diff --git a/1/1SC.cif b/1/1SC.cif index ee0f705ec..7c6c15950 100644 --- a/1/1SC.cif +++ b/1/1SC.cif @@ -7,7 +7,7 @@ _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level -1SC 1SC "5'-O-THIOPHOSPHONOCYTIDINE" NON-POLYMER 34 21 . +1SC 1SC "5'-O-THIOPHOSPHONOCYTIDINE" NON-POLYMER 33 21 . data_comp_1SC loop_ @@ -19,40 +19,77 @@ _chem_comp_atom.charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z -1SC O3P O OP -1 -12.310 -3.334 44.206 -1SC P P P 0 -13.057 -2.106 43.805 -1SC O1P O O 0 -12.571 -1.437 42.561 -1SC "O5'" O O2 0 -14.585 -2.517 43.567 -1SC "C5'" C CH2 0 -14.891 -3.567 42.613 -1SC "C4'" C CH1 0 -16.387 -3.725 42.485 -1SC "O4'" O O2 0 -16.976 -3.960 43.787 -1SC "C3'" C CH1 0 -17.161 -2.510 41.962 -1SC "O3'" O OH1 0 -17.079 -2.428 40.544 -1SC "C2'" C CH1 0 -18.586 -2.789 42.468 -1SC "O2'" O OH1 0 -19.366 -3.544 41.562 -1SC "C1'" C CH1 0 -18.343 -3.607 43.748 -1SC N1 N NR6 0 -18.679 -2.847 44.989 -1SC C2 C CR6 0 -19.763 -3.238 45.797 -1SC O2 O O 0 -20.445 -4.227 45.482 -1SC N3 N NRD6 0 -20.043 -2.520 46.918 -1SC C4 C CR6 0 -19.303 -1.451 47.254 -1SC N4 N NH2 0 -19.625 -0.790 48.360 -1SC C5 C CR16 0 -18.204 -1.037 46.447 -1SC C6 C CR16 0 -17.934 -1.752 45.340 -1SC S S SH1 0 -13.103 -0.728 45.375 -1SC "H5'1" H H 0 -14.493 -4.420 42.916 -1SC "H5'2" H H 0 -14.506 -3.339 41.731 -1SC "H4'" H H 0 -16.568 -4.501 41.912 -1SC "H3'" H H 0 -16.816 -1.677 42.372 -1SC "HO3'" H H 0 -17.596 -1.810 40.276 -1SC "H2'" H H 0 -19.036 -1.948 42.681 -1SC "HO2'" H H 0 -18.944 -4.243 41.328 -1SC "H1'" H H 0 -18.876 -4.434 43.709 -1SC HN41 H H 0 -20.340 -1.018 48.815 -1SC HN42 H H 0 -19.121 -0.126 48.634 -1SC H5 H H 0 -17.682 -0.289 46.677 -1SC H6 H H 0 -17.219 -1.505 44.789 -1SC HS H HSH1 0 -14.183 -0.773 45.921 +1SC O3P O OP -1 -12.426 -3.185 44.260 +1SC P P P 0 -13.144 -1.925 43.896 +1SC O1P O OP -1 -12.638 -1.449 42.569 +1SC "O5'" O O2 0 -14.653 -2.384 43.562 +1SC "C5'" C CH2 0 -14.888 -3.414 42.580 +1SC "C4'" C CH1 0 -16.364 -3.716 42.489 +1SC "O4'" O O2 0 -16.915 -4.002 43.792 +1SC "C3'" C CH1 0 -17.240 -2.579 41.957 +1SC "O3'" O OH1 0 -17.187 -2.538 40.536 +1SC "C2'" C CH1 0 -18.630 -2.947 42.500 +1SC "O2'" O OH1 0 -19.372 -3.776 41.625 +1SC "C1'" C CH1 0 -18.294 -3.714 43.790 +1SC N1 N NR6 0 -18.616 -2.953 45.036 +1SC C2 C CR6 0 -19.586 -3.409 45.948 +1SC O2 O O 0 -20.198 -4.466 45.736 +1SC N3 N NRD6 0 -19.835 -2.670 47.062 +1SC C4 C CR6 0 -19.173 -1.524 47.294 +1SC N4 N NH2 0 -19.460 -0.846 48.399 +1SC C5 C CR16 0 -18.190 -1.048 46.379 +1SC C6 C CR16 0 -17.949 -1.785 45.280 +1SC S S S1 0 -13.048 -0.526 45.242 +1SC "H5'1" H H 0 -14.400 -4.238 42.832 +1SC "H5'2" H H 0 -14.558 -3.116 41.694 +1SC "H4'" H H 0 -16.482 -4.512 41.912 +1SC "H3'" H H 0 -16.949 -1.711 42.334 +1SC "HO3'" H H 0 -17.748 -1.983 40.253 +1SC "H2'" H H 0 -19.140 -2.133 42.711 +1SC "HO2'" H H 0 -20.150 -3.878 41.923 +1SC "H1'" H H 0 -18.796 -4.571 43.779 +1SC HN41 H H 0 -19.041 -0.096 48.571 +1SC HN42 H H 0 -20.066 -1.145 48.957 +1SC H5 H H 0 -17.723 -0.245 46.538 +1SC H6 H H 0 -17.308 -1.497 44.660 + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +1SC O3P O(POOS) +1SC P P(OC)(O)2(S) +1SC O1P O(POOS) +1SC "O5'" O(CC[5]HH)(POOS) +1SC "C5'" C(C[5]C[5]O[5]H)(OP)(H)2 +1SC "C4'" C[5](C[5]C[5]HO)(O[5]C[5])(CHHO)(H){1|N<3>,1|O<2>,2|H<1>} +1SC "O4'" O[5](C[5]N[6a]C[5]H)(C[5]C[5]CH){2|C<3>,2|H<1>,2|O<2>} +1SC "C3'" C[5](C[5]C[5]HO)(C[5]O[5]CH)(OH)(H){1|H<1>,1|N<3>} +1SC "O3'" O(C[5]C[5]2H)(H) +1SC "C2'" C[5](C[5]N[6a]O[5]H)(C[5]C[5]HO)(OH)(H){1|C<4>,1|H<1>,2|C<3>} +1SC "O2'" O(C[5]C[5]2H)(H) +1SC "C1'" C[5](N[6a]C[6a]2)(C[5]C[5]HO)(O[5]C[5])(H){1|C<3>,1|C<4>,1|N<2>,1|O<1>,1|O<2>,3|H<1>} +1SC N1 N[6a](C[5]C[5]O[5]H)(C[6a]C[6a]H)(C[6a]N[6a]O){1|C<3>,1|O<2>,2|C<4>,2|H<1>} +1SC C2 C[6a](N[6a]C[6a]C[5])(N[6a]C[6a])(O){1|C<3>,1|C<4>,1|N<3>,1|O<2>,2|H<1>} +1SC O2 O(C[6a]N[6a]2) +1SC N3 N[6a](C[6a]C[6a]N)(C[6a]N[6a]O){1|C<3>,1|C<4>,1|H<1>} +1SC C4 C[6a](C[6a]C[6a]H)(N[6a]C[6a])(NHH){1|H<1>,1|N<3>,1|O<1>} +1SC N4 N(C[6a]C[6a]N[6a])(H)2 +1SC C5 C[6a](C[6a]N[6a]H)(C[6a]N[6a]N)(H){1|C<3>,1|C<4>} +1SC C6 C[6a](N[6a]C[6a]C[5])(C[6a]C[6a]H)(H){1|C<4>,1|H<1>,1|N<2>,1|N<3>,1|O<1>,1|O<2>} +1SC S S(PO3) +1SC "H5'1" H(CC[5]HO) +1SC "H5'2" H(CC[5]HO) +1SC "H4'" H(C[5]C[5]O[5]C) +1SC "H3'" H(C[5]C[5]2O) +1SC "HO3'" H(OC[5]) +1SC "H2'" H(C[5]C[5]2O) +1SC "HO2'" H(OC[5]) +1SC "H1'" H(C[5]N[6a]C[5]O[5]) +1SC HN41 H(NC[6a]H) +1SC HN42 H(NC[6a]H) +1SC H5 H(C[6a]C[6a]2) +1SC H6 H(C[6a]C[6a]N[6a]) loop_ _chem_comp_bond.comp_id @@ -64,41 +101,40 @@ _chem_comp_bond.value_dist_nucleus _chem_comp_bond.value_dist_nucleus_esd _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd -1SC O3P P SINGLE n 1.493 0.0157 1.493 0.0157 -1SC P O1P DOUBLE n 1.493 0.0157 1.493 0.0157 -1SC P "O5'" SINGLE n 1.601 0.0114 1.601 0.0114 -1SC P S SINGLE n 2.091 0.0200 2.091 0.0200 -1SC "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 -1SC "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 -1SC "C4'" "O4'" SINGLE n 1.451 0.0111 1.451 0.0111 -1SC "C4'" "C3'" SINGLE n 1.535 0.0100 1.535 0.0100 -1SC "O4'" "C1'" SINGLE n 1.411 0.0100 1.411 0.0100 -1SC "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 -1SC "C3'" "C2'" SINGLE n 1.533 0.0109 1.533 0.0109 -1SC "C2'" "O2'" SINGLE n 1.412 0.0100 1.412 0.0100 -1SC "C2'" "C1'" SINGLE n 1.532 0.0100 1.532 0.0100 -1SC "C1'" N1 SINGLE n 1.487 0.0100 1.487 0.0100 -1SC N1 C2 SINGLE y 1.397 0.0100 1.397 0.0100 -1SC N1 C6 SINGLE y 1.364 0.0108 1.364 0.0108 -1SC C2 O2 DOUBLE n 1.241 0.0100 1.241 0.0100 -1SC C2 N3 SINGLE y 1.355 0.0119 1.355 0.0119 -1SC N3 C4 DOUBLE y 1.339 0.0110 1.339 0.0110 -1SC C4 N4 SINGLE n 1.325 0.0109 1.325 0.0109 -1SC C4 C5 SINGLE y 1.422 0.0123 1.422 0.0123 -1SC C5 C6 DOUBLE y 1.342 0.0100 1.342 0.0100 -1SC "C5'" "H5'1" SINGLE n 1.089 0.0100 0.989 0.0200 -1SC "C5'" "H5'2" SINGLE n 1.089 0.0100 0.989 0.0200 -1SC "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200 -1SC "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200 -1SC "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 -1SC "C2'" "H2'" SINGLE n 1.089 0.0100 0.978 0.0200 -1SC "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200 -1SC "C1'" "H1'" SINGLE n 1.089 0.0100 0.985 0.0100 -1SC N4 HN41 SINGLE n 1.016 0.0100 0.877 0.0200 -1SC N4 HN42 SINGLE n 1.016 0.0100 0.877 0.0200 -1SC C5 H5 SINGLE n 1.082 0.0130 0.941 0.0174 -1SC C6 H6 SINGLE n 1.082 0.0130 0.935 0.0143 -1SC S HS SINGLE n 1.338 0.0100 1.211 0.0200 +1SC O3P P SINGLE n 1.497 0.0143 1.497 0.0143 +1SC P O1P SINGLE n 1.497 0.0143 1.497 0.0143 +1SC P "O5'" SINGLE n 1.613 0.0200 1.613 0.0200 +1SC P S DOUBLE n 1.949 0.0200 1.949 0.0200 +1SC "O5'" "C5'" SINGLE n 1.438 0.0200 1.438 0.0200 +1SC "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 +1SC "C4'" "O4'" SINGLE n 1.445 0.0100 1.445 0.0100 +1SC "C4'" "C3'" SINGLE n 1.532 0.0100 1.532 0.0100 +1SC "O4'" "C1'" SINGLE n 1.408 0.0100 1.408 0.0100 +1SC "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +1SC "C3'" "C2'" SINGLE n 1.534 0.0111 1.534 0.0111 +1SC "C2'" "O2'" SINGLE n 1.415 0.0100 1.415 0.0100 +1SC "C2'" "C1'" SINGLE n 1.533 0.0100 1.533 0.0100 +1SC "C1'" N1 SINGLE n 1.489 0.0100 1.489 0.0100 +1SC N1 C2 SINGLE y 1.398 0.0100 1.398 0.0100 +1SC N1 C6 SINGLE y 1.361 0.0100 1.361 0.0100 +1SC C2 O2 DOUBLE n 1.238 0.0116 1.238 0.0116 +1SC C2 N3 SINGLE y 1.355 0.0100 1.355 0.0100 +1SC N3 C4 DOUBLE y 1.341 0.0104 1.341 0.0104 +1SC C4 N4 SINGLE n 1.326 0.0110 1.326 0.0110 +1SC C4 C5 SINGLE y 1.422 0.0101 1.422 0.0101 +1SC C5 C6 DOUBLE y 1.342 0.0100 1.342 0.0100 +1SC "C5'" "H5'1" SINGLE n 1.092 0.0100 0.991 0.0200 +1SC "C5'" "H5'2" SINGLE n 1.092 0.0100 0.991 0.0200 +1SC "C4'" "H4'" SINGLE n 1.092 0.0100 0.990 0.0200 +1SC "C3'" "H3'" SINGLE n 1.092 0.0100 0.991 0.0200 +1SC "O3'" "HO3'" SINGLE n 0.972 0.0180 0.839 0.0200 +1SC "C2'" "H2'" SINGLE n 1.092 0.0100 0.983 0.0200 +1SC "O2'" "HO2'" SINGLE n 0.972 0.0180 0.839 0.0200 +1SC "C1'" "H1'" SINGLE n 1.092 0.0100 0.994 0.0122 +1SC N4 HN41 SINGLE n 1.013 0.0120 0.875 0.0200 +1SC N4 HN42 SINGLE n 1.013 0.0120 0.875 0.0200 +1SC C5 H5 SINGLE n 1.085 0.0150 0.942 0.0165 +1SC C6 H6 SINGLE n 1.085 0.0150 0.938 0.0143 loop_ _chem_comp_angle.comp_id @@ -107,66 +143,65 @@ _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd -1SC O3P P O1P 116.964 2.85 -1SC O3P P "O5'" 108.530 2.45 -1SC O3P P S 111.281 3.00 -1SC O1P P "O5'" 108.530 2.45 -1SC O1P P S 111.281 3.00 -1SC "O5'" P S 105.685 3.00 -1SC P "O5'" "C5'" 119.135 1.78 -1SC "O5'" "C5'" "C4'" 109.510 1.50 -1SC "O5'" "C5'" "H5'1" 109.821 1.50 -1SC "O5'" "C5'" "H5'2" 109.821 1.50 -1SC "C4'" "C5'" "H5'1" 109.624 1.50 -1SC "C4'" "C5'" "H5'2" 109.624 1.50 -1SC "H5'1" "C5'" "H5'2" 108.472 1.50 -1SC "C5'" "C4'" "O4'" 109.615 1.50 -1SC "C5'" "C4'" "C3'" 116.008 1.52 -1SC "C5'" "C4'" "H4'" 108.268 1.50 -1SC "O4'" "C4'" "C3'" 104.439 1.50 -1SC "O4'" "C4'" "H4'" 108.698 1.50 -1SC "C3'" "C4'" "H4'" 109.363 1.86 -1SC "C4'" "O4'" "C1'" 109.578 1.50 -1SC "C4'" "C3'" "O3'" 111.281 2.46 -1SC "C4'" "C3'" "C2'" 102.071 1.50 -1SC "C4'" "C3'" "H3'" 110.452 2.54 -1SC "O3'" "C3'" "C2'" 111.993 3.00 -1SC "O3'" "C3'" "H3'" 110.380 1.67 -1SC "C2'" "C3'" "H3'" 110.108 1.66 -1SC "C3'" "O3'" "HO3'" 108.744 3.00 -1SC "C3'" "C2'" "O2'" 112.861 2.52 -1SC "C3'" "C2'" "C1'" 101.269 1.50 -1SC "C3'" "C2'" "H2'" 110.799 1.82 -1SC "O2'" "C2'" "C1'" 109.476 3.00 -1SC "O2'" "C2'" "H2'" 111.022 1.77 -1SC "C1'" "C2'" "H2'" 110.760 1.63 -1SC "C2'" "O2'" "HO2'" 109.449 1.85 -1SC "O4'" "C1'" "C2'" 106.825 1.50 -1SC "O4'" "C1'" N1 108.667 1.50 -1SC "O4'" "C1'" "H1'" 109.327 1.50 -1SC "C2'" "C1'" N1 112.859 1.50 -1SC "C2'" "C1'" "H1'" 109.776 1.83 -1SC N1 "C1'" "H1'" 109.166 1.50 -1SC "C1'" N1 C2 118.189 2.26 -1SC "C1'" N1 C6 121.301 1.52 -1SC C2 N1 C6 120.510 1.50 -1SC N1 C2 O2 118.710 1.50 -1SC N1 C2 N3 118.927 1.50 -1SC O2 C2 N3 122.370 1.50 -1SC C2 N3 C4 120.266 1.50 -1SC N3 C4 N4 117.855 1.50 -1SC N3 C4 C5 121.269 1.50 -1SC N4 C4 C5 120.876 1.50 -1SC C4 N4 HN41 119.818 1.59 -1SC C4 N4 HN42 119.818 1.59 -1SC HN41 N4 HN42 120.363 1.85 -1SC C4 C5 C6 117.808 1.50 -1SC C4 C5 H5 121.350 1.50 -1SC C6 C5 H5 120.848 1.50 -1SC N1 C6 C5 121.215 1.50 -1SC N1 C6 H6 118.510 1.50 -1SC C5 C6 H6 120.275 1.75 -1SC P S HS 109.471 3.00 +1SC O3P P O1P 112.844 3.00 +1SC O3P P "O5'" 106.327 3.00 +1SC O3P P S 116.458 3.00 +1SC O1P P "O5'" 106.327 3.00 +1SC O1P P S 116.458 3.00 +1SC "O5'" P S 114.928 3.00 +1SC P "O5'" "C5'" 119.085 2.00 +1SC "O5'" "C5'" "C4'" 109.482 2.30 +1SC "O5'" "C5'" "H5'1" 109.954 1.50 +1SC "O5'" "C5'" "H5'2" 109.954 1.50 +1SC "C4'" "C5'" "H5'1" 109.589 1.50 +1SC "C4'" "C5'" "H5'2" 109.589 1.50 +1SC "H5'1" "C5'" "H5'2" 108.471 1.50 +1SC "C5'" "C4'" "O4'" 110.351 1.93 +1SC "C5'" "C4'" "C3'" 115.288 1.50 +1SC "C5'" "C4'" "H4'" 108.351 1.59 +1SC "O4'" "C4'" "C3'" 105.071 1.50 +1SC "O4'" "C4'" "H4'" 108.778 1.50 +1SC "C3'" "C4'" "H4'" 109.322 2.54 +1SC "C4'" "O4'" "C1'" 109.821 1.50 +1SC "C4'" "C3'" "O3'" 110.713 3.00 +1SC "C4'" "C3'" "C2'" 102.776 1.50 +1SC "C4'" "C3'" "H3'" 110.577 3.00 +1SC "O3'" "C3'" "C2'" 111.936 3.00 +1SC "O3'" "C3'" "H3'" 110.541 2.08 +1SC "C2'" "C3'" "H3'" 110.235 2.42 +1SC "C3'" "O3'" "HO3'" 109.389 3.00 +1SC "C3'" "C2'" "O2'" 113.012 3.00 +1SC "C3'" "C2'" "C1'" 101.479 1.50 +1SC "C3'" "C2'" "H2'" 110.640 2.20 +1SC "O2'" "C2'" "C1'" 109.825 3.00 +1SC "O2'" "C2'" "H2'" 110.739 1.98 +1SC "C1'" "C2'" "H2'" 110.219 1.50 +1SC "C2'" "O2'" "HO2'" 109.730 3.00 +1SC "O4'" "C1'" "C2'" 106.541 2.94 +1SC "O4'" "C1'" N1 108.138 1.50 +1SC "O4'" "C1'" "H1'" 109.439 1.50 +1SC "C2'" "C1'" N1 113.288 2.34 +1SC "C2'" "C1'" "H1'" 109.838 3.00 +1SC N1 "C1'" "H1'" 109.374 1.50 +1SC "C1'" N1 C2 118.289 3.00 +1SC "C1'" N1 C6 121.103 2.33 +1SC C2 N1 C6 120.608 1.50 +1SC N1 C2 O2 118.915 2.14 +1SC N1 C2 N3 118.792 1.50 +1SC O2 C2 N3 122.293 1.50 +1SC C2 N3 C4 120.397 1.50 +1SC N3 C4 N4 117.915 1.50 +1SC N3 C4 C5 121.314 1.50 +1SC N4 C4 C5 120.770 1.50 +1SC C4 N4 HN41 119.693 3.00 +1SC C4 N4 HN42 119.693 3.00 +1SC HN41 N4 HN42 120.613 3.00 +1SC C4 C5 C6 117.770 1.50 +1SC C4 C5 H5 121.221 1.50 +1SC C6 C5 H5 121.009 1.50 +1SC N1 C6 C5 121.118 1.50 +1SC N1 C6 H6 118.411 1.84 +1SC C5 C6 H6 120.471 3.00 loop_ _chem_comp_tor.comp_id @@ -178,31 +213,29 @@ _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period -1SC C2e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 -1SC C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 -1SC C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 -1SC C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 -1SC C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 -1SC C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 -1SC C3e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 -1SC C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 -1SC C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 -1SC C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 -1SC C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 -1SC C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 -1SC beta P "O5'" "C5'" "C4'" 180.000 10.00 3 -1SC epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 -1SC gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 -1SC sp3_sp3_52 "C3'" "C2'" "O2'" "HO2'" 180.000 10.00 3 -1SC const_sp2_sp2_4 O2 C2 N1 "C1'" 0.000 5.0 2 -1SC const_18 C5 C6 N1 "C1'" 180.000 10.0 2 -1SC const_sp2_sp2_6 O2 C2 N3 C4 180.000 5.0 2 -1SC const_sp2_sp2_8 N4 C4 N3 C2 180.000 5.0 2 -1SC sp2_sp2_3 N3 C4 N4 HN41 0.000 5.0 2 -1SC const_11 N4 C4 C5 C6 180.000 10.0 2 -1SC const_13 C4 C5 C6 N1 0.000 10.0 2 -1SC sp3_sp3_28 O3P P S HS 180.000 10.0 3 -1SC sp3_sp3_26 "C5'" "O5'" P O3P -60.000 10.0 3 +1SC sp2_sp3_1 C2 N1 "C1'" "O4'" 150.000 10.0 6 +1SC const_sp2_sp2_1 N3 C2 N1 C6 0.000 0.0 1 +1SC const_sp2_sp2_4 O2 C2 N1 "C1'" 0.000 0.0 1 +1SC const_17 C5 C6 N1 C2 0.000 0.0 1 +1SC const_20 H6 C6 N1 "C1'" 0.000 0.0 1 +1SC const_sp2_sp2_5 N1 C2 N3 C4 0.000 0.0 1 +1SC const_sp2_sp2_7 C5 C4 N3 C2 0.000 0.0 1 +1SC sp2_sp2_21 C5 C4 N4 HN41 180.000 20 2 +1SC sp2_sp2_24 N3 C4 N4 HN42 180.000 20 2 +1SC const_sp2_sp2_9 N3 C4 C5 C6 0.000 0.0 1 +1SC const_12 N4 C4 C5 H5 0.000 0.0 1 +1SC const_13 C4 C5 C6 N1 0.000 0.0 1 +1SC const_16 H5 C5 C6 H6 0.000 0.0 1 +1SC sp3_sp3_26 "C5'" "O5'" P O3P -60.000 10.0 3 +1SC sp3_sp3_28 "C4'" "C5'" "O5'" P 180.000 10.0 3 +1SC sp3_sp3_31 "O4'" "C4'" "C5'" "O5'" 180.000 10.0 3 +1SC sp3_sp3_2 "C5'" "C4'" "O4'" "C1'" -60.000 10.0 3 +1SC sp3_sp3_44 "O3'" "C3'" "C4'" "C5'" 180.000 10.0 3 +1SC sp3_sp3_4 "C2'" "C1'" "O4'" "C4'" -60.000 10.0 3 +1SC sp3_sp3_49 "C4'" "C3'" "O3'" "HO3'" 180.000 10.0 3 +1SC sp3_sp3_20 "O2'" "C2'" "C3'" "O3'" -60.000 10.0 3 +1SC sp3_sp3_52 "C3'" "C2'" "O2'" "HO2'" 180.000 10.0 3 +1SC sp3_sp3_8 "O4'" "C1'" "C2'" "O2'" 180.000 10.0 3 loop_ _chem_comp_chir.comp_id @@ -212,11 +245,11 @@ _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign -1SC chir_1 P S "O5'" O3P both +1SC chir_1 P S "O5'" O3P both 1SC chir_2 "C4'" "O4'" "C3'" "C5'" negative 1SC chir_3 "C3'" "O3'" "C4'" "C2'" positive 1SC chir_4 "C2'" "O2'" "C1'" "C3'" negative -1SC chir_5 "C1'" "O4'" N1 "C2'" negative +1SC chir_5 "C1'" "O4'" N1 "C2'" negative loop_ _chem_comp_plane_atom.comp_id @@ -224,20 +257,20 @@ _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd 1SC plan-1 "C1'" 0.020 -1SC plan-1 C2 0.020 -1SC plan-1 C4 0.020 -1SC plan-1 C5 0.020 -1SC plan-1 C6 0.020 -1SC plan-1 H5 0.020 -1SC plan-1 H6 0.020 -1SC plan-1 N1 0.020 -1SC plan-1 N3 0.020 -1SC plan-1 N4 0.020 -1SC plan-1 O2 0.020 -1SC plan-2 C4 0.020 -1SC plan-2 HN41 0.020 -1SC plan-2 HN42 0.020 -1SC plan-2 N4 0.020 +1SC plan-1 C2 0.020 +1SC plan-1 C4 0.020 +1SC plan-1 C5 0.020 +1SC plan-1 C6 0.020 +1SC plan-1 H5 0.020 +1SC plan-1 H6 0.020 +1SC plan-1 N1 0.020 +1SC plan-1 N3 0.020 +1SC plan-1 N4 0.020 +1SC plan-1 O2 0.020 +1SC plan-2 C4 0.020 +1SC plan-2 HN41 0.020 +1SC plan-2 HN42 0.020 +1SC plan-2 N4 0.020 loop_ _pdbx_chem_comp_descriptor.comp_id @@ -245,20 +278,29 @@ _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor -1SC SMILES ACDLabs 10.04 O=P(O)(S)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O -1SC SMILES_CANONICAL CACTVS 3.341 NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@](O)(S)=O)[C@@H](O)[C@H]2O -1SC SMILES CACTVS 3.341 NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(S)=O)[CH](O)[CH]2O +1SC SMILES ACDLabs 10.04 O=P(O)(S)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O +1SC SMILES_CANONICAL CACTVS 3.341 NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@](O)(S)=O)[C@@H](O)[C@H]2O +1SC SMILES CACTVS 3.341 NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(S)=O)[CH](O)[CH]2O 1SC SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@](=O)(O)S)O)O -1SC SMILES "OpenEye OEToolkits" 1.5.0 C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)S)O)O -1SC InChI InChI 1.03 InChI=1S/C9H14N3O7PS/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(19-8)3-18-20(16,17)21/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,21)/t4-,6-,7-,8-/m1/s1 -1SC InChIKey InChI 1.03 JOENGNVCVILJEG-XVFCMESISA-N +1SC SMILES "OpenEye OEToolkits" 1.5.0 C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)S)O)O +1SC InChI InChI 1.03 InChI=1S/C9H14N3O7PS/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(19-8)3-18-20(16,17)21/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,21)/t4-,6-,7-,8-/m1/s1 +1SC InChIKey InChI 1.03 JOENGNVCVILJEG-XVFCMESISA-N loop_ _pdbx_chem_comp_description_generator.comp_id _pdbx_chem_comp_description_generator.program_name _pdbx_chem_comp_description_generator.program_version _pdbx_chem_comp_description_generator.descriptor -1SC acedrg 243 "dictionary generator" -1SC acedrg_database 11 "data source" -1SC rdkit 2017.03.2 "Chemoinformatics tool" -1SC refmac5 5.8.0238 "optimization tool" +1SC acedrg 277 "dictionary generator" +1SC acedrg_database 12 "data source" +1SC rdkit 2019.09.1 "Chemoinformatics tool" +1SC refmac5 5.8.0425 "optimization tool" + +loop_ +_chem_comp_alias.comp_id +_chem_comp_alias.group +_chem_comp_alias.atom_id +_chem_comp_alias.atom_id_standard +1SC S-NA O3P OP3 +1SC S-NA S S2P +1SC S-NA O1P OP1 diff --git a/4/48Z.cif b/4/48Z.cif index 9d4451b57..64744a043 100644 --- a/4/48Z.cif +++ b/4/48Z.cif @@ -7,7 +7,7 @@ _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level -48Z 48Z 2-deoxy-2-fluoro-5-O-thiophosphono-alpha-D-arabinofuranose NON-POLYMER 23 14 . +48Z 48Z 2-deoxy-2-fluoro-5-O-thiophosphono-alpha-D-arabinofuranose NON-POLYMER 22 14 . data_comp_48Z loop_ @@ -19,29 +19,55 @@ _chem_comp_atom.charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z -48Z O1 O OH1 0 1.992 -2.787 2.610 -48Z P P P 0 5.475 -3.195 -2.829 -48Z C1 C CH1 0 3.110 -2.571 1.832 -48Z C2 C CH1 0 2.989 -1.256 1.081 -48Z F2 F F 0 4.252 -0.782 0.717 -48Z C3 C CH1 0 2.196 -1.624 -0.166 -48Z O3 O OH1 0 0.825 -1.318 -0.013 -48Z C4 C CH1 0 2.448 -3.130 -0.323 -48Z O4 O O2 0 3.220 -3.555 0.822 -48Z C5 C CH2 0 3.181 -3.526 -1.582 -48Z O5 O O2 0 4.497 -2.916 -1.594 -48Z OP1 O O 0 4.935 -2.454 -4.008 -48Z OP2 O OP -1 5.595 -4.672 -3.001 -48Z SP3 S SH1 0 7.312 -2.376 -2.262 -48Z HO1 H H 0 2.050 -3.541 2.996 -48Z H1 H H 0 3.924 -2.583 2.396 -48Z H2 H H 0 2.500 -0.588 1.621 -48Z H3 H H 0 2.555 -1.145 -0.942 -48Z HO3 H H 0 0.531 -1.723 0.674 -48Z H4 H H 0 1.584 -3.606 -0.313 -48Z H52 H H 0 2.667 -3.227 -2.372 -48Z H51 H H 0 3.268 -4.510 -1.619 -48Z HSP3 H HSH1 0 7.192 -1.180 -2.116 +48Z O1 O OH1 0 1.909 -2.766 2.618 +48Z P P P 0 5.565 -3.226 -2.698 +48Z C1 C CH1 0 3.051 -2.635 1.854 +48Z C2 C CH1 0 3.064 -1.284 1.140 +48Z F2 F F 0 4.330 -0.930 0.817 +48Z C3 C CH1 0 2.272 -1.557 -0.129 +48Z O3 O OH1 0 0.924 -1.168 0.023 +48Z C4 C CH1 0 2.409 -3.071 -0.349 +48Z O4 O O2 0 3.074 -3.602 0.816 +48Z C5 C CH2 0 3.184 -3.471 -1.580 +48Z O5 O O2 0 4.521 -2.939 -1.506 +48Z OP1 O OP -1 4.886 -2.632 -3.892 +48Z OP2 O OP -1 5.593 -4.712 -2.853 +48Z SP3 S S1 0 7.309 -2.420 -2.396 +48Z HO1 H H 0 1.900 -3.520 2.986 +48Z H1 H H 0 3.859 -2.735 2.425 +48Z H2 H H 0 2.633 -0.592 1.689 +48Z H3 H H 0 2.685 -1.062 -0.879 +48Z HO3 H H 0 0.587 -1.574 0.677 +48Z H4 H H 0 1.508 -3.478 -0.409 +48Z H52 H H 0 2.725 -3.123 -2.386 +48Z H51 H H 0 3.216 -4.460 -1.642 + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +48Z O1 O(C[5]C[5]O[5]H)(H) +48Z P P(OC)(O)2(S) +48Z C1 C[5](C[5]C[5]FH)(O[5]C[5])(OH)(H){1|C<4>,1|O<2>,2|H<1>} +48Z C2 C[5](C[5]C[5]HO)(C[5]O[5]HO)(F)(H){1|C<4>,1|H<1>} +48Z F2 F(C[5]C[5]2H) +48Z C3 C[5](C[5]C[5]FH)(C[5]O[5]CH)(OH)(H){1|H<1>,1|O<2>} +48Z O3 O(C[5]C[5]2H)(H) +48Z C4 C[5](C[5]C[5]HO)(O[5]C[5])(CHHO)(H){1|F<1>,1|O<2>,2|H<1>} +48Z O4 O[5](C[5]C[5]CH)(C[5]C[5]HO){1|F<1>,1|O<2>,2|H<1>} +48Z C5 C(C[5]C[5]O[5]H)(OP)(H)2 +48Z O5 O(CC[5]HH)(POOS) +48Z OP1 O(POOS) +48Z OP2 O(POOS) +48Z SP3 S(PO3) +48Z HO1 H(OC[5]) +48Z H1 H(C[5]C[5]O[5]O) +48Z H2 H(C[5]C[5]2F) +48Z H3 H(C[5]C[5]2O) +48Z HO3 H(OC[5]) +48Z H4 H(C[5]C[5]O[5]C) +48Z H52 H(CC[5]HO) +48Z H51 H(CC[5]HO) loop_ _chem_comp_bond.comp_id @@ -53,29 +79,28 @@ _chem_comp_bond.value_dist_nucleus _chem_comp_bond.value_dist_nucleus_esd _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd -48Z P SP3 SINGLE n 2.091 0.0200 2.091 0.0200 -48Z P OP2 SINGLE n 1.493 0.0157 1.493 0.0157 -48Z P O5 SINGLE n 1.601 0.0114 1.601 0.0114 -48Z O1 C1 SINGLE n 1.380 0.0200 1.380 0.0200 -48Z C1 C2 SINGLE n 1.525 0.0145 1.525 0.0145 -48Z C2 F2 SINGLE n 1.398 0.0100 1.398 0.0100 -48Z C2 C3 SINGLE n 1.521 0.0111 1.521 0.0111 -48Z C3 O3 SINGLE n 1.411 0.0121 1.411 0.0121 -48Z C3 C4 SINGLE n 1.528 0.0117 1.528 0.0117 -48Z C4 O4 SINGLE n 1.443 0.0100 1.443 0.0100 -48Z C1 O4 SINGLE n 1.423 0.0192 1.423 0.0192 -48Z C4 C5 SINGLE n 1.509 0.0100 1.509 0.0100 -48Z C5 O5 SINGLE n 1.450 0.0166 1.450 0.0166 -48Z P OP1 DOUBLE n 1.493 0.0157 1.493 0.0157 -48Z O1 HO1 SINGLE n 0.970 0.0120 0.849 0.0200 -48Z C1 H1 SINGLE n 1.089 0.0100 0.990 0.0166 -48Z C2 H2 SINGLE n 1.089 0.0100 0.988 0.0103 -48Z C3 H3 SINGLE n 1.089 0.0100 0.980 0.0100 -48Z O3 HO3 SINGLE n 0.970 0.0120 0.849 0.0200 -48Z C4 H4 SINGLE n 1.089 0.0100 0.986 0.0200 -48Z C5 H52 SINGLE n 1.089 0.0100 0.989 0.0200 -48Z C5 H51 SINGLE n 1.089 0.0100 0.989 0.0200 -48Z SP3 HSP3 SINGLE n 1.338 0.0100 1.211 0.0200 +48Z P SP3 DOUBLE n 1.949 0.0200 1.949 0.0200 +48Z P OP2 SINGLE n 1.497 0.0143 1.497 0.0143 +48Z P O5 SINGLE n 1.613 0.0200 1.613 0.0200 +48Z O1 C1 SINGLE n 1.380 0.0200 1.380 0.0200 +48Z C1 C2 SINGLE n 1.533 0.0139 1.533 0.0139 +48Z C2 F2 SINGLE n 1.354 0.0200 1.354 0.0200 +48Z C2 C3 SINGLE n 1.520 0.0110 1.520 0.0110 +48Z C3 O3 SINGLE n 1.410 0.0100 1.410 0.0100 +48Z C3 C4 SINGLE n 1.530 0.0119 1.530 0.0119 +48Z C4 O4 SINGLE n 1.441 0.0100 1.441 0.0100 +48Z C1 O4 SINGLE n 1.423 0.0158 1.423 0.0158 +48Z C4 C5 SINGLE n 1.508 0.0100 1.508 0.0100 +48Z C5 O5 SINGLE n 1.438 0.0200 1.438 0.0200 +48Z P OP1 SINGLE n 1.497 0.0143 1.497 0.0143 +48Z O1 HO1 SINGLE n 0.972 0.0180 0.839 0.0200 +48Z C1 H1 SINGLE n 1.092 0.0100 0.994 0.0100 +48Z C2 H2 SINGLE n 1.092 0.0100 0.982 0.0171 +48Z C3 H3 SINGLE n 1.092 0.0100 0.989 0.0103 +48Z O3 HO3 SINGLE n 0.972 0.0180 0.839 0.0200 +48Z C4 H4 SINGLE n 1.092 0.0100 0.990 0.0200 +48Z C5 H52 SINGLE n 1.092 0.0100 0.991 0.0200 +48Z C5 H51 SINGLE n 1.092 0.0100 0.991 0.0200 loop_ _chem_comp_angle.comp_id @@ -84,47 +109,46 @@ _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd -48Z C1 O1 HO1 109.854 2.80 -48Z SP3 P OP2 111.281 3.00 -48Z SP3 P O5 105.685 3.00 -48Z SP3 P OP1 111.281 3.00 -48Z OP2 P O5 108.530 2.45 -48Z OP2 P OP1 116.964 2.85 -48Z O5 P OP1 108.530 2.45 -48Z O1 C1 C2 110.383 1.65 -48Z O1 C1 O4 110.867 1.50 -48Z O1 C1 H1 110.005 1.50 -48Z C2 C1 O4 105.977 1.50 -48Z C2 C1 H1 110.953 2.33 -48Z O4 C1 H1 109.510 2.59 -48Z C1 C2 F2 110.700 1.96 -48Z C1 C2 C3 104.443 2.26 -48Z C1 C2 H2 110.945 1.50 -48Z F2 C2 C3 110.051 1.88 -48Z F2 C2 H2 111.335 1.50 -48Z C3 C2 H2 110.826 1.50 -48Z C2 C3 O3 111.623 3.00 -48Z C2 C3 C4 102.056 1.52 -48Z C2 C3 H3 110.299 1.50 -48Z O3 C3 C4 112.431 2.44 -48Z O3 C3 H3 109.964 1.50 -48Z C4 C3 H3 109.965 1.50 -48Z C3 O3 HO3 108.182 1.86 -48Z C3 C4 O4 105.508 1.50 -48Z C3 C4 C5 114.866 1.63 -48Z C3 C4 H4 109.385 1.50 -48Z O4 C4 C5 109.123 1.50 -48Z O4 C4 H4 109.199 2.08 -48Z C5 C4 H4 108.268 1.50 -48Z C4 O4 C1 108.379 1.72 -48Z C4 C5 O5 109.510 1.50 -48Z C4 C5 H52 109.624 1.50 -48Z C4 C5 H51 109.624 1.50 -48Z O5 C5 H52 109.821 1.50 -48Z O5 C5 H51 109.821 1.50 -48Z H52 C5 H51 108.472 1.50 -48Z P O5 C5 119.135 1.78 -48Z P SP3 HSP3 109.471 3.00 +48Z C1 O1 HO1 109.708 3.00 +48Z SP3 P OP2 116.458 3.00 +48Z SP3 P O5 114.928 3.00 +48Z SP3 P OP1 116.458 3.00 +48Z OP2 P O5 106.327 3.00 +48Z OP2 P OP1 112.844 3.00 +48Z O5 P OP1 106.327 3.00 +48Z O1 C1 C2 110.590 2.70 +48Z O1 C1 O4 110.735 1.50 +48Z O1 C1 H1 110.390 2.72 +48Z C2 C1 O4 105.987 1.50 +48Z C2 C1 H1 110.781 3.00 +48Z O4 C1 H1 109.981 3.00 +48Z C1 C2 F2 110.545 3.00 +48Z C1 C2 C3 104.595 3.00 +48Z C1 C2 H2 110.979 1.50 +48Z F2 C2 C3 109.584 2.51 +48Z F2 C2 H2 111.293 3.00 +48Z C3 C2 H2 111.401 1.52 +48Z C2 C3 O3 111.747 3.00 +48Z C2 C3 C4 102.238 2.63 +48Z C2 C3 H3 110.152 2.42 +48Z O3 C3 C4 112.166 3.00 +48Z O3 C3 H3 110.652 1.50 +48Z C4 C3 H3 110.639 1.50 +48Z C3 O3 HO3 108.613 2.59 +48Z C3 C4 O4 105.543 1.50 +48Z C3 C4 C5 114.817 2.32 +48Z C3 C4 H4 109.427 1.50 +48Z O4 C4 C5 109.156 1.74 +48Z O4 C4 H4 109.143 2.48 +48Z C5 C4 H4 108.351 1.59 +48Z C4 O4 C1 108.677 2.31 +48Z C4 C5 O5 109.482 2.30 +48Z C4 C5 H52 109.589 1.50 +48Z C4 C5 H51 109.589 1.50 +48Z O5 C5 H52 109.954 1.50 +48Z O5 C5 H51 109.954 1.50 +48Z H52 C5 H51 108.471 1.50 +48Z P O5 C5 119.085 2.00 loop_ _chem_comp_tor.comp_id @@ -136,17 +160,16 @@ _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period -48Z sp3_sp3_37 C2 C1 O1 HO1 180.000 10.0 3 -48Z sp3_sp3_34 C5 O5 P SP3 180.000 10.0 3 -48Z sp3_sp3_31 OP2 P SP3 HSP3 180.000 10.0 3 -48Z sp3_sp3_5 O1 C1 C2 F2 60.000 10.0 3 -48Z sp3_sp3_44 O1 C1 O4 C4 60.000 10.0 3 -48Z sp3_sp3_14 F2 C2 C3 O3 -60.000 10.0 3 -48Z sp3_sp3_40 C2 C3 O3 HO3 180.000 10.0 3 -48Z sp3_sp3_23 O3 C3 C4 C5 60.000 10.0 3 -48Z sp3_sp3_29 C5 C4 O4 C1 180.000 10.0 3 -48Z sp3_sp3_46 C3 C4 C5 O5 180.000 10.0 3 -48Z sp3_sp3_55 C4 C5 O5 P 180.000 10.0 3 +48Z sp3_sp3_34 C2 C1 O1 HO1 180.000 10.0 3 +48Z sp3_sp3_31 C5 O5 P SP3 180.000 10.0 3 +48Z sp3_sp3_5 O1 C1 C2 F2 60.000 10.0 3 +48Z sp3_sp3_41 O1 C1 O4 C4 60.000 10.0 3 +48Z sp3_sp3_14 F2 C2 C3 O3 -60.000 10.0 3 +48Z sp3_sp3_37 C2 C3 O3 HO3 180.000 10.0 3 +48Z sp3_sp3_23 O3 C3 C4 C5 60.000 10.0 3 +48Z sp3_sp3_29 C5 C4 O4 C1 180.000 10.0 3 +48Z sp3_sp3_43 C3 C4 C5 O5 180.000 10.0 3 +48Z sp3_sp3_52 C4 C5 O5 P 180.000 10.0 3 loop_ _chem_comp_chir.comp_id @@ -156,11 +179,11 @@ _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign -48Z chir_1 P SP3 O5 OP2 both -48Z chir_2 C1 O4 O1 C2 positive -48Z chir_3 C2 F2 C1 C3 positive -48Z chir_4 C3 O3 C2 C4 negative -48Z chir_5 C4 O4 C3 C5 negative +48Z chir_1 P SP3 O5 OP2 both +48Z chir_2 C1 O4 O1 C2 positive +48Z chir_3 C2 F2 C1 C3 positive +48Z chir_4 C3 O3 C2 C4 negative +48Z chir_5 C4 O4 C3 C5 negative loop_ _pdbx_chem_comp_descriptor.comp_id @@ -168,20 +191,33 @@ _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor -48Z SMILES ACDLabs 12.01 FC1C(O)C(OC1O)COP(=O)(O)S -48Z InChI InChI 1.03 InChI=1S/C5H10FO6PS/c6-3-4(7)2(12-5(3)8)1-11-13(9,10)14/h2-5,7-8H,1H2,(H2,9,10,14)/t2-,3+,4-,5+/m1/s1 -48Z InChIKey InChI 1.03 ACXIGHNBDAUOFX-LECHCGJUSA-N -48Z SMILES_CANONICAL CACTVS 3.370 O[C@H]1O[C@H](CO[P](O)(S)=O)[C@@H](O)[C@@H]1F -48Z SMILES CACTVS 3.370 O[CH]1O[CH](CO[P](O)(S)=O)[CH](O)[CH]1F +48Z SMILES ACDLabs 12.01 FC1C(O)C(OC1O)COP(=O)(O)S +48Z InChI InChI 1.03 InChI=1S/C5H10FO6PS/c6-3-4(7)2(12-5(3)8)1-11-13(9,10)14/h2-5,7-8H,1H2,(H2,9,10,14)/t2-,3+,4-,5+/m1/s1 +48Z InChIKey InChI 1.03 ACXIGHNBDAUOFX-LECHCGJUSA-N +48Z SMILES_CANONICAL CACTVS 3.370 O[C@H]1O[C@H](CO[P](O)(S)=O)[C@@H](O)[C@@H]1F +48Z SMILES CACTVS 3.370 O[CH]1O[CH](CO[P](O)(S)=O)[CH](O)[CH]1F 48Z SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 C([C@@H]1[C@H]([C@@H]([C@H](O1)O)F)O)O[P@](=O)(O)S -48Z SMILES "OpenEye OEToolkits" 1.7.6 C(C1C(C(C(O1)O)F)O)OP(=O)(O)S +48Z SMILES "OpenEye OEToolkits" 1.7.6 C(C1C(C(C(O1)O)F)O)OP(=O)(O)S loop_ _pdbx_chem_comp_description_generator.comp_id _pdbx_chem_comp_description_generator.program_name _pdbx_chem_comp_description_generator.program_version _pdbx_chem_comp_description_generator.descriptor -48Z acedrg 243 "dictionary generator" -48Z acedrg_database 11 "data source" -48Z rdkit 2017.03.2 "Chemoinformatics tool" -48Z refmac5 5.8.0238 "optimization tool" +48Z acedrg 277 "dictionary generator" +48Z acedrg_database 12 "data source" +48Z rdkit 2019.09.1 "Chemoinformatics tool" +48Z refmac5 5.8.0425 "optimization tool" + +loop_ +_chem_comp_alias.comp_id +_chem_comp_alias.group +_chem_comp_alias.atom_id +_chem_comp_alias.atom_id_standard +48Z S-NA SP3 S2P +48Z S-NA OP2 OP3 +48Z S-NA O5 O5' +48Z S-NA C4 C4' +48Z S-NA C3 C3' +48Z S-NA O3 O3' +48Z S-NA HO3 HO3' diff --git a/6/6NW.cif b/6/6NW.cif index 0ca227d20..ff87227b2 100644 --- a/6/6NW.cif +++ b/6/6NW.cif @@ -7,7 +7,7 @@ _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level -6NW 6NW "2'-O-methyl-5'-O-thiophosphonoadenosine" NON-POLYMER 39 24 . +6NW 6NW "2'-O-methyl-5'-O-thiophosphonoadenosine" NON-POLYMER 38 24 . data_comp_6NW loop_ @@ -19,45 +19,87 @@ _chem_comp_atom.charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z -6NW P P P 0 -22.353 32.507 33.673 -6NW SP1 S SH1 0 -20.970 30.949 33.844 -6NW OP2 O O 0 -23.344 32.185 32.604 -6NW "O5'" O O2 0 -23.134 32.546 35.070 -6NW "C5'" C CH2 0 -23.862 31.372 35.512 -6NW "C4'" C CH1 0 -24.708 31.721 36.712 -6NW "O4'" O O2 0 -25.685 32.723 36.330 -6NW "C3'" C CH1 0 -25.520 30.566 37.310 -6NW "O3'" O OH1 0 -24.768 29.874 38.300 -6NW "C2'" C CH1 0 -26.747 31.281 37.882 -6NW "O2'" O O2 0 -26.530 31.806 39.189 -6NW "C1'" C CH1 0 -26.949 32.414 36.876 -6NW "CM'" C CH3 0 -27.715 31.905 39.976 -6NW N9 N NR5 0 -27.874 32.055 35.802 -6NW C8 C CR15 0 -27.591 31.833 34.475 -6NW N7 N NRD5 0 -28.645 31.529 33.760 -6NW C5 C CR56 0 -29.694 31.550 34.666 -6NW C6 C CR6 0 -31.079 31.310 34.525 -6NW N6 N NH2 0 -31.657 30.990 33.371 -6NW N1 N NRD6 0 -31.852 31.414 35.637 -6NW C2 C CR16 0 -31.262 31.738 36.799 -6NW N3 N NRD6 0 -29.975 31.985 37.047 -6NW C4 C CR56 0 -29.232 31.876 35.929 -6NW OP3 O OP -1 -21.643 33.809 33.510 -6NW H1 H HSH1 0 -19.882 31.332 33.476 -6NW "H5''" H H 0 -23.226 30.655 35.755 -6NW "H5'" H H 0 -24.442 31.042 34.783 -6NW "H4'" H H 0 -24.121 32.097 37.403 -6NW "H3'" H H 0 -25.797 29.939 36.592 -6NW "HO3'" H H 0 -25.269 29.297 38.670 -6NW "H2'" H H 0 -27.515 30.657 37.884 -6NW H7 H H 0 -27.300 33.202 37.350 -6NW H11 H H 0 -27.513 32.367 40.806 -6NW H9 H H 0 -28.046 31.014 40.175 -6NW H10 H H 0 -28.391 32.401 39.486 -6NW H8 H H 0 -26.724 31.893 34.112 -6NW H61 H H 0 -32.475 31.261 33.204 -6NW H62 H H 0 -31.218 30.510 32.783 -6NW H2 H H 0 -31.839 31.799 37.544 +6NW P P P 0 -22.090 32.460 33.954 +6NW SP1 S S1 0 -20.565 31.357 34.444 +6NW OP2 O OP -1 -22.834 31.894 32.784 +6NW "O5'" O O2 0 -23.224 32.535 35.093 +6NW "C5'" C CH2 0 -23.941 31.341 35.452 +6NW "C4'" C CH1 0 -24.756 31.596 36.697 +6NW "O4'" O O2 0 -25.701 32.656 36.437 +6NW "C3'" C CH1 0 -25.599 30.410 37.177 +6NW "O3'" O OH1 0 -24.847 29.593 38.068 +6NW "C2'" C CH1 0 -26.788 31.095 37.853 +6NW "O2'" O O2 0 -26.513 31.491 39.186 +6NW "C1'" C CH1 0 -26.982 32.315 36.958 +6NW "CM'" C CH3 0 -27.673 31.651 39.987 +6NW N9 N NR5 0 -27.909 32.062 35.853 +6NW C8 C CR15 0 -27.648 31.874 34.518 +6NW N7 N NRD5 0 -28.720 31.669 33.793 +6NW C5 C CR56 0 -29.760 31.723 34.710 +6NW C6 C CR6 0 -31.157 31.580 34.566 +6NW N6 N NH2 0 -31.760 31.345 33.400 +6NW N1 N NRD6 0 -31.919 31.691 35.688 +6NW C2 C CR16 0 -31.308 31.927 36.858 +6NW N3 N NRD6 0 -30.008 32.079 37.109 +6NW C4 C CR56 0 -29.274 31.966 35.984 +6NW OP3 O OP -1 -21.758 33.887 33.661 +6NW "H5''" H H 0 -23.304 30.601 35.620 +6NW "H5'" H H 0 -24.543 31.073 34.712 +6NW "H4'" H H 0 -24.142 31.878 37.420 +6NW "H3'" H H 0 -25.911 29.877 36.403 +6NW "HO3'" H H 0 -25.346 29.002 38.391 +6NW "H2'" H H 0 -27.571 30.489 37.819 +6NW H7 H H 0 -27.332 33.088 37.517 +6NW H11 H H 0 -27.422 32.014 40.848 +6NW H9 H H 0 -28.101 30.792 40.112 +6NW H10 H H 0 -28.289 32.258 39.549 +6NW H8 H H 0 -26.778 31.892 34.158 +6NW H61 H H 0 -32.636 31.262 33.362 +6NW H62 H H 0 -31.281 31.273 32.664 +6NW H2 H H 0 -31.879 31.995 37.609 + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +6NW P P(OC)(O)2(S) +6NW SP1 S(PO3) +6NW OP2 O(POOS) +6NW "O5'" O(CC[5]HH)(POOS) +6NW "C5'" C(C[5]C[5]O[5]H)(OP)(H)2 +6NW "C4'" C[5](C[5]C[5]HO)(O[5]C[5])(CHHO)(H){1|N<3>,1|O<2>,2|H<1>} +6NW "O4'" O[5](C[5]N[5a]C[5]H)(C[5]C[5]CH){2|C<3>,2|H<1>,2|O<2>} +6NW "C3'" C[5](C[5]C[5]HO)(C[5]O[5]CH)(OH)(H){1|H<1>,1|N<3>} +6NW "O3'" O(C[5]C[5]2H)(H) +6NW "C2'" C[5](C[5]N[5a]O[5]H)(C[5]C[5]HO)(OC)(H){1|C<4>,1|H<1>,2|C<3>} +6NW "O2'" O(C[5]C[5]2H)(CH3) +6NW "C1'" C[5](N[5a]C[5a,6a]C[5a])(C[5]C[5]HO)(O[5]C[5])(H){1|C<3>,1|C<4>,1|O<2>,2|N<2>,3|H<1>} +6NW "CM'" C(OC[5])(H)3 +6NW N9 N[5a](C[5a,6a]C[5a,6a]N[6a])(C[5]C[5]O[5]H)(C[5a]N[5a]H){1|H<1>,1|O<2>,2|C<3>,2|C<4>} +6NW C8 C[5a](N[5a]C[5a,6a]C[5])(N[5a]C[5a,6a])(H){1|C<3>,1|C<4>,1|H<1>,1|N<2>,1|O<2>} +6NW N7 N[5a](C[5a,6a]C[5a,6a]C[6a])(C[5a]N[5a]H){1|C<4>,1|N<3>,2|N<2>} +6NW C5 C[5a,6a](C[5a,6a]N[5a]N[6a])(C[6a]N[6a]N)(N[5a]C[5a]){1|C<3>,1|C<4>,1|H<1>} +6NW C6 C[6a](C[5a,6a]C[5a,6a]N[5a])(N[6a]C[6a])(NHH){1|C<3>,1|H<1>,1|N<2>,1|N<3>} +6NW N6 N(C[6a]C[5a,6a]N[6a])(H)2 +6NW N1 N[6a](C[6a]C[5a,6a]N)(C[6a]N[6a]H){1|C<3>,1|N<2>} +6NW C2 C[6a](N[6a]C[5a,6a])(N[6a]C[6a])(H){1|C<3>,2|N<3>} +6NW N3 N[6a](C[5a,6a]C[5a,6a]N[5a])(C[6a]N[6a]H){1|C<4>,1|N<2>,2|C<3>} +6NW C4 C[5a,6a](C[5a,6a]C[6a]N[5a])(N[5a]C[5a]C[5])(N[6a]C[6a]){1|C<4>,1|N<2>,1|N<3>,1|O<2>,3|H<1>} +6NW OP3 O(POOS) +6NW "H5''" H(CC[5]HO) +6NW "H5'" H(CC[5]HO) +6NW "H4'" H(C[5]C[5]O[5]C) +6NW "H3'" H(C[5]C[5]2O) +6NW "HO3'" H(OC[5]) +6NW "H2'" H(C[5]C[5]2O) +6NW H7 H(C[5]N[5a]C[5]O[5]) +6NW H11 H(CHHO) +6NW H9 H(CHHO) +6NW H10 H(CHHO) +6NW H8 H(C[5a]N[5a]2) +6NW H61 H(NC[6a]H) +6NW H62 H(NC[6a]H) +6NW H2 H(C[6a]N[6a]2) loop_ _chem_comp_bond.comp_id @@ -69,47 +111,46 @@ _chem_comp_bond.value_dist_nucleus _chem_comp_bond.value_dist_nucleus_esd _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd -6NW P SP1 SINGLE n 2.091 0.0200 2.091 0.0200 -6NW P OP2 DOUBLE n 1.493 0.0157 1.493 0.0157 -6NW P "O5'" SINGLE n 1.601 0.0114 1.601 0.0114 -6NW "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 -6NW "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 -6NW "C4'" "O4'" SINGLE n 1.451 0.0100 1.451 0.0100 -6NW "C4'" "C3'" SINGLE n 1.535 0.0100 1.535 0.0100 -6NW "O4'" "C1'" SINGLE n 1.409 0.0100 1.409 0.0100 -6NW "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 -6NW "C3'" "C2'" SINGLE n 1.530 0.0134 1.530 0.0134 -6NW "C2'" "O2'" SINGLE n 1.423 0.0100 1.423 0.0100 -6NW "C2'" "C1'" SINGLE n 1.527 0.0100 1.527 0.0100 -6NW "O2'" "CM'" SINGLE n 1.423 0.0131 1.423 0.0131 -6NW "C1'" N9 SINGLE n 1.458 0.0100 1.458 0.0100 -6NW N9 C8 SINGLE y 1.372 0.0100 1.372 0.0100 -6NW N9 C4 SINGLE y 1.374 0.0101 1.374 0.0101 -6NW C8 N7 DOUBLE y 1.310 0.0100 1.310 0.0100 -6NW N7 C5 SINGLE y 1.388 0.0100 1.388 0.0100 -6NW C5 C6 SINGLE y 1.408 0.0100 1.408 0.0100 -6NW C5 C4 DOUBLE y 1.381 0.0100 1.381 0.0100 -6NW C6 N6 SINGLE n 1.330 0.0100 1.330 0.0100 -6NW C6 N1 DOUBLE y 1.354 0.0100 1.354 0.0100 -6NW N1 C2 SINGLE y 1.339 0.0100 1.339 0.0100 -6NW C2 N3 DOUBLE y 1.330 0.0100 1.330 0.0100 -6NW N3 C4 SINGLE y 1.343 0.0100 1.343 0.0100 -6NW P OP3 SINGLE n 1.493 0.0157 1.493 0.0157 -6NW SP1 H1 SINGLE n 1.338 0.0100 1.211 0.0200 -6NW "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200 -6NW "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 -6NW "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200 -6NW "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200 -6NW "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 -6NW "C2'" "H2'" SINGLE n 1.089 0.0100 0.988 0.0200 -6NW "C1'" H7 SINGLE n 1.089 0.0100 0.984 0.0200 -6NW "CM'" H11 SINGLE n 1.089 0.0100 0.971 0.0146 -6NW "CM'" H9 SINGLE n 1.089 0.0100 0.971 0.0146 -6NW "CM'" H10 SINGLE n 1.089 0.0100 0.971 0.0146 -6NW C8 H8 SINGLE n 1.082 0.0130 0.942 0.0170 -6NW N6 H61 SINGLE n 1.016 0.0100 0.877 0.0200 -6NW N6 H62 SINGLE n 1.016 0.0100 0.877 0.0200 -6NW C2 H2 SINGLE n 1.082 0.0130 0.945 0.0200 +6NW P SP1 DOUBLE n 1.949 0.0200 1.949 0.0200 +6NW P OP2 SINGLE n 1.497 0.0143 1.497 0.0143 +6NW P "O5'" SINGLE n 1.613 0.0200 1.613 0.0200 +6NW "O5'" "C5'" SINGLE n 1.438 0.0200 1.438 0.0200 +6NW "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 +6NW "C4'" "O4'" SINGLE n 1.444 0.0100 1.444 0.0100 +6NW "C4'" "C3'" SINGLE n 1.532 0.0100 1.532 0.0100 +6NW "O4'" "C1'" SINGLE n 1.423 0.0100 1.423 0.0100 +6NW "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +6NW "C3'" "C2'" SINGLE n 1.529 0.0100 1.529 0.0100 +6NW "C2'" "O2'" SINGLE n 1.415 0.0100 1.415 0.0100 +6NW "C2'" "C1'" SINGLE n 1.524 0.0126 1.524 0.0126 +6NW "O2'" "CM'" SINGLE n 1.415 0.0136 1.415 0.0136 +6NW "C1'" N9 SINGLE n 1.462 0.0102 1.462 0.0102 +6NW N9 C8 SINGLE y 1.371 0.0100 1.371 0.0100 +6NW N9 C4 SINGLE y 1.374 0.0101 1.374 0.0101 +6NW C8 N7 DOUBLE y 1.311 0.0100 1.311 0.0100 +6NW N7 C5 SINGLE y 1.388 0.0100 1.388 0.0100 +6NW C5 C6 SINGLE y 1.407 0.0100 1.407 0.0100 +6NW C5 C4 DOUBLE y 1.382 0.0100 1.382 0.0100 +6NW C6 N6 SINGLE n 1.332 0.0107 1.332 0.0107 +6NW C6 N1 DOUBLE y 1.355 0.0106 1.355 0.0106 +6NW N1 C2 SINGLE y 1.338 0.0100 1.338 0.0100 +6NW C2 N3 DOUBLE y 1.329 0.0100 1.329 0.0100 +6NW N3 C4 SINGLE y 1.344 0.0100 1.344 0.0100 +6NW P OP3 SINGLE n 1.497 0.0143 1.497 0.0143 +6NW "C5'" "H5''" SINGLE n 1.092 0.0100 0.991 0.0200 +6NW "C5'" "H5'" SINGLE n 1.092 0.0100 0.991 0.0200 +6NW "C4'" "H4'" SINGLE n 1.092 0.0100 0.990 0.0200 +6NW "C3'" "H3'" SINGLE n 1.092 0.0100 0.991 0.0200 +6NW "O3'" "HO3'" SINGLE n 0.972 0.0180 0.839 0.0200 +6NW "C2'" "H2'" SINGLE n 1.092 0.0100 0.990 0.0134 +6NW "C1'" H7 SINGLE n 1.092 0.0100 1.016 0.0200 +6NW "CM'" H11 SINGLE n 1.092 0.0100 0.968 0.0164 +6NW "CM'" H9 SINGLE n 1.092 0.0100 0.968 0.0164 +6NW "CM'" H10 SINGLE n 1.092 0.0100 0.968 0.0164 +6NW C8 H8 SINGLE n 1.085 0.0150 0.942 0.0168 +6NW N6 H61 SINGLE n 1.013 0.0120 0.880 0.0200 +6NW N6 H62 SINGLE n 1.013 0.0120 0.880 0.0200 +6NW C2 H2 SINGLE n 1.085 0.0150 0.946 0.0200 loop_ _chem_comp_angle.comp_id @@ -118,77 +159,76 @@ _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd -6NW SP1 P OP2 111.281 3.00 -6NW SP1 P "O5'" 105.685 3.00 -6NW SP1 P OP3 111.281 3.00 -6NW OP2 P "O5'" 108.530 2.45 -6NW OP2 P OP3 116.964 2.85 -6NW "O5'" P OP3 108.530 2.45 -6NW P SP1 H1 109.471 3.00 -6NW P "O5'" "C5'" 119.135 1.78 -6NW "O5'" "C5'" "C4'" 109.510 1.50 -6NW "O5'" "C5'" "H5''" 109.821 1.50 -6NW "O5'" "C5'" "H5'" 109.821 1.50 -6NW "C4'" "C5'" "H5''" 109.624 1.50 -6NW "C4'" "C5'" "H5'" 109.624 1.50 -6NW "H5''" "C5'" "H5'" 108.472 1.50 -6NW "C5'" "C4'" "O4'" 109.123 1.50 -6NW "C5'" "C4'" "C3'" 116.008 1.52 -6NW "C5'" "C4'" "H4'" 108.268 1.50 -6NW "O4'" "C4'" "C3'" 105.388 1.50 -6NW "O4'" "C4'" "H4'" 108.947 1.50 -6NW "C3'" "C4'" "H4'" 109.363 1.86 -6NW "C4'" "O4'" "C1'" 109.903 1.50 -6NW "C4'" "C3'" "O3'" 111.281 2.46 -6NW "C4'" "C3'" "C2'" 102.352 1.50 -6NW "C4'" "C3'" "H3'" 110.452 2.54 -6NW "O3'" "C3'" "C2'" 112.463 2.73 -6NW "O3'" "C3'" "H3'" 110.380 1.67 -6NW "C2'" "C3'" "H3'" 110.255 2.04 -6NW "C3'" "O3'" "HO3'" 108.744 3.00 -6NW "C3'" "C2'" "O2'" 112.623 3.00 -6NW "C3'" "C2'" "C1'" 101.388 1.50 -6NW "C3'" "C2'" "H2'" 110.255 2.04 -6NW "O2'" "C2'" "C1'" 110.738 2.44 -6NW "O2'" "C2'" "H2'" 110.257 1.68 -6NW "C1'" "C2'" "H2'" 111.584 1.94 -6NW "C2'" "O2'" "CM'" 113.084 1.50 -6NW "O4'" "C1'" "C2'" 106.765 1.50 -6NW "O4'" "C1'" N9 108.477 1.50 -6NW "O4'" "C1'" H7 109.807 1.50 -6NW "C2'" "C1'" N9 112.584 1.50 -6NW "C2'" "C1'" H7 109.263 1.50 -6NW N9 "C1'" H7 109.561 1.50 -6NW "O2'" "CM'" H11 109.434 1.50 -6NW "O2'" "CM'" H9 109.434 1.50 -6NW "O2'" "CM'" H10 109.434 1.50 -6NW H11 "CM'" H9 109.541 1.50 -6NW H11 "CM'" H10 109.541 1.50 -6NW H9 "CM'" H10 109.541 1.50 -6NW "C1'" N9 C8 126.848 1.91 -6NW "C1'" N9 C4 127.459 1.80 -6NW C8 N9 C4 105.693 1.50 -6NW N9 C8 N7 113.469 1.50 -6NW N9 C8 H8 123.206 1.50 -6NW N7 C8 H8 123.326 1.50 -6NW C8 N7 C5 104.739 1.50 -6NW N7 C5 C6 132.250 1.50 -6NW N7 C5 C4 110.483 1.50 -6NW C6 C5 C4 117.267 1.50 -6NW C5 C6 N6 123.792 1.50 -6NW C5 C6 N1 117.409 1.50 -6NW N6 C6 N1 118.799 1.50 -6NW C6 N6 H61 119.723 1.50 -6NW C6 N6 H62 119.723 1.50 -6NW H61 N6 H62 120.554 1.88 -6NW C6 N1 C2 118.521 1.50 -6NW N1 C2 N3 129.332 1.50 -6NW N1 C2 H2 115.313 1.50 -6NW N3 C2 H2 115.355 1.50 -6NW C2 N3 C4 110.982 1.50 -6NW N9 C4 C5 105.616 1.50 -6NW N9 C4 N3 127.895 1.50 -6NW C5 C4 N3 126.489 1.50 +6NW SP1 P OP2 116.458 3.00 +6NW SP1 P "O5'" 114.928 3.00 +6NW SP1 P OP3 116.458 3.00 +6NW OP2 P "O5'" 106.327 3.00 +6NW OP2 P OP3 112.844 3.00 +6NW "O5'" P OP3 106.327 3.00 +6NW P "O5'" "C5'" 119.085 2.00 +6NW "O5'" "C5'" "C4'" 109.482 2.30 +6NW "O5'" "C5'" "H5''" 109.954 1.50 +6NW "O5'" "C5'" "H5'" 109.954 1.50 +6NW "C4'" "C5'" "H5''" 109.589 1.50 +6NW "C4'" "C5'" "H5'" 109.589 1.50 +6NW "H5''" "C5'" "H5'" 108.471 1.50 +6NW "C5'" "C4'" "O4'" 109.154 1.50 +6NW "C5'" "C4'" "C3'" 115.288 1.50 +6NW "C5'" "C4'" "H4'" 108.351 1.59 +6NW "O4'" "C4'" "C3'" 105.318 1.50 +6NW "O4'" "C4'" "H4'" 109.120 1.50 +6NW "C3'" "C4'" "H4'" 109.322 2.54 +6NW "C4'" "O4'" "C1'" 109.502 2.85 +6NW "C4'" "C3'" "O3'" 110.713 3.00 +6NW "C4'" "C3'" "C2'" 102.511 1.50 +6NW "C4'" "C3'" "H3'" 110.577 3.00 +6NW "O3'" "C3'" "C2'" 112.059 3.00 +6NW "O3'" "C3'" "H3'" 110.541 2.08 +6NW "C2'" "C3'" "H3'" 110.368 2.92 +6NW "C3'" "O3'" "HO3'" 109.389 3.00 +6NW "C3'" "C2'" "O2'" 112.208 3.00 +6NW "C3'" "C2'" "C1'" 101.348 1.50 +6NW "C3'" "C2'" "H2'" 110.368 2.92 +6NW "O2'" "C2'" "C1'" 110.752 3.00 +6NW "O2'" "C2'" "H2'" 110.191 2.23 +6NW "C1'" "C2'" "H2'" 111.584 3.00 +6NW "C2'" "O2'" "CM'" 112.888 1.50 +6NW "O4'" "C1'" "C2'" 106.765 1.50 +6NW "O4'" "C1'" N9 108.577 1.50 +6NW "O4'" "C1'" H7 109.833 2.53 +6NW "C2'" "C1'" N9 112.584 1.50 +6NW "C2'" "C1'" H7 109.263 1.50 +6NW N9 "C1'" H7 109.411 1.50 +6NW "O2'" "CM'" H11 109.455 1.50 +6NW "O2'" "CM'" H9 109.455 1.50 +6NW "O2'" "CM'" H10 109.455 1.50 +6NW H11 "CM'" H9 109.475 1.50 +6NW H11 "CM'" H10 109.475 1.50 +6NW H9 "CM'" H10 109.475 1.50 +6NW "C1'" N9 C8 127.072 3.00 +6NW "C1'" N9 C4 126.969 2.94 +6NW C8 N9 C4 105.958 1.50 +6NW N9 C8 N7 113.692 1.50 +6NW N9 C8 H8 122.949 1.50 +6NW N7 C8 H8 123.359 1.50 +6NW C8 N7 C5 103.906 1.50 +6NW N7 C5 C6 131.998 1.50 +6NW N7 C5 C4 110.646 1.50 +6NW C6 C5 C4 117.356 1.50 +6NW C5 C6 N6 123.773 1.50 +6NW C5 C6 N1 117.375 1.50 +6NW N6 C6 N1 118.852 1.50 +6NW C6 N6 H61 119.818 3.00 +6NW C6 N6 H62 119.818 3.00 +6NW H61 N6 H62 120.363 3.00 +6NW C6 N1 C2 118.603 1.50 +6NW N1 C2 N3 129.210 1.50 +6NW N1 C2 H2 115.363 1.50 +6NW N3 C2 H2 115.427 1.50 +6NW C2 N3 C4 111.101 1.50 +6NW N9 C4 C5 105.797 1.50 +6NW N9 C4 N3 127.848 1.50 +6NW C5 C4 N3 126.355 1.50 loop_ _chem_comp_tor.comp_id @@ -200,36 +240,34 @@ _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period -6NW C2e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 -6NW C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 -6NW C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 -6NW C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 -6NW C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 -6NW C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 -6NW C3e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 -6NW C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 -6NW C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 -6NW C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 -6NW C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 -6NW C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 -6NW beta P "O5'" "C5'" "C4'" 180.000 10.00 3 -6NW epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 -6NW gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 -6NW sp3_sp3_27 OP2 P SP1 H1 -60.000 10.0 3 -6NW sp3_sp3_28 "C5'" "O5'" P SP1 180.000 10.0 3 -6NW sp3_sp3_58 H11 "CM'" "O2'" "C2'" 180.000 10.0 3 -6NW const_14 N7 C8 N9 "C1'" 180.000 10.0 2 -6NW const_26 C5 C4 N9 "C1'" 180.000 10.0 2 -6NW const_17 N9 C8 N7 C5 0.000 10.0 2 -6NW const_20 C6 C5 N7 C8 180.000 10.0 2 -6NW const_sp2_sp2_4 N7 C5 C6 N6 0.000 5.0 2 -6NW const_21 N9 C4 C5 N7 0.000 10.0 2 -6NW sp2_sp2_1 C5 C6 N6 H61 180.000 5.0 2 -6NW const_sp2_sp2_6 N6 C6 N1 C2 180.000 5.0 2 -6NW const_sp2_sp2_7 N3 C2 N1 C6 0.000 5.0 2 -6NW const_sp2_sp2_9 N1 C2 N3 C4 0.000 5.0 2 -6NW const_12 N9 C4 N3 C2 180.000 10.0 2 -6NW sp3_sp3_55 "C3'" "C2'" "O2'" "CM'" 180.000 10.0 3 +6NW sp3_sp3_25 "C5'" "O5'" P SP1 180.000 10.0 3 +6NW sp3_sp3_55 H11 "CM'" "O2'" "C2'" 180.000 10.0 3 +6NW sp2_sp3_1 C8 N9 "C1'" "O4'" 150.000 10.0 6 +6NW const_13 N7 C8 N9 C4 0.000 0.0 1 +6NW const_16 H8 C8 N9 "C1'" 0.000 0.0 1 +6NW const_25 C5 C4 N9 C8 0.000 0.0 1 +6NW const_28 N3 C4 N9 "C1'" 0.000 0.0 1 +6NW const_17 N9 C8 N7 C5 0.000 0.0 1 +6NW const_19 C4 C5 N7 C8 0.000 0.0 1 +6NW const_sp2_sp2_1 C4 C5 C6 N1 0.000 0.0 1 +6NW const_sp2_sp2_4 N7 C5 C6 N6 0.000 0.0 1 +6NW const_21 N9 C4 C5 N7 0.000 0.0 1 +6NW const_24 N3 C4 C5 C6 0.000 0.0 1 +6NW sp2_sp2_29 C5 C6 N6 H61 180.000 20 2 +6NW sp2_sp2_32 N1 C6 N6 H62 180.000 20 2 +6NW const_sp2_sp2_5 C5 C6 N1 C2 0.000 0.0 1 +6NW const_sp2_sp2_7 N3 C2 N1 C6 0.000 0.0 1 +6NW const_sp2_sp2_9 N1 C2 N3 C4 0.000 0.0 1 +6NW const_11 C5 C4 N3 C2 0.000 0.0 1 +6NW sp3_sp3_28 "C4'" "C5'" "O5'" P 180.000 10.0 3 +6NW sp3_sp3_31 "O4'" "C4'" "C5'" "O5'" 180.000 10.0 3 +6NW sp3_sp3_2 "C5'" "C4'" "O4'" "C1'" -60.000 10.0 3 +6NW sp3_sp3_44 "O3'" "C3'" "C4'" "C5'" 180.000 10.0 3 +6NW sp3_sp3_4 "C2'" "C1'" "O4'" "C4'" -60.000 10.0 3 +6NW sp3_sp3_49 "C4'" "C3'" "O3'" "HO3'" 180.000 10.0 3 +6NW sp3_sp3_20 "O2'" "C2'" "C3'" "O3'" -60.000 10.0 3 +6NW sp3_sp3_52 "C3'" "C2'" "O2'" "CM'" 180.000 10.0 3 +6NW sp3_sp3_8 "O4'" "C1'" "C2'" "O2'" 180.000 10.0 3 loop_ _chem_comp_chir.comp_id @@ -239,11 +277,11 @@ _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign -6NW chir_1 P SP1 "O5'" OP3 both +6NW chir_1 P SP1 "O5'" OP3 both 6NW chir_2 "C4'" "O4'" "C3'" "C5'" negative 6NW chir_3 "C3'" "O3'" "C2'" "C4'" negative 6NW chir_4 "C2'" "O2'" "C1'" "C3'" negative -6NW chir_5 "C1'" "O4'" N9 "C2'" negative +6NW chir_5 "C1'" "O4'" N9 "C2'" negative loop_ _chem_comp_plane_atom.comp_id @@ -251,22 +289,28 @@ _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd 6NW plan-1 "C1'" 0.020 -6NW plan-1 C2 0.020 -6NW plan-1 C4 0.020 -6NW plan-1 C5 0.020 -6NW plan-1 C6 0.020 -6NW plan-1 C8 0.020 -6NW plan-1 H2 0.020 -6NW plan-1 H8 0.020 -6NW plan-1 N1 0.020 -6NW plan-1 N3 0.020 -6NW plan-1 N6 0.020 -6NW plan-1 N7 0.020 -6NW plan-1 N9 0.020 -6NW plan-2 C6 0.020 -6NW plan-2 H61 0.020 -6NW plan-2 H62 0.020 -6NW plan-2 N6 0.020 +6NW plan-1 C4 0.020 +6NW plan-1 C5 0.020 +6NW plan-1 C6 0.020 +6NW plan-1 C8 0.020 +6NW plan-1 H8 0.020 +6NW plan-1 N3 0.020 +6NW plan-1 N7 0.020 +6NW plan-1 N9 0.020 +6NW plan-2 C2 0.020 +6NW plan-2 C4 0.020 +6NW plan-2 C5 0.020 +6NW plan-2 C6 0.020 +6NW plan-2 H2 0.020 +6NW plan-2 N1 0.020 +6NW plan-2 N3 0.020 +6NW plan-2 N6 0.020 +6NW plan-2 N7 0.020 +6NW plan-2 N9 0.020 +6NW plan-3 C6 0.020 +6NW plan-3 H61 0.020 +6NW plan-3 H62 0.020 +6NW plan-3 N6 0.020 loop_ _pdbx_chem_comp_descriptor.comp_id @@ -274,20 +318,28 @@ _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor -6NW SMILES ACDLabs 12.01 P(S)(=O)(OCC1OC(C(C1O)OC)n2cnc3c(N)ncnc23)O -6NW InChI InChI 1.03 InChI=1S/C11H16N5O6PS/c1-20-8-7(17)5(2-21-23(18,19)24)22-11(8)16-4-15-6-9(12)13-3-14-10(6)16/h3-5,7-8,11,17H,2H2,1H3,(H2,12,13,14)(H2,18,19,24)/t5-,7-,8-,11-/m1/s1 -6NW InChIKey InChI 1.03 OXNLMRLCWQEYRW-IOSLPCCCSA-N -6NW SMILES_CANONICAL CACTVS 3.385 CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(S)=O)O[C@H]1n2cnc3c(N)ncnc23 -6NW SMILES CACTVS 3.385 CO[CH]1[CH](O)[CH](CO[P](O)(S)=O)O[CH]1n2cnc3c(N)ncnc23 +6NW SMILES ACDLabs 12.01 P(S)(=O)(OCC1OC(C(C1O)OC)n2cnc3c(N)ncnc23)O +6NW InChI InChI 1.03 InChI=1S/C11H16N5O6PS/c1-20-8-7(17)5(2-21-23(18,19)24)22-11(8)16-4-15-6-9(12)13-3-14-10(6)16/h3-5,7-8,11,17H,2H2,1H3,(H2,12,13,14)(H2,18,19,24)/t5-,7-,8-,11-/m1/s1 +6NW InChIKey InChI 1.03 OXNLMRLCWQEYRW-IOSLPCCCSA-N +6NW SMILES_CANONICAL CACTVS 3.385 CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(S)=O)O[C@H]1n2cnc3c(N)ncnc23 +6NW SMILES CACTVS 3.385 CO[CH]1[CH](O)[CH](CO[P](O)(S)=O)O[CH]1n2cnc3c(N)ncnc23 6NW SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 CO[C@@H]1[C@@H]([C@H](O[C@H]1n2cnc3c2ncnc3N)COP(=O)(O)S)O -6NW SMILES "OpenEye OEToolkits" 2.0.4 COC1C(C(OC1n2cnc3c2ncnc3N)COP(=O)(O)S)O +6NW SMILES "OpenEye OEToolkits" 2.0.4 COC1C(C(OC1n2cnc3c2ncnc3N)COP(=O)(O)S)O loop_ _pdbx_chem_comp_description_generator.comp_id _pdbx_chem_comp_description_generator.program_name _pdbx_chem_comp_description_generator.program_version _pdbx_chem_comp_description_generator.descriptor -6NW acedrg 243 "dictionary generator" -6NW acedrg_database 11 "data source" -6NW rdkit 2017.03.2 "Chemoinformatics tool" -6NW refmac5 5.8.0238 "optimization tool" +6NW acedrg 277 "dictionary generator" +6NW acedrg_database 12 "data source" +6NW rdkit 2019.09.1 "Chemoinformatics tool" +6NW refmac5 5.8.0425 "optimization tool" + +loop_ +_chem_comp_alias.comp_id +_chem_comp_alias.group +_chem_comp_alias.atom_id +_chem_comp_alias.atom_id_standard +6NW S-NA OP2 OP1 +6NW S-NA SP1 S2P diff --git a/6/6OO.cif b/6/6OO.cif index 4fe495917..a7f85080c 100644 --- a/6/6OO.cif +++ b/6/6OO.cif @@ -7,7 +7,7 @@ _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level -6OO 6OO "2'-O-methyl-5'-O-thiophosphonocytidine" NON-POLYMER 37 22 . +6OO 6OO "2'-O-methyl-5'-O-thiophosphonocytidine" NON-POLYMER 36 22 . data_comp_6OO loop_ @@ -19,43 +19,42 @@ _chem_comp_atom.charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z -6OO C2 C CR6 0 -31.844 25.390 38.490 -6OO C4 C CR6 0 -29.866 26.186 37.494 -6OO C5 C CR16 0 -29.073 25.565 38.500 -6OO C6 C CR16 0 -29.710 24.877 39.463 -6OO O2 O O 0 -33.079 25.299 38.504 -6OO P P P 0 -27.349 24.828 43.714 -6OO SP1 S SH1 0 -27.679 24.955 45.754 -6OO OP2 O O 0 -26.544 23.608 43.384 -6OO "O5'" O O2 0 -28.779 24.638 43.022 -6OO "C5'" C CH2 0 -29.843 23.926 43.702 -6OO "C4'" C CH1 0 -30.863 23.445 42.698 -6OO "O4'" O O2 0 -31.274 24.519 41.826 -6OO "C3'" C CH1 0 -30.379 22.350 41.745 -6OO "O3'" O OH1 0 -30.442 21.080 42.384 -6OO "C2'" C CH1 0 -31.345 22.489 40.563 -6OO "O2'" O O2 0 -32.499 21.688 40.723 -6OO "C1'" C CH1 0 -31.710 23.988 40.595 -6OO "CM'" C CH3 0 -33.178 21.430 39.504 -6OO N1 N NR6 0 -31.073 24.772 39.493 -6OO N3 N NRD6 0 -31.207 26.087 37.512 -6OO N4 N NH2 0 -29.302 26.880 36.512 -6OO O1 O OP -1 -26.775 26.109 43.188 -6OO H1 H H 0 -28.133 25.632 38.491 -6OO H2 H H 0 -29.213 24.459 40.139 -6OO H3 H HSH1 0 -27.459 27.072 45.467 -6OO H4 H H 0 -30.283 24.525 44.357 -6OO H5 H H 0 -29.470 23.148 44.191 -6OO H6 H H 0 -31.655 23.117 43.194 -6OO H7 H H 0 -29.452 22.534 41.451 -6OO H8 H H 0 -30.766 21.184 43.174 -6OO H9 H H 0 -30.855 22.251 39.724 -6OO H10 H H 0 -32.697 24.082 40.546 -6OO H11 H H 0 -33.989 20.934 39.688 -6OO H12 H H 0 -32.609 20.908 38.920 -6OO H13 H H 0 -33.404 22.266 39.073 -6OO H14 H H 0 -28.430 26.960 36.481 -6OO H15 H H 0 -29.797 27.259 35.896 +6OO C2 C CR6 0 -32.212 25.615 38.999 +6OO C4 C CR6 0 -30.456 26.873 38.066 +6OO C5 C CR16 0 -29.492 26.145 38.821 +6OO C6 C CR16 0 -29.940 25.176 39.639 +6OO O2 O O 0 -33.421 25.361 39.093 +6OO P P P 0 -27.283 24.498 43.874 +6OO SP1 S S1 0 -27.318 24.009 45.758 +6OO OP2 O OP -1 -26.269 23.703 43.112 +6OO "O5'" O O2 0 -28.642 24.190 43.065 +6OO "C5'" C CH2 0 -29.594 23.248 43.596 +6OO "C4'" C CH1 0 -30.619 22.900 42.544 +6OO "O4'" O O2 0 -31.197 24.091 41.969 +6OO "C3'" C CH1 0 -30.086 22.128 41.335 +6OO "O3'" O OH1 0 -29.946 20.749 41.655 +6OO "C2'" C CH1 0 -31.154 22.407 40.272 +6OO "O2'" O O2 0 -32.188 21.442 40.290 +6OO "C1'" C CH1 0 -31.692 23.794 40.683 +6OO "CM'" C CH3 0 -32.929 21.388 39.082 +6OO N1 N NR6 0 -31.272 24.889 39.754 +6OO N3 N NRD6 0 -31.768 26.596 38.170 +6OO N4 N NH2 0 -30.084 27.843 37.239 +6OO O1 O OP -1 -27.036 25.954 43.632 +6OO H1 H H 0 -28.573 26.336 38.752 +6OO H2 H H 0 -29.329 24.681 40.149 +6OO H4 H H 0 -30.050 23.639 44.385 +6OO H5 H H 0 -29.127 22.423 43.884 +6OO H6 H H 0 -31.339 22.374 42.974 +6OO H7 H H 0 -29.216 22.499 41.045 +6OO H8 H H 0 -29.346 20.656 42.234 +6OO H9 H H 0 -30.708 22.438 39.377 +6OO H10 H H 0 -32.683 23.756 40.729 +6OO H11 H H 0 -33.656 20.756 39.180 +6OO H12 H H 0 -32.351 21.103 38.360 +6OO H13 H H 0 -33.290 22.264 38.881 +6OO H14 H H 0 -29.234 28.041 37.155 +6OO H15 H H 0 -30.683 28.285 36.777 loop_ _chem_comp_acedrg.comp_id @@ -66,8 +65,8 @@ _chem_comp_acedrg.atom_type 6OO C5 C[6a](C[6a]N[6a]H)(C[6a]N[6a]N)(H){1|C<3>,1|C<4>} 6OO C6 C[6a](N[6a]C[6a]C[5])(C[6a]C[6a]H)(H){1|C<4>,1|H<1>,1|N<2>,1|N<3>,1|O<1>,1|O<2>} 6OO O2 O(C[6a]N[6a]2) -6OO P P(OC)(SH)(O)2 -6OO SP1 S(PO3)(H) +6OO P P(OC)(O)2(S) +6OO SP1 S(PO3) 6OO OP2 O(POOS) 6OO "O5'" O(CC[5]HH)(POOS) 6OO "C5'" C(C[5]C[5]O[5]H)(OP)(H)2 @@ -85,7 +84,6 @@ _chem_comp_acedrg.atom_type 6OO O1 O(POOS) 6OO H1 H(C[6a]C[6a]2) 6OO H2 H(C[6a]C[6a]N[6a]) -6OO H3 H(SP) 6OO H4 H(CC[5]HO) 6OO H5 H(CC[5]HO) 6OO H6 H(C[5]C[5]O[5]C) @@ -126,27 +124,26 @@ _chem_comp_bond.value_dist_esd 6OO "C4'" "O4'" SINGLE n 1.445 0.0100 1.445 0.0100 6OO "C4'" "C3'" SINGLE n 1.532 0.0100 1.532 0.0100 6OO "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 -6OO P "O5'" SINGLE n 1.599 0.0100 1.599 0.0100 -6OO "O5'" "C5'" SINGLE n 1.445 0.0200 1.445 0.0200 -6OO P OP2 DOUBLE n 1.499 0.0184 1.499 0.0184 +6OO P "O5'" SINGLE n 1.613 0.0200 1.613 0.0200 +6OO "O5'" "C5'" SINGLE n 1.438 0.0200 1.438 0.0200 +6OO P OP2 SINGLE n 1.497 0.0143 1.497 0.0143 6OO "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 -6OO P SP1 SINGLE n 2.071 0.0200 2.071 0.0200 -6OO P O1 SINGLE n 1.499 0.0184 1.499 0.0184 -6OO C5 H1 SINGLE n 1.082 0.0130 0.942 0.0165 -6OO C6 H2 SINGLE n 1.082 0.0130 0.938 0.0143 -6OO SP1 H3 SINGLE n 1.338 0.0100 1.212 0.0200 -6OO "C5'" H4 SINGLE n 1.089 0.0100 0.991 0.0200 -6OO "C5'" H5 SINGLE n 1.089 0.0100 0.991 0.0200 -6OO "C4'" H6 SINGLE n 1.089 0.0100 0.990 0.0200 -6OO "C3'" H7 SINGLE n 1.089 0.0100 0.991 0.0200 -6OO "O3'" H8 SINGLE n 0.970 0.0120 0.839 0.0200 -6OO "C2'" H9 SINGLE n 1.089 0.0100 1.000 0.0100 -6OO "C1'" H10 SINGLE n 1.089 0.0100 0.994 0.0122 -6OO "CM'" H11 SINGLE n 1.089 0.0100 0.968 0.0164 -6OO "CM'" H12 SINGLE n 1.089 0.0100 0.968 0.0164 -6OO "CM'" H13 SINGLE n 1.089 0.0100 0.968 0.0164 -6OO N4 H14 SINGLE n 1.016 0.0100 0.875 0.0200 -6OO N4 H15 SINGLE n 1.016 0.0100 0.875 0.0200 +6OO P SP1 DOUBLE n 1.949 0.0200 1.949 0.0200 +6OO P O1 SINGLE n 1.497 0.0143 1.497 0.0143 +6OO C5 H1 SINGLE n 1.085 0.0150 0.942 0.0165 +6OO C6 H2 SINGLE n 1.085 0.0150 0.938 0.0143 +6OO "C5'" H4 SINGLE n 1.092 0.0100 0.991 0.0200 +6OO "C5'" H5 SINGLE n 1.092 0.0100 0.991 0.0200 +6OO "C4'" H6 SINGLE n 1.092 0.0100 0.990 0.0200 +6OO "C3'" H7 SINGLE n 1.092 0.0100 0.991 0.0200 +6OO "O3'" H8 SINGLE n 0.972 0.0180 0.839 0.0200 +6OO "C2'" H9 SINGLE n 1.092 0.0100 1.000 0.0100 +6OO "C1'" H10 SINGLE n 1.092 0.0100 0.994 0.0122 +6OO "CM'" H11 SINGLE n 1.092 0.0100 0.968 0.0164 +6OO "CM'" H12 SINGLE n 1.092 0.0100 0.968 0.0164 +6OO "CM'" H13 SINGLE n 1.092 0.0100 0.968 0.0164 +6OO N4 H14 SINGLE n 1.013 0.0120 0.875 0.0200 +6OO N4 H15 SINGLE n 1.013 0.0120 0.875 0.0200 loop_ _chem_comp_angle.comp_id @@ -167,14 +164,13 @@ _chem_comp_angle.value_angle_esd 6OO C5 C6 N1 121.118 1.50 6OO C5 C6 H2 120.471 3.00 6OO N1 C6 H2 118.411 1.84 -6OO "O5'" P OP2 108.260 3.00 -6OO "O5'" P SP1 106.008 3.00 -6OO "O5'" P O1 108.260 3.00 -6OO OP2 P SP1 112.238 3.00 -6OO OP2 P O1 116.064 3.00 -6OO SP1 P O1 112.238 3.00 -6OO P SP1 H3 109.471 3.00 -6OO P "O5'" "C5'" 118.610 3.00 +6OO "O5'" P OP2 106.327 3.00 +6OO "O5'" P SP1 114.928 3.00 +6OO "O5'" P O1 106.327 3.00 +6OO OP2 P SP1 116.458 3.00 +6OO OP2 P O1 112.844 3.00 +6OO SP1 P O1 116.458 3.00 +6OO P "O5'" "C5'" 119.085 2.00 6OO "O5'" "C5'" "C4'" 109.482 2.30 6OO "O5'" "C5'" H4 109.954 1.50 6OO "O5'" "C5'" H5 109.954 1.50 @@ -232,31 +228,30 @@ _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period -6OO C2e-chi "C2'" "C1'" N1 C2 210.000 10.000 6 -6OO C2e-nyu0 "C4'" "O4'" "C1'" N1 340.700 6.300 1 -6OO C2e-nyu1 N1 "C1'" "C2'" "O2'" 32.800 4.900 1 -6OO C2e-nyu2 "O2'" "C2'" "C3'" "O3'" 326.9 3.600 1 -6OO C2e-nyu4 "C5'" "C4'" "O4'" "C1'" 357.700 6.100 1 -6OO C3e-chi "C2'" "C1'" N1 C2 210.000 10.000 6 -6OO C3e-nyu0 "C4'" "O4'" "C1'" N1 2.8 6.100 1 -6OO C3e-nyu1 N1 "C1'" "C2'" "O2'" 335.00 4.900 1 -6OO C3e-nyu2 "O2'" "C2'" "C3'" "O3'" 35.9 2.800 1 -6OO C3e-nyu4 "C5'" "C4'" "O4'" "C1'" 20.500 5.100 1 -6OO alpha "C5'" "O5'" P OP2 -60.000 10.00 3 -6OO beta P "O5'" "C5'" "C4'" 180.000 10.00 3 -6OO delta "O3'" "C3'" "C4'" "C5'" 80.000 10.00 3 -6OO gamma "O5'" "C5'" "C4'" "O4'" 180.000 10.00 3 -6OO const_23 O2 C2 N1 C6 180.000 0.0 2 -6OO const_sp2_sp2_2 O2 C2 N3 C4 180.000 0.0 2 -6OO sp3_sp3_40 "C2'" "C3'" "O3'" H8 180.000 10.0 3 -6OO sp3_sp3_28 "C1'" "C2'" "O2'" "CM'" 180.000 10.0 3 -6OO sp3_sp3_25 H11 "CM'" "O2'" "C2'" 180.000 10.0 3 -6OO const_sp2_sp2_4 N4 C4 N3 C2 180.000 0.0 2 -6OO const_sp2_sp2_7 N4 C4 C5 C6 180.000 0.0 2 -6OO sp2_sp2_19 N3 C4 N4 H14 0.000 20 2 -6OO const_sp2_sp2_9 C4 C5 C6 N1 0.000 0.0 2 -6OO const_13 C5 C6 N1 C2 0.000 0.0 2 -6OO sp3_sp3_59 "O5'" P SP1 H3 60.000 10.0 3 +6OO const_21 N3 C2 N1 C6 0.000 0.0 1 +6OO const_24 O2 C2 N1 "C1'" 0.000 0.0 1 +6OO const_sp2_sp2_1 N1 C2 N3 C4 0.000 0.0 1 +6OO sp3_sp3_2 "C5'" "C4'" "O4'" "C1'" -60.000 10.0 3 +6OO sp3_sp3_35 "O3'" "C3'" "C4'" "C5'" 180.000 10.0 3 +6OO sp3_sp3_5 N1 "C1'" "O4'" "C4'" 180.000 10.0 3 +6OO sp3_sp3_40 "C2'" "C3'" "O3'" H8 180.000 10.0 3 +6OO sp3_sp3_20 "O2'" "C2'" "C3'" "O3'" -60.000 10.0 3 +6OO sp3_sp3_28 "C1'" "C2'" "O2'" "CM'" 180.000 10.0 3 +6OO sp3_sp3_11 N1 "C1'" "C2'" "O2'" 60.000 10.0 3 +6OO sp3_sp3_25 H11 "CM'" "O2'" "C2'" 180.000 10.0 3 +6OO sp2_sp3_1 C2 N1 "C1'" "C2'" 150.000 10.0 6 +6OO const_sp2_sp2_3 C5 C4 N3 C2 0.000 0.0 1 +6OO const_sp2_sp2_5 N3 C4 C5 C6 0.000 0.0 1 +6OO const_sp2_sp2_8 N4 C4 C5 H1 0.000 0.0 1 +6OO sp2_sp2_17 C5 C4 N4 H14 180.000 20 2 +6OO sp2_sp2_20 N3 C4 N4 H15 180.000 20 2 +6OO const_sp2_sp2_9 C4 C5 C6 N1 0.000 0.0 1 +6OO const_12 H1 C5 C6 H2 0.000 0.0 1 +6OO const_13 C5 C6 N1 C2 0.000 0.0 1 +6OO const_16 H2 C6 N1 "C1'" 0.000 0.0 1 +6OO sp3_sp3_45 "C5'" "O5'" P OP2 60.000 10.0 3 +6OO sp3_sp3_46 "C4'" "C5'" "O5'" P 180.000 10.0 3 +6OO sp3_sp3_49 "O4'" "C4'" "C5'" "O5'" 180.000 10.0 3 loop_ _chem_comp_chir.comp_id @@ -311,7 +306,17 @@ _pdbx_chem_comp_description_generator.comp_id _pdbx_chem_comp_description_generator.program_name _pdbx_chem_comp_description_generator.program_version _pdbx_chem_comp_description_generator.descriptor -6OO acedrg 275 "dictionary generator" +6OO acedrg 277 "dictionary generator" 6OO acedrg_database 12 "data source" 6OO rdkit 2019.09.1 "Chemoinformatics tool" -6OO refmac5 5.8.0411 "optimization tool" +6OO refmac5 5.8.0425 "optimization tool" + +loop_ +_chem_comp_alias.comp_id +_chem_comp_alias.group +_chem_comp_alias.atom_id +_chem_comp_alias.atom_id_standard +6OO S-NA OP2 OP1 +6OO S-NA SP1 S2P +6OO S-NA O1 OP3 +6OO S-NA H8 HO3' diff --git a/a/AS.cif b/a/AS.cif index 733257681..3bb2acaae 100644 --- a/a/AS.cif +++ b/a/AS.cif @@ -7,7 +7,7 @@ _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level -AS AS "2-DEOXY-ADENOSINE -5'-THIO-MONOPHOSPHATE" NON-POLYMER 34 22 . +AS AS "2-DEOXY-ADENOSINE -5'-THIO-MONOPHOSPHATE" S-NA 34 22 . data_comp_AS loop_ @@ -19,40 +19,40 @@ _chem_comp_atom.charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z -AS P P P 0 3.040 -8.571 -5.404 -AS OP1 O OP -1 3.409 -10.027 -5.427 -AS S2P S S1 0 1.180 -8.171 -5.799 -AS OP3 O OP -1 4.040 -7.812 -6.241 -AS "O5'" O O2 0 3.413 -8.087 -3.912 -AS "C5'" C CH2 0 4.786 -8.193 -3.450 -AS "C4'" C CH1 0 4.862 -7.857 -1.980 -AS "O4'" O O2 0 4.214 -6.595 -1.728 -AS "C3'" C CH1 0 4.162 -8.832 -1.044 -AS "O3'" O OH1 0 4.986 -9.963 -0.778 -AS "C2'" C CH2 0 3.974 -7.969 0.201 -AS "C1'" C CH1 0 3.781 -6.567 -0.368 -AS N9 N NT 0 2.390 -6.106 -0.316 -AS C8 C CR15 0 1.422 -6.185 -1.296 -AS N7 N NRD5 0 0.272 -5.678 -0.912 -AS C5 C CR56 0 0.492 -5.248 0.391 -AS C6 C CR6 0 -0.338 -4.623 1.347 -AS N6 N NH2 0 -1.612 -4.310 1.127 -AS N1 N NRD6 0 0.207 -4.330 2.557 -AS C2 C CR16 0 1.494 -4.647 2.775 -AS N3 N NRD6 0 2.366 -5.234 1.953 -AS C4 C CR56 0 1.795 -5.511 0.765 -AS "H5'" H H 0 5.361 -7.569 -3.958 -AS "H5''" H H 0 5.120 -9.112 -3.595 -AS "H4'" H H 0 5.813 -7.788 -1.724 -AS "H3'" H H 0 3.290 -9.112 -1.414 -AS "HO3'" H H 0 4.583 -10.477 -0.236 -AS "H2'" H H 0 4.761 -8.009 0.777 -AS "H2''" H H 0 3.191 -8.255 0.711 -AS "H1'" H H 0 4.352 -5.931 0.137 -AS H8 H H 0 1.558 -6.555 -2.151 -AS HN61 H H 0 -2.198 -4.389 1.775 -AS HN62 H H 0 -1.859 -4.027 0.335 -AS H2 H H 0 1.829 -4.424 3.630 +AS P P P 0 3.040 -8.571 -5.404 +AS OP1 O OP -1 3.409 -10.027 -5.427 +AS S2P S S1 0 1.180 -8.171 -5.799 +AS OP3 O OP -1 4.040 -7.812 -6.241 +AS "O5'" O O2 0 3.413 -8.087 -3.912 +AS "C5'" C CH2 0 4.786 -8.193 -3.450 +AS "C4'" C CH1 0 4.862 -7.857 -1.980 +AS "O4'" O O2 0 4.214 -6.595 -1.728 +AS "C3'" C CH1 0 4.162 -8.832 -1.044 +AS "O3'" O OH1 0 4.986 -9.963 -0.778 +AS "C2'" C CH2 0 3.974 -7.969 0.201 +AS "C1'" C CH1 0 3.781 -6.567 -0.368 +AS N9 N NT 0 2.390 -6.106 -0.316 +AS C8 C CR15 0 1.422 -6.185 -1.296 +AS N7 N NRD5 0 0.272 -5.678 -0.912 +AS C5 C CR56 0 0.492 -5.248 0.391 +AS C6 C CR6 0 -0.338 -4.623 1.347 +AS N6 N NH2 0 -1.612 -4.310 1.127 +AS N1 N NRD6 0 0.207 -4.330 2.557 +AS C2 C CR16 0 1.494 -4.647 2.775 +AS N3 N NRD6 0 2.366 -5.234 1.953 +AS C4 C CR56 0 1.795 -5.511 0.765 +AS "H5'" H H 0 5.361 -7.569 -3.958 +AS "H5''" H H 0 5.120 -9.112 -3.595 +AS "H4'" H H 0 5.813 -7.788 -1.724 +AS "H3'" H H 0 3.290 -9.112 -1.414 +AS "HO3'" H H 0 4.583 -10.477 -0.236 +AS "H2'" H H 0 4.761 -8.009 0.777 +AS "H2''" H H 0 3.191 -8.255 0.711 +AS "H1'" H H 0 4.352 -5.931 0.137 +AS H8 H H 0 1.558 -6.555 -2.151 +AS HN61 H H 0 -2.198 -4.389 1.775 +AS HN62 H H 0 -1.859 -4.027 0.335 +AS H2 H H 0 1.829 -4.424 3.630 loop_ _chem_comp_bond.comp_id @@ -64,42 +64,42 @@ _chem_comp_bond.value_dist_nucleus _chem_comp_bond.value_dist_nucleus_esd _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd -AS P OP1 SINGLE n 1.509 0.0200 1.509 0.0200 -AS P S2P DOUBLE n 1.949 0.0200 1.949 0.0200 -AS P OP3 SINGLE n 1.509 0.0200 1.509 0.0200 -AS P "O5'" SINGLE n 1.614 0.0178 1.614 0.0178 -AS "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 -AS "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 -AS "C4'" "O4'" SINGLE n 1.442 0.0100 1.442 0.0100 -AS "C4'" "C3'" SINGLE n 1.526 0.0115 1.526 0.0115 -AS "O4'" "C1'" SINGLE n 1.425 0.0100 1.425 0.0100 -AS "C3'" "O3'" SINGLE n 1.424 0.0100 1.424 0.0100 -AS "C3'" "C2'" SINGLE n 1.526 0.0101 1.526 0.0101 -AS "C2'" "C1'" SINGLE n 1.521 0.0118 1.521 0.0118 -AS "C1'" N9 SINGLE n 1.458 0.0200 1.458 0.0200 -AS N9 C8 SINGLE y 1.372 0.0200 1.372 0.0200 -AS N9 C4 SINGLE y 1.372 0.0100 1.372 0.0100 -AS C8 N7 DOUBLE y 1.310 0.0100 1.310 0.0100 -AS N7 C5 SINGLE y 1.388 0.0100 1.388 0.0100 -AS C5 C6 SINGLE y 1.408 0.0100 1.408 0.0100 -AS C5 C4 DOUBLE y 1.381 0.0100 1.381 0.0100 -AS C6 N6 SINGLE n 1.330 0.0100 1.330 0.0100 -AS C6 N1 DOUBLE y 1.354 0.0100 1.354 0.0100 -AS N1 C2 SINGLE y 1.339 0.0100 1.339 0.0100 -AS C2 N3 DOUBLE y 1.330 0.0100 1.330 0.0100 -AS N3 C4 SINGLE y 1.343 0.0100 1.343 0.0100 -AS "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 +AS P OP1 SINGLE n 1.509 0.0200 1.509 0.0200 +AS P S2P DOUBLE n 1.949 0.0200 1.949 0.0200 +AS P OP3 SINGLE n 1.509 0.0200 1.509 0.0200 +AS P "O5'" SINGLE n 1.614 0.0178 1.614 0.0178 +AS "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 +AS "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 +AS "C4'" "O4'" SINGLE n 1.442 0.0100 1.442 0.0100 +AS "C4'" "C3'" SINGLE n 1.526 0.0115 1.526 0.0115 +AS "O4'" "C1'" SINGLE n 1.425 0.0100 1.425 0.0100 +AS "C3'" "O3'" SINGLE n 1.424 0.0100 1.424 0.0100 +AS "C3'" "C2'" SINGLE n 1.526 0.0101 1.526 0.0101 +AS "C2'" "C1'" SINGLE n 1.521 0.0118 1.521 0.0118 +AS "C1'" N9 SINGLE n 1.458 0.0200 1.458 0.0200 +AS N9 C8 SINGLE y 1.372 0.0200 1.372 0.0200 +AS N9 C4 SINGLE y 1.372 0.0100 1.372 0.0100 +AS C8 N7 DOUBLE y 1.310 0.0100 1.310 0.0100 +AS N7 C5 SINGLE y 1.388 0.0100 1.388 0.0100 +AS C5 C6 SINGLE y 1.408 0.0100 1.408 0.0100 +AS C5 C4 DOUBLE y 1.381 0.0100 1.381 0.0100 +AS C6 N6 SINGLE n 1.330 0.0100 1.330 0.0100 +AS C6 N1 DOUBLE y 1.354 0.0100 1.354 0.0100 +AS N1 C2 SINGLE y 1.339 0.0100 1.339 0.0100 +AS C2 N3 DOUBLE y 1.330 0.0100 1.330 0.0100 +AS N3 C4 SINGLE y 1.343 0.0100 1.343 0.0100 +AS "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 AS "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200 -AS "C4'" "H4'" SINGLE n 1.089 0.0100 0.987 0.0170 -AS "C3'" "H3'" SINGLE n 1.089 0.0100 0.988 0.0189 +AS "C4'" "H4'" SINGLE n 1.089 0.0100 0.987 0.0170 +AS "C3'" "H3'" SINGLE n 1.089 0.0100 0.988 0.0189 AS "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 -AS "C2'" "H2'" SINGLE n 1.089 0.0100 0.977 0.0113 +AS "C2'" "H2'" SINGLE n 1.089 0.0100 0.977 0.0113 AS "C2'" "H2''" SINGLE n 1.089 0.0100 0.977 0.0113 -AS "C1'" "H1'" SINGLE n 1.089 0.0100 0.993 0.0101 -AS C8 H8 SINGLE n 1.082 0.0130 0.942 0.0170 -AS N6 HN61 SINGLE n 1.016 0.0100 0.877 0.0200 -AS N6 HN62 SINGLE n 1.016 0.0100 0.877 0.0200 -AS C2 H2 SINGLE n 1.082 0.0130 0.945 0.0200 +AS "C1'" "H1'" SINGLE n 1.089 0.0100 0.993 0.0101 +AS C8 H8 SINGLE n 1.082 0.0130 0.942 0.0170 +AS N6 HN61 SINGLE n 1.016 0.0100 0.877 0.0200 +AS N6 HN62 SINGLE n 1.016 0.0100 0.877 0.0200 +AS C2 H2 SINGLE n 1.082 0.0130 0.945 0.0200 loop_ _chem_comp_angle.comp_id @@ -108,69 +108,69 @@ _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd -AS OP1 P S2P 116.650 1.50 -AS OP1 P OP3 113.206 2.54 -AS OP1 P "O5'" 106.518 3.00 -AS S2P P OP3 116.650 1.50 -AS S2P P "O5'" 113.924 3.00 -AS OP3 P "O5'" 106.518 3.00 -AS P "O5'" "C5'" 118.783 1.50 -AS "O5'" "C5'" "C4'" 109.510 1.50 -AS "O5'" "C5'" "H5'" 109.821 1.50 +AS OP1 P S2P 116.650 1.50 +AS OP1 P OP3 113.206 2.54 +AS OP1 P "O5'" 106.518 3.00 +AS S2P P OP3 116.650 1.50 +AS S2P P "O5'" 113.924 3.00 +AS OP3 P "O5'" 106.518 3.00 +AS P "O5'" "C5'" 118.783 1.50 +AS "O5'" "C5'" "C4'" 109.510 1.50 +AS "O5'" "C5'" "H5'" 109.821 1.50 AS "O5'" "C5'" "H5''" 109.821 1.50 -AS "C4'" "C5'" "H5'" 109.624 1.50 +AS "C4'" "C5'" "H5'" 109.624 1.50 AS "C4'" "C5'" "H5''" 109.624 1.50 AS "H5'" "C5'" "H5''" 108.472 1.50 -AS "C5'" "C4'" "O4'" 109.123 1.50 -AS "C5'" "C4'" "C3'" 114.866 1.63 -AS "C5'" "C4'" "H4'" 108.268 1.50 -AS "O4'" "C4'" "C3'" 105.506 1.50 -AS "O4'" "C4'" "H4'" 108.947 1.50 -AS "C3'" "C4'" "H4'" 109.069 1.50 -AS "C4'" "O4'" "C1'" 108.795 1.50 -AS "C4'" "C3'" "O3'" 110.527 2.37 -AS "C4'" "C3'" "C2'" 102.433 1.50 -AS "C4'" "C3'" "H3'" 110.775 1.50 -AS "O3'" "C3'" "C2'" 111.424 1.96 -AS "O3'" "C3'" "H3'" 110.713 1.50 -AS "C2'" "C3'" "H3'" 110.846 1.50 +AS "C5'" "C4'" "O4'" 109.123 1.50 +AS "C5'" "C4'" "C3'" 114.866 1.63 +AS "C5'" "C4'" "H4'" 108.268 1.50 +AS "O4'" "C4'" "C3'" 105.506 1.50 +AS "O4'" "C4'" "H4'" 108.947 1.50 +AS "C3'" "C4'" "H4'" 109.069 1.50 +AS "C4'" "O4'" "C1'" 108.795 1.50 +AS "C4'" "C3'" "O3'" 110.527 2.37 +AS "C4'" "C3'" "C2'" 102.433 1.50 +AS "C4'" "C3'" "H3'" 110.775 1.50 +AS "O3'" "C3'" "C2'" 111.424 1.96 +AS "O3'" "C3'" "H3'" 110.713 1.50 +AS "C2'" "C3'" "H3'" 110.846 1.50 AS "C3'" "O3'" "HO3'" 109.026 2.38 -AS "C3'" "C2'" "C1'" 102.663 1.50 -AS "C3'" "C2'" "H2'" 111.194 1.50 +AS "C3'" "C2'" "C1'" 102.663 1.50 +AS "C3'" "C2'" "H2'" 111.194 1.50 AS "C3'" "C2'" "H2''" 111.194 1.50 -AS "C1'" "C2'" "H2'" 111.213 1.50 +AS "C1'" "C2'" "H2'" 111.213 1.50 AS "C1'" "C2'" "H2''" 111.213 1.50 AS "H2'" "C2'" "H2''" 109.148 1.50 -AS "O4'" "C1'" "C2'" 106.035 1.50 -AS "O4'" "C1'" N9 108.167 1.51 -AS "O4'" "C1'" "H1'" 109.059 1.50 -AS "C2'" "C1'" N9 113.752 2.20 -AS "C2'" "C1'" "H1'" 109.272 1.50 -AS N9 "C1'" "H1'" 109.246 1.50 -AS "C1'" N9 C8 126.078 2.46 -AS "C1'" N9 C4 125.158 1.54 -AS C8 N9 C4 107.594 1.50 -AS N9 C8 N7 112.130 1.94 -AS N9 C8 H8 124.701 2.19 -AS N7 C8 H8 123.170 1.50 -AS C8 N7 C5 103.927 1.50 -AS N7 C5 C6 132.145 1.50 -AS N7 C5 C4 110.588 1.50 -AS C6 C5 C4 117.267 1.50 -AS C5 C6 N6 123.792 1.50 -AS C5 C6 N1 117.409 1.50 -AS N6 C6 N1 118.799 1.50 -AS C6 N6 HN61 119.723 1.50 -AS C6 N6 HN62 119.723 1.50 -AS HN61 N6 HN62 120.554 1.88 -AS C6 N1 C2 118.521 1.50 -AS N1 C2 N3 129.332 1.50 -AS N1 C2 H2 115.313 1.50 -AS N3 C2 H2 115.355 1.50 -AS C2 N3 C4 110.982 1.50 -AS N9 C4 C5 107.666 1.69 -AS N9 C4 N3 125.845 1.50 -AS C5 C4 N3 126.489 1.50 +AS "O4'" "C1'" "C2'" 106.035 1.50 +AS "O4'" "C1'" N9 108.167 1.51 +AS "O4'" "C1'" "H1'" 109.059 1.50 +AS "C2'" "C1'" N9 113.752 2.20 +AS "C2'" "C1'" "H1'" 109.272 1.50 +AS N9 "C1'" "H1'" 109.246 1.50 +AS "C1'" N9 C8 126.078 2.46 +AS "C1'" N9 C4 125.158 1.54 +AS C8 N9 C4 107.594 1.50 +AS N9 C8 N7 112.130 1.94 +AS N9 C8 H8 124.701 2.19 +AS N7 C8 H8 123.170 1.50 +AS C8 N7 C5 103.927 1.50 +AS N7 C5 C6 132.145 1.50 +AS N7 C5 C4 110.588 1.50 +AS C6 C5 C4 117.267 1.50 +AS C5 C6 N6 123.792 1.50 +AS C5 C6 N1 117.409 1.50 +AS N6 C6 N1 118.799 1.50 +AS C6 N6 HN61 119.723 1.50 +AS C6 N6 HN62 119.723 1.50 +AS HN61 N6 HN62 120.554 1.88 +AS C6 N1 C2 118.521 1.50 +AS N1 C2 N3 129.332 1.50 +AS N1 C2 H2 115.313 1.50 +AS N3 C2 H2 115.355 1.50 +AS C2 N3 C4 110.982 1.50 +AS N9 C4 C5 107.666 1.69 +AS N9 C4 N3 125.845 1.50 +AS C5 C4 N3 126.489 1.50 loop_ _chem_comp_tor.comp_id @@ -182,33 +182,33 @@ _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period -AS C2e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 -AS C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 -AS C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 -AS C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 -AS C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 -AS C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 -AS C3e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 -AS C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 -AS C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 -AS C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 -AS C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 -AS C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 -AS alpha "C5'" "O5'" P OP3 -60.000 10.00 3 -AS beta P "O5'" "C5'" "C4'" 180.000 10.00 3 -AS epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 -AS gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 -AS const_14 N7 C8 N9 "C1'" 180.000 10.0 2 -AS const_26 C5 C4 N9 "C1'" 180.000 10.0 2 -AS const_17 N9 C8 N7 C5 0.000 10.0 2 -AS const_20 C6 C5 N7 C8 180.000 10.0 2 -AS const_sp2_sp2_4 N7 C5 C6 N6 0.000 5.0 2 -AS const_21 N9 C4 C5 N7 0.000 10.0 2 -AS sp2_sp2_1 C5 C6 N6 HN61 180.000 5.0 2 -AS const_sp2_sp2_6 N6 C6 N1 C2 180.000 5.0 2 -AS const_sp2_sp2_7 N3 C2 N1 C6 0.000 5.0 2 -AS const_sp2_sp2_9 N1 C2 N3 C4 0.000 5.0 2 -AS const_12 N9 C4 N3 C2 180.000 10.0 2 +AS C2e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 +AS C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 +AS C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 +AS C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 +AS C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 +AS C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 +AS C3e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 +AS C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 +AS C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 +AS C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 +AS C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 +AS C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 +AS alpha "C5'" "O5'" P OP3 -60.000 10.00 3 +AS beta P "O5'" "C5'" "C4'" 180.000 10.00 3 +AS epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 +AS gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 +AS const_14 N7 C8 N9 "C1'" 180.000 10.0 2 +AS const_26 C5 C4 N9 "C1'" 180.000 10.0 2 +AS const_17 N9 C8 N7 C5 0.000 10.0 2 +AS const_20 C6 C5 N7 C8 180.000 10.0 2 +AS const_sp2_sp2_4 N7 C5 C6 N6 0.000 5.0 2 +AS const_21 N9 C4 C5 N7 0.000 10.0 2 +AS sp2_sp2_1 C5 C6 N6 HN61 180.000 5.0 2 +AS const_sp2_sp2_6 N6 C6 N1 C2 180.000 5.0 2 +AS const_sp2_sp2_7 N3 C2 N1 C6 0.000 5.0 2 +AS const_sp2_sp2_9 N1 C2 N3 C4 0.000 5.0 2 +AS const_12 N9 C4 N3 C2 180.000 10.0 2 loop_ _chem_comp_chir.comp_id @@ -218,10 +218,10 @@ _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign -AS chir_1 P S2P "O5'" OP1 both +AS chir_1 P S2P "O5'" OP1 both AS chir_2 "C4'" "O4'" "C3'" "C5'" negative AS chir_3 "C3'" "O3'" "C4'" "C2'" positive -AS chir_4 "C1'" "O4'" N9 "C2'" negative +AS chir_4 "C1'" "O4'" N9 "C2'" negative loop_ _chem_comp_plane_atom.comp_id @@ -229,22 +229,22 @@ _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd AS plan-1 "C1'" 0.020 -AS plan-1 C2 0.020 -AS plan-1 C4 0.020 -AS plan-1 C5 0.020 -AS plan-1 C6 0.020 -AS plan-1 C8 0.020 -AS plan-1 H2 0.020 -AS plan-1 H8 0.020 -AS plan-1 N1 0.020 -AS plan-1 N3 0.020 -AS plan-1 N6 0.020 -AS plan-1 N7 0.020 -AS plan-1 N9 0.020 -AS plan-2 C6 0.020 -AS plan-2 HN61 0.020 -AS plan-2 HN62 0.020 -AS plan-2 N6 0.020 +AS plan-1 C2 0.020 +AS plan-1 C4 0.020 +AS plan-1 C5 0.020 +AS plan-1 C6 0.020 +AS plan-1 C8 0.020 +AS plan-1 H2 0.020 +AS plan-1 H8 0.020 +AS plan-1 N1 0.020 +AS plan-1 N3 0.020 +AS plan-1 N6 0.020 +AS plan-1 N7 0.020 +AS plan-1 N9 0.020 +AS plan-2 C6 0.020 +AS plan-2 HN61 0.020 +AS plan-2 HN62 0.020 +AS plan-2 N6 0.020 loop_ _pdbx_chem_comp_descriptor.comp_id @@ -252,20 +252,20 @@ _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor -AS SMILES ACDLabs 10.04 S=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O -AS SMILES_CANONICAL CACTVS 3.341 Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=S)O3 -AS SMILES CACTVS 3.341 Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(O)=S)O3 +AS SMILES ACDLabs 10.04 S=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O +AS SMILES_CANONICAL CACTVS 3.341 Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=S)O3 +AS SMILES CACTVS 3.341 Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(O)=S)O3 AS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=S)(O)O)O)N -AS SMILES "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=S)(O)O)O)N -AS InChI InChI 1.03 InChI=1S/C10H14N5O5PS/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(20-7)2-19-21(17,18)22/h3-7,16H,1-2H2,(H2,11,12,13)(H2,17,18,22)/t5-,6+,7+/m0/s1 -AS InChIKey InChI 1.03 ULJYSQHUKIZEGB-RRKCRQDMSA-N +AS SMILES "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=S)(O)O)O)N +AS InChI InChI 1.03 InChI=1S/C10H14N5O5PS/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(20-7)2-19-21(17,18)22/h3-7,16H,1-2H2,(H2,11,12,13)(H2,17,18,22)/t5-,6+,7+/m0/s1 +AS InChIKey InChI 1.03 ULJYSQHUKIZEGB-RRKCRQDMSA-N loop_ _pdbx_chem_comp_description_generator.comp_id _pdbx_chem_comp_description_generator.program_name _pdbx_chem_comp_description_generator.program_version _pdbx_chem_comp_description_generator.descriptor -AS acedrg 243 "dictionary generator" -AS acedrg_database 11 "data source" -AS rdkit 2017.03.2 "Chemoinformatics tool" -AS refmac5 5.8.0238 "optimization tool" +AS acedrg 243 "dictionary generator" +AS acedrg_database 11 "data source" +AS rdkit 2017.03.2 "Chemoinformatics tool" +AS refmac5 5.8.0238 "optimization tool" diff --git a/c/C7R.cif b/c/C7R.cif index 469e735c7..2061ef14c 100644 --- a/c/C7R.cif +++ b/c/C7R.cif @@ -7,7 +7,7 @@ _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level -C7R C7R "2'-deoxy-5'-O-thiophosphonocytidine" NON-POLYMER 33 20 . +C7R C7R "2'-deoxy-5'-O-thiophosphonocytidine" NON-POLYMER 32 20 . data_comp_C7R loop_ @@ -19,39 +19,75 @@ _chem_comp_atom.charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z -C7R P P P 0 2.510 14.762 -11.240 -C7R "C5'" C CH2 0 4.616 15.459 -12.659 -C7R "O5'" O O2 0 3.380 14.704 -12.583 -C7R "C4'" C CH1 0 5.292 15.188 -13.981 -C7R "O4'" O O2 0 6.430 16.068 -14.130 -C7R "C3'" C CH1 0 5.824 13.767 -14.153 -C7R "O3'" O OH1 0 5.684 13.331 -15.502 -C7R "C2'" C CH2 0 7.295 13.910 -13.790 -C7R "C1'" C CH1 0 7.619 15.315 -14.272 -C7R N1 N NR6 0 8.692 15.997 -13.495 -C7R C2 C CR6 0 9.929 16.290 -14.099 -C7R O2 O O 0 10.128 15.983 -15.286 -C7R N3 N NRD6 0 10.890 16.911 -13.363 -C7R C4 C CR6 0 10.670 17.240 -12.079 -C7R N4 N NH2 0 11.645 17.844 -11.412 -C7R C5 C CR16 0 9.424 16.948 -11.451 -C7R C6 C CR16 0 8.479 16.335 -12.186 -C7R OP1 O O 0 1.249 14.003 -11.489 -C7R SP2 S SH1 0 3.656 13.770 -9.802 -C7R OP3 O OP -1 2.332 16.196 -10.867 -C7R "H5'2" H H 0 5.217 15.194 -11.919 -C7R "H5'1" H H 0 4.425 16.425 -12.576 -C7R "H4'" H H 0 4.647 15.382 -14.702 -C7R "H3'" H H 0 5.369 13.144 -13.536 -C7R H1 H H 0 5.665 12.483 -15.518 -C7R "H2'1" H H 0 7.843 13.241 -14.254 -C7R "H2'2" H H 0 7.433 13.820 -12.823 -C7R "H1'" H H 0 7.861 15.281 -15.231 -C7R H42 H H 0 11.509 18.114 -10.588 -C7R H41 H H 0 12.426 17.972 -11.795 -C7R H5 H H 0 9.264 17.176 -10.552 -C7R H6 H H 0 7.653 16.128 -11.802 -C7R HSP2 H HSH1 0 3.935 14.538 -8.908 +C7R P P P 0 2.527 14.776 -11.232 +C7R "C5'" C CH2 0 4.641 15.422 -12.655 +C7R "O5'" O O2 0 3.380 14.732 -12.595 +C7R "C4'" C CH1 0 5.277 15.188 -14.001 +C7R "O4'" O O2 0 6.415 16.062 -14.177 +C7R "C3'" C CH1 0 5.804 13.765 -14.204 +C7R "O3'" O OH1 0 5.697 13.371 -15.570 +C7R "C2'" C CH2 0 7.266 13.898 -13.801 +C7R "C1'" C CH1 0 7.603 15.307 -14.300 +C7R N1 N NR6 0 8.677 15.996 -13.522 +C7R C2 C CR6 0 9.913 16.297 -14.123 +C7R O2 O O 0 10.128 15.997 -15.306 +C7R N3 N NRD6 0 10.864 16.923 -13.381 +C7R C4 C CR6 0 10.637 17.249 -12.097 +C7R N4 N NH2 0 11.606 17.859 -11.423 +C7R C5 C CR16 0 9.392 16.949 -11.475 +C7R C6 C CR16 0 8.456 16.330 -12.217 +C7R OP1 O OP -1 1.241 14.125 -11.635 +C7R SP2 S S1 0 3.380 13.844 -9.754 +C7R OP3 O OP -1 2.273 16.230 -10.990 +C7R "H5'2" H H 0 5.242 15.089 -11.941 +C7R "H5'1" H H 0 4.501 16.394 -12.519 +C7R "H4'" H H 0 4.608 15.389 -14.702 +C7R "H3'" H H 0 5.330 13.125 -13.615 +C7R H1 H H 0 5.881 12.555 -15.629 +C7R "H2'1" H H 0 7.816 13.229 -14.238 +C7R "H2'2" H H 0 7.375 13.823 -12.841 +C7R "H1'" H H 0 7.853 15.263 -15.260 +C7R H42 H H 0 11.480 18.081 -10.585 +C7R H41 H H 0 12.369 18.041 -11.813 +C7R H5 H H 0 9.227 17.175 -10.576 +C7R H6 H H 0 7.626 16.118 -11.834 + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +C7R P P(OC)(O)2(S) +C7R "C5'" C(C[5]C[5]O[5]H)(OP)(H)2 +C7R "O5'" O(CC[5]HH)(POOS) +C7R "C4'" C[5](C[5]C[5]HO)(O[5]C[5])(CHHO)(H){1|N<3>,3|H<1>} +C7R "O4'" O[5](C[5]N[6a]C[5]H)(C[5]C[5]CH){1|O<2>,2|C<3>,3|H<1>} +C7R "C3'" C[5](C[5]C[5]HH)(C[5]O[5]CH)(OH)(H){1|H<1>,1|N<3>} +C7R "O3'" O(C[5]C[5]2H)(H) +C7R "C2'" C[5](C[5]N[6a]O[5]H)(C[5]C[5]HO)(H)2{1|C<4>,1|H<1>,2|C<3>} +C7R "C1'" C[5](N[6a]C[6a]2)(C[5]C[5]HH)(O[5]C[5])(H){1|C<3>,1|C<4>,1|N<2>,1|O<1>,1|O<2>,3|H<1>} +C7R N1 N[6a](C[5]C[5]O[5]H)(C[6a]C[6a]H)(C[6a]N[6a]O){1|C<3>,2|C<4>,3|H<1>} +C7R C2 C[6a](N[6a]C[6a]C[5])(N[6a]C[6a])(O){1|C<3>,1|C<4>,1|N<3>,1|O<2>,2|H<1>} +C7R O2 O(C[6a]N[6a]2) +C7R N3 N[6a](C[6a]C[6a]N)(C[6a]N[6a]O){1|C<3>,1|C<4>,1|H<1>} +C7R C4 C[6a](C[6a]C[6a]H)(N[6a]C[6a])(NHH){1|H<1>,1|N<3>,1|O<1>} +C7R N4 N(C[6a]C[6a]N[6a])(H)2 +C7R C5 C[6a](C[6a]N[6a]H)(C[6a]N[6a]N)(H){1|C<3>,1|C<4>} +C7R C6 C[6a](N[6a]C[6a]C[5])(C[6a]C[6a]H)(H){1|C<4>,1|H<1>,1|N<2>,1|N<3>,1|O<1>,1|O<2>} +C7R OP1 O(POOS) +C7R SP2 S(PO3) +C7R OP3 O(POOS) +C7R "H5'2" H(CC[5]HO) +C7R "H5'1" H(CC[5]HO) +C7R "H4'" H(C[5]C[5]O[5]C) +C7R "H3'" H(C[5]C[5]2O) +C7R H1 H(OC[5]) +C7R "H2'1" H(C[5]C[5]2H) +C7R "H2'2" H(C[5]C[5]2H) +C7R "H1'" H(C[5]N[6a]C[5]O[5]) +C7R H42 H(NC[6a]H) +C7R H41 H(NC[6a]H) +C7R H5 H(C[6a]C[6a]2) +C7R H6 H(C[6a]C[6a]N[6a]) loop_ _chem_comp_bond.comp_id @@ -63,40 +99,39 @@ _chem_comp_bond.value_dist_nucleus _chem_comp_bond.value_dist_nucleus_esd _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd -C7R "C3'" "O3'" SINGLE n 1.424 0.0100 1.424 0.0100 -C7R C2 O2 DOUBLE n 1.241 0.0100 1.241 0.0100 -C7R "O4'" "C1'" SINGLE n 1.413 0.0100 1.413 0.0100 -C7R "C4'" "O4'" SINGLE n 1.445 0.0100 1.445 0.0100 -C7R "C2'" "C1'" SINGLE n 1.520 0.0100 1.520 0.0100 -C7R "C1'" N1 SINGLE n 1.480 0.0115 1.480 0.0115 -C7R "C4'" "C3'" SINGLE n 1.526 0.0115 1.526 0.0115 -C7R "C3'" "C2'" SINGLE n 1.522 0.0100 1.522 0.0100 -C7R "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 -C7R N1 C2 SINGLE y 1.397 0.0100 1.397 0.0100 -C7R C2 N3 SINGLE y 1.355 0.0119 1.355 0.0119 -C7R N1 C6 SINGLE y 1.360 0.0118 1.360 0.0118 -C7R N3 C4 DOUBLE y 1.339 0.0110 1.339 0.0110 -C7R "C5'" "O5'" SINGLE n 1.450 0.0166 1.450 0.0166 -C7R P "O5'" SINGLE n 1.601 0.0114 1.601 0.0114 -C7R C5 C6 DOUBLE y 1.342 0.0100 1.342 0.0100 -C7R C4 C5 SINGLE y 1.422 0.0123 1.422 0.0123 -C7R C4 N4 SINGLE n 1.325 0.0109 1.325 0.0109 -C7R P OP1 DOUBLE n 1.493 0.0157 1.493 0.0157 -C7R P SP2 SINGLE n 2.091 0.0200 2.091 0.0200 -C7R P OP3 SINGLE n 1.493 0.0157 1.493 0.0157 -C7R "C5'" "H5'2" SINGLE n 1.089 0.0100 0.989 0.0200 -C7R "C5'" "H5'1" SINGLE n 1.089 0.0100 0.989 0.0200 -C7R "C4'" "H4'" SINGLE n 1.089 0.0100 0.987 0.0170 -C7R "C3'" "H3'" SINGLE n 1.089 0.0100 0.988 0.0189 -C7R "O3'" H1 SINGLE n 0.970 0.0120 0.849 0.0200 -C7R "C2'" "H2'1" SINGLE n 1.089 0.0100 0.982 0.0200 -C7R "C2'" "H2'2" SINGLE n 1.089 0.0100 0.982 0.0200 -C7R "C1'" "H1'" SINGLE n 1.089 0.0100 0.991 0.0103 -C7R N4 H42 SINGLE n 1.016 0.0100 0.877 0.0200 -C7R N4 H41 SINGLE n 1.016 0.0100 0.877 0.0200 -C7R C5 H5 SINGLE n 1.082 0.0130 0.941 0.0174 -C7R C6 H6 SINGLE n 1.082 0.0130 0.935 0.0143 -C7R SP2 HSP2 SINGLE n 1.338 0.0100 1.211 0.0200 +C7R "C3'" "O3'" SINGLE n 1.425 0.0128 1.425 0.0128 +C7R C2 O2 DOUBLE n 1.238 0.0116 1.238 0.0116 +C7R "O4'" "C1'" SINGLE n 1.412 0.0100 1.412 0.0100 +C7R "C4'" "O4'" SINGLE n 1.445 0.0100 1.445 0.0100 +C7R "C2'" "C1'" SINGLE n 1.532 0.0100 1.532 0.0100 +C7R "C1'" N1 SINGLE n 1.481 0.0136 1.481 0.0136 +C7R "C4'" "C3'" SINGLE n 1.530 0.0119 1.530 0.0119 +C7R "C3'" "C2'" SINGLE n 1.523 0.0101 1.523 0.0101 +C7R "C5'" "C4'" SINGLE n 1.507 0.0100 1.507 0.0100 +C7R N1 C2 SINGLE y 1.397 0.0100 1.397 0.0100 +C7R C2 N3 SINGLE y 1.355 0.0100 1.355 0.0100 +C7R N1 C6 SINGLE y 1.359 0.0100 1.359 0.0100 +C7R N3 C4 DOUBLE y 1.341 0.0104 1.341 0.0104 +C7R "C5'" "O5'" SINGLE n 1.438 0.0200 1.438 0.0200 +C7R P "O5'" SINGLE n 1.613 0.0200 1.613 0.0200 +C7R C5 C6 DOUBLE y 1.342 0.0100 1.342 0.0100 +C7R C4 C5 SINGLE y 1.422 0.0101 1.422 0.0101 +C7R C4 N4 SINGLE n 1.326 0.0110 1.326 0.0110 +C7R P OP1 SINGLE n 1.497 0.0143 1.497 0.0143 +C7R P SP2 DOUBLE n 1.949 0.0200 1.949 0.0200 +C7R P OP3 SINGLE n 1.497 0.0143 1.497 0.0143 +C7R "C5'" "H5'2" SINGLE n 1.092 0.0100 0.991 0.0200 +C7R "C5'" "H5'1" SINGLE n 1.092 0.0100 0.991 0.0200 +C7R "C4'" "H4'" SINGLE n 1.092 0.0100 0.990 0.0200 +C7R "C3'" "H3'" SINGLE n 1.092 0.0100 0.991 0.0181 +C7R "O3'" H1 SINGLE n 0.972 0.0180 0.839 0.0200 +C7R "C2'" "H2'1" SINGLE n 1.092 0.0100 0.970 0.0100 +C7R "C2'" "H2'2" SINGLE n 1.092 0.0100 0.970 0.0100 +C7R "C1'" "H1'" SINGLE n 1.092 0.0100 0.993 0.0100 +C7R N4 H42 SINGLE n 1.013 0.0120 0.875 0.0200 +C7R N4 H41 SINGLE n 1.013 0.0120 0.875 0.0200 +C7R C5 H5 SINGLE n 1.085 0.0150 0.942 0.0165 +C7R C6 H6 SINGLE n 1.085 0.0150 0.938 0.0143 loop_ _chem_comp_angle.comp_id @@ -105,65 +140,64 @@ _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd -C7R "O5'" P OP1 108.530 2.45 -C7R "O5'" P SP2 105.685 3.00 -C7R "O5'" P OP3 108.530 2.45 -C7R OP1 P SP2 111.281 3.00 -C7R OP1 P OP3 116.964 2.85 -C7R SP2 P OP3 111.281 3.00 -C7R "C4'" "C5'" "O5'" 109.510 1.50 -C7R "C4'" "C5'" "H5'2" 109.624 1.50 -C7R "C4'" "C5'" "H5'1" 109.624 1.50 -C7R "O5'" "C5'" "H5'2" 109.821 1.50 -C7R "O5'" "C5'" "H5'1" 109.821 1.50 -C7R "H5'2" "C5'" "H5'1" 108.472 1.50 -C7R "C5'" "O5'" P 119.135 1.78 -C7R "O4'" "C4'" "C3'" 105.770 1.50 -C7R "O4'" "C4'" "C5'" 109.615 1.50 -C7R "O4'" "C4'" "H4'" 108.698 1.50 -C7R "C3'" "C4'" "C5'" 114.866 1.63 -C7R "C3'" "C4'" "H4'" 109.069 1.50 -C7R "C5'" "C4'" "H4'" 108.268 1.50 -C7R "C1'" "O4'" "C4'" 109.692 1.50 -C7R "O3'" "C3'" "C4'" 110.527 2.37 -C7R "O3'" "C3'" "C2'" 110.636 2.59 -C7R "O3'" "C3'" "H3'" 110.713 1.50 -C7R "C4'" "C3'" "C2'" 102.800 1.50 -C7R "C4'" "C3'" "H3'" 110.775 1.50 -C7R "C2'" "C3'" "H3'" 110.862 1.50 -C7R "C3'" "O3'" H1 109.026 2.38 -C7R "C1'" "C2'" "C3'" 102.834 1.50 -C7R "C1'" "C2'" "H2'1" 111.187 1.50 -C7R "C1'" "C2'" "H2'2" 111.187 1.50 -C7R "C3'" "C2'" "H2'1" 111.310 1.50 -C7R "C3'" "C2'" "H2'2" 111.310 1.50 -C7R "H2'1" "C2'" "H2'2" 108.952 1.50 -C7R "O4'" "C1'" "C2'" 106.308 1.50 -C7R "O4'" "C1'" N1 107.584 1.50 -C7R "O4'" "C1'" "H1'" 109.550 1.50 -C7R "C2'" "C1'" N1 114.268 1.50 -C7R "C2'" "C1'" "H1'" 109.741 1.50 -C7R N1 "C1'" "H1'" 109.342 1.50 -C7R "C1'" N1 C2 118.777 1.50 -C7R "C1'" N1 C6 120.713 1.50 -C7R C2 N1 C6 120.510 1.50 -C7R O2 C2 N1 118.710 1.50 -C7R O2 C2 N3 122.370 1.50 -C7R N1 C2 N3 118.927 1.50 -C7R C2 N3 C4 120.266 1.50 -C7R N3 C4 C5 121.269 1.50 -C7R N3 C4 N4 117.855 1.50 -C7R C5 C4 N4 120.876 1.50 -C7R C4 N4 H42 119.818 1.59 -C7R C4 N4 H41 119.818 1.59 -C7R H42 N4 H41 120.363 1.85 -C7R C6 C5 C4 117.808 1.50 -C7R C6 C5 H5 120.848 1.50 -C7R C4 C5 H5 121.350 1.50 -C7R N1 C6 C5 121.215 1.50 -C7R N1 C6 H6 118.510 1.50 -C7R C5 C6 H6 120.275 1.75 -C7R P SP2 HSP2 109.471 3.00 +C7R "O5'" P OP1 106.327 3.00 +C7R "O5'" P SP2 114.928 3.00 +C7R "O5'" P OP3 106.327 3.00 +C7R OP1 P SP2 116.458 3.00 +C7R OP1 P OP3 112.844 3.00 +C7R SP2 P OP3 116.458 3.00 +C7R "C4'" "C5'" "O5'" 109.482 2.30 +C7R "C4'" "C5'" "H5'2" 109.589 1.50 +C7R "C4'" "C5'" "H5'1" 109.589 1.50 +C7R "O5'" "C5'" "H5'2" 109.954 1.50 +C7R "O5'" "C5'" "H5'1" 109.954 1.50 +C7R "H5'2" "C5'" "H5'1" 108.471 1.50 +C7R "C5'" "O5'" P 119.085 2.00 +C7R "O4'" "C4'" "C3'" 105.546 1.50 +C7R "O4'" "C4'" "C5'" 110.351 1.93 +C7R "O4'" "C4'" "H4'" 108.778 1.50 +C7R "C3'" "C4'" "C5'" 113.954 2.40 +C7R "C3'" "C4'" "H4'" 109.033 1.50 +C7R "C5'" "C4'" "H4'" 108.351 1.59 +C7R "C1'" "O4'" "C4'" 109.881 1.50 +C7R "O3'" "C3'" "C4'" 110.611 3.00 +C7R "O3'" "C3'" "C2'" 110.452 3.00 +C7R "O3'" "C3'" "H3'" 110.786 1.88 +C7R "C4'" "C3'" "C2'" 102.581 1.50 +C7R "C4'" "C3'" "H3'" 110.734 1.65 +C7R "C2'" "C3'" "H3'" 110.938 1.50 +C7R "C3'" "O3'" H1 108.690 3.00 +C7R "C1'" "C2'" "C3'" 102.658 2.13 +C7R "C1'" "C2'" "H2'1" 111.181 1.50 +C7R "C1'" "C2'" "H2'2" 111.181 1.50 +C7R "C3'" "C2'" "H2'1" 111.287 1.86 +C7R "C3'" "C2'" "H2'2" 111.287 1.86 +C7R "H2'1" "C2'" "H2'2" 109.095 1.50 +C7R "O4'" "C1'" "C2'" 106.263 1.50 +C7R "O4'" "C1'" N1 107.769 1.50 +C7R "O4'" "C1'" "H1'" 109.467 1.50 +C7R "C2'" "C1'" N1 114.169 1.50 +C7R "C2'" "C1'" "H1'" 109.883 1.50 +C7R N1 "C1'" "H1'" 109.124 1.71 +C7R "C1'" N1 C2 118.555 2.04 +C7R "C1'" N1 C6 120.837 1.65 +C7R C2 N1 C6 120.608 1.50 +C7R O2 C2 N1 118.915 2.14 +C7R O2 C2 N3 122.293 1.50 +C7R N1 C2 N3 118.792 1.50 +C7R C2 N3 C4 120.397 1.50 +C7R N3 C4 C5 121.314 1.50 +C7R N3 C4 N4 117.915 1.50 +C7R C5 C4 N4 120.770 1.50 +C7R C4 N4 H42 119.693 3.00 +C7R C4 N4 H41 119.693 3.00 +C7R H42 N4 H41 120.613 3.00 +C7R C6 C5 C4 117.770 1.50 +C7R C6 C5 H5 121.009 1.50 +C7R C4 C5 H5 121.221 1.50 +C7R N1 C6 C5 121.118 1.50 +C7R N1 C6 H6 118.411 1.84 +C7R C5 C6 H6 120.471 3.00 loop_ _chem_comp_tor.comp_id @@ -175,30 +209,28 @@ _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period -C7R C2e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 -C7R C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 -C7R C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 -C7R C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 -C7R C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 -C7R C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 -C7R C3e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 -C7R C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 -C7R C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 -C7R C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 -C7R C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 -C7R C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 -C7R alpha "C5'" "O5'" P OP3 -60.000 10.00 3 -C7R beta P "O5'" "C5'" "C4'" 180.000 10.00 3 -C7R gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 -C7R sp3_sp3_53 "O5'" P SP2 HSP2 60.000 10.0 3 -C7R const_sp2_sp2_6 O2 C2 N3 C4 180.000 5.0 2 -C7R const_sp2_sp2_8 N4 C4 N3 C2 180.000 5.0 2 -C7R sp2_sp2_3 N3 C4 N4 H42 0.000 5.0 2 -C7R const_11 N4 C4 C5 C6 180.000 10.0 2 -C7R const_13 C4 C5 C6 N1 0.000 10.0 2 -C7R sp3_sp3_25 "C4'" "C3'" "O3'" H1 180.000 10.0 3 -C7R const_sp2_sp2_4 O2 C2 N1 "C1'" 0.000 5.0 2 -C7R const_18 C5 C6 N1 "C1'" 180.000 10.0 2 +C7R sp3_sp3_51 "C5'" "O5'" P OP1 60.000 10.0 3 +C7R const_sp2_sp2_5 N1 C2 N3 C4 0.000 0.0 1 +C7R const_sp2_sp2_7 C5 C4 N3 C2 0.000 0.0 1 +C7R sp2_sp2_21 C5 C4 N4 H42 180.000 20 2 +C7R sp2_sp2_24 N3 C4 N4 H41 180.000 20 2 +C7R const_sp2_sp2_9 N3 C4 C5 C6 0.000 0.0 1 +C7R const_12 N4 C4 C5 H5 0.000 0.0 1 +C7R const_13 C4 C5 C6 N1 0.000 0.0 1 +C7R const_16 H5 C5 C6 H6 0.000 0.0 1 +C7R sp3_sp3_46 "C4'" "C5'" "O5'" P 180.000 10.0 3 +C7R sp3_sp3_37 "O4'" "C4'" "C5'" "O5'" 180.000 10.0 3 +C7R sp3_sp3_2 "C5'" "C4'" "O4'" "C1'" -60.000 10.0 3 +C7R sp3_sp3_32 "O3'" "C3'" "C4'" "C5'" 180.000 10.0 3 +C7R sp3_sp3_4 "C2'" "C1'" "O4'" "C4'" -60.000 10.0 3 +C7R sp3_sp3_25 "C4'" "C3'" "O3'" H1 180.000 10.0 3 +C7R sp3_sp3_17 "C1'" "C2'" "C3'" "O3'" 60.000 10.0 3 +C7R sp3_sp3_7 "O4'" "C1'" "C2'" "C3'" 60.000 10.0 3 +C7R sp2_sp3_1 C2 N1 "C1'" "O4'" 150.000 10.0 6 +C7R const_sp2_sp2_1 N3 C2 N1 C6 0.000 0.0 1 +C7R const_sp2_sp2_4 O2 C2 N1 "C1'" 0.000 0.0 1 +C7R const_17 C5 C6 N1 C2 0.000 0.0 1 +C7R const_20 H6 C6 N1 "C1'" 0.000 0.0 1 loop_ _chem_comp_chir.comp_id @@ -208,10 +240,10 @@ _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign -C7R chir_1 P SP2 "O5'" OP3 both +C7R chir_1 P SP2 "O5'" OP3 both C7R chir_2 "C4'" "O4'" "C3'" "C5'" negative C7R chir_3 "C3'" "O3'" "C4'" "C2'" positive -C7R chir_4 "C1'" "O4'" N1 "C2'" negative +C7R chir_4 "C1'" "O4'" N1 "C2'" negative loop_ _chem_comp_plane_atom.comp_id @@ -219,20 +251,20 @@ _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd C7R plan-1 "C1'" 0.020 -C7R plan-1 C2 0.020 -C7R plan-1 C4 0.020 -C7R plan-1 C5 0.020 -C7R plan-1 C6 0.020 -C7R plan-1 H5 0.020 -C7R plan-1 H6 0.020 -C7R plan-1 N1 0.020 -C7R plan-1 N3 0.020 -C7R plan-1 N4 0.020 -C7R plan-1 O2 0.020 -C7R plan-2 C4 0.020 -C7R plan-2 H41 0.020 -C7R plan-2 H42 0.020 -C7R plan-2 N4 0.020 +C7R plan-1 C2 0.020 +C7R plan-1 C4 0.020 +C7R plan-1 C5 0.020 +C7R plan-1 C6 0.020 +C7R plan-1 H5 0.020 +C7R plan-1 H6 0.020 +C7R plan-1 N1 0.020 +C7R plan-1 N3 0.020 +C7R plan-1 N4 0.020 +C7R plan-1 O2 0.020 +C7R plan-2 C4 0.020 +C7R plan-2 H41 0.020 +C7R plan-2 H42 0.020 +C7R plan-2 N4 0.020 loop_ _pdbx_chem_comp_descriptor.comp_id @@ -240,20 +272,28 @@ _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor -C7R SMILES ACDLabs 12.01 P(S)(O)(OCC1OC(CC1O)N2C=CC(=NC2=O)N)=O -C7R InChI InChI 1.03 InChI=1S/C9H14N3O6PS/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(18-8)4-17-19(15,16)20/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,20)/t5-,6+,8+/m0/s1 -C7R InChIKey InChI 1.03 FHBXKBNKQMSUIJ-SHYZEUOFSA-N -C7R SMILES_CANONICAL CACTVS 3.385 NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(S)=O)O2 -C7R SMILES CACTVS 3.385 NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(S)=O)O2 +C7R SMILES ACDLabs 12.01 P(S)(O)(OCC1OC(CC1O)N2C=CC(=NC2=O)N)=O +C7R InChI InChI 1.03 InChI=1S/C9H14N3O6PS/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(18-8)4-17-19(15,16)20/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,20)/t5-,6+,8+/m0/s1 +C7R InChIKey InChI 1.03 FHBXKBNKQMSUIJ-SHYZEUOFSA-N +C7R SMILES_CANONICAL CACTVS 3.385 NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(S)=O)O2 +C7R SMILES CACTVS 3.385 NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(S)=O)O2 C7R SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)S)O -C7R SMILES "OpenEye OEToolkits" 2.0.4 C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)S)O +C7R SMILES "OpenEye OEToolkits" 2.0.4 C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)S)O loop_ _pdbx_chem_comp_description_generator.comp_id _pdbx_chem_comp_description_generator.program_name _pdbx_chem_comp_description_generator.program_version _pdbx_chem_comp_description_generator.descriptor -C7R acedrg 243 "dictionary generator" -C7R acedrg_database 11 "data source" -C7R rdkit 2017.03.2 "Chemoinformatics tool" -C7R refmac5 5.8.0238 "optimization tool" +C7R acedrg 277 "dictionary generator" +C7R acedrg_database 12 "data source" +C7R rdkit 2019.09.1 "Chemoinformatics tool" +C7R refmac5 5.8.0425 "optimization tool" + +loop_ +_chem_comp_alias.comp_id +_chem_comp_alias.group +_chem_comp_alias.atom_id +_chem_comp_alias.atom_id_standard +C7R S-NA SP2 S2P +C7R S-NA H1 HO3' diff --git a/c/C7S.cif b/c/C7S.cif index 28469cc2a..0b0c0edc0 100644 --- a/c/C7S.cif +++ b/c/C7S.cif @@ -7,7 +7,7 @@ _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level -C7S C7S "2'-deoxy-5'-O-thiophosphonocytidine" NON-POLYMER 33 20 . +C7S C7S "2'-deoxy-5'-O-thiophosphonocytidine" NON-POLYMER 32 20 . data_comp_C7S loop_ @@ -19,39 +19,75 @@ _chem_comp_atom.charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z -C7S P P P 0 3.515 15.366 -10.897 -C7S "C5'" C CH2 0 3.931 15.595 -13.487 -C7S "O5'" O O2 0 4.449 15.209 -12.188 -C7S "C4'" C CH1 0 4.956 15.291 -14.552 -C7S "O4'" O O2 0 6.167 16.033 -14.283 -C7S "C3'" C CH1 0 5.357 13.817 -14.661 -C7S "O3'" O OH1 0 5.270 13.367 -16.009 -C7S "C2'" C CH2 0 6.806 13.793 -14.194 -C7S "C1'" C CH1 0 7.286 15.201 -14.504 -C7S N1 N NR6 0 8.402 15.678 -13.641 -C7S C2 C CR6 0 9.676 15.911 -14.192 -C7S O2 O O 0 9.870 15.723 -15.404 -C7S N3 N NRD6 0 10.676 16.343 -13.378 -C7S C4 C CR6 0 10.460 16.542 -12.068 -C7S N4 N NH2 0 11.474 16.964 -11.325 -C7S C5 C CR16 0 9.178 16.309 -11.492 -C7S C6 C CR16 0 8.194 15.883 -12.303 -C7S SP1 S SH1 0 2.007 13.940 -11.140 -C7S OP2 O O 0 4.341 15.025 -9.701 -C7S OP3 O OP -1 2.939 16.742 -10.906 -C7S H1 H H 0 3.725 16.562 -13.491 -C7S H2 H H 0 3.097 15.097 -13.677 -C7S H3 H H 0 4.591 15.591 -15.420 -C7S H4 H H 0 4.792 13.258 -14.073 -C7S H5 H H 0 5.244 12.519 -16.017 -C7S H6 H H 0 7.329 13.125 -14.689 -C7S H7 H H 0 6.867 13.596 -13.235 -C7S H8 H H 0 7.542 15.256 -15.459 -C7S H9 H H 0 11.319 17.443 -10.606 -C7S H10 H H 0 12.298 16.762 -11.552 -C7S H11 H H 0 9.020 16.447 -10.574 -C7S H12 H H 0 7.342 15.719 -11.955 -C7S HSP1 H HSH1 0 0.927 14.461 -10.968 +C7S P P P 0 3.565 15.153 -10.934 +C7S "C5'" C CH2 0 3.963 15.664 -13.484 +C7S "O5'" O O2 0 4.520 15.241 -12.226 +C7S "C4'" C CH1 0 4.944 15.380 -14.593 +C7S "O4'" O O2 0 6.184 16.086 -14.359 +C7S "C3'" C CH1 0 5.309 13.896 -14.747 +C7S "O3'" O OH1 0 5.295 13.505 -16.118 +C7S "C2'" C CH2 0 6.729 13.819 -14.202 +C7S "C1'" C CH1 0 7.274 15.209 -14.541 +C7S N1 N NR6 0 8.398 15.666 -13.669 +C7S C2 C CR6 0 9.676 15.893 -14.213 +C7S O2 O O 0 9.886 15.719 -15.422 +C7S N3 N NRD6 0 10.673 16.307 -13.386 +C7S C4 C CR6 0 10.451 16.497 -12.074 +C7S N4 N NH2 0 11.464 16.902 -11.318 +C7S C5 C CR16 0 9.163 16.270 -11.511 +C7S C6 C CR16 0 8.182 15.861 -12.335 +C7S SP1 S S1 0 2.445 13.564 -10.908 +C7S OP2 O OP -1 4.548 15.162 -9.805 +C7S OP3 O OP -1 2.812 16.444 -10.922 +C7S H1 H H 0 3.767 16.635 -13.456 +C7S H2 H H 0 3.117 15.178 -13.658 +C7S H3 H H 0 4.550 15.705 -15.442 +C7S H4 H H 0 4.696 13.326 -14.216 +C7S H5 H H 0 5.289 12.667 -16.159 +C7S H6 H H 0 7.241 13.124 -14.645 +C7S H7 H H 0 6.731 13.657 -13.246 +C7S H8 H H 0 7.547 15.232 -15.494 +C7S H9 H H 0 11.343 17.031 -10.461 +C7S H10 H H 0 12.254 17.040 -11.673 +C7S H11 H H 0 9.001 16.401 -10.592 +C7S H12 H H 0 7.323 15.702 -11.993 + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +C7S P P(OC)(O)2(S) +C7S "C5'" C(C[5]C[5]O[5]H)(OP)(H)2 +C7S "O5'" O(CC[5]HH)(POOS) +C7S "C4'" C[5](C[5]C[5]HO)(O[5]C[5])(CHHO)(H){1|N<3>,3|H<1>} +C7S "O4'" O[5](C[5]N[6a]C[5]H)(C[5]C[5]CH){1|O<2>,2|C<3>,3|H<1>} +C7S "C3'" C[5](C[5]C[5]HH)(C[5]O[5]CH)(OH)(H){1|H<1>,1|N<3>} +C7S "O3'" O(C[5]C[5]2H)(H) +C7S "C2'" C[5](C[5]N[6a]O[5]H)(C[5]C[5]HO)(H)2{1|C<4>,1|H<1>,2|C<3>} +C7S "C1'" C[5](N[6a]C[6a]2)(C[5]C[5]HH)(O[5]C[5])(H){1|C<3>,1|C<4>,1|N<2>,1|O<1>,1|O<2>,3|H<1>} +C7S N1 N[6a](C[5]C[5]O[5]H)(C[6a]C[6a]H)(C[6a]N[6a]O){1|C<3>,2|C<4>,3|H<1>} +C7S C2 C[6a](N[6a]C[6a]C[5])(N[6a]C[6a])(O){1|C<3>,1|C<4>,1|N<3>,1|O<2>,2|H<1>} +C7S O2 O(C[6a]N[6a]2) +C7S N3 N[6a](C[6a]C[6a]N)(C[6a]N[6a]O){1|C<3>,1|C<4>,1|H<1>} +C7S C4 C[6a](C[6a]C[6a]H)(N[6a]C[6a])(NHH){1|H<1>,1|N<3>,1|O<1>} +C7S N4 N(C[6a]C[6a]N[6a])(H)2 +C7S C5 C[6a](C[6a]N[6a]H)(C[6a]N[6a]N)(H){1|C<3>,1|C<4>} +C7S C6 C[6a](N[6a]C[6a]C[5])(C[6a]C[6a]H)(H){1|C<4>,1|H<1>,1|N<2>,1|N<3>,1|O<1>,1|O<2>} +C7S SP1 S(PO3) +C7S OP2 O(POOS) +C7S OP3 O(POOS) +C7S H1 H(CC[5]HO) +C7S H2 H(CC[5]HO) +C7S H3 H(C[5]C[5]O[5]C) +C7S H4 H(C[5]C[5]2O) +C7S H5 H(OC[5]) +C7S H6 H(C[5]C[5]2H) +C7S H7 H(C[5]C[5]2H) +C7S H8 H(C[5]N[6a]C[5]O[5]) +C7S H9 H(NC[6a]H) +C7S H10 H(NC[6a]H) +C7S H11 H(C[6a]C[6a]2) +C7S H12 H(C[6a]C[6a]N[6a]) loop_ _chem_comp_bond.comp_id @@ -63,40 +99,39 @@ _chem_comp_bond.value_dist_nucleus _chem_comp_bond.value_dist_nucleus_esd _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd -C7S "C3'" "O3'" SINGLE n 1.424 0.0100 1.424 0.0100 -C7S C2 O2 DOUBLE n 1.241 0.0100 1.241 0.0100 -C7S "C4'" "C3'" SINGLE n 1.526 0.0115 1.526 0.0115 +C7S "C3'" "O3'" SINGLE n 1.425 0.0128 1.425 0.0128 +C7S C2 O2 DOUBLE n 1.238 0.0116 1.238 0.0116 +C7S "C4'" "C3'" SINGLE n 1.530 0.0119 1.530 0.0119 C7S "C4'" "O4'" SINGLE n 1.445 0.0100 1.445 0.0100 -C7S "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 -C7S "O4'" "C1'" SINGLE n 1.413 0.0100 1.413 0.0100 -C7S "C2'" "C1'" SINGLE n 1.520 0.0100 1.520 0.0100 -C7S "C1'" N1 SINGLE n 1.480 0.0115 1.480 0.0115 -C7S "C3'" "C2'" SINGLE n 1.522 0.0100 1.522 0.0100 -C7S N1 C2 SINGLE y 1.397 0.0100 1.397 0.0100 -C7S C2 N3 SINGLE y 1.355 0.0119 1.355 0.0119 -C7S "C5'" "O5'" SINGLE n 1.450 0.0166 1.450 0.0166 -C7S N1 C6 SINGLE y 1.360 0.0118 1.360 0.0118 -C7S N3 C4 DOUBLE y 1.339 0.0110 1.339 0.0110 -C7S P "O5'" SINGLE n 1.601 0.0114 1.601 0.0114 -C7S C5 C6 DOUBLE y 1.342 0.0100 1.342 0.0100 -C7S C4 N4 SINGLE n 1.325 0.0109 1.325 0.0109 -C7S C4 C5 SINGLE y 1.422 0.0123 1.422 0.0123 -C7S P SP1 SINGLE n 2.091 0.0200 2.091 0.0200 -C7S P OP2 DOUBLE n 1.493 0.0157 1.493 0.0157 -C7S P OP3 SINGLE n 1.493 0.0157 1.493 0.0157 -C7S "C5'" H1 SINGLE n 1.089 0.0100 0.989 0.0200 -C7S "C5'" H2 SINGLE n 1.089 0.0100 0.989 0.0200 -C7S "C4'" H3 SINGLE n 1.089 0.0100 0.987 0.0170 -C7S "C3'" H4 SINGLE n 1.089 0.0100 0.988 0.0189 -C7S "O3'" H5 SINGLE n 0.970 0.0120 0.849 0.0200 -C7S "C2'" H6 SINGLE n 1.089 0.0100 0.982 0.0200 -C7S "C2'" H7 SINGLE n 1.089 0.0100 0.982 0.0200 -C7S "C1'" H8 SINGLE n 1.089 0.0100 0.991 0.0103 -C7S N4 H9 SINGLE n 1.016 0.0100 0.877 0.0200 -C7S N4 H10 SINGLE n 1.016 0.0100 0.877 0.0200 -C7S C5 H11 SINGLE n 1.082 0.0130 0.941 0.0174 -C7S C6 H12 SINGLE n 1.082 0.0130 0.935 0.0143 -C7S SP1 HSP1 SINGLE n 1.338 0.0100 1.211 0.0200 +C7S "C5'" "C4'" SINGLE n 1.507 0.0100 1.507 0.0100 +C7S "O4'" "C1'" SINGLE n 1.412 0.0100 1.412 0.0100 +C7S "C2'" "C1'" SINGLE n 1.532 0.0100 1.532 0.0100 +C7S "C1'" N1 SINGLE n 1.481 0.0136 1.481 0.0136 +C7S "C3'" "C2'" SINGLE n 1.523 0.0101 1.523 0.0101 +C7S N1 C2 SINGLE y 1.397 0.0100 1.397 0.0100 +C7S C2 N3 SINGLE y 1.355 0.0100 1.355 0.0100 +C7S "C5'" "O5'" SINGLE n 1.438 0.0200 1.438 0.0200 +C7S N1 C6 SINGLE y 1.359 0.0100 1.359 0.0100 +C7S N3 C4 DOUBLE y 1.341 0.0104 1.341 0.0104 +C7S P "O5'" SINGLE n 1.613 0.0200 1.613 0.0200 +C7S C5 C6 DOUBLE y 1.342 0.0100 1.342 0.0100 +C7S C4 N4 SINGLE n 1.326 0.0110 1.326 0.0110 +C7S C4 C5 SINGLE y 1.422 0.0101 1.422 0.0101 +C7S P SP1 DOUBLE n 1.949 0.0200 1.949 0.0200 +C7S P OP2 SINGLE n 1.497 0.0143 1.497 0.0143 +C7S P OP3 SINGLE n 1.497 0.0143 1.497 0.0143 +C7S "C5'" H1 SINGLE n 1.092 0.0100 0.991 0.0200 +C7S "C5'" H2 SINGLE n 1.092 0.0100 0.991 0.0200 +C7S "C4'" H3 SINGLE n 1.092 0.0100 0.990 0.0200 +C7S "C3'" H4 SINGLE n 1.092 0.0100 0.991 0.0181 +C7S "O3'" H5 SINGLE n 0.972 0.0180 0.839 0.0200 +C7S "C2'" H6 SINGLE n 1.092 0.0100 0.970 0.0100 +C7S "C2'" H7 SINGLE n 1.092 0.0100 0.970 0.0100 +C7S "C1'" H8 SINGLE n 1.092 0.0100 0.993 0.0100 +C7S N4 H9 SINGLE n 1.013 0.0120 0.875 0.0200 +C7S N4 H10 SINGLE n 1.013 0.0120 0.875 0.0200 +C7S C5 H11 SINGLE n 1.085 0.0150 0.942 0.0165 +C7S C6 H12 SINGLE n 1.085 0.0150 0.938 0.0143 loop_ _chem_comp_angle.comp_id @@ -105,65 +140,64 @@ _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd -C7S "O5'" P SP1 105.685 3.00 -C7S "O5'" P OP2 108.530 2.45 -C7S "O5'" P OP3 108.530 2.45 -C7S SP1 P OP2 111.281 3.00 -C7S SP1 P OP3 111.281 3.00 -C7S OP2 P OP3 116.964 2.85 -C7S "C4'" "C5'" "O5'" 109.510 1.50 -C7S "C4'" "C5'" H1 109.624 1.50 -C7S "C4'" "C5'" H2 109.624 1.50 -C7S "O5'" "C5'" H1 109.821 1.50 -C7S "O5'" "C5'" H2 109.821 1.50 -C7S H1 "C5'" H2 108.472 1.50 -C7S "C5'" "O5'" P 119.135 1.78 -C7S "C3'" "C4'" "O4'" 105.770 1.50 -C7S "C3'" "C4'" "C5'" 114.866 1.63 -C7S "C3'" "C4'" H3 109.069 1.50 -C7S "O4'" "C4'" "C5'" 109.615 1.50 -C7S "O4'" "C4'" H3 108.698 1.50 -C7S "C5'" "C4'" H3 108.268 1.50 -C7S "C4'" "O4'" "C1'" 109.692 1.50 -C7S "O3'" "C3'" "C4'" 110.527 2.37 -C7S "O3'" "C3'" "C2'" 110.636 2.59 -C7S "O3'" "C3'" H4 110.713 1.50 -C7S "C4'" "C3'" "C2'" 102.800 1.50 -C7S "C4'" "C3'" H4 110.775 1.50 -C7S "C2'" "C3'" H4 110.862 1.50 -C7S "C3'" "O3'" H5 109.026 2.38 -C7S "C1'" "C2'" "C3'" 102.834 1.50 -C7S "C1'" "C2'" H6 111.187 1.50 -C7S "C1'" "C2'" H7 111.187 1.50 -C7S "C3'" "C2'" H6 111.310 1.50 -C7S "C3'" "C2'" H7 111.310 1.50 -C7S H6 "C2'" H7 108.952 1.50 -C7S "O4'" "C1'" "C2'" 106.308 1.50 -C7S "O4'" "C1'" N1 107.584 1.50 -C7S "O4'" "C1'" H8 109.550 1.50 -C7S "C2'" "C1'" N1 114.268 1.50 -C7S "C2'" "C1'" H8 109.741 1.50 -C7S N1 "C1'" H8 109.342 1.50 -C7S "C1'" N1 C2 118.777 1.50 -C7S "C1'" N1 C6 120.713 1.50 -C7S C2 N1 C6 120.510 1.50 -C7S O2 C2 N1 118.710 1.50 -C7S O2 C2 N3 122.370 1.50 -C7S N1 C2 N3 118.927 1.50 -C7S C2 N3 C4 120.266 1.50 -C7S N3 C4 N4 117.855 1.50 -C7S N3 C4 C5 121.269 1.50 -C7S N4 C4 C5 120.876 1.50 -C7S C4 N4 H9 119.818 1.59 -C7S C4 N4 H10 119.818 1.59 -C7S H9 N4 H10 120.363 1.85 -C7S C6 C5 C4 117.808 1.50 -C7S C6 C5 H11 120.848 1.50 -C7S C4 C5 H11 121.350 1.50 -C7S N1 C6 C5 121.215 1.50 -C7S N1 C6 H12 118.510 1.50 -C7S C5 C6 H12 120.275 1.75 -C7S P SP1 HSP1 109.471 3.00 +C7S "O5'" P SP1 114.928 3.00 +C7S "O5'" P OP2 106.327 3.00 +C7S "O5'" P OP3 106.327 3.00 +C7S SP1 P OP2 116.458 3.00 +C7S SP1 P OP3 116.458 3.00 +C7S OP2 P OP3 112.844 3.00 +C7S "C4'" "C5'" "O5'" 109.482 2.30 +C7S "C4'" "C5'" H1 109.589 1.50 +C7S "C4'" "C5'" H2 109.589 1.50 +C7S "O5'" "C5'" H1 109.954 1.50 +C7S "O5'" "C5'" H2 109.954 1.50 +C7S H1 "C5'" H2 108.471 1.50 +C7S "C5'" "O5'" P 119.085 2.00 +C7S "C3'" "C4'" "O4'" 105.546 1.50 +C7S "C3'" "C4'" "C5'" 113.954 2.40 +C7S "C3'" "C4'" H3 109.033 1.50 +C7S "O4'" "C4'" "C5'" 110.351 1.93 +C7S "O4'" "C4'" H3 108.778 1.50 +C7S "C5'" "C4'" H3 108.351 1.59 +C7S "C4'" "O4'" "C1'" 109.881 1.50 +C7S "O3'" "C3'" "C4'" 110.611 3.00 +C7S "O3'" "C3'" "C2'" 110.452 3.00 +C7S "O3'" "C3'" H4 110.786 1.88 +C7S "C4'" "C3'" "C2'" 102.581 1.50 +C7S "C4'" "C3'" H4 110.734 1.65 +C7S "C2'" "C3'" H4 110.938 1.50 +C7S "C3'" "O3'" H5 108.690 3.00 +C7S "C1'" "C2'" "C3'" 102.658 2.13 +C7S "C1'" "C2'" H6 111.181 1.50 +C7S "C1'" "C2'" H7 111.181 1.50 +C7S "C3'" "C2'" H6 111.287 1.86 +C7S "C3'" "C2'" H7 111.287 1.86 +C7S H6 "C2'" H7 109.095 1.50 +C7S "O4'" "C1'" "C2'" 106.263 1.50 +C7S "O4'" "C1'" N1 107.769 1.50 +C7S "O4'" "C1'" H8 109.467 1.50 +C7S "C2'" "C1'" N1 114.169 1.50 +C7S "C2'" "C1'" H8 109.883 1.50 +C7S N1 "C1'" H8 109.124 1.71 +C7S "C1'" N1 C2 118.555 2.04 +C7S "C1'" N1 C6 120.837 1.65 +C7S C2 N1 C6 120.608 1.50 +C7S O2 C2 N1 118.915 2.14 +C7S O2 C2 N3 122.293 1.50 +C7S N1 C2 N3 118.792 1.50 +C7S C2 N3 C4 120.397 1.50 +C7S N3 C4 N4 117.915 1.50 +C7S N3 C4 C5 121.314 1.50 +C7S N4 C4 C5 120.770 1.50 +C7S C4 N4 H9 119.693 3.00 +C7S C4 N4 H10 119.693 3.00 +C7S H9 N4 H10 120.613 3.00 +C7S C6 C5 C4 117.770 1.50 +C7S C6 C5 H11 121.009 1.50 +C7S C4 C5 H11 121.221 1.50 +C7S N1 C6 C5 121.118 1.50 +C7S N1 C6 H12 118.411 1.84 +C7S C5 C6 H12 120.471 3.00 loop_ _chem_comp_tor.comp_id @@ -175,30 +209,28 @@ _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period -C7S C2e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 -C7S C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 -C7S C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 -C7S C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 -C7S C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 -C7S C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 -C7S C3e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 -C7S C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 -C7S C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 -C7S C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 -C7S C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 -C7S C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 -C7S beta P "O5'" "C5'" "C4'" 180.000 10.00 3 -C7S gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 -C7S sp3_sp3_53 "O5'" P SP1 HSP1 60.000 10.0 3 -C7S sp3_sp3_49 "C5'" "O5'" P SP1 180.000 10.0 3 -C7S const_sp2_sp2_6 O2 C2 N3 C4 180.000 5.0 2 -C7S const_sp2_sp2_8 N4 C4 N3 C2 180.000 5.0 2 -C7S sp2_sp2_3 N3 C4 N4 H9 0.000 5.0 2 -C7S const_11 N4 C4 C5 C6 180.000 10.0 2 -C7S const_13 C4 C5 C6 N1 0.000 10.0 2 -C7S sp3_sp3_31 "C4'" "C3'" "O3'" H5 180.000 10.0 3 -C7S const_sp2_sp2_4 O2 C2 N1 "C1'" 0.000 5.0 2 -C7S const_18 C5 C6 N1 "C1'" 180.000 10.0 2 +C7S sp3_sp3_49 "C5'" "O5'" P SP1 180.000 10.0 3 +C7S const_sp2_sp2_5 N1 C2 N3 C4 0.000 0.0 1 +C7S const_sp2_sp2_7 C5 C4 N3 C2 0.000 0.0 1 +C7S sp2_sp2_21 C5 C4 N4 H9 180.000 20 2 +C7S sp2_sp2_24 N3 C4 N4 H10 180.000 20 2 +C7S const_sp2_sp2_9 N3 C4 C5 C6 0.000 0.0 1 +C7S const_12 N4 C4 C5 H11 0.000 0.0 1 +C7S const_13 C4 C5 C6 N1 0.000 0.0 1 +C7S const_16 H11 C5 C6 H12 0.000 0.0 1 +C7S sp3_sp3_46 "C4'" "C5'" "O5'" P 180.000 10.0 3 +C7S sp3_sp3_37 "C3'" "C4'" "C5'" "O5'" 180.000 10.0 3 +C7S sp3_sp3_35 "C5'" "C4'" "O4'" "C1'" 60.000 10.0 3 +C7S sp3_sp3_5 "O3'" "C3'" "C4'" "C5'" 60.000 10.0 3 +C7S sp3_sp3_28 "C2'" "C1'" "O4'" "C4'" -60.000 10.0 3 +C7S sp3_sp3_31 "C4'" "C3'" "O3'" H5 180.000 10.0 3 +C7S sp3_sp3_11 "C1'" "C2'" "C3'" "O3'" 60.000 10.0 3 +C7S sp3_sp3_19 "O4'" "C1'" "C2'" "C3'" 60.000 10.0 3 +C7S sp2_sp3_1 C2 N1 "C1'" "O4'" 150.000 10.0 6 +C7S const_sp2_sp2_1 N3 C2 N1 C6 0.000 0.0 1 +C7S const_sp2_sp2_4 O2 C2 N1 "C1'" 0.000 0.0 1 +C7S const_17 C5 C6 N1 C2 0.000 0.0 1 +C7S const_20 H12 C6 N1 "C1'" 0.000 0.0 1 loop_ _chem_comp_chir.comp_id @@ -208,10 +240,10 @@ _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign -C7S chir_1 P SP1 "O5'" OP3 both +C7S chir_1 P SP1 "O5'" OP3 both C7S chir_2 "C4'" "O4'" "C3'" "C5'" negative C7S chir_3 "C3'" "O3'" "C4'" "C2'" positive -C7S chir_4 "C1'" "O4'" N1 "C2'" negative +C7S chir_4 "C1'" "O4'" N1 "C2'" negative loop_ _chem_comp_plane_atom.comp_id @@ -219,20 +251,20 @@ _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd C7S plan-1 "C1'" 0.020 -C7S plan-1 C2 0.020 -C7S plan-1 C4 0.020 -C7S plan-1 C5 0.020 -C7S plan-1 C6 0.020 -C7S plan-1 H11 0.020 -C7S plan-1 H12 0.020 -C7S plan-1 N1 0.020 -C7S plan-1 N3 0.020 -C7S plan-1 N4 0.020 -C7S plan-1 O2 0.020 -C7S plan-2 C4 0.020 -C7S plan-2 H10 0.020 -C7S plan-2 H9 0.020 -C7S plan-2 N4 0.020 +C7S plan-1 C2 0.020 +C7S plan-1 C4 0.020 +C7S plan-1 C5 0.020 +C7S plan-1 C6 0.020 +C7S plan-1 H11 0.020 +C7S plan-1 H12 0.020 +C7S plan-1 N1 0.020 +C7S plan-1 N3 0.020 +C7S plan-1 N4 0.020 +C7S plan-1 O2 0.020 +C7S plan-2 C4 0.020 +C7S plan-2 H10 0.020 +C7S plan-2 H9 0.020 +C7S plan-2 N4 0.020 loop_ _pdbx_chem_comp_descriptor.comp_id @@ -240,20 +272,29 @@ _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor -C7S SMILES ACDLabs 12.01 P(=O)(O)(OCC1C(CC(O1)N2C=CC(=NC2=O)N)O)S -C7S InChI InChI 1.03 InChI=1S/C9H14N3O6PS/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(18-8)4-17-19(15,16)20/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,20)/t5-,6+,8+/m0/s1 -C7S InChIKey InChI 1.03 FHBXKBNKQMSUIJ-SHYZEUOFSA-N -C7S SMILES_CANONICAL CACTVS 3.385 NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(S)=O)O2 -C7S SMILES CACTVS 3.385 NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(S)=O)O2 +C7S SMILES ACDLabs 12.01 P(=O)(O)(OCC1C(CC(O1)N2C=CC(=NC2=O)N)O)S +C7S InChI InChI 1.03 InChI=1S/C9H14N3O6PS/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(18-8)4-17-19(15,16)20/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,20)/t5-,6+,8+/m0/s1 +C7S InChIKey InChI 1.03 FHBXKBNKQMSUIJ-SHYZEUOFSA-N +C7S SMILES_CANONICAL CACTVS 3.385 NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(S)=O)O2 +C7S SMILES CACTVS 3.385 NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(S)=O)O2 C7S SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)S)O -C7S SMILES "OpenEye OEToolkits" 2.0.4 C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)S)O +C7S SMILES "OpenEye OEToolkits" 2.0.4 C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)S)O loop_ _pdbx_chem_comp_description_generator.comp_id _pdbx_chem_comp_description_generator.program_name _pdbx_chem_comp_description_generator.program_version _pdbx_chem_comp_description_generator.descriptor -C7S acedrg 243 "dictionary generator" -C7S acedrg_database 11 "data source" -C7S rdkit 2017.03.2 "Chemoinformatics tool" -C7S refmac5 5.8.0238 "optimization tool" +C7S acedrg 277 "dictionary generator" +C7S acedrg_database 12 "data source" +C7S rdkit 2019.09.1 "Chemoinformatics tool" +C7S refmac5 5.8.0425 "optimization tool" + +loop_ +_chem_comp_alias.comp_id +_chem_comp_alias.group +_chem_comp_alias.atom_id +_chem_comp_alias.atom_id_standard +C7S S-NA OP2 OP1 +C7S S-NA SP1 S2P +C7S S-NA H5 HO3' diff --git a/d/DV3.cif b/d/DV3.cif index cf7e64707..710697888 100644 --- a/d/DV3.cif +++ b/d/DV3.cif @@ -1,4 +1,3 @@ -# data_comp_list loop_ _chem_comp.id @@ -8,10 +7,9 @@ _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level -DV3 DV3 1,4-anhydro-2-deoxy-5-O-thiophosphono-D-erythro-pentitol NON-POLYMER 22 12 . -# +DV3 DV3 1,4-anhydro-2-deoxy-5-O-thiophosphono-D-erythro-pentitol NON-POLYMER 21 12 . + data_comp_DV3 -# loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id @@ -21,28 +19,54 @@ _chem_comp_atom.charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z -DV3 "O5'" O O2 0 -3.402 -39.236 2.279 -DV3 P P P 0 -2.393 -38.993 3.498 -DV3 SP3 S SH1 0 -2.643 -36.986 4.025 -DV3 OP2 O O 0 -1.006 -39.212 2.993 -DV3 OP3 O OP -1 -2.810 -39.881 4.621 -DV3 "C2'" C CH2 0 -3.484 -40.286 -1.771 -DV3 "C5'" C CH2 0 -3.168 -38.565 1.014 -DV3 "C4'" C CH1 0 -4.252 -38.946 0.035 -DV3 "O4'" O O2 0 -4.128 -38.127 -1.150 -DV3 "C1'" C CH2 0 -3.855 -38.938 -2.276 -DV3 "C3'" C CH1 0 -4.209 -40.399 -0.438 -DV3 "O3'" O OH1 0 -5.522 -40.928 -0.607 -DV3 H1 H HSH1 0 -2.902 -36.908 5.206 -DV3 H3 H H 0 -3.780 -40.991 -2.389 -DV3 H4 H H 0 -2.512 -40.364 -1.647 -DV3 H5 H H 0 -2.286 -38.830 0.651 -DV3 H6 H H 0 -3.170 -37.586 1.147 -DV3 H7 H H 0 -5.125 -38.770 0.459 -DV3 H8 H H 0 -3.118 -38.556 -2.798 -DV3 H9 H H 0 -4.646 -38.996 -2.851 -DV3 H10 H H 0 -3.693 -40.954 0.194 -DV3 H11 H H 0 -5.978 -40.419 -1.111 +DV3 "O5'" O O2 0 -3.350 -39.316 2.248 +DV3 P P P 0 -2.499 -38.927 3.557 +DV3 SP3 S S1 0 -2.910 -37.157 4.251 +DV3 OP2 O OP -1 -1.083 -39.022 3.080 +DV3 OP3 O OP -1 -2.751 -40.047 4.514 +DV3 "C2'" C CH2 0 -3.568 -40.334 -1.781 +DV3 "C5'" C CH2 0 -3.059 -38.671 0.993 +DV3 "C4'" C CH1 0 -4.192 -38.918 0.028 +DV3 "O4'" O O2 0 -3.991 -38.121 -1.153 +DV3 "C1'" C CH2 0 -3.780 -38.957 -2.275 +DV3 "C3'" C CH1 0 -4.314 -40.369 -0.447 +DV3 "O3'" O OH1 0 -5.677 -40.752 -0.626 +DV3 H3 H H 0 -3.940 -40.996 -2.405 +DV3 H4 H H 0 -2.613 -40.521 -1.650 +DV3 H5 H H 0 -2.217 -39.032 0.615 +DV3 H6 H H 0 -2.948 -37.696 1.131 +DV3 H7 H H 0 -5.039 -38.645 0.462 +DV3 H8 H H 0 -2.996 -38.653 -2.778 +DV3 H9 H H 0 -4.560 -38.926 -2.867 +DV3 H10 H H 0 -3.862 -40.984 0.184 +DV3 H11 H H 0 -6.067 -40.204 -1.128 + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +DV3 "O5'" O(CC[5]HH)(POOS) +DV3 P P(OC)(O)2(S) +DV3 SP3 S(PO3) +DV3 OP2 O(POOS) +DV3 OP3 O(POOS) +DV3 "C2'" C[5](C[5]C[5]HO)(C[5]O[5]HH)(H)2{1|C<4>,1|H<1>} +DV3 "C5'" C(C[5]C[5]O[5]H)(OP)(H)2 +DV3 "C4'" C[5](C[5]C[5]HO)(O[5]C[5])(CHHO)(H){4|H<1>} +DV3 "O4'" O[5](C[5]C[5]CH)(C[5]C[5]HH){1|O<2>,3|H<1>} +DV3 "C1'" C[5](C[5]C[5]HH)(O[5]C[5])(H)2{1|C<4>,1|O<2>,2|H<1>} +DV3 "C3'" C[5](C[5]C[5]HH)(C[5]O[5]CH)(OH)(H){2|H<1>} +DV3 "O3'" O(C[5]C[5]2H)(H) +DV3 H3 H(C[5]C[5]2H) +DV3 H4 H(C[5]C[5]2H) +DV3 H5 H(CC[5]HO) +DV3 H6 H(CC[5]HO) +DV3 H7 H(C[5]C[5]O[5]C) +DV3 H8 H(C[5]C[5]O[5]H) +DV3 H9 H(C[5]C[5]O[5]H) +DV3 H10 H(C[5]C[5]2O) +DV3 H11 H(OC[5]) + loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 @@ -53,28 +77,28 @@ _chem_comp_bond.value_dist_nucleus _chem_comp_bond.value_dist_nucleus_esd _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd -DV3 "C2'" "C1'" SINGLE n 1.489 0.0200 1.489 0.0200 -DV3 "O4'" "C1'" SINGLE n 1.415 0.0200 1.415 0.0200 -DV3 "C2'" "C3'" SINGLE n 1.521 0.0137 1.521 0.0137 -DV3 "C4'" "O4'" SINGLE n 1.444 0.0115 1.444 0.0115 -DV3 "C3'" "O3'" SINGLE n 1.424 0.0100 1.424 0.0100 -DV3 "C4'" "C3'" SINGLE n 1.527 0.0115 1.527 0.0115 -DV3 "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 -DV3 "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 -DV3 "O5'" P SINGLE n 1.601 0.0114 1.601 0.0114 -DV3 P OP2 DOUBLE n 1.493 0.0157 1.493 0.0157 -DV3 P SP3 SINGLE n 2.091 0.0200 2.091 0.0200 -DV3 P OP3 SINGLE n 1.493 0.0157 1.493 0.0157 -DV3 SP3 H1 SINGLE n 1.338 0.0100 1.211 0.0200 -DV3 "C2'" H3 SINGLE n 1.089 0.0100 0.983 0.0154 -DV3 "C2'" H4 SINGLE n 1.089 0.0100 0.983 0.0154 -DV3 "C5'" H5 SINGLE n 1.089 0.0100 0.989 0.0200 -DV3 "C5'" H6 SINGLE n 1.089 0.0100 0.989 0.0200 -DV3 "C4'" H7 SINGLE n 1.089 0.0100 0.986 0.0200 -DV3 "C1'" H8 SINGLE n 1.089 0.0100 0.980 0.0111 -DV3 "C1'" H9 SINGLE n 1.089 0.0100 0.980 0.0111 -DV3 "C3'" H10 SINGLE n 1.089 0.0100 0.987 0.0182 -DV3 "O3'" H11 SINGLE n 0.970 0.0120 0.849 0.0200 +DV3 "C2'" "C1'" SINGLE n 1.480 0.0200 1.480 0.0200 +DV3 "O4'" "C1'" SINGLE n 1.412 0.0200 1.412 0.0200 +DV3 "C2'" "C3'" SINGLE n 1.530 0.0123 1.530 0.0123 +DV3 "C4'" "O4'" SINGLE n 1.438 0.0100 1.438 0.0100 +DV3 "C3'" "O3'" SINGLE n 1.425 0.0122 1.425 0.0122 +DV3 "C4'" "C3'" SINGLE n 1.530 0.0119 1.530 0.0119 +DV3 "C5'" "C4'" SINGLE n 1.508 0.0100 1.508 0.0100 +DV3 "O5'" "C5'" SINGLE n 1.438 0.0200 1.438 0.0200 +DV3 "O5'" P SINGLE n 1.613 0.0200 1.613 0.0200 +DV3 P OP2 SINGLE n 1.497 0.0143 1.497 0.0143 +DV3 P SP3 DOUBLE n 1.949 0.0200 1.949 0.0200 +DV3 P OP3 SINGLE n 1.497 0.0143 1.497 0.0143 +DV3 "C2'" H3 SINGLE n 1.092 0.0100 0.982 0.0143 +DV3 "C2'" H4 SINGLE n 1.092 0.0100 0.982 0.0143 +DV3 "C5'" H5 SINGLE n 1.092 0.0100 0.991 0.0200 +DV3 "C5'" H6 SINGLE n 1.092 0.0100 0.991 0.0200 +DV3 "C4'" H7 SINGLE n 1.092 0.0100 0.990 0.0200 +DV3 "C1'" H8 SINGLE n 1.092 0.0100 0.980 0.0111 +DV3 "C1'" H9 SINGLE n 1.092 0.0100 0.980 0.0111 +DV3 "C3'" H10 SINGLE n 1.092 0.0100 0.990 0.0179 +DV3 "O3'" H11 SINGLE n 0.972 0.0180 0.839 0.0200 + loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 @@ -82,46 +106,46 @@ _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd -DV3 "C5'" "O5'" P 119.135 1.78 -DV3 "O5'" P OP2 108.530 2.45 -DV3 "O5'" P SP3 105.685 3.00 -DV3 "O5'" P OP3 108.530 2.45 -DV3 OP2 P SP3 111.281 3.00 -DV3 OP2 P OP3 116.964 2.85 -DV3 SP3 P OP3 111.281 3.00 -DV3 P SP3 H1 109.471 3.00 -DV3 "C1'" "C2'" "C3'" 104.443 2.26 -DV3 "C1'" "C2'" H3 111.353 1.50 -DV3 "C1'" "C2'" H4 111.353 1.50 -DV3 "C3'" "C2'" H3 110.947 1.50 -DV3 "C3'" "C2'" H4 110.947 1.50 -DV3 H3 "C2'" H4 108.877 1.50 -DV3 "C4'" "C5'" "O5'" 109.510 1.50 -DV3 "C4'" "C5'" H5 109.624 1.50 -DV3 "C4'" "C5'" H6 109.624 1.50 -DV3 "O5'" "C5'" H5 109.821 1.50 -DV3 "O5'" "C5'" H6 109.821 1.50 -DV3 H5 "C5'" H6 108.472 1.50 -DV3 "O4'" "C4'" "C3'" 105.508 1.50 -DV3 "O4'" "C4'" "C5'" 109.123 1.50 -DV3 "O4'" "C4'" H7 109.115 1.50 -DV3 "C3'" "C4'" "C5'" 114.866 1.63 -DV3 "C3'" "C4'" H7 109.069 1.50 -DV3 "C5'" "C4'" H7 108.268 1.50 -DV3 "C1'" "O4'" "C4'" 107.967 2.51 -DV3 "C2'" "C1'" "O4'" 106.763 3.00 -DV3 "C2'" "C1'" H8 110.363 1.50 -DV3 "C2'" "C1'" H9 110.363 1.50 -DV3 "O4'" "C1'" H8 110.225 1.50 -DV3 "O4'" "C1'" H9 110.225 1.50 -DV3 H8 "C1'" H9 108.637 1.50 -DV3 "C2'" "C3'" "O3'" 111.015 2.41 -DV3 "C2'" "C3'" "C4'" 102.085 1.51 -DV3 "C2'" "C3'" H10 111.076 1.50 -DV3 "O3'" "C3'" "C4'" 110.527 2.37 -DV3 "O3'" "C3'" H10 110.713 1.50 -DV3 "C4'" "C3'" H10 110.775 1.50 -DV3 "C3'" "O3'" H11 109.026 2.38 +DV3 "C5'" "O5'" P 119.085 2.00 +DV3 "O5'" P OP2 106.327 3.00 +DV3 "O5'" P SP3 114.928 3.00 +DV3 "O5'" P OP3 106.327 3.00 +DV3 OP2 P SP3 116.458 3.00 +DV3 OP2 P OP3 112.844 3.00 +DV3 SP3 P OP3 116.458 3.00 +DV3 "C1'" "C2'" "C3'" 104.595 3.00 +DV3 "C1'" "C2'" H3 111.353 1.50 +DV3 "C1'" "C2'" H4 111.353 1.50 +DV3 "C3'" "C2'" H3 110.924 1.50 +DV3 "C3'" "C2'" H4 110.924 1.50 +DV3 H3 "C2'" H4 109.193 1.50 +DV3 "C4'" "C5'" "O5'" 109.482 2.30 +DV3 "C4'" "C5'" H5 109.589 1.50 +DV3 "C4'" "C5'" H6 109.589 1.50 +DV3 "O5'" "C5'" H5 109.954 1.50 +DV3 "O5'" "C5'" H6 109.954 1.50 +DV3 H5 "C5'" H6 108.471 1.50 +DV3 "O4'" "C4'" "C3'" 105.543 1.50 +DV3 "O4'" "C4'" "C5'" 109.156 1.74 +DV3 "O4'" "C4'" H7 108.884 1.50 +DV3 "C3'" "C4'" "C5'" 113.954 2.40 +DV3 "C3'" "C4'" H7 109.033 1.50 +DV3 "C5'" "C4'" H7 108.351 1.59 +DV3 "C1'" "O4'" "C4'" 109.212 1.50 +DV3 "C2'" "C1'" "O4'" 106.725 3.00 +DV3 "C2'" "C1'" H8 110.363 1.50 +DV3 "C2'" "C1'" H9 110.363 1.50 +DV3 "O4'" "C1'" H8 110.224 1.50 +DV3 "O4'" "C1'" H9 110.224 1.50 +DV3 H8 "C1'" H9 108.674 1.50 +DV3 "C2'" "C3'" "O3'" 110.663 3.00 +DV3 "C2'" "C3'" "C4'" 102.105 1.79 +DV3 "C2'" "C3'" H10 111.013 3.00 +DV3 "O3'" "C3'" "C4'" 110.611 3.00 +DV3 "O3'" "C3'" H10 110.786 1.88 +DV3 "C4'" "C3'" H10 110.734 1.65 +DV3 "C3'" "O3'" H11 108.690 3.00 + loop_ _chem_comp_tor.comp_id _chem_comp_tor.id @@ -132,16 +156,16 @@ _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period -DV3 sp3_sp3_51 "C5'" "O5'" P OP2 60.000 10.0 3 -DV3 sp3_sp3_46 "C4'" "C5'" "O5'" P 180.000 10.0 3 -DV3 sp3_sp3_34 "C2'" "C3'" "O3'" H11 180.000 10.0 3 -DV3 sp3_sp3_53 "O5'" P SP3 H1 60.000 10.0 3 -DV3 sp3_sp3_26 "C1'" "C2'" "C3'" "O3'" -60.000 10.0 3 -DV3 sp3_sp3_1 "O4'" "C1'" "C2'" "C3'" 60.000 10.0 3 -DV3 sp3_sp3_37 "O4'" "C4'" "C5'" "O5'" 180.000 10.0 3 -DV3 sp3_sp3_20 "O3'" "C3'" "C4'" "C5'" -60.000 10.0 3 -DV3 sp3_sp3_14 "C5'" "C4'" "O4'" "C1'" -60.000 10.0 3 -DV3 sp3_sp3_10 "C2'" "C1'" "O4'" "C4'" -60.000 10.0 3 +DV3 sp3_sp3_51 "C5'" "O5'" P OP2 60.000 10.0 3 +DV3 sp3_sp3_46 "C4'" "C5'" "O5'" P 180.000 10.0 3 +DV3 sp3_sp3_34 "C2'" "C3'" "O3'" H11 180.000 10.0 3 +DV3 sp3_sp3_26 "C1'" "C2'" "C3'" "O3'" -60.000 10.0 3 +DV3 sp3_sp3_1 "O4'" "C1'" "C2'" "C3'" 60.000 10.0 3 +DV3 sp3_sp3_37 "O4'" "C4'" "C5'" "O5'" 180.000 10.0 3 +DV3 sp3_sp3_20 "O3'" "C3'" "C4'" "C5'" -60.000 10.0 3 +DV3 sp3_sp3_14 "C5'" "C4'" "O4'" "C1'" -60.000 10.0 3 +DV3 sp3_sp3_10 "C2'" "C1'" "O4'" "C4'" -60.000 10.0 3 + loop_ _chem_comp_chir.comp_id _chem_comp_chir.id @@ -150,28 +174,39 @@ _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign -DV3 chir_1 P SP3 "O5'" OP3 both -DV3 chir_2 "C4'" "O4'" "C3'" "C5'" negative -DV3 chir_3 "C3'" "O3'" "C4'" "C2'" positive +DV3 chir_1 P SP3 "O5'" OP3 both +DV3 chir_2 "C4'" "O4'" "C3'" "C5'" negative +DV3 chir_3 "C3'" "O3'" "C4'" "C2'" positive + loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor -DV3 SMILES ACDLabs 12.01 O(P(S)(O)=O)CC1OCCC1O -DV3 InChI InChI 1.03 InChI=1S/C5H11O5PS/c6-4-1-2-9-5(4)3-10-11(7,8)12/h4-6H,1-3H2,(H2,7,8,12)/t4-,5+/m0/s1 -DV3 InChIKey InChI 1.03 PPLIRDZWRNAVLB-CRCLSJGQSA-N -DV3 SMILES_CANONICAL CACTVS 3.385 O[C@H]1CCO[C@@H]1CO[P](O)(S)=O -DV3 SMILES CACTVS 3.385 O[CH]1CCO[CH]1CO[P](O)(S)=O -DV3 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 C1CO[C@@H]([C@H]1O)COP(=O)(O)S -DV3 SMILES "OpenEye OEToolkits" 2.0.6 C1COC(C1O)COP(=O)(O)S +DV3 SMILES ACDLabs 12.01 O(P(S)(O)=O)CC1OCCC1O +DV3 InChI InChI 1.03 InChI=1S/C5H11O5PS/c6-4-1-2-9-5(4)3-10-11(7,8)12/h4-6H,1-3H2,(H2,7,8,12)/t4-,5+/m0/s1 +DV3 InChIKey InChI 1.03 PPLIRDZWRNAVLB-CRCLSJGQSA-N +DV3 SMILES_CANONICAL CACTVS 3.385 O[C@H]1CCO[C@@H]1CO[P](O)(S)=O +DV3 SMILES CACTVS 3.385 O[CH]1CCO[CH]1CO[P](O)(S)=O +DV3 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 C1CO[C@@H]([C@H]1O)COP(=O)(O)S +DV3 SMILES "OpenEye OEToolkits" 2.0.6 C1COC(C1O)COP(=O)(O)S + loop_ _pdbx_chem_comp_description_generator.comp_id _pdbx_chem_comp_description_generator.program_name _pdbx_chem_comp_description_generator.program_version _pdbx_chem_comp_description_generator.descriptor -DV3 acedrg 243 "dictionary generator" -DV3 acedrg_database 11 "data source" -DV3 rdkit 2017.03.2 "Chemoinformatics tool" -DV3 refmac5 5.8.0238 "optimization tool" +DV3 acedrg 277 "dictionary generator" +DV3 acedrg_database 12 "data source" +DV3 rdkit 2019.09.1 "Chemoinformatics tool" +DV3 refmac5 5.8.0425 "optimization tool" + +loop_ +_chem_comp_alias.comp_id +_chem_comp_alias.group +_chem_comp_alias.atom_id +_chem_comp_alias.atom_id_standard +DV3 S-NA OP2 OP1 +DV3 S-NA SP3 S2P +DV3 S-NA H11 HO3' diff --git a/f/F2T.cif b/f/F2T.cif index 6a6e5bc03..604b29369 100644 --- a/f/F2T.cif +++ b/f/F2T.cif @@ -7,7 +7,7 @@ _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level -F2T F2T "2'-deoxy-2'-fluoro-5'-O-thiophosphonouridine" NON-POLYMER 32 21 . +F2T F2T "2'-deoxy-2'-fluoro-5'-O-thiophosphonouridine" NON-POLYMER 31 21 . data_comp_F2T loop_ @@ -19,38 +19,73 @@ _chem_comp_atom.charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z -F2T P P P 0 -25.210 31.236 28.230 -F2T SP1 S SH1 0 -27.244 31.311 27.755 -F2T OP2 O O 0 -24.849 29.860 28.684 -F2T "O5'" O O2 0 -25.040 32.219 29.481 -F2T "C5'" C CH2 0 -23.704 32.546 29.944 -F2T "C4'" C CH1 0 -23.783 33.401 31.186 -F2T "O4'" O O2 0 -24.630 34.546 30.949 -F2T "C3'" C CH1 0 -24.389 32.723 32.411 -F2T "O3'" O OH1 0 -23.446 31.932 33.102 -F2T "C2'" C CH1 0 -24.869 33.917 33.228 -F2T "F2'" F F 0 -23.859 34.348 34.095 -F2T "C1'" C CH1 0 -25.137 35.013 32.189 -F2T N1 N NR6 0 -26.580 35.335 32.014 -F2T C2 C CR6 0 -27.043 36.594 32.373 -F2T O2 O O 0 -26.328 37.479 32.828 -F2T N3 N NR6 0 -28.392 36.793 32.178 -F2T C4 C CR6 0 -29.308 35.885 31.677 -F2T O4 O O 0 -30.488 36.216 31.562 -F2T C5 C CR16 0 -28.755 34.606 31.332 -F2T C6 C CR16 0 -27.442 34.381 31.512 -F2T OP3 O OP -1 -24.392 31.777 27.106 -F2T H11 H HSH1 0 -27.377 31.323 26.551 -F2T "H5'" H H 0 -23.216 33.035 29.236 -F2T "H5''" H H 0 -23.208 31.714 30.146 -F2T "H4'" H H 0 -22.875 33.718 31.403 -F2T "H3'" H H 0 -25.153 32.170 32.143 -F2T "HO3'" H H 0 -23.826 31.604 33.787 -F2T "H2'" H H 0 -25.691 33.690 33.725 -F2T "H1'" H H 0 -24.642 35.825 32.446 -F2T H3 H H 0 -28.699 37.598 32.403 -F2T H5 H H 0 -29.306 33.934 30.986 -F2T H6 H H 0 -27.092 33.541 31.283 +F2T P P P 0 -25.329 31.268 28.225 +F2T SP1 S S1 0 -27.194 30.827 27.898 +F2T OP2 O OP -1 -24.515 30.039 28.486 +F2T "O5'" O O2 0 -25.109 32.147 29.556 +F2T "C5'" C CH2 0 -23.773 32.486 29.978 +F2T "C4'" C CH1 0 -23.823 33.384 31.190 +F2T "O4'" O O2 0 -24.633 34.552 30.936 +F2T "C3'" C CH1 0 -24.441 32.772 32.443 +F2T "O3'" O OH1 0 -23.508 32.017 33.185 +F2T "C2'" C CH1 0 -24.848 34.009 33.231 +F2T "F2'" F F 0 -23.790 34.461 34.018 +F2T "C1'" C CH1 0 -25.122 35.055 32.159 +F2T N1 N NR6 0 -26.544 35.382 31.984 +F2T C2 C CR6 0 -26.993 36.670 32.255 +F2T O2 O O 0 -26.269 37.580 32.634 +F2T N3 N NR16 0 -28.345 36.864 32.062 +F2T C4 C CR6 0 -29.275 35.929 31.639 +F2T O4 O O 0 -30.457 36.256 31.513 +F2T C5 C CR16 0 -28.735 34.622 31.384 +F2T C6 C CR16 0 -27.421 34.400 31.564 +F2T OP3 O OP -1 -24.680 32.049 27.128 +F2T "H5'" H H 0 -23.296 32.950 29.245 +F2T "H5''" H H 0 -23.271 31.661 30.203 +F2T "H4'" H H 0 -22.900 33.679 31.392 +F2T "H3'" H H 0 -25.230 32.222 32.213 +F2T "HO3'" H H 0 -23.906 31.663 33.833 +F2T "H2'" H H 0 -25.660 33.829 33.786 +F2T "H1'" H H 0 -24.610 35.882 32.388 +F2T H3 H H 0 -28.638 37.670 32.226 +F2T H5 H H 0 -29.298 33.929 31.094 +F2T H6 H H 0 -27.079 33.537 31.392 + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +F2T P P(OC)(O)2(S) +F2T SP1 S(PO3) +F2T OP2 O(POOS) +F2T "O5'" O(CC[5]HH)(POOS) +F2T "C5'" C(C[5]C[5]O[5]H)(OP)(H)2 +F2T "C4'" C[5](C[5]C[5]HO)(O[5]C[5])(CHHO)(H){1|F<1>,1|N<3>,2|H<1>} +F2T "O4'" O[5](C[5]N[6a]C[5]H)(C[5]C[5]CH){1|F<1>,1|O<2>,2|C<3>,2|H<1>} +F2T "C3'" C[5](C[5]C[5]FH)(C[5]O[5]CH)(OH)(H){1|H<1>,1|N<3>} +F2T "O3'" O(C[5]C[5]2H)(H) +F2T "C2'" C[5](C[5]N[6a]O[5]H)(C[5]C[5]HO)(F)(H){1|C<4>,1|H<1>,2|C<3>} +F2T "F2'" F(C[5]C[5]2H) +F2T "C1'" C[5](N[6a]C[6a]2)(C[5]C[5]FH)(O[5]C[5])(H){1|C<3>,1|C<4>,1|N<3>,1|O<1>,1|O<2>,3|H<1>} +F2T N1 N[6a](C[5]C[5]O[5]H)(C[6a]C[6a]H)(C[6a]N[6a]O){1|C<3>,1|F<1>,2|C<4>,3|H<1>} +F2T C2 C[6a](N[6a]C[6a]C[5])(N[6a]C[6a]H)(O){1|C<3>,1|C<4>,1|O<1>,1|O<2>,2|H<1>} +F2T O2 O(C[6a]N[6a]2) +F2T N3 N[6a](C[6a]C[6a]O)(C[6a]N[6a]O)(H){1|C<3>,1|C<4>,1|H<1>} +F2T C4 C[6a](C[6a]C[6a]H)(N[6a]C[6a]H)(O){1|H<1>,1|N<3>,1|O<1>} +F2T O4 O(C[6a]C[6a]N[6a]) +F2T C5 C[6a](C[6a]N[6a]H)(C[6a]N[6a]O)(H){1|C<3>,1|C<4>,1|H<1>} +F2T C6 C[6a](N[6a]C[6a]C[5])(C[6a]C[6a]H)(H){1|C<4>,1|H<1>,1|N<3>,1|O<2>,2|O<1>} +F2T OP3 O(POOS) +F2T "H5'" H(CC[5]HO) +F2T "H5''" H(CC[5]HO) +F2T "H4'" H(C[5]C[5]O[5]C) +F2T "H3'" H(C[5]C[5]2O) +F2T "HO3'" H(OC[5]) +F2T "H2'" H(C[5]C[5]2F) +F2T "H1'" H(C[5]N[6a]C[5]O[5]) +F2T H3 H(N[6a]C[6a]2) +F2T H5 H(C[6a]C[6a]2) +F2T H6 H(C[6a]C[6a]N[6a]) loop_ _chem_comp_bond.comp_id @@ -62,39 +97,38 @@ _chem_comp_bond.value_dist_nucleus _chem_comp_bond.value_dist_nucleus_esd _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd -F2T P SP1 SINGLE n 2.091 0.0200 2.091 0.0200 -F2T P OP2 DOUBLE n 1.493 0.0157 1.493 0.0157 -F2T P "O5'" SINGLE n 1.601 0.0114 1.601 0.0114 -F2T "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 -F2T "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 -F2T "C4'" "O4'" SINGLE n 1.446 0.0100 1.446 0.0100 -F2T "C4'" "C3'" SINGLE n 1.528 0.0117 1.528 0.0117 -F2T "O4'" "C1'" SINGLE n 1.417 0.0100 1.417 0.0100 -F2T "C3'" "O3'" SINGLE n 1.411 0.0121 1.411 0.0121 -F2T "C3'" "C2'" SINGLE n 1.522 0.0100 1.522 0.0100 -F2T "C2'" "F2'" SINGLE n 1.398 0.0100 1.398 0.0100 -F2T "C2'" "C1'" SINGLE n 1.530 0.0100 1.530 0.0100 -F2T "C1'" N1 SINGLE n 1.476 0.0146 1.476 0.0146 -F2T N1 C2 SINGLE y 1.379 0.0100 1.379 0.0100 -F2T N1 C6 SINGLE y 1.375 0.0100 1.375 0.0100 -F2T C2 O2 DOUBLE n 1.224 0.0111 1.224 0.0111 -F2T C2 N3 SINGLE y 1.372 0.0112 1.372 0.0112 -F2T N3 C4 SINGLE y 1.381 0.0100 1.381 0.0100 -F2T C4 O4 DOUBLE n 1.231 0.0100 1.231 0.0100 -F2T C4 C5 SINGLE y 1.434 0.0100 1.434 0.0100 -F2T C5 C6 DOUBLE y 1.342 0.0100 1.342 0.0100 -F2T P OP3 SINGLE n 1.493 0.0157 1.493 0.0157 -F2T SP1 H11 SINGLE n 1.338 0.0100 1.211 0.0200 -F2T "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 -F2T "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200 -F2T "C4'" "H4'" SINGLE n 1.089 0.0100 0.986 0.0200 -F2T "C3'" "H3'" SINGLE n 1.089 0.0100 0.980 0.0100 -F2T "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 -F2T "C2'" "H2'" SINGLE n 1.089 0.0100 0.988 0.0103 -F2T "C1'" "H1'" SINGLE n 1.089 0.0100 0.987 0.0200 -F2T N3 H3 SINGLE n 1.016 0.0100 0.889 0.0200 -F2T C5 H5 SINGLE n 1.082 0.0130 0.935 0.0100 -F2T C6 H6 SINGLE n 1.082 0.0130 0.938 0.0107 +F2T P SP1 DOUBLE n 1.949 0.0200 1.949 0.0200 +F2T P OP2 SINGLE n 1.497 0.0143 1.497 0.0143 +F2T P "O5'" SINGLE n 1.613 0.0200 1.613 0.0200 +F2T "O5'" "C5'" SINGLE n 1.438 0.0200 1.438 0.0200 +F2T "C5'" "C4'" SINGLE n 1.508 0.0100 1.508 0.0100 +F2T "C4'" "O4'" SINGLE n 1.447 0.0100 1.447 0.0100 +F2T "C4'" "C3'" SINGLE n 1.530 0.0119 1.530 0.0119 +F2T "O4'" "C1'" SINGLE n 1.408 0.0100 1.408 0.0100 +F2T "C3'" "O3'" SINGLE n 1.410 0.0100 1.410 0.0100 +F2T "C3'" "C2'" SINGLE n 1.519 0.0100 1.519 0.0100 +F2T "C2'" "F2'" SINGLE n 1.393 0.0100 1.393 0.0100 +F2T "C2'" "C1'" SINGLE n 1.516 0.0100 1.516 0.0100 +F2T "C1'" N1 SINGLE n 1.463 0.0100 1.463 0.0100 +F2T N1 C2 SINGLE y 1.381 0.0100 1.381 0.0100 +F2T N1 C6 SINGLE y 1.377 0.0100 1.377 0.0100 +F2T C2 O2 DOUBLE n 1.221 0.0100 1.221 0.0100 +F2T C2 N3 SINGLE y 1.375 0.0100 1.375 0.0100 +F2T N3 C4 SINGLE y 1.382 0.0100 1.382 0.0100 +F2T C4 O4 DOUBLE n 1.233 0.0100 1.233 0.0100 +F2T C4 C5 SINGLE y 1.435 0.0100 1.435 0.0100 +F2T C5 C6 DOUBLE y 1.342 0.0100 1.342 0.0100 +F2T P OP3 SINGLE n 1.497 0.0143 1.497 0.0143 +F2T "C5'" "H5'" SINGLE n 1.092 0.0100 0.991 0.0200 +F2T "C5'" "H5''" SINGLE n 1.092 0.0100 0.991 0.0200 +F2T "C4'" "H4'" SINGLE n 1.092 0.0100 0.990 0.0200 +F2T "C3'" "H3'" SINGLE n 1.092 0.0100 0.989 0.0103 +F2T "O3'" "HO3'" SINGLE n 0.972 0.0180 0.839 0.0200 +F2T "C2'" "H2'" SINGLE n 1.092 0.0100 1.000 0.0100 +F2T "C1'" "H1'" SINGLE n 1.092 0.0100 1.000 0.0100 +F2T N3 H3 SINGLE n 1.013 0.0120 0.872 0.0200 +F2T C5 H5 SINGLE n 1.085 0.0150 0.939 0.0100 +F2T C6 H6 SINGLE n 1.085 0.0150 0.944 0.0121 loop_ _chem_comp_angle.comp_id @@ -103,64 +137,63 @@ _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd -F2T SP1 P OP2 111.281 3.00 -F2T SP1 P "O5'" 105.685 3.00 -F2T SP1 P OP3 111.281 3.00 -F2T OP2 P "O5'" 108.530 2.45 -F2T OP2 P OP3 116.964 2.85 -F2T "O5'" P OP3 108.530 2.45 -F2T P SP1 H11 109.471 3.00 -F2T P "O5'" "C5'" 119.135 1.78 -F2T "O5'" "C5'" "C4'" 109.510 1.50 -F2T "O5'" "C5'" "H5'" 109.821 1.50 -F2T "O5'" "C5'" "H5''" 109.821 1.50 -F2T "C4'" "C5'" "H5'" 109.624 1.50 -F2T "C4'" "C5'" "H5''" 109.624 1.50 -F2T "H5'" "C5'" "H5''" 108.472 1.50 -F2T "C5'" "C4'" "O4'" 109.615 1.50 -F2T "C5'" "C4'" "C3'" 114.866 1.63 -F2T "C5'" "C4'" "H4'" 108.268 1.50 -F2T "O4'" "C4'" "C3'" 105.508 1.50 -F2T "O4'" "C4'" "H4'" 108.698 1.50 -F2T "C3'" "C4'" "H4'" 109.385 1.50 -F2T "C4'" "O4'" "C1'" 109.375 1.70 -F2T "C4'" "C3'" "O3'" 112.431 2.44 -F2T "C4'" "C3'" "C2'" 102.302 1.50 -F2T "C4'" "C3'" "H3'" 109.965 1.50 -F2T "O3'" "C3'" "C2'" 111.623 3.00 -F2T "O3'" "C3'" "H3'" 109.964 1.50 -F2T "C2'" "C3'" "H3'" 110.299 1.50 -F2T "C3'" "O3'" "HO3'" 108.182 1.86 -F2T "C3'" "C2'" "F2'" 110.051 1.88 -F2T "C3'" "C2'" "C1'" 103.185 1.56 -F2T "C3'" "C2'" "H2'" 110.826 1.50 -F2T "F2'" "C2'" "C1'" 109.343 1.50 -F2T "F2'" "C2'" "H2'" 111.335 1.50 -F2T "C1'" "C2'" "H2'" 111.301 1.50 -F2T "O4'" "C1'" "C2'" 105.973 1.50 -F2T "O4'" "C1'" N1 108.092 1.50 -F2T "O4'" "C1'" "H1'" 109.395 1.50 -F2T "C2'" "C1'" N1 113.961 1.50 -F2T "C2'" "C1'" "H1'" 109.391 1.50 -F2T N1 "C1'" "H1'" 108.901 1.50 -F2T "C1'" N1 C2 117.571 1.50 -F2T "C1'" N1 C6 121.009 1.50 -F2T C2 N1 C6 121.419 1.50 -F2T N1 C2 O2 122.841 1.50 -F2T N1 C2 N3 114.848 1.50 -F2T O2 C2 N3 122.311 1.50 -F2T C2 N3 C4 126.992 1.50 -F2T C2 N3 H3 115.772 1.79 -F2T C4 N3 H3 117.236 1.73 -F2T N3 C4 O4 119.401 1.50 -F2T N3 C4 C5 114.659 1.50 -F2T O4 C4 C5 125.940 1.50 -F2T C4 C5 C6 119.525 1.50 -F2T C4 C5 H5 120.151 1.50 -F2T C6 C5 H5 120.325 1.50 -F2T N1 C6 C5 122.557 1.50 -F2T N1 C6 H6 118.477 1.50 -F2T C5 C6 H6 118.966 1.50 +F2T SP1 P OP2 116.458 3.00 +F2T SP1 P "O5'" 114.928 3.00 +F2T SP1 P OP3 116.458 3.00 +F2T OP2 P "O5'" 106.327 3.00 +F2T OP2 P OP3 112.844 3.00 +F2T "O5'" P OP3 106.327 3.00 +F2T P "O5'" "C5'" 119.085 2.00 +F2T "O5'" "C5'" "C4'" 109.482 2.30 +F2T "O5'" "C5'" "H5'" 109.954 1.50 +F2T "O5'" "C5'" "H5''" 109.954 1.50 +F2T "C4'" "C5'" "H5'" 109.589 1.50 +F2T "C4'" "C5'" "H5''" 109.589 1.50 +F2T "H5'" "C5'" "H5''" 108.471 1.50 +F2T "C5'" "C4'" "O4'" 110.351 1.93 +F2T "C5'" "C4'" "C3'" 114.817 2.32 +F2T "C5'" "C4'" "H4'" 108.351 1.59 +F2T "O4'" "C4'" "C3'" 106.265 1.50 +F2T "O4'" "C4'" "H4'" 108.778 1.50 +F2T "C3'" "C4'" "H4'" 109.427 1.50 +F2T "C4'" "O4'" "C1'" 109.807 1.50 +F2T "C4'" "C3'" "O3'" 112.166 3.00 +F2T "C4'" "C3'" "C2'" 102.628 1.50 +F2T "C4'" "C3'" "H3'" 110.639 1.50 +F2T "O3'" "C3'" "C2'" 107.383 3.00 +F2T "O3'" "C3'" "H3'" 110.652 1.50 +F2T "C2'" "C3'" "H3'" 111.124 1.50 +F2T "C3'" "O3'" "HO3'" 108.613 2.59 +F2T "C3'" "C2'" "F2'" 109.728 3.00 +F2T "C3'" "C2'" "C1'" 101.995 1.50 +F2T "C3'" "C2'" "H2'" 111.579 2.10 +F2T "F2'" "C2'" "C1'" 108.424 1.50 +F2T "F2'" "C2'" "H2'" 111.510 1.50 +F2T "C1'" "C2'" "H2'" 111.813 1.50 +F2T "O4'" "C1'" "C2'" 106.016 1.50 +F2T "O4'" "C1'" N1 107.966 1.50 +F2T "O4'" "C1'" "H1'" 109.496 1.50 +F2T "C2'" "C1'" N1 115.046 2.16 +F2T "C2'" "C1'" "H1'" 109.140 1.50 +F2T N1 "C1'" "H1'" 109.169 1.50 +F2T "C1'" N1 C2 118.040 1.54 +F2T "C1'" N1 C6 120.480 1.50 +F2T C2 N1 C6 121.480 1.50 +F2T N1 C2 O2 122.982 1.50 +F2T N1 C2 N3 114.684 1.50 +F2T O2 C2 N3 122.337 1.50 +F2T C2 N3 C4 127.033 1.50 +F2T C2 N3 H3 115.708 3.00 +F2T C4 N3 H3 117.259 3.00 +F2T N3 C4 O4 119.595 1.50 +F2T N3 C4 C5 114.643 1.50 +F2T O4 C4 C5 125.762 1.50 +F2T C4 C5 C6 119.580 1.50 +F2T C4 C5 H5 120.071 1.50 +F2T C6 C5 H5 120.349 1.50 +F2T N1 C6 C5 122.580 1.50 +F2T N1 C6 H6 118.439 1.84 +F2T C5 C6 H6 118.980 1.53 loop_ _chem_comp_tor.comp_id @@ -172,27 +205,28 @@ _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period -F2T C2e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 -F2T C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 -F2T C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 -F2T C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 -F2T C3e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 -F2T C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 -F2T C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 -F2T C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 -F2T beta P "O5'" "C5'" "C4'" 180.000 10.00 3 -F2T epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 -F2T gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 -F2T sp3_sp3_27 OP2 P SP1 H11 -60.000 10.0 3 -F2T sp3_sp3_28 "C5'" "O5'" P SP1 180.000 10.0 3 -F2T const_sp2_sp2_4 O2 C2 N1 "C1'" 0.000 5.0 2 -F2T const_22 C5 C6 N1 "C1'" 180.000 10.0 2 -F2T const_sp2_sp2_7 O2 C2 N3 C4 180.000 5.0 2 -F2T const_11 O4 C4 N3 C2 180.000 10.0 2 -F2T const_15 O4 C4 C5 C6 180.000 10.0 2 -F2T const_17 C4 C5 C6 N1 0.000 10.0 2 -F2T sp3_sp3_20 "F2'" "C2'" "C3'" "O3'" -60.000 10.0 3 -F2T sp3_sp3_8 "O4'" "C1'" "C2'" "F2'" 180.000 10.0 3 +F2T sp3_sp3_25 "C5'" "O5'" P SP1 180.000 10.0 3 +F2T sp2_sp3_1 C2 N1 "C1'" "O4'" 150.000 10.0 6 +F2T const_sp2_sp2_1 N3 C2 N1 C6 0.000 0.0 1 +F2T const_sp2_sp2_4 O2 C2 N1 "C1'" 0.000 0.0 1 +F2T const_21 C5 C6 N1 C2 0.000 0.0 1 +F2T const_24 H6 C6 N1 "C1'" 0.000 0.0 1 +F2T const_sp2_sp2_5 N1 C2 N3 C4 0.000 0.0 1 +F2T const_sp2_sp2_8 O2 C2 N3 H3 0.000 0.0 1 +F2T const_sp2_sp2_9 C5 C4 N3 C2 0.000 0.0 1 +F2T const_12 O4 C4 N3 H3 0.000 0.0 1 +F2T const_13 N3 C4 C5 C6 0.000 0.0 1 +F2T const_16 O4 C4 C5 H5 0.000 0.0 1 +F2T const_17 C4 C5 C6 N1 0.000 0.0 1 +F2T const_20 H5 C5 C6 H6 0.000 0.0 1 +F2T sp3_sp3_28 "C4'" "C5'" "O5'" P 180.000 10.0 3 +F2T sp3_sp3_31 "O4'" "C4'" "C5'" "O5'" 180.000 10.0 3 +F2T sp3_sp3_2 "C5'" "C4'" "O4'" "C1'" -60.000 10.0 3 +F2T sp3_sp3_44 "O3'" "C3'" "C4'" "C5'" 180.000 10.0 3 +F2T sp3_sp3_4 "C2'" "C1'" "O4'" "C4'" -60.000 10.0 3 +F2T sp3_sp3_49 "C4'" "C3'" "O3'" "HO3'" 180.000 10.0 3 +F2T sp3_sp3_20 "F2'" "C2'" "C3'" "O3'" -60.000 10.0 3 +F2T sp3_sp3_8 "O4'" "C1'" "C2'" "F2'" 180.000 10.0 3 loop_ _chem_comp_chir.comp_id @@ -202,11 +236,11 @@ _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign -F2T chir_1 P SP1 "O5'" OP3 both +F2T chir_1 P SP1 "O5'" OP3 both F2T chir_2 "C4'" "O4'" "C3'" "C5'" negative F2T chir_3 "C3'" "O3'" "C2'" "C4'" negative F2T chir_4 "C2'" "F2'" "C1'" "C3'" negative -F2T chir_5 "C1'" "O4'" N1 "C2'" negative +F2T chir_5 "C1'" "O4'" N1 "C2'" negative loop_ _chem_comp_plane_atom.comp_id @@ -214,17 +248,17 @@ _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd F2T plan-1 "C1'" 0.020 -F2T plan-1 C2 0.020 -F2T plan-1 C4 0.020 -F2T plan-1 C5 0.020 -F2T plan-1 C6 0.020 -F2T plan-1 H3 0.020 -F2T plan-1 H5 0.020 -F2T plan-1 H6 0.020 -F2T plan-1 N1 0.020 -F2T plan-1 N3 0.020 -F2T plan-1 O2 0.020 -F2T plan-1 O4 0.020 +F2T plan-1 C2 0.020 +F2T plan-1 C4 0.020 +F2T plan-1 C5 0.020 +F2T plan-1 C6 0.020 +F2T plan-1 H3 0.020 +F2T plan-1 H5 0.020 +F2T plan-1 H6 0.020 +F2T plan-1 N1 0.020 +F2T plan-1 N3 0.020 +F2T plan-1 O2 0.020 +F2T plan-1 O4 0.020 loop_ _pdbx_chem_comp_descriptor.comp_id @@ -232,20 +266,28 @@ _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor -F2T SMILES ACDLabs 12.01 P(S)(=O)(OCC1OC(C(C1O)F)N2C(=O)NC(=O)C=C2)O -F2T InChI InChI 1.03 InChI=1S/C9H12FN2O7PS/c10-6-7(14)4(3-18-20(16,17)21)19-8(6)12-2-1-5(13)11-9(12)15/h1-2,4,6-8,14H,3H2,(H,11,13,15)(H2,16,17,21)/t4-,6-,7-,8-/m1/s1 -F2T InChIKey InChI 1.03 GAVMOIRMDKJPDM-XVFCMESISA-N -F2T SMILES_CANONICAL CACTVS 3.385 O[C@H]1[C@@H](F)[C@@H](O[C@@H]1CO[P](O)(S)=O)N2C=CC(=O)NC2=O -F2T SMILES CACTVS 3.385 O[CH]1[CH](F)[CH](O[CH]1CO[P](O)(S)=O)N2C=CC(=O)NC2=O +F2T SMILES ACDLabs 12.01 P(S)(=O)(OCC1OC(C(C1O)F)N2C(=O)NC(=O)C=C2)O +F2T InChI InChI 1.03 InChI=1S/C9H12FN2O7PS/c10-6-7(14)4(3-18-20(16,17)21)19-8(6)12-2-1-5(13)11-9(12)15/h1-2,4,6-8,14H,3H2,(H,11,13,15)(H2,16,17,21)/t4-,6-,7-,8-/m1/s1 +F2T InChIKey InChI 1.03 GAVMOIRMDKJPDM-XVFCMESISA-N +F2T SMILES_CANONICAL CACTVS 3.385 O[C@H]1[C@@H](F)[C@@H](O[C@@H]1CO[P](O)(S)=O)N2C=CC(=O)NC2=O +F2T SMILES CACTVS 3.385 O[CH]1[CH](F)[CH](O[CH]1CO[P](O)(S)=O)N2C=CC(=O)NC2=O F2T SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)S)O)F -F2T SMILES "OpenEye OEToolkits" 2.0.4 C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)S)O)F +F2T SMILES "OpenEye OEToolkits" 2.0.4 C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)S)O)F loop_ _pdbx_chem_comp_description_generator.comp_id _pdbx_chem_comp_description_generator.program_name _pdbx_chem_comp_description_generator.program_version _pdbx_chem_comp_description_generator.descriptor -F2T acedrg 243 "dictionary generator" -F2T acedrg_database 11 "data source" -F2T rdkit 2017.03.2 "Chemoinformatics tool" -F2T refmac5 5.8.0238 "optimization tool" +F2T acedrg 277 "dictionary generator" +F2T acedrg_database 12 "data source" +F2T rdkit 2019.09.1 "Chemoinformatics tool" +F2T refmac5 5.8.0425 "optimization tool" + +loop_ +_chem_comp_alias.comp_id +_chem_comp_alias.group +_chem_comp_alias.atom_id +_chem_comp_alias.atom_id_standard +F2T S-NA OP2 OP1 +F2T S-NA SP1 S2P diff --git a/g/G46.cif b/g/G46.cif index fd055272b..6d2287c70 100644 --- a/g/G46.cif +++ b/g/G46.cif @@ -7,7 +7,7 @@ _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level -G46 G46 "GUANOSINE-5'-MONOTHIOPHOSPHATE" NON-POLYMER 37 24 . +G46 G46 "GUANOSINE-5'-MONOTHIOPHOSPHATE" NON-POLYMER 36 24 . data_comp_G46 loop_ @@ -19,43 +19,83 @@ _chem_comp_atom.charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z -G46 P P P 0 10.148 -3.511 32.973 -G46 O1P O OP -1 8.817 -3.597 33.641 -G46 S2P S SH1 0 11.530 -4.739 33.946 -G46 O3P O O 0 10.709 -2.135 32.830 -G46 "O5'" O O2 0 10.004 -4.130 31.505 -G46 "C5'" C CH2 0 9.328 -5.403 31.340 -G46 "C4'" C CH1 0 9.497 -5.897 29.923 -G46 "O4'" O O2 0 9.032 -4.884 28.996 -G46 "C3'" C CH1 0 10.931 -6.195 29.473 -G46 "O3'" O OH1 0 11.323 -7.508 29.856 -G46 "C2'" C CH1 0 10.832 -6.029 27.952 -G46 "C1'" C CH1 0 9.794 -4.914 27.807 -G46 "O2'" O OH1 0 10.424 -7.206 27.286 -G46 N9 N NR5 0 10.376 -3.594 27.567 -G46 C8 C CR15 0 10.360 -2.495 28.394 -G46 N7 N NRD5 0 10.968 -1.451 27.886 -G46 C5 C CR56 0 11.413 -1.884 26.644 -G46 C6 C CR6 0 12.138 -1.191 25.638 -G46 O6 O O 0 12.539 -0.018 25.657 -G46 N1 N NR6 0 12.388 -2.004 24.526 -G46 C2 C CR6 0 11.990 -3.316 24.400 -G46 N2 N NH2 0 12.318 -3.943 23.261 -G46 N3 N NRD6 0 11.307 -3.971 25.345 -G46 C4 C CR56 0 11.052 -3.200 26.434 -G46 HS H HSH1 0 11.751 -5.717 33.266 -G46 "H5'1" H H 0 8.365 -5.298 31.540 -G46 "H5'2" H H 0 9.707 -6.066 31.968 -G46 "H4'" H H 0 8.949 -6.703 29.812 -G46 "H3'" H H 0 11.559 -5.528 29.850 -G46 HA H H 0 12.086 -7.674 29.523 -G46 "H2'" H H 0 11.708 -5.735 27.587 -G46 "H1'" H H 0 9.202 -5.138 27.053 -G46 HB H H 0 9.669 -7.459 27.583 -G46 H8 H H 0 9.954 -2.491 29.243 -G46 H1 H H 0 12.843 -1.634 23.846 -G46 H2N1 H H 0 12.612 -4.769 23.286 -G46 H2N2 H H 0 12.238 -3.525 22.494 +G46 P P P 0 10.382 -3.515 32.980 +G46 O1P O OP -1 9.426 -4.206 33.897 +G46 S2P S S1 0 12.225 -3.500 33.600 +G46 O3P O OP -1 9.873 -2.132 32.713 +G46 "O5'" O O2 0 10.197 -4.232 31.549 +G46 "C5'" C CH2 0 10.002 -5.659 31.488 +G46 "C4'" C CH1 0 10.204 -6.156 30.076 +G46 "O4'" O O2 0 9.370 -5.405 29.169 +G46 "C3'" C CH1 0 11.620 -6.002 29.515 +G46 "O3'" O OH1 0 12.438 -7.094 29.918 +G46 "C2'" C CH1 0 11.369 -5.976 28.003 +G46 "C1'" C CH1 0 10.028 -5.239 27.915 +G46 "O2'" O OH1 0 11.277 -7.262 27.422 +G46 N9 N NR5 0 10.163 -3.810 27.620 +G46 C8 C CR15 0 9.950 -2.726 28.435 +G46 N7 N NRD5 0 10.162 -1.573 27.849 +G46 C5 C CR56 0 10.543 -1.917 26.557 +G46 C6 C CR6 0 10.901 -1.090 25.458 +G46 O6 O O 0 10.951 0.149 25.419 +G46 N1 N NR16 0 11.222 -1.842 24.322 +G46 C2 C CR6 0 11.200 -3.221 24.251 +G46 N2 N NH2 0 11.539 -3.783 23.076 +G46 N3 N NRD6 0 10.863 -4.000 25.284 +G46 C4 C CR56 0 10.548 -3.288 26.397 +G46 "H5'1" H H 0 9.084 -5.884 31.787 +G46 "H5'2" H H 0 10.645 -6.112 32.091 +G46 "H4'" H H 0 9.942 -7.110 30.042 +G46 "H3'" H H 0 12.021 -5.146 29.811 +G46 HA H H 0 13.181 -7.044 29.531 +G46 "H2'" H H 0 12.076 -5.446 27.554 +G46 "H1'" H H 0 9.461 -5.673 27.191 +G46 HB H H 0 10.660 -7.706 27.776 +G46 H8 H H 0 9.675 -2.803 29.332 +G46 H1 H H 0 11.457 -1.382 23.592 +G46 H2N1 H H 0 11.765 -3.287 22.390 +G46 H2N2 H H 0 11.533 -4.658 22.995 + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +G46 P P(OC)(O)2(S) +G46 O1P O(POOS) +G46 S2P S(PO3) +G46 O3P O(POOS) +G46 "O5'" O(CC[5]HH)(POOS) +G46 "C5'" C(C[5]C[5]O[5]H)(OP)(H)2 +G46 "C4'" C[5](C[5]C[5]HO)(O[5]C[5])(CHHO)(H){1|N<3>,1|O<2>,2|H<1>} +G46 "O4'" O[5](C[5]N[5a]C[5]H)(C[5]C[5]CH){2|C<3>,2|H<1>,2|O<2>} +G46 "C3'" C[5](C[5]C[5]HO)(C[5]O[5]CH)(OH)(H){1|H<1>,1|N<3>} +G46 "O3'" O(C[5]C[5]2H)(H) +G46 "C2'" C[5](C[5]N[5a]O[5]H)(C[5]C[5]HO)(OH)(H){1|C<4>,1|H<1>,2|C<3>} +G46 "C1'" C[5](N[5a]C[5a,6a]C[5a])(C[5]C[5]HO)(O[5]C[5])(H){1|C<3>,1|C<4>,1|O<2>,2|N<2>,3|H<1>} +G46 "O2'" O(C[5]C[5]2H)(H) +G46 N9 N[5a](C[5a,6a]C[5a,6a]N[6a])(C[5]C[5]O[5]H)(C[5a]N[5a]H){1|H<1>,1|O<2>,2|C<3>,2|C<4>} +G46 C8 C[5a](N[5a]C[5a,6a]C[5])(N[5a]C[5a,6a])(H){1|C<3>,1|C<4>,1|H<1>,1|N<2>,1|O<2>} +G46 N7 N[5a](C[5a,6a]C[5a,6a]C[6a])(C[5a]N[5a]H){1|C<4>,1|N<2>,1|N<3>,1|O<1>} +G46 C5 C[5a,6a](C[5a,6a]N[5a]N[6a])(C[6a]N[6a]O)(N[5a]C[5a]){1|C<3>,1|C<4>,2|H<1>} +G46 C6 C[6a](C[5a,6a]C[5a,6a]N[5a])(N[6a]C[6a]H)(O){1|C<3>,1|N<2>,2|N<3>} +G46 O6 O(C[6a]C[5a,6a]N[6a]) +G46 N1 N[6a](C[6a]C[5a,6a]O)(C[6a]N[6a]N)(H){1|C<3>,1|N<2>} +G46 C2 C[6a](N[6a]C[5a,6a])(N[6a]C[6a]H)(NHH){1|C<3>,1|N<3>,1|O<1>} +G46 N2 N(C[6a]N[6a]2)(H)2 +G46 N3 N[6a](C[5a,6a]C[5a,6a]N[5a])(C[6a]N[6a]N){1|C<4>,1|H<1>,1|N<2>,2|C<3>} +G46 C4 C[5a,6a](C[5a,6a]C[6a]N[5a])(N[5a]C[5a]C[5])(N[6a]C[6a]){1|C<4>,1|O<1>,1|O<2>,2|H<1>,2|N<3>} +G46 "H5'1" H(CC[5]HO) +G46 "H5'2" H(CC[5]HO) +G46 "H4'" H(C[5]C[5]O[5]C) +G46 "H3'" H(C[5]C[5]2O) +G46 HA H(OC[5]) +G46 "H2'" H(C[5]C[5]2O) +G46 "H1'" H(C[5]N[5a]C[5]O[5]) +G46 HB H(OC[5]) +G46 H8 H(C[5a]N[5a]2) +G46 H1 H(N[6a]C[6a]2) +G46 H2N1 H(NC[6a]H) +G46 H2N2 H(NC[6a]H) loop_ _chem_comp_bond.comp_id @@ -67,45 +107,44 @@ _chem_comp_bond.value_dist_nucleus _chem_comp_bond.value_dist_nucleus_esd _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd -G46 P O1P SINGLE n 1.493 0.0157 1.493 0.0157 -G46 P S2P SINGLE n 2.091 0.0200 2.091 0.0200 -G46 P O3P DOUBLE n 1.493 0.0157 1.493 0.0157 -G46 P "O5'" SINGLE n 1.601 0.0114 1.601 0.0114 -G46 "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 -G46 "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 -G46 "C4'" "O4'" SINGLE n 1.451 0.0100 1.451 0.0100 -G46 "C4'" "C3'" SINGLE n 1.535 0.0100 1.535 0.0100 -G46 "O4'" "C1'" SINGLE n 1.409 0.0100 1.409 0.0100 -G46 "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 -G46 "C3'" "C2'" SINGLE n 1.531 0.0100 1.531 0.0100 -G46 "C2'" "C1'" SINGLE n 1.525 0.0100 1.525 0.0100 -G46 "C2'" "O2'" SINGLE n 1.411 0.0100 1.411 0.0100 -G46 "C1'" N9 SINGLE n 1.458 0.0100 1.458 0.0100 -G46 N9 C8 SINGLE y 1.372 0.0100 1.372 0.0100 -G46 N9 C4 SINGLE y 1.375 0.0100 1.375 0.0100 -G46 C8 N7 DOUBLE y 1.312 0.0100 1.312 0.0100 -G46 N7 C5 SINGLE y 1.390 0.0100 1.390 0.0100 -G46 C5 C6 SINGLE y 1.417 0.0103 1.417 0.0103 -G46 C5 C4 DOUBLE y 1.377 0.0100 1.377 0.0100 -G46 C6 O6 DOUBLE n 1.239 0.0100 1.239 0.0100 -G46 C6 N1 SINGLE y 1.396 0.0107 1.396 0.0107 -G46 N1 C2 SINGLE y 1.374 0.0100 1.374 0.0100 -G46 C2 N2 SINGLE n 1.340 0.0101 1.340 0.0101 -G46 C2 N3 DOUBLE y 1.333 0.0104 1.333 0.0104 -G46 N3 C4 SINGLE y 1.355 0.0100 1.355 0.0100 -G46 S2P HS SINGLE n 1.338 0.0100 1.211 0.0200 -G46 "C5'" "H5'1" SINGLE n 1.089 0.0100 0.989 0.0200 -G46 "C5'" "H5'2" SINGLE n 1.089 0.0100 0.989 0.0200 -G46 "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200 -G46 "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200 -G46 "O3'" HA SINGLE n 0.970 0.0120 0.849 0.0200 -G46 "C2'" "H2'" SINGLE n 1.089 0.0100 0.994 0.0200 -G46 "C1'" "H1'" SINGLE n 1.089 0.0100 0.984 0.0200 -G46 "O2'" HB SINGLE n 0.970 0.0120 0.849 0.0200 -G46 C8 H8 SINGLE n 1.082 0.0130 0.942 0.0170 -G46 N1 H1 SINGLE n 1.016 0.0100 0.897 0.0200 -G46 N2 H2N1 SINGLE n 1.016 0.0100 0.877 0.0200 -G46 N2 H2N2 SINGLE n 1.016 0.0100 0.877 0.0200 +G46 P O1P SINGLE n 1.497 0.0143 1.497 0.0143 +G46 P S2P DOUBLE n 1.949 0.0200 1.949 0.0200 +G46 P O3P SINGLE n 1.497 0.0143 1.497 0.0143 +G46 P "O5'" SINGLE n 1.613 0.0200 1.613 0.0200 +G46 "O5'" "C5'" SINGLE n 1.438 0.0200 1.438 0.0200 +G46 "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 +G46 "C4'" "O4'" SINGLE n 1.444 0.0100 1.444 0.0100 +G46 "C4'" "C3'" SINGLE n 1.532 0.0100 1.532 0.0100 +G46 "O4'" "C1'" SINGLE n 1.423 0.0100 1.423 0.0100 +G46 "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +G46 "C3'" "C2'" SINGLE n 1.532 0.0103 1.532 0.0103 +G46 "C2'" "C1'" SINGLE n 1.528 0.0100 1.528 0.0100 +G46 "C2'" "O2'" SINGLE n 1.412 0.0100 1.412 0.0100 +G46 "C1'" N9 SINGLE n 1.462 0.0102 1.462 0.0102 +G46 N9 C8 SINGLE y 1.371 0.0100 1.371 0.0100 +G46 N9 C4 SINGLE y 1.383 0.0114 1.383 0.0114 +G46 C8 N7 DOUBLE y 1.311 0.0104 1.311 0.0104 +G46 N7 C5 SINGLE y 1.390 0.0100 1.390 0.0100 +G46 C5 C6 SINGLE y 1.418 0.0111 1.418 0.0111 +G46 C5 C4 DOUBLE y 1.377 0.0100 1.377 0.0100 +G46 C6 O6 DOUBLE n 1.240 0.0104 1.240 0.0104 +G46 C6 N1 SINGLE y 1.394 0.0120 1.394 0.0120 +G46 N1 C2 SINGLE y 1.374 0.0124 1.374 0.0124 +G46 C2 N2 SINGLE n 1.341 0.0143 1.341 0.0143 +G46 C2 N3 DOUBLE y 1.331 0.0119 1.331 0.0119 +G46 N3 C4 SINGLE y 1.355 0.0100 1.355 0.0100 +G46 "C5'" "H5'1" SINGLE n 1.092 0.0100 0.991 0.0200 +G46 "C5'" "H5'2" SINGLE n 1.092 0.0100 0.991 0.0200 +G46 "C4'" "H4'" SINGLE n 1.092 0.0100 0.990 0.0200 +G46 "C3'" "H3'" SINGLE n 1.092 0.0100 0.991 0.0200 +G46 "O3'" HA SINGLE n 0.972 0.0180 0.839 0.0200 +G46 "C2'" "H2'" SINGLE n 1.092 0.0100 0.991 0.0200 +G46 "C1'" "H1'" SINGLE n 1.092 0.0100 1.016 0.0200 +G46 "O2'" HB SINGLE n 0.972 0.0180 0.839 0.0200 +G46 C8 H8 SINGLE n 1.085 0.0150 0.942 0.0168 +G46 N1 H1 SINGLE n 1.013 0.0120 0.894 0.0200 +G46 N2 H2N1 SINGLE n 1.013 0.0120 0.877 0.0200 +G46 N2 H2N2 SINGLE n 1.013 0.0120 0.877 0.0200 loop_ _chem_comp_angle.comp_id @@ -114,73 +153,72 @@ _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd -G46 O1P P S2P 111.281 3.00 -G46 O1P P O3P 116.964 2.85 -G46 O1P P "O5'" 108.530 2.45 -G46 S2P P O3P 111.281 3.00 -G46 S2P P "O5'" 105.685 3.00 -G46 O3P P "O5'" 108.530 2.45 -G46 P S2P HS 109.471 3.00 -G46 P "O5'" "C5'" 119.135 1.78 -G46 "O5'" "C5'" "C4'" 109.510 1.50 -G46 "O5'" "C5'" "H5'1" 109.821 1.50 -G46 "O5'" "C5'" "H5'2" 109.821 1.50 -G46 "C4'" "C5'" "H5'1" 109.624 1.50 -G46 "C4'" "C5'" "H5'2" 109.624 1.50 -G46 "H5'1" "C5'" "H5'2" 108.472 1.50 -G46 "C5'" "C4'" "O4'" 109.123 1.50 -G46 "C5'" "C4'" "C3'" 116.008 1.52 -G46 "C5'" "C4'" "H4'" 108.268 1.50 -G46 "O4'" "C4'" "C3'" 105.388 1.50 -G46 "O4'" "C4'" "H4'" 108.947 1.50 -G46 "C3'" "C4'" "H4'" 109.363 1.86 -G46 "C4'" "O4'" "C1'" 109.903 1.50 -G46 "C4'" "C3'" "O3'" 111.281 2.46 -G46 "C4'" "C3'" "C2'" 102.602 1.50 -G46 "C4'" "C3'" "H3'" 110.452 2.54 -G46 "O3'" "C3'" "C2'" 111.581 2.83 -G46 "O3'" "C3'" "H3'" 110.380 1.67 -G46 "C2'" "C3'" "H3'" 110.504 1.75 -G46 "C3'" "O3'" HA 108.744 3.00 -G46 "C3'" "C2'" "C1'" 101.239 1.50 -G46 "C3'" "C2'" "O2'" 112.782 2.45 -G46 "C3'" "C2'" "H2'" 110.596 1.51 -G46 "C1'" "C2'" "O2'" 111.715 2.69 -G46 "C1'" "C2'" "H2'" 110.636 1.70 -G46 "O2'" "C2'" "H2'" 110.448 1.97 -G46 "O4'" "C1'" "C2'" 106.047 1.50 -G46 "O4'" "C1'" N9 108.477 1.50 -G46 "O4'" "C1'" "H1'" 109.807 1.50 -G46 "C2'" "C1'" N9 113.824 1.50 -G46 "C2'" "C1'" "H1'" 109.015 1.50 -G46 N9 "C1'" "H1'" 109.561 1.50 -G46 "C2'" "O2'" HB 109.103 2.13 -G46 "C1'" N9 C8 126.829 1.91 -G46 "C1'" N9 C4 127.440 1.80 -G46 C8 N9 C4 105.731 1.50 -G46 N9 C8 N7 113.507 1.50 -G46 N9 C8 H8 123.187 1.50 -G46 N7 C8 H8 123.307 1.50 -G46 C8 N7 C5 104.778 1.50 -G46 N7 C5 C6 130.030 1.50 -G46 N7 C5 C4 110.574 1.50 -G46 C6 C5 C4 119.397 1.50 -G46 C5 C6 O6 128.244 1.50 -G46 C5 C6 N1 111.367 1.50 -G46 O6 C6 N1 120.389 1.50 -G46 C6 N1 C2 125.351 1.50 -G46 C6 N1 H1 116.978 2.44 -G46 C2 N1 H1 117.677 2.71 -G46 N1 C2 N2 116.576 1.50 -G46 N1 C2 N3 123.602 1.50 -G46 N2 C2 N3 119.821 1.50 -G46 C2 N2 H2N1 119.868 1.50 -G46 C2 N2 H2N2 119.868 1.50 -G46 H2N1 N2 H2N2 120.263 1.96 -G46 C2 N3 C4 112.066 1.50 -G46 N9 C4 C5 105.411 1.50 -G46 N9 C4 N3 126.378 1.50 -G46 C5 C4 N3 128.211 1.50 +G46 O1P P S2P 116.458 3.00 +G46 O1P P O3P 112.844 3.00 +G46 O1P P "O5'" 106.327 3.00 +G46 S2P P O3P 116.458 3.00 +G46 S2P P "O5'" 114.928 3.00 +G46 O3P P "O5'" 106.327 3.00 +G46 P "O5'" "C5'" 119.085 2.00 +G46 "O5'" "C5'" "C4'" 109.482 2.30 +G46 "O5'" "C5'" "H5'1" 109.954 1.50 +G46 "O5'" "C5'" "H5'2" 109.954 1.50 +G46 "C4'" "C5'" "H5'1" 109.589 1.50 +G46 "C4'" "C5'" "H5'2" 109.589 1.50 +G46 "H5'1" "C5'" "H5'2" 108.471 1.50 +G46 "C5'" "C4'" "O4'" 109.154 1.50 +G46 "C5'" "C4'" "C3'" 115.288 1.50 +G46 "C5'" "C4'" "H4'" 108.351 1.59 +G46 "O4'" "C4'" "C3'" 105.318 1.50 +G46 "O4'" "C4'" "H4'" 109.120 1.50 +G46 "C3'" "C4'" "H4'" 109.322 2.54 +G46 "C4'" "O4'" "C1'" 109.502 2.85 +G46 "C4'" "C3'" "O3'" 110.713 3.00 +G46 "C4'" "C3'" "C2'" 102.593 1.50 +G46 "C4'" "C3'" "H3'" 110.577 3.00 +G46 "O3'" "C3'" "C2'" 111.671 3.00 +G46 "O3'" "C3'" "H3'" 110.541 2.08 +G46 "C2'" "C3'" "H3'" 110.454 1.85 +G46 "C3'" "O3'" HA 109.389 3.00 +G46 "C3'" "C2'" "C1'" 101.406 1.50 +G46 "C3'" "C2'" "O2'" 112.677 3.00 +G46 "C3'" "C2'" "H2'" 110.788 1.91 +G46 "C1'" "C2'" "O2'" 110.814 3.00 +G46 "C1'" "C2'" "H2'" 110.342 1.91 +G46 "O2'" "C2'" "H2'" 110.904 1.50 +G46 "O4'" "C1'" "C2'" 106.114 1.65 +G46 "O4'" "C1'" N9 108.577 1.50 +G46 "O4'" "C1'" "H1'" 109.833 2.53 +G46 "C2'" "C1'" N9 113.380 2.77 +G46 "C2'" "C1'" "H1'" 109.222 1.50 +G46 N9 "C1'" "H1'" 109.411 1.50 +G46 "C2'" "O2'" HB 109.217 3.00 +G46 "C1'" N9 C8 127.058 3.00 +G46 "C1'" N9 C4 126.955 2.94 +G46 C8 N9 C4 105.987 1.50 +G46 N9 C8 N7 113.721 1.50 +G46 N9 C8 H8 122.935 1.50 +G46 N7 C8 H8 123.345 1.50 +G46 C8 N7 C5 103.926 1.50 +G46 N7 C5 C6 129.926 1.50 +G46 N7 C5 C4 110.770 1.50 +G46 C6 C5 C4 119.304 1.50 +G46 C5 C6 O6 128.237 1.50 +G46 C5 C6 N1 111.514 1.50 +G46 O6 C6 N1 120.248 1.50 +G46 C6 N1 C2 125.452 1.50 +G46 C6 N1 H1 117.160 2.45 +G46 C2 N1 H1 117.387 2.97 +G46 N1 C2 N2 116.657 1.50 +G46 N1 C2 N3 123.538 1.50 +G46 N2 C2 N3 119.805 1.50 +G46 C2 N2 H2N1 119.712 3.00 +G46 C2 N2 H2N2 119.712 3.00 +G46 H2N1 N2 H2N2 120.576 3.00 +G46 C2 N3 C4 111.926 1.50 +G46 N9 C4 C5 105.596 1.50 +G46 N9 C4 N3 126.138 1.50 +G46 C5 C4 N3 128.265 1.50 loop_ _chem_comp_tor.comp_id @@ -192,35 +230,35 @@ _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period -G46 C2e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 -G46 C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 -G46 C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 -G46 C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 -G46 C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 -G46 C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 -G46 C3e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 -G46 C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 -G46 C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 -G46 C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 -G46 C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 -G46 C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 -G46 beta P "O5'" "C5'" "C4'" 180.000 10.00 3 -G46 gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 -G46 sp3_sp3_25 O1P P S2P HS 180.000 10.0 3 -G46 sp3_sp3_29 "C5'" "O5'" P O1P -60.000 10.0 3 -G46 sp3_sp3_55 "C3'" "C2'" "O2'" HB 180.000 10.0 3 -G46 const_18 N7 C8 N9 "C1'" 180.000 10.0 2 -G46 const_30 C5 C4 N9 "C1'" 180.000 10.0 2 -G46 const_21 N9 C8 N7 C5 0.000 10.0 2 -G46 const_24 C6 C5 N7 C8 180.000 10.0 2 -G46 const_sp2_sp2_4 N7 C5 C6 O6 0.000 5.0 2 -G46 const_25 N9 C4 C5 N7 0.000 10.0 2 -G46 const_sp2_sp2_7 O6 C6 N1 C2 180.000 5.0 2 -G46 const_11 N2 C2 N1 C6 180.000 10.0 2 -G46 sp2_sp2_1 N1 C2 N2 H2N1 180.000 5.0 2 -G46 const_14 N2 C2 N3 C4 180.000 10.0 2 -G46 const_16 N9 C4 N3 C2 180.000 10.0 2 -G46 sp3_sp3_52 "C4'" "C3'" "O3'" HA 180.000 10.0 3 +G46 sp3_sp3_26 "C5'" "O5'" P O1P -60.000 10.0 3 +G46 sp3_sp3_8 "O4'" "C1'" "C2'" "O2'" 180.000 10.0 3 +G46 sp3_sp3_52 "C3'" "C2'" "O2'" HB 180.000 10.0 3 +G46 sp2_sp3_1 C8 N9 "C1'" "O4'" 150.000 10.0 6 +G46 const_17 N7 C8 N9 C4 0.000 0.0 1 +G46 const_20 H8 C8 N9 "C1'" 0.000 0.0 1 +G46 const_29 C5 C4 N9 C8 0.000 0.0 1 +G46 const_32 N3 C4 N9 "C1'" 0.000 0.0 1 +G46 const_21 N9 C8 N7 C5 0.000 0.0 1 +G46 const_23 C4 C5 N7 C8 0.000 0.0 1 +G46 const_sp2_sp2_1 C4 C5 C6 N1 0.000 0.0 1 +G46 const_sp2_sp2_4 N7 C5 C6 O6 0.000 0.0 1 +G46 const_25 N9 C4 C5 N7 0.000 0.0 1 +G46 const_28 N3 C4 C5 C6 0.000 0.0 1 +G46 const_sp2_sp2_5 C5 C6 N1 C2 0.000 0.0 1 +G46 const_sp2_sp2_8 O6 C6 N1 H1 0.000 0.0 1 +G46 const_sp2_sp2_9 N3 C2 N1 C6 0.000 0.0 1 +G46 const_12 N2 C2 N1 H1 0.000 0.0 1 +G46 sp2_sp2_33 N1 C2 N2 H2N1 180.000 20 2 +G46 sp2_sp2_36 N3 C2 N2 H2N2 180.000 20 2 +G46 const_13 N1 C2 N3 C4 0.000 0.0 1 +G46 const_15 C5 C4 N3 C2 0.000 0.0 1 +G46 sp3_sp3_28 "C4'" "C5'" "O5'" P 180.000 10.0 3 +G46 sp3_sp3_31 "O4'" "C4'" "C5'" "O5'" 180.000 10.0 3 +G46 sp3_sp3_2 "C5'" "C4'" "O4'" "C1'" -60.000 10.0 3 +G46 sp3_sp3_44 "O3'" "C3'" "C4'" "C5'" 180.000 10.0 3 +G46 sp3_sp3_4 "C2'" "C1'" "O4'" "C4'" -60.000 10.0 3 +G46 sp3_sp3_20 "O2'" "C2'" "C3'" "O3'" -60.000 10.0 3 +G46 sp3_sp3_49 "C4'" "C3'" "O3'" HA 180.000 10.0 3 loop_ _chem_comp_chir.comp_id @@ -230,11 +268,11 @@ _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign -G46 chir_1 P S2P "O5'" O1P both +G46 chir_1 P S2P "O5'" O1P both G46 chir_2 "C4'" "O4'" "C3'" "C5'" negative G46 chir_3 "C3'" "O3'" "C4'" "C2'" positive G46 chir_4 "C2'" "O2'" "C1'" "C3'" negative -G46 chir_5 "C1'" "O4'" N9 "C2'" negative +G46 chir_5 "C1'" "O4'" N9 "C2'" negative loop_ _chem_comp_plane_atom.comp_id @@ -242,23 +280,29 @@ _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd G46 plan-1 "C1'" 0.020 -G46 plan-1 C2 0.020 -G46 plan-1 C4 0.020 -G46 plan-1 C5 0.020 -G46 plan-1 C6 0.020 -G46 plan-1 C8 0.020 -G46 plan-1 H1 0.020 -G46 plan-1 H8 0.020 -G46 plan-1 N1 0.020 -G46 plan-1 N2 0.020 -G46 plan-1 N3 0.020 -G46 plan-1 N7 0.020 -G46 plan-1 N9 0.020 -G46 plan-1 O6 0.020 -G46 plan-2 C2 0.020 -G46 plan-2 H2N1 0.020 -G46 plan-2 H2N2 0.020 -G46 plan-2 N2 0.020 +G46 plan-1 C4 0.020 +G46 plan-1 C5 0.020 +G46 plan-1 C6 0.020 +G46 plan-1 C8 0.020 +G46 plan-1 H8 0.020 +G46 plan-1 N3 0.020 +G46 plan-1 N7 0.020 +G46 plan-1 N9 0.020 +G46 plan-2 C2 0.020 +G46 plan-2 C4 0.020 +G46 plan-2 C5 0.020 +G46 plan-2 C6 0.020 +G46 plan-2 H1 0.020 +G46 plan-2 N1 0.020 +G46 plan-2 N2 0.020 +G46 plan-2 N3 0.020 +G46 plan-2 N7 0.020 +G46 plan-2 N9 0.020 +G46 plan-2 O6 0.020 +G46 plan-3 C2 0.020 +G46 plan-3 H2N1 0.020 +G46 plan-3 H2N2 0.020 +G46 plan-3 N2 0.020 loop_ _pdbx_chem_comp_descriptor.comp_id @@ -266,20 +310,29 @@ _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor -G46 SMILES ACDLabs 12.01 O=P(O)(S)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O -G46 InChI InChI 1.03 InChI=1S/C10H14N5O7PS/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(22-9)1-21-23(19,20)24/h2-3,5-6,9,16-17H,1H2,(H2,19,20,24)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1 -G46 InChIKey InChI 1.03 DIDGPCDGNMIUNX-UUOKFMHZSA-N -G46 SMILES_CANONICAL CACTVS 3.385 NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(S)=O)[C@@H](O)[C@H]3O -G46 SMILES CACTVS 3.385 NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(S)=O)[CH](O)[CH]3O +G46 SMILES ACDLabs 12.01 O=P(O)(S)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O +G46 InChI InChI 1.03 InChI=1S/C10H14N5O7PS/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(22-9)1-21-23(19,20)24/h2-3,5-6,9,16-17H,1H2,(H2,19,20,24)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1 +G46 InChIKey InChI 1.03 DIDGPCDGNMIUNX-UUOKFMHZSA-N +G46 SMILES_CANONICAL CACTVS 3.385 NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(S)=O)[C@@H](O)[C@H]3O +G46 SMILES CACTVS 3.385 NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(S)=O)[CH](O)[CH]3O G46 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)S)O)O)N=C(NC2=O)N -G46 SMILES "OpenEye OEToolkits" 1.7.6 c1nc2c(n1C3C(C(C(O3)COP(=O)(O)S)O)O)N=C(NC2=O)N +G46 SMILES "OpenEye OEToolkits" 1.7.6 c1nc2c(n1C3C(C(C(O3)COP(=O)(O)S)O)O)N=C(NC2=O)N loop_ _pdbx_chem_comp_description_generator.comp_id _pdbx_chem_comp_description_generator.program_name _pdbx_chem_comp_description_generator.program_version _pdbx_chem_comp_description_generator.descriptor -G46 acedrg 243 "dictionary generator" -G46 acedrg_database 11 "data source" -G46 rdkit 2017.03.2 "Chemoinformatics tool" -G46 refmac5 5.8.0238 "optimization tool" +G46 acedrg 277 "dictionary generator" +G46 acedrg_database 12 "data source" +G46 rdkit 2019.09.1 "Chemoinformatics tool" +G46 refmac5 5.8.0425 "optimization tool" + +loop_ +_chem_comp_alias.comp_id +_chem_comp_alias.group +_chem_comp_alias.atom_id +_chem_comp_alias.atom_id_standard +G46 S-NA O3P OP3 +G46 S-NA O1P OP1 +G46 S-NA HA HO3' diff --git a/g/GS.cif b/g/GS.cif index 8aec142db..e4b8cb185 100644 --- a/g/GS.cif +++ b/g/GS.cif @@ -7,7 +7,7 @@ _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level -GS GS "GUANOSINE-5'-THIO-MONOPHOSPHATE" NON-POLYMER 36 23 . +GS GS "GUANOSINE-5'-THIO-MONOPHOSPHATE" S-NA 35 23 . data_comp_GS loop_ @@ -19,42 +19,81 @@ _chem_comp_atom.charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z -GS P P P 0 -8.010 3.936 -5.266 -GS OP1 O O 0 -9.195 3.222 -5.826 -GS S2P S SH1 0 -7.678 3.311 -3.300 -GS OP3 O OP -1 -8.064 5.427 -5.337 -GS "O5'" O O2 0 -6.720 3.448 -6.078 -GS "C5'" C CH2 0 -6.709 3.561 -7.525 -GS "C4'" C CH1 0 -5.410 3.020 -8.074 -GS "O4'" O O2 0 -4.301 3.679 -7.431 -GS "C3'" C CH1 0 -5.170 1.534 -7.844 -GS "O3'" O OH1 0 -5.797 0.762 -8.864 -GS "C2'" C CH2 0 -3.649 1.445 -7.932 -GS "C1'" C CH1 0 -3.179 2.798 -7.408 -GS N9 N NR5 0 -2.660 2.761 -6.040 -GS C8 C CR15 0 -3.363 2.419 -4.911 -GS N7 N NRD5 0 -2.646 2.472 -3.815 -GS C5 C CR56 0 -1.389 2.874 -4.248 -GS C6 C CR6 0 -0.198 3.105 -3.509 -GS O6 O O 0 -0.025 2.992 -2.287 -GS N1 N NR6 0 0.858 3.504 -4.337 -GS C2 C CR6 0 0.776 3.661 -5.703 -GS N2 N NH2 0 1.892 4.051 -6.336 -GS N3 N NRD6 0 -0.343 3.445 -6.401 -GS C4 C CR56 0 -1.383 3.056 -5.617 -GS HSP2 H HSH1 0 -6.571 2.826 -3.212 -GS "H5'" H H 0 -6.809 4.510 -7.786 -GS "H5''" H H 0 -7.466 3.052 -7.906 -GS "H4'" H H 0 -5.379 3.208 -9.042 -GS "H3'" H H 0 -5.487 1.257 -6.951 -GS "HO3'" H H 0 -5.608 -0.057 -8.746 -GS "H2'" H H 0 -3.359 1.307 -8.855 -GS "H2''" H H 0 -3.308 0.715 -7.379 -GS "H1'" H H 0 -2.480 3.155 -8.016 -GS H8 H H 0 -4.272 2.171 -4.924 -GS HN1 H H 0 1.647 3.669 -3.940 -GS HN21 H H 0 1.845 4.653 -6.972 -GS HN22 H H 0 2.665 3.703 -6.112 +GS P P P 0 -7.877 4.041 -5.112 +GS OP1 O OP -1 -9.127 3.566 -5.786 +GS S2P S S1 0 -7.818 3.480 -3.251 +GS OP3 O OP -1 -7.759 5.521 -5.314 +GS "O5'" O O2 0 -6.706 3.391 -6.005 +GS "C5'" C CH2 0 -6.717 3.564 -7.436 +GS "C4'" C CH1 0 -5.432 3.044 -8.031 +GS "O4'" O O2 0 -4.308 3.682 -7.390 +GS "C3'" C CH1 0 -5.189 1.546 -7.855 +GS "O3'" O OH1 0 -5.799 0.811 -8.913 +GS "C2'" C CH2 0 -3.667 1.456 -7.931 +GS "C1'" C CH1 0 -3.195 2.795 -7.380 +GS N9 N NR5 0 -2.673 2.733 -6.018 +GS C8 C CR15 0 -3.387 2.403 -4.893 +GS N7 N NRD5 0 -2.676 2.422 -3.792 +GS C5 C CR56 0 -1.406 2.788 -4.221 +GS C6 C CR6 0 -0.209 2.973 -3.476 +GS O6 O O 0 -0.042 2.843 -2.254 +GS N1 N NR16 0 0.863 3.345 -4.295 +GS C2 C CR6 0 0.793 3.518 -5.664 +GS N2 N NH2 0 1.924 3.879 -6.298 +GS N3 N NRD6 0 -0.331 3.345 -6.366 +GS C4 C CR56 0 -1.385 2.983 -5.587 +GS "H5'" H H 0 -6.818 4.525 -7.657 +GS "H5''" H H 0 -7.482 3.072 -7.829 +GS "H4'" H H 0 -5.424 3.263 -8.997 +GS "H3'" H H 0 -5.518 1.233 -6.975 +GS "HO3'" H H 0 -5.647 -0.005 -8.796 +GS "H2'" H H 0 -3.373 1.333 -8.847 +GS "H2''" H H 0 -3.336 0.720 -7.393 +GS "H1'" H H 0 -2.491 3.157 -7.980 +GS H8 H H 0 -4.304 2.186 -4.914 +GS HN1 H H 0 1.649 3.478 -3.889 +GS HN21 H H 0 2.671 3.997 -5.853 +GS HN22 H H 0 1.916 3.997 -7.168 + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +GS P P(OC)(O)2(S) +GS OP1 O(POOS) +GS S2P S(PO3) +GS OP3 O(POOS) +GS "O5'" O(CC[5]HH)(POOS) +GS "C5'" C(C[5]C[5]O[5]H)(OP)(H)2 +GS "C4'" C[5](C[5]C[5]HO)(O[5]C[5])(CHHO)(H){1|N<3>,3|H<1>} +GS "O4'" O[5](C[5]N[5a]C[5]H)(C[5]C[5]CH){1|O<2>,2|C<3>,3|H<1>} +GS "C3'" C[5](C[5]C[5]HH)(C[5]O[5]CH)(OH)(H){1|H<1>,1|N<3>} +GS "O3'" O(C[5]C[5]2H)(H) +GS "C2'" C[5](C[5]N[5a]O[5]H)(C[5]C[5]HO)(H)2{1|C<4>,1|H<1>,2|C<3>} +GS "C1'" C[5](N[5a]C[5a,6a]C[5a])(C[5]C[5]HH)(O[5]C[5])(H){1|C<3>,1|C<4>,1|O<2>,2|N<2>,3|H<1>} +GS N9 N[5a](C[5a,6a]C[5a,6a]N[6a])(C[5]C[5]O[5]H)(C[5a]N[5a]H){2|C<3>,2|C<4>,2|H<1>} +GS C8 C[5a](N[5a]C[5a,6a]C[5])(N[5a]C[5a,6a])(H){1|C<3>,1|C<4>,1|H<1>,1|N<2>,1|O<2>} +GS N7 N[5a](C[5a,6a]C[5a,6a]C[6a])(C[5a]N[5a]H){1|C<4>,1|N<2>,1|N<3>,1|O<1>} +GS C5 C[5a,6a](C[5a,6a]N[5a]N[6a])(C[6a]N[6a]O)(N[5a]C[5a]){1|C<3>,1|C<4>,2|H<1>} +GS C6 C[6a](C[5a,6a]C[5a,6a]N[5a])(N[6a]C[6a]H)(O){1|C<3>,1|N<2>,2|N<3>} +GS O6 O(C[6a]C[5a,6a]N[6a]) +GS N1 N[6a](C[6a]C[5a,6a]O)(C[6a]N[6a]N)(H){1|C<3>,1|N<2>} +GS C2 C[6a](N[6a]C[5a,6a])(N[6a]C[6a]H)(NHH){1|C<3>,1|N<3>,1|O<1>} +GS N2 N(C[6a]N[6a]2)(H)2 +GS N3 N[6a](C[5a,6a]C[5a,6a]N[5a])(C[6a]N[6a]N){1|C<4>,1|H<1>,1|N<2>,2|C<3>} +GS C4 C[5a,6a](C[5a,6a]C[6a]N[5a])(N[5a]C[5a]C[5])(N[6a]C[6a]){1|C<4>,1|O<1>,1|O<2>,2|H<1>,2|N<3>} +GS "H5'" H(CC[5]HO) +GS "H5''" H(CC[5]HO) +GS "H4'" H(C[5]C[5]O[5]C) +GS "H3'" H(C[5]C[5]2O) +GS "HO3'" H(OC[5]) +GS "H2'" H(C[5]C[5]2H) +GS "H2''" H(C[5]C[5]2H) +GS "H1'" H(C[5]N[5a]C[5]O[5]) +GS H8 H(C[5a]N[5a]2) +GS HN1 H(N[6a]C[6a]2) +GS HN21 H(NC[6a]H) +GS HN22 H(NC[6a]H) loop_ _chem_comp_bond.comp_id @@ -66,44 +105,43 @@ _chem_comp_bond.value_dist_nucleus _chem_comp_bond.value_dist_nucleus_esd _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd -GS P OP1 DOUBLE n 1.493 0.0157 1.493 0.0157 -GS P S2P SINGLE n 2.091 0.0200 2.091 0.0200 -GS P OP3 SINGLE n 1.493 0.0157 1.493 0.0157 -GS P "O5'" SINGLE n 1.601 0.0114 1.601 0.0114 -GS "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 -GS "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 -GS "C4'" "O4'" SINGLE n 1.442 0.0100 1.442 0.0100 -GS "C4'" "C3'" SINGLE n 1.526 0.0115 1.526 0.0115 -GS "O4'" "C1'" SINGLE n 1.425 0.0100 1.425 0.0100 -GS "C3'" "O3'" SINGLE n 1.424 0.0100 1.424 0.0100 -GS "C3'" "C2'" SINGLE n 1.526 0.0101 1.526 0.0101 -GS "C2'" "C1'" SINGLE n 1.521 0.0118 1.521 0.0118 -GS "C1'" N9 SINGLE n 1.462 0.0111 1.462 0.0111 -GS N9 C8 SINGLE y 1.373 0.0100 1.373 0.0100 -GS N9 C4 SINGLE y 1.375 0.0100 1.375 0.0100 -GS C8 N7 DOUBLE y 1.312 0.0100 1.312 0.0100 -GS N7 C5 SINGLE y 1.390 0.0100 1.390 0.0100 -GS C5 C6 SINGLE y 1.417 0.0103 1.417 0.0103 -GS C5 C4 DOUBLE y 1.377 0.0100 1.377 0.0100 -GS C6 O6 DOUBLE n 1.239 0.0100 1.239 0.0100 -GS C6 N1 SINGLE y 1.396 0.0107 1.396 0.0107 -GS N1 C2 SINGLE y 1.374 0.0100 1.374 0.0100 -GS C2 N2 SINGLE n 1.340 0.0101 1.340 0.0101 -GS C2 N3 DOUBLE y 1.333 0.0104 1.333 0.0104 -GS N3 C4 SINGLE y 1.355 0.0100 1.355 0.0100 -GS S2P HSP2 SINGLE n 1.338 0.0100 1.211 0.0200 -GS "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 -GS "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200 -GS "C4'" "H4'" SINGLE n 1.089 0.0100 0.987 0.0170 -GS "C3'" "H3'" SINGLE n 1.089 0.0100 0.988 0.0189 -GS "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 -GS "C2'" "H2'" SINGLE n 1.089 0.0100 0.977 0.0113 -GS "C2'" "H2''" SINGLE n 1.089 0.0100 0.977 0.0113 -GS "C1'" "H1'" SINGLE n 1.089 0.0100 0.993 0.0101 -GS C8 H8 SINGLE n 1.082 0.0130 0.942 0.0170 -GS N1 HN1 SINGLE n 1.016 0.0100 0.897 0.0200 -GS N2 HN21 SINGLE n 1.016 0.0100 0.877 0.0200 -GS N2 HN22 SINGLE n 1.016 0.0100 0.877 0.0200 +GS P OP1 SINGLE n 1.497 0.0143 1.497 0.0143 +GS P S2P DOUBLE n 1.949 0.0200 1.949 0.0200 +GS P OP3 SINGLE n 1.497 0.0143 1.497 0.0143 +GS P "O5'" SINGLE n 1.613 0.0200 1.613 0.0200 +GS "O5'" "C5'" SINGLE n 1.438 0.0200 1.438 0.0200 +GS "C5'" "C4'" SINGLE n 1.507 0.0100 1.507 0.0100 +GS "C4'" "O4'" SINGLE n 1.444 0.0100 1.444 0.0100 +GS "C4'" "C3'" SINGLE n 1.530 0.0119 1.530 0.0119 +GS "O4'" "C1'" SINGLE n 1.422 0.0100 1.422 0.0100 +GS "C3'" "O3'" SINGLE n 1.425 0.0128 1.425 0.0128 +GS "C3'" "C2'" SINGLE n 1.526 0.0100 1.526 0.0100 +GS "C2'" "C1'" SINGLE n 1.520 0.0114 1.520 0.0114 +GS "C1'" N9 SINGLE n 1.459 0.0100 1.459 0.0100 +GS N9 C8 SINGLE y 1.373 0.0100 1.373 0.0100 +GS N9 C4 SINGLE y 1.379 0.0100 1.379 0.0100 +GS C8 N7 DOUBLE y 1.311 0.0104 1.311 0.0104 +GS N7 C5 SINGLE y 1.390 0.0100 1.390 0.0100 +GS C5 C6 SINGLE y 1.418 0.0111 1.418 0.0111 +GS C5 C4 DOUBLE y 1.377 0.0100 1.377 0.0100 +GS C6 O6 DOUBLE n 1.240 0.0104 1.240 0.0104 +GS C6 N1 SINGLE y 1.394 0.0120 1.394 0.0120 +GS N1 C2 SINGLE y 1.374 0.0124 1.374 0.0124 +GS C2 N2 SINGLE n 1.341 0.0143 1.341 0.0143 +GS C2 N3 DOUBLE y 1.331 0.0119 1.331 0.0119 +GS N3 C4 SINGLE y 1.355 0.0100 1.355 0.0100 +GS "C5'" "H5'" SINGLE n 1.092 0.0100 0.991 0.0200 +GS "C5'" "H5''" SINGLE n 1.092 0.0100 0.991 0.0200 +GS "C4'" "H4'" SINGLE n 1.092 0.0100 0.990 0.0200 +GS "C3'" "H3'" SINGLE n 1.092 0.0100 0.991 0.0181 +GS "O3'" "HO3'" SINGLE n 0.972 0.0180 0.839 0.0200 +GS "C2'" "H2'" SINGLE n 1.092 0.0100 0.970 0.0100 +GS "C2'" "H2''" SINGLE n 1.092 0.0100 0.970 0.0100 +GS "C1'" "H1'" SINGLE n 1.092 0.0100 0.993 0.0100 +GS C8 H8 SINGLE n 1.085 0.0150 0.942 0.0168 +GS N1 HN1 SINGLE n 1.013 0.0120 0.894 0.0200 +GS N2 HN21 SINGLE n 1.013 0.0120 0.877 0.0200 +GS N2 HN22 SINGLE n 1.013 0.0120 0.877 0.0200 loop_ _chem_comp_angle.comp_id @@ -112,72 +150,71 @@ _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd -GS OP1 P S2P 111.281 3.00 -GS OP1 P OP3 116.964 2.85 -GS OP1 P "O5'" 108.530 2.45 -GS S2P P OP3 111.281 3.00 -GS S2P P "O5'" 105.685 3.00 -GS OP3 P "O5'" 108.530 2.45 -GS P S2P HSP2 109.471 3.00 -GS P "O5'" "C5'" 119.135 1.78 -GS "O5'" "C5'" "C4'" 109.510 1.50 -GS "O5'" "C5'" "H5'" 109.821 1.50 -GS "O5'" "C5'" "H5''" 109.821 1.50 -GS "C4'" "C5'" "H5'" 109.624 1.50 -GS "C4'" "C5'" "H5''" 109.624 1.50 -GS "H5'" "C5'" "H5''" 108.472 1.50 -GS "C5'" "C4'" "O4'" 109.123 1.50 -GS "C5'" "C4'" "C3'" 114.866 1.63 -GS "C5'" "C4'" "H4'" 108.268 1.50 -GS "O4'" "C4'" "C3'" 105.506 1.50 -GS "O4'" "C4'" "H4'" 108.947 1.50 -GS "C3'" "C4'" "H4'" 109.069 1.50 -GS "C4'" "O4'" "C1'" 108.795 1.50 -GS "C4'" "C3'" "O3'" 110.527 2.37 -GS "C4'" "C3'" "C2'" 102.433 1.50 -GS "C4'" "C3'" "H3'" 110.775 1.50 -GS "O3'" "C3'" "C2'" 111.424 1.96 -GS "O3'" "C3'" "H3'" 110.713 1.50 -GS "C2'" "C3'" "H3'" 110.846 1.50 -GS "C3'" "O3'" "HO3'" 109.026 2.38 -GS "C3'" "C2'" "C1'" 102.663 1.50 -GS "C3'" "C2'" "H2'" 111.194 1.50 -GS "C3'" "C2'" "H2''" 111.194 1.50 -GS "C1'" "C2'" "H2'" 111.213 1.50 -GS "C1'" "C2'" "H2''" 111.213 1.50 -GS "H2'" "C2'" "H2''" 109.148 1.50 -GS "O4'" "C1'" "C2'" 106.035 1.50 -GS "O4'" "C1'" N9 108.236 1.50 -GS "O4'" "C1'" "H1'" 109.059 1.50 -GS "C2'" "C1'" N9 114.190 1.67 -GS "C2'" "C1'" "H1'" 109.272 1.50 -GS N9 "C1'" "H1'" 109.282 1.50 -GS "C1'" N9 C8 127.617 2.81 -GS "C1'" N9 C4 126.652 2.93 -GS C8 N9 C4 105.731 1.50 -GS N9 C8 N7 113.507 1.50 -GS N9 C8 H8 123.187 1.50 -GS N7 C8 H8 123.307 1.50 -GS C8 N7 C5 104.778 1.50 -GS N7 C5 C6 130.030 1.50 -GS N7 C5 C4 110.574 1.50 -GS C6 C5 C4 119.397 1.50 -GS C5 C6 O6 128.244 1.50 -GS C5 C6 N1 111.367 1.50 -GS O6 C6 N1 120.389 1.50 -GS C6 N1 C2 125.351 1.50 -GS C6 N1 HN1 116.978 2.44 -GS C2 N1 HN1 117.677 2.71 -GS N1 C2 N2 116.576 1.50 -GS N1 C2 N3 123.602 1.50 -GS N2 C2 N3 119.821 1.50 -GS C2 N2 HN21 119.868 1.50 -GS C2 N2 HN22 119.868 1.50 -GS HN21 N2 HN22 120.263 1.96 -GS C2 N3 C4 112.066 1.50 -GS N9 C4 C5 105.411 1.50 -GS N9 C4 N3 126.378 1.50 -GS C5 C4 N3 128.211 1.50 +GS OP1 P S2P 116.458 3.00 +GS OP1 P OP3 112.844 3.00 +GS OP1 P "O5'" 106.327 3.00 +GS S2P P OP3 116.458 3.00 +GS S2P P "O5'" 114.928 3.00 +GS OP3 P "O5'" 106.327 3.00 +GS P "O5'" "C5'" 119.085 2.00 +GS "O5'" "C5'" "C4'" 109.482 2.30 +GS "O5'" "C5'" "H5'" 109.954 1.50 +GS "O5'" "C5'" "H5''" 109.954 1.50 +GS "C4'" "C5'" "H5'" 109.589 1.50 +GS "C4'" "C5'" "H5''" 109.589 1.50 +GS "H5'" "C5'" "H5''" 108.471 1.50 +GS "C5'" "C4'" "O4'" 109.154 1.50 +GS "C5'" "C4'" "C3'" 113.954 2.40 +GS "C5'" "C4'" "H4'" 108.351 1.59 +GS "O4'" "C4'" "C3'" 105.638 1.50 +GS "O4'" "C4'" "H4'" 109.120 1.50 +GS "C3'" "C4'" "H4'" 109.033 1.50 +GS "C4'" "O4'" "C1'" 109.382 3.00 +GS "C4'" "C3'" "O3'" 110.611 3.00 +GS "C4'" "C3'" "C2'" 102.567 1.50 +GS "C4'" "C3'" "H3'" 110.734 1.65 +GS "O3'" "C3'" "C2'" 111.092 3.00 +GS "O3'" "C3'" "H3'" 110.786 1.88 +GS "C2'" "C3'" "H3'" 110.933 1.50 +GS "C3'" "O3'" "HO3'" 108.690 3.00 +GS "C3'" "C2'" "C1'" 102.504 1.94 +GS "C3'" "C2'" "H2'" 111.186 1.50 +GS "C3'" "C2'" "H2''" 111.186 1.50 +GS "C1'" "C2'" "H2'" 111.303 1.50 +GS "C1'" "C2'" "H2''" 111.303 1.50 +GS "H2'" "C2'" "H2''" 109.191 1.50 +GS "O4'" "C1'" "C2'" 106.199 1.82 +GS "O4'" "C1'" N9 108.364 1.50 +GS "O4'" "C1'" "H1'" 109.179 1.50 +GS "C2'" "C1'" N9 114.470 2.72 +GS "C2'" "C1'" "H1'" 109.048 1.50 +GS N9 "C1'" "H1'" 108.921 1.50 +GS "C1'" N9 C8 126.947 3.00 +GS "C1'" N9 C4 127.066 3.00 +GS C8 N9 C4 105.987 1.50 +GS N9 C8 N7 113.721 1.50 +GS N9 C8 H8 122.935 1.50 +GS N7 C8 H8 123.345 1.50 +GS C8 N7 C5 103.926 1.50 +GS N7 C5 C6 129.926 1.50 +GS N7 C5 C4 110.770 1.50 +GS C6 C5 C4 119.304 1.50 +GS C5 C6 O6 128.237 1.50 +GS C5 C6 N1 111.514 1.50 +GS O6 C6 N1 120.248 1.50 +GS C6 N1 C2 125.452 1.50 +GS C6 N1 HN1 117.160 2.45 +GS C2 N1 HN1 117.387 2.97 +GS N1 C2 N2 116.657 1.50 +GS N1 C2 N3 123.538 1.50 +GS N2 C2 N3 119.805 1.50 +GS C2 N2 HN21 119.712 3.00 +GS C2 N2 HN22 119.712 3.00 +GS HN21 N2 HN22 120.576 3.00 +GS C2 N3 C4 111.926 1.50 +GS N9 C4 C5 105.596 1.50 +GS N9 C4 N3 126.138 1.50 +GS C5 C4 N3 128.265 1.50 loop_ _chem_comp_tor.comp_id @@ -189,34 +226,34 @@ _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period -GS C2e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 -GS C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 -GS C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 -GS C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 -GS C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 -GS C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 -GS C3e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 -GS C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 -GS C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 -GS C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 -GS C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 -GS C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 -GS alpha "C5'" "O5'" P OP3 -60.000 10.00 3 -GS beta P "O5'" "C5'" "C4'" 180.000 10.00 3 -GS epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 -GS gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 -GS sp3_sp3_27 OP1 P S2P HSP2 -60.000 10.0 3 -GS const_18 N7 C8 N9 "C1'" 180.000 10.0 2 -GS const_30 C5 C4 N9 "C1'" 180.000 10.0 2 -GS const_21 N9 C8 N7 C5 0.000 10.0 2 -GS const_24 C6 C5 N7 C8 180.000 10.0 2 -GS const_sp2_sp2_4 N7 C5 C6 O6 0.000 5.0 2 -GS const_25 N9 C4 C5 N7 0.000 10.0 2 -GS const_sp2_sp2_7 O6 C6 N1 C2 180.000 5.0 2 -GS const_11 N2 C2 N1 C6 180.000 10.0 2 -GS sp2_sp2_1 N1 C2 N2 HN21 180.000 5.0 2 -GS const_14 N2 C2 N3 C4 180.000 10.0 2 -GS const_16 N9 C4 N3 C2 180.000 10.0 2 +GS sp3_sp3_27 "C5'" "O5'" P OP1 60.000 10.0 3 +GS sp3_sp3_7 "O4'" "C1'" "C2'" "C3'" 60.000 10.0 3 +GS sp2_sp3_1 C8 N9 "C1'" "O4'" 150.000 10.0 6 +GS const_17 N7 C8 N9 C4 0.000 0.0 1 +GS const_20 H8 C8 N9 "C1'" 0.000 0.0 1 +GS const_29 C5 C4 N9 C8 0.000 0.0 1 +GS const_32 N3 C4 N9 "C1'" 0.000 0.0 1 +GS const_21 N9 C8 N7 C5 0.000 0.0 1 +GS const_23 C4 C5 N7 C8 0.000 0.0 1 +GS const_sp2_sp2_1 C4 C5 C6 N1 0.000 0.0 1 +GS const_sp2_sp2_4 N7 C5 C6 O6 0.000 0.0 1 +GS const_25 N9 C4 C5 N7 0.000 0.0 1 +GS const_28 N3 C4 C5 C6 0.000 0.0 1 +GS const_sp2_sp2_5 C5 C6 N1 C2 0.000 0.0 1 +GS const_sp2_sp2_8 O6 C6 N1 HN1 0.000 0.0 1 +GS const_sp2_sp2_9 N3 C2 N1 C6 0.000 0.0 1 +GS const_12 N2 C2 N1 HN1 0.000 0.0 1 +GS sp2_sp2_33 N1 C2 N2 HN21 180.000 20 2 +GS sp2_sp2_36 N3 C2 N2 HN22 180.000 20 2 +GS const_13 N1 C2 N3 C4 0.000 0.0 1 +GS const_15 C5 C4 N3 C2 0.000 0.0 1 +GS sp3_sp3_28 "C4'" "C5'" "O5'" P 180.000 10.0 3 +GS sp3_sp3_31 "O4'" "C4'" "C5'" "O5'" 180.000 10.0 3 +GS sp3_sp3_2 "C5'" "C4'" "O4'" "C1'" -60.000 10.0 3 +GS sp3_sp3_44 "O3'" "C3'" "C4'" "C5'" 180.000 10.0 3 +GS sp3_sp3_4 "C2'" "C1'" "O4'" "C4'" -60.000 10.0 3 +GS sp3_sp3_17 "C1'" "C2'" "C3'" "O3'" 60.000 10.0 3 +GS sp3_sp3_49 "C4'" "C3'" "O3'" "HO3'" 180.000 10.0 3 loop_ _chem_comp_chir.comp_id @@ -226,10 +263,10 @@ _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign -GS chir_1 P S2P "O5'" OP3 both +GS chir_1 P S2P "O5'" OP3 both GS chir_2 "C4'" "O4'" "C3'" "C5'" negative GS chir_3 "C3'" "O3'" "C4'" "C2'" positive -GS chir_4 "C1'" "O4'" N9 "C2'" negative +GS chir_4 "C1'" "O4'" N9 "C2'" negative loop_ _chem_comp_plane_atom.comp_id @@ -237,23 +274,29 @@ _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd GS plan-1 "C1'" 0.020 -GS plan-1 C2 0.020 -GS plan-1 C4 0.020 -GS plan-1 C5 0.020 -GS plan-1 C6 0.020 -GS plan-1 C8 0.020 -GS plan-1 H8 0.020 -GS plan-1 HN1 0.020 -GS plan-1 N1 0.020 -GS plan-1 N2 0.020 -GS plan-1 N3 0.020 -GS plan-1 N7 0.020 -GS plan-1 N9 0.020 -GS plan-1 O6 0.020 -GS plan-2 C2 0.020 -GS plan-2 HN21 0.020 -GS plan-2 HN22 0.020 -GS plan-2 N2 0.020 +GS plan-1 C4 0.020 +GS plan-1 C5 0.020 +GS plan-1 C6 0.020 +GS plan-1 C8 0.020 +GS plan-1 H8 0.020 +GS plan-1 N3 0.020 +GS plan-1 N7 0.020 +GS plan-1 N9 0.020 +GS plan-2 C2 0.020 +GS plan-2 C4 0.020 +GS plan-2 C5 0.020 +GS plan-2 C6 0.020 +GS plan-2 HN1 0.020 +GS plan-2 N1 0.020 +GS plan-2 N2 0.020 +GS plan-2 N3 0.020 +GS plan-2 N7 0.020 +GS plan-2 N9 0.020 +GS plan-2 O6 0.020 +GS plan-3 C2 0.020 +GS plan-3 HN21 0.020 +GS plan-3 HN22 0.020 +GS plan-3 N2 0.020 loop_ _pdbx_chem_comp_descriptor.comp_id @@ -261,20 +304,20 @@ _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor -GS SMILES ACDLabs 10.04 O=P(O)(S)OCC3OC(n2cnc1c2N=C(N)NC1=O)CC3O -GS SMILES_CANONICAL CACTVS 3.341 NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P@](O)(S)=O)O3 -GS SMILES CACTVS 3.341 NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(S)=O)O3 +GS SMILES ACDLabs 10.04 O=P(O)(S)OCC3OC(n2cnc1c2N=C(N)NC1=O)CC3O +GS SMILES_CANONICAL CACTVS 3.341 NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P@](O)(S)=O)O3 +GS SMILES CACTVS 3.341 NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(S)=O)O3 GS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@](=O)(O)S)O)N=C(NC2=O)N -GS SMILES "OpenEye OEToolkits" 1.5.0 c1nc2c(n1C3CC(C(O3)COP(=O)(O)S)O)N=C(NC2=O)N -GS InChI InChI 1.03 InChI=1S/C10H14N5O6PS/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(21-6)2-20-22(18,19)23/h3-6,16H,1-2H2,(H2,18,19,23)(H3,11,13,14,17)/t4-,5+,6+/m0/s1 -GS InChIKey InChI 1.03 PSIUGNOLTIFXCJ-KVQBGUIXSA-N +GS SMILES "OpenEye OEToolkits" 1.5.0 c1nc2c(n1C3CC(C(O3)COP(=O)(O)S)O)N=C(NC2=O)N +GS InChI InChI 1.03 InChI=1S/C10H14N5O6PS/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(21-6)2-20-22(18,19)23/h3-6,16H,1-2H2,(H2,18,19,23)(H3,11,13,14,17)/t4-,5+,6+/m0/s1 +GS InChIKey InChI 1.03 PSIUGNOLTIFXCJ-KVQBGUIXSA-N loop_ _pdbx_chem_comp_description_generator.comp_id _pdbx_chem_comp_description_generator.program_name _pdbx_chem_comp_description_generator.program_version _pdbx_chem_comp_description_generator.descriptor -GS acedrg 243 "dictionary generator" -GS acedrg_database 11 "data source" -GS rdkit 2017.03.2 "Chemoinformatics tool" -GS refmac5 5.8.0238 "optimization tool" +GS acedrg 277 "dictionary generator" +GS acedrg_database 12 "data source" +GS rdkit 2019.09.1 "Chemoinformatics tool" +GS refmac5 5.8.0425 "optimization tool" diff --git a/k/K39.cif b/k/K39.cif index 88e0d5228..46ecc5a85 100644 --- a/k/K39.cif +++ b/k/K39.cif @@ -1,4 +1,3 @@ -# data_comp_list loop_ _chem_comp.id @@ -8,10 +7,9 @@ _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level -K39 K39 "2'-methoxyethyl-guanosine-5'-thiophosphate" NON-POLYMER 46 28 . -# +K39 K39 "2'-methoxyethyl-guanosine-5'-thiophosphate" NON-POLYMER 46 28 . + data_comp_K39 -# loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id @@ -21,52 +19,53 @@ _chem_comp_atom.charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z -K39 "C1'" C CH1 0 -9.965 -21.717 -25.076 -K39 C2 C CR6 0 -8.489 -20.705 -21.081 -K39 "C2'" C CH1 0 -11.259 -22.521 -24.943 -K39 "C3'" C CH1 0 -12.002 -22.135 -26.223 -K39 C4 C CR56 0 -9.493 -20.269 -23.037 -K39 "C4'" C CH1 0 -10.847 -22.016 -27.219 -K39 C5 C CR56 0 -9.759 -18.949 -22.736 -K39 "C5'" C CH2 0 -11.124 -21.195 -28.456 -K39 C6 C CR6 0 -9.354 -18.430 -21.475 -K39 C8 C CR15 0 -10.536 -19.267 -24.692 -K39 "CA'" C CH2 0 -10.716 -24.401 -23.562 -K39 "CB'" C CH2 0 -10.322 -25.838 -23.632 -K39 "CD'" C CH3 0 -11.126 -27.994 -24.197 -K39 N1 N NR6 0 -8.713 -19.400 -20.696 -K39 N2 N NH2 0 -7.857 -21.498 -20.202 -K39 N3 N NRD6 0 -8.868 -21.196 -22.264 -K39 N7 N NRD5 0 -10.417 -18.324 -23.788 -K39 N9 N NR5 0 -9.997 -20.470 -24.310 -K39 "O2'" O O2 0 -10.983 -23.920 -24.882 -K39 "O3'" O OH1 0 -12.938 -23.114 -26.655 -K39 "O4'" O O2 0 -9.784 -21.409 -26.456 -K39 "O5'" O O2 0 -11.421 -19.832 -28.097 -K39 O6 O O 0 -9.507 -17.280 -21.037 -K39 "OC'" O O2 0 -11.410 -26.613 -24.093 -K39 OP2 O OP -1 -12.227 -19.342 -30.382 -K39 P P P 0 -11.488 -18.707 -29.248 -K39 SP1 S S1 0 -12.231 -17.018 -28.632 -K39 OP3 O OP -1 -10.050 -18.582 -29.643 -K39 "H1'" H H 0 -9.184 -22.284 -24.761 -K39 "H2'" H H 0 -11.789 -22.234 -24.157 -K39 "H3'" H H 0 -12.452 -21.261 -26.097 -K39 "H4'" H H 0 -10.566 -22.922 -27.503 -K39 "H5'" H H 0 -11.892 -21.588 -28.944 -K39 "H5''" H H 0 -10.332 -21.220 -29.051 -K39 H8 H H 0 -10.948 -19.133 -25.527 -K39 H2 H H 0 -9.987 -23.871 -23.153 -K39 H9 H H 0 -11.524 -24.299 -22.999 -K39 H10 H H 0 -10.048 -26.149 -22.741 -K39 H11 H H 0 -9.559 -25.941 -24.243 -K39 H12 H H 0 -11.912 -28.461 -24.517 -K39 H13 H H 0 -10.878 -28.340 -23.327 -K39 H14 H H 0 -10.397 -28.128 -24.820 -K39 H1 H H 0 -8.428 -19.148 -19.885 -K39 H21 H H 0 -8.248 -22.229 -19.917 -K39 H22 H H 0 -7.057 -21.280 -19.917 -K39 "HO3'" H H 0 -13.423 -22.918 -25.785 +K39 "C1'" C CH1 0 -9.965 -21.717 -25.076 +K39 C2 C CR6 0 -8.489 -20.705 -21.081 +K39 "C2'" C CH1 0 -11.259 -22.521 -24.943 +K39 "C3'" C CH1 0 -12.002 -22.135 -26.223 +K39 C4 C CR56 0 -9.493 -20.269 -23.037 +K39 "C4'" C CH1 0 -10.847 -22.016 -27.219 +K39 C5 C CR56 0 -9.759 -18.949 -22.736 +K39 "C5'" C CH2 0 -11.124 -21.195 -28.456 +K39 C6 C CR6 0 -9.354 -18.430 -21.475 +K39 C8 C CR15 0 -10.536 -19.267 -24.692 +K39 "CA'" C CH2 0 -10.716 -24.401 -23.562 +K39 "CB'" C CH2 0 -10.322 -25.838 -23.632 +K39 "CD'" C CH3 0 -11.126 -27.994 -24.197 +K39 N1 N NR6 0 -8.713 -19.400 -20.696 +K39 N2 N NH2 0 -7.857 -21.498 -20.202 +K39 N3 N NRD6 0 -8.868 -21.196 -22.264 +K39 N7 N NRD5 0 -10.417 -18.324 -23.788 +K39 N9 N NR5 0 -9.997 -20.470 -24.310 +K39 "O2'" O O2 0 -10.983 -23.920 -24.882 +K39 "O3'" O OH1 0 -12.938 -23.114 -26.655 +K39 "O4'" O O2 0 -9.784 -21.409 -26.456 +K39 "O5'" O O2 0 -11.421 -19.832 -28.097 +K39 O6 O O 0 -9.507 -17.280 -21.037 +K39 "OC'" O O2 0 -11.410 -26.613 -24.093 +K39 OP2 O OP -1 -12.227 -19.342 -30.382 +K39 P P P 0 -11.488 -18.707 -29.248 +K39 SP1 S S1 0 -12.231 -17.018 -28.632 +K39 OP3 O OP -1 -10.050 -18.582 -29.643 +K39 "H1'" H H 0 -9.184 -22.284 -24.761 +K39 "H2'" H H 0 -11.789 -22.234 -24.157 +K39 "H3'" H H 0 -12.452 -21.261 -26.097 +K39 "H4'" H H 0 -10.566 -22.922 -27.503 +K39 "H5'" H H 0 -11.892 -21.588 -28.944 +K39 "H5''" H H 0 -10.332 -21.220 -29.051 +K39 H8 H H 0 -10.948 -19.133 -25.527 +K39 H2 H H 0 -9.987 -23.871 -23.153 +K39 H9 H H 0 -11.524 -24.299 -22.999 +K39 H10 H H 0 -10.048 -26.149 -22.741 +K39 H11 H H 0 -9.559 -25.941 -24.243 +K39 H12 H H 0 -11.912 -28.461 -24.517 +K39 H13 H H 0 -10.878 -28.340 -23.327 +K39 H14 H H 0 -10.397 -28.128 -24.820 +K39 H1 H H 0 -8.428 -19.148 -19.885 +K39 H21 H H 0 -8.248 -22.229 -19.917 +K39 H22 H H 0 -7.057 -21.280 -19.917 +K39 "HO3'" H H 0 -13.423 -22.918 -25.785 + loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 @@ -77,54 +76,55 @@ _chem_comp_bond.value_dist_nucleus _chem_comp_bond.value_dist_nucleus_esd _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd -K39 OP2 P SINGLE n 1.497 0.0143 1.497 0.0143 -K39 "O5'" P SINGLE n 1.613 0.0200 1.613 0.0200 -K39 P SP1 DOUBLE n 1.949 0.0200 1.949 0.0200 -K39 "C5'" "O5'" SINGLE n 1.438 0.0200 1.438 0.0200 -K39 "C4'" "C5'" SINGLE n 1.509 0.0100 1.509 0.0100 -K39 "C4'" "O4'" SINGLE n 1.444 0.0100 1.444 0.0100 -K39 "C3'" "C4'" SINGLE n 1.532 0.0100 1.532 0.0100 -K39 "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 -K39 "C1'" "O4'" SINGLE n 1.423 0.0100 1.423 0.0100 -K39 "C2'" "C3'" SINGLE n 1.529 0.0100 1.529 0.0100 -K39 "CD'" "OC'" SINGLE n 1.413 0.0146 1.413 0.0146 -K39 "CB'" "OC'" SINGLE n 1.410 0.0200 1.410 0.0200 -K39 "C1'" "C2'" SINGLE n 1.524 0.0126 1.524 0.0126 -K39 "C1'" N9 SINGLE n 1.462 0.0102 1.462 0.0102 -K39 C8 N9 SINGLE y 1.371 0.0100 1.371 0.0100 -K39 C8 N7 DOUBLE y 1.311 0.0104 1.311 0.0104 -K39 "C2'" "O2'" SINGLE n 1.423 0.0137 1.423 0.0137 -K39 "CA'" "O2'" SINGLE n 1.429 0.0100 1.429 0.0100 -K39 C4 N9 SINGLE y 1.383 0.0114 1.383 0.0114 -K39 C5 N7 SINGLE y 1.390 0.0100 1.390 0.0100 -K39 "CA'" "CB'" SINGLE n 1.492 0.0193 1.492 0.0193 -K39 C4 C5 DOUBLE y 1.377 0.0100 1.377 0.0100 -K39 C4 N3 SINGLE y 1.355 0.0100 1.355 0.0100 -K39 C5 C6 SINGLE y 1.418 0.0111 1.418 0.0111 -K39 C2 N3 DOUBLE y 1.331 0.0119 1.331 0.0119 -K39 C6 O6 DOUBLE n 1.240 0.0104 1.240 0.0104 -K39 C6 N1 SINGLE y 1.394 0.0120 1.394 0.0120 -K39 C2 N1 SINGLE y 1.374 0.0124 1.374 0.0124 -K39 C2 N2 SINGLE n 1.341 0.0143 1.341 0.0143 -K39 P OP3 SINGLE n 1.497 0.0143 1.497 0.0143 -K39 "C1'" "H1'" SINGLE n 1.089 0.0100 1.016 0.0200 -K39 "C2'" "H2'" SINGLE n 1.089 0.0100 0.990 0.0134 -K39 "C3'" "H3'" SINGLE n 1.089 0.0100 0.991 0.0200 -K39 "C4'" "H4'" SINGLE n 1.089 0.0100 0.990 0.0200 -K39 "C5'" "H5'" SINGLE n 1.089 0.0100 0.991 0.0200 -K39 "C5'" "H5''" SINGLE n 1.089 0.0100 0.991 0.0200 -K39 C8 H8 SINGLE n 1.082 0.0130 0.942 0.0168 -K39 "CA'" H2 SINGLE n 1.089 0.0100 0.990 0.0100 -K39 "CA'" H9 SINGLE n 1.089 0.0100 0.990 0.0100 -K39 "CB'" H10 SINGLE n 1.089 0.0100 0.983 0.0114 -K39 "CB'" H11 SINGLE n 1.089 0.0100 0.983 0.0114 -K39 "CD'" H12 SINGLE n 1.089 0.0100 0.968 0.0164 -K39 "CD'" H13 SINGLE n 1.089 0.0100 0.968 0.0164 -K39 "CD'" H14 SINGLE n 1.089 0.0100 0.968 0.0164 -K39 N1 H1 SINGLE n 1.016 0.0100 0.894 0.0200 -K39 N2 H21 SINGLE n 1.016 0.0100 0.877 0.0200 -K39 N2 H22 SINGLE n 1.016 0.0100 0.877 0.0200 -K39 "O3'" "HO3'" SINGLE n 0.970 0.0120 0.839 0.0200 +K39 OP2 P SINGLE n 1.497 0.0143 1.497 0.0143 +K39 "O5'" P SINGLE n 1.613 0.0200 1.613 0.0200 +K39 P SP1 DOUBLE n 1.949 0.0200 1.949 0.0200 +K39 "C5'" "O5'" SINGLE n 1.438 0.0200 1.438 0.0200 +K39 "C4'" "C5'" SINGLE n 1.509 0.0100 1.509 0.0100 +K39 "C4'" "O4'" SINGLE n 1.444 0.0100 1.444 0.0100 +K39 "C3'" "C4'" SINGLE n 1.532 0.0100 1.532 0.0100 +K39 "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +K39 "C1'" "O4'" SINGLE n 1.423 0.0100 1.423 0.0100 +K39 "C2'" "C3'" SINGLE n 1.529 0.0100 1.529 0.0100 +K39 "CD'" "OC'" SINGLE n 1.413 0.0146 1.413 0.0146 +K39 "CB'" "OC'" SINGLE n 1.410 0.0200 1.410 0.0200 +K39 "C1'" "C2'" SINGLE n 1.524 0.0126 1.524 0.0126 +K39 "C1'" N9 SINGLE n 1.462 0.0102 1.462 0.0102 +K39 C8 N9 SINGLE y 1.371 0.0100 1.371 0.0100 +K39 C8 N7 DOUBLE y 1.311 0.0104 1.311 0.0104 +K39 "C2'" "O2'" SINGLE n 1.423 0.0137 1.423 0.0137 +K39 "CA'" "O2'" SINGLE n 1.429 0.0100 1.429 0.0100 +K39 C4 N9 SINGLE y 1.383 0.0114 1.383 0.0114 +K39 C5 N7 SINGLE y 1.390 0.0100 1.390 0.0100 +K39 "CA'" "CB'" SINGLE n 1.492 0.0193 1.492 0.0193 +K39 C4 C5 DOUBLE y 1.377 0.0100 1.377 0.0100 +K39 C4 N3 SINGLE y 1.355 0.0100 1.355 0.0100 +K39 C5 C6 SINGLE y 1.418 0.0111 1.418 0.0111 +K39 C2 N3 DOUBLE y 1.331 0.0119 1.331 0.0119 +K39 C6 O6 DOUBLE n 1.240 0.0104 1.240 0.0104 +K39 C6 N1 SINGLE y 1.394 0.0120 1.394 0.0120 +K39 C2 N1 SINGLE y 1.374 0.0124 1.374 0.0124 +K39 C2 N2 SINGLE n 1.341 0.0143 1.341 0.0143 +K39 P OP3 SINGLE n 1.497 0.0143 1.497 0.0143 +K39 "C1'" "H1'" SINGLE n 1.089 0.0100 1.016 0.0200 +K39 "C2'" "H2'" SINGLE n 1.089 0.0100 0.990 0.0134 +K39 "C3'" "H3'" SINGLE n 1.089 0.0100 0.991 0.0200 +K39 "C4'" "H4'" SINGLE n 1.089 0.0100 0.990 0.0200 +K39 "C5'" "H5'" SINGLE n 1.089 0.0100 0.991 0.0200 +K39 "C5'" "H5''" SINGLE n 1.089 0.0100 0.991 0.0200 +K39 C8 H8 SINGLE n 1.082 0.0130 0.942 0.0168 +K39 "CA'" H2 SINGLE n 1.089 0.0100 0.990 0.0100 +K39 "CA'" H9 SINGLE n 1.089 0.0100 0.990 0.0100 +K39 "CB'" H10 SINGLE n 1.089 0.0100 0.983 0.0114 +K39 "CB'" H11 SINGLE n 1.089 0.0100 0.983 0.0114 +K39 "CD'" H12 SINGLE n 1.089 0.0100 0.968 0.0164 +K39 "CD'" H13 SINGLE n 1.089 0.0100 0.968 0.0164 +K39 "CD'" H14 SINGLE n 1.089 0.0100 0.968 0.0164 +K39 N1 H1 SINGLE n 1.016 0.0100 0.894 0.0200 +K39 N2 H21 SINGLE n 1.016 0.0100 0.877 0.0200 +K39 N2 H22 SINGLE n 1.016 0.0100 0.877 0.0200 +K39 "O3'" "HO3'" SINGLE n 0.970 0.0120 0.839 0.0200 + loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 @@ -132,91 +132,92 @@ _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd -K39 "O4'" "C1'" "C2'" 106.765 1.50 -K39 "O4'" "C1'" N9 108.577 1.50 -K39 "O4'" "C1'" "H1'" 109.833 2.53 -K39 "C2'" "C1'" N9 112.584 1.50 -K39 "C2'" "C1'" "H1'" 109.263 1.50 -K39 N9 "C1'" "H1'" 109.411 1.50 -K39 N3 C2 N1 123.538 1.50 -K39 N3 C2 N2 119.805 1.50 -K39 N1 C2 N2 116.657 1.50 -K39 "C3'" "C2'" "C1'" 101.348 1.50 -K39 "C3'" "C2'" "O2'" 112.208 3.50 -K39 "C3'" "C2'" "H2'" 110.368 2.92 -K39 "C1'" "C2'" "O2'" 110.752 3.50 -K39 "C1'" "C2'" "H2'" 111.584 3.50 -K39 "O2'" "C2'" "H2'" 110.191 2.23 -K39 "C4'" "C3'" "O3'" 110.713 3.50 -K39 "C4'" "C3'" "C2'" 102.511 1.50 -K39 "C4'" "C3'" "H3'" 110.577 3.50 -K39 "O3'" "C3'" "C2'" 112.059 3.50 -K39 "O3'" "C3'" "H3'" 110.541 2.08 -K39 "C2'" "C3'" "H3'" 110.368 2.92 -K39 N9 C4 C5 105.596 1.50 -K39 N9 C4 N3 126.138 1.50 -K39 C5 C4 N3 128.265 1.50 -K39 "C5'" "C4'" "O4'" 109.154 1.50 -K39 "C5'" "C4'" "C3'" 115.288 1.50 -K39 "C5'" "C4'" "H4'" 108.351 1.59 -K39 "O4'" "C4'" "C3'" 105.318 1.50 -K39 "O4'" "C4'" "H4'" 109.120 1.50 -K39 "C3'" "C4'" "H4'" 109.322 2.54 -K39 N7 C5 C4 110.770 1.50 -K39 N7 C5 C6 129.926 1.50 -K39 C4 C5 C6 119.304 1.50 -K39 "O5'" "C5'" "C4'" 109.482 2.30 -K39 "O5'" "C5'" "H5'" 109.954 1.50 -K39 "O5'" "C5'" "H5''" 109.954 1.50 -K39 "C4'" "C5'" "H5'" 109.589 1.50 -K39 "C4'" "C5'" "H5''" 109.589 1.50 -K39 "H5'" "C5'" "H5''" 108.471 1.50 -K39 C5 C6 O6 128.237 1.50 -K39 C5 C6 N1 111.514 1.50 -K39 O6 C6 N1 120.249 1.50 -K39 N9 C8 N7 113.721 1.50 -K39 N9 C8 H8 122.935 1.50 -K39 N7 C8 H8 123.345 1.50 -K39 "O2'" "CA'" "CB'" 109.739 3.50 -K39 "O2'" "CA'" H2 109.754 1.50 -K39 "O2'" "CA'" H9 109.754 1.50 -K39 "CB'" "CA'" H2 109.989 1.50 -K39 "CB'" "CA'" H9 109.989 1.50 -K39 H2 "CA'" H9 108.199 1.50 -K39 "OC'" "CB'" "CA'" 110.005 3.50 -K39 "OC'" "CB'" H10 109.650 1.50 -K39 "OC'" "CB'" H11 109.650 1.50 -K39 "CA'" "CB'" H10 109.619 1.50 -K39 "CA'" "CB'" H11 109.619 1.50 -K39 H10 "CB'" H11 108.266 1.87 -K39 "OC'" "CD'" H12 109.428 1.50 -K39 "OC'" "CD'" H13 109.428 1.50 -K39 "OC'" "CD'" H14 109.428 1.50 -K39 H12 "CD'" H13 109.526 2.98 -K39 H12 "CD'" H14 109.526 2.98 -K39 H13 "CD'" H14 109.526 2.98 -K39 C6 N1 C2 125.452 1.50 -K39 C6 N1 H1 117.160 2.45 -K39 C2 N1 H1 117.387 2.97 -K39 C2 N2 H21 119.712 3.50 -K39 C2 N2 H22 119.712 3.50 -K39 H21 N2 H22 120.576 3.50 -K39 C4 N3 C2 111.926 1.50 -K39 C8 N7 C5 103.926 1.50 -K39 "C1'" N9 C8 127.058 3.17 -K39 "C1'" N9 C4 126.955 2.94 -K39 C8 N9 C4 105.987 1.50 -K39 "C2'" "O2'" "CA'" 113.047 1.50 -K39 "C3'" "O3'" "HO3'" 109.389 3.50 -K39 "C4'" "O4'" "C1'" 109.502 2.85 -K39 P "O5'" "C5'" 119.085 2.00 -K39 "CD'" "OC'" "CB'" 112.460 3.50 -K39 OP2 P "O5'" 106.327 3.50 -K39 OP2 P SP1 116.458 3.12 -K39 OP2 P OP3 112.844 3.50 -K39 "O5'" P SP1 114.928 3.50 -K39 "O5'" P OP3 106.327 3.50 -K39 SP1 P OP3 116.458 3.12 +K39 "O4'" "C1'" "C2'" 106.765 1.50 +K39 "O4'" "C1'" N9 108.577 1.50 +K39 "O4'" "C1'" "H1'" 109.833 2.53 +K39 "C2'" "C1'" N9 112.584 1.50 +K39 "C2'" "C1'" "H1'" 109.263 1.50 +K39 N9 "C1'" "H1'" 109.411 1.50 +K39 N3 C2 N1 123.538 1.50 +K39 N3 C2 N2 119.805 1.50 +K39 N1 C2 N2 116.657 1.50 +K39 "C3'" "C2'" "C1'" 101.348 1.50 +K39 "C3'" "C2'" "O2'" 112.208 3.50 +K39 "C3'" "C2'" "H2'" 110.368 2.92 +K39 "C1'" "C2'" "O2'" 110.752 3.50 +K39 "C1'" "C2'" "H2'" 111.584 3.50 +K39 "O2'" "C2'" "H2'" 110.191 2.23 +K39 "C4'" "C3'" "O3'" 110.713 3.50 +K39 "C4'" "C3'" "C2'" 102.511 1.50 +K39 "C4'" "C3'" "H3'" 110.577 3.50 +K39 "O3'" "C3'" "C2'" 112.059 3.50 +K39 "O3'" "C3'" "H3'" 110.541 2.08 +K39 "C2'" "C3'" "H3'" 110.368 2.92 +K39 N9 C4 C5 105.596 1.50 +K39 N9 C4 N3 126.138 1.50 +K39 C5 C4 N3 128.265 1.50 +K39 "C5'" "C4'" "O4'" 109.154 1.50 +K39 "C5'" "C4'" "C3'" 115.288 1.50 +K39 "C5'" "C4'" "H4'" 108.351 1.59 +K39 "O4'" "C4'" "C3'" 105.318 1.50 +K39 "O4'" "C4'" "H4'" 109.120 1.50 +K39 "C3'" "C4'" "H4'" 109.322 2.54 +K39 N7 C5 C4 110.770 1.50 +K39 N7 C5 C6 129.926 1.50 +K39 C4 C5 C6 119.304 1.50 +K39 "O5'" "C5'" "C4'" 109.482 2.30 +K39 "O5'" "C5'" "H5'" 109.954 1.50 +K39 "O5'" "C5'" "H5''" 109.954 1.50 +K39 "C4'" "C5'" "H5'" 109.589 1.50 +K39 "C4'" "C5'" "H5''" 109.589 1.50 +K39 "H5'" "C5'" "H5''" 108.471 1.50 +K39 C5 C6 O6 128.237 1.50 +K39 C5 C6 N1 111.514 1.50 +K39 O6 C6 N1 120.249 1.50 +K39 N9 C8 N7 113.721 1.50 +K39 N9 C8 H8 122.935 1.50 +K39 N7 C8 H8 123.345 1.50 +K39 "O2'" "CA'" "CB'" 109.739 3.50 +K39 "O2'" "CA'" H2 109.754 1.50 +K39 "O2'" "CA'" H9 109.754 1.50 +K39 "CB'" "CA'" H2 109.989 1.50 +K39 "CB'" "CA'" H9 109.989 1.50 +K39 H2 "CA'" H9 108.199 1.50 +K39 "OC'" "CB'" "CA'" 110.005 3.50 +K39 "OC'" "CB'" H10 109.650 1.50 +K39 "OC'" "CB'" H11 109.650 1.50 +K39 "CA'" "CB'" H10 109.619 1.50 +K39 "CA'" "CB'" H11 109.619 1.50 +K39 H10 "CB'" H11 108.266 1.87 +K39 "OC'" "CD'" H12 109.428 1.50 +K39 "OC'" "CD'" H13 109.428 1.50 +K39 "OC'" "CD'" H14 109.428 1.50 +K39 H12 "CD'" H13 109.526 2.98 +K39 H12 "CD'" H14 109.526 2.98 +K39 H13 "CD'" H14 109.526 2.98 +K39 C6 N1 C2 125.452 1.50 +K39 C6 N1 H1 117.160 2.45 +K39 C2 N1 H1 117.387 2.97 +K39 C2 N2 H21 119.712 3.50 +K39 C2 N2 H22 119.712 3.50 +K39 H21 N2 H22 120.576 3.50 +K39 C4 N3 C2 111.926 1.50 +K39 C8 N7 C5 103.926 1.50 +K39 "C1'" N9 C8 127.058 3.17 +K39 "C1'" N9 C4 126.955 2.94 +K39 C8 N9 C4 105.987 1.50 +K39 "C2'" "O2'" "CA'" 113.047 1.50 +K39 "C3'" "O3'" "HO3'" 109.389 3.50 +K39 "C4'" "O4'" "C1'" 109.502 2.85 +K39 P "O5'" "C5'" 119.085 2.00 +K39 "CD'" "OC'" "CB'" 112.460 3.50 +K39 OP2 P "O5'" 106.327 3.50 +K39 OP2 P SP1 116.458 3.12 +K39 OP2 P OP3 112.844 3.50 +K39 "O5'" P SP1 114.928 3.50 +K39 "O5'" P OP3 106.327 3.50 +K39 SP1 P OP3 116.458 3.12 + loop_ _chem_comp_tor.comp_id _chem_comp_tor.id @@ -227,38 +228,39 @@ _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period -K39 C2e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 -K39 C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 -K39 C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 -K39 C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 -K39 C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 -K39 C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 -K39 C3e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 -K39 C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 -K39 C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 -K39 C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 -K39 C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 -K39 C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 -K39 alpha "C5'" "O5'" P OP3 -60.000 10.00 3 -K39 beta P "O5'" "C5'" "C4'" 180.000 10.00 3 -K39 epsilon "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 -K39 gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 -K39 sp3_sp3_64 "O2'" "CA'" "CB'" "OC'" 180.000 10.0 3 -K39 sp3_sp3_61 "CB'" "CA'" "O2'" "C2'" 180.000 10.0 3 -K39 sp3_sp3_46 "CA'" "CB'" "OC'" "CD'" 180.000 10.0 3 -K39 sp3_sp3_43 H12 "CD'" "OC'" "CB'" 180.000 10.0 3 -K39 const_31 N2 C2 N1 C6 180.000 5.0 2 -K39 sp2_sp2_3 N3 C2 N2 H21 0.000 5.0 2 -K39 const_sp2_sp2_2 N2 C2 N3 C4 180.000 5.0 2 -K39 sp3_sp3_58 "C3'" "C2'" "O2'" "CA'" 180.000 10.0 3 -K39 const_sp2_sp2_4 N9 C4 N3 C2 180.000 5.0 2 -K39 const_18 C5 C4 N9 "C1'" 180.000 5.0 2 -K39 const_sp2_sp2_5 N9 C4 C5 N7 0.000 5.0 2 -K39 const_27 C4 C5 N7 C8 0.000 5.0 2 -K39 const_12 N7 C5 C6 O6 0.000 5.0 2 -K39 const_15 O6 C6 N1 C2 180.000 5.0 2 -K39 const_25 N9 C8 N7 C5 0.000 5.0 2 -K39 const_22 N7 C8 N9 "C1'" 180.000 5.0 2 +K39 C2e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 +K39 C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 +K39 C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 +K39 C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 +K39 C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 +K39 C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 +K39 C3e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 +K39 C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 +K39 C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 +K39 C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 +K39 C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 +K39 C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 +K39 alpha "C5'" "O5'" P OP3 -60.000 10.00 3 +K39 beta P "O5'" "C5'" "C4'" 180.000 10.00 3 +K39 epsilon "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 +K39 gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 +K39 sp3_sp3_64 "O2'" "CA'" "CB'" "OC'" 180.000 10.0 3 +K39 sp3_sp3_61 "CB'" "CA'" "O2'" "C2'" 180.000 10.0 3 +K39 sp3_sp3_46 "CA'" "CB'" "OC'" "CD'" 180.000 10.0 3 +K39 sp3_sp3_43 H12 "CD'" "OC'" "CB'" 180.000 10.0 3 +K39 const_31 N2 C2 N1 C6 180.000 5.0 2 +K39 sp2_sp2_3 N3 C2 N2 H21 0.000 5.0 2 +K39 const_sp2_sp2_2 N2 C2 N3 C4 180.000 5.0 2 +K39 sp3_sp3_58 "C3'" "C2'" "O2'" "CA'" 180.000 10.0 3 +K39 const_sp2_sp2_4 N9 C4 N3 C2 180.000 5.0 2 +K39 const_18 C5 C4 N9 "C1'" 180.000 5.0 2 +K39 const_sp2_sp2_5 N9 C4 C5 N7 0.000 5.0 2 +K39 const_27 C4 C5 N7 C8 0.000 5.0 2 +K39 const_12 N7 C5 C6 O6 0.000 5.0 2 +K39 const_15 O6 C6 N1 C2 180.000 5.0 2 +K39 const_25 N9 C8 N7 C5 0.000 5.0 2 +K39 const_22 N7 C8 N9 "C1'" 180.000 5.0 2 + loop_ _chem_comp_chir.comp_id _chem_comp_chir.id @@ -267,34 +269,36 @@ _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign -K39 chir_1 "C1'" "O4'" N9 "C2'" negative -K39 chir_2 "C2'" "O2'" "C1'" "C3'" negative -K39 chir_3 "C3'" "O3'" "C2'" "C4'" negative -K39 chir_4 "C4'" "O4'" "C3'" "C5'" negative -K39 chir_5 P SP1 "O5'" OP2 both +K39 chir_1 "C1'" "O4'" N9 "C2'" negative +K39 chir_2 "C2'" "O2'" "C1'" "C3'" negative +K39 chir_3 "C3'" "O3'" "C2'" "C4'" negative +K39 chir_4 "C4'" "O4'" "C3'" "C5'" negative +K39 chir_5 P SP1 "O5'" OP2 both + loop_ _chem_comp_plane_atom.comp_id _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd -K39 plan-1 "C1'" 0.020 -K39 plan-1 C2 0.020 -K39 plan-1 C4 0.020 -K39 plan-1 C5 0.020 -K39 plan-1 C6 0.020 -K39 plan-1 C8 0.020 -K39 plan-1 H1 0.020 -K39 plan-1 H8 0.020 -K39 plan-1 N1 0.020 -K39 plan-1 N2 0.020 -K39 plan-1 N3 0.020 -K39 plan-1 N7 0.020 -K39 plan-1 N9 0.020 -K39 plan-1 O6 0.020 -K39 plan-2 C2 0.020 -K39 plan-2 H21 0.020 -K39 plan-2 H22 0.020 -K39 plan-2 N2 0.020 +K39 plan-1 "C1'" 0.020 +K39 plan-1 C2 0.020 +K39 plan-1 C4 0.020 +K39 plan-1 C5 0.020 +K39 plan-1 C6 0.020 +K39 plan-1 C8 0.020 +K39 plan-1 H1 0.020 +K39 plan-1 H8 0.020 +K39 plan-1 N1 0.020 +K39 plan-1 N2 0.020 +K39 plan-1 N3 0.020 +K39 plan-1 N7 0.020 +K39 plan-1 N9 0.020 +K39 plan-1 O6 0.020 +K39 plan-2 C2 0.020 +K39 plan-2 H21 0.020 +K39 plan-2 H22 0.020 +K39 plan-2 N2 0.020 + loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type @@ -307,12 +311,21 @@ K39 SMILES_CANONICAL CACTVS 3.385 "COCCO[C@@H]1[C@H](O)[C@@H](CO[P K39 SMILES CACTVS 3.385 "COCCO[CH]1[CH](O)[CH](CO[P](O)(O)=S)O[CH]1n2cnc3C(=O)NC(=Nc23)N" K39 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "COCCO[C@@H]1[C@@H]([C@H](O[C@H]1n2cnc3c2N=C(NC3=O)N)COP(=S)(O)O)O" K39 SMILES "OpenEye OEToolkits" 2.0.7 "COCCOC1C(C(OC1n2cnc3c2N=C(NC3=O)N)COP(=S)(O)O)O" + loop_ _pdbx_chem_comp_description_generator.comp_id _pdbx_chem_comp_description_generator.program_name _pdbx_chem_comp_description_generator.program_version _pdbx_chem_comp_description_generator.descriptor -K39 acedrg 249 "dictionary generator" -K39 acedrg_database 12 "data source" -K39 rdkit 2019.09.1 "Chemoinformatics tool" -K39 refmac5 5.8.0352 "optimization tool" +K39 acedrg 249 "dictionary generator" +K39 acedrg_database 12 "data source" +K39 rdkit 2019.09.1 "Chemoinformatics tool" +K39 refmac5 5.8.0352 "optimization tool" + +loop_ +_chem_comp_alias.comp_id +_chem_comp_alias.group +_chem_comp_alias.atom_id +_chem_comp_alias.atom_id_standard +K39 S-NA OP2 OP1 +K39 S-NA SP1 S2P diff --git a/links_and_mods.cif b/links_and_mods.cif index 0fa509a80..4348644f6 100644 --- a/links_and_mods.cif +++ b/links_and_mods.cif @@ -24,6 +24,7 @@ pept-SUI . DEL-OXT peptide SUI SUImod1 NON-POLYMER pept-SUI SUI-pept SUI SUImod2 NON-POLYMER . DEL-HN1 peptide SUI-pept gap . . . . . . gap-link p . DEL_HO3p DNA/RNA . DEL_OP3 DNA/RNA default-DNA/RNA-link +p-S . DEL_HO3p DNA/RNA . DEL_OP3S S-NA DNA/RNA-S-NA-link AA-RNA . DEL-OXT peptide . DEL_HO3p DNA/RNA aminoacyl-RNA RNA-F86 . DEL_HO3p DNA/RNA F86 F86m1 NON-POLYMER RNA-F86 FOR_C-N FOR FORm1 NON-POLYMER . DEL-HN1 peptide bond_FOR-C_=_N-peptide @@ -145,6 +146,7 @@ p5*END DNA/RNA-p5*-terminus . DNA/RNA p3*END DNA/RNA-p3*-terminus . DNA/RNA DEL_OP3 DN/RNA-OP3-delete . DNA/RNA DEL_HO3p DNA/RNA-OP3-delete . DNA/RNA +DEL_OP3S S-NA-OP3-delete . S-NA F86m1 "[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" F86 NON-POLYMER FOR-N N-terminus_of_formyl . . FOR-C C-terminus_of_formyl . . @@ -1086,6 +1088,64 @@ _chem_link_chir.atom_id_3 _chem_link_chir.volume_sign p 2 P 2 "O5'" 1 "O3'" 2 OP2 both +data_link_p-S +loop_ +_chem_link_bond.link_id +_chem_link_bond.atom_1_comp_id +_chem_link_bond.atom_id_1 +_chem_link_bond.atom_2_comp_id +_chem_link_bond.atom_id_2 +_chem_link_bond.type +_chem_link_bond.value_dist +_chem_link_bond.value_dist_esd +p-S 1 "O3'" 2 P SINGLE 1.602 0.0155 + +loop_ +_chem_link_angle.link_id +_chem_link_angle.atom_1_comp_id +_chem_link_angle.atom_id_1 +_chem_link_angle.atom_2_comp_id +_chem_link_angle.atom_id_2 +_chem_link_angle.atom_3_comp_id +_chem_link_angle.atom_id_3 +_chem_link_angle.value_angle +_chem_link_angle.value_angle_esd +p-S 1 "C3'" 1 "O3'" 2 P 120.945 1.50 +p-S 2 OP1 2 P 1 "O3'" 108.260 3.00 +p-S 2 S2P 2 P 1 "O3'" 109.083 3.00 +p-S 2 "O5'" 2 P 1 "O3'" 101.205 3.00 + +loop_ +_chem_link_tor.link_id +_chem_link_tor.id +_chem_link_tor.atom_1_comp_id +_chem_link_tor.atom_id_1 +_chem_link_tor.atom_2_comp_id +_chem_link_tor.atom_id_2 +_chem_link_tor.atom_3_comp_id +_chem_link_tor.atom_id_3 +_chem_link_tor.atom_4_comp_id +_chem_link_tor.atom_id_4 +_chem_link_tor.value_angle +_chem_link_tor.value_angle_esd +_chem_link_tor.period +p-S zeta 1 "C3'" 1 "O3'" 2 P 2 "O5'" 60.000 10.0 3 +p-S epsilon 1 "C4'" 1 "C3'" 1 "O3'" 2 P 180.000 10.0 3 +p-S alpha 1 "O3'" 2 "P" 2 "O5'" 2 "C5'" 180.000 10.00 3 + +loop_ +_chem_link_chir.link_id +_chem_link_chir.atom_centre_comp_id +_chem_link_chir.atom_id_centre +_chem_link_chir.atom_1_comp_id +_chem_link_chir.atom_id_1 +_chem_link_chir.atom_2_comp_id +_chem_link_chir.atom_id_2 +_chem_link_chir.atom_3_comp_id +_chem_link_chir.atom_id_3 +_chem_link_chir.volume_sign +p-S 2 P 2 S2P 2 "O5'" 2 OP1 both + data_link_AA-RNA loop_ _chem_link_bond.link_id @@ -6603,6 +6663,43 @@ _chem_mod_tor.new_value_angle _chem_mod_tor.new_value_angle_esd DEL_OP3 delete "C5'" "O5'" P OP3 . . +data_mod_DEL_OP3S +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +DEL_OP3S delete OP3 . O OP -1 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +DEL_OP3S delete P OP3 single . . . . + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +DEL_OP3S delete OP1 P OP3 . . +DEL_OP3S delete S2P P OP3 . . +DEL_OP3S delete OP3 P "O5'" . . +DEL_OP3S change S2P P "O5'" 109.083 3.00 +DEL_OP3S change P "O5'" "C5'" 118.610 3.00 + data_mod_DEL_HO3p loop_ _chem_mod_atom.mod_id diff --git a/list/mon_lib_list.cif b/list/mon_lib_list.cif index 44670ed38..d9d922ffc 100644 --- a/list/mon_lib_list.cif +++ b/list/mon_lib_list.cif @@ -12136,7 +12136,7 @@ ARV ARV 5-N-ALLYL-ARGININE peptide 34 15 . ARW ARW 'METHYL BETA-D-ARABINOPYRANOSIDE' pyranose 23 11 . ARX ARX (2S,3S,4R,5R)-5-(6-amino-9H-purin-9- NON-POLYMER 97 50 . ARZ ARZ '(3S,5S,7S)-N-(5-sulfamoyl-1,3,4-thiadiazol-2-yl)tricyclo[3.3.1.1~3,7~]decane-1-carboxamide' NON-POLYMER 40 22 . -AS AS '.' NON-POLYMER 36 22 . +AS AS '.' S-NA 36 22 . AS0 AS0 '4-[(11BETA,17BETA)-17-METHOXY-17-(METHOXYMETHYL)-3-OXOESTRA-4,9-DIEN-11-YL]BENZALDEHYDE OXIME' NON-POLYMER 68 33 . AS1 AS1 ARGININOSUCCINATE NON-POLYMER 37 20 . AS2 AS2 '(2R)-2-AMINO-4-OXOBUTANOIC ACID' NON-POLYMER 15 8 . @@ -18983,7 +18983,7 @@ GRW GRW '(2~{S})-~{N}-[(2~{S},3~{R})-1-[[(2~{S})-1-[4-(aminomethyl)phenyl]-4-met GRX GRX (S)-1-beta-phosphonofluoromethylene-1-deoxy-D-glucopyranose NON-POLYMER 29 17 . GRY GRY '~{N}1-(4,6-dimethylpyrimidin-2-yl)benzene-1,4-diamine' NON-POLYMER 30 16 . GRZ GRZ '1-[5-chloranyl-2-(4-fluoranylphenoxy)phenyl]-~{N}-oxidanyl-1,2,3-triazole-4-carboxamide' NON-POLYMER 34 24 . -GS GS "GUANOSINE-5'-THIO-MONOPHOSPHATE" NON-POLYMER 37 23 . +GS GS "GUANOSINE-5'-THIO-MONOPHOSPHATE" S-NA 37 23 . GS1 GS1 1-THIO-BETA-D-GLUCOPYRANOSE pyranose 24 12 . GS2 GS2 '2-[(2-{[1-(N,N-dimethylglycyl)-5-methoxy-1H-indol-6-yl]amino}-7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]-6-fluoro-N-methylbenzamide' NON-POLYMER 66 39 . GS3 GS3 '2-fluoro-6-{[2-({2-methoxy-4-[4-(1-methylethyl)piperazin-1-yl]phenyl}amino)-7H-pyrrolo[2,3-d]pyrimidin-4-yl]amino}benzamide' NON-POLYMER 69 38 . @@ -29778,7 +29778,7 @@ SBW SBW N-(3-hydroxybenzyl)-4-sulfamoylbenzamide NON-POLYMER 35 21 . SBX SBX '1-CYCLOHEXYL-3-PHENYL-1-PROPYL-1-(3,3-DIMETHYL-1,2-DIOXYPENTYL)-2-PIPERIDINE CARBOXYLATE' NON-POLYMER 74 33 . SBY SBY '3-[DODECYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE' NON-POLYMER 59 22 . SBZ SBZ '[4-(1,3,2-DIOXABOROLAN-2-YLOXY)METHYL]BENZAMIDINE' NON-POLYMER 30 16 . -SC SC "2-DEOXY-CYTIDINE-5'-THIOPHOSPHORATE" NON-POLYMER 34 20 . +SC SC "2-DEOXY-CYTIDINE-5'-THIOPHOSPHORATE" S-NA 34 20 . SC0 SC0 (6E,11E)-HEPTADECA-6,11-DIENE-9,9-DIYLBIS(PHOSPHONICACID) NON-POLYMER 55 25 . SC1 SC1 '[3R-[3A,4A,5B(S*)]]-5-(1-CARBOXY-1-PHOSPHONOETHOXY)-4-HYDROXY-3-(PHOSPHONOOXY)-1-CYCLOHEXENE-1-CARBOXYLICACID' NON-POLYMER 35 25 . SC2 SC2 N-ACETYL-L-CYSTEINE NON-POLYMER 18 10 . @@ -30220,7 +30220,7 @@ SR5 SR5 '(2~{S})-2-[[1-(7-chloranylquinolin-4-yl)-5-(2,6-dimethoxyphenyl)pyrazol SR7 SR7 'N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide' NON-POLYMER 57 34 . SR8 SR8 1-(5-TERT-BUTYL-1,2-OXAZOL-3-YL)-3-(4-PYRIDIN-4-YLOXYPHENYL)UREA NON-POLYMER 46 26 . SR9 SR9 '(2~{S})-4-methyl-2-[(1-quinolin-8-ylsulfonylindol-3-yl)carbonylamino]pentanoic acid' NON-POLYMER 55 33 . -SRA SRA '.' NON-POLYMER 37 23 . +SRA SRA '.' S-NA 37 23 . SRB SRB 'L-1-NAPHTHYL-2-ACETAMIDO-ETHANE BORONIC ACID' NON-POLYMER 37 20 . SRD SRD 'D-1-NAPHTHYL-2-ACETAMIDO-ETHANE BORONIC ACID' NON-POLYMER 37 20 . SRE SRE (1S,4S)-4-(3,4-dichlorophenyl)-N-methyl-1,2,3,4-tetrahydronaphthalen-1-amine NON-POLYMER 37 20 . @@ -35924,6 +35924,7 @@ pept-SUI . DEL-OXT peptide SUI SUImod1 NON-POLYMER pept-SUI SUI-pept SUI SUImod2 NON-POLYMER . DEL-HN1 peptide SUI-pept gap . . . . . . gap-link p . DEL_HO3p DNA/RNA . DEL_OP3 DNA/RNA default-DNA/RNA-link +p-S . DEL_HO3p DNA/RNA . DEL_OP3S S-NA DNA/RNA-S-NA-link AA-RNA . DEL-OXT peptide . DEL_HO3p DNA/RNA aminoacyl-RNA RNA-F86 . DEL_HO3p DNA/RNA F86 F86m1 NON-POLYMER RNA-F86 FOR_C-N FOR FORm1 NON-POLYMER . DEL-HN1 peptide bond_FOR-C_=_N-peptide @@ -36045,6 +36046,7 @@ p5*END DNA/RNA-p5*-terminus . DNA/RNA p3*END DNA/RNA-p3*-terminus . DNA/RNA DEL_OP3 DN/RNA-OP3-delete . DNA/RNA DEL_HO3p DNA/RNA-OP3-delete . DNA/RNA +DEL_OP3S S-NA-OP3-delete . S-NA F86m1 "[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" F86 NON-POLYMER FOR-N N-terminus_of_formyl . . FOR-C C-terminus_of_formyl . . @@ -36986,6 +36988,64 @@ _chem_link_chir.atom_id_3 _chem_link_chir.volume_sign p 2 P 2 "O5'" 1 "O3'" 2 OP2 both +data_link_p-S +loop_ +_chem_link_bond.link_id +_chem_link_bond.atom_1_comp_id +_chem_link_bond.atom_id_1 +_chem_link_bond.atom_2_comp_id +_chem_link_bond.atom_id_2 +_chem_link_bond.type +_chem_link_bond.value_dist +_chem_link_bond.value_dist_esd +p-S 1 "O3'" 2 P SINGLE 1.602 0.0155 + +loop_ +_chem_link_angle.link_id +_chem_link_angle.atom_1_comp_id +_chem_link_angle.atom_id_1 +_chem_link_angle.atom_2_comp_id +_chem_link_angle.atom_id_2 +_chem_link_angle.atom_3_comp_id +_chem_link_angle.atom_id_3 +_chem_link_angle.value_angle +_chem_link_angle.value_angle_esd +p-S 1 "C3'" 1 "O3'" 2 P 120.945 1.50 +p-S 2 OP1 2 P 1 "O3'" 108.260 3.00 +p-S 2 S2P 2 P 1 "O3'" 109.083 3.00 +p-S 2 "O5'" 2 P 1 "O3'" 101.205 3.00 + +loop_ +_chem_link_tor.link_id +_chem_link_tor.id +_chem_link_tor.atom_1_comp_id +_chem_link_tor.atom_id_1 +_chem_link_tor.atom_2_comp_id +_chem_link_tor.atom_id_2 +_chem_link_tor.atom_3_comp_id +_chem_link_tor.atom_id_3 +_chem_link_tor.atom_4_comp_id +_chem_link_tor.atom_id_4 +_chem_link_tor.value_angle +_chem_link_tor.value_angle_esd +_chem_link_tor.period +p-S zeta 1 "C3'" 1 "O3'" 2 P 2 "O5'" 60.000 10.0 3 +p-S epsilon 1 "C4'" 1 "C3'" 1 "O3'" 2 P 180.000 10.0 3 +p-S alpha 1 "O3'" 2 "P" 2 "O5'" 2 "C5'" 180.000 10.00 3 + +loop_ +_chem_link_chir.link_id +_chem_link_chir.atom_centre_comp_id +_chem_link_chir.atom_id_centre +_chem_link_chir.atom_1_comp_id +_chem_link_chir.atom_id_1 +_chem_link_chir.atom_2_comp_id +_chem_link_chir.atom_id_2 +_chem_link_chir.atom_3_comp_id +_chem_link_chir.atom_id_3 +_chem_link_chir.volume_sign +p-S 2 P 2 S2P 2 "O5'" 2 OP1 both + data_link_AA-RNA loop_ _chem_link_bond.link_id @@ -42503,6 +42563,43 @@ _chem_mod_tor.new_value_angle _chem_mod_tor.new_value_angle_esd DEL_OP3 delete "C5'" "O5'" P OP3 . . +data_mod_DEL_OP3S +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +DEL_OP3S delete OP3 . O OP -1 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +DEL_OP3S delete P OP3 single . . . . + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +DEL_OP3S delete OP1 P OP3 . . +DEL_OP3S delete S2P P OP3 . . +DEL_OP3S delete OP3 P "O5'" . . +DEL_OP3S change S2P P "O5'" 109.083 3.00 +DEL_OP3S change P "O5'" "C5'" 118.610 3.00 + data_mod_DEL_HO3p loop_ _chem_mod_atom.mod_id diff --git a/n/N7X.cif b/n/N7X.cif index e25e1ed53..cd2bf1c62 100644 --- a/n/N7X.cif +++ b/n/N7X.cif @@ -19,52 +19,52 @@ _chem_comp_atom.charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z -N7X C C CH2 0 -2.555 -2.648 -1.281 -N7X C1 C CH2 0 -3.706 -3.546 -0.956 -N7X "C1'" C CH1 0 -0.828 -0.218 0.947 -N7X C12 C CH3 0 -5.933 -3.559 -0.139 -N7X C2 C CR6 0 -1.090 1.947 -0.331 -N7X "C2'" C CH1 0 -0.899 -1.264 -0.166 -N7X "C3'" C CH1 0 0.329 -2.116 0.169 -N7X C4 C CR6 0 -2.924 3.352 0.109 -N7X "C4'" C CH1 0 1.340 -1.076 0.679 -N7X C5 C CR6 0 -3.419 2.460 1.097 -N7X "C5'" C CH2 0 2.351 -0.590 -0.331 -N7X C6 C CR16 0 -2.712 1.339 1.324 -N7X C7 C CH3 0 -4.683 2.769 1.849 -N7X N1 N NR6 0 -1.557 1.050 0.646 -N7X N3 N NRD6 0 -1.796 3.084 -0.569 -N7X N4 N NH2 0 -3.556 4.500 -0.193 -N7X O12 O O2 0 -4.801 -2.779 -0.485 -N7X O2 O O 0 -0.047 1.695 -0.957 -N7X "O2'" O O2 0 -2.132 -1.972 -0.086 -N7X "O3'" O OH1 0 0.063 -3.097 1.164 -N7X "O4'" O O2 0 0.544 0.045 1.151 -N7X "O5'" O O2 0 3.209 0.407 0.284 -N7X OP2 O OP -1 5.012 2.061 0.256 -N7X P P P 0 4.602 0.789 -0.429 -N7X S S S1 0 5.872 -0.678 -0.316 -N7X OP3 O OP -1 4.142 1.125 -1.827 -N7X H1 H H 0 -2.823 -1.990 -1.954 -N7X H2 H H 0 -1.812 -3.174 -1.642 -N7X H3 H H 0 -3.435 -4.193 -0.268 -N7X H4 H H 0 -3.973 -4.044 -1.760 -N7X H5 H H 0 -1.195 -0.611 1.773 -N7X H6 H H 0 -6.638 -2.977 0.188 -N7X H7 H H 0 -5.689 -4.193 0.555 -N7X H8 H H 0 -6.247 -4.040 -0.922 -N7X H9 H H 0 -0.795 -0.847 -1.055 -N7X H10 H H 0 0.674 -2.549 -0.654 -N7X H11 H H 0 1.831 -1.451 1.442 -N7X H12 H H 0 1.881 -0.196 -1.107 -N7X H13 H H 0 2.894 -1.353 -0.648 -N7X H14 H H 0 -3.021 0.723 1.980 -N7X H15 H H 0 -4.869 2.062 2.488 -N7X H16 H H 0 -5.423 2.840 1.225 -N7X H17 H H 0 -4.581 3.610 2.323 -N7X H18 H H 0 -3.738 5.079 0.440 -N7X H19 H H 0 -3.779 4.670 -1.025 -N7X "HO3'" H H 0 0.743 -3.599 1.241 +N7X C C CH2 0 -2.555 -2.648 -1.281 +N7X C1 C CH2 0 -3.706 -3.546 -0.956 +N7X "C1'" C CH1 0 -0.828 -0.218 0.947 +N7X C12 C CH3 0 -5.933 -3.559 -0.139 +N7X C2 C CR6 0 -1.090 1.947 -0.331 +N7X "C2'" C CH1 0 -0.899 -1.264 -0.166 +N7X "C3'" C CH1 0 0.329 -2.116 0.169 +N7X C4 C CR6 0 -2.924 3.352 0.109 +N7X "C4'" C CH1 0 1.340 -1.076 0.679 +N7X C5 C CR6 0 -3.419 2.460 1.097 +N7X "C5'" C CH2 0 2.351 -0.590 -0.331 +N7X C6 C CR16 0 -2.712 1.339 1.324 +N7X C7 C CH3 0 -4.683 2.769 1.849 +N7X N1 N NR6 0 -1.557 1.050 0.646 +N7X N3 N NRD6 0 -1.796 3.084 -0.569 +N7X N4 N NH2 0 -3.556 4.500 -0.193 +N7X O12 O O2 0 -4.801 -2.779 -0.485 +N7X O2 O O 0 -0.047 1.695 -0.957 +N7X "O2'" O O2 0 -2.132 -1.972 -0.086 +N7X "O3'" O OH1 0 0.063 -3.097 1.164 +N7X "O4'" O O2 0 0.544 0.045 1.151 +N7X "O5'" O O2 0 3.209 0.407 0.284 +N7X OP2 O OP -1 5.012 2.061 0.256 +N7X P P P 0 4.602 0.789 -0.429 +N7X S S S1 0 5.872 -0.678 -0.316 +N7X OP3 O OP -1 4.142 1.125 -1.827 +N7X H1 H H 0 -2.823 -1.990 -1.954 +N7X H2 H H 0 -1.812 -3.174 -1.642 +N7X H3 H H 0 -3.435 -4.193 -0.268 +N7X H4 H H 0 -3.973 -4.044 -1.760 +N7X H5 H H 0 -1.195 -0.611 1.773 +N7X H6 H H 0 -6.638 -2.977 0.188 +N7X H7 H H 0 -5.689 -4.193 0.555 +N7X H8 H H 0 -6.247 -4.040 -0.922 +N7X H9 H H 0 -0.795 -0.847 -1.055 +N7X H10 H H 0 0.674 -2.549 -0.654 +N7X H11 H H 0 1.831 -1.451 1.442 +N7X H12 H H 0 1.881 -0.196 -1.107 +N7X H13 H H 0 2.894 -1.353 -0.648 +N7X H14 H H 0 -3.021 0.723 1.980 +N7X H15 H H 0 -4.869 2.062 2.488 +N7X H16 H H 0 -5.423 2.840 1.225 +N7X H17 H H 0 -4.581 3.610 2.323 +N7X H18 H H 0 -3.738 5.079 0.440 +N7X H19 H H 0 -3.779 4.670 -1.025 +N7X "HO3'" H H 0 0.743 -3.599 1.241 loop_ _chem_comp_bond.comp_id @@ -76,52 +76,52 @@ _chem_comp_bond.value_dist_nucleus _chem_comp_bond.value_dist_nucleus_esd _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd -N7X "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 -N7X "C2'" "C3'" SINGLE n 1.530 0.0134 1.530 0.0134 -N7X "C3'" "C4'" SINGLE n 1.535 0.0100 1.535 0.0100 -N7X P S DOUBLE n 1.949 0.0200 1.949 0.0200 -N7X "C2'" "O2'" SINGLE n 1.423 0.0100 1.423 0.0100 -N7X "C1'" "C2'" SINGLE n 1.531 0.0100 1.531 0.0100 -N7X OP2 P SINGLE n 1.509 0.0200 1.509 0.0200 -N7X C "O2'" SINGLE n 1.434 0.0200 1.434 0.0200 -N7X "O5'" P SINGLE n 1.614 0.0178 1.614 0.0178 -N7X "C5'" "O5'" SINGLE n 1.450 0.0166 1.450 0.0166 -N7X C C1 SINGLE n 1.495 0.0146 1.495 0.0146 -N7X "C4'" "C5'" SINGLE n 1.509 0.0100 1.509 0.0100 -N7X C1 O12 SINGLE n 1.414 0.0200 1.414 0.0200 -N7X "C4'" "O4'" SINGLE n 1.451 0.0111 1.451 0.0111 -N7X C4 N4 SINGLE n 1.343 0.0151 1.343 0.0151 -N7X C4 N3 DOUBLE y 1.341 0.0100 1.341 0.0100 -N7X C2 N3 SINGLE y 1.353 0.0117 1.353 0.0117 -N7X C4 C5 SINGLE y 1.416 0.0131 1.416 0.0131 -N7X C2 O2 DOUBLE n 1.241 0.0100 1.241 0.0100 -N7X C2 N1 SINGLE y 1.395 0.0100 1.395 0.0100 -N7X C5 C7 SINGLE n 1.501 0.0100 1.501 0.0100 -N7X C5 C6 DOUBLE y 1.342 0.0102 1.342 0.0102 -N7X C6 N1 SINGLE y 1.364 0.0100 1.364 0.0100 -N7X "C1'" N1 SINGLE n 1.485 0.0100 1.485 0.0100 -N7X "C1'" "O4'" SINGLE n 1.411 0.0100 1.411 0.0100 -N7X C12 O12 SINGLE n 1.415 0.0200 1.415 0.0200 -N7X P OP3 SINGLE n 1.509 0.0200 1.509 0.0200 -N7X C H1 SINGLE n 1.089 0.0100 0.979 0.0200 -N7X C H2 SINGLE n 1.089 0.0100 0.979 0.0200 -N7X C1 H3 SINGLE n 1.089 0.0100 0.982 0.0175 -N7X C1 H4 SINGLE n 1.089 0.0100 0.982 0.0175 -N7X "C1'" H5 SINGLE n 1.089 0.0100 0.985 0.0100 -N7X C12 H6 SINGLE n 1.089 0.0100 0.971 0.0146 -N7X C12 H7 SINGLE n 1.089 0.0100 0.971 0.0146 -N7X C12 H8 SINGLE n 1.089 0.0100 0.971 0.0146 -N7X "C2'" H9 SINGLE n 1.089 0.0100 0.988 0.0200 -N7X "C3'" H10 SINGLE n 1.089 0.0100 0.992 0.0200 -N7X "C4'" H11 SINGLE n 1.089 0.0100 0.981 0.0200 -N7X "C5'" H12 SINGLE n 1.089 0.0100 0.989 0.0200 -N7X "C5'" H13 SINGLE n 1.089 0.0100 0.989 0.0200 -N7X C6 H14 SINGLE n 1.082 0.0130 0.951 0.0200 -N7X C7 H15 SINGLE n 1.089 0.0100 0.971 0.0135 -N7X C7 H16 SINGLE n 1.089 0.0100 0.971 0.0135 -N7X C7 H17 SINGLE n 1.089 0.0100 0.971 0.0135 -N7X N4 H18 SINGLE n 1.016 0.0100 0.877 0.0200 -N7X N4 H19 SINGLE n 1.016 0.0100 0.877 0.0200 +N7X "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +N7X "C2'" "C3'" SINGLE n 1.530 0.0134 1.530 0.0134 +N7X "C3'" "C4'" SINGLE n 1.535 0.0100 1.535 0.0100 +N7X P S DOUBLE n 1.949 0.0200 1.949 0.0200 +N7X "C2'" "O2'" SINGLE n 1.423 0.0100 1.423 0.0100 +N7X "C1'" "C2'" SINGLE n 1.531 0.0100 1.531 0.0100 +N7X OP2 P SINGLE n 1.509 0.0200 1.509 0.0200 +N7X C "O2'" SINGLE n 1.434 0.0200 1.434 0.0200 +N7X "O5'" P SINGLE n 1.614 0.0178 1.614 0.0178 +N7X "C5'" "O5'" SINGLE n 1.450 0.0166 1.450 0.0166 +N7X C C1 SINGLE n 1.495 0.0146 1.495 0.0146 +N7X "C4'" "C5'" SINGLE n 1.509 0.0100 1.509 0.0100 +N7X C1 O12 SINGLE n 1.414 0.0200 1.414 0.0200 +N7X "C4'" "O4'" SINGLE n 1.451 0.0111 1.451 0.0111 +N7X C4 N4 SINGLE n 1.343 0.0151 1.343 0.0151 +N7X C4 N3 DOUBLE y 1.341 0.0100 1.341 0.0100 +N7X C2 N3 SINGLE y 1.353 0.0117 1.353 0.0117 +N7X C4 C5 SINGLE y 1.416 0.0131 1.416 0.0131 +N7X C2 O2 DOUBLE n 1.241 0.0100 1.241 0.0100 +N7X C2 N1 SINGLE y 1.395 0.0100 1.395 0.0100 +N7X C5 C7 SINGLE n 1.501 0.0100 1.501 0.0100 +N7X C5 C6 DOUBLE y 1.342 0.0102 1.342 0.0102 +N7X C6 N1 SINGLE y 1.364 0.0100 1.364 0.0100 +N7X "C1'" N1 SINGLE n 1.485 0.0100 1.485 0.0100 +N7X "C1'" "O4'" SINGLE n 1.411 0.0100 1.411 0.0100 +N7X C12 O12 SINGLE n 1.415 0.0200 1.415 0.0200 +N7X P OP3 SINGLE n 1.509 0.0200 1.509 0.0200 +N7X C H1 SINGLE n 1.089 0.0100 0.979 0.0200 +N7X C H2 SINGLE n 1.089 0.0100 0.979 0.0200 +N7X C1 H3 SINGLE n 1.089 0.0100 0.982 0.0175 +N7X C1 H4 SINGLE n 1.089 0.0100 0.982 0.0175 +N7X "C1'" H5 SINGLE n 1.089 0.0100 0.985 0.0100 +N7X C12 H6 SINGLE n 1.089 0.0100 0.971 0.0146 +N7X C12 H7 SINGLE n 1.089 0.0100 0.971 0.0146 +N7X C12 H8 SINGLE n 1.089 0.0100 0.971 0.0146 +N7X "C2'" H9 SINGLE n 1.089 0.0100 0.988 0.0200 +N7X "C3'" H10 SINGLE n 1.089 0.0100 0.992 0.0200 +N7X "C4'" H11 SINGLE n 1.089 0.0100 0.981 0.0200 +N7X "C5'" H12 SINGLE n 1.089 0.0100 0.989 0.0200 +N7X "C5'" H13 SINGLE n 1.089 0.0100 0.989 0.0200 +N7X C6 H14 SINGLE n 1.082 0.0130 0.951 0.0200 +N7X C7 H15 SINGLE n 1.089 0.0100 0.971 0.0135 +N7X C7 H16 SINGLE n 1.089 0.0100 0.971 0.0135 +N7X C7 H17 SINGLE n 1.089 0.0100 0.971 0.0135 +N7X N4 H18 SINGLE n 1.016 0.0100 0.877 0.0200 +N7X N4 H19 SINGLE n 1.016 0.0100 0.877 0.0200 N7X "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 loop_ @@ -131,90 +131,90 @@ _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd -N7X "O2'" C C1 109.293 1.78 -N7X "O2'" C H1 109.660 1.50 -N7X "O2'" C H2 109.660 1.50 -N7X C1 C H1 110.041 1.50 -N7X C1 C H2 110.041 1.50 -N7X H1 C H2 108.356 1.50 -N7X C C1 O12 109.863 1.99 -N7X C C1 H3 109.614 1.50 -N7X C C1 H4 109.614 1.50 -N7X O12 C1 H3 109.622 1.50 -N7X O12 C1 H4 109.622 1.50 -N7X H3 C1 H4 108.274 1.50 -N7X "C2'" "C1'" N1 113.620 1.99 -N7X "C2'" "C1'" "O4'" 106.391 1.51 -N7X "C2'" "C1'" H5 109.527 1.54 -N7X N1 "C1'" "O4'" 108.667 1.50 -N7X N1 "C1'" H5 109.166 1.50 -N7X "O4'" "C1'" H5 109.327 1.50 -N7X O12 C12 H6 109.470 1.50 -N7X O12 C12 H7 109.470 1.50 -N7X O12 C12 H8 109.470 1.50 -N7X H6 C12 H7 109.532 1.53 -N7X H6 C12 H8 109.532 1.53 -N7X H7 C12 H8 109.532 1.53 -N7X N3 C2 O2 122.606 1.50 -N7X N3 C2 N1 118.440 1.50 -N7X O2 C2 N1 118.953 1.50 -N7X "C3'" "C2'" "O2'" 112.623 3.00 -N7X "C3'" "C2'" "C1'" 101.207 1.50 -N7X "C3'" "C2'" H9 110.255 2.04 -N7X "O2'" "C2'" "C1'" 110.738 2.44 -N7X "O2'" "C2'" H9 110.257 1.68 -N7X "C1'" "C2'" H9 110.561 1.96 -N7X "O3'" "C3'" "C2'" 112.463 2.73 -N7X "O3'" "C3'" "C4'" 111.281 2.46 -N7X "O3'" "C3'" H10 110.380 1.67 -N7X "C2'" "C3'" "C4'" 102.352 1.50 -N7X "C2'" "C3'" H10 110.255 2.04 -N7X "C4'" "C3'" H10 110.452 2.54 -N7X N4 C4 N3 117.013 1.55 -N7X N4 C4 C5 121.437 1.50 -N7X N3 C4 C5 121.550 1.50 -N7X "C3'" "C4'" "C5'" 116.008 1.52 -N7X "C3'" "C4'" "O4'" 104.439 1.50 -N7X "C3'" "C4'" H11 109.363 1.86 -N7X "C5'" "C4'" "O4'" 109.615 1.50 -N7X "C5'" "C4'" H11 108.268 1.50 -N7X "O4'" "C4'" H11 108.698 1.50 -N7X C4 C5 C7 120.410 1.50 -N7X C4 C5 C6 117.857 1.50 -N7X C7 C5 C6 121.734 1.50 -N7X "O5'" "C5'" "C4'" 109.510 1.50 -N7X "O5'" "C5'" H12 109.821 1.50 -N7X "O5'" "C5'" H13 109.821 1.50 -N7X "C4'" "C5'" H12 109.624 1.50 -N7X "C4'" "C5'" H13 109.624 1.50 -N7X H12 "C5'" H13 108.472 1.50 -N7X C5 C6 N1 121.998 1.50 -N7X C5 C6 H14 119.342 1.50 -N7X N1 C6 H14 118.660 1.56 -N7X C5 C7 H15 109.580 1.50 -N7X C5 C7 H16 109.580 1.50 -N7X C5 C7 H17 109.580 1.50 -N7X H15 C7 H16 109.348 1.50 -N7X H15 C7 H17 109.348 1.50 -N7X H16 C7 H17 109.348 1.50 -N7X C2 N1 C6 120.242 1.50 -N7X C2 N1 "C1'" 118.572 2.26 -N7X C6 N1 "C1'" 121.186 1.50 -N7X C4 N3 C2 119.913 1.50 -N7X C4 N4 H18 119.860 1.50 -N7X C4 N4 H19 119.860 1.50 -N7X H18 N4 H19 120.280 1.85 -N7X C1 O12 C12 112.505 3.00 -N7X "C2'" "O2'" C 114.719 2.29 +N7X "O2'" C C1 109.293 1.78 +N7X "O2'" C H1 109.660 1.50 +N7X "O2'" C H2 109.660 1.50 +N7X C1 C H1 110.041 1.50 +N7X C1 C H2 110.041 1.50 +N7X H1 C H2 108.356 1.50 +N7X C C1 O12 109.863 1.99 +N7X C C1 H3 109.614 1.50 +N7X C C1 H4 109.614 1.50 +N7X O12 C1 H3 109.622 1.50 +N7X O12 C1 H4 109.622 1.50 +N7X H3 C1 H4 108.274 1.50 +N7X "C2'" "C1'" N1 113.620 1.99 +N7X "C2'" "C1'" "O4'" 106.391 1.51 +N7X "C2'" "C1'" H5 109.527 1.54 +N7X N1 "C1'" "O4'" 108.667 1.50 +N7X N1 "C1'" H5 109.166 1.50 +N7X "O4'" "C1'" H5 109.327 1.50 +N7X O12 C12 H6 109.470 1.50 +N7X O12 C12 H7 109.470 1.50 +N7X O12 C12 H8 109.470 1.50 +N7X H6 C12 H7 109.532 1.53 +N7X H6 C12 H8 109.532 1.53 +N7X H7 C12 H8 109.532 1.53 +N7X N3 C2 O2 122.606 1.50 +N7X N3 C2 N1 118.440 1.50 +N7X O2 C2 N1 118.953 1.50 +N7X "C3'" "C2'" "O2'" 112.623 3.00 +N7X "C3'" "C2'" "C1'" 101.207 1.50 +N7X "C3'" "C2'" H9 110.255 2.04 +N7X "O2'" "C2'" "C1'" 110.738 2.44 +N7X "O2'" "C2'" H9 110.257 1.68 +N7X "C1'" "C2'" H9 110.561 1.96 +N7X "O3'" "C3'" "C2'" 112.463 2.73 +N7X "O3'" "C3'" "C4'" 111.281 2.46 +N7X "O3'" "C3'" H10 110.380 1.67 +N7X "C2'" "C3'" "C4'" 102.352 1.50 +N7X "C2'" "C3'" H10 110.255 2.04 +N7X "C4'" "C3'" H10 110.452 2.54 +N7X N4 C4 N3 117.013 1.55 +N7X N4 C4 C5 121.437 1.50 +N7X N3 C4 C5 121.550 1.50 +N7X "C3'" "C4'" "C5'" 116.008 1.52 +N7X "C3'" "C4'" "O4'" 104.439 1.50 +N7X "C3'" "C4'" H11 109.363 1.86 +N7X "C5'" "C4'" "O4'" 109.615 1.50 +N7X "C5'" "C4'" H11 108.268 1.50 +N7X "O4'" "C4'" H11 108.698 1.50 +N7X C4 C5 C7 120.410 1.50 +N7X C4 C5 C6 117.857 1.50 +N7X C7 C5 C6 121.734 1.50 +N7X "O5'" "C5'" "C4'" 109.510 1.50 +N7X "O5'" "C5'" H12 109.821 1.50 +N7X "O5'" "C5'" H13 109.821 1.50 +N7X "C4'" "C5'" H12 109.624 1.50 +N7X "C4'" "C5'" H13 109.624 1.50 +N7X H12 "C5'" H13 108.472 1.50 +N7X C5 C6 N1 121.998 1.50 +N7X C5 C6 H14 119.342 1.50 +N7X N1 C6 H14 118.660 1.56 +N7X C5 C7 H15 109.580 1.50 +N7X C5 C7 H16 109.580 1.50 +N7X C5 C7 H17 109.580 1.50 +N7X H15 C7 H16 109.348 1.50 +N7X H15 C7 H17 109.348 1.50 +N7X H16 C7 H17 109.348 1.50 +N7X C2 N1 C6 120.242 1.50 +N7X C2 N1 "C1'" 118.572 2.26 +N7X C6 N1 "C1'" 121.186 1.50 +N7X C4 N3 C2 119.913 1.50 +N7X C4 N4 H18 119.860 1.50 +N7X C4 N4 H19 119.860 1.50 +N7X H18 N4 H19 120.280 1.85 +N7X C1 O12 C12 112.505 3.00 +N7X "C2'" "O2'" C 114.719 2.29 N7X "C3'" "O3'" "HO3'" 108.744 3.00 -N7X "C4'" "O4'" "C1'" 109.578 1.50 -N7X P "O5'" "C5'" 118.783 1.50 -N7X S P OP2 116.650 1.50 -N7X S P "O5'" 113.924 3.00 -N7X S P OP3 116.650 1.50 -N7X OP2 P "O5'" 106.518 3.00 -N7X OP2 P OP3 113.206 2.54 -N7X "O5'" P OP3 106.518 3.00 +N7X "C4'" "O4'" "C1'" 109.578 1.50 +N7X P "O5'" "C5'" 118.783 1.50 +N7X S P OP2 116.650 1.50 +N7X S P "O5'" 113.924 3.00 +N7X S P OP3 116.650 1.50 +N7X OP2 P "O5'" 106.518 3.00 +N7X OP2 P OP3 113.206 2.54 +N7X "O5'" P OP3 106.518 3.00 loop_ _chem_comp_tor.comp_id @@ -226,35 +226,35 @@ _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period -N7X C2e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 -N7X C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 -N7X C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 -N7X C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 -N7X C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 -N7X C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 -N7X C3e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 -N7X C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 -N7X C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 -N7X C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 -N7X C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 -N7X C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 -N7X beta P "O5'" "C5'" "C4'" 180.000 10.00 3 -N7X epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 -N7X gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 -N7X sp3_sp3_46 "O2'" C C1 O12 180.000 10.0 3 -N7X sp3_sp3_37 C1 C "O2'" "C2'" 180.000 10.0 3 -N7X const_13 C5 C6 N1 C2 0.000 10.0 2 -N7X sp3_sp3_64 C C1 O12 C12 180.000 10.0 3 -N7X sp3_sp3_40 "C5'" "O5'" P S 180.000 10.0 3 -N7X sp3_sp3_70 H6 C12 O12 C1 180.000 10.0 3 -N7X const_19 O2 C2 N1 C6 180.000 10.0 2 -N7X const_sp2_sp2_2 O2 C2 N3 C4 180.000 5.0 2 -N7X sp3_sp3_34 "C3'" "C2'" "O2'" C 180.000 10.0 3 -N7X const_sp2_sp2_4 N4 C4 N3 C2 180.000 5.0 2 -N7X sp2_sp2_3 N3 C4 N4 H18 0.000 5.0 2 -N7X const_sp2_sp2_8 N4 C4 C5 C7 0.000 5.0 2 -N7X const_11 C7 C5 C6 N1 180.000 10.0 2 -N7X sp2_sp3_1 C4 C5 C7 H15 150.000 10.0 6 +N7X C2e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 +N7X C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 +N7X C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 +N7X C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 +N7X C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 +N7X C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 +N7X C3e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 +N7X C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 +N7X C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 +N7X C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 +N7X C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 +N7X C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 +N7X beta P "O5'" "C5'" "C4'" 180.000 10.00 3 +N7X epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 +N7X gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 +N7X sp3_sp3_46 "O2'" C C1 O12 180.000 10.0 3 +N7X sp3_sp3_37 C1 C "O2'" "C2'" 180.000 10.0 3 +N7X const_13 C5 C6 N1 C2 0.000 10.0 2 +N7X sp3_sp3_64 C C1 O12 C12 180.000 10.0 3 +N7X sp3_sp3_40 "C5'" "O5'" P S 180.000 10.0 3 +N7X sp3_sp3_70 H6 C12 O12 C1 180.000 10.0 3 +N7X const_19 O2 C2 N1 C6 180.000 10.0 2 +N7X const_sp2_sp2_2 O2 C2 N3 C4 180.000 5.0 2 +N7X sp3_sp3_34 "C3'" "C2'" "O2'" C 180.000 10.0 3 +N7X const_sp2_sp2_4 N4 C4 N3 C2 180.000 5.0 2 +N7X sp2_sp2_3 N3 C4 N4 H18 0.000 5.0 2 +N7X const_sp2_sp2_8 N4 C4 C5 C7 0.000 5.0 2 +N7X const_11 C7 C5 C6 N1 180.000 10.0 2 +N7X sp2_sp3_1 C4 C5 C7 H15 150.000 10.0 6 loop_ _chem_comp_chir.comp_id @@ -264,11 +264,11 @@ _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign -N7X chir_1 "C1'" "O4'" N1 "C2'" negative +N7X chir_1 "C1'" "O4'" N1 "C2'" negative N7X chir_2 "C2'" "O2'" "C1'" "C3'" negative N7X chir_3 "C3'" "O3'" "C2'" "C4'" negative N7X chir_4 "C4'" "O4'" "C3'" "C5'" negative -N7X chir_5 P S "O5'" OP2 both +N7X chir_5 P S "O5'" OP2 both loop_ _chem_comp_plane_atom.comp_id @@ -276,20 +276,20 @@ _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd N7X plan-1 "C1'" 0.020 -N7X plan-1 C2 0.020 -N7X plan-1 C4 0.020 -N7X plan-1 C5 0.020 -N7X plan-1 C6 0.020 -N7X plan-1 C7 0.020 -N7X plan-1 H14 0.020 -N7X plan-1 N1 0.020 -N7X plan-1 N3 0.020 -N7X plan-1 N4 0.020 -N7X plan-1 O2 0.020 -N7X plan-2 C4 0.020 -N7X plan-2 H18 0.020 -N7X plan-2 H19 0.020 -N7X plan-2 N4 0.020 +N7X plan-1 C2 0.020 +N7X plan-1 C4 0.020 +N7X plan-1 C5 0.020 +N7X plan-1 C6 0.020 +N7X plan-1 C7 0.020 +N7X plan-1 H14 0.020 +N7X plan-1 N1 0.020 +N7X plan-1 N3 0.020 +N7X plan-1 N4 0.020 +N7X plan-1 O2 0.020 +N7X plan-2 C4 0.020 +N7X plan-2 H18 0.020 +N7X plan-2 H19 0.020 +N7X plan-2 N4 0.020 loop_ _pdbx_chem_comp_descriptor.comp_id @@ -297,20 +297,28 @@ _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor -N7X SMILES ACDLabs 12.01 C(COC)OC1C(OC(C1O)COP(O)(O)=S)N2C(N=C(C(C)=C2)N)=O -N7X InChI InChI 1.03 InChI=1S/C13H22N3O8PS/c1-7-5-16(13(18)15-11(7)14)12-10(22-4-3-21-2)9(17)8(24-12)6-23-25(19,20)26/h5,8-10,12,17H,3-4,6H2,1-2H3,(H2,14,15,18)(H2,19,20,26)/t8-,9-,10-,12-/m1/s1 -N7X InChIKey InChI 1.03 UINDLFLAAYRFRN-DNRKLUKYSA-N -N7X SMILES_CANONICAL CACTVS 3.385 COCCO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=S)O[C@H]1N2C=C(C)C(=NC2=O)N -N7X SMILES CACTVS 3.385 COCCO[CH]1[CH](O)[CH](CO[P](O)(O)=S)O[CH]1N2C=C(C)C(=NC2=O)N +N7X SMILES ACDLabs 12.01 C(COC)OC1C(OC(C1O)COP(O)(O)=S)N2C(N=C(C(C)=C2)N)=O +N7X InChI InChI 1.03 InChI=1S/C13H22N3O8PS/c1-7-5-16(13(18)15-11(7)14)12-10(22-4-3-21-2)9(17)8(24-12)6-23-25(19,20)26/h5,8-10,12,17H,3-4,6H2,1-2H3,(H2,14,15,18)(H2,19,20,26)/t8-,9-,10-,12-/m1/s1 +N7X InChIKey InChI 1.03 UINDLFLAAYRFRN-DNRKLUKYSA-N +N7X SMILES_CANONICAL CACTVS 3.385 COCCO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=S)O[C@H]1N2C=C(C)C(=NC2=O)N +N7X SMILES CACTVS 3.385 COCCO[CH]1[CH](O)[CH](CO[P](O)(O)=S)O[CH]1N2C=C(C)C(=NC2=O)N N7X SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CC1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=S)(O)O)O)OCCOC -N7X SMILES "OpenEye OEToolkits" 2.0.7 CC1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=S)(O)O)O)OCCOC +N7X SMILES "OpenEye OEToolkits" 2.0.7 CC1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=S)(O)O)O)OCCOC loop_ _pdbx_chem_comp_description_generator.comp_id _pdbx_chem_comp_description_generator.program_name _pdbx_chem_comp_description_generator.program_version _pdbx_chem_comp_description_generator.descriptor -N7X acedrg 243 "dictionary generator" -N7X acedrg_database 11 "data source" -N7X rdkit 2017.03.2 "Chemoinformatics tool" -N7X refmac5 5.8.0238 "optimization tool" +N7X acedrg 243 "dictionary generator" +N7X acedrg_database 11 "data source" +N7X rdkit 2017.03.2 "Chemoinformatics tool" +N7X refmac5 5.8.0238 "optimization tool" + +loop_ +_chem_comp_alias.comp_id +_chem_comp_alias.group +_chem_comp_alias.atom_id +_chem_comp_alias.atom_id_standard +N7X S-NA OP2 OP1 +N7X S-NA S S2P diff --git a/o/OKN.cif b/o/OKN.cif index 25d564fef..7643699a2 100644 --- a/o/OKN.cif +++ b/o/OKN.cif @@ -7,7 +7,7 @@ _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level -OKN OKN "5'-methyl-2'-deoxycytidine-5'-phosphorothioate" NON-POLYMER 36 21 . +OKN OKN "5'-methyl-2'-deoxycytidine-5'-phosphorothioate" NON-POLYMER 35 21 . data_comp_OKN loop_ @@ -19,42 +19,81 @@ _chem_comp_atom.charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z -OKN C2 C CR6 0 -8.147 -29.933 39.378 -OKN C4 C CR6 0 -10.428 -29.896 38.806 -OKN "C1'" C CH1 0 -6.403 -29.474 37.622 -OKN "C2'" C CH2 0 -5.933 -30.510 36.614 -OKN "C3'" C CH1 0 -4.862 -29.756 35.841 -OKN "C4'" C CH1 0 -5.386 -28.322 35.847 -OKN C5 C CR6 0 -10.125 -29.584 37.453 -OKN "C5'" C CH2 0 -6.126 -27.910 34.598 -OKN C6 C CR16 0 -8.826 -29.458 37.127 -OKN CM5 C CH3 0 -11.220 -29.402 36.440 -OKN N1 N NR6 0 -7.823 -29.623 38.046 -OKN N3 N NRD6 0 -9.457 -30.061 39.720 -OKN N4 N NH2 0 -11.695 -30.041 39.234 -OKN O2 O O 0 -7.244 -30.084 40.218 -OKN "O3'" O OH1 0 -3.609 -29.842 36.513 -OKN "O4'" O O2 0 -6.268 -28.217 36.988 -OKN "O5'" O O2 0 -5.194 -27.826 33.489 -OKN OP1 O O 0 -6.732 -28.682 31.710 -OKN P P P 0 -5.751 -27.595 32.006 -OKN S01 S SH1 0 -6.735 -25.752 32.060 -OKN OP3 O OP -1 -4.581 -27.527 31.084 -OKN H1 H H 0 -5.807 -29.497 38.413 -OKN H2 H H 0 -5.560 -31.299 37.064 -OKN H3 H H 0 -6.662 -30.796 36.023 -OKN H4 H H 0 -4.787 -30.099 34.918 -OKN H5 H H 0 -4.629 -27.701 35.976 -OKN H6 H H 0 -6.556 -27.031 34.743 -OKN H7 H H 0 -6.831 -28.573 34.397 -OKN H8 H H 0 -8.591 -29.252 36.229 -OKN H9 H H 0 -11.859 -30.129 36.518 -OKN H10 H H 0 -10.843 -29.401 35.545 -OKN H11 H H 0 -11.672 -28.558 36.599 -OKN H12 H H 0 -11.948 -30.796 39.600 -OKN H13 H H 0 -12.264 -29.380 39.145 -OKN H14 H H 0 -3.319 -30.638 36.457 -OKN H15 H HSH1 0 -6.294 -25.033 31.191 +OKN C2 C CR6 0 -8.173 -29.942 39.386 +OKN C4 C CR6 0 -10.457 -30.002 38.761 +OKN "C1'" C CH1 0 -6.417 -29.405 37.660 +OKN "C2'" C CH2 0 -5.873 -30.455 36.685 +OKN "C3'" C CH1 0 -4.818 -29.663 35.926 +OKN "C4'" C CH1 0 -5.444 -28.268 35.850 +OKN C5 C CR6 0 -10.144 -29.675 37.417 +OKN "C5'" C CH2 0 -6.202 -28.001 34.575 +OKN C6 C CR16 0 -8.845 -29.495 37.114 +OKN CM5 C CH3 0 -11.224 -29.539 36.374 +OKN N1 N NR6 0 -7.839 -29.616 38.059 +OKN N3 N NRD6 0 -9.483 -30.127 39.700 +OKN N4 N NH2 0 -11.721 -30.205 39.179 +OKN O2 O O 0 -7.289 -30.058 40.248 +OKN "O3'" O OH1 0 -3.595 -29.636 36.657 +OKN "O4'" O O2 0 -6.327 -28.164 36.990 +OKN "O5'" O O2 0 -5.274 -27.658 33.530 +OKN OP1 O OP -1 -6.718 -28.248 31.671 +OKN P P P 0 -5.835 -27.125 32.119 +OKN S01 S S1 0 -6.808 -25.445 32.249 +OKN OP3 O OP -1 -4.636 -27.076 31.229 +OKN H1 H H 0 -5.838 -29.374 38.465 +OKN H2 H H 0 -5.481 -31.205 37.159 +OKN H3 H H 0 -6.566 -30.782 36.090 +OKN H4 H H 0 -4.678 -30.038 35.019 +OKN H5 H H 0 -4.730 -27.588 35.936 +OKN H6 H H 0 -6.840 -27.256 34.719 +OKN H7 H H 0 -6.716 -28.809 34.319 +OKN H8 H H 0 -8.606 -29.276 36.220 +OKN H9 H H 0 -11.849 -30.279 36.455 +OKN H10 H H 0 -10.828 -29.549 35.486 +OKN H11 H H 0 -11.699 -28.701 36.505 +OKN H12 H H 0 -12.396 -29.805 38.793 +OKN H13 H H 0 -11.874 -30.737 39.859 +OKN H14 H H 0 -3.264 -30.406 36.656 + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +OKN C2 C[6a](N[6a]C[6a]C[5])(N[6a]C[6a])(O){1|C<3>,1|C<4>,1|N<3>,1|O<2>,2|H<1>} +OKN C4 C[6a](C[6a]C[6a]C)(N[6a]C[6a])(NHH){1|H<1>,1|N<3>,1|O<1>} +OKN "C1'" C[5](N[6a]C[6a]2)(C[5]C[5]HH)(O[5]C[5])(H){1|C<3>,1|C<4>,1|N<2>,1|O<1>,1|O<2>,3|H<1>} +OKN "C2'" C[5](C[5]N[6a]O[5]H)(C[5]C[5]HO)(H)2{1|C<4>,1|H<1>,2|C<3>} +OKN "C3'" C[5](C[5]C[5]HH)(C[5]O[5]CH)(OH)(H){1|H<1>,1|N<3>} +OKN "C4'" C[5](C[5]C[5]HO)(O[5]C[5])(CHHO)(H){1|N<3>,3|H<1>} +OKN C5 C[6a](C[6a]N[6a]H)(C[6a]N[6a]N)(CH3){1|C<3>,1|C<4>} +OKN "C5'" C(C[5]C[5]O[5]H)(OP)(H)2 +OKN C6 C[6a](N[6a]C[6a]C[5])(C[6a]C[6a]C)(H){1|C<4>,1|H<1>,1|N<2>,1|N<3>,1|O<1>,1|O<2>} +OKN CM5 C(C[6a]C[6a]2)(H)3 +OKN N1 N[6a](C[5]C[5]O[5]H)(C[6a]C[6a]H)(C[6a]N[6a]O){1|C<3>,2|H<1>,3|C<4>} +OKN N3 N[6a](C[6a]C[6a]N)(C[6a]N[6a]O){1|C<3>,2|C<4>} +OKN N4 N(C[6a]C[6a]N[6a])(H)2 +OKN O2 O(C[6a]N[6a]2) +OKN "O3'" O(C[5]C[5]2H)(H) +OKN "O4'" O[5](C[5]N[6a]C[5]H)(C[5]C[5]CH){1|O<2>,2|C<3>,3|H<1>} +OKN "O5'" O(CC[5]HH)(POOS) +OKN OP1 O(POOS) +OKN P P(OC)(O)2(S) +OKN S01 S(PO3) +OKN OP3 O(POOS) +OKN H1 H(C[5]N[6a]C[5]O[5]) +OKN H2 H(C[5]C[5]2H) +OKN H3 H(C[5]C[5]2H) +OKN H4 H(C[5]C[5]2O) +OKN H5 H(C[5]C[5]O[5]C) +OKN H6 H(CC[5]HO) +OKN H7 H(CC[5]HO) +OKN H8 H(C[6a]C[6a]N[6a]) +OKN H9 H(CC[6a]HH) +OKN H10 H(CC[6a]HH) +OKN H11 H(CC[6a]HH) +OKN H12 H(NC[6a]H) +OKN H13 H(NC[6a]H) +OKN H14 H(OC[5]) loop_ _chem_comp_bond.comp_id @@ -66,43 +105,42 @@ _chem_comp_bond.value_dist_nucleus _chem_comp_bond.value_dist_nucleus_esd _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd -OKN OP1 P DOUBLE n 1.493 0.0157 1.493 0.0157 -OKN P S01 SINGLE n 2.091 0.0200 2.091 0.0200 -OKN "O5'" P SINGLE n 1.601 0.0114 1.601 0.0114 -OKN "C5'" "O5'" SINGLE n 1.450 0.0166 1.450 0.0166 -OKN "C4'" "C5'" SINGLE n 1.509 0.0100 1.509 0.0100 -OKN "C3'" "C4'" SINGLE n 1.526 0.0115 1.526 0.0115 -OKN "C3'" "O3'" SINGLE n 1.424 0.0100 1.424 0.0100 -OKN "C2'" "C3'" SINGLE n 1.522 0.0100 1.522 0.0100 +OKN OP1 P SINGLE n 1.497 0.0143 1.497 0.0143 +OKN P S01 DOUBLE n 1.949 0.0200 1.949 0.0200 +OKN "O5'" P SINGLE n 1.613 0.0200 1.613 0.0200 +OKN "C5'" "O5'" SINGLE n 1.438 0.0200 1.438 0.0200 +OKN "C4'" "C5'" SINGLE n 1.507 0.0100 1.507 0.0100 +OKN "C3'" "C4'" SINGLE n 1.530 0.0119 1.530 0.0119 +OKN "C3'" "O3'" SINGLE n 1.425 0.0128 1.425 0.0128 +OKN "C2'" "C3'" SINGLE n 1.523 0.0101 1.523 0.0101 OKN "C4'" "O4'" SINGLE n 1.445 0.0100 1.445 0.0100 -OKN "C1'" "C2'" SINGLE n 1.520 0.0100 1.520 0.0100 -OKN C5 CM5 SINGLE n 1.501 0.0100 1.501 0.0100 -OKN "C1'" "O4'" SINGLE n 1.413 0.0100 1.413 0.0100 -OKN C5 C6 DOUBLE y 1.342 0.0102 1.342 0.0102 -OKN C6 N1 SINGLE y 1.364 0.0100 1.364 0.0100 -OKN "C1'" N1 SINGLE n 1.480 0.0115 1.480 0.0115 -OKN C4 C5 SINGLE y 1.416 0.0131 1.416 0.0131 -OKN C2 N1 SINGLE y 1.395 0.0100 1.395 0.0100 -OKN C4 N4 SINGLE n 1.343 0.0151 1.343 0.0151 -OKN C4 N3 DOUBLE y 1.341 0.0100 1.341 0.0100 -OKN C2 N3 SINGLE y 1.353 0.0117 1.353 0.0117 -OKN C2 O2 DOUBLE n 1.241 0.0100 1.241 0.0100 -OKN P OP3 SINGLE n 1.493 0.0157 1.493 0.0157 -OKN "C1'" H1 SINGLE n 1.089 0.0100 0.991 0.0103 -OKN "C2'" H2 SINGLE n 1.089 0.0100 0.982 0.0200 -OKN "C2'" H3 SINGLE n 1.089 0.0100 0.982 0.0200 -OKN "C3'" H4 SINGLE n 1.089 0.0100 0.988 0.0189 -OKN "C4'" H5 SINGLE n 1.089 0.0100 0.987 0.0170 -OKN "C5'" H6 SINGLE n 1.089 0.0100 0.989 0.0200 -OKN "C5'" H7 SINGLE n 1.089 0.0100 0.989 0.0200 -OKN C6 H8 SINGLE n 1.082 0.0130 0.951 0.0200 -OKN CM5 H9 SINGLE n 1.089 0.0100 0.971 0.0135 -OKN CM5 H10 SINGLE n 1.089 0.0100 0.971 0.0135 -OKN CM5 H11 SINGLE n 1.089 0.0100 0.971 0.0135 -OKN N4 H12 SINGLE n 1.016 0.0100 0.877 0.0200 -OKN N4 H13 SINGLE n 1.016 0.0100 0.877 0.0200 -OKN "O3'" H14 SINGLE n 0.970 0.0120 0.849 0.0200 -OKN S01 H15 SINGLE n 1.338 0.0100 1.211 0.0200 +OKN "C1'" "C2'" SINGLE n 1.532 0.0100 1.532 0.0100 +OKN C5 CM5 SINGLE n 1.506 0.0109 1.506 0.0109 +OKN "C1'" "O4'" SINGLE n 1.412 0.0100 1.412 0.0100 +OKN C5 C6 DOUBLE y 1.343 0.0100 1.343 0.0100 +OKN C6 N1 SINGLE y 1.381 0.0100 1.381 0.0100 +OKN "C1'" N1 SINGLE n 1.478 0.0148 1.478 0.0148 +OKN C4 C5 SINGLE y 1.408 0.0144 1.408 0.0144 +OKN C2 N1 SINGLE y 1.397 0.0100 1.397 0.0100 +OKN C4 N4 SINGLE n 1.344 0.0100 1.344 0.0100 +OKN C4 N3 DOUBLE y 1.351 0.0140 1.351 0.0140 +OKN C2 N3 SINGLE y 1.355 0.0100 1.355 0.0100 +OKN C2 O2 DOUBLE n 1.238 0.0116 1.238 0.0116 +OKN P OP3 SINGLE n 1.497 0.0143 1.497 0.0143 +OKN "C1'" H1 SINGLE n 1.092 0.0100 0.993 0.0100 +OKN "C2'" H2 SINGLE n 1.092 0.0100 0.970 0.0100 +OKN "C2'" H3 SINGLE n 1.092 0.0100 0.970 0.0100 +OKN "C3'" H4 SINGLE n 1.092 0.0100 0.991 0.0181 +OKN "C4'" H5 SINGLE n 1.092 0.0100 0.990 0.0200 +OKN "C5'" H6 SINGLE n 1.092 0.0100 0.991 0.0200 +OKN "C5'" H7 SINGLE n 1.092 0.0100 0.991 0.0200 +OKN C6 H8 SINGLE n 1.085 0.0150 0.951 0.0200 +OKN CM5 H9 SINGLE n 1.092 0.0100 0.972 0.0144 +OKN CM5 H10 SINGLE n 1.092 0.0100 0.972 0.0144 +OKN CM5 H11 SINGLE n 1.092 0.0100 0.972 0.0144 +OKN N4 H12 SINGLE n 1.013 0.0120 0.875 0.0200 +OKN N4 H13 SINGLE n 1.013 0.0120 0.875 0.0200 +OKN "O3'" H14 SINGLE n 0.972 0.0180 0.839 0.0200 loop_ _chem_comp_angle.comp_id @@ -111,71 +149,70 @@ _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd -OKN N1 C2 N3 118.440 1.50 -OKN N1 C2 O2 118.953 1.50 -OKN N3 C2 O2 122.606 1.50 -OKN C5 C4 N4 121.437 1.50 -OKN C5 C4 N3 121.550 1.50 -OKN N4 C4 N3 117.013 1.55 -OKN "C2'" "C1'" "O4'" 106.308 1.50 -OKN "C2'" "C1'" N1 114.268 1.50 -OKN "C2'" "C1'" H1 109.741 1.50 -OKN "O4'" "C1'" N1 107.584 1.50 -OKN "O4'" "C1'" H1 109.550 1.50 -OKN N1 "C1'" H1 109.342 1.50 -OKN "C3'" "C2'" "C1'" 102.834 1.50 -OKN "C3'" "C2'" H2 111.310 1.50 -OKN "C3'" "C2'" H3 111.310 1.50 -OKN "C1'" "C2'" H2 111.187 1.50 -OKN "C1'" "C2'" H3 111.187 1.50 -OKN H2 "C2'" H3 108.952 1.50 -OKN "C4'" "C3'" "O3'" 110.527 2.37 -OKN "C4'" "C3'" "C2'" 102.800 1.50 -OKN "C4'" "C3'" H4 110.775 1.50 -OKN "O3'" "C3'" "C2'" 110.636 2.59 -OKN "O3'" "C3'" H4 110.713 1.50 -OKN "C2'" "C3'" H4 110.862 1.50 -OKN "C5'" "C4'" "C3'" 114.866 1.63 -OKN "C5'" "C4'" "O4'" 109.615 1.50 -OKN "C5'" "C4'" H5 108.268 1.50 -OKN "C3'" "C4'" "O4'" 105.770 1.50 -OKN "C3'" "C4'" H5 109.069 1.50 -OKN "O4'" "C4'" H5 108.698 1.50 -OKN CM5 C5 C6 121.734 1.50 -OKN CM5 C5 C4 120.410 1.50 -OKN C6 C5 C4 117.857 1.50 -OKN "O5'" "C5'" "C4'" 109.510 1.50 -OKN "O5'" "C5'" H6 109.821 1.50 -OKN "O5'" "C5'" H7 109.821 1.50 -OKN "C4'" "C5'" H6 109.624 1.50 -OKN "C4'" "C5'" H7 109.624 1.50 -OKN H6 "C5'" H7 108.472 1.50 -OKN C5 C6 N1 121.998 1.50 -OKN C5 C6 H8 119.342 1.50 -OKN N1 C6 H8 118.660 1.56 -OKN C5 CM5 H9 109.580 1.50 -OKN C5 CM5 H10 109.580 1.50 -OKN C5 CM5 H11 109.580 1.50 -OKN H9 CM5 H10 109.348 1.50 -OKN H9 CM5 H11 109.348 1.50 -OKN H10 CM5 H11 109.348 1.50 -OKN C6 N1 "C1'" 120.512 1.50 -OKN C6 N1 C2 120.242 1.50 -OKN "C1'" N1 C2 119.246 1.50 -OKN C4 N3 C2 119.913 1.50 -OKN C4 N4 H12 119.860 1.50 -OKN C4 N4 H13 119.860 1.50 -OKN H12 N4 H13 120.280 1.85 -OKN "C3'" "O3'" H14 109.026 2.38 -OKN "C4'" "O4'" "C1'" 109.692 1.50 -OKN P "O5'" "C5'" 119.135 1.78 -OKN OP1 P S01 111.281 3.00 -OKN OP1 P "O5'" 108.530 2.45 -OKN OP1 P OP3 116.964 2.85 -OKN S01 P "O5'" 105.685 3.00 -OKN S01 P OP3 111.281 3.00 -OKN "O5'" P OP3 108.530 2.45 -OKN P S01 H15 109.471 3.00 +OKN N1 C2 N3 118.368 1.50 +OKN N1 C2 O2 119.127 2.14 +OKN N3 C2 O2 122.505 1.50 +OKN C5 C4 N4 121.554 1.50 +OKN C5 C4 N3 121.462 1.50 +OKN N4 C4 N3 116.984 1.54 +OKN "C2'" "C1'" "O4'" 106.263 1.50 +OKN "C2'" "C1'" N1 114.169 1.50 +OKN "C2'" "C1'" H1 109.883 1.50 +OKN "O4'" "C1'" N1 107.769 1.50 +OKN "O4'" "C1'" H1 109.467 1.50 +OKN N1 "C1'" H1 109.124 1.71 +OKN "C3'" "C2'" "C1'" 102.658 2.13 +OKN "C3'" "C2'" H2 111.287 1.86 +OKN "C3'" "C2'" H3 111.287 1.86 +OKN "C1'" "C2'" H2 111.181 1.50 +OKN "C1'" "C2'" H3 111.181 1.50 +OKN H2 "C2'" H3 109.095 1.50 +OKN "C4'" "C3'" "O3'" 110.611 3.00 +OKN "C4'" "C3'" "C2'" 102.581 1.50 +OKN "C4'" "C3'" H4 110.734 1.65 +OKN "O3'" "C3'" "C2'" 110.452 3.00 +OKN "O3'" "C3'" H4 110.786 1.88 +OKN "C2'" "C3'" H4 110.938 1.50 +OKN "C5'" "C4'" "C3'" 113.954 2.40 +OKN "C5'" "C4'" "O4'" 110.351 1.93 +OKN "C5'" "C4'" H5 108.351 1.59 +OKN "C3'" "C4'" "O4'" 105.546 1.50 +OKN "C3'" "C4'" H5 109.033 1.50 +OKN "O4'" "C4'" H5 108.778 1.50 +OKN CM5 C5 C6 121.831 1.50 +OKN CM5 C5 C4 120.260 1.50 +OKN C6 C5 C4 117.910 1.50 +OKN "O5'" "C5'" "C4'" 109.482 2.30 +OKN "O5'" "C5'" H6 109.954 1.50 +OKN "O5'" "C5'" H7 109.954 1.50 +OKN "C4'" "C5'" H6 109.589 1.50 +OKN "C4'" "C5'" H7 109.589 1.50 +OKN H6 "C5'" H7 108.471 1.50 +OKN C5 C6 N1 122.038 1.50 +OKN C5 C6 H8 119.290 2.38 +OKN N1 C6 H8 118.672 1.83 +OKN C5 CM5 H9 109.477 1.50 +OKN C5 CM5 H10 109.477 1.50 +OKN C5 CM5 H11 109.477 1.50 +OKN H9 CM5 H10 109.334 1.91 +OKN H9 CM5 H11 109.334 1.91 +OKN H10 CM5 H11 109.334 1.91 +OKN C6 N1 "C1'" 120.996 1.69 +OKN C6 N1 C2 120.373 1.50 +OKN "C1'" N1 C2 118.630 2.04 +OKN C4 N3 C2 119.848 1.50 +OKN C4 N4 H12 119.897 3.00 +OKN C4 N4 H13 119.897 3.00 +OKN H12 N4 H13 120.206 3.00 +OKN "C3'" "O3'" H14 108.690 3.00 +OKN "C4'" "O4'" "C1'" 109.881 1.50 +OKN P "O5'" "C5'" 119.085 2.00 +OKN OP1 P S01 116.458 3.00 +OKN OP1 P "O5'" 106.327 3.00 +OKN OP1 P OP3 112.844 3.00 +OKN S01 P "O5'" 114.928 3.00 +OKN S01 P OP3 116.458 3.00 +OKN "O5'" P OP3 106.327 3.00 loop_ _chem_comp_tor.comp_id @@ -187,31 +224,29 @@ _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period -OKN C2e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 -OKN C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 -OKN C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 -OKN C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 -OKN C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 -OKN C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 -OKN C3e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 -OKN C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 -OKN C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 -OKN C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 -OKN C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 -OKN C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 -OKN alpha "C5'" "O5'" P OP3 -60.000 10.00 3 -OKN beta P "O5'" "C5'" "C4'" 180.000 10.00 3 -OKN gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 -OKN const_sp2_sp2_3 O2 C2 N1 C6 180.000 5.0 2 -OKN const_20 O2 C2 N3 C4 180.000 10.0 2 -OKN sp3_sp3_33 OP1 P S01 H15 -60.000 10.0 3 -OKN const_18 N4 C4 N3 C2 180.000 10.0 2 -OKN sp2_sp2_1 C5 C4 N4 H12 180.000 5.0 2 -OKN const_16 N4 C4 C5 CM5 0.000 10.0 2 -OKN sp3_sp3_49 "C4'" "C3'" "O3'" H14 180.000 10.0 3 -OKN const_11 CM5 C5 C6 N1 180.000 10.0 2 -OKN sp2_sp3_1 C6 C5 CM5 H9 150.000 10.0 6 -OKN const_sp2_sp2_6 C5 C6 N1 "C1'" 180.000 5.0 2 +OKN const_sp2_sp2_1 N3 C2 N1 C6 0.000 0.0 1 +OKN const_sp2_sp2_4 O2 C2 N1 "C1'" 0.000 0.0 1 +OKN const_23 N1 C2 N3 C4 0.000 0.0 1 +OKN sp3_sp3_33 "C5'" "O5'" P OP1 60.000 10.0 3 +OKN const_17 C5 C4 N3 C2 0.000 0.0 1 +OKN sp2_sp2_19 C5 C4 N4 H12 180.000 20 2 +OKN sp2_sp2_22 N3 C4 N4 H13 180.000 20 2 +OKN const_13 N3 C4 C5 C6 0.000 0.0 1 +OKN const_16 N4 C4 C5 CM5 0.000 0.0 1 +OKN sp2_sp3_7 C6 N1 "C1'" "C2'" 150.000 10.0 6 +OKN sp3_sp3_49 "C2'" "C1'" "O4'" "C4'" 180.000 10.0 3 +OKN sp3_sp3_1 "O4'" "C1'" "C2'" "C3'" 60.000 10.0 3 +OKN sp3_sp3_11 "C1'" "C2'" "C3'" "O3'" 60.000 10.0 3 +OKN sp3_sp3_46 "C4'" "C3'" "O3'" H14 180.000 10.0 3 +OKN sp3_sp3_23 "O3'" "C3'" "C4'" "C5'" 60.000 10.0 3 +OKN sp3_sp3_29 "C5'" "C4'" "O4'" "C1'" 180.000 10.0 3 +OKN sp3_sp3_37 "C3'" "C4'" "C5'" "O5'" 180.000 10.0 3 +OKN const_sp2_sp2_9 C4 C5 C6 N1 0.000 0.0 1 +OKN const_12 CM5 C5 C6 H8 0.000 0.0 1 +OKN sp2_sp3_1 C6 C5 CM5 H9 150.000 10.0 6 +OKN sp3_sp3_34 "C4'" "C5'" "O5'" P 180.000 10.0 3 +OKN const_sp2_sp2_5 C5 C6 N1 C2 0.000 0.0 1 +OKN const_sp2_sp2_8 H8 C6 N1 "C1'" 0.000 0.0 1 loop_ _chem_comp_chir.comp_id @@ -221,10 +256,10 @@ _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign -OKN chir_1 "C1'" "O4'" N1 "C2'" negative +OKN chir_1 "C1'" "O4'" N1 "C2'" negative OKN chir_2 "C3'" "O3'" "C4'" "C2'" positive OKN chir_3 "C4'" "O4'" "C3'" "C5'" negative -OKN chir_4 P S01 "O5'" OP3 both +OKN chir_4 P S01 "O5'" OP3 both loop_ _chem_comp_plane_atom.comp_id @@ -232,20 +267,20 @@ _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd OKN plan-1 "C1'" 0.020 -OKN plan-1 C2 0.020 -OKN plan-1 C4 0.020 -OKN plan-1 C5 0.020 -OKN plan-1 C6 0.020 -OKN plan-1 CM5 0.020 -OKN plan-1 H8 0.020 -OKN plan-1 N1 0.020 -OKN plan-1 N3 0.020 -OKN plan-1 N4 0.020 -OKN plan-1 O2 0.020 -OKN plan-2 C4 0.020 -OKN plan-2 H12 0.020 -OKN plan-2 H13 0.020 -OKN plan-2 N4 0.020 +OKN plan-1 C2 0.020 +OKN plan-1 C4 0.020 +OKN plan-1 C5 0.020 +OKN plan-1 C6 0.020 +OKN plan-1 CM5 0.020 +OKN plan-1 H8 0.020 +OKN plan-1 N1 0.020 +OKN plan-1 N3 0.020 +OKN plan-1 N4 0.020 +OKN plan-1 O2 0.020 +OKN plan-2 C4 0.020 +OKN plan-2 H12 0.020 +OKN plan-2 H13 0.020 +OKN plan-2 N4 0.020 loop_ _pdbx_chem_comp_descriptor.comp_id @@ -253,19 +288,27 @@ _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor -OKN InChI InChI 1.03 InChI=1S/C10H16N3O6PS/c1-5-3-13(10(15)12-9(5)11)8-2-6(14)7(19-8)4-18-20(16,17)21/h3,6-8,14H,2,4H2,1H3,(H2,11,12,15)(H2,16,17,21)/t6-,7+,8+/m0/s1 -OKN InChIKey InChI 1.03 UZWQYGFEEXJOHY-XLPZGREQSA-N -OKN SMILES_CANONICAL CACTVS 3.385 CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(S)=O)O2)C(=O)N=C1N -OKN SMILES CACTVS 3.385 CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(S)=O)O2)C(=O)N=C1N +OKN InChI InChI 1.03 InChI=1S/C10H16N3O6PS/c1-5-3-13(10(15)12-9(5)11)8-2-6(14)7(19-8)4-18-20(16,17)21/h3,6-8,14H,2,4H2,1H3,(H2,11,12,15)(H2,16,17,21)/t6-,7+,8+/m0/s1 +OKN InChIKey InChI 1.03 UZWQYGFEEXJOHY-XLPZGREQSA-N +OKN SMILES_CANONICAL CACTVS 3.385 CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(S)=O)O2)C(=O)N=C1N +OKN SMILES CACTVS 3.385 CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(S)=O)O2)C(=O)N=C1N OKN SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CC1=CN(C(=O)N=C1N)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)S)O -OKN SMILES "OpenEye OEToolkits" 2.0.7 CC1=CN(C(=O)N=C1N)C2CC(C(O2)COP(=O)(O)S)O +OKN SMILES "OpenEye OEToolkits" 2.0.7 CC1=CN(C(=O)N=C1N)C2CC(C(O2)COP(=O)(O)S)O loop_ _pdbx_chem_comp_description_generator.comp_id _pdbx_chem_comp_description_generator.program_name _pdbx_chem_comp_description_generator.program_version _pdbx_chem_comp_description_generator.descriptor -OKN acedrg 243 "dictionary generator" -OKN acedrg_database 11 "data source" -OKN rdkit 2017.03.2 "Chemoinformatics tool" -OKN refmac5 5.8.0238 "optimization tool" +OKN acedrg 277 "dictionary generator" +OKN acedrg_database 12 "data source" +OKN rdkit 2019.09.1 "Chemoinformatics tool" +OKN refmac5 5.8.0425 "optimization tool" + +loop_ +_chem_comp_alias.comp_id +_chem_comp_alias.group +_chem_comp_alias.atom_id +_chem_comp_alias.atom_id_standard +OKN S-NA S01 S2P +OKN S-NA H14 HO3' diff --git a/o/OKQ.cif b/o/OKQ.cif index cbe13b74a..e1a9b6a8b 100644 --- a/o/OKQ.cif +++ b/o/OKQ.cif @@ -7,7 +7,7 @@ _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level -OKQ OKQ "2'-O-methylcytidine-5'-phosphorothioate" NON-POLYMER 37 22 . +OKQ OKQ "2'-O-methylcytidine-5'-phosphorothioate" NON-POLYMER 36 22 . data_comp_OKQ loop_ @@ -19,43 +19,83 @@ _chem_comp_atom.charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z -OKQ C2 C CR6 0 -1.933 -1.232 0.185 -OKQ C4 C CR6 0 -3.953 -2.352 -0.260 -OKQ C5 C CR16 0 -4.389 -1.290 -1.104 -OKQ C6 C CR16 0 -3.567 -0.237 -1.264 -OKQ O2 O O 0 -0.829 -1.182 0.752 -OKQ "C1'" C CH1 0 -1.476 1.025 -0.859 -OKQ "C2'" C CH1 0 -1.335 1.924 0.371 -OKQ "C3'" C CH1 0 -0.042 2.666 0.025 -OKQ "C4'" C CH1 0 0.794 1.587 -0.682 -OKQ "C5'" C CH2 0 1.806 0.871 0.179 -OKQ CM2 C CH3 0 -2.671 3.299 1.797 -OKQ N1 N NR6 0 -2.344 -0.174 -0.649 -OKQ N3 N NRD6 0 -2.759 -2.300 0.352 -OKQ N4 N NH2 0 -4.714 -3.419 -0.058 -OKQ "O2'" O O2 0 -2.477 2.767 0.490 -OKQ "O3'" O OH1 0 -0.261 3.782 -0.829 -OKQ "O4'" O O2 0 -0.166 0.628 -1.203 -OKQ "O5'" O O2 0 2.486 -0.141 -0.610 -OKQ P1 P P 0 3.622 -1.039 0.072 -OKQ O1 O O 0 4.612 -0.118 0.704 -OKQ S1 S SH1 0 2.648 -2.152 1.548 -OKQ OP3 O OP -1 4.172 -1.959 -0.966 -OKQ H1 H H 0 -5.224 -1.320 -1.536 -OKQ H2 H H 0 -3.829 0.474 -1.812 -OKQ H3 H H 0 -1.843 1.561 -1.600 -OKQ H4 H H 0 -1.211 1.386 1.190 -OKQ H5 H H 0 0.414 2.957 0.857 -OKQ H6 H H 0 1.271 1.992 -1.437 -OKQ H7 H H 0 1.348 0.447 0.946 -OKQ H8 H H 0 2.464 1.522 0.528 -OKQ H9 H H 0 -3.411 3.927 1.783 -OKQ H10 H H 0 -1.864 3.756 2.084 -OKQ H11 H H 0 -2.871 2.576 2.414 -OKQ H12 H H 0 -4.425 -4.077 0.448 -OKQ H13 H H 0 -5.508 -3.467 -0.431 -OKQ H14 H H 0 -0.554 4.429 -0.363 -OKQ H17 H HSH1 0 2.830 -3.333 1.350 +OKQ C2 C CR6 0 -1.953 -1.203 0.265 +OKQ C4 C CR6 0 -3.951 -2.363 -0.185 +OKQ C5 C CR16 0 -4.371 -1.350 -1.092 +OKQ C6 C CR16 0 -3.553 -0.299 -1.280 +OKQ O2 O O 0 -0.870 -1.120 0.861 +OKQ "C1'" C CH1 0 -1.507 1.012 -0.899 +OKQ "C2'" C CH1 0 -1.342 1.965 0.293 +OKQ "C3'" C CH1 0 -0.047 2.678 -0.100 +OKQ "C4'" C CH1 0 0.770 1.543 -0.729 +OKQ "C5'" C CH2 0 1.734 0.859 0.210 +OKQ CM2 C CH3 0 -2.549 3.485 1.645 +OKQ N1 N NR6 0 -2.353 -0.193 -0.631 +OKQ N3 N NRD6 0 -2.775 -2.268 0.460 +OKQ N4 N NH2 0 -4.709 -3.428 0.048 +OKQ "O2'" O O2 0 -2.454 2.833 0.389 +OKQ "O3'" O OH1 0 -0.258 3.724 -1.041 +OKQ "O4'" O O2 0 -0.203 0.599 -1.235 +OKQ "O5'" O O2 0 2.322 -0.287 -0.438 +OKQ P1 P P 0 3.645 -0.967 0.182 +OKQ O1 O OP -1 4.729 -0.397 -0.679 +OKQ S1 S S1 0 3.952 -0.595 2.068 +OKQ OP3 O OP -1 3.510 -2.428 -0.124 +OKQ H1 H H 0 -5.194 -1.412 -1.546 +OKQ H2 H H 0 -3.810 0.381 -1.873 +OKQ H3 H H 0 -1.886 1.519 -1.666 +OKQ H4 H H 0 -1.201 1.464 1.147 +OKQ H5 H H 0 0.409 3.028 0.708 +OKQ H6 H H 0 1.288 1.903 -1.492 +OKQ H7 H H 0 1.252 0.572 1.027 +OKQ H8 H H 0 2.444 1.498 0.474 +OKQ H9 H H 0 -3.288 4.110 1.626 +OKQ H10 H H 0 -1.728 3.964 1.828 +OKQ H11 H H 0 -2.702 2.828 2.340 +OKQ H12 H H 0 -5.480 -3.510 -0.360 +OKQ H13 H H 0 -4.443 -4.048 0.607 +OKQ H14 H H 0 -0.643 4.366 -0.663 + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +OKQ C2 C[6a](N[6a]C[6a]C[5])(N[6a]C[6a])(O){1|C<3>,1|C<4>,1|N<3>,1|O<2>,2|H<1>} +OKQ C4 C[6a](C[6a]C[6a]H)(N[6a]C[6a])(NHH){1|H<1>,1|N<3>,1|O<1>} +OKQ C5 C[6a](C[6a]N[6a]H)(C[6a]N[6a]N)(H){1|C<3>,1|C<4>} +OKQ C6 C[6a](N[6a]C[6a]C[5])(C[6a]C[6a]H)(H){1|C<4>,1|H<1>,1|N<2>,1|N<3>,1|O<1>,1|O<2>} +OKQ O2 O(C[6a]N[6a]2) +OKQ "C1'" C[5](N[6a]C[6a]2)(C[5]C[5]HO)(O[5]C[5])(H){1|C<3>,1|C<4>,1|N<2>,1|O<1>,1|O<2>,3|H<1>} +OKQ "C2'" C[5](C[5]N[6a]O[5]H)(C[5]C[5]HO)(OC)(H){1|C<4>,1|H<1>,2|C<3>} +OKQ "C3'" C[5](C[5]C[5]HO)(C[5]O[5]CH)(OH)(H){1|H<1>,1|N<3>} +OKQ "C4'" C[5](C[5]C[5]HO)(O[5]C[5])(CHHO)(H){1|N<3>,1|O<2>,2|H<1>} +OKQ "C5'" C(C[5]C[5]O[5]H)(OP)(H)2 +OKQ CM2 C(OC[5])(H)3 +OKQ N1 N[6a](C[5]C[5]O[5]H)(C[6a]C[6a]H)(C[6a]N[6a]O){1|C<3>,1|O<2>,2|C<4>,2|H<1>} +OKQ N3 N[6a](C[6a]C[6a]N)(C[6a]N[6a]O){1|C<3>,1|C<4>,1|H<1>} +OKQ N4 N(C[6a]C[6a]N[6a])(H)2 +OKQ "O2'" O(C[5]C[5]2H)(CH3) +OKQ "O3'" O(C[5]C[5]2H)(H) +OKQ "O4'" O[5](C[5]N[6a]C[5]H)(C[5]C[5]CH){2|C<3>,2|H<1>,2|O<2>} +OKQ "O5'" O(CC[5]HH)(POOS) +OKQ P1 P(OC)(O)2(S) +OKQ O1 O(POOS) +OKQ S1 S(PO3) +OKQ OP3 O(POOS) +OKQ H1 H(C[6a]C[6a]2) +OKQ H2 H(C[6a]C[6a]N[6a]) +OKQ H3 H(C[5]N[6a]C[5]O[5]) +OKQ H4 H(C[5]C[5]2O) +OKQ H5 H(C[5]C[5]2O) +OKQ H6 H(C[5]C[5]O[5]C) +OKQ H7 H(CC[5]HO) +OKQ H8 H(CC[5]HO) +OKQ H9 H(CHHO) +OKQ H10 H(CHHO) +OKQ H11 H(CHHO) +OKQ H12 H(NC[6a]H) +OKQ H13 H(NC[6a]H) +OKQ H14 H(OC[5]) loop_ _chem_comp_bond.comp_id @@ -67,44 +107,43 @@ _chem_comp_bond.value_dist_nucleus _chem_comp_bond.value_dist_nucleus_esd _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd -OKQ "C5'" "O5'" SINGLE n 1.450 0.0166 1.450 0.0166 +OKQ "C5'" "O5'" SINGLE n 1.438 0.0200 1.438 0.0200 OKQ "C4'" "C5'" SINGLE n 1.509 0.0100 1.509 0.0100 -OKQ "C4'" "O4'" SINGLE n 1.451 0.0111 1.451 0.0111 -OKQ "C3'" "C4'" SINGLE n 1.535 0.0100 1.535 0.0100 -OKQ "C1'" "O4'" SINGLE n 1.411 0.0100 1.411 0.0100 -OKQ C5 C6 DOUBLE y 1.342 0.0100 1.342 0.0100 -OKQ C6 N1 SINGLE y 1.364 0.0108 1.364 0.0108 -OKQ "C2'" "C3'" SINGLE n 1.530 0.0134 1.530 0.0134 +OKQ "C4'" "O4'" SINGLE n 1.445 0.0100 1.445 0.0100 +OKQ "C3'" "C4'" SINGLE n 1.532 0.0100 1.532 0.0100 +OKQ "C1'" "O4'" SINGLE n 1.408 0.0100 1.408 0.0100 +OKQ C5 C6 DOUBLE y 1.342 0.0100 1.342 0.0100 +OKQ C6 N1 SINGLE y 1.361 0.0100 1.361 0.0100 +OKQ "C2'" "C3'" SINGLE n 1.530 0.0100 1.530 0.0100 OKQ "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 -OKQ C4 C5 SINGLE y 1.422 0.0123 1.422 0.0123 -OKQ "C1'" "C2'" SINGLE n 1.531 0.0100 1.531 0.0100 -OKQ "C2'" "O2'" SINGLE n 1.423 0.0100 1.423 0.0100 -OKQ "C1'" N1 SINGLE n 1.487 0.0100 1.487 0.0100 -OKQ C2 N1 SINGLE y 1.397 0.0100 1.397 0.0100 -OKQ C4 N4 SINGLE n 1.325 0.0109 1.325 0.0109 -OKQ C4 N3 DOUBLE y 1.339 0.0110 1.339 0.0110 -OKQ C2 N3 SINGLE y 1.355 0.0119 1.355 0.0119 -OKQ C2 O2 DOUBLE n 1.241 0.0100 1.241 0.0100 -OKQ CM2 "O2'" SINGLE n 1.423 0.0131 1.423 0.0131 -OKQ "O5'" P1 SINGLE n 1.601 0.0114 1.601 0.0114 -OKQ P1 O1 DOUBLE n 1.493 0.0157 1.493 0.0157 -OKQ P1 S1 SINGLE n 2.091 0.0200 2.091 0.0200 -OKQ P1 OP3 SINGLE n 1.493 0.0157 1.493 0.0157 -OKQ C5 H1 SINGLE n 1.082 0.0130 0.941 0.0174 -OKQ C6 H2 SINGLE n 1.082 0.0130 0.935 0.0143 -OKQ "C1'" H3 SINGLE n 1.089 0.0100 0.985 0.0100 -OKQ "C2'" H4 SINGLE n 1.089 0.0100 0.988 0.0200 -OKQ "C3'" H5 SINGLE n 1.089 0.0100 0.992 0.0200 -OKQ "C4'" H6 SINGLE n 1.089 0.0100 0.981 0.0200 -OKQ "C5'" H7 SINGLE n 1.089 0.0100 0.989 0.0200 -OKQ "C5'" H8 SINGLE n 1.089 0.0100 0.989 0.0200 -OKQ CM2 H9 SINGLE n 1.089 0.0100 0.971 0.0146 -OKQ CM2 H10 SINGLE n 1.089 0.0100 0.971 0.0146 -OKQ CM2 H11 SINGLE n 1.089 0.0100 0.971 0.0146 -OKQ N4 H12 SINGLE n 1.016 0.0100 0.877 0.0200 -OKQ N4 H13 SINGLE n 1.016 0.0100 0.877 0.0200 -OKQ "O3'" H14 SINGLE n 0.970 0.0120 0.849 0.0200 -OKQ S1 H17 SINGLE n 1.338 0.0100 1.211 0.0200 +OKQ C4 C5 SINGLE y 1.422 0.0101 1.422 0.0101 +OKQ "C1'" "C2'" SINGLE n 1.536 0.0135 1.536 0.0135 +OKQ "C2'" "O2'" SINGLE n 1.411 0.0100 1.411 0.0100 +OKQ "C1'" N1 SINGLE n 1.489 0.0100 1.489 0.0100 +OKQ C2 N1 SINGLE y 1.398 0.0100 1.398 0.0100 +OKQ C4 N4 SINGLE n 1.326 0.0110 1.326 0.0110 +OKQ C4 N3 DOUBLE y 1.341 0.0104 1.341 0.0104 +OKQ C2 N3 SINGLE y 1.355 0.0100 1.355 0.0100 +OKQ C2 O2 DOUBLE n 1.238 0.0116 1.238 0.0116 +OKQ CM2 "O2'" SINGLE n 1.415 0.0136 1.415 0.0136 +OKQ "O5'" P1 SINGLE n 1.613 0.0200 1.613 0.0200 +OKQ P1 O1 SINGLE n 1.497 0.0143 1.497 0.0143 +OKQ P1 S1 DOUBLE n 1.949 0.0200 1.949 0.0200 +OKQ P1 OP3 SINGLE n 1.497 0.0143 1.497 0.0143 +OKQ C5 H1 SINGLE n 1.085 0.0150 0.942 0.0165 +OKQ C6 H2 SINGLE n 1.085 0.0150 0.938 0.0143 +OKQ "C1'" H3 SINGLE n 1.092 0.0100 0.994 0.0122 +OKQ "C2'" H4 SINGLE n 1.092 0.0100 1.000 0.0100 +OKQ "C3'" H5 SINGLE n 1.092 0.0100 0.991 0.0200 +OKQ "C4'" H6 SINGLE n 1.092 0.0100 0.990 0.0200 +OKQ "C5'" H7 SINGLE n 1.092 0.0100 0.991 0.0200 +OKQ "C5'" H8 SINGLE n 1.092 0.0100 0.991 0.0200 +OKQ CM2 H9 SINGLE n 1.092 0.0100 0.968 0.0164 +OKQ CM2 H10 SINGLE n 1.092 0.0100 0.968 0.0164 +OKQ CM2 H11 SINGLE n 1.092 0.0100 0.968 0.0164 +OKQ N4 H12 SINGLE n 1.013 0.0120 0.875 0.0200 +OKQ N4 H13 SINGLE n 1.013 0.0120 0.875 0.0200 +OKQ "O3'" H14 SINGLE n 0.972 0.0180 0.839 0.0200 loop_ _chem_comp_angle.comp_id @@ -113,72 +152,71 @@ _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd -OKQ N1 C2 N3 118.920 1.50 -OKQ N1 C2 O2 118.716 1.50 -OKQ N3 C2 O2 122.370 1.50 -OKQ C5 C4 N4 120.876 1.50 -OKQ C5 C4 N3 121.269 1.50 -OKQ N4 C4 N3 117.855 1.50 -OKQ C6 C5 C4 117.808 1.50 -OKQ C6 C5 H1 120.848 1.50 -OKQ C4 C5 H1 121.350 1.50 -OKQ C5 C6 N1 121.215 1.50 -OKQ C5 C6 H2 120.275 1.75 -OKQ N1 C6 H2 118.510 1.50 -OKQ "O4'" "C1'" "C2'" 106.391 1.51 -OKQ "O4'" "C1'" N1 108.667 1.50 -OKQ "O4'" "C1'" H3 109.327 1.50 -OKQ "C2'" "C1'" N1 113.620 1.99 -OKQ "C2'" "C1'" H3 109.527 1.54 -OKQ N1 "C1'" H3 109.166 1.50 -OKQ "C3'" "C2'" "C1'" 101.207 1.50 -OKQ "C3'" "C2'" "O2'" 112.623 3.00 -OKQ "C3'" "C2'" H4 110.255 2.04 -OKQ "C1'" "C2'" "O2'" 110.738 2.44 -OKQ "C1'" "C2'" H4 110.561 1.96 -OKQ "O2'" "C2'" H4 110.257 1.68 -OKQ "C4'" "C3'" "C2'" 102.352 1.50 -OKQ "C4'" "C3'" "O3'" 111.281 2.46 -OKQ "C4'" "C3'" H5 110.452 2.54 -OKQ "C2'" "C3'" "O3'" 112.463 2.73 -OKQ "C2'" "C3'" H5 110.255 2.04 -OKQ "O3'" "C3'" H5 110.380 1.67 -OKQ "C5'" "C4'" "O4'" 109.615 1.50 -OKQ "C5'" "C4'" "C3'" 116.008 1.52 -OKQ "C5'" "C4'" H6 108.268 1.50 -OKQ "O4'" "C4'" "C3'" 104.439 1.50 -OKQ "O4'" "C4'" H6 108.698 1.50 -OKQ "C3'" "C4'" H6 109.363 1.86 -OKQ "O5'" "C5'" "C4'" 109.510 1.50 -OKQ "O5'" "C5'" H7 109.821 1.50 -OKQ "O5'" "C5'" H8 109.821 1.50 -OKQ "C4'" "C5'" H7 109.624 1.50 -OKQ "C4'" "C5'" H8 109.624 1.50 -OKQ H7 "C5'" H8 108.472 1.50 -OKQ "O2'" CM2 H9 109.434 1.50 -OKQ "O2'" CM2 H10 109.434 1.50 -OKQ "O2'" CM2 H11 109.434 1.50 -OKQ H9 CM2 H10 109.541 1.50 -OKQ H9 CM2 H11 109.541 1.50 -OKQ H10 CM2 H11 109.541 1.50 -OKQ C6 N1 "C1'" 121.301 1.52 -OKQ C6 N1 C2 120.510 1.50 -OKQ "C1'" N1 C2 118.189 2.26 -OKQ C4 N3 C2 120.266 1.50 -OKQ C4 N4 H12 119.818 1.59 -OKQ C4 N4 H13 119.818 1.59 -OKQ H12 N4 H13 120.363 1.85 -OKQ "C2'" "O2'" CM2 113.084 1.50 -OKQ "C3'" "O3'" H14 108.744 3.00 -OKQ "C4'" "O4'" "C1'" 109.578 1.50 -OKQ "C5'" "O5'" P1 119.135 1.78 -OKQ "O5'" P1 O1 108.530 2.45 -OKQ "O5'" P1 S1 105.685 3.00 -OKQ "O5'" P1 OP3 108.530 2.45 -OKQ O1 P1 S1 111.281 3.00 -OKQ O1 P1 OP3 116.964 2.85 -OKQ S1 P1 OP3 111.281 3.00 -OKQ P1 S1 H17 109.471 3.00 +OKQ N1 C2 N3 118.792 1.50 +OKQ N1 C2 O2 118.915 2.14 +OKQ N3 C2 O2 122.293 1.50 +OKQ C5 C4 N4 120.770 1.50 +OKQ C5 C4 N3 121.314 1.50 +OKQ N4 C4 N3 117.915 1.50 +OKQ C6 C5 C4 117.770 1.50 +OKQ C6 C5 H1 121.009 1.50 +OKQ C4 C5 H1 121.221 1.50 +OKQ C5 C6 N1 121.118 1.50 +OKQ C5 C6 H2 120.471 3.00 +OKQ N1 C6 H2 118.411 1.84 +OKQ "O4'" "C1'" "C2'" 106.317 2.77 +OKQ "O4'" "C1'" N1 108.138 1.50 +OKQ "O4'" "C1'" H3 109.439 1.50 +OKQ "C2'" "C1'" N1 113.630 2.26 +OKQ "C2'" "C1'" H3 109.683 1.50 +OKQ N1 "C1'" H3 109.374 1.50 +OKQ "C3'" "C2'" "C1'" 101.790 1.50 +OKQ "C3'" "C2'" "O2'" 112.208 3.00 +OKQ "C3'" "C2'" H4 110.368 2.92 +OKQ "C1'" "C2'" "O2'" 111.051 2.25 +OKQ "C1'" "C2'" H4 111.550 1.50 +OKQ "O2'" "C2'" H4 110.925 1.50 +OKQ "C4'" "C3'" "C2'" 102.511 1.50 +OKQ "C4'" "C3'" "O3'" 110.713 3.00 +OKQ "C4'" "C3'" H5 110.577 3.00 +OKQ "C2'" "C3'" "O3'" 112.059 3.00 +OKQ "C2'" "C3'" H5 110.368 2.92 +OKQ "O3'" "C3'" H5 110.541 2.08 +OKQ "C5'" "C4'" "O4'" 110.351 1.93 +OKQ "C5'" "C4'" "C3'" 115.288 1.50 +OKQ "C5'" "C4'" H6 108.351 1.59 +OKQ "O4'" "C4'" "C3'" 105.071 1.50 +OKQ "O4'" "C4'" H6 108.778 1.50 +OKQ "C3'" "C4'" H6 109.322 2.54 +OKQ "O5'" "C5'" "C4'" 109.482 2.30 +OKQ "O5'" "C5'" H7 109.954 1.50 +OKQ "O5'" "C5'" H8 109.954 1.50 +OKQ "C4'" "C5'" H7 109.589 1.50 +OKQ "C4'" "C5'" H8 109.589 1.50 +OKQ H7 "C5'" H8 108.471 1.50 +OKQ "O2'" CM2 H9 109.455 1.50 +OKQ "O2'" CM2 H10 109.455 1.50 +OKQ "O2'" CM2 H11 109.455 1.50 +OKQ H9 CM2 H10 109.475 1.50 +OKQ H9 CM2 H11 109.475 1.50 +OKQ H10 CM2 H11 109.475 1.50 +OKQ C6 N1 "C1'" 121.103 2.33 +OKQ C6 N1 C2 120.608 1.50 +OKQ "C1'" N1 C2 118.289 3.00 +OKQ C4 N3 C2 120.397 1.50 +OKQ C4 N4 H12 119.693 3.00 +OKQ C4 N4 H13 119.693 3.00 +OKQ H12 N4 H13 120.613 3.00 +OKQ "C2'" "O2'" CM2 112.131 1.50 +OKQ "C3'" "O3'" H14 109.389 3.00 +OKQ "C4'" "O4'" "C1'" 109.821 1.50 +OKQ "C5'" "O5'" P1 119.085 2.00 +OKQ "O5'" P1 O1 106.327 3.00 +OKQ "O5'" P1 S1 114.928 3.00 +OKQ "O5'" P1 OP3 106.327 3.00 +OKQ O1 P1 S1 116.458 3.00 +OKQ O1 P1 OP3 112.844 3.00 +OKQ S1 P1 OP3 116.458 3.00 loop_ _chem_comp_tor.comp_id @@ -190,32 +228,30 @@ _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period -OKQ C2e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 -OKQ C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 -OKQ C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 -OKQ C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 -OKQ C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 -OKQ C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 -OKQ C3e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 -OKQ C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 -OKQ C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 -OKQ C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 -OKQ C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 -OKQ C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 -OKQ gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 -OKQ const_sp2_sp2_3 O2 C2 N1 C6 180.000 5.0 2 -OKQ const_20 O2 C2 N3 C4 180.000 10.0 2 -OKQ sp3_sp3_52 H9 CM2 "O2'" "C2'" 180.000 10.0 3 -OKQ sp3_sp3_57 "C5'" "O5'" P1 O1 60.000 10.0 3 -OKQ sp3_sp3_59 "O5'" P1 S1 H17 60.000 10.0 3 -OKQ const_18 N4 C4 N3 C2 180.000 10.0 2 -OKQ sp2_sp2_1 C5 C4 N4 H12 180.000 5.0 2 -OKQ const_15 N4 C4 C5 C6 180.000 10.0 2 -OKQ const_sp2_sp2_9 C4 C5 C6 N1 0.000 5.0 2 -OKQ const_sp2_sp2_6 C5 C6 N1 "C1'" 180.000 5.0 2 -OKQ sp3_sp3_49 "C3'" "C2'" "O2'" CM2 180.000 10.0 3 -OKQ sp3_sp3_37 "C4'" "C3'" "O3'" H14 180.000 10.0 3 -OKQ sp3_sp3_25 "C4'" "C5'" "O5'" P1 180.000 10.0 3 +OKQ const_sp2_sp2_1 N3 C2 N1 C6 0.000 0.0 1 +OKQ const_sp2_sp2_4 O2 C2 N1 "C1'" 0.000 0.0 1 +OKQ const_23 N1 C2 N3 C4 0.000 0.0 1 +OKQ sp3_sp3_52 H9 CM2 "O2'" "C2'" 180.000 10.0 3 +OKQ sp3_sp3_57 "C5'" "O5'" P1 O1 60.000 10.0 3 +OKQ const_17 C5 C4 N3 C2 0.000 0.0 1 +OKQ sp2_sp2_19 C5 C4 N4 H12 180.000 20 2 +OKQ sp2_sp2_22 N3 C4 N4 H13 180.000 20 2 +OKQ const_13 N3 C4 C5 C6 0.000 0.0 1 +OKQ const_16 N4 C4 C5 H1 0.000 0.0 1 +OKQ const_sp2_sp2_9 C4 C5 C6 N1 0.000 0.0 1 +OKQ const_12 H1 C5 C6 H2 0.000 0.0 1 +OKQ const_sp2_sp2_5 C5 C6 N1 C2 0.000 0.0 1 +OKQ const_sp2_sp2_8 H2 C6 N1 "C1'" 0.000 0.0 1 +OKQ sp2_sp3_1 C6 N1 "C1'" "O4'" 150.000 10.0 6 +OKQ sp3_sp3_1 "C2'" "C1'" "O4'" "C4'" 60.000 10.0 3 +OKQ sp3_sp3_41 "O4'" "C1'" "C2'" "O2'" -60.000 10.0 3 +OKQ sp3_sp3_49 "C3'" "C2'" "O2'" CM2 180.000 10.0 3 +OKQ sp3_sp3_20 "O2'" "C2'" "C3'" "O3'" -60.000 10.0 3 +OKQ sp3_sp3_37 "C4'" "C3'" "O3'" H14 180.000 10.0 3 +OKQ sp3_sp3_11 "O3'" "C3'" "C4'" "C5'" 60.000 10.0 3 +OKQ sp3_sp3_5 "C5'" "C4'" "O4'" "C1'" 180.000 10.0 3 +OKQ sp3_sp3_28 "O4'" "C4'" "C5'" "O5'" 180.000 10.0 3 +OKQ sp3_sp3_25 "C4'" "C5'" "O5'" P1 180.000 10.0 3 loop_ _chem_comp_chir.comp_id @@ -225,11 +261,11 @@ _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign -OKQ chir_1 "C1'" "O4'" N1 "C2'" negative +OKQ chir_1 "C1'" "O4'" N1 "C2'" negative OKQ chir_2 "C2'" "O2'" "C1'" "C3'" negative OKQ chir_3 "C3'" "O3'" "C2'" "C4'" negative OKQ chir_4 "C4'" "O4'" "C3'" "C5'" negative -OKQ chir_5 P1 S1 "O5'" OP3 both +OKQ chir_5 P1 S1 "O5'" OP3 both loop_ _chem_comp_plane_atom.comp_id @@ -237,20 +273,20 @@ _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd OKQ plan-1 "C1'" 0.020 -OKQ plan-1 C2 0.020 -OKQ plan-1 C4 0.020 -OKQ plan-1 C5 0.020 -OKQ plan-1 C6 0.020 -OKQ plan-1 H1 0.020 -OKQ plan-1 H2 0.020 -OKQ plan-1 N1 0.020 -OKQ plan-1 N3 0.020 -OKQ plan-1 N4 0.020 -OKQ plan-1 O2 0.020 -OKQ plan-2 C4 0.020 -OKQ plan-2 H12 0.020 -OKQ plan-2 H13 0.020 -OKQ plan-2 N4 0.020 +OKQ plan-1 C2 0.020 +OKQ plan-1 C4 0.020 +OKQ plan-1 C5 0.020 +OKQ plan-1 C6 0.020 +OKQ plan-1 H1 0.020 +OKQ plan-1 H2 0.020 +OKQ plan-1 N1 0.020 +OKQ plan-1 N3 0.020 +OKQ plan-1 N4 0.020 +OKQ plan-1 O2 0.020 +OKQ plan-2 C4 0.020 +OKQ plan-2 H12 0.020 +OKQ plan-2 H13 0.020 +OKQ plan-2 N4 0.020 loop_ _pdbx_chem_comp_descriptor.comp_id @@ -258,19 +294,29 @@ _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor -OKQ InChI InChI 1.03 InChI=1S/C10H16N3O7PS/c1-18-8-7(14)5(4-19-21(16,17)22)20-9(8)13-3-2-6(11)12-10(13)15/h2-3,5,7-9,14H,4H2,1H3,(H2,11,12,15)(H2,16,17,22)/t5-,7-,8-,9-/m1/s1 -OKQ InChIKey InChI 1.03 JKIZWHJBBPPNBB-ZOQUXTDFSA-N -OKQ SMILES_CANONICAL CACTVS 3.385 CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(S)=O)O[C@H]1N2C=CC(=NC2=O)N -OKQ SMILES CACTVS 3.385 CO[CH]1[CH](O)[CH](CO[P](O)(S)=O)O[CH]1N2C=CC(=NC2=O)N +OKQ InChI InChI 1.03 InChI=1S/C10H16N3O7PS/c1-18-8-7(14)5(4-19-21(16,17)22)20-9(8)13-3-2-6(11)12-10(13)15/h2-3,5,7-9,14H,4H2,1H3,(H2,11,12,15)(H2,16,17,22)/t5-,7-,8-,9-/m1/s1 +OKQ InChIKey InChI 1.03 JKIZWHJBBPPNBB-ZOQUXTDFSA-N +OKQ SMILES_CANONICAL CACTVS 3.385 CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(S)=O)O[C@H]1N2C=CC(=NC2=O)N +OKQ SMILES CACTVS 3.385 CO[CH]1[CH](O)[CH](CO[P](O)(S)=O)O[CH]1N2C=CC(=NC2=O)N OKQ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CO[C@@H]1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)S)O -OKQ SMILES "OpenEye OEToolkits" 2.0.7 COC1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)S)O +OKQ SMILES "OpenEye OEToolkits" 2.0.7 COC1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)S)O loop_ _pdbx_chem_comp_description_generator.comp_id _pdbx_chem_comp_description_generator.program_name _pdbx_chem_comp_description_generator.program_version _pdbx_chem_comp_description_generator.descriptor -OKQ acedrg 243 "dictionary generator" -OKQ acedrg_database 11 "data source" -OKQ rdkit 2017.03.2 "Chemoinformatics tool" -OKQ refmac5 5.8.0238 "optimization tool" +OKQ acedrg 277 "dictionary generator" +OKQ acedrg_database 12 "data source" +OKQ rdkit 2019.09.1 "Chemoinformatics tool" +OKQ refmac5 5.8.0425 "optimization tool" + +loop_ +_chem_comp_alias.comp_id +_chem_comp_alias.group +_chem_comp_alias.atom_id +_chem_comp_alias.atom_id_standard +OKQ S-NA P1 P +OKQ S-NA O1 OP1 +OKQ S-NA S1 S2P +OKQ S-NA H14 HO3' diff --git a/o/OKT.cif b/o/OKT.cif index 1b015e92c..0b560213e 100644 --- a/o/OKT.cif +++ b/o/OKT.cif @@ -7,7 +7,7 @@ _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level -OKT OKT "2'-O-methyluridine-5'-phosphorothioate" NON-POLYMER 36 22 . +OKT OKT "2'-O-methyluridine-5'-phosphorothioate" NON-POLYMER 35 22 . data_comp_OKT loop_ @@ -19,42 +19,81 @@ _chem_comp_atom.charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z -OKT C02 C CH3 0 2.545 -3.603 1.456 -OKT "C1'" C CH1 0 1.495 -0.975 -0.918 -OKT C2 C CR6 0 2.230 1.077 0.280 -OKT "C2'" C CH1 0 1.308 -1.963 0.235 -OKT "C3'" C CH1 0 -0.077 -2.522 -0.101 -OKT C4 C CR6 0 4.448 2.060 -0.199 -OKT "C4'" C CH1 0 -0.815 -1.294 -0.658 -OKT C5 C CR16 0 4.663 1.006 -1.151 -OKT "C5'" C CH2 0 -1.695 -0.555 0.320 -OKT C6 C CR16 0 3.708 0.079 -1.341 -OKT N1 N NR6 0 2.506 0.089 -0.662 -OKT N3 N NR6 0 3.228 2.010 0.451 -OKT O01 O O2 0 2.349 -2.935 0.213 -OKT O2 O O 0 1.186 1.139 0.921 -OKT "O3'" O OH1 0 -0.028 -3.568 -1.065 -OKT O4 O O 0 5.240 2.965 0.065 -OKT "O4'" O O2 0 0.224 -0.403 -1.148 -OKT "O5'" O O2 0 -2.348 0.550 -0.357 -OKT OP1 O O 0 -2.630 1.961 1.688 -OKT P P P 0 -3.344 1.499 0.461 -OKT S01 S SH1 0 -4.956 0.283 0.998 -OKT OP3 O OP -1 -3.801 2.580 -0.458 -OKT H1 H H 0 3.208 -4.304 1.344 -OKT H2 H H 0 1.706 -3.994 1.750 -OKT H3 H H 0 2.857 -2.966 2.120 -OKT H4 H H 0 1.757 -1.476 -1.719 -OKT H5 H H 0 1.284 -1.496 1.105 -OKT H6 H H 0 -0.523 -2.840 0.726 -OKT H7 H H 0 -1.372 -1.570 -1.418 -OKT H8 H H 0 5.462 0.967 -1.634 -OKT H9 H H 0 -1.147 -0.214 1.069 -OKT H10 H H 0 -2.375 -1.173 0.686 -OKT H11 H H 0 3.864 -0.603 -1.966 -OKT H12 H H 0 3.060 2.649 1.049 -OKT H13 H H 0 0.206 -4.285 -0.676 -OKT H15 H HSH1 0 -5.991 0.809 0.655 +OKT C02 C CH3 0 2.463 -3.633 1.514 +OKT "C1'" C CH1 0 1.533 -0.997 -0.906 +OKT C2 C CR6 0 2.241 1.091 0.266 +OKT "C2'" C CH1 0 1.339 -1.963 0.272 +OKT "C3'" C CH1 0 -0.039 -2.537 -0.062 +OKT C4 C CR6 0 4.422 2.121 -0.297 +OKT "C4'" C CH1 0 -0.775 -1.320 -0.634 +OKT C5 C CR16 0 4.632 1.062 -1.245 +OKT "C5'" C CH2 0 -1.647 -0.577 0.349 +OKT C6 C CR16 0 3.695 0.110 -1.397 +OKT N1 N NR6 0 2.514 0.098 -0.675 +OKT N3 N NR16 0 3.224 2.050 0.394 +OKT O01 O O2 0 2.365 -2.935 0.283 +OKT O2 O O 0 1.219 1.136 0.936 +OKT "O3'" O OH1 0 0.019 -3.584 -1.024 +OKT O4 O O 0 5.205 3.046 -0.069 +OKT "O4'" O O2 0 0.255 -0.444 -1.150 +OKT "O5'" O O2 0 -2.281 0.530 -0.317 +OKT OP1 O OP -1 -2.661 1.904 1.647 +OKT P P P 0 -3.405 1.381 0.457 +OKT S01 S S1 0 -4.965 0.340 0.975 +OKT OP3 O OP -1 -3.705 2.518 -0.465 +OKT H1 H H 0 3.137 -4.324 1.437 +OKT H2 H H 0 1.610 -4.039 1.728 +OKT H3 H H 0 2.714 -3.017 2.217 +OKT H4 H H 0 1.808 -1.518 -1.704 +OKT H5 H H 0 1.294 -1.477 1.144 +OKT H6 H H 0 -0.485 -2.854 0.765 +OKT H7 H H 0 -1.346 -1.613 -1.389 +OKT H8 H H 0 5.420 1.037 -1.755 +OKT H9 H H 0 -1.093 -0.247 1.101 +OKT H10 H H 0 -2.333 -1.192 0.712 +OKT H11 H H 0 3.848 -0.579 -2.024 +OKT H12 H H 0 3.065 2.679 0.979 +OKT H13 H H 0 0.403 -4.250 -0.688 + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +OKT C02 C(OC[5])(H)3 +OKT "C1'" C[5](N[6a]C[6a]2)(C[5]C[5]HO)(O[5]C[5])(H){1|C<3>,1|C<4>,1|N<3>,1|O<1>,1|O<2>,3|H<1>} +OKT C2 C[6a](N[6a]C[6a]C[5])(N[6a]C[6a]H)(O){1|C<3>,1|C<4>,1|O<1>,1|O<2>,2|H<1>} +OKT "C2'" C[5](C[5]N[6a]O[5]H)(C[5]C[5]HO)(OC)(H){1|C<4>,1|H<1>,2|C<3>} +OKT "C3'" C[5](C[5]C[5]HO)(C[5]O[5]CH)(OH)(H){1|H<1>,1|N<3>} +OKT C4 C[6a](C[6a]C[6a]H)(N[6a]C[6a]H)(O){1|H<1>,1|N<3>,1|O<1>} +OKT "C4'" C[5](C[5]C[5]HO)(O[5]C[5])(CHHO)(H){1|N<3>,1|O<2>,2|H<1>} +OKT C5 C[6a](C[6a]N[6a]H)(C[6a]N[6a]O)(H){1|C<3>,1|C<4>,1|H<1>} +OKT "C5'" C(C[5]C[5]O[5]H)(OP)(H)2 +OKT C6 C[6a](N[6a]C[6a]C[5])(C[6a]C[6a]H)(H){1|C<4>,1|H<1>,1|N<3>,1|O<2>,2|O<1>} +OKT N1 N[6a](C[5]C[5]O[5]H)(C[6a]C[6a]H)(C[6a]N[6a]O){1|C<3>,1|O<2>,2|C<4>,3|H<1>} +OKT N3 N[6a](C[6a]C[6a]O)(C[6a]N[6a]O)(H){1|C<3>,1|C<4>,1|H<1>} +OKT O01 O(C[5]C[5]2H)(CH3) +OKT O2 O(C[6a]N[6a]2) +OKT "O3'" O(C[5]C[5]2H)(H) +OKT O4 O(C[6a]C[6a]N[6a]) +OKT "O4'" O[5](C[5]N[6a]C[5]H)(C[5]C[5]CH){2|C<3>,2|H<1>,2|O<2>} +OKT "O5'" O(CC[5]HH)(POOS) +OKT OP1 O(POOS) +OKT P P(OC)(O)2(S) +OKT S01 S(PO3) +OKT OP3 O(POOS) +OKT H1 H(CHHO) +OKT H2 H(CHHO) +OKT H3 H(CHHO) +OKT H4 H(C[5]N[6a]C[5]O[5]) +OKT H5 H(C[5]C[5]2O) +OKT H6 H(C[5]C[5]2O) +OKT H7 H(C[5]C[5]O[5]C) +OKT H8 H(C[6a]C[6a]2) +OKT H9 H(CC[5]HO) +OKT H10 H(CC[5]HO) +OKT H11 H(C[6a]C[6a]N[6a]) +OKT H12 H(N[6a]C[6a]2) +OKT H13 H(OC[5]) loop_ _chem_comp_bond.comp_id @@ -66,43 +105,42 @@ _chem_comp_bond.value_dist_nucleus _chem_comp_bond.value_dist_nucleus_esd _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd -OKT P S01 SINGLE n 2.091 0.0200 2.091 0.0200 -OKT OP1 P DOUBLE n 1.493 0.0157 1.493 0.0157 -OKT "O5'" P SINGLE n 1.601 0.0114 1.601 0.0114 -OKT C4 O4 DOUBLE n 1.231 0.0100 1.231 0.0100 -OKT C4 C5 SINGLE y 1.434 0.0100 1.434 0.0100 -OKT C5 C6 DOUBLE y 1.342 0.0100 1.342 0.0100 -OKT C4 N3 SINGLE y 1.381 0.0100 1.381 0.0100 -OKT "C5'" "O5'" SINGLE n 1.450 0.0166 1.450 0.0166 -OKT C6 N1 SINGLE y 1.375 0.0106 1.375 0.0106 -OKT C2 N3 SINGLE y 1.372 0.0112 1.372 0.0112 +OKT P S01 DOUBLE n 1.949 0.0200 1.949 0.0200 +OKT OP1 P SINGLE n 1.497 0.0143 1.497 0.0143 +OKT "O5'" P SINGLE n 1.613 0.0200 1.613 0.0200 +OKT C4 O4 DOUBLE n 1.233 0.0100 1.233 0.0100 +OKT C4 C5 SINGLE y 1.435 0.0100 1.435 0.0100 +OKT C5 C6 DOUBLE y 1.342 0.0100 1.342 0.0100 +OKT C4 N3 SINGLE y 1.382 0.0100 1.382 0.0100 +OKT "C5'" "O5'" SINGLE n 1.438 0.0200 1.438 0.0200 +OKT C6 N1 SINGLE y 1.378 0.0100 1.378 0.0100 +OKT C2 N3 SINGLE y 1.375 0.0100 1.375 0.0100 OKT "C4'" "C5'" SINGLE n 1.509 0.0100 1.509 0.0100 -OKT C2 N1 SINGLE y 1.383 0.0100 1.383 0.0100 -OKT "C1'" N1 SINGLE n 1.476 0.0133 1.476 0.0133 -OKT "C4'" "O4'" SINGLE n 1.451 0.0111 1.451 0.0111 +OKT C2 N1 SINGLE y 1.386 0.0100 1.386 0.0100 +OKT "C1'" N1 SINGLE n 1.477 0.0120 1.477 0.0120 +OKT "C4'" "O4'" SINGLE n 1.445 0.0100 1.445 0.0100 OKT "C1'" "O4'" SINGLE n 1.412 0.0100 1.412 0.0100 -OKT C2 O2 DOUBLE n 1.224 0.0111 1.224 0.0111 -OKT "C3'" "C4'" SINGLE n 1.535 0.0100 1.535 0.0100 -OKT "C1'" "C2'" SINGLE n 1.531 0.0100 1.531 0.0100 -OKT "C2'" "C3'" SINGLE n 1.530 0.0134 1.530 0.0134 +OKT C2 O2 DOUBLE n 1.221 0.0100 1.221 0.0100 +OKT "C3'" "C4'" SINGLE n 1.532 0.0100 1.532 0.0100 +OKT "C1'" "C2'" SINGLE n 1.536 0.0135 1.536 0.0135 +OKT "C2'" "C3'" SINGLE n 1.530 0.0100 1.530 0.0100 OKT "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 -OKT "C2'" O01 SINGLE n 1.423 0.0100 1.423 0.0100 -OKT C02 O01 SINGLE n 1.423 0.0131 1.423 0.0131 -OKT P OP3 SINGLE n 1.493 0.0157 1.493 0.0157 -OKT C02 H1 SINGLE n 1.089 0.0100 0.971 0.0146 -OKT C02 H2 SINGLE n 1.089 0.0100 0.971 0.0146 -OKT C02 H3 SINGLE n 1.089 0.0100 0.971 0.0146 -OKT "C1'" H4 SINGLE n 1.089 0.0100 0.981 0.0118 -OKT "C2'" H5 SINGLE n 1.089 0.0100 0.988 0.0200 -OKT "C3'" H6 SINGLE n 1.089 0.0100 0.992 0.0200 -OKT "C4'" H7 SINGLE n 1.089 0.0100 0.981 0.0200 -OKT C5 H8 SINGLE n 1.082 0.0130 0.935 0.0100 -OKT "C5'" H9 SINGLE n 1.089 0.0100 0.989 0.0200 -OKT "C5'" H10 SINGLE n 1.089 0.0100 0.989 0.0200 -OKT C6 H11 SINGLE n 1.082 0.0130 0.938 0.0107 -OKT N3 H12 SINGLE n 1.016 0.0100 0.889 0.0200 -OKT "O3'" H13 SINGLE n 0.970 0.0120 0.849 0.0200 -OKT S01 H15 SINGLE n 1.338 0.0100 1.211 0.0200 +OKT "C2'" O01 SINGLE n 1.411 0.0100 1.411 0.0100 +OKT C02 O01 SINGLE n 1.415 0.0136 1.415 0.0136 +OKT P OP3 SINGLE n 1.497 0.0143 1.497 0.0143 +OKT C02 H1 SINGLE n 1.092 0.0100 0.968 0.0164 +OKT C02 H2 SINGLE n 1.092 0.0100 0.968 0.0164 +OKT C02 H3 SINGLE n 1.092 0.0100 0.968 0.0164 +OKT "C1'" H4 SINGLE n 1.092 0.0100 0.992 0.0194 +OKT "C2'" H5 SINGLE n 1.092 0.0100 1.000 0.0100 +OKT "C3'" H6 SINGLE n 1.092 0.0100 0.991 0.0200 +OKT "C4'" H7 SINGLE n 1.092 0.0100 0.990 0.0200 +OKT C5 H8 SINGLE n 1.085 0.0150 0.939 0.0100 +OKT "C5'" H9 SINGLE n 1.092 0.0100 0.991 0.0200 +OKT "C5'" H10 SINGLE n 1.092 0.0100 0.991 0.0200 +OKT C6 H11 SINGLE n 1.085 0.0150 0.944 0.0121 +OKT N3 H12 SINGLE n 1.013 0.0120 0.872 0.0200 +OKT "O3'" H13 SINGLE n 0.972 0.0180 0.839 0.0200 loop_ _chem_comp_angle.comp_id @@ -111,71 +149,70 @@ _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd -OKT O01 C02 H1 109.434 1.50 -OKT O01 C02 H2 109.434 1.50 -OKT O01 C02 H3 109.434 1.50 -OKT H1 C02 H2 109.541 1.50 -OKT H1 C02 H3 109.541 1.50 -OKT H2 C02 H3 109.541 1.50 -OKT N1 "C1'" "O4'" 108.667 1.50 -OKT N1 "C1'" "C2'" 113.620 1.99 -OKT N1 "C1'" H4 109.166 1.50 -OKT "O4'" "C1'" "C2'" 106.391 1.51 -OKT "O4'" "C1'" H4 109.327 1.50 -OKT "C2'" "C1'" H4 109.527 1.54 -OKT N3 C2 N1 114.848 1.50 -OKT N3 C2 O2 122.311 1.50 -OKT N1 C2 O2 122.841 1.50 -OKT "C1'" "C2'" "C3'" 101.207 1.50 -OKT "C1'" "C2'" O01 110.738 2.44 -OKT "C1'" "C2'" H5 110.561 1.96 -OKT "C3'" "C2'" O01 112.623 3.00 -OKT "C3'" "C2'" H5 110.255 2.04 -OKT O01 "C2'" H5 110.257 1.68 -OKT "C4'" "C3'" "C2'" 102.352 1.50 -OKT "C4'" "C3'" "O3'" 111.281 2.46 -OKT "C4'" "C3'" H6 110.452 2.54 -OKT "C2'" "C3'" "O3'" 112.463 2.73 -OKT "C2'" "C3'" H6 110.255 2.04 -OKT "O3'" "C3'" H6 110.380 1.67 -OKT O4 C4 C5 125.940 1.50 -OKT O4 C4 N3 119.401 1.50 -OKT C5 C4 N3 114.659 1.50 -OKT "C5'" "C4'" "O4'" 109.615 1.50 -OKT "C5'" "C4'" "C3'" 116.008 1.52 -OKT "C5'" "C4'" H7 108.268 1.50 -OKT "O4'" "C4'" "C3'" 104.439 1.50 -OKT "O4'" "C4'" H7 108.698 1.50 -OKT "C3'" "C4'" H7 109.363 1.86 -OKT C4 C5 C6 119.525 1.50 -OKT C4 C5 H8 120.151 1.50 -OKT C6 C5 H8 120.325 1.50 -OKT "O5'" "C5'" "C4'" 109.510 1.50 -OKT "O5'" "C5'" H9 109.821 1.50 -OKT "O5'" "C5'" H10 109.821 1.50 -OKT "C4'" "C5'" H9 109.624 1.50 -OKT "C4'" "C5'" H10 109.624 1.50 -OKT H9 "C5'" H10 108.472 1.50 -OKT C5 C6 N1 122.557 1.50 -OKT C5 C6 H11 118.966 1.50 -OKT N1 C6 H11 118.477 1.50 -OKT C6 N1 C2 121.419 1.50 -OKT C6 N1 "C1'" 121.471 1.52 -OKT C2 N1 "C1'" 117.109 1.50 -OKT C4 N3 C2 126.992 1.50 -OKT C4 N3 H12 117.236 1.73 -OKT C2 N3 H12 115.772 1.79 -OKT "C2'" O01 C02 113.084 1.50 -OKT "C3'" "O3'" H13 108.744 3.00 -OKT "C4'" "O4'" "C1'" 109.578 1.50 -OKT P "O5'" "C5'" 119.135 1.78 -OKT S01 P OP1 111.281 3.00 -OKT S01 P "O5'" 105.685 3.00 -OKT S01 P OP3 111.281 3.00 -OKT OP1 P "O5'" 108.530 2.45 -OKT OP1 P OP3 116.964 2.85 -OKT "O5'" P OP3 108.530 2.45 -OKT P S01 H15 109.471 3.00 +OKT O01 C02 H1 109.455 1.50 +OKT O01 C02 H2 109.455 1.50 +OKT O01 C02 H3 109.455 1.50 +OKT H1 C02 H2 109.475 1.50 +OKT H1 C02 H3 109.475 1.50 +OKT H2 C02 H3 109.475 1.50 +OKT N1 "C1'" "O4'" 108.138 1.50 +OKT N1 "C1'" "C2'" 113.630 2.26 +OKT N1 "C1'" H4 109.374 1.50 +OKT "O4'" "C1'" "C2'" 106.317 2.77 +OKT "O4'" "C1'" H4 109.439 1.50 +OKT "C2'" "C1'" H4 109.683 1.50 +OKT N3 C2 N1 114.681 1.50 +OKT N3 C2 O2 122.337 1.50 +OKT N1 C2 O2 122.984 1.50 +OKT "C1'" "C2'" "C3'" 101.790 1.50 +OKT "C1'" "C2'" O01 111.051 2.25 +OKT "C1'" "C2'" H5 111.550 1.50 +OKT "C3'" "C2'" O01 112.208 3.00 +OKT "C3'" "C2'" H5 110.368 2.92 +OKT O01 "C2'" H5 110.925 1.50 +OKT "C4'" "C3'" "C2'" 102.511 1.50 +OKT "C4'" "C3'" "O3'" 110.713 3.00 +OKT "C4'" "C3'" H6 110.577 3.00 +OKT "C2'" "C3'" "O3'" 112.059 3.00 +OKT "C2'" "C3'" H6 110.368 2.92 +OKT "O3'" "C3'" H6 110.541 2.08 +OKT O4 C4 C5 125.762 1.50 +OKT O4 C4 N3 119.595 1.50 +OKT C5 C4 N3 114.643 1.50 +OKT "C5'" "C4'" "O4'" 110.351 1.93 +OKT "C5'" "C4'" "C3'" 115.288 1.50 +OKT "C5'" "C4'" H7 108.351 1.59 +OKT "O4'" "C4'" "C3'" 105.071 1.50 +OKT "O4'" "C4'" H7 108.778 1.50 +OKT "C3'" "C4'" H7 109.322 2.54 +OKT C4 C5 C6 119.580 1.50 +OKT C4 C5 H8 120.071 1.50 +OKT C6 C5 H8 120.349 1.50 +OKT "O5'" "C5'" "C4'" 109.482 2.30 +OKT "O5'" "C5'" H9 109.954 1.50 +OKT "O5'" "C5'" H10 109.954 1.50 +OKT "C4'" "C5'" H9 109.589 1.50 +OKT "C4'" "C5'" H10 109.589 1.50 +OKT H9 "C5'" H10 108.471 1.50 +OKT C5 C6 N1 122.580 1.50 +OKT C5 C6 H11 118.980 1.53 +OKT N1 C6 H11 118.439 1.84 +OKT C6 N1 C2 121.480 1.50 +OKT C6 N1 "C1'" 120.804 2.33 +OKT C2 N1 "C1'" 117.716 1.50 +OKT C4 N3 C2 127.033 1.50 +OKT C4 N3 H12 117.259 3.00 +OKT C2 N3 H12 115.708 3.00 +OKT "C2'" O01 C02 112.131 1.50 +OKT "C3'" "O3'" H13 109.389 3.00 +OKT "C4'" "O4'" "C1'" 109.821 1.50 +OKT P "O5'" "C5'" 119.085 2.00 +OKT S01 P OP1 116.458 3.00 +OKT S01 P "O5'" 114.928 3.00 +OKT S01 P OP3 116.458 3.00 +OKT OP1 P "O5'" 106.327 3.00 +OKT OP1 P OP3 112.844 3.00 +OKT "O5'" P OP3 106.327 3.00 loop_ _chem_comp_tor.comp_id @@ -187,29 +224,30 @@ _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period -OKT C2e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 -OKT C2e-nyu0 "C4'" "O4'" "C1'" "C2" 340.700 6.300 1 -OKT C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 -OKT C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 -OKT C3e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 -OKT C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 -OKT C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 -OKT C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 -OKT beta P "O5'" "C5'" "C4'" 180.000 10.00 3 -OKT gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 -OKT sp3_sp3_58 H1 C02 O01 "C2'" 180.000 10.0 3 -OKT sp3_sp3_28 "C5'" "O5'" P S01 180.000 10.0 3 -OKT sp3_sp3_27 OP1 P S01 H15 -60.000 10.0 3 -OKT sp3_sp3_47 N1 "C1'" "C2'" O01 180.000 10.0 3 -OKT const_23 O2 C2 N1 C6 180.000 10.0 2 -OKT const_sp2_sp2_3 O2 C2 N3 C4 180.000 5.0 2 -OKT sp3_sp3_55 "C1'" "C2'" O01 C02 180.000 10.0 3 -OKT sp3_sp3_20 O01 "C2'" "C3'" "O3'" -60.000 10.0 3 -OKT sp3_sp3_52 "C4'" "C3'" "O3'" H13 180.000 10.0 3 -OKT const_sp2_sp2_7 O4 C4 N3 C2 180.000 5.0 2 -OKT const_11 O4 C4 C5 C6 180.000 10.0 2 -OKT const_13 C4 C5 C6 N1 0.000 10.0 2 -OKT const_17 C5 C6 N1 C2 0.000 10.0 2 +OKT sp3_sp3_55 H1 C02 O01 "C2'" 180.000 10.0 3 +OKT sp3_sp3_25 "C5'" "O5'" P S01 180.000 10.0 3 +OKT sp2_sp3_1 C6 N1 "C1'" "O4'" 150.000 10.0 6 +OKT sp3_sp3_2 N1 "C1'" "O4'" "C4'" -60.000 10.0 3 +OKT sp3_sp3_44 N1 "C1'" "C2'" O01 180.000 10.0 3 +OKT const_21 N3 C2 N1 C6 0.000 0.0 1 +OKT const_24 O2 C2 N1 "C1'" 0.000 0.0 1 +OKT const_sp2_sp2_1 N1 C2 N3 C4 0.000 0.0 1 +OKT const_sp2_sp2_4 O2 C2 N3 H12 0.000 0.0 1 +OKT sp3_sp3_52 "C1'" "C2'" O01 C02 180.000 10.0 3 +OKT sp3_sp3_20 O01 "C2'" "C3'" "O3'" -60.000 10.0 3 +OKT sp3_sp3_49 "C4'" "C3'" "O3'" H13 180.000 10.0 3 +OKT sp3_sp3_11 "O3'" "C3'" "C4'" "C5'" 60.000 10.0 3 +OKT const_sp2_sp2_5 C5 C4 N3 C2 0.000 0.0 1 +OKT const_sp2_sp2_8 O4 C4 N3 H12 0.000 0.0 1 +OKT const_sp2_sp2_9 N3 C4 C5 C6 0.000 0.0 1 +OKT const_12 O4 C4 C5 H8 0.000 0.0 1 +OKT sp3_sp3_5 "C5'" "C4'" "O4'" "C1'" 180.000 10.0 3 +OKT sp3_sp3_31 "O4'" "C4'" "C5'" "O5'" 180.000 10.0 3 +OKT const_13 C4 C5 C6 N1 0.000 0.0 1 +OKT const_16 H8 C5 C6 H11 0.000 0.0 1 +OKT sp3_sp3_28 "C4'" "C5'" "O5'" P 180.000 10.0 3 +OKT const_17 C5 C6 N1 C2 0.000 0.0 1 +OKT const_20 H11 C6 N1 "C1'" 0.000 0.0 1 loop_ _chem_comp_chir.comp_id @@ -219,11 +257,11 @@ _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign -OKT chir_1 "C1'" "O4'" N1 "C2'" negative -OKT chir_2 "C2'" O01 "C1'" "C3'" negative +OKT chir_1 "C1'" "O4'" N1 "C2'" negative +OKT chir_2 "C2'" O01 "C1'" "C3'" negative OKT chir_3 "C3'" "O3'" "C2'" "C4'" negative OKT chir_4 "C4'" "O4'" "C3'" "C5'" negative -OKT chir_5 P S01 "O5'" OP3 both +OKT chir_5 P S01 "O5'" OP3 both loop_ _chem_comp_plane_atom.comp_id @@ -231,17 +269,17 @@ _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd OKT plan-1 "C1'" 0.020 -OKT plan-1 C2 0.020 -OKT plan-1 C4 0.020 -OKT plan-1 C5 0.020 -OKT plan-1 C6 0.020 -OKT plan-1 H11 0.020 -OKT plan-1 H12 0.020 -OKT plan-1 H8 0.020 -OKT plan-1 N1 0.020 -OKT plan-1 N3 0.020 -OKT plan-1 O2 0.020 -OKT plan-1 O4 0.020 +OKT plan-1 C2 0.020 +OKT plan-1 C4 0.020 +OKT plan-1 C5 0.020 +OKT plan-1 C6 0.020 +OKT plan-1 H11 0.020 +OKT plan-1 H12 0.020 +OKT plan-1 H8 0.020 +OKT plan-1 N1 0.020 +OKT plan-1 N3 0.020 +OKT plan-1 O2 0.020 +OKT plan-1 O4 0.020 loop_ _pdbx_chem_comp_descriptor.comp_id @@ -249,19 +287,27 @@ _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor -OKT InChI InChI 1.03 InChI=1S/C10H15N2O8PS/c1-18-8-7(14)5(4-19-21(16,17)22)20-9(8)12-3-2-6(13)11-10(12)15/h2-3,5,7-9,14H,4H2,1H3,(H,11,13,15)(H2,16,17,22)/t5-,7-,8-,9-/m1/s1 -OKT InChIKey InChI 1.03 IEWLRLDHDVZUFQ-ZOQUXTDFSA-N -OKT SMILES_CANONICAL CACTVS 3.385 CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(S)=O)O[C@H]1N2C=CC(=O)NC2=O -OKT SMILES CACTVS 3.385 CO[CH]1[CH](O)[CH](CO[P](O)(S)=O)O[CH]1N2C=CC(=O)NC2=O +OKT InChI InChI 1.03 InChI=1S/C10H15N2O8PS/c1-18-8-7(14)5(4-19-21(16,17)22)20-9(8)12-3-2-6(13)11-10(12)15/h2-3,5,7-9,14H,4H2,1H3,(H,11,13,15)(H2,16,17,22)/t5-,7-,8-,9-/m1/s1 +OKT InChIKey InChI 1.03 IEWLRLDHDVZUFQ-ZOQUXTDFSA-N +OKT SMILES_CANONICAL CACTVS 3.385 CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(S)=O)O[C@H]1N2C=CC(=O)NC2=O +OKT SMILES CACTVS 3.385 CO[CH]1[CH](O)[CH](CO[P](O)(S)=O)O[CH]1N2C=CC(=O)NC2=O OKT SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CO[C@@H]1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)S)O -OKT SMILES "OpenEye OEToolkits" 2.0.7 COC1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)S)O +OKT SMILES "OpenEye OEToolkits" 2.0.7 COC1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)S)O loop_ _pdbx_chem_comp_description_generator.comp_id _pdbx_chem_comp_description_generator.program_name _pdbx_chem_comp_description_generator.program_version _pdbx_chem_comp_description_generator.descriptor -OKT acedrg 243 "dictionary generator" -OKT acedrg_database 11 "data source" -OKT rdkit 2017.03.2 "Chemoinformatics tool" -OKT refmac5 5.8.0238 "optimization tool" +OKT acedrg 277 "dictionary generator" +OKT acedrg_database 12 "data source" +OKT rdkit 2019.09.1 "Chemoinformatics tool" +OKT refmac5 5.8.0425 "optimization tool" + +loop_ +_chem_comp_alias.comp_id +_chem_comp_alias.group +_chem_comp_alias.atom_id +_chem_comp_alias.atom_id_standard +OKT S-NA S01 S2P +OKT S-NA H13 HO3' diff --git a/p/PST.cif b/p/PST.cif index 0ec1af418..965767ffb 100644 --- a/p/PST.cif +++ b/p/PST.cif @@ -297,3 +297,12 @@ PST acedrg 275 "dictionary generator" PST acedrg_database 12 "data source" PST rdkit 2019.09.1 "Chemoinformatics tool" PST refmac5 5.8.0411 "optimization tool" + +loop_ +_chem_comp_alias.comp_id +_chem_comp_alias.group +_chem_comp_alias.atom_id +_chem_comp_alias.atom_id_standard +PST S-NA SP S2P +PST S-NA OP2 OP3 +PST S-NA HO3 HO3' diff --git a/r/RFJ.cif b/r/RFJ.cif index 796a26d49..7b5d1e5ba 100644 --- a/r/RFJ.cif +++ b/r/RFJ.cif @@ -19,45 +19,45 @@ _chem_comp_atom.charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z -RFJ C C CH3 0 2.028 3.227 -1.409 -RFJ "C1'" C CH1 0 0.666 0.803 0.881 -RFJ C2 C CR6 0 4.916 0.189 0.341 -RFJ "C2'" C CH1 0 0.472 1.895 -0.170 -RFJ "C3'" C CH1 0 -0.855 2.514 0.274 -RFJ C4 C CR56 0 2.766 -0.430 0.243 -RFJ "C4'" C CH1 0 -1.628 1.287 0.775 -RFJ C5 C CR56 0 3.030 -1.679 -0.277 -RFJ "C5'" C CH2 0 -2.454 0.558 -0.256 -RFJ C6 C CR6 0 4.377 -2.057 -0.522 -RFJ C8 C CR15 0 0.901 -1.559 -0.082 -RFJ N1 N NR6 0 5.273 -1.038 -0.175 -RFJ N2 N NH2 0 5.912 1.043 0.615 -RFJ N3 N NRD6 0 3.650 0.548 0.574 -RFJ N7 N NRD5 0 1.847 -2.382 -0.477 -RFJ N9 N NT 0 1.404 -0.357 0.370 -RFJ "O2'" O O2 0 1.563 2.811 -0.128 -RFJ "O3'" O OH1 0 -0.703 3.477 1.311 -RFJ "O4'" O O2 0 -0.617 0.386 1.294 -RFJ "O5'" O O2 0 -3.129 -0.563 0.371 -RFJ O6 O O 0 4.798 -3.129 -0.981 -RFJ OP2 O OP -1 -4.527 -2.567 0.375 -RFJ P P P 0 -4.307 -1.316 -0.427 -RFJ S S S1 0 -5.863 -0.171 -0.643 -RFJ OP3 O OP -1 -3.609 -1.689 -1.712 -RFJ H1 H H 0 2.713 3.906 -1.299 -RFJ H2 H H 0 1.288 3.594 -1.920 -RFJ H3 H H 0 2.402 2.465 -1.881 -RFJ H4 H H 0 1.152 1.180 1.650 -RFJ H5 H H 0 0.375 1.504 -1.074 -RFJ H6 H H 0 -1.320 2.918 -0.504 -RFJ H7 H H 0 -2.222 1.555 1.509 -RFJ H8 H H 0 -1.866 0.233 -0.982 -RFJ H9 H H 0 -3.119 1.177 -0.647 -RFJ H10 H H 0 -0.014 -1.782 -0.107 -RFJ H11 H H 0 6.146 -1.204 -0.303 -RFJ H12 H H 0 5.892 1.516 1.353 -RFJ H13 H H 0 6.582 1.127 0.055 -RFJ "HO3'" H H 0 -0.449 4.210 0.967 +RFJ C C CH3 0 2.028 3.227 -1.409 +RFJ "C1'" C CH1 0 0.666 0.803 0.881 +RFJ C2 C CR6 0 4.916 0.189 0.341 +RFJ "C2'" C CH1 0 0.472 1.895 -0.170 +RFJ "C3'" C CH1 0 -0.855 2.514 0.274 +RFJ C4 C CR56 0 2.766 -0.430 0.243 +RFJ "C4'" C CH1 0 -1.628 1.287 0.775 +RFJ C5 C CR56 0 3.030 -1.679 -0.277 +RFJ "C5'" C CH2 0 -2.454 0.558 -0.256 +RFJ C6 C CR6 0 4.377 -2.057 -0.522 +RFJ C8 C CR15 0 0.901 -1.559 -0.082 +RFJ N1 N NR6 0 5.273 -1.038 -0.175 +RFJ N2 N NH2 0 5.912 1.043 0.615 +RFJ N3 N NRD6 0 3.650 0.548 0.574 +RFJ N7 N NRD5 0 1.847 -2.382 -0.477 +RFJ N9 N NT 0 1.404 -0.357 0.370 +RFJ "O2'" O O2 0 1.563 2.811 -0.128 +RFJ "O3'" O OH1 0 -0.703 3.477 1.311 +RFJ "O4'" O O2 0 -0.617 0.386 1.294 +RFJ "O5'" O O2 0 -3.129 -0.563 0.371 +RFJ O6 O O 0 4.798 -3.129 -0.981 +RFJ OP2 O OP -1 -4.527 -2.567 0.375 +RFJ P P P 0 -4.307 -1.316 -0.427 +RFJ S S S1 0 -5.863 -0.171 -0.643 +RFJ OP3 O OP -1 -3.609 -1.689 -1.712 +RFJ H1 H H 0 2.713 3.906 -1.299 +RFJ H2 H H 0 1.288 3.594 -1.920 +RFJ H3 H H 0 2.402 2.465 -1.881 +RFJ H4 H H 0 1.152 1.180 1.650 +RFJ H5 H H 0 0.375 1.504 -1.074 +RFJ H6 H H 0 -1.320 2.918 -0.504 +RFJ H7 H H 0 -2.222 1.555 1.509 +RFJ H8 H H 0 -1.866 0.233 -0.982 +RFJ H9 H H 0 -3.119 1.177 -0.647 +RFJ H10 H H 0 -0.014 -1.782 -0.107 +RFJ H11 H H 0 6.146 -1.204 -0.303 +RFJ H12 H H 0 5.892 1.516 1.353 +RFJ H13 H H 0 6.582 1.127 0.055 +RFJ "HO3'" H H 0 -0.449 4.210 0.967 loop_ _chem_comp_bond.comp_id @@ -69,46 +69,46 @@ _chem_comp_bond.value_dist_nucleus _chem_comp_bond.value_dist_nucleus_esd _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd -RFJ P S DOUBLE n 1.949 0.0200 1.949 0.0200 -RFJ OP2 P SINGLE n 1.509 0.0200 1.509 0.0200 -RFJ "O5'" P SINGLE n 1.614 0.0178 1.614 0.0178 -RFJ "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 -RFJ "C5'" "O5'" SINGLE n 1.450 0.0166 1.450 0.0166 -RFJ "C4'" "C5'" SINGLE n 1.509 0.0100 1.509 0.0100 -RFJ "C3'" "C4'" SINGLE n 1.535 0.0100 1.535 0.0100 -RFJ "C2'" "C3'" SINGLE n 1.530 0.0134 1.530 0.0134 -RFJ "C4'" "O4'" SINGLE n 1.451 0.0100 1.451 0.0100 -RFJ "C2'" "O2'" SINGLE n 1.423 0.0100 1.423 0.0100 -RFJ "C1'" "C2'" SINGLE n 1.527 0.0100 1.527 0.0100 -RFJ "C1'" "O4'" SINGLE n 1.409 0.0100 1.409 0.0100 -RFJ C8 N7 DOUBLE y 1.312 0.0100 1.312 0.0100 -RFJ C8 N9 SINGLE y 1.372 0.0200 1.372 0.0200 -RFJ C "O2'" SINGLE n 1.423 0.0131 1.423 0.0131 -RFJ C5 N7 SINGLE y 1.390 0.0100 1.390 0.0100 -RFJ "C1'" N9 SINGLE n 1.458 0.0200 1.458 0.0200 -RFJ C4 N9 SINGLE y 1.372 0.0100 1.372 0.0100 -RFJ C4 C5 DOUBLE y 1.377 0.0100 1.377 0.0100 -RFJ C5 C6 SINGLE y 1.417 0.0103 1.417 0.0103 -RFJ C4 N3 SINGLE y 1.355 0.0100 1.355 0.0100 -RFJ C6 O6 DOUBLE n 1.239 0.0100 1.239 0.0100 -RFJ C6 N1 SINGLE y 1.396 0.0107 1.396 0.0107 -RFJ C2 N3 DOUBLE y 1.333 0.0104 1.333 0.0104 -RFJ C2 N1 SINGLE y 1.374 0.0100 1.374 0.0100 -RFJ C2 N2 SINGLE n 1.340 0.0101 1.340 0.0101 -RFJ P OP3 SINGLE n 1.509 0.0200 1.509 0.0200 -RFJ C H1 SINGLE n 1.089 0.0100 0.971 0.0146 -RFJ C H2 SINGLE n 1.089 0.0100 0.971 0.0146 -RFJ C H3 SINGLE n 1.089 0.0100 0.971 0.0146 -RFJ "C1'" H4 SINGLE n 1.089 0.0100 0.984 0.0200 -RFJ "C2'" H5 SINGLE n 1.089 0.0100 0.988 0.0200 -RFJ "C3'" H6 SINGLE n 1.089 0.0100 0.992 0.0200 -RFJ "C4'" H7 SINGLE n 1.089 0.0100 0.981 0.0200 -RFJ "C5'" H8 SINGLE n 1.089 0.0100 0.989 0.0200 -RFJ "C5'" H9 SINGLE n 1.089 0.0100 0.989 0.0200 -RFJ C8 H10 SINGLE n 1.082 0.0130 0.942 0.0170 -RFJ N1 H11 SINGLE n 1.016 0.0100 0.897 0.0200 -RFJ N2 H12 SINGLE n 1.016 0.0100 0.877 0.0200 -RFJ N2 H13 SINGLE n 1.016 0.0100 0.877 0.0200 +RFJ P S DOUBLE n 1.949 0.0200 1.949 0.0200 +RFJ OP2 P SINGLE n 1.509 0.0200 1.509 0.0200 +RFJ "O5'" P SINGLE n 1.614 0.0178 1.614 0.0178 +RFJ "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +RFJ "C5'" "O5'" SINGLE n 1.450 0.0166 1.450 0.0166 +RFJ "C4'" "C5'" SINGLE n 1.509 0.0100 1.509 0.0100 +RFJ "C3'" "C4'" SINGLE n 1.535 0.0100 1.535 0.0100 +RFJ "C2'" "C3'" SINGLE n 1.530 0.0134 1.530 0.0134 +RFJ "C4'" "O4'" SINGLE n 1.451 0.0100 1.451 0.0100 +RFJ "C2'" "O2'" SINGLE n 1.423 0.0100 1.423 0.0100 +RFJ "C1'" "C2'" SINGLE n 1.527 0.0100 1.527 0.0100 +RFJ "C1'" "O4'" SINGLE n 1.409 0.0100 1.409 0.0100 +RFJ C8 N7 DOUBLE y 1.312 0.0100 1.312 0.0100 +RFJ C8 N9 SINGLE y 1.372 0.0200 1.372 0.0200 +RFJ C "O2'" SINGLE n 1.423 0.0131 1.423 0.0131 +RFJ C5 N7 SINGLE y 1.390 0.0100 1.390 0.0100 +RFJ "C1'" N9 SINGLE n 1.458 0.0200 1.458 0.0200 +RFJ C4 N9 SINGLE y 1.372 0.0100 1.372 0.0100 +RFJ C4 C5 DOUBLE y 1.377 0.0100 1.377 0.0100 +RFJ C5 C6 SINGLE y 1.417 0.0103 1.417 0.0103 +RFJ C4 N3 SINGLE y 1.355 0.0100 1.355 0.0100 +RFJ C6 O6 DOUBLE n 1.239 0.0100 1.239 0.0100 +RFJ C6 N1 SINGLE y 1.396 0.0107 1.396 0.0107 +RFJ C2 N3 DOUBLE y 1.333 0.0104 1.333 0.0104 +RFJ C2 N1 SINGLE y 1.374 0.0100 1.374 0.0100 +RFJ C2 N2 SINGLE n 1.340 0.0101 1.340 0.0101 +RFJ P OP3 SINGLE n 1.509 0.0200 1.509 0.0200 +RFJ C H1 SINGLE n 1.089 0.0100 0.971 0.0146 +RFJ C H2 SINGLE n 1.089 0.0100 0.971 0.0146 +RFJ C H3 SINGLE n 1.089 0.0100 0.971 0.0146 +RFJ "C1'" H4 SINGLE n 1.089 0.0100 0.984 0.0200 +RFJ "C2'" H5 SINGLE n 1.089 0.0100 0.988 0.0200 +RFJ "C3'" H6 SINGLE n 1.089 0.0100 0.992 0.0200 +RFJ "C4'" H7 SINGLE n 1.089 0.0100 0.981 0.0200 +RFJ "C5'" H8 SINGLE n 1.089 0.0100 0.989 0.0200 +RFJ "C5'" H9 SINGLE n 1.089 0.0100 0.989 0.0200 +RFJ C8 H10 SINGLE n 1.082 0.0130 0.942 0.0170 +RFJ N1 H11 SINGLE n 1.016 0.0100 0.897 0.0200 +RFJ N2 H12 SINGLE n 1.016 0.0100 0.877 0.0200 +RFJ N2 H13 SINGLE n 1.016 0.0100 0.877 0.0200 RFJ "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 loop_ @@ -118,78 +118,78 @@ _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd -RFJ "O2'" C H1 109.434 1.50 -RFJ "O2'" C H2 109.434 1.50 -RFJ "O2'" C H3 109.434 1.50 -RFJ H1 C H2 109.541 1.50 -RFJ H1 C H3 109.541 1.50 -RFJ H2 C H3 109.541 1.50 -RFJ "C2'" "C1'" "O4'" 106.765 1.50 -RFJ "C2'" "C1'" N9 113.752 2.20 -RFJ "C2'" "C1'" H4 109.263 1.50 -RFJ "O4'" "C1'" N9 108.167 1.51 -RFJ "O4'" "C1'" H4 109.807 1.50 -RFJ N9 "C1'" H4 109.246 1.50 -RFJ N3 C2 N1 123.603 1.50 -RFJ N3 C2 N2 119.821 1.50 -RFJ N1 C2 N2 116.575 1.50 -RFJ "C3'" "C2'" "O2'" 112.623 3.00 -RFJ "C3'" "C2'" "C1'" 101.388 1.50 -RFJ "C3'" "C2'" H5 110.255 2.04 -RFJ "O2'" "C2'" "C1'" 110.738 2.44 -RFJ "O2'" "C2'" H5 110.257 1.68 -RFJ "C1'" "C2'" H5 111.584 1.94 -RFJ "O3'" "C3'" "C4'" 111.281 2.46 -RFJ "O3'" "C3'" "C2'" 112.463 2.73 -RFJ "O3'" "C3'" H6 110.380 1.67 -RFJ "C4'" "C3'" "C2'" 102.352 1.50 -RFJ "C4'" "C3'" H6 110.452 2.54 -RFJ "C2'" "C3'" H6 110.255 2.04 -RFJ N9 C4 C5 106.805 1.69 -RFJ N9 C4 N3 124.984 1.50 -RFJ C5 C4 N3 128.211 1.50 -RFJ "C5'" "C4'" "C3'" 116.008 1.52 -RFJ "C5'" "C4'" "O4'" 109.123 1.50 -RFJ "C5'" "C4'" H7 108.268 1.50 -RFJ "C3'" "C4'" "O4'" 105.388 1.50 -RFJ "C3'" "C4'" H7 109.363 1.86 -RFJ "O4'" "C4'" H7 108.947 1.50 -RFJ N7 C5 C4 110.629 1.50 -RFJ N7 C5 C6 129.975 1.50 -RFJ C4 C5 C6 119.397 1.50 -RFJ "O5'" "C5'" "C4'" 109.510 1.50 -RFJ "O5'" "C5'" H8 109.821 1.50 -RFJ "O5'" "C5'" H9 109.821 1.50 -RFJ "C4'" "C5'" H8 109.624 1.50 -RFJ "C4'" "C5'" H9 109.624 1.50 -RFJ H8 "C5'" H9 108.472 1.50 -RFJ C5 C6 O6 128.244 1.50 -RFJ C5 C6 N1 111.367 1.50 -RFJ O6 C6 N1 120.389 1.50 -RFJ N7 C8 N9 112.130 1.94 -RFJ N7 C8 H10 123.170 1.50 -RFJ N9 C8 H10 124.701 2.19 -RFJ C6 N1 C2 125.351 1.50 -RFJ C6 N1 H11 116.978 2.44 -RFJ C2 N1 H11 117.677 2.71 -RFJ C2 N2 H12 119.868 1.50 -RFJ C2 N2 H13 119.868 1.50 -RFJ H12 N2 H13 120.263 1.96 -RFJ C4 N3 C2 112.066 1.50 -RFJ C8 N7 C5 103.927 1.50 -RFJ C8 N9 "C1'" 126.078 2.46 -RFJ C8 N9 C4 107.594 1.50 -RFJ "C1'" N9 C4 125.158 1.54 -RFJ "C2'" "O2'" C 113.084 1.50 +RFJ "O2'" C H1 109.434 1.50 +RFJ "O2'" C H2 109.434 1.50 +RFJ "O2'" C H3 109.434 1.50 +RFJ H1 C H2 109.541 1.50 +RFJ H1 C H3 109.541 1.50 +RFJ H2 C H3 109.541 1.50 +RFJ "C2'" "C1'" "O4'" 106.765 1.50 +RFJ "C2'" "C1'" N9 113.752 2.20 +RFJ "C2'" "C1'" H4 109.263 1.50 +RFJ "O4'" "C1'" N9 108.167 1.51 +RFJ "O4'" "C1'" H4 109.807 1.50 +RFJ N9 "C1'" H4 109.246 1.50 +RFJ N3 C2 N1 123.603 1.50 +RFJ N3 C2 N2 119.821 1.50 +RFJ N1 C2 N2 116.575 1.50 +RFJ "C3'" "C2'" "O2'" 112.623 3.00 +RFJ "C3'" "C2'" "C1'" 101.388 1.50 +RFJ "C3'" "C2'" H5 110.255 2.04 +RFJ "O2'" "C2'" "C1'" 110.738 2.44 +RFJ "O2'" "C2'" H5 110.257 1.68 +RFJ "C1'" "C2'" H5 111.584 1.94 +RFJ "O3'" "C3'" "C4'" 111.281 2.46 +RFJ "O3'" "C3'" "C2'" 112.463 2.73 +RFJ "O3'" "C3'" H6 110.380 1.67 +RFJ "C4'" "C3'" "C2'" 102.352 1.50 +RFJ "C4'" "C3'" H6 110.452 2.54 +RFJ "C2'" "C3'" H6 110.255 2.04 +RFJ N9 C4 C5 106.805 1.69 +RFJ N9 C4 N3 124.984 1.50 +RFJ C5 C4 N3 128.211 1.50 +RFJ "C5'" "C4'" "C3'" 116.008 1.52 +RFJ "C5'" "C4'" "O4'" 109.123 1.50 +RFJ "C5'" "C4'" H7 108.268 1.50 +RFJ "C3'" "C4'" "O4'" 105.388 1.50 +RFJ "C3'" "C4'" H7 109.363 1.86 +RFJ "O4'" "C4'" H7 108.947 1.50 +RFJ N7 C5 C4 110.629 1.50 +RFJ N7 C5 C6 129.975 1.50 +RFJ C4 C5 C6 119.397 1.50 +RFJ "O5'" "C5'" "C4'" 109.510 1.50 +RFJ "O5'" "C5'" H8 109.821 1.50 +RFJ "O5'" "C5'" H9 109.821 1.50 +RFJ "C4'" "C5'" H8 109.624 1.50 +RFJ "C4'" "C5'" H9 109.624 1.50 +RFJ H8 "C5'" H9 108.472 1.50 +RFJ C5 C6 O6 128.244 1.50 +RFJ C5 C6 N1 111.367 1.50 +RFJ O6 C6 N1 120.389 1.50 +RFJ N7 C8 N9 112.130 1.94 +RFJ N7 C8 H10 123.170 1.50 +RFJ N9 C8 H10 124.701 2.19 +RFJ C6 N1 C2 125.351 1.50 +RFJ C6 N1 H11 116.978 2.44 +RFJ C2 N1 H11 117.677 2.71 +RFJ C2 N2 H12 119.868 1.50 +RFJ C2 N2 H13 119.868 1.50 +RFJ H12 N2 H13 120.263 1.96 +RFJ C4 N3 C2 112.066 1.50 +RFJ C8 N7 C5 103.927 1.50 +RFJ C8 N9 "C1'" 126.078 2.46 +RFJ C8 N9 C4 107.594 1.50 +RFJ "C1'" N9 C4 125.158 1.54 +RFJ "C2'" "O2'" C 113.084 1.50 RFJ "C3'" "O3'" "HO3'" 108.744 3.00 -RFJ "C4'" "O4'" "C1'" 109.903 1.50 -RFJ P "O5'" "C5'" 118.783 1.50 -RFJ S P OP2 116.650 1.50 -RFJ S P "O5'" 113.924 3.00 -RFJ S P OP3 116.650 1.50 -RFJ OP2 P "O5'" 106.518 3.00 -RFJ OP2 P OP3 113.206 2.54 -RFJ "O5'" P OP3 106.518 3.00 +RFJ "C4'" "O4'" "C1'" 109.903 1.50 +RFJ P "O5'" "C5'" 118.783 1.50 +RFJ S P OP2 116.650 1.50 +RFJ S P "O5'" 113.924 3.00 +RFJ S P OP3 116.650 1.50 +RFJ OP2 P "O5'" 106.518 3.00 +RFJ OP2 P OP3 113.206 2.54 +RFJ "O5'" P OP3 106.518 3.00 loop_ _chem_comp_tor.comp_id @@ -201,35 +201,35 @@ _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period -RFJ C2e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 -RFJ C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 -RFJ C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 -RFJ C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 -RFJ C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 -RFJ C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 -RFJ C3e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 -RFJ C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 -RFJ C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 -RFJ C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 -RFJ C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 -RFJ C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 -RFJ beta P "O5'" "C5'" "C4'" 180.000 10.00 3 -RFJ epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 -RFJ gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 -RFJ sp3_sp3_55 H1 C "O2'" "C2'" 180.000 10.0 3 -RFJ const_25 N9 C8 N7 C5 0.000 10.0 2 -RFJ const_22 N7 C8 N9 "C1'" 180.000 10.0 2 -RFJ sp3_sp3_31 "C5'" "O5'" P S 180.000 10.0 3 -RFJ const_31 N2 C2 N1 C6 180.000 10.0 2 -RFJ sp2_sp2_3 N3 C2 N2 H12 0.000 5.0 2 -RFJ const_sp2_sp2_2 N2 C2 N3 C4 180.000 5.0 2 -RFJ sp3_sp3_49 "C3'" "C2'" "O2'" C 180.000 10.0 3 -RFJ const_sp2_sp2_4 N9 C4 N3 C2 180.000 5.0 2 -RFJ const_17 C5 C4 N9 C8 0.000 10.0 2 -RFJ const_sp2_sp2_5 N9 C4 C5 N7 0.000 5.0 2 -RFJ const_27 C4 C5 N7 C8 0.000 10.0 2 -RFJ const_12 N7 C5 C6 O6 0.000 10.0 2 -RFJ const_15 O6 C6 N1 C2 180.000 10.0 2 +RFJ C2e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 +RFJ C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 +RFJ C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 +RFJ C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 +RFJ C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 +RFJ C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 +RFJ C3e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 +RFJ C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 +RFJ C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 +RFJ C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 +RFJ C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 +RFJ C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 +RFJ beta P "O5'" "C5'" "C4'" 180.000 10.00 3 +RFJ epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 +RFJ gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 +RFJ sp3_sp3_55 H1 C "O2'" "C2'" 180.000 10.0 3 +RFJ const_25 N9 C8 N7 C5 0.000 10.0 2 +RFJ const_22 N7 C8 N9 "C1'" 180.000 10.0 2 +RFJ sp3_sp3_31 "C5'" "O5'" P S 180.000 10.0 3 +RFJ const_31 N2 C2 N1 C6 180.000 10.0 2 +RFJ sp2_sp2_3 N3 C2 N2 H12 0.000 5.0 2 +RFJ const_sp2_sp2_2 N2 C2 N3 C4 180.000 5.0 2 +RFJ sp3_sp3_49 "C3'" "C2'" "O2'" C 180.000 10.0 3 +RFJ const_sp2_sp2_4 N9 C4 N3 C2 180.000 5.0 2 +RFJ const_17 C5 C4 N9 C8 0.000 10.0 2 +RFJ const_sp2_sp2_5 N9 C4 C5 N7 0.000 5.0 2 +RFJ const_27 C4 C5 N7 C8 0.000 10.0 2 +RFJ const_12 N7 C5 C6 O6 0.000 10.0 2 +RFJ const_15 O6 C6 N1 C2 180.000 10.0 2 loop_ _chem_comp_chir.comp_id @@ -239,11 +239,11 @@ _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign -RFJ chir_1 "C1'" "O4'" N9 "C2'" negative +RFJ chir_1 "C1'" "O4'" N9 "C2'" negative RFJ chir_2 "C2'" "O2'" "C1'" "C3'" negative RFJ chir_3 "C3'" "O3'" "C2'" "C4'" negative RFJ chir_4 "C4'" "O4'" "C3'" "C5'" negative -RFJ chir_5 P S "O5'" OP2 both +RFJ chir_5 P S "O5'" OP2 both loop_ _chem_comp_plane_atom.comp_id @@ -251,23 +251,23 @@ _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd RFJ plan-1 "C1'" 0.020 -RFJ plan-1 C2 0.020 -RFJ plan-1 C4 0.020 -RFJ plan-1 C5 0.020 -RFJ plan-1 C6 0.020 -RFJ plan-1 C8 0.020 -RFJ plan-1 H10 0.020 -RFJ plan-1 H11 0.020 -RFJ plan-1 N1 0.020 -RFJ plan-1 N2 0.020 -RFJ plan-1 N3 0.020 -RFJ plan-1 N7 0.020 -RFJ plan-1 N9 0.020 -RFJ plan-1 O6 0.020 -RFJ plan-2 C2 0.020 -RFJ plan-2 H12 0.020 -RFJ plan-2 H13 0.020 -RFJ plan-2 N2 0.020 +RFJ plan-1 C2 0.020 +RFJ plan-1 C4 0.020 +RFJ plan-1 C5 0.020 +RFJ plan-1 C6 0.020 +RFJ plan-1 C8 0.020 +RFJ plan-1 H10 0.020 +RFJ plan-1 H11 0.020 +RFJ plan-1 N1 0.020 +RFJ plan-1 N2 0.020 +RFJ plan-1 N3 0.020 +RFJ plan-1 N7 0.020 +RFJ plan-1 N9 0.020 +RFJ plan-1 O6 0.020 +RFJ plan-2 C2 0.020 +RFJ plan-2 H12 0.020 +RFJ plan-2 H13 0.020 +RFJ plan-2 N2 0.020 loop_ _pdbx_chem_comp_descriptor.comp_id @@ -275,20 +275,28 @@ _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor -RFJ SMILES ACDLabs 12.01 COC3C(n2c1N=C(N)NC(c1nc2)=O)OC(C3O)COP(O)(O)=S -RFJ InChI InChI 1.03 InChI=1S/C11H16N5O7PS/c1-21-7-6(17)4(2-22-24(19,20)25)23-10(7)16-3-13-5-8(16)14-11(12)15-9(5)18/h3-4,6-7,10,17H,2H2,1H3,(H2,19,20,25)(H3,12,14,15,18)/t4-,6-,7-,10-/m1/s1 -RFJ InChIKey InChI 1.03 QUDYZWLGVZGRFN-KQYNXXCUSA-N -RFJ SMILES_CANONICAL CACTVS 3.385 CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=S)O[C@H]1n2cnc3C(=O)NC(=Nc23)N -RFJ SMILES CACTVS 3.385 CO[CH]1[CH](O)[CH](CO[P](O)(O)=S)O[CH]1n2cnc3C(=O)NC(=Nc23)N +RFJ SMILES ACDLabs 12.01 COC3C(n2c1N=C(N)NC(c1nc2)=O)OC(C3O)COP(O)(O)=S +RFJ InChI InChI 1.03 InChI=1S/C11H16N5O7PS/c1-21-7-6(17)4(2-22-24(19,20)25)23-10(7)16-3-13-5-8(16)14-11(12)15-9(5)18/h3-4,6-7,10,17H,2H2,1H3,(H2,19,20,25)(H3,12,14,15,18)/t4-,6-,7-,10-/m1/s1 +RFJ InChIKey InChI 1.03 QUDYZWLGVZGRFN-KQYNXXCUSA-N +RFJ SMILES_CANONICAL CACTVS 3.385 CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=S)O[C@H]1n2cnc3C(=O)NC(=Nc23)N +RFJ SMILES CACTVS 3.385 CO[CH]1[CH](O)[CH](CO[P](O)(O)=S)O[CH]1n2cnc3C(=O)NC(=Nc23)N RFJ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CO[C@@H]1[C@@H]([C@H](O[C@H]1n2cnc3c2N=C(NC3=O)N)COP(=S)(O)O)O -RFJ SMILES "OpenEye OEToolkits" 2.0.7 COC1C(C(OC1n2cnc3c2N=C(NC3=O)N)COP(=S)(O)O)O +RFJ SMILES "OpenEye OEToolkits" 2.0.7 COC1C(C(OC1n2cnc3c2N=C(NC3=O)N)COP(=S)(O)O)O loop_ _pdbx_chem_comp_description_generator.comp_id _pdbx_chem_comp_description_generator.program_name _pdbx_chem_comp_description_generator.program_version _pdbx_chem_comp_description_generator.descriptor -RFJ acedrg 243 "dictionary generator" -RFJ acedrg_database 11 "data source" -RFJ rdkit 2017.03.2 "Chemoinformatics tool" -RFJ refmac5 5.8.0238 "optimization tool" +RFJ acedrg 243 "dictionary generator" +RFJ acedrg_database 11 "data source" +RFJ rdkit 2017.03.2 "Chemoinformatics tool" +RFJ refmac5 5.8.0238 "optimization tool" + +loop_ +_chem_comp_alias.comp_id +_chem_comp_alias.group +_chem_comp_alias.atom_id +_chem_comp_alias.atom_id_standard +RFJ S-NA OP2 OP1 +RFJ S-NA S S2P diff --git a/s/SC.cif b/s/SC.cif index a2d1dc140..5348ea37d 100644 --- a/s/SC.cif +++ b/s/SC.cif @@ -7,7 +7,7 @@ _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level -SC SC "2-DEOXY-CYTIDINE-5'-THIOPHOSPHORATE" NON-POLYMER 32 20 . +SC SC "2-DEOXY-CYTIDINE-5'-THIOPHOSPHORATE" S-NA 32 20 . data_comp_SC loop_ @@ -19,38 +19,38 @@ _chem_comp_atom.charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z -SC N1 N NR6 0 2.160 -3.489 -3.830 -SC C2 C CR6 0 2.502 -2.766 -2.672 -SC N3 N NRD6 0 1.514 -2.382 -1.820 -SC C4 C CR6 0 0.232 -2.692 -2.069 -SC C5 C CR16 0 -0.133 -3.430 -3.232 -SC C6 C CR16 0 0.850 -3.807 -4.070 -SC O2 O O 0 3.690 -2.483 -2.447 -SC N4 N NH2 0 -0.686 -2.290 -1.200 -SC "C1'" C CH1 0 3.223 -3.931 -4.776 -SC "C2'" C CH2 0 3.514 -5.425 -4.718 -SC "C3'" C CH1 0 3.020 -5.964 -6.055 -SC "C4'" C CH1 0 3.110 -4.742 -6.958 -SC "O4'" O O2 0 2.801 -3.629 -6.093 -SC "O3'" O OH1 0 3.874 -7.001 -6.528 -SC "C5'" C CH2 0 2.187 -4.749 -8.153 -SC "O5'" O O2 0 0.805 -4.667 -7.711 -SC P P P 0 -0.377 -5.043 -8.740 -SC OP1 O OP -1 -0.176 -6.508 -9.008 -SC S2P S S1 0 -2.105 -4.554 -7.998 -SC OP3 O OP -1 0.021 -4.270 -9.974 -SC H5 H H 0 -1.030 -3.650 -3.411 -SC H6 H H 0 0.641 -4.293 -4.841 -SC HN41 H H 0 -1.499 -2.110 -1.477 -SC HN42 H H 0 -0.480 -2.208 -0.350 -SC "H1'" H H 0 4.060 -3.433 -4.596 -SC "H2'" H H 0 4.476 -5.589 -4.606 -SC "H2''" H H 0 3.036 -5.848 -3.971 -SC "H3'" H H 0 2.088 -6.282 -5.983 -SC "H4'" H H 0 4.038 -4.645 -7.282 -SC "HO3'" H H 0 3.579 -7.284 -7.272 -SC "H5'" H H 0 2.326 -5.580 -8.672 -SC "H5''" H H 0 2.398 -3.979 -8.737 +SC N1 N NR6 0 2.160 -3.489 -3.830 +SC C2 C CR6 0 2.502 -2.766 -2.672 +SC N3 N NRD6 0 1.514 -2.382 -1.820 +SC C4 C CR6 0 0.232 -2.692 -2.069 +SC C5 C CR16 0 -0.133 -3.430 -3.232 +SC C6 C CR16 0 0.850 -3.807 -4.070 +SC O2 O O 0 3.690 -2.483 -2.447 +SC N4 N NH2 0 -0.686 -2.290 -1.200 +SC "C1'" C CH1 0 3.223 -3.931 -4.776 +SC "C2'" C CH2 0 3.514 -5.425 -4.718 +SC "C3'" C CH1 0 3.020 -5.964 -6.055 +SC "C4'" C CH1 0 3.110 -4.742 -6.958 +SC "O4'" O O2 0 2.801 -3.629 -6.093 +SC "O3'" O OH1 0 3.874 -7.001 -6.528 +SC "C5'" C CH2 0 2.187 -4.749 -8.153 +SC "O5'" O O2 0 0.805 -4.667 -7.711 +SC P P P 0 -0.377 -5.043 -8.740 +SC OP1 O OP -1 -0.176 -6.508 -9.008 +SC S2P S S1 0 -2.105 -4.554 -7.998 +SC OP3 O OP -1 0.021 -4.270 -9.974 +SC H5 H H 0 -1.030 -3.650 -3.411 +SC H6 H H 0 0.641 -4.293 -4.841 +SC HN41 H H 0 -1.499 -2.110 -1.477 +SC HN42 H H 0 -0.480 -2.208 -0.350 +SC "H1'" H H 0 4.060 -3.433 -4.596 +SC "H2'" H H 0 4.476 -5.589 -4.606 +SC "H2''" H H 0 3.036 -5.848 -3.971 +SC "H3'" H H 0 2.088 -6.282 -5.983 +SC "H4'" H H 0 4.038 -4.645 -7.282 +SC "HO3'" H H 0 3.579 -7.284 -7.272 +SC "H5'" H H 0 2.326 -5.580 -8.672 +SC "H5''" H H 0 2.398 -3.979 -8.737 loop_ _chem_comp_bond.comp_id @@ -62,38 +62,38 @@ _chem_comp_bond.value_dist_nucleus _chem_comp_bond.value_dist_nucleus_esd _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd -SC N1 C2 SINGLE y 1.397 0.0100 1.397 0.0100 -SC N1 C6 SINGLE y 1.360 0.0118 1.360 0.0118 -SC N1 "C1'" SINGLE n 1.480 0.0115 1.480 0.0115 -SC C2 N3 SINGLE y 1.355 0.0119 1.355 0.0119 -SC C2 O2 DOUBLE n 1.241 0.0100 1.241 0.0100 -SC N3 C4 DOUBLE y 1.339 0.0110 1.339 0.0110 -SC C4 C5 SINGLE y 1.422 0.0123 1.422 0.0123 -SC C4 N4 SINGLE n 1.325 0.0109 1.325 0.0109 -SC C5 C6 DOUBLE y 1.342 0.0100 1.342 0.0100 -SC "C1'" "C2'" SINGLE n 1.520 0.0100 1.520 0.0100 -SC "C1'" "O4'" SINGLE n 1.413 0.0100 1.413 0.0100 -SC "C2'" "C3'" SINGLE n 1.522 0.0100 1.522 0.0100 -SC "C3'" "C4'" SINGLE n 1.526 0.0115 1.526 0.0115 -SC "C3'" "O3'" SINGLE n 1.424 0.0100 1.424 0.0100 -SC "C4'" "O4'" SINGLE n 1.445 0.0100 1.445 0.0100 -SC "C4'" "C5'" SINGLE n 1.509 0.0100 1.509 0.0100 -SC "C5'" "O5'" SINGLE n 1.450 0.0166 1.450 0.0166 -SC "O5'" P SINGLE n 1.614 0.0178 1.614 0.0178 -SC P OP1 SINGLE n 1.509 0.0200 1.509 0.0200 -SC P S2P DOUBLE n 1.949 0.0200 1.949 0.0200 -SC P OP3 SINGLE n 1.509 0.0200 1.509 0.0200 -SC C5 H5 SINGLE n 1.082 0.0130 0.941 0.0174 -SC C6 H6 SINGLE n 1.082 0.0130 0.935 0.0143 -SC N4 HN41 SINGLE n 1.016 0.0100 0.877 0.0200 -SC N4 HN42 SINGLE n 1.016 0.0100 0.877 0.0200 -SC "C1'" "H1'" SINGLE n 1.089 0.0100 0.991 0.0103 -SC "C2'" "H2'" SINGLE n 1.089 0.0100 0.982 0.0200 +SC N1 C2 SINGLE y 1.397 0.0100 1.397 0.0100 +SC N1 C6 SINGLE y 1.360 0.0118 1.360 0.0118 +SC N1 "C1'" SINGLE n 1.480 0.0115 1.480 0.0115 +SC C2 N3 SINGLE y 1.355 0.0119 1.355 0.0119 +SC C2 O2 DOUBLE n 1.241 0.0100 1.241 0.0100 +SC N3 C4 DOUBLE y 1.339 0.0110 1.339 0.0110 +SC C4 C5 SINGLE y 1.422 0.0123 1.422 0.0123 +SC C4 N4 SINGLE n 1.325 0.0109 1.325 0.0109 +SC C5 C6 DOUBLE y 1.342 0.0100 1.342 0.0100 +SC "C1'" "C2'" SINGLE n 1.520 0.0100 1.520 0.0100 +SC "C1'" "O4'" SINGLE n 1.413 0.0100 1.413 0.0100 +SC "C2'" "C3'" SINGLE n 1.522 0.0100 1.522 0.0100 +SC "C3'" "C4'" SINGLE n 1.526 0.0115 1.526 0.0115 +SC "C3'" "O3'" SINGLE n 1.424 0.0100 1.424 0.0100 +SC "C4'" "O4'" SINGLE n 1.445 0.0100 1.445 0.0100 +SC "C4'" "C5'" SINGLE n 1.509 0.0100 1.509 0.0100 +SC "C5'" "O5'" SINGLE n 1.450 0.0166 1.450 0.0166 +SC "O5'" P SINGLE n 1.614 0.0178 1.614 0.0178 +SC P OP1 SINGLE n 1.509 0.0200 1.509 0.0200 +SC P S2P DOUBLE n 1.949 0.0200 1.949 0.0200 +SC P OP3 SINGLE n 1.509 0.0200 1.509 0.0200 +SC C5 H5 SINGLE n 1.082 0.0130 0.941 0.0174 +SC C6 H6 SINGLE n 1.082 0.0130 0.935 0.0143 +SC N4 HN41 SINGLE n 1.016 0.0100 0.877 0.0200 +SC N4 HN42 SINGLE n 1.016 0.0100 0.877 0.0200 +SC "C1'" "H1'" SINGLE n 1.089 0.0100 0.991 0.0103 +SC "C2'" "H2'" SINGLE n 1.089 0.0100 0.982 0.0200 SC "C2'" "H2''" SINGLE n 1.089 0.0100 0.982 0.0200 -SC "C3'" "H3'" SINGLE n 1.089 0.0100 0.988 0.0189 -SC "C4'" "H4'" SINGLE n 1.089 0.0100 0.987 0.0170 +SC "C3'" "H3'" SINGLE n 1.089 0.0100 0.988 0.0189 +SC "C4'" "H4'" SINGLE n 1.089 0.0100 0.987 0.0170 SC "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 -SC "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 +SC "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 SC "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200 loop_ @@ -103,64 +103,64 @@ _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd -SC C2 N1 C6 120.510 1.50 -SC C2 N1 "C1'" 118.777 1.50 -SC C6 N1 "C1'" 120.713 1.50 -SC N1 C2 N3 118.920 1.50 -SC N1 C2 O2 118.716 1.50 -SC N3 C2 O2 122.370 1.50 -SC C2 N3 C4 120.266 1.50 -SC N3 C4 C5 121.269 1.50 -SC N3 C4 N4 117.855 1.50 -SC C5 C4 N4 120.876 1.50 -SC C4 C5 C6 117.808 1.50 -SC C4 C5 H5 121.350 1.50 -SC C6 C5 H5 120.848 1.50 -SC N1 C6 C5 121.215 1.50 -SC N1 C6 H6 118.510 1.50 -SC C5 C6 H6 120.275 1.75 -SC C4 N4 HN41 119.818 1.59 -SC C4 N4 HN42 119.818 1.59 -SC HN41 N4 HN42 120.363 1.85 -SC N1 "C1'" "C2'" 114.268 1.50 -SC N1 "C1'" "O4'" 107.584 1.50 -SC N1 "C1'" "H1'" 109.342 1.50 -SC "C2'" "C1'" "O4'" 106.308 1.50 -SC "C2'" "C1'" "H1'" 109.741 1.50 -SC "O4'" "C1'" "H1'" 109.550 1.50 -SC "C1'" "C2'" "C3'" 102.834 1.50 -SC "C1'" "C2'" "H2'" 111.187 1.50 +SC C2 N1 C6 120.510 1.50 +SC C2 N1 "C1'" 118.777 1.50 +SC C6 N1 "C1'" 120.713 1.50 +SC N1 C2 N3 118.920 1.50 +SC N1 C2 O2 118.716 1.50 +SC N3 C2 O2 122.370 1.50 +SC C2 N3 C4 120.266 1.50 +SC N3 C4 C5 121.269 1.50 +SC N3 C4 N4 117.855 1.50 +SC C5 C4 N4 120.876 1.50 +SC C4 C5 C6 117.808 1.50 +SC C4 C5 H5 121.350 1.50 +SC C6 C5 H5 120.848 1.50 +SC N1 C6 C5 121.215 1.50 +SC N1 C6 H6 118.510 1.50 +SC C5 C6 H6 120.275 1.75 +SC C4 N4 HN41 119.818 1.59 +SC C4 N4 HN42 119.818 1.59 +SC HN41 N4 HN42 120.363 1.85 +SC N1 "C1'" "C2'" 114.268 1.50 +SC N1 "C1'" "O4'" 107.584 1.50 +SC N1 "C1'" "H1'" 109.342 1.50 +SC "C2'" "C1'" "O4'" 106.308 1.50 +SC "C2'" "C1'" "H1'" 109.741 1.50 +SC "O4'" "C1'" "H1'" 109.550 1.50 +SC "C1'" "C2'" "C3'" 102.834 1.50 +SC "C1'" "C2'" "H2'" 111.187 1.50 SC "C1'" "C2'" "H2''" 111.187 1.50 -SC "C3'" "C2'" "H2'" 111.310 1.50 +SC "C3'" "C2'" "H2'" 111.310 1.50 SC "C3'" "C2'" "H2''" 111.310 1.50 SC "H2'" "C2'" "H2''" 108.952 1.50 -SC "C2'" "C3'" "C4'" 102.800 1.50 -SC "C2'" "C3'" "O3'" 110.636 2.59 -SC "C2'" "C3'" "H3'" 110.862 1.50 -SC "C4'" "C3'" "O3'" 110.527 2.37 -SC "C4'" "C3'" "H3'" 110.775 1.50 -SC "O3'" "C3'" "H3'" 110.713 1.50 -SC "C3'" "C4'" "O4'" 105.770 1.50 -SC "C3'" "C4'" "C5'" 114.866 1.63 -SC "C3'" "C4'" "H4'" 109.069 1.50 -SC "O4'" "C4'" "C5'" 109.615 1.50 -SC "O4'" "C4'" "H4'" 108.698 1.50 -SC "C5'" "C4'" "H4'" 108.268 1.50 -SC "C1'" "O4'" "C4'" 109.692 1.50 +SC "C2'" "C3'" "C4'" 102.800 1.50 +SC "C2'" "C3'" "O3'" 110.636 2.59 +SC "C2'" "C3'" "H3'" 110.862 1.50 +SC "C4'" "C3'" "O3'" 110.527 2.37 +SC "C4'" "C3'" "H3'" 110.775 1.50 +SC "O3'" "C3'" "H3'" 110.713 1.50 +SC "C3'" "C4'" "O4'" 105.770 1.50 +SC "C3'" "C4'" "C5'" 114.866 1.63 +SC "C3'" "C4'" "H4'" 109.069 1.50 +SC "O4'" "C4'" "C5'" 109.615 1.50 +SC "O4'" "C4'" "H4'" 108.698 1.50 +SC "C5'" "C4'" "H4'" 108.268 1.50 +SC "C1'" "O4'" "C4'" 109.692 1.50 SC "C3'" "O3'" "HO3'" 109.026 2.38 -SC "C4'" "C5'" "O5'" 109.510 1.50 -SC "C4'" "C5'" "H5'" 109.624 1.50 +SC "C4'" "C5'" "O5'" 109.510 1.50 +SC "C4'" "C5'" "H5'" 109.624 1.50 SC "C4'" "C5'" "H5''" 109.624 1.50 -SC "O5'" "C5'" "H5'" 109.821 1.50 +SC "O5'" "C5'" "H5'" 109.821 1.50 SC "O5'" "C5'" "H5''" 109.821 1.50 SC "H5'" "C5'" "H5''" 108.472 1.50 -SC "C5'" "O5'" P 118.783 1.50 -SC "O5'" P OP1 106.518 3.00 -SC "O5'" P S2P 113.924 3.00 -SC "O5'" P OP3 106.518 3.00 -SC OP1 P S2P 116.650 1.50 -SC OP1 P OP3 113.206 2.54 -SC S2P P OP3 116.650 1.50 +SC "C5'" "O5'" P 118.783 1.50 +SC "O5'" P OP1 106.518 3.00 +SC "O5'" P S2P 113.924 3.00 +SC "O5'" P OP3 106.518 3.00 +SC OP1 P S2P 116.650 1.50 +SC OP1 P OP3 113.206 2.54 +SC S2P P OP3 116.650 1.50 loop_ _chem_comp_tor.comp_id @@ -172,29 +172,29 @@ _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period -SC C2e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 -SC C2e-nyu0 "C4'" "O4'" "C1'" "C2" 340.700 6.300 1 -SC C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 -SC C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 -SC C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 -SC C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 -SC C3e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 -SC C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 -SC C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 -SC C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 -SC C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 -SC C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 -SC alpha "C5'" "O5'" P OP3 -60.000 10.00 3 -SC beta P "O5'" "C5'" "C4'" 180.000 10.00 3 -SC epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 -SC gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 -SC const_sp2_sp2_3 O2 C2 N1 C6 180.000 5.0 2 -SC const_17 C5 C6 N1 C2 0.000 10.0 2 -SC const_sp2_sp2_6 O2 C2 N3 C4 180.000 5.0 2 -SC const_sp2_sp2_8 N4 C4 N3 C2 180.000 5.0 2 -SC const_11 N4 C4 C5 C6 180.000 10.0 2 -SC sp2_sp2_3 N3 C4 N4 HN41 0.000 5.0 2 -SC const_13 C4 C5 C6 N1 0.000 10.0 2 +SC C2e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 +SC C2e-nyu0 "C4'" "O4'" "C1'" "C2" 340.700 6.300 1 +SC C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 +SC C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 +SC C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 +SC C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 +SC C3e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 +SC C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 +SC C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 +SC C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 +SC C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 +SC C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 +SC alpha "C5'" "O5'" P OP3 -60.000 10.00 3 +SC beta P "O5'" "C5'" "C4'" 180.000 10.00 3 +SC epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 +SC gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 +SC const_sp2_sp2_3 O2 C2 N1 C6 180.000 5.0 2 +SC const_17 C5 C6 N1 C2 0.000 10.0 2 +SC const_sp2_sp2_6 O2 C2 N3 C4 180.000 5.0 2 +SC const_sp2_sp2_8 N4 C4 N3 C2 180.000 5.0 2 +SC const_11 N4 C4 C5 C6 180.000 10.0 2 +SC sp2_sp2_3 N3 C4 N4 HN41 0.000 5.0 2 +SC const_13 C4 C5 C6 N1 0.000 10.0 2 loop_ _chem_comp_chir.comp_id @@ -204,10 +204,10 @@ _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign -SC chir_1 "C1'" "O4'" N1 "C2'" negative +SC chir_1 "C1'" "O4'" N1 "C2'" negative SC chir_2 "C3'" "O3'" "C4'" "C2'" positive SC chir_3 "C4'" "O4'" "C3'" "C5'" negative -SC chir_4 P S2P "O5'" OP1 both +SC chir_4 P S2P "O5'" OP1 both loop_ _chem_comp_plane_atom.comp_id @@ -215,20 +215,20 @@ _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd SC plan-1 "C1'" 0.020 -SC plan-1 C2 0.020 -SC plan-1 C4 0.020 -SC plan-1 C5 0.020 -SC plan-1 C6 0.020 -SC plan-1 H5 0.020 -SC plan-1 H6 0.020 -SC plan-1 N1 0.020 -SC plan-1 N3 0.020 -SC plan-1 N4 0.020 -SC plan-1 O2 0.020 -SC plan-2 C4 0.020 -SC plan-2 HN41 0.020 -SC plan-2 HN42 0.020 -SC plan-2 N4 0.020 +SC plan-1 C2 0.020 +SC plan-1 C4 0.020 +SC plan-1 C5 0.020 +SC plan-1 C6 0.020 +SC plan-1 H5 0.020 +SC plan-1 H6 0.020 +SC plan-1 N1 0.020 +SC plan-1 N3 0.020 +SC plan-1 N4 0.020 +SC plan-1 O2 0.020 +SC plan-2 C4 0.020 +SC plan-2 HN41 0.020 +SC plan-2 HN42 0.020 +SC plan-2 N4 0.020 loop_ _pdbx_chem_comp_descriptor.comp_id @@ -236,20 +236,20 @@ _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor -SC SMILES ACDLabs 10.04 O=C1N=C(N)C=CN1C2OC(C(O)C2)COP(=S)(O)O -SC SMILES_CANONICAL CACTVS 3.341 NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=S)O2 -SC SMILES CACTVS 3.341 NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(O)=S)O2 +SC SMILES ACDLabs 10.04 O=C1N=C(N)C=CN1C2OC(C(O)C2)COP(=S)(O)O +SC SMILES_CANONICAL CACTVS 3.341 NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=S)O2 +SC SMILES CACTVS 3.341 NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(O)=S)O2 SC SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=S)(O)O)O -SC SMILES "OpenEye OEToolkits" 1.5.0 C1C(C(OC1N2C=CC(=NC2=O)N)COP(=S)(O)O)O -SC InChI InChI 1.03 InChI=1S/C9H14N3O6PS/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(18-8)4-17-19(15,16)20/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,20)/t5-,6+,8+/m0/s1 -SC InChIKey InChI 1.03 FHBXKBNKQMSUIJ-SHYZEUOFSA-N +SC SMILES "OpenEye OEToolkits" 1.5.0 C1C(C(OC1N2C=CC(=NC2=O)N)COP(=S)(O)O)O +SC InChI InChI 1.03 InChI=1S/C9H14N3O6PS/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(18-8)4-17-19(15,16)20/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,20)/t5-,6+,8+/m0/s1 +SC InChIKey InChI 1.03 FHBXKBNKQMSUIJ-SHYZEUOFSA-N loop_ _pdbx_chem_comp_description_generator.comp_id _pdbx_chem_comp_description_generator.program_name _pdbx_chem_comp_description_generator.program_version _pdbx_chem_comp_description_generator.descriptor -SC acedrg 243 "dictionary generator" -SC acedrg_database 11 "data source" -SC rdkit 2017.03.2 "Chemoinformatics tool" -SC refmac5 5.8.0238 "optimization tool" +SC acedrg 243 "dictionary generator" +SC acedrg_database 11 "data source" +SC rdkit 2017.03.2 "Chemoinformatics tool" +SC refmac5 5.8.0238 "optimization tool" diff --git a/s/SRA.cif b/s/SRA.cif index ddce6cefd..0c53231bd 100644 --- a/s/SRA.cif +++ b/s/SRA.cif @@ -7,7 +7,7 @@ _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level -SRA SRA "ADENOSINE -5'-THIO-MONOPHOSPHATE" NON-POLYMER 35 23 . +SRA SRA "ADENOSINE -5'-THIO-MONOPHOSPHATE" S-NA 35 23 . data_comp_SRA loop_ @@ -19,41 +19,41 @@ _chem_comp_atom.charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z -SRA P P P 0 -2.967 -1.628 2.851 -SRA OP1 O OP -1 -2.307 -0.278 2.956 -SRA S2P S S1 0 -4.710 -1.642 1.994 -SRA OP3 O OP -1 -2.932 -2.278 4.214 -SRA "O5'" O O2 0 -1.928 -2.511 1.989 -SRA "C5'" C CH2 0 -0.759 -3.084 2.633 -SRA "C4'" C CH1 0 0.228 -3.545 1.587 -SRA "O4'" O O2 0 -0.439 -4.410 0.632 -SRA "C3'" C CH1 0 0.865 -2.451 0.725 -SRA "O3'" O OH1 0 1.980 -1.861 1.382 -SRA "C2'" C CH1 0 1.264 -3.241 -0.525 -SRA "C1'" C CH1 0 0.104 -4.228 -0.660 -SRA N9 N NR5 0 -0.944 -3.785 -1.577 -SRA C8 C CR15 0 -2.241 -3.436 -1.283 -SRA N7 N NRD5 0 -2.941 -3.086 -2.333 -SRA C5 C CR56 0 -2.058 -3.213 -3.393 -SRA C6 C CR6 0 -2.197 -2.988 -4.780 -SRA N6 N NH2 0 -3.325 -2.572 -5.349 -SRA N1 N NRD6 0 -1.113 -3.211 -5.567 -SRA C2 C CR16 0 0.022 -3.631 -4.987 -SRA N3 N NRD6 0 0.267 -3.875 -3.698 -SRA C4 C CR56 0 -0.823 -3.648 -2.941 -SRA "O2'" O OH1 0 2.493 -3.920 -0.375 -SRA "H5'" H H 0 -1.028 -3.854 3.193 -SRA "H5''" H H 0 -0.332 -2.408 3.215 -SRA "H4'" H H 0 0.935 -4.055 2.037 -SRA "H3'" H H 0 0.195 -1.757 0.495 -SRA "HO3'" H H 0 2.364 -1.328 0.844 -SRA "H2'" H H 0 1.306 -2.639 -1.314 -SRA "H1'" H H 0 0.463 -5.087 -0.981 -SRA H8 H H 0 -2.595 -3.445 -0.412 -SRA HN61 H H 0 -3.537 -2.852 -6.154 -SRA HN62 H H 0 -3.853 -2.021 -4.916 -SRA H2 H H 0 0.750 -3.774 -5.573 -SRA "HO2'" H H 0 2.764 -4.176 -1.138 +SRA P P P 0 -2.967 -1.628 2.851 +SRA OP1 O OP -1 -2.307 -0.278 2.956 +SRA S2P S S1 0 -4.710 -1.642 1.994 +SRA OP3 O OP -1 -2.932 -2.278 4.214 +SRA "O5'" O O2 0 -1.928 -2.511 1.989 +SRA "C5'" C CH2 0 -0.759 -3.084 2.633 +SRA "C4'" C CH1 0 0.228 -3.545 1.587 +SRA "O4'" O O2 0 -0.439 -4.410 0.632 +SRA "C3'" C CH1 0 0.865 -2.451 0.725 +SRA "O3'" O OH1 0 1.980 -1.861 1.382 +SRA "C2'" C CH1 0 1.264 -3.241 -0.525 +SRA "C1'" C CH1 0 0.104 -4.228 -0.660 +SRA N9 N NR5 0 -0.944 -3.785 -1.577 +SRA C8 C CR15 0 -2.241 -3.436 -1.283 +SRA N7 N NRD5 0 -2.941 -3.086 -2.333 +SRA C5 C CR56 0 -2.058 -3.213 -3.393 +SRA C6 C CR6 0 -2.197 -2.988 -4.780 +SRA N6 N NH2 0 -3.325 -2.572 -5.349 +SRA N1 N NRD6 0 -1.113 -3.211 -5.567 +SRA C2 C CR16 0 0.022 -3.631 -4.987 +SRA N3 N NRD6 0 0.267 -3.875 -3.698 +SRA C4 C CR56 0 -0.823 -3.648 -2.941 +SRA "O2'" O OH1 0 2.493 -3.920 -0.375 +SRA "H5'" H H 0 -1.028 -3.854 3.193 +SRA "H5''" H H 0 -0.332 -2.408 3.215 +SRA "H4'" H H 0 0.935 -4.055 2.037 +SRA "H3'" H H 0 0.195 -1.757 0.495 +SRA "HO3'" H H 0 2.364 -1.328 0.844 +SRA "H2'" H H 0 1.306 -2.639 -1.314 +SRA "H1'" H H 0 0.463 -5.087 -0.981 +SRA H8 H H 0 -2.595 -3.445 -0.412 +SRA HN61 H H 0 -3.537 -2.852 -6.154 +SRA HN62 H H 0 -3.853 -2.021 -4.916 +SRA H2 H H 0 0.750 -3.774 -5.573 +SRA "HO2'" H H 0 2.764 -4.176 -1.138 loop_ _chem_comp_bond.comp_id @@ -65,42 +65,42 @@ _chem_comp_bond.value_dist_nucleus _chem_comp_bond.value_dist_nucleus_esd _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd -SRA P OP1 SINGLE n 1.509 0.0200 1.509 0.0200 -SRA P S2P DOUBLE n 1.949 0.0200 1.949 0.0200 -SRA P OP3 SINGLE n 1.509 0.0200 1.509 0.0200 -SRA P "O5'" SINGLE n 1.614 0.0178 1.614 0.0178 -SRA "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 -SRA "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 -SRA "C4'" "O4'" SINGLE n 1.451 0.0100 1.451 0.0100 -SRA "C4'" "C3'" SINGLE n 1.535 0.0100 1.535 0.0100 -SRA "O4'" "C1'" SINGLE n 1.409 0.0100 1.409 0.0100 -SRA "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 -SRA "C3'" "C2'" SINGLE n 1.531 0.0100 1.531 0.0100 -SRA "C2'" "C1'" SINGLE n 1.525 0.0100 1.525 0.0100 -SRA "C2'" "O2'" SINGLE n 1.411 0.0100 1.411 0.0100 -SRA "C1'" N9 SINGLE n 1.458 0.0100 1.458 0.0100 -SRA N9 C8 SINGLE y 1.372 0.0100 1.372 0.0100 -SRA N9 C4 SINGLE y 1.374 0.0101 1.374 0.0101 -SRA C8 N7 DOUBLE y 1.310 0.0100 1.310 0.0100 -SRA N7 C5 SINGLE y 1.388 0.0100 1.388 0.0100 -SRA C5 C6 SINGLE y 1.408 0.0100 1.408 0.0100 -SRA C5 C4 DOUBLE y 1.381 0.0100 1.381 0.0100 -SRA C6 N6 SINGLE n 1.330 0.0100 1.330 0.0100 -SRA C6 N1 DOUBLE y 1.354 0.0100 1.354 0.0100 -SRA N1 C2 SINGLE y 1.339 0.0100 1.339 0.0100 -SRA C2 N3 DOUBLE y 1.330 0.0100 1.330 0.0100 -SRA N3 C4 SINGLE y 1.343 0.0100 1.343 0.0100 -SRA "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 +SRA P OP1 SINGLE n 1.509 0.0200 1.509 0.0200 +SRA P S2P DOUBLE n 1.949 0.0200 1.949 0.0200 +SRA P OP3 SINGLE n 1.509 0.0200 1.509 0.0200 +SRA P "O5'" SINGLE n 1.614 0.0178 1.614 0.0178 +SRA "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 +SRA "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 +SRA "C4'" "O4'" SINGLE n 1.451 0.0100 1.451 0.0100 +SRA "C4'" "C3'" SINGLE n 1.535 0.0100 1.535 0.0100 +SRA "O4'" "C1'" SINGLE n 1.409 0.0100 1.409 0.0100 +SRA "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +SRA "C3'" "C2'" SINGLE n 1.531 0.0100 1.531 0.0100 +SRA "C2'" "C1'" SINGLE n 1.525 0.0100 1.525 0.0100 +SRA "C2'" "O2'" SINGLE n 1.411 0.0100 1.411 0.0100 +SRA "C1'" N9 SINGLE n 1.458 0.0100 1.458 0.0100 +SRA N9 C8 SINGLE y 1.372 0.0100 1.372 0.0100 +SRA N9 C4 SINGLE y 1.374 0.0101 1.374 0.0101 +SRA C8 N7 DOUBLE y 1.310 0.0100 1.310 0.0100 +SRA N7 C5 SINGLE y 1.388 0.0100 1.388 0.0100 +SRA C5 C6 SINGLE y 1.408 0.0100 1.408 0.0100 +SRA C5 C4 DOUBLE y 1.381 0.0100 1.381 0.0100 +SRA C6 N6 SINGLE n 1.330 0.0100 1.330 0.0100 +SRA C6 N1 DOUBLE y 1.354 0.0100 1.354 0.0100 +SRA N1 C2 SINGLE y 1.339 0.0100 1.339 0.0100 +SRA C2 N3 DOUBLE y 1.330 0.0100 1.330 0.0100 +SRA N3 C4 SINGLE y 1.343 0.0100 1.343 0.0100 +SRA "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 SRA "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200 -SRA "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200 -SRA "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200 +SRA "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200 +SRA "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200 SRA "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 -SRA "C2'" "H2'" SINGLE n 1.089 0.0100 0.994 0.0200 -SRA "C1'" "H1'" SINGLE n 1.089 0.0100 0.984 0.0200 -SRA C8 H8 SINGLE n 1.082 0.0130 0.942 0.0170 -SRA N6 HN61 SINGLE n 1.016 0.0100 0.877 0.0200 -SRA N6 HN62 SINGLE n 1.016 0.0100 0.877 0.0200 -SRA C2 H2 SINGLE n 1.082 0.0130 0.945 0.0200 +SRA "C2'" "H2'" SINGLE n 1.089 0.0100 0.994 0.0200 +SRA "C1'" "H1'" SINGLE n 1.089 0.0100 0.984 0.0200 +SRA C8 H8 SINGLE n 1.082 0.0130 0.942 0.0170 +SRA N6 HN61 SINGLE n 1.016 0.0100 0.877 0.0200 +SRA N6 HN62 SINGLE n 1.016 0.0100 0.877 0.0200 +SRA C2 H2 SINGLE n 1.082 0.0130 0.945 0.0200 SRA "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200 loop_ @@ -110,69 +110,69 @@ _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd -SRA OP1 P S2P 116.650 1.50 -SRA OP1 P OP3 113.206 2.54 -SRA OP1 P "O5'" 106.518 3.00 -SRA S2P P OP3 116.650 1.50 -SRA S2P P "O5'" 113.924 3.00 -SRA OP3 P "O5'" 106.518 3.00 -SRA P "O5'" "C5'" 118.783 1.50 -SRA "O5'" "C5'" "C4'" 109.510 1.50 -SRA "O5'" "C5'" "H5'" 109.821 1.50 +SRA OP1 P S2P 116.650 1.50 +SRA OP1 P OP3 113.206 2.54 +SRA OP1 P "O5'" 106.518 3.00 +SRA S2P P OP3 116.650 1.50 +SRA S2P P "O5'" 113.924 3.00 +SRA OP3 P "O5'" 106.518 3.00 +SRA P "O5'" "C5'" 118.783 1.50 +SRA "O5'" "C5'" "C4'" 109.510 1.50 +SRA "O5'" "C5'" "H5'" 109.821 1.50 SRA "O5'" "C5'" "H5''" 109.821 1.50 -SRA "C4'" "C5'" "H5'" 109.624 1.50 +SRA "C4'" "C5'" "H5'" 109.624 1.50 SRA "C4'" "C5'" "H5''" 109.624 1.50 SRA "H5'" "C5'" "H5''" 108.472 1.50 -SRA "C5'" "C4'" "O4'" 109.123 1.50 -SRA "C5'" "C4'" "C3'" 116.008 1.52 -SRA "C5'" "C4'" "H4'" 108.268 1.50 -SRA "O4'" "C4'" "C3'" 105.388 1.50 -SRA "O4'" "C4'" "H4'" 108.947 1.50 -SRA "C3'" "C4'" "H4'" 109.363 1.86 -SRA "C4'" "O4'" "C1'" 109.903 1.50 -SRA "C4'" "C3'" "O3'" 111.281 2.46 -SRA "C4'" "C3'" "C2'" 102.602 1.50 -SRA "C4'" "C3'" "H3'" 110.452 2.54 -SRA "O3'" "C3'" "C2'" 111.581 2.83 -SRA "O3'" "C3'" "H3'" 110.380 1.67 -SRA "C2'" "C3'" "H3'" 110.504 1.75 +SRA "C5'" "C4'" "O4'" 109.123 1.50 +SRA "C5'" "C4'" "C3'" 116.008 1.52 +SRA "C5'" "C4'" "H4'" 108.268 1.50 +SRA "O4'" "C4'" "C3'" 105.388 1.50 +SRA "O4'" "C4'" "H4'" 108.947 1.50 +SRA "C3'" "C4'" "H4'" 109.363 1.86 +SRA "C4'" "O4'" "C1'" 109.903 1.50 +SRA "C4'" "C3'" "O3'" 111.281 2.46 +SRA "C4'" "C3'" "C2'" 102.602 1.50 +SRA "C4'" "C3'" "H3'" 110.452 2.54 +SRA "O3'" "C3'" "C2'" 111.581 2.83 +SRA "O3'" "C3'" "H3'" 110.380 1.67 +SRA "C2'" "C3'" "H3'" 110.504 1.75 SRA "C3'" "O3'" "HO3'" 108.744 3.00 -SRA "C3'" "C2'" "C1'" 101.239 1.50 -SRA "C3'" "C2'" "O2'" 112.782 2.45 -SRA "C3'" "C2'" "H2'" 110.596 1.51 -SRA "C1'" "C2'" "O2'" 111.715 2.69 -SRA "C1'" "C2'" "H2'" 110.636 1.70 -SRA "O2'" "C2'" "H2'" 110.448 1.97 -SRA "O4'" "C1'" "C2'" 106.047 1.50 -SRA "O4'" "C1'" N9 108.477 1.50 -SRA "O4'" "C1'" "H1'" 109.807 1.50 -SRA "C2'" "C1'" N9 113.824 1.50 -SRA "C2'" "C1'" "H1'" 109.015 1.50 -SRA N9 "C1'" "H1'" 109.561 1.50 -SRA "C1'" N9 C8 126.848 1.91 -SRA "C1'" N9 C4 127.459 1.80 -SRA C8 N9 C4 105.693 1.50 -SRA N9 C8 N7 113.469 1.50 -SRA N9 C8 H8 123.206 1.50 -SRA N7 C8 H8 123.326 1.50 -SRA C8 N7 C5 104.739 1.50 -SRA N7 C5 C6 132.250 1.50 -SRA N7 C5 C4 110.483 1.50 -SRA C6 C5 C4 117.267 1.50 -SRA C5 C6 N6 123.792 1.50 -SRA C5 C6 N1 117.409 1.50 -SRA N6 C6 N1 118.799 1.50 -SRA C6 N6 HN61 119.723 1.50 -SRA C6 N6 HN62 119.723 1.50 -SRA HN61 N6 HN62 120.554 1.88 -SRA C6 N1 C2 118.521 1.50 -SRA N1 C2 N3 129.332 1.50 -SRA N1 C2 H2 115.313 1.50 -SRA N3 C2 H2 115.355 1.50 -SRA C2 N3 C4 110.982 1.50 -SRA N9 C4 C5 105.616 1.50 -SRA N9 C4 N3 127.895 1.50 -SRA C5 C4 N3 126.489 1.50 +SRA "C3'" "C2'" "C1'" 101.239 1.50 +SRA "C3'" "C2'" "O2'" 112.782 2.45 +SRA "C3'" "C2'" "H2'" 110.596 1.51 +SRA "C1'" "C2'" "O2'" 111.715 2.69 +SRA "C1'" "C2'" "H2'" 110.636 1.70 +SRA "O2'" "C2'" "H2'" 110.448 1.97 +SRA "O4'" "C1'" "C2'" 106.047 1.50 +SRA "O4'" "C1'" N9 108.477 1.50 +SRA "O4'" "C1'" "H1'" 109.807 1.50 +SRA "C2'" "C1'" N9 113.824 1.50 +SRA "C2'" "C1'" "H1'" 109.015 1.50 +SRA N9 "C1'" "H1'" 109.561 1.50 +SRA "C1'" N9 C8 126.848 1.91 +SRA "C1'" N9 C4 127.459 1.80 +SRA C8 N9 C4 105.693 1.50 +SRA N9 C8 N7 113.469 1.50 +SRA N9 C8 H8 123.206 1.50 +SRA N7 C8 H8 123.326 1.50 +SRA C8 N7 C5 104.739 1.50 +SRA N7 C5 C6 132.250 1.50 +SRA N7 C5 C4 110.483 1.50 +SRA C6 C5 C4 117.267 1.50 +SRA C5 C6 N6 123.792 1.50 +SRA C5 C6 N1 117.409 1.50 +SRA N6 C6 N1 118.799 1.50 +SRA C6 N6 HN61 119.723 1.50 +SRA C6 N6 HN62 119.723 1.50 +SRA HN61 N6 HN62 120.554 1.88 +SRA C6 N1 C2 118.521 1.50 +SRA N1 C2 N3 129.332 1.50 +SRA N1 C2 H2 115.313 1.50 +SRA N3 C2 H2 115.355 1.50 +SRA C2 N3 C4 110.982 1.50 +SRA N9 C4 C5 105.616 1.50 +SRA N9 C4 N3 127.895 1.50 +SRA C5 C4 N3 126.489 1.50 SRA "C2'" "O2'" "HO2'" 109.103 2.13 loop_ @@ -185,34 +185,34 @@ _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period -SRA C2e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 -SRA C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 -SRA C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 -SRA C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 -SRA C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 -SRA C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 -SRA C3e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 -SRA C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 -SRA C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 -SRA C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 -SRA C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 -SRA C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 -SRA alpha "C5'" "O5'" P OP3 -60.000 10.00 3 -SRA beta P "O5'" "C5'" "C4'" 180.000 10.00 3 -SRA epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 -SRA gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 -SRA sp3_sp3_52 "C3'" "C2'" "O2'" "HO2'" 180.000 10.00 3 -SRA const_14 N7 C8 N9 "C1'" 180.000 10.0 2 -SRA const_26 C5 C4 N9 "C1'" 180.000 10.0 2 -SRA const_17 N9 C8 N7 C5 0.000 10.0 2 -SRA const_20 C6 C5 N7 C8 180.000 10.0 2 -SRA const_sp2_sp2_4 N7 C5 C6 N6 0.000 5.0 2 -SRA const_21 N9 C4 C5 N7 0.000 10.0 2 -SRA sp2_sp2_1 C5 C6 N6 HN61 180.000 5.0 2 -SRA const_sp2_sp2_6 N6 C6 N1 C2 180.000 5.0 2 -SRA const_sp2_sp2_7 N3 C2 N1 C6 0.000 5.0 2 -SRA const_sp2_sp2_9 N1 C2 N3 C4 0.000 5.0 2 -SRA const_12 N9 C4 N3 C2 180.000 10.0 2 +SRA C2e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 +SRA C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 +SRA C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 +SRA C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 +SRA C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 +SRA C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 +SRA C3e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 +SRA C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 +SRA C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 +SRA C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 +SRA C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 +SRA C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 +SRA alpha "C5'" "O5'" P OP3 -60.000 10.00 3 +SRA beta P "O5'" "C5'" "C4'" 180.000 10.00 3 +SRA epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 +SRA gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 +SRA sp3_sp3_52 "C3'" "C2'" "O2'" "HO2'" 180.000 10.00 3 +SRA const_14 N7 C8 N9 "C1'" 180.000 10.0 2 +SRA const_26 C5 C4 N9 "C1'" 180.000 10.0 2 +SRA const_17 N9 C8 N7 C5 0.000 10.0 2 +SRA const_20 C6 C5 N7 C8 180.000 10.0 2 +SRA const_sp2_sp2_4 N7 C5 C6 N6 0.000 5.0 2 +SRA const_21 N9 C4 C5 N7 0.000 10.0 2 +SRA sp2_sp2_1 C5 C6 N6 HN61 180.000 5.0 2 +SRA const_sp2_sp2_6 N6 C6 N1 C2 180.000 5.0 2 +SRA const_sp2_sp2_7 N3 C2 N1 C6 0.000 5.0 2 +SRA const_sp2_sp2_9 N1 C2 N3 C4 0.000 5.0 2 +SRA const_12 N9 C4 N3 C2 180.000 10.0 2 loop_ _chem_comp_chir.comp_id @@ -222,11 +222,11 @@ _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign -SRA chir_1 P S2P "O5'" OP1 both +SRA chir_1 P S2P "O5'" OP1 both SRA chir_2 "C4'" "O4'" "C3'" "C5'" negative SRA chir_3 "C3'" "O3'" "C4'" "C2'" positive SRA chir_4 "C2'" "O2'" "C1'" "C3'" negative -SRA chir_5 "C1'" "O4'" N9 "C2'" negative +SRA chir_5 "C1'" "O4'" N9 "C2'" negative loop_ _chem_comp_plane_atom.comp_id @@ -234,22 +234,22 @@ _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd SRA plan-1 "C1'" 0.020 -SRA plan-1 C2 0.020 -SRA plan-1 C4 0.020 -SRA plan-1 C5 0.020 -SRA plan-1 C6 0.020 -SRA plan-1 C8 0.020 -SRA plan-1 H2 0.020 -SRA plan-1 H8 0.020 -SRA plan-1 N1 0.020 -SRA plan-1 N3 0.020 -SRA plan-1 N6 0.020 -SRA plan-1 N7 0.020 -SRA plan-1 N9 0.020 -SRA plan-2 C6 0.020 -SRA plan-2 HN61 0.020 -SRA plan-2 HN62 0.020 -SRA plan-2 N6 0.020 +SRA plan-1 C2 0.020 +SRA plan-1 C4 0.020 +SRA plan-1 C5 0.020 +SRA plan-1 C6 0.020 +SRA plan-1 C8 0.020 +SRA plan-1 H2 0.020 +SRA plan-1 H8 0.020 +SRA plan-1 N1 0.020 +SRA plan-1 N3 0.020 +SRA plan-1 N6 0.020 +SRA plan-1 N7 0.020 +SRA plan-1 N9 0.020 +SRA plan-2 C6 0.020 +SRA plan-2 HN61 0.020 +SRA plan-2 HN62 0.020 +SRA plan-2 N6 0.020 loop_ _pdbx_chem_comp_descriptor.comp_id @@ -257,20 +257,20 @@ _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor -SRA SMILES ACDLabs 10.04 S=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O -SRA SMILES_CANONICAL CACTVS 3.341 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=S)[C@@H](O)[C@H]3O -SRA SMILES CACTVS 3.341 Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=S)[CH](O)[CH]3O +SRA SMILES ACDLabs 10.04 S=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O +SRA SMILES_CANONICAL CACTVS 3.341 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=S)[C@@H](O)[C@H]3O +SRA SMILES CACTVS 3.341 Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=S)[CH](O)[CH]3O SRA SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=S)(O)O)O)O)N -SRA SMILES "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=S)(O)O)O)O)N -SRA InChI InChI 1.03 InChI=1S/C10H14N5O6PS/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(21-10)1-20-22(18,19)23/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,23)/t4-,6-,7-,10-/m1/s1 -SRA InChIKey InChI 1.03 UBCPYVAQZGCDJO-KQYNXXCUSA-N +SRA SMILES "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=S)(O)O)O)O)N +SRA InChI InChI 1.03 InChI=1S/C10H14N5O6PS/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(21-10)1-20-22(18,19)23/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,23)/t4-,6-,7-,10-/m1/s1 +SRA InChIKey InChI 1.03 UBCPYVAQZGCDJO-KQYNXXCUSA-N loop_ _pdbx_chem_comp_description_generator.comp_id _pdbx_chem_comp_description_generator.program_name _pdbx_chem_comp_description_generator.program_version _pdbx_chem_comp_description_generator.descriptor -SRA acedrg 243 "dictionary generator" -SRA acedrg_database 11 "data source" -SRA rdkit 2017.03.2 "Chemoinformatics tool" -SRA refmac5 5.8.0238 "optimization tool" +SRA acedrg 243 "dictionary generator" +SRA acedrg_database 11 "data source" +SRA rdkit 2017.03.2 "Chemoinformatics tool" +SRA refmac5 5.8.0238 "optimization tool" diff --git a/s/SSU.cif b/s/SSU.cif index 662baa5f4..4118c65c6 100644 --- a/s/SSU.cif +++ b/s/SSU.cif @@ -19,38 +19,38 @@ _chem_comp_atom.charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z -SSU "O2'" O OH1 0 1.450 0.577 2.522 -SSU "C2'" C CH1 0 0.838 0.578 1.249 -SSU "C1'" C CH1 0 1.064 1.936 0.574 -SSU "O4'" O O2 0 2.064 1.773 -0.411 -SSU "C4'" C CH1 0 2.638 0.447 -0.312 -SSU "C5'" C CH2 0 3.167 0.016 -1.658 -SSU "O5'" O O2 0 4.246 0.897 -2.062 -SSU P P P 0 4.780 0.827 -3.578 -SSU S1P S S1 0 3.516 1.654 -4.802 -SSU OP2 O OP -1 5.042 -0.638 -3.802 -SSU OP3 O OP -1 6.104 1.540 -3.453 -SSU "C3'" C CH1 0 1.499 -0.400 0.267 -SSU "O3'" O OH1 0 2.001 -1.569 0.902 -SSU N1 N NR6 0 -0.168 2.472 -0.068 -SSU C6 C CR16 0 -0.650 1.922 -1.239 -SSU C5 C CR16 0 -1.759 2.370 -1.854 -SSU C4 C CR6 0 -2.495 3.462 -1.282 -SSU O4 O O 0 -3.521 3.961 -1.745 -SSU N3 N NR6 0 -1.963 3.964 -0.107 -SSU C2 C CR6 0 -0.832 3.531 0.547 -SSU O2 O O 0 -0.458 4.058 1.589 -SSU "HO2'" H H 0 1.357 -0.187 2.880 -SSU "H2'" H H 0 -0.118 0.387 1.327 -SSU "H1'" H H 0 1.394 2.575 1.241 -SSU "H4'" H H 0 3.386 0.471 0.323 -SSU "H5'" H H 0 2.439 0.049 -2.326 -SSU "H5''" H H 0 3.498 -0.915 -1.601 -SSU "H3'" H H 0 0.858 -0.647 -0.449 -SSU "HO3'" H H 0 2.383 -2.056 0.320 -SSU H6 H H 0 -0.181 1.207 -1.625 -SSU H5 H H 0 -2.051 1.973 -2.648 -SSU H3 H H 0 -2.394 4.643 0.276 +SSU "O2'" O OH1 0 1.450 0.577 2.522 +SSU "C2'" C CH1 0 0.838 0.578 1.249 +SSU "C1'" C CH1 0 1.064 1.936 0.574 +SSU "O4'" O O2 0 2.064 1.773 -0.411 +SSU "C4'" C CH1 0 2.638 0.447 -0.312 +SSU "C5'" C CH2 0 3.167 0.016 -1.658 +SSU "O5'" O O2 0 4.246 0.897 -2.062 +SSU P P P 0 4.780 0.827 -3.578 +SSU S1P S S1 0 3.516 1.654 -4.802 +SSU OP2 O OP -1 5.042 -0.638 -3.802 +SSU OP3 O OP -1 6.104 1.540 -3.453 +SSU "C3'" C CH1 0 1.499 -0.400 0.267 +SSU "O3'" O OH1 0 2.001 -1.569 0.902 +SSU N1 N NR6 0 -0.168 2.472 -0.068 +SSU C6 C CR16 0 -0.650 1.922 -1.239 +SSU C5 C CR16 0 -1.759 2.370 -1.854 +SSU C4 C CR6 0 -2.495 3.462 -1.282 +SSU O4 O O 0 -3.521 3.961 -1.745 +SSU N3 N NR6 0 -1.963 3.964 -0.107 +SSU C2 C CR6 0 -0.832 3.531 0.547 +SSU O2 O O 0 -0.458 4.058 1.589 +SSU "HO2'" H H 0 1.357 -0.187 2.880 +SSU "H2'" H H 0 -0.118 0.387 1.327 +SSU "H1'" H H 0 1.394 2.575 1.241 +SSU "H4'" H H 0 3.386 0.471 0.323 +SSU "H5'" H H 0 2.439 0.049 -2.326 +SSU "H5''" H H 0 3.498 -0.915 -1.601 +SSU "H3'" H H 0 0.858 -0.647 -0.449 +SSU "HO3'" H H 0 2.383 -2.056 0.320 +SSU H6 H H 0 -0.181 1.207 -1.625 +SSU H5 H H 0 -2.051 1.973 -2.648 +SSU H3 H H 0 -2.394 4.643 0.276 loop_ _chem_comp_bond.comp_id @@ -62,39 +62,39 @@ _chem_comp_bond.value_dist_nucleus _chem_comp_bond.value_dist_nucleus_esd _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd -SSU "O2'" "C2'" SINGLE n 1.412 0.0100 1.412 0.0100 -SSU "C2'" "C1'" SINGLE n 1.529 0.0100 1.529 0.0100 -SSU "C2'" "C3'" SINGLE n 1.533 0.0109 1.533 0.0109 -SSU "C1'" "O4'" SINGLE n 1.412 0.0100 1.412 0.0100 -SSU "C1'" N1 SINGLE n 1.476 0.0133 1.476 0.0133 -SSU "O4'" "C4'" SINGLE n 1.451 0.0111 1.451 0.0111 -SSU "C4'" "C5'" SINGLE n 1.509 0.0100 1.509 0.0100 -SSU "C4'" "C3'" SINGLE n 1.535 0.0100 1.535 0.0100 -SSU "C5'" "O5'" SINGLE n 1.450 0.0166 1.450 0.0166 -SSU "O5'" P SINGLE n 1.614 0.0178 1.614 0.0178 -SSU P S1P DOUBLE n 1.949 0.0200 1.949 0.0200 -SSU P OP2 SINGLE n 1.509 0.0200 1.509 0.0200 -SSU P OP3 SINGLE n 1.509 0.0200 1.509 0.0200 -SSU "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 -SSU N1 C6 SINGLE y 1.375 0.0106 1.375 0.0106 -SSU N1 C2 SINGLE y 1.383 0.0100 1.383 0.0100 -SSU C6 C5 DOUBLE y 1.342 0.0100 1.342 0.0100 -SSU C5 C4 SINGLE y 1.434 0.0100 1.434 0.0100 -SSU C4 O4 DOUBLE n 1.231 0.0100 1.231 0.0100 -SSU C4 N3 SINGLE y 1.381 0.0100 1.381 0.0100 -SSU N3 C2 SINGLE y 1.372 0.0112 1.372 0.0112 -SSU C2 O2 DOUBLE n 1.224 0.0111 1.224 0.0111 +SSU "O2'" "C2'" SINGLE n 1.412 0.0100 1.412 0.0100 +SSU "C2'" "C1'" SINGLE n 1.529 0.0100 1.529 0.0100 +SSU "C2'" "C3'" SINGLE n 1.533 0.0109 1.533 0.0109 +SSU "C1'" "O4'" SINGLE n 1.412 0.0100 1.412 0.0100 +SSU "C1'" N1 SINGLE n 1.476 0.0133 1.476 0.0133 +SSU "O4'" "C4'" SINGLE n 1.451 0.0111 1.451 0.0111 +SSU "C4'" "C5'" SINGLE n 1.509 0.0100 1.509 0.0100 +SSU "C4'" "C3'" SINGLE n 1.535 0.0100 1.535 0.0100 +SSU "C5'" "O5'" SINGLE n 1.450 0.0166 1.450 0.0166 +SSU "O5'" P SINGLE n 1.614 0.0178 1.614 0.0178 +SSU P S1P DOUBLE n 1.949 0.0200 1.949 0.0200 +SSU P OP2 SINGLE n 1.509 0.0200 1.509 0.0200 +SSU P OP3 SINGLE n 1.509 0.0200 1.509 0.0200 +SSU "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +SSU N1 C6 SINGLE y 1.375 0.0106 1.375 0.0106 +SSU N1 C2 SINGLE y 1.383 0.0100 1.383 0.0100 +SSU C6 C5 DOUBLE y 1.342 0.0100 1.342 0.0100 +SSU C5 C4 SINGLE y 1.434 0.0100 1.434 0.0100 +SSU C4 O4 DOUBLE n 1.231 0.0100 1.231 0.0100 +SSU C4 N3 SINGLE y 1.381 0.0100 1.381 0.0100 +SSU N3 C2 SINGLE y 1.372 0.0112 1.372 0.0112 +SSU C2 O2 DOUBLE n 1.224 0.0111 1.224 0.0111 SSU "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200 -SSU "C2'" "H2'" SINGLE n 1.089 0.0100 0.978 0.0200 -SSU "C1'" "H1'" SINGLE n 1.089 0.0100 0.981 0.0118 -SSU "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200 -SSU "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 +SSU "C2'" "H2'" SINGLE n 1.089 0.0100 0.978 0.0200 +SSU "C1'" "H1'" SINGLE n 1.089 0.0100 0.981 0.0118 +SSU "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200 +SSU "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 SSU "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200 -SSU "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200 +SSU "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200 SSU "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 -SSU C6 H6 SINGLE n 1.082 0.0130 0.938 0.0107 -SSU C5 H5 SINGLE n 1.082 0.0130 0.935 0.0100 -SSU N3 H3 SINGLE n 1.016 0.0100 0.889 0.0200 +SSU C6 H6 SINGLE n 1.082 0.0130 0.938 0.0107 +SSU C5 H5 SINGLE n 1.082 0.0130 0.935 0.0100 +SSU N3 H3 SINGLE n 1.016 0.0100 0.889 0.0200 loop_ _chem_comp_angle.comp_id @@ -104,63 +104,63 @@ _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd SSU "C2'" "O2'" "HO2'" 109.449 1.85 -SSU "O2'" "C2'" "C1'" 109.476 3.00 -SSU "O2'" "C2'" "C3'" 112.861 2.52 -SSU "O2'" "C2'" "H2'" 111.022 1.77 -SSU "C1'" "C2'" "C3'" 101.269 1.50 -SSU "C1'" "C2'" "H2'" 110.760 1.63 -SSU "C3'" "C2'" "H2'" 110.799 1.82 -SSU "C2'" "C1'" "O4'" 106.825 1.50 -SSU "C2'" "C1'" N1 112.859 1.50 -SSU "C2'" "C1'" "H1'" 109.776 1.83 -SSU "O4'" "C1'" N1 108.667 1.50 -SSU "O4'" "C1'" "H1'" 109.327 1.50 -SSU N1 "C1'" "H1'" 109.166 1.50 -SSU "C1'" "O4'" "C4'" 109.578 1.50 -SSU "O4'" "C4'" "C5'" 109.615 1.50 -SSU "O4'" "C4'" "C3'" 104.439 1.50 -SSU "O4'" "C4'" "H4'" 108.698 1.50 -SSU "C5'" "C4'" "C3'" 116.008 1.52 -SSU "C5'" "C4'" "H4'" 108.268 1.50 -SSU "C3'" "C4'" "H4'" 109.363 1.86 -SSU "C4'" "C5'" "O5'" 109.510 1.50 -SSU "C4'" "C5'" "H5'" 109.624 1.50 +SSU "O2'" "C2'" "C1'" 109.476 3.00 +SSU "O2'" "C2'" "C3'" 112.861 2.52 +SSU "O2'" "C2'" "H2'" 111.022 1.77 +SSU "C1'" "C2'" "C3'" 101.269 1.50 +SSU "C1'" "C2'" "H2'" 110.760 1.63 +SSU "C3'" "C2'" "H2'" 110.799 1.82 +SSU "C2'" "C1'" "O4'" 106.825 1.50 +SSU "C2'" "C1'" N1 112.859 1.50 +SSU "C2'" "C1'" "H1'" 109.776 1.83 +SSU "O4'" "C1'" N1 108.667 1.50 +SSU "O4'" "C1'" "H1'" 109.327 1.50 +SSU N1 "C1'" "H1'" 109.166 1.50 +SSU "C1'" "O4'" "C4'" 109.578 1.50 +SSU "O4'" "C4'" "C5'" 109.615 1.50 +SSU "O4'" "C4'" "C3'" 104.439 1.50 +SSU "O4'" "C4'" "H4'" 108.698 1.50 +SSU "C5'" "C4'" "C3'" 116.008 1.52 +SSU "C5'" "C4'" "H4'" 108.268 1.50 +SSU "C3'" "C4'" "H4'" 109.363 1.86 +SSU "C4'" "C5'" "O5'" 109.510 1.50 +SSU "C4'" "C5'" "H5'" 109.624 1.50 SSU "C4'" "C5'" "H5''" 109.624 1.50 -SSU "O5'" "C5'" "H5'" 109.821 1.50 +SSU "O5'" "C5'" "H5'" 109.821 1.50 SSU "O5'" "C5'" "H5''" 109.821 1.50 SSU "H5'" "C5'" "H5''" 108.472 1.50 -SSU "C5'" "O5'" P 118.783 1.50 -SSU "O5'" P S1P 113.924 3.00 -SSU "O5'" P OP2 106.518 3.00 -SSU "O5'" P OP3 106.518 3.00 -SSU S1P P OP2 116.650 1.50 -SSU S1P P OP3 116.650 1.50 -SSU OP2 P OP3 113.206 2.54 -SSU "C2'" "C3'" "C4'" 102.071 1.50 -SSU "C2'" "C3'" "O3'" 111.993 3.00 -SSU "C2'" "C3'" "H3'" 110.108 1.66 -SSU "C4'" "C3'" "O3'" 111.281 2.46 -SSU "C4'" "C3'" "H3'" 110.452 2.54 -SSU "O3'" "C3'" "H3'" 110.380 1.67 +SSU "C5'" "O5'" P 118.783 1.50 +SSU "O5'" P S1P 113.924 3.00 +SSU "O5'" P OP2 106.518 3.00 +SSU "O5'" P OP3 106.518 3.00 +SSU S1P P OP2 116.650 1.50 +SSU S1P P OP3 116.650 1.50 +SSU OP2 P OP3 113.206 2.54 +SSU "C2'" "C3'" "C4'" 102.071 1.50 +SSU "C2'" "C3'" "O3'" 111.993 3.00 +SSU "C2'" "C3'" "H3'" 110.108 1.66 +SSU "C4'" "C3'" "O3'" 111.281 2.46 +SSU "C4'" "C3'" "H3'" 110.452 2.54 +SSU "O3'" "C3'" "H3'" 110.380 1.67 SSU "C3'" "O3'" "HO3'" 108.744 3.00 -SSU "C1'" N1 C6 121.471 1.52 -SSU "C1'" N1 C2 117.109 1.50 -SSU C6 N1 C2 121.419 1.50 -SSU N1 C6 C5 122.557 1.50 -SSU N1 C6 H6 118.477 1.50 -SSU C5 C6 H6 118.966 1.50 -SSU C6 C5 C4 119.525 1.50 -SSU C6 C5 H5 120.325 1.50 -SSU C4 C5 H5 120.151 1.50 -SSU C5 C4 O4 125.940 1.50 -SSU C5 C4 N3 114.659 1.50 -SSU O4 C4 N3 119.401 1.50 -SSU C4 N3 C2 126.992 1.50 -SSU C4 N3 H3 117.236 1.73 -SSU C2 N3 H3 115.772 1.79 -SSU N1 C2 N3 114.848 1.50 -SSU N1 C2 O2 122.841 1.50 -SSU N3 C2 O2 122.311 1.50 +SSU "C1'" N1 C6 121.471 1.52 +SSU "C1'" N1 C2 117.109 1.50 +SSU C6 N1 C2 121.419 1.50 +SSU N1 C6 C5 122.557 1.50 +SSU N1 C6 H6 118.477 1.50 +SSU C5 C6 H6 118.966 1.50 +SSU C6 C5 C4 119.525 1.50 +SSU C6 C5 H5 120.325 1.50 +SSU C4 C5 H5 120.151 1.50 +SSU C5 C4 O4 125.940 1.50 +SSU C5 C4 N3 114.659 1.50 +SSU O4 C4 N3 119.401 1.50 +SSU C4 N3 C2 126.992 1.50 +SSU C4 N3 H3 117.236 1.73 +SSU C2 N3 H3 115.772 1.79 +SSU N1 C2 N3 114.848 1.50 +SSU N1 C2 O2 122.841 1.50 +SSU N3 C2 O2 122.311 1.50 loop_ _chem_comp_tor.comp_id @@ -172,29 +172,29 @@ _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period -SSU C2e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 -SSU C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 -SSU C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 -SSU C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 -SSU C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 -SSU C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 -SSU C3e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 -SSU C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 -SSU C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 -SSU C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 -SSU C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 -SSU C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 -SSU beta P "O5'" "C5'" "C4'" 180.000 10.00 3 -SSU epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 -SSU gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 -SSU sp3_sp3_25 "C1'" "C2'" "O2'" "HO2'" 180.000 10.0 3 -SSU const_sp2_sp2_2 C5 C6 N1 "C1'" 180.000 5.0 2 -SSU const_24 O2 C2 N1 "C1'" 0.000 10.0 2 -SSU const_sp2_sp2_5 C4 C5 C6 N1 0.000 5.0 2 -SSU const_11 O4 C4 C5 C6 180.000 10.0 2 -SSU const_15 O4 C4 N3 C2 180.000 10.0 2 -SSU const_19 O2 C2 N3 C4 180.000 10.0 2 -SSU sp3_sp3_49 "C5'" "O5'" P S1P 180.000 10.0 3 +SSU C2e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 +SSU C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 +SSU C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 +SSU C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 +SSU C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 +SSU C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 +SSU C3e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 +SSU C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 +SSU C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 +SSU C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 +SSU C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 +SSU C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 +SSU beta P "O5'" "C5'" "C4'" 180.000 10.00 3 +SSU epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 +SSU gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 +SSU sp3_sp3_25 "C1'" "C2'" "O2'" "HO2'" 180.000 10.0 3 +SSU const_sp2_sp2_2 C5 C6 N1 "C1'" 180.000 5.0 2 +SSU const_24 O2 C2 N1 "C1'" 0.000 10.0 2 +SSU const_sp2_sp2_5 C4 C5 C6 N1 0.000 5.0 2 +SSU const_11 O4 C4 C5 C6 180.000 10.0 2 +SSU const_15 O4 C4 N3 C2 180.000 10.0 2 +SSU const_19 O2 C2 N3 C4 180.000 10.0 2 +SSU sp3_sp3_49 "C5'" "O5'" P S1P 180.000 10.0 3 loop_ _chem_comp_chir.comp_id @@ -205,9 +205,9 @@ _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign SSU chir_1 "C2'" "O2'" "C1'" "C3'" negative -SSU chir_2 "C1'" "O4'" N1 "C2'" negative +SSU chir_2 "C1'" "O4'" N1 "C2'" negative SSU chir_3 "C4'" "O4'" "C3'" "C5'" negative -SSU chir_4 P S1P "O5'" OP2 both +SSU chir_4 P S1P "O5'" OP2 both SSU chir_5 "C3'" "O3'" "C4'" "C2'" positive loop_ @@ -216,17 +216,17 @@ _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd SSU plan-1 "C1'" 0.020 -SSU plan-1 C2 0.020 -SSU plan-1 C4 0.020 -SSU plan-1 C5 0.020 -SSU plan-1 C6 0.020 -SSU plan-1 H3 0.020 -SSU plan-1 H5 0.020 -SSU plan-1 H6 0.020 -SSU plan-1 N1 0.020 -SSU plan-1 N3 0.020 -SSU plan-1 O2 0.020 -SSU plan-1 O4 0.020 +SSU plan-1 C2 0.020 +SSU plan-1 C4 0.020 +SSU plan-1 C5 0.020 +SSU plan-1 C6 0.020 +SSU plan-1 H3 0.020 +SSU plan-1 H5 0.020 +SSU plan-1 H6 0.020 +SSU plan-1 N1 0.020 +SSU plan-1 N3 0.020 +SSU plan-1 O2 0.020 +SSU plan-1 O4 0.020 loop_ _pdbx_chem_comp_descriptor.comp_id @@ -234,20 +234,28 @@ _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor -SSU SMILES ACDLabs 10.04 O=C1NC(=O)N(C=C1)C2OC(C(O)C2O)COP(=S)(O)O -SSU SMILES_CANONICAL CACTVS 3.341 O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=S)N2C=CC(=O)NC2=O -SSU SMILES CACTVS 3.341 O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=S)N2C=CC(=O)NC2=O +SSU SMILES ACDLabs 10.04 O=C1NC(=O)N(C=C1)C2OC(C(O)C2O)COP(=S)(O)O +SSU SMILES_CANONICAL CACTVS 3.341 O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=S)N2C=CC(=O)NC2=O +SSU SMILES CACTVS 3.341 O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=S)N2C=CC(=O)NC2=O SSU SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=S)(O)O)O)O -SSU SMILES "OpenEye OEToolkits" 1.5.0 C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=S)(O)O)O)O -SSU InChI InChI 1.03 InChI=1S/C9H13N2O8PS/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(19-8)3-18-20(16,17)21/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,21)/t4-,6-,7-,8-/m1/s1 -SSU InChIKey InChI 1.03 NSEBKRRODBXALJ-XVFCMESISA-N +SSU SMILES "OpenEye OEToolkits" 1.5.0 C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=S)(O)O)O)O +SSU InChI InChI 1.03 InChI=1S/C9H13N2O8PS/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(19-8)3-18-20(16,17)21/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,21)/t4-,6-,7-,8-/m1/s1 +SSU InChIKey InChI 1.03 NSEBKRRODBXALJ-XVFCMESISA-N loop_ _pdbx_chem_comp_description_generator.comp_id _pdbx_chem_comp_description_generator.program_name _pdbx_chem_comp_description_generator.program_version _pdbx_chem_comp_description_generator.descriptor -SSU acedrg 243 "dictionary generator" -SSU acedrg_database 11 "data source" -SSU rdkit 2017.03.2 "Chemoinformatics tool" -SSU refmac5 5.8.0238 "optimization tool" +SSU acedrg 243 "dictionary generator" +SSU acedrg_database 11 "data source" +SSU rdkit 2017.03.2 "Chemoinformatics tool" +SSU refmac5 5.8.0238 "optimization tool" + +loop_ +_chem_comp_alias.comp_id +_chem_comp_alias.group +_chem_comp_alias.atom_id +_chem_comp_alias.atom_id_standard +SSU S-NA OP2 OP1 +SSU S-NA S1P S2P diff --git a/u/U37.cif b/u/U37.cif index ae4bee6a5..7a8746a3a 100644 --- a/u/U37.cif +++ b/u/U37.cif @@ -7,7 +7,7 @@ _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level -U37 U37 "URIDINE 5'-MONOTHIOPHOSPHATE" NON-POLYMER 33 21 . +U37 U37 "URIDINE 5'-MONOTHIOPHOSPHATE" NON-POLYMER 32 21 . data_comp_U37 loop_ @@ -19,39 +19,75 @@ _chem_comp_atom.charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z -U37 O3P O O 0 -16.340 -0.634 38.532 -U37 P P P 0 -17.208 -1.272 37.497 -U37 S S SH1 0 -16.792 -0.446 35.623 -U37 O1P O OP -1 -17.146 -2.763 37.438 -U37 "O5'" O O2 0 -18.720 -0.852 37.810 -U37 "C5'" C CH2 0 -19.343 -1.320 39.033 -U37 "C4'" C CH1 0 -20.720 -0.716 39.161 -U37 "O4'" O O2 0 -21.332 -1.155 40.399 -U37 "C3'" C CH1 0 -20.781 0.814 39.246 -U37 "O3'" O OH1 0 -20.697 1.410 37.957 -U37 "C2'" C CH1 0 -22.130 1.048 39.942 -U37 "O2'" O OH1 0 -23.221 1.115 39.045 -U37 "C1'" C CH1 0 -22.261 -0.187 40.845 -U37 N1 N NR6 0 -21.987 0.115 42.276 -U37 C2 C CR6 0 -23.044 0.071 43.183 -U37 O2 O O 0 -24.197 -0.208 42.875 -U37 N3 N NR6 0 -22.703 0.365 44.485 -U37 C4 C CR6 0 -21.448 0.695 44.967 -U37 O4 O O 0 -21.303 0.934 46.166 -U37 C5 C CR16 0 -20.412 0.723 43.973 -U37 C6 C CR16 0 -20.712 0.441 42.693 -U37 HS H HSH1 0 -17.817 -0.029 35.129 -U37 "H5'1" H H 0 -18.792 -1.058 39.811 -U37 "H5'2" H H 0 -19.413 -2.306 39.017 -U37 "H4'" H H 0 -21.267 -1.029 38.409 -U37 "H3'" H H 0 -20.044 1.148 39.819 -U37 HA H H 0 -21.347 1.150 37.477 -U37 "H2'" H H 0 -22.090 1.861 40.484 -U37 HB H H 0 -23.275 0.396 38.594 -U37 "H1'" H H 0 -23.163 -0.560 40.751 -U37 H3 H H 0 -23.370 0.338 45.074 -U37 H5 H H 0 -19.535 0.937 44.216 -U37 H6 H H 0 -20.025 0.462 42.056 +U37 O3P O OP -1 -16.453 -0.732 38.675 +U37 P P P 0 -17.219 -1.251 37.499 +U37 S S S1 0 -16.555 -0.504 35.831 +U37 O1P O OP -1 -17.219 -2.749 37.548 +U37 "O5'" O O2 0 -18.732 -0.812 37.831 +U37 "C5'" C CH2 0 -19.388 -1.332 39.004 +U37 "C4'" C CH1 0 -20.754 -0.704 39.134 +U37 "O4'" O O2 0 -21.388 -1.125 40.360 +U37 "C3'" C CH1 0 -20.769 0.825 39.205 +U37 "O3'" O OH1 0 -20.717 1.380 37.896 +U37 "C2'" C CH1 0 -22.089 1.122 39.933 +U37 "O2'" O OH1 0 -23.194 1.282 39.061 +U37 "C1'" C CH1 0 -22.279 -0.123 40.803 +U37 N1 N NR6 0 -22.017 0.127 42.245 +U37 C2 C CR6 0 -23.064 0.032 43.161 +U37 O2 O O 0 -24.213 -0.255 42.857 +U37 N3 N NR16 0 -22.708 0.286 44.469 +U37 C4 C CR6 0 -21.452 0.620 44.948 +U37 O4 O O 0 -21.291 0.819 46.154 +U37 C5 C CR16 0 -20.428 0.701 43.942 +U37 C6 C CR16 0 -20.739 0.460 42.657 +U37 "H5'1" H H 0 -18.851 -1.126 39.812 +U37 "H5'2" H H 0 -19.481 -2.315 38.932 +U37 "H4'" H H 0 -21.308 -1.002 38.369 +U37 "H3'" H H 0 -20.003 1.150 39.743 +U37 HA H H 0 -20.821 2.211 37.942 +U37 "H2'" H H 0 -21.989 1.919 40.501 +U37 HB H H 0 -23.248 0.629 38.536 +U37 "H1'" H H 0 -23.207 -0.448 40.679 +U37 H3 H H 0 -23.355 0.228 45.054 +U37 H5 H H 0 -19.548 0.922 44.184 +U37 H6 H H 0 -20.058 0.515 42.007 + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +U37 O3P O(POOS) +U37 P P(OC)(O)2(S) +U37 S S(PO3) +U37 O1P O(POOS) +U37 "O5'" O(CC[5]HH)(POOS) +U37 "C5'" C(C[5]C[5]O[5]H)(OP)(H)2 +U37 "C4'" C[5](C[5]C[5]HO)(O[5]C[5])(CHHO)(H){1|N<3>,1|O<2>,2|H<1>} +U37 "O4'" O[5](C[5]N[6a]C[5]H)(C[5]C[5]CH){2|C<3>,2|H<1>,2|O<2>} +U37 "C3'" C[5](C[5]C[5]HO)(C[5]O[5]CH)(OH)(H){1|H<1>,1|N<3>} +U37 "O3'" O(C[5]C[5]2H)(H) +U37 "C2'" C[5](C[5]N[6a]O[5]H)(C[5]C[5]HO)(OH)(H){1|C<4>,1|H<1>,2|C<3>} +U37 "O2'" O(C[5]C[5]2H)(H) +U37 "C1'" C[5](N[6a]C[6a]2)(C[5]C[5]HO)(O[5]C[5])(H){1|C<3>,1|C<4>,1|N<3>,1|O<1>,1|O<2>,3|H<1>} +U37 N1 N[6a](C[5]C[5]O[5]H)(C[6a]C[6a]H)(C[6a]N[6a]O){1|C<3>,1|O<2>,2|C<4>,3|H<1>} +U37 C2 C[6a](N[6a]C[6a]C[5])(N[6a]C[6a]H)(O){1|C<3>,1|C<4>,1|O<1>,1|O<2>,2|H<1>} +U37 O2 O(C[6a]N[6a]2) +U37 N3 N[6a](C[6a]C[6a]O)(C[6a]N[6a]O)(H){1|C<3>,1|C<4>,1|H<1>} +U37 C4 C[6a](C[6a]C[6a]H)(N[6a]C[6a]H)(O){1|H<1>,1|N<3>,1|O<1>} +U37 O4 O(C[6a]C[6a]N[6a]) +U37 C5 C[6a](C[6a]N[6a]H)(C[6a]N[6a]O)(H){1|C<3>,1|C<4>,1|H<1>} +U37 C6 C[6a](N[6a]C[6a]C[5])(C[6a]C[6a]H)(H){1|C<4>,1|H<1>,1|N<3>,1|O<2>,2|O<1>} +U37 "H5'1" H(CC[5]HO) +U37 "H5'2" H(CC[5]HO) +U37 "H4'" H(C[5]C[5]O[5]C) +U37 "H3'" H(C[5]C[5]2O) +U37 HA H(OC[5]) +U37 "H2'" H(C[5]C[5]2O) +U37 HB H(OC[5]) +U37 "H1'" H(C[5]N[6a]C[5]O[5]) +U37 H3 H(N[6a]C[6a]2) +U37 H5 H(C[6a]C[6a]2) +U37 H6 H(C[6a]C[6a]N[6a]) loop_ _chem_comp_bond.comp_id @@ -63,40 +99,39 @@ _chem_comp_bond.value_dist_nucleus _chem_comp_bond.value_dist_nucleus_esd _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd -U37 O3P P DOUBLE n 1.493 0.0157 1.493 0.0157 -U37 P S SINGLE n 2.091 0.0200 2.091 0.0200 -U37 P O1P SINGLE n 1.493 0.0157 1.493 0.0157 -U37 P "O5'" SINGLE n 1.601 0.0114 1.601 0.0114 -U37 "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 -U37 "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 -U37 "C4'" "O4'" SINGLE n 1.451 0.0111 1.451 0.0111 -U37 "C4'" "C3'" SINGLE n 1.535 0.0100 1.535 0.0100 -U37 "O4'" "C1'" SINGLE n 1.412 0.0100 1.412 0.0100 -U37 "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 -U37 "C3'" "C2'" SINGLE n 1.533 0.0109 1.533 0.0109 -U37 "C2'" "O2'" SINGLE n 1.412 0.0100 1.412 0.0100 -U37 "C2'" "C1'" SINGLE n 1.529 0.0100 1.529 0.0100 -U37 "C1'" N1 SINGLE n 1.476 0.0133 1.476 0.0133 -U37 N1 C2 SINGLE y 1.383 0.0100 1.383 0.0100 -U37 N1 C6 SINGLE y 1.375 0.0106 1.375 0.0106 -U37 C2 O2 DOUBLE n 1.224 0.0111 1.224 0.0111 -U37 C2 N3 SINGLE y 1.372 0.0112 1.372 0.0112 -U37 N3 C4 SINGLE y 1.381 0.0100 1.381 0.0100 -U37 C4 O4 DOUBLE n 1.231 0.0100 1.231 0.0100 -U37 C4 C5 SINGLE y 1.434 0.0100 1.434 0.0100 -U37 C5 C6 DOUBLE y 1.342 0.0100 1.342 0.0100 -U37 S HS SINGLE n 1.338 0.0100 1.211 0.0200 -U37 "C5'" "H5'1" SINGLE n 1.089 0.0100 0.989 0.0200 -U37 "C5'" "H5'2" SINGLE n 1.089 0.0100 0.989 0.0200 -U37 "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200 -U37 "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200 -U37 "O3'" HA SINGLE n 0.970 0.0120 0.849 0.0200 -U37 "C2'" "H2'" SINGLE n 1.089 0.0100 0.978 0.0200 -U37 "O2'" HB SINGLE n 0.970 0.0120 0.849 0.0200 -U37 "C1'" "H1'" SINGLE n 1.089 0.0100 0.981 0.0118 -U37 N3 H3 SINGLE n 1.016 0.0100 0.889 0.0200 -U37 C5 H5 SINGLE n 1.082 0.0130 0.935 0.0100 -U37 C6 H6 SINGLE n 1.082 0.0130 0.938 0.0107 +U37 O3P P SINGLE n 1.497 0.0143 1.497 0.0143 +U37 P S DOUBLE n 1.949 0.0200 1.949 0.0200 +U37 P O1P SINGLE n 1.497 0.0143 1.497 0.0143 +U37 P "O5'" SINGLE n 1.613 0.0200 1.613 0.0200 +U37 "O5'" "C5'" SINGLE n 1.438 0.0200 1.438 0.0200 +U37 "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 +U37 "C4'" "O4'" SINGLE n 1.445 0.0100 1.445 0.0100 +U37 "C4'" "C3'" SINGLE n 1.532 0.0100 1.532 0.0100 +U37 "O4'" "C1'" SINGLE n 1.412 0.0100 1.412 0.0100 +U37 "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +U37 "C3'" "C2'" SINGLE n 1.534 0.0111 1.534 0.0111 +U37 "C2'" "O2'" SINGLE n 1.415 0.0100 1.415 0.0100 +U37 "C2'" "C1'" SINGLE n 1.526 0.0100 1.526 0.0100 +U37 "C1'" N1 SINGLE n 1.477 0.0120 1.477 0.0120 +U37 N1 C2 SINGLE y 1.386 0.0100 1.386 0.0100 +U37 N1 C6 SINGLE y 1.378 0.0100 1.378 0.0100 +U37 C2 O2 DOUBLE n 1.221 0.0100 1.221 0.0100 +U37 C2 N3 SINGLE y 1.375 0.0100 1.375 0.0100 +U37 N3 C4 SINGLE y 1.382 0.0100 1.382 0.0100 +U37 C4 O4 DOUBLE n 1.233 0.0100 1.233 0.0100 +U37 C4 C5 SINGLE y 1.435 0.0100 1.435 0.0100 +U37 C5 C6 DOUBLE y 1.342 0.0100 1.342 0.0100 +U37 "C5'" "H5'1" SINGLE n 1.092 0.0100 0.991 0.0200 +U37 "C5'" "H5'2" SINGLE n 1.092 0.0100 0.991 0.0200 +U37 "C4'" "H4'" SINGLE n 1.092 0.0100 0.990 0.0200 +U37 "C3'" "H3'" SINGLE n 1.092 0.0100 0.991 0.0200 +U37 "O3'" HA SINGLE n 0.972 0.0180 0.839 0.0200 +U37 "C2'" "H2'" SINGLE n 1.092 0.0100 0.983 0.0200 +U37 "O2'" HB SINGLE n 0.972 0.0180 0.839 0.0200 +U37 "C1'" "H1'" SINGLE n 1.092 0.0100 0.992 0.0194 +U37 N3 H3 SINGLE n 1.013 0.0120 0.872 0.0200 +U37 C5 H5 SINGLE n 1.085 0.0150 0.939 0.0100 +U37 C6 H6 SINGLE n 1.085 0.0150 0.944 0.0121 loop_ _chem_comp_angle.comp_id @@ -105,65 +140,64 @@ _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd -U37 O3P P S 111.281 3.00 -U37 O3P P O1P 116.964 2.85 -U37 O3P P "O5'" 108.530 2.45 -U37 S P O1P 111.281 3.00 -U37 S P "O5'" 105.685 3.00 -U37 O1P P "O5'" 108.530 2.45 -U37 P S HS 109.471 3.00 -U37 P "O5'" "C5'" 119.135 1.78 -U37 "O5'" "C5'" "C4'" 109.510 1.50 -U37 "O5'" "C5'" "H5'1" 109.821 1.50 -U37 "O5'" "C5'" "H5'2" 109.821 1.50 -U37 "C4'" "C5'" "H5'1" 109.624 1.50 -U37 "C4'" "C5'" "H5'2" 109.624 1.50 -U37 "H5'1" "C5'" "H5'2" 108.472 1.50 -U37 "C5'" "C4'" "O4'" 109.615 1.50 -U37 "C5'" "C4'" "C3'" 116.008 1.52 -U37 "C5'" "C4'" "H4'" 108.268 1.50 -U37 "O4'" "C4'" "C3'" 104.439 1.50 -U37 "O4'" "C4'" "H4'" 108.698 1.50 -U37 "C3'" "C4'" "H4'" 109.363 1.86 -U37 "C4'" "O4'" "C1'" 109.578 1.50 -U37 "C4'" "C3'" "O3'" 111.281 2.46 -U37 "C4'" "C3'" "C2'" 102.071 1.50 -U37 "C4'" "C3'" "H3'" 110.452 2.54 -U37 "O3'" "C3'" "C2'" 111.993 3.00 -U37 "O3'" "C3'" "H3'" 110.380 1.67 -U37 "C2'" "C3'" "H3'" 110.108 1.66 -U37 "C3'" "O3'" HA 108.744 3.00 -U37 "C3'" "C2'" "O2'" 112.861 2.52 -U37 "C3'" "C2'" "C1'" 101.269 1.50 -U37 "C3'" "C2'" "H2'" 110.799 1.82 -U37 "O2'" "C2'" "C1'" 109.476 3.00 -U37 "O2'" "C2'" "H2'" 111.022 1.77 -U37 "C1'" "C2'" "H2'" 110.760 1.63 -U37 "C2'" "O2'" HB 109.449 1.85 -U37 "O4'" "C1'" "C2'" 106.825 1.50 -U37 "O4'" "C1'" N1 108.667 1.50 -U37 "O4'" "C1'" "H1'" 109.327 1.50 -U37 "C2'" "C1'" N1 112.859 1.50 -U37 "C2'" "C1'" "H1'" 109.776 1.83 -U37 N1 "C1'" "H1'" 109.166 1.50 -U37 "C1'" N1 C2 117.109 1.50 -U37 "C1'" N1 C6 121.471 1.52 -U37 C2 N1 C6 121.419 1.50 -U37 N1 C2 O2 122.841 1.50 -U37 N1 C2 N3 114.848 1.50 -U37 O2 C2 N3 122.311 1.50 -U37 C2 N3 C4 126.992 1.50 -U37 C2 N3 H3 115.772 1.79 -U37 C4 N3 H3 117.236 1.73 -U37 N3 C4 O4 119.401 1.50 -U37 N3 C4 C5 114.659 1.50 -U37 O4 C4 C5 125.940 1.50 -U37 C4 C5 C6 119.525 1.50 -U37 C4 C5 H5 120.151 1.50 -U37 C6 C5 H5 120.325 1.50 -U37 N1 C6 C5 122.557 1.50 -U37 N1 C6 H6 118.477 1.50 -U37 C5 C6 H6 118.966 1.50 +U37 O3P P S 116.458 3.00 +U37 O3P P O1P 112.844 3.00 +U37 O3P P "O5'" 106.327 3.00 +U37 S P O1P 116.458 3.00 +U37 S P "O5'" 114.928 3.00 +U37 O1P P "O5'" 106.327 3.00 +U37 P "O5'" "C5'" 119.085 2.00 +U37 "O5'" "C5'" "C4'" 109.482 2.30 +U37 "O5'" "C5'" "H5'1" 109.954 1.50 +U37 "O5'" "C5'" "H5'2" 109.954 1.50 +U37 "C4'" "C5'" "H5'1" 109.589 1.50 +U37 "C4'" "C5'" "H5'2" 109.589 1.50 +U37 "H5'1" "C5'" "H5'2" 108.471 1.50 +U37 "C5'" "C4'" "O4'" 110.351 1.93 +U37 "C5'" "C4'" "C3'" 115.288 1.50 +U37 "C5'" "C4'" "H4'" 108.351 1.59 +U37 "O4'" "C4'" "C3'" 105.071 1.50 +U37 "O4'" "C4'" "H4'" 108.778 1.50 +U37 "C3'" "C4'" "H4'" 109.322 2.54 +U37 "C4'" "O4'" "C1'" 109.821 1.50 +U37 "C4'" "C3'" "O3'" 110.713 3.00 +U37 "C4'" "C3'" "C2'" 102.776 1.50 +U37 "C4'" "C3'" "H3'" 110.577 3.00 +U37 "O3'" "C3'" "C2'" 111.936 3.00 +U37 "O3'" "C3'" "H3'" 110.541 2.08 +U37 "C2'" "C3'" "H3'" 110.235 2.42 +U37 "C3'" "O3'" HA 109.389 3.00 +U37 "C3'" "C2'" "O2'" 113.012 3.00 +U37 "C3'" "C2'" "C1'" 101.479 1.50 +U37 "C3'" "C2'" "H2'" 110.640 2.20 +U37 "O2'" "C2'" "C1'" 109.825 3.00 +U37 "O2'" "C2'" "H2'" 110.739 1.98 +U37 "C1'" "C2'" "H2'" 110.219 1.50 +U37 "C2'" "O2'" HB 109.730 3.00 +U37 "O4'" "C1'" "C2'" 106.541 2.94 +U37 "O4'" "C1'" N1 108.138 1.50 +U37 "O4'" "C1'" "H1'" 109.439 1.50 +U37 "C2'" "C1'" N1 113.288 2.34 +U37 "C2'" "C1'" "H1'" 109.838 3.00 +U37 N1 "C1'" "H1'" 109.374 1.50 +U37 "C1'" N1 C2 117.716 1.50 +U37 "C1'" N1 C6 120.804 2.33 +U37 C2 N1 C6 121.480 1.50 +U37 N1 C2 O2 122.982 1.50 +U37 N1 C2 N3 114.684 1.50 +U37 O2 C2 N3 122.337 1.50 +U37 C2 N3 C4 127.033 1.50 +U37 C2 N3 H3 115.708 3.00 +U37 C4 N3 H3 117.259 3.00 +U37 N3 C4 O4 119.595 1.50 +U37 N3 C4 C5 114.643 1.50 +U37 O4 C4 C5 125.762 1.50 +U37 C4 C5 C6 119.580 1.50 +U37 C4 C5 H5 120.071 1.50 +U37 C6 C5 H5 120.349 1.50 +U37 N1 C6 C5 122.580 1.50 +U37 N1 C6 H6 118.439 1.84 +U37 C5 C6 H6 118.980 1.53 loop_ _chem_comp_tor.comp_id @@ -175,30 +209,29 @@ _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period -U37 C2e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 -U37 C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 -U37 C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 -U37 C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 -U37 C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 -U37 C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 -U37 C3e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 -U37 C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 -U37 C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 -U37 C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 -U37 C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 -U37 C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 -U37 beta P "O5'" "C5'" "C4'" 180.000 10.00 3 -U37 gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 -U37 sp3_sp3_55 "C3'" "C2'" "O2'" HB 180.000 10.0 3 -U37 const_sp2_sp2_4 O2 C2 N1 "C1'" 0.000 5.0 2 -U37 const_22 C5 C6 N1 "C1'" 180.000 10.0 2 -U37 const_sp2_sp2_7 O2 C2 N3 C4 180.000 5.0 2 -U37 const_11 O4 C4 N3 C2 180.000 10.0 2 -U37 const_15 O4 C4 C5 C6 180.000 10.0 2 -U37 const_17 C4 C5 C6 N1 0.000 10.0 2 -U37 sp3_sp3_27 O3P P S HS -60.000 10.0 3 -U37 sp3_sp3_30 "C5'" "O5'" P O3P 60.000 10.0 3 -U37 sp3_sp3_52 "C4'" "C3'" "O3'" HA 180.000 10.0 3 +U37 sp3_sp3_52 "C3'" "C2'" "O2'" HB 180.000 10.0 3 +U37 sp3_sp3_8 "O4'" "C1'" "C2'" "O2'" 180.000 10.0 3 +U37 sp2_sp3_1 C2 N1 "C1'" "O4'" 150.000 10.0 6 +U37 const_sp2_sp2_1 N3 C2 N1 C6 0.000 0.0 1 +U37 const_sp2_sp2_4 O2 C2 N1 "C1'" 0.000 0.0 1 +U37 const_21 C5 C6 N1 C2 0.000 0.0 1 +U37 const_24 H6 C6 N1 "C1'" 0.000 0.0 1 +U37 const_sp2_sp2_5 N1 C2 N3 C4 0.000 0.0 1 +U37 const_sp2_sp2_8 O2 C2 N3 H3 0.000 0.0 1 +U37 const_sp2_sp2_9 C5 C4 N3 C2 0.000 0.0 1 +U37 const_12 O4 C4 N3 H3 0.000 0.0 1 +U37 const_13 N3 C4 C5 C6 0.000 0.0 1 +U37 const_16 O4 C4 C5 H5 0.000 0.0 1 +U37 const_17 C4 C5 C6 N1 0.000 0.0 1 +U37 const_20 H5 C5 C6 H6 0.000 0.0 1 +U37 sp3_sp3_27 "C5'" "O5'" P O3P 60.000 10.0 3 +U37 sp3_sp3_28 "C4'" "C5'" "O5'" P 180.000 10.0 3 +U37 sp3_sp3_31 "O4'" "C4'" "C5'" "O5'" 180.000 10.0 3 +U37 sp3_sp3_2 "C5'" "C4'" "O4'" "C1'" -60.000 10.0 3 +U37 sp3_sp3_44 "O3'" "C3'" "C4'" "C5'" 180.000 10.0 3 +U37 sp3_sp3_4 "C2'" "C1'" "O4'" "C4'" -60.000 10.0 3 +U37 sp3_sp3_20 "O2'" "C2'" "C3'" "O3'" -60.000 10.0 3 +U37 sp3_sp3_49 "C4'" "C3'" "O3'" HA 180.000 10.0 3 loop_ _chem_comp_chir.comp_id @@ -208,11 +241,11 @@ _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign -U37 chir_1 P S "O5'" O1P both +U37 chir_1 P S "O5'" O1P both U37 chir_2 "C4'" "O4'" "C3'" "C5'" negative U37 chir_3 "C3'" "O3'" "C4'" "C2'" positive U37 chir_4 "C2'" "O2'" "C1'" "C3'" negative -U37 chir_5 "C1'" "O4'" N1 "C2'" negative +U37 chir_5 "C1'" "O4'" N1 "C2'" negative loop_ _chem_comp_plane_atom.comp_id @@ -220,17 +253,17 @@ _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd U37 plan-1 "C1'" 0.020 -U37 plan-1 C2 0.020 -U37 plan-1 C4 0.020 -U37 plan-1 C5 0.020 -U37 plan-1 C6 0.020 -U37 plan-1 H3 0.020 -U37 plan-1 H5 0.020 -U37 plan-1 H6 0.020 -U37 plan-1 N1 0.020 -U37 plan-1 N3 0.020 -U37 plan-1 O2 0.020 -U37 plan-1 O4 0.020 +U37 plan-1 C2 0.020 +U37 plan-1 C4 0.020 +U37 plan-1 C5 0.020 +U37 plan-1 C6 0.020 +U37 plan-1 H3 0.020 +U37 plan-1 H5 0.020 +U37 plan-1 H6 0.020 +U37 plan-1 N1 0.020 +U37 plan-1 N3 0.020 +U37 plan-1 O2 0.020 +U37 plan-1 O4 0.020 loop_ _pdbx_chem_comp_descriptor.comp_id @@ -238,20 +271,30 @@ _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor -U37 SMILES ACDLabs 10.04 O=P(O)(S)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O -U37 SMILES_CANONICAL CACTVS 3.341 O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P@@](O)(S)=O)N2C=CC(=O)NC2=O -U37 SMILES CACTVS 3.341 O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(S)=O)N2C=CC(=O)NC2=O +U37 SMILES ACDLabs 10.04 O=P(O)(S)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O +U37 SMILES_CANONICAL CACTVS 3.341 O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P@@](O)(S)=O)N2C=CC(=O)NC2=O +U37 SMILES CACTVS 3.341 O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(S)=O)N2C=CC(=O)NC2=O U37 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)S)O)O -U37 SMILES "OpenEye OEToolkits" 1.5.0 C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)S)O)O -U37 InChI InChI 1.03 InChI=1S/C9H13N2O8PS/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(19-8)3-18-20(16,17)21/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,21)/t4-,6-,7-,8-/m1/s1 -U37 InChIKey InChI 1.03 NSEBKRRODBXALJ-XVFCMESISA-N +U37 SMILES "OpenEye OEToolkits" 1.5.0 C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)S)O)O +U37 InChI InChI 1.03 InChI=1S/C9H13N2O8PS/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(19-8)3-18-20(16,17)21/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,21)/t4-,6-,7-,8-/m1/s1 +U37 InChIKey InChI 1.03 NSEBKRRODBXALJ-XVFCMESISA-N loop_ _pdbx_chem_comp_description_generator.comp_id _pdbx_chem_comp_description_generator.program_name _pdbx_chem_comp_description_generator.program_version _pdbx_chem_comp_description_generator.descriptor -U37 acedrg 243 "dictionary generator" -U37 acedrg_database 11 "data source" -U37 rdkit 2017.03.2 "Chemoinformatics tool" -U37 refmac5 5.8.0238 "optimization tool" +U37 acedrg 277 "dictionary generator" +U37 acedrg_database 12 "data source" +U37 rdkit 2019.09.1 "Chemoinformatics tool" +U37 refmac5 5.8.0425 "optimization tool" + +loop_ +_chem_comp_alias.comp_id +_chem_comp_alias.group +_chem_comp_alias.atom_id +_chem_comp_alias.atom_id_standard +U37 S-NA O3P OP3 +U37 S-NA S S2P +U37 S-NA O1P OP1 +U37 S-NA HA HO3' diff --git a/u/UPS.cif b/u/UPS.cif index ea58ce269..28e449bde 100644 --- a/u/UPS.cif +++ b/u/UPS.cif @@ -19,37 +19,37 @@ _chem_comp_atom.charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z -UPS OP3 O OP -1 3.644 3.350 -32.996 -UPS P P P 0 4.046 1.900 -32.888 -UPS S1P S S1 0 3.868 0.848 -34.512 -UPS OP2 O OP -1 3.383 1.306 -31.670 -UPS "O5'" O O2 0 5.580 1.965 -32.403 -UPS "C5'" C CH2 0 6.531 2.729 -33.189 -UPS "C4'" C CH1 0 7.922 2.531 -32.637 -UPS "O4'" O O2 0 7.963 2.975 -31.263 -UPS "C1'" C CH1 0 8.731 2.059 -30.496 -UPS N1 N NR6 0 8.244 2.109 -29.084 -UPS C2 C CR6 0 9.164 2.273 -28.054 -UPS O2 O O 0 10.372 2.386 -28.231 -UPS N3 N NR6 0 8.620 2.304 -26.790 -UPS C4 C CR6 0 7.283 2.188 -26.451 -UPS O4 O O 0 6.951 2.235 -25.266 -UPS C5 C CR16 0 6.395 2.019 -27.566 -UPS C6 C CR16 0 6.896 1.985 -28.814 -UPS "C2'" C CH2 0 8.548 0.712 -31.179 -UPS "C3'" C CH1 0 8.424 1.084 -32.652 -UPS "O3'" O OH1 0 9.694 0.993 -33.295 -UPS "H5'" H H 0 6.297 3.689 -33.159 -UPS "H5'A" H H 0 6.503 2.429 -34.132 -UPS "H4'" H H 0 8.540 3.093 -33.165 -UPS "H1'" H H 0 9.687 2.325 -30.541 -UPS HN3 H H 0 9.200 2.410 -26.123 -UPS H5 H H 0 5.475 1.933 -27.425 -UPS H6 H H 0 6.304 1.873 -29.533 -UPS "H2'" H H 0 7.741 0.256 -30.860 -UPS "H2'A" H H 0 9.324 0.130 -31.023 -UPS "H3'" H H 0 7.771 0.496 -33.102 -UPS "HO3'" H H 0 10.259 1.479 -32.886 +UPS OP3 O OP -1 3.644 3.350 -32.996 +UPS P P P 0 4.046 1.900 -32.888 +UPS S1P S S1 0 3.868 0.848 -34.512 +UPS OP2 O OP -1 3.383 1.306 -31.670 +UPS "O5'" O O2 0 5.580 1.965 -32.403 +UPS "C5'" C CH2 0 6.531 2.729 -33.189 +UPS "C4'" C CH1 0 7.922 2.531 -32.637 +UPS "O4'" O O2 0 7.963 2.975 -31.263 +UPS "C1'" C CH1 0 8.731 2.059 -30.496 +UPS N1 N NR6 0 8.244 2.109 -29.084 +UPS C2 C CR6 0 9.164 2.273 -28.054 +UPS O2 O O 0 10.372 2.386 -28.231 +UPS N3 N NR6 0 8.620 2.304 -26.790 +UPS C4 C CR6 0 7.283 2.188 -26.451 +UPS O4 O O 0 6.951 2.235 -25.266 +UPS C5 C CR16 0 6.395 2.019 -27.566 +UPS C6 C CR16 0 6.896 1.985 -28.814 +UPS "C2'" C CH2 0 8.548 0.712 -31.179 +UPS "C3'" C CH1 0 8.424 1.084 -32.652 +UPS "O3'" O OH1 0 9.694 0.993 -33.295 +UPS "H5'" H H 0 6.297 3.689 -33.159 +UPS "H5'A" H H 0 6.503 2.429 -34.132 +UPS "H4'" H H 0 8.540 3.093 -33.165 +UPS "H1'" H H 0 9.687 2.325 -30.541 +UPS HN3 H H 0 9.200 2.410 -26.123 +UPS H5 H H 0 5.475 1.933 -27.425 +UPS H6 H H 0 6.304 1.873 -29.533 +UPS "H2'" H H 0 7.741 0.256 -30.860 +UPS "H2'A" H H 0 9.324 0.130 -31.023 +UPS "H3'" H H 0 7.771 0.496 -33.102 +UPS "HO3'" H H 0 10.259 1.479 -32.886 loop_ _chem_comp_bond.comp_id @@ -61,37 +61,37 @@ _chem_comp_bond.value_dist_nucleus _chem_comp_bond.value_dist_nucleus_esd _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd -UPS OP3 P SINGLE n 1.509 0.0200 1.509 0.0200 -UPS P S1P DOUBLE n 1.949 0.0200 1.949 0.0200 -UPS P OP2 SINGLE n 1.509 0.0200 1.509 0.0200 -UPS P "O5'" SINGLE n 1.614 0.0178 1.614 0.0178 -UPS "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 -UPS "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 -UPS "C4'" "C3'" SINGLE n 1.526 0.0115 1.526 0.0115 -UPS "C4'" "O4'" SINGLE n 1.445 0.0100 1.445 0.0100 -UPS "O4'" "C1'" SINGLE n 1.422 0.0100 1.422 0.0100 -UPS "C1'" "C2'" SINGLE n 1.523 0.0130 1.523 0.0130 -UPS "C1'" N1 SINGLE n 1.476 0.0163 1.476 0.0163 -UPS N1 C6 SINGLE y 1.375 0.0100 1.375 0.0100 -UPS N1 C2 SINGLE y 1.381 0.0100 1.381 0.0100 -UPS C2 O2 DOUBLE n 1.224 0.0111 1.224 0.0111 -UPS C2 N3 SINGLE y 1.372 0.0112 1.372 0.0112 -UPS N3 C4 SINGLE y 1.381 0.0100 1.381 0.0100 -UPS C4 C5 SINGLE y 1.434 0.0100 1.434 0.0100 -UPS C4 O4 DOUBLE n 1.231 0.0100 1.231 0.0100 -UPS C5 C6 DOUBLE y 1.342 0.0100 1.342 0.0100 -UPS "C2'" "C3'" SINGLE n 1.522 0.0100 1.522 0.0100 -UPS "C3'" "O3'" SINGLE n 1.424 0.0100 1.424 0.0100 -UPS "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 +UPS OP3 P SINGLE n 1.509 0.0200 1.509 0.0200 +UPS P S1P DOUBLE n 1.949 0.0200 1.949 0.0200 +UPS P OP2 SINGLE n 1.509 0.0200 1.509 0.0200 +UPS P "O5'" SINGLE n 1.614 0.0178 1.614 0.0178 +UPS "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 +UPS "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 +UPS "C4'" "C3'" SINGLE n 1.526 0.0115 1.526 0.0115 +UPS "C4'" "O4'" SINGLE n 1.445 0.0100 1.445 0.0100 +UPS "O4'" "C1'" SINGLE n 1.422 0.0100 1.422 0.0100 +UPS "C1'" "C2'" SINGLE n 1.523 0.0130 1.523 0.0130 +UPS "C1'" N1 SINGLE n 1.476 0.0163 1.476 0.0163 +UPS N1 C6 SINGLE y 1.375 0.0100 1.375 0.0100 +UPS N1 C2 SINGLE y 1.381 0.0100 1.381 0.0100 +UPS C2 O2 DOUBLE n 1.224 0.0111 1.224 0.0111 +UPS C2 N3 SINGLE y 1.372 0.0112 1.372 0.0112 +UPS N3 C4 SINGLE y 1.381 0.0100 1.381 0.0100 +UPS C4 C5 SINGLE y 1.434 0.0100 1.434 0.0100 +UPS C4 O4 DOUBLE n 1.231 0.0100 1.231 0.0100 +UPS C5 C6 DOUBLE y 1.342 0.0100 1.342 0.0100 +UPS "C2'" "C3'" SINGLE n 1.522 0.0100 1.522 0.0100 +UPS "C3'" "O3'" SINGLE n 1.424 0.0100 1.424 0.0100 +UPS "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 UPS "C5'" "H5'A" SINGLE n 1.089 0.0100 0.989 0.0200 -UPS "C4'" "H4'" SINGLE n 1.089 0.0100 0.987 0.0170 -UPS "C1'" "H1'" SINGLE n 1.089 0.0100 0.996 0.0200 -UPS N3 HN3 SINGLE n 1.016 0.0100 0.889 0.0200 -UPS C5 H5 SINGLE n 1.082 0.0130 0.935 0.0100 -UPS C6 H6 SINGLE n 1.082 0.0130 0.938 0.0107 -UPS "C2'" "H2'" SINGLE n 1.089 0.0100 0.982 0.0200 +UPS "C4'" "H4'" SINGLE n 1.089 0.0100 0.987 0.0170 +UPS "C1'" "H1'" SINGLE n 1.089 0.0100 0.996 0.0200 +UPS N3 HN3 SINGLE n 1.016 0.0100 0.889 0.0200 +UPS C5 H5 SINGLE n 1.082 0.0130 0.935 0.0100 +UPS C6 H6 SINGLE n 1.082 0.0130 0.938 0.0107 +UPS "C2'" "H2'" SINGLE n 1.089 0.0100 0.982 0.0200 UPS "C2'" "H2'A" SINGLE n 1.089 0.0100 0.982 0.0200 -UPS "C3'" "H3'" SINGLE n 1.089 0.0100 0.988 0.0189 +UPS "C3'" "H3'" SINGLE n 1.089 0.0100 0.988 0.0189 UPS "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 loop_ @@ -101,62 +101,62 @@ _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd -UPS OP3 P S1P 116.650 1.50 -UPS OP3 P OP2 113.206 2.54 -UPS OP3 P "O5'" 106.518 3.00 -UPS S1P P OP2 116.650 1.50 -UPS S1P P "O5'" 113.924 3.00 -UPS OP2 P "O5'" 106.518 3.00 -UPS P "O5'" "C5'" 118.783 1.50 -UPS "O5'" "C5'" "C4'" 109.510 1.50 -UPS "O5'" "C5'" "H5'" 109.821 1.50 +UPS OP3 P S1P 116.650 1.50 +UPS OP3 P OP2 113.206 2.54 +UPS OP3 P "O5'" 106.518 3.00 +UPS S1P P OP2 116.650 1.50 +UPS S1P P "O5'" 113.924 3.00 +UPS OP2 P "O5'" 106.518 3.00 +UPS P "O5'" "C5'" 118.783 1.50 +UPS "O5'" "C5'" "C4'" 109.510 1.50 +UPS "O5'" "C5'" "H5'" 109.821 1.50 UPS "O5'" "C5'" "H5'A" 109.821 1.50 -UPS "C4'" "C5'" "H5'" 109.624 1.50 +UPS "C4'" "C5'" "H5'" 109.624 1.50 UPS "C4'" "C5'" "H5'A" 109.624 1.50 UPS "H5'" "C5'" "H5'A" 108.472 1.50 -UPS "C5'" "C4'" "C3'" 114.866 1.63 -UPS "C5'" "C4'" "O4'" 109.615 1.50 -UPS "C5'" "C4'" "H4'" 108.268 1.50 -UPS "C3'" "C4'" "O4'" 105.770 1.50 -UPS "C3'" "C4'" "H4'" 109.069 1.50 -UPS "O4'" "C4'" "H4'" 108.698 1.50 -UPS "C4'" "O4'" "C1'" 109.692 1.50 -UPS "O4'" "C1'" "C2'" 106.308 1.50 -UPS "O4'" "C1'" N1 107.584 1.50 -UPS "O4'" "C1'" "H1'" 109.550 1.50 -UPS "C2'" "C1'" N1 114.268 1.50 -UPS "C2'" "C1'" "H1'" 109.741 1.50 -UPS N1 "C1'" "H1'" 109.342 1.50 -UPS "C1'" N1 C6 120.739 1.50 -UPS "C1'" N1 C2 117.841 1.50 -UPS C6 N1 C2 121.419 1.50 -UPS N1 C2 O2 122.841 1.50 -UPS N1 C2 N3 114.848 1.50 -UPS O2 C2 N3 122.311 1.50 -UPS C2 N3 C4 126.992 1.50 -UPS C2 N3 HN3 115.772 1.79 -UPS C4 N3 HN3 117.236 1.73 -UPS N3 C4 C5 114.659 1.50 -UPS N3 C4 O4 119.401 1.50 -UPS C5 C4 O4 125.940 1.50 -UPS C4 C5 C6 119.525 1.50 -UPS C4 C5 H5 120.151 1.50 -UPS C6 C5 H5 120.325 1.50 -UPS N1 C6 C5 122.557 1.50 -UPS N1 C6 H6 118.477 1.50 -UPS C5 C6 H6 118.966 1.50 -UPS "C1'" "C2'" "C3'" 102.834 1.50 -UPS "C1'" "C2'" "H2'" 111.187 1.50 +UPS "C5'" "C4'" "C3'" 114.866 1.63 +UPS "C5'" "C4'" "O4'" 109.615 1.50 +UPS "C5'" "C4'" "H4'" 108.268 1.50 +UPS "C3'" "C4'" "O4'" 105.770 1.50 +UPS "C3'" "C4'" "H4'" 109.069 1.50 +UPS "O4'" "C4'" "H4'" 108.698 1.50 +UPS "C4'" "O4'" "C1'" 109.692 1.50 +UPS "O4'" "C1'" "C2'" 106.308 1.50 +UPS "O4'" "C1'" N1 107.584 1.50 +UPS "O4'" "C1'" "H1'" 109.550 1.50 +UPS "C2'" "C1'" N1 114.268 1.50 +UPS "C2'" "C1'" "H1'" 109.741 1.50 +UPS N1 "C1'" "H1'" 109.342 1.50 +UPS "C1'" N1 C6 120.739 1.50 +UPS "C1'" N1 C2 117.841 1.50 +UPS C6 N1 C2 121.419 1.50 +UPS N1 C2 O2 122.841 1.50 +UPS N1 C2 N3 114.848 1.50 +UPS O2 C2 N3 122.311 1.50 +UPS C2 N3 C4 126.992 1.50 +UPS C2 N3 HN3 115.772 1.79 +UPS C4 N3 HN3 117.236 1.73 +UPS N3 C4 C5 114.659 1.50 +UPS N3 C4 O4 119.401 1.50 +UPS C5 C4 O4 125.940 1.50 +UPS C4 C5 C6 119.525 1.50 +UPS C4 C5 H5 120.151 1.50 +UPS C6 C5 H5 120.325 1.50 +UPS N1 C6 C5 122.557 1.50 +UPS N1 C6 H6 118.477 1.50 +UPS C5 C6 H6 118.966 1.50 +UPS "C1'" "C2'" "C3'" 102.834 1.50 +UPS "C1'" "C2'" "H2'" 111.187 1.50 UPS "C1'" "C2'" "H2'A" 111.187 1.50 -UPS "C3'" "C2'" "H2'" 111.310 1.50 +UPS "C3'" "C2'" "H2'" 111.310 1.50 UPS "C3'" "C2'" "H2'A" 111.310 1.50 UPS "H2'" "C2'" "H2'A" 108.952 1.50 -UPS "C4'" "C3'" "C2'" 102.800 1.50 -UPS "C4'" "C3'" "O3'" 110.527 2.37 -UPS "C4'" "C3'" "H3'" 110.775 1.50 -UPS "C2'" "C3'" "O3'" 110.636 2.59 -UPS "C2'" "C3'" "H3'" 110.862 1.50 -UPS "O3'" "C3'" "H3'" 110.713 1.50 +UPS "C4'" "C3'" "C2'" 102.800 1.50 +UPS "C4'" "C3'" "O3'" 110.527 2.37 +UPS "C4'" "C3'" "H3'" 110.775 1.50 +UPS "C2'" "C3'" "O3'" 110.636 2.59 +UPS "C2'" "C3'" "H3'" 110.862 1.50 +UPS "O3'" "C3'" "H3'" 110.713 1.50 UPS "C3'" "O3'" "HO3'" 109.026 2.38 loop_ @@ -169,28 +169,28 @@ _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period -UPS C2e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 -UPS C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 -UPS C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 -UPS C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 -UPS C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 -UPS C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 -UPS C3e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 -UPS C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 -UPS C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 -UPS C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 -UPS C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 -UPS C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 -UPS alpha "C5'" "O5'" P OP3 -60.000 10.00 3 -UPS beta P "O5'" "C5'" "C4'" 180.000 10.00 3 -UPS epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 -UPS gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 -UPS const_19 O2 C2 N3 C4 180.000 10.0 2 -UPS const_15 O4 C4 N3 C2 180.000 10.0 2 -UPS const_11 O4 C4 C5 C6 180.000 10.0 2 -UPS const_sp2_sp2_5 C4 C5 C6 N1 0.000 5.0 2 -UPS const_24 O2 C2 N1 "C1'" 0.000 10.0 2 -UPS const_sp2_sp2_2 C5 C6 N1 "C1'" 180.000 5.0 2 +UPS C2e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 +UPS C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 +UPS C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 +UPS C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 +UPS C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 +UPS C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 +UPS C3e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 +UPS C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 +UPS C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 +UPS C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 +UPS C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 +UPS C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 +UPS alpha "C5'" "O5'" P OP3 -60.000 10.00 3 +UPS beta P "O5'" "C5'" "C4'" 180.000 10.00 3 +UPS epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 +UPS gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 +UPS const_19 O2 C2 N3 C4 180.000 10.0 2 +UPS const_15 O4 C4 N3 C2 180.000 10.0 2 +UPS const_11 O4 C4 C5 C6 180.000 10.0 2 +UPS const_sp2_sp2_5 C4 C5 C6 N1 0.000 5.0 2 +UPS const_24 O2 C2 N1 "C1'" 0.000 10.0 2 +UPS const_sp2_sp2_2 C5 C6 N1 "C1'" 180.000 5.0 2 loop_ _chem_comp_chir.comp_id @@ -200,9 +200,9 @@ _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign -UPS chir_1 P S1P "O5'" OP3 both +UPS chir_1 P S1P "O5'" OP3 both UPS chir_2 "C4'" "O4'" "C3'" "C5'" negative -UPS chir_3 "C1'" "O4'" N1 "C2'" negative +UPS chir_3 "C1'" "O4'" N1 "C2'" negative UPS chir_4 "C3'" "O3'" "C4'" "C2'" positive loop_ @@ -211,17 +211,17 @@ _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd UPS plan-1 "C1'" 0.020 -UPS plan-1 C2 0.020 -UPS plan-1 C4 0.020 -UPS plan-1 C5 0.020 -UPS plan-1 C6 0.020 -UPS plan-1 H5 0.020 -UPS plan-1 H6 0.020 -UPS plan-1 HN3 0.020 -UPS plan-1 N1 0.020 -UPS plan-1 N3 0.020 -UPS plan-1 O2 0.020 -UPS plan-1 O4 0.020 +UPS plan-1 C2 0.020 +UPS plan-1 C4 0.020 +UPS plan-1 C5 0.020 +UPS plan-1 C6 0.020 +UPS plan-1 H5 0.020 +UPS plan-1 H6 0.020 +UPS plan-1 HN3 0.020 +UPS plan-1 N1 0.020 +UPS plan-1 N3 0.020 +UPS plan-1 O2 0.020 +UPS plan-1 O4 0.020 loop_ _pdbx_chem_comp_descriptor.comp_id @@ -229,20 +229,28 @@ _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor -UPS SMILES ACDLabs 10.04 O=C1NC(=O)N(C=C1)C2OC(C(O)C2)COP(=S)(O)O -UPS SMILES_CANONICAL CACTVS 3.341 O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=S)N2C=CC(=O)NC2=O -UPS SMILES CACTVS 3.341 O[CH]1C[CH](O[CH]1CO[P](O)(O)=S)N2C=CC(=O)NC2=O +UPS SMILES ACDLabs 10.04 O=C1NC(=O)N(C=C1)C2OC(C(O)C2)COP(=S)(O)O +UPS SMILES_CANONICAL CACTVS 3.341 O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=S)N2C=CC(=O)NC2=O +UPS SMILES CACTVS 3.341 O[CH]1C[CH](O[CH]1CO[P](O)(O)=S)N2C=CC(=O)NC2=O UPS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=S)(O)O)O -UPS SMILES "OpenEye OEToolkits" 1.5.0 C1C(C(OC1N2C=CC(=O)NC2=O)COP(=S)(O)O)O -UPS InChI InChI 1.03 InChI=1S/C9H13N2O7PS/c12-5-3-8(11-2-1-7(13)10-9(11)14)18-6(5)4-17-19(15,16)20/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,20)/t5-,6+,8+/m0/s1 -UPS InChIKey InChI 1.03 LGZBLTPUGKWVDT-SHYZEUOFSA-N +UPS SMILES "OpenEye OEToolkits" 1.5.0 C1C(C(OC1N2C=CC(=O)NC2=O)COP(=S)(O)O)O +UPS InChI InChI 1.03 InChI=1S/C9H13N2O7PS/c12-5-3-8(11-2-1-7(13)10-9(11)14)18-6(5)4-17-19(15,16)20/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,20)/t5-,6+,8+/m0/s1 +UPS InChIKey InChI 1.03 LGZBLTPUGKWVDT-SHYZEUOFSA-N loop_ _pdbx_chem_comp_description_generator.comp_id _pdbx_chem_comp_description_generator.program_name _pdbx_chem_comp_description_generator.program_version _pdbx_chem_comp_description_generator.descriptor -UPS acedrg 243 "dictionary generator" -UPS acedrg_database 11 "data source" -UPS rdkit 2017.03.2 "Chemoinformatics tool" -UPS refmac5 5.8.0238 "optimization tool" +UPS acedrg 243 "dictionary generator" +UPS acedrg_database 11 "data source" +UPS rdkit 2017.03.2 "Chemoinformatics tool" +UPS refmac5 5.8.0238 "optimization tool" + +loop_ +_chem_comp_alias.comp_id +_chem_comp_alias.group +_chem_comp_alias.atom_id +_chem_comp_alias.atom_id_standard +UPS S-NA OP2 OP1 +UPS S-NA S1P S2P diff --git a/y/YA4.cif b/y/YA4.cif index ee67f406e..33b58569b 100644 --- a/y/YA4.cif +++ b/y/YA4.cif @@ -7,7 +7,7 @@ _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level -YA4 YA4 "[(2~{R},3~{S},4~{S})-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphinic acid" NON-POLYMER 23 13 . +YA4 YA4 "[(2~{R},3~{S},4~{S})-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphinic acid" NON-POLYMER 22 13 . data_comp_YA4 loop_ @@ -19,29 +19,55 @@ _chem_comp_atom.charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z -YA4 "C1'" C CH2 0 -148.989 -53.025 -68.735 -YA4 "C2'" C CH1 0 -149.996 -54.159 -68.809 -YA4 "C3'" C CH1 0 -149.954 -54.735 -67.394 -YA4 "C4'" C CH1 0 -149.705 -53.484 -66.539 -YA4 "C5'" C CH2 0 -148.923 -53.706 -65.268 -YA4 "O2'" O OH1 0 -151.272 -53.629 -69.145 -YA4 "O3'" O OH1 0 -151.165 -55.380 -67.016 -YA4 "O4'" O O2 0 -148.975 -52.564 -67.383 -YA4 "O5'" O O2 0 -148.832 -52.462 -64.530 -YA4 OP1 O O 0 -148.157 -51.075 -62.567 -YA4 P P P 0 -147.936 -52.406 -63.205 -YA4 SP3 S SH1 0 -145.964 -52.549 -63.879 -YA4 OP3 O OP -1 -148.284 -53.588 -62.363 -YA4 "H1'" H H 0 -148.096 -53.337 -68.983 -YA4 "H1''" H H 0 -149.245 -52.292 -69.330 -YA4 "H2'" H H 0 -149.710 -54.856 -69.462 -YA4 "H3'" H H 0 -149.192 -55.363 -67.307 -YA4 "H4'" H H 0 -150.571 -53.080 -66.299 -YA4 "H5'" H H 0 -148.015 -54.031 -65.490 -YA4 "H5''" H H 0 -149.374 -54.391 -64.716 -YA4 "HO2'" H H 0 -151.897 -54.202 -69.110 -YA4 "HO3'" H H 0 -151.087 -55.662 -66.220 -YA4 HSP3 H HSH1 0 -145.572 -53.687 -63.745 +YA4 "C1'" C CH2 0 -149.007 -53.070 -68.716 +YA4 "C2'" C CH1 0 -150.115 -54.109 -68.787 +YA4 "C3'" C CH1 0 -150.015 -54.703 -67.379 +YA4 "C4'" C CH1 0 -149.733 -53.465 -66.521 +YA4 "C5'" C CH2 0 -148.892 -53.712 -65.293 +YA4 "O2'" O OH1 0 -151.351 -53.452 -69.024 +YA4 "O3'" O OH1 0 -151.218 -55.339 -66.966 +YA4 "O4'" O O2 0 -149.048 -52.540 -67.383 +YA4 "O5'" O O2 0 -148.956 -52.562 -64.430 +YA4 OP1 O OP -1 -148.602 -51.473 -62.296 +YA4 P P P 0 -147.906 -52.426 -63.218 +YA4 SP3 S S1 0 -146.167 -51.756 -63.773 +YA4 OP3 O OP -1 -147.877 -53.776 -62.578 +YA4 "H1'" H H 0 -148.135 -53.481 -68.896 +YA4 "H1''" H H 0 -149.157 -52.359 -69.373 +YA4 "H2'" H H 0 -149.927 -54.805 -69.473 +YA4 "H3'" H H 0 -149.254 -55.337 -67.330 +YA4 "H4'" H H 0 -150.591 -53.062 -66.235 +YA4 "H5'" H H 0 -147.953 -53.880 -65.564 +YA4 "H5''" H H 0 -149.229 -54.512 -64.816 +YA4 "HO2'" H H 0 -152.015 -53.941 -68.872 +YA4 "HO3'" H H 0 -151.118 -55.648 -66.192 + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +YA4 "C1'" C[5](C[5]C[5]HO)(O[5]C[5])(H)2{1|C<4>,1|O<2>,2|H<1>} +YA4 "C2'" C[5](C[5]C[5]HO)(C[5]O[5]HH)(OH)(H){1|C<4>,1|H<1>} +YA4 "C3'" C[5](C[5]C[5]HO)(C[5]O[5]CH)(OH)(H){2|H<1>} +YA4 "C4'" C[5](C[5]C[5]HO)(O[5]C[5])(CHHO)(H){1|O<2>,3|H<1>} +YA4 "C5'" C(C[5]C[5]O[5]H)(OP)(H)2 +YA4 "O2'" O(C[5]C[5]2H)(H) +YA4 "O3'" O(C[5]C[5]2H)(H) +YA4 "O4'" O[5](C[5]C[5]CH)(C[5]C[5]HH){2|H<1>,2|O<2>} +YA4 "O5'" O(CC[5]HH)(POOS) +YA4 OP1 O(POOS) +YA4 P P(OC)(O)2(S) +YA4 SP3 S(PO3) +YA4 OP3 O(POOS) +YA4 "H1'" H(C[5]C[5]O[5]H) +YA4 "H1''" H(C[5]C[5]O[5]H) +YA4 "H2'" H(C[5]C[5]2O) +YA4 "H3'" H(C[5]C[5]2O) +YA4 "H4'" H(C[5]C[5]O[5]C) +YA4 "H5'" H(CC[5]HO) +YA4 "H5''" H(CC[5]HO) +YA4 "HO2'" H(OC[5]) +YA4 "HO3'" H(OC[5]) loop_ _chem_comp_bond.comp_id @@ -53,29 +79,28 @@ _chem_comp_bond.value_dist_nucleus _chem_comp_bond.value_dist_nucleus_esd _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd -YA4 "C2'" "O2'" SINGLE n 1.421 0.0100 1.421 0.0100 -YA4 "C1'" "C2'" SINGLE n 1.520 0.0161 1.520 0.0161 -YA4 "C2'" "C3'" SINGLE n 1.529 0.0127 1.529 0.0127 -YA4 "C1'" "O4'" SINGLE n 1.427 0.0200 1.427 0.0200 -YA4 "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 -YA4 "C3'" "C4'" SINGLE n 1.535 0.0100 1.535 0.0100 -YA4 "C4'" "O4'" SINGLE n 1.444 0.0115 1.444 0.0115 -YA4 "C4'" "C5'" SINGLE n 1.509 0.0100 1.509 0.0100 -YA4 "C5'" "O5'" SINGLE n 1.450 0.0166 1.450 0.0166 -YA4 "O5'" P SINGLE n 1.601 0.0114 1.601 0.0114 -YA4 P SP3 SINGLE n 2.091 0.0200 2.091 0.0200 -YA4 OP1 P DOUBLE n 1.493 0.0157 1.493 0.0157 -YA4 P OP3 SINGLE n 1.493 0.0157 1.493 0.0157 -YA4 "C1'" "H1'" SINGLE n 1.089 0.0100 0.978 0.0200 -YA4 "C1'" "H1''" SINGLE n 1.089 0.0100 0.978 0.0200 -YA4 "C2'" "H2'" SINGLE n 1.089 0.0100 0.998 0.0100 -YA4 "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200 -YA4 "C4'" "H4'" SINGLE n 1.089 0.0100 0.986 0.0200 -YA4 "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 -YA4 "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200 -YA4 "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200 -YA4 "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 -YA4 SP3 HSP3 SINGLE n 1.338 0.0100 1.211 0.0200 +YA4 "C2'" "O2'" SINGLE n 1.420 0.0100 1.420 0.0100 +YA4 "C1'" "C2'" SINGLE n 1.521 0.0117 1.521 0.0117 +YA4 "C2'" "C3'" SINGLE n 1.531 0.0126 1.531 0.0126 +YA4 "C1'" "O4'" SINGLE n 1.435 0.0100 1.435 0.0100 +YA4 "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +YA4 "C3'" "C4'" SINGLE n 1.532 0.0100 1.532 0.0100 +YA4 "C4'" "O4'" SINGLE n 1.438 0.0100 1.438 0.0100 +YA4 "C4'" "C5'" SINGLE n 1.508 0.0100 1.508 0.0100 +YA4 "C5'" "O5'" SINGLE n 1.438 0.0200 1.438 0.0200 +YA4 "O5'" P SINGLE n 1.613 0.0200 1.613 0.0200 +YA4 P SP3 DOUBLE n 1.949 0.0200 1.949 0.0200 +YA4 OP1 P SINGLE n 1.497 0.0143 1.497 0.0143 +YA4 P OP3 SINGLE n 1.497 0.0143 1.497 0.0143 +YA4 "C1'" "H1'" SINGLE n 1.092 0.0100 0.980 0.0112 +YA4 "C1'" "H1''" SINGLE n 1.092 0.0100 0.980 0.0112 +YA4 "C2'" "H2'" SINGLE n 1.092 0.0100 0.995 0.0100 +YA4 "C3'" "H3'" SINGLE n 1.092 0.0100 0.991 0.0200 +YA4 "C4'" "H4'" SINGLE n 1.092 0.0100 0.990 0.0200 +YA4 "C5'" "H5'" SINGLE n 1.092 0.0100 0.991 0.0200 +YA4 "C5'" "H5''" SINGLE n 1.092 0.0100 0.991 0.0200 +YA4 "O2'" "HO2'" SINGLE n 0.972 0.0180 0.839 0.0200 +YA4 "O3'" "HO3'" SINGLE n 0.972 0.0180 0.839 0.0200 loop_ _chem_comp_angle.comp_id @@ -84,47 +109,46 @@ _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd -YA4 "C2'" "C1'" "O4'" 106.664 2.41 -YA4 "C2'" "C1'" "H1'" 110.717 1.50 -YA4 "C2'" "C1'" "H1''" 110.717 1.50 -YA4 "O4'" "C1'" "H1'" 109.245 3.00 -YA4 "O4'" "C1'" "H1''" 109.245 3.00 -YA4 "H1'" "C1'" "H1''" 108.734 2.05 -YA4 "O2'" "C2'" "C1'" 109.430 1.50 -YA4 "O2'" "C2'" "C3'" 112.463 2.73 -YA4 "O2'" "C2'" "H2'" 111.638 1.50 -YA4 "C1'" "C2'" "C3'" 104.443 2.26 -YA4 "C1'" "C2'" "H2'" 111.679 1.50 -YA4 "C3'" "C2'" "H2'" 110.255 2.04 -YA4 "C2'" "C3'" "O3'" 112.463 2.73 -YA4 "C2'" "C3'" "C4'" 102.352 1.50 -YA4 "C2'" "C3'" "H3'" 110.255 2.04 -YA4 "O3'" "C3'" "C4'" 111.281 2.46 -YA4 "O3'" "C3'" "H3'" 110.380 1.67 -YA4 "C4'" "C3'" "H3'" 110.452 2.54 -YA4 "C3'" "C4'" "O4'" 105.508 1.50 -YA4 "C3'" "C4'" "C5'" 116.008 1.52 -YA4 "C3'" "C4'" "H4'" 109.363 1.86 -YA4 "O4'" "C4'" "C5'" 109.123 1.50 -YA4 "O4'" "C4'" "H4'" 109.115 1.50 -YA4 "C5'" "C4'" "H4'" 108.268 1.50 -YA4 "C4'" "C5'" "O5'" 109.510 1.50 -YA4 "C4'" "C5'" "H5'" 109.624 1.50 -YA4 "C4'" "C5'" "H5''" 109.624 1.50 -YA4 "O5'" "C5'" "H5'" 109.821 1.50 -YA4 "O5'" "C5'" "H5''" 109.821 1.50 -YA4 "H5'" "C5'" "H5''" 108.472 1.50 -YA4 "C2'" "O2'" "HO2'" 113.614 3.00 -YA4 "C3'" "O3'" "HO3'" 108.744 3.00 -YA4 "C1'" "O4'" "C4'" 107.967 2.51 -YA4 "C5'" "O5'" P 119.135 1.78 -YA4 "O5'" P SP3 105.685 3.00 -YA4 "O5'" P OP1 108.530 2.45 -YA4 "O5'" P OP3 108.530 2.45 -YA4 SP3 P OP1 111.281 3.00 -YA4 SP3 P OP3 111.281 3.00 -YA4 OP1 P OP3 116.964 2.85 -YA4 P SP3 HSP3 109.471 3.00 +YA4 "C2'" "C1'" "O4'" 106.006 1.50 +YA4 "C2'" "C1'" "H1'" 110.715 1.50 +YA4 "C2'" "C1'" "H1''" 110.715 1.50 +YA4 "O4'" "C1'" "H1'" 110.530 1.50 +YA4 "O4'" "C1'" "H1''" 110.530 1.50 +YA4 "H1'" "C1'" "H1''" 108.613 1.50 +YA4 "O2'" "C2'" "C1'" 109.061 1.90 +YA4 "O2'" "C2'" "C3'" 112.059 3.00 +YA4 "O2'" "C2'" "H2'" 111.862 1.50 +YA4 "C1'" "C2'" "C3'" 101.111 3.00 +YA4 "C1'" "C2'" "H2'" 111.807 1.50 +YA4 "C3'" "C2'" "H2'" 110.368 2.92 +YA4 "C2'" "C3'" "O3'" 112.059 3.00 +YA4 "C2'" "C3'" "C4'" 102.511 1.50 +YA4 "C2'" "C3'" "H3'" 110.368 2.92 +YA4 "O3'" "C3'" "C4'" 110.713 3.00 +YA4 "O3'" "C3'" "H3'" 110.541 2.08 +YA4 "C4'" "C3'" "H3'" 110.577 3.00 +YA4 "C3'" "C4'" "O4'" 105.543 1.50 +YA4 "C3'" "C4'" "C5'" 115.288 1.50 +YA4 "C3'" "C4'" "H4'" 109.322 2.54 +YA4 "O4'" "C4'" "C5'" 109.156 1.74 +YA4 "O4'" "C4'" "H4'" 108.884 1.50 +YA4 "C5'" "C4'" "H4'" 108.351 1.59 +YA4 "C4'" "C5'" "O5'" 109.482 2.30 +YA4 "C4'" "C5'" "H5'" 109.589 1.50 +YA4 "C4'" "C5'" "H5''" 109.589 1.50 +YA4 "O5'" "C5'" "H5'" 109.954 1.50 +YA4 "O5'" "C5'" "H5''" 109.954 1.50 +YA4 "H5'" "C5'" "H5''" 108.471 1.50 +YA4 "C2'" "O2'" "HO2'" 112.908 3.00 +YA4 "C3'" "O3'" "HO3'" 109.389 3.00 +YA4 "C1'" "O4'" "C4'" 109.212 1.50 +YA4 "C5'" "O5'" P 119.085 2.00 +YA4 "O5'" P SP3 114.928 3.00 +YA4 "O5'" P OP1 106.327 3.00 +YA4 "O5'" P OP3 106.327 3.00 +YA4 SP3 P OP1 116.458 3.00 +YA4 SP3 P OP3 116.458 3.00 +YA4 OP1 P OP3 112.844 3.00 loop_ _chem_comp_tor.comp_id @@ -136,22 +160,16 @@ _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period -YA4 C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 -YA4 C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 -YA4 C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 -YA4 C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 -YA4 C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 -YA4 C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 -YA4 C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 -YA4 C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 -YA4 C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 -YA4 C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 -YA4 beta P "O5'" "C5'" "C4'" 180.000 10.00 3 -YA4 epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 -YA4 gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 -YA4 sp3_sp3_56 "O5'" P SP3 HSP3 60.000 10.0 3 +YA4 sp3_sp3_2 "O4'" "C1'" "C2'" "O2'" 180.000 10.0 3 +YA4 sp3_sp3_34 "C2'" "C1'" "O4'" "C4'" 180.000 10.0 3 +YA4 sp3_sp3_14 "O2'" "C2'" "C3'" "O3'" -60.000 10.0 3 YA4 sp3_sp3_31 "C1'" "C2'" "O2'" "HO2'" 180.000 10.0 3 -YA4 sp3_sp3_52 "C5'" "O5'" P SP3 180.000 10.0 3 +YA4 sp3_sp3_23 "O3'" "C3'" "C4'" "C5'" 60.000 10.0 3 +YA4 sp3_sp3_37 "C2'" "C3'" "O3'" "HO3'" 180.000 10.0 3 +YA4 sp3_sp3_40 "C3'" "C4'" "C5'" "O5'" 180.000 10.0 3 +YA4 sp3_sp3_29 "C5'" "C4'" "O4'" "C1'" 180.000 10.0 3 +YA4 sp3_sp3_49 "C4'" "C5'" "O5'" P 180.000 10.0 3 +YA4 sp3_sp3_52 "C5'" "O5'" P SP3 180.000 10.0 3 loop_ _chem_comp_chir.comp_id @@ -164,7 +182,7 @@ _chem_comp_chir.volume_sign YA4 chir_1 "C2'" "O2'" "C3'" "C1'" positive YA4 chir_2 "C3'" "O3'" "C4'" "C2'" positive YA4 chir_3 "C4'" "O4'" "C3'" "C5'" negative -YA4 chir_4 P SP3 "O5'" OP3 both +YA4 chir_4 P SP3 "O5'" OP3 both loop_ _pdbx_chem_comp_descriptor.comp_id @@ -172,19 +190,26 @@ _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor -YA4 InChI InChI 1.03 InChI=1S/C5H11O6PS/c6-3-1-10-4(5(3)7)2-11-12(8,9)13/h3-7H,1-2H2,(H2,8,9,13)/t3-,4+,5-/m0/s1 -YA4 InChIKey InChI 1.03 HBCHIJUQXWEATM-LMVFSUKVSA-N -YA4 SMILES_CANONICAL CACTVS 3.385 O[C@H]1CO[C@H](CO[P](O)(S)=O)[C@H]1O -YA4 SMILES CACTVS 3.385 O[CH]1CO[CH](CO[P](O)(S)=O)[CH]1O +YA4 InChI InChI 1.03 InChI=1S/C5H11O6PS/c6-3-1-10-4(5(3)7)2-11-12(8,9)13/h3-7H,1-2H2,(H2,8,9,13)/t3-,4+,5-/m0/s1 +YA4 InChIKey InChI 1.03 HBCHIJUQXWEATM-LMVFSUKVSA-N +YA4 SMILES_CANONICAL CACTVS 3.385 O[C@H]1CO[C@H](CO[P](O)(S)=O)[C@H]1O +YA4 SMILES CACTVS 3.385 O[CH]1CO[CH](CO[P](O)(S)=O)[CH]1O YA4 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 C1[C@@H]([C@@H]([C@H](O1)COP(=O)(O)S)O)O -YA4 SMILES "OpenEye OEToolkits" 2.0.7 C1C(C(C(O1)COP(=O)(O)S)O)O +YA4 SMILES "OpenEye OEToolkits" 2.0.7 C1C(C(C(O1)COP(=O)(O)S)O)O loop_ _pdbx_chem_comp_description_generator.comp_id _pdbx_chem_comp_description_generator.program_name _pdbx_chem_comp_description_generator.program_version _pdbx_chem_comp_description_generator.descriptor -YA4 acedrg 243 "dictionary generator" -YA4 acedrg_database 11 "data source" -YA4 rdkit 2017.03.2 "Chemoinformatics tool" -YA4 refmac5 5.8.0238 "optimization tool" +YA4 acedrg 277 "dictionary generator" +YA4 acedrg_database 12 "data source" +YA4 rdkit 2019.09.1 "Chemoinformatics tool" +YA4 refmac5 5.8.0425 "optimization tool" + +loop_ +_chem_comp_alias.comp_id +_chem_comp_alias.group +_chem_comp_alias.atom_id +_chem_comp_alias.atom_id_standard +YA4 S-NA SP3 S2P