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new group for phosphorothioate DNA #53

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efc6347
fix P-SH to P=S: 1SC 48Z 6NW 6OO C7R C7S DV3 F2T G46 GS OKN OKQ OKT U…
keitaroyam Apr 10, 2024
1a1030c
new group: S-NA
keitaroyam Apr 10, 2024
326f286
link for S-NA added
keitaroyam Apr 10, 2024
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404 changes: 223 additions & 181 deletions 1/1SC.cif
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264 changes: 150 additions & 114 deletions 4/48Z.cif
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Original file line number Diff line number Diff line change
Expand Up @@ -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_
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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
Expand All @@ -156,32 +179,45 @@ _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
_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'
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