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ener_lib: fix for sp2 nitrogen #64

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Merged
keitaroyam merged 4 commits into from
Aug 5, 2025
Merged

ener_lib: fix for sp2 nitrogen #64

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6c86e6e
ener_lib: fix for nitrogen
keitaroyam Jul 15, 2025
93c37d7
new types
keitaroyam Jul 24, 2025
0cec187
HB type of N21 (sp2 N with two bonds attached to one hydrogen atoms) …
keitaroyam Aug 5, 2025
c5d0d1d
newline accidentally inserted
keitaroyam Aug 5, 2025
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20 changes: 15 additions & 5 deletions ener_lib.cif
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Original file line number Diff line number Diff line change
Expand Up @@ -52,19 +52,27 @@ data_energy
#ATOMTYPE NS = without hydrogen ( triple bond ) = NSP
#ATOMTYPE NS1 = connected to 1 hydrogen = NSP1
#HEADER N Nitrogen SP2
#ATOMTYPE NC1 = connected to 1 hyd. in a charged group ( NE of ARG )
#ATOMTYPE NC2 = connected to 2 hyd. in a charged group ( NH2 of ARG )
## N with three bonds
#ATOMTYPE NH0 = connected to 0 hydrogen
#ATOMTYPE NH1 = connected to 1 hydrogen ( N of main chain )
#ATOMTYPE NH2 = connected to 2 hydrogen ( NE2 of GLU )
## N with two bonds
#ATOMTYPE N20 = connected to 0 hydrogen
#ATOMTYPE N21 = connected to 1 hydrogen
## OBSOLETE
#ATOMTYPE NC1 = connected to 1 hyd. in a charged group ( NE of ARG )
#ATOMTYPE NC2 = connected to 2 hyd. in a charged group ( NH2 of ARG )
#ATOMTYPE NPA = without hydrogen ( NA and NC of HEME )
#ATOMTYPE NPB = without hydrogen ( NB and ND of HEME )
#ATOMTYPE NRD5 = without hydrogen but with electronic doublet in 5 atoms ring
#ATOMTYPE NRD6 = without hydrogen but with electronic doublet in 6 atoms ring
#ATOMTYPE NR15 = connected to 1 hyd. in 5 atoms ring ( ND1 of HIS )
#ATOMTYPE NR16 = connected to 1 hyd. in 6 atoms ring
#ATOMTYPE NR5 = connected to 3 non-hydrogen atoms in 5 atoms ring
#ATOMTYPE NR55 = between two atoms in 5-5 rings
#ATOMTYPE NR56 = between two atoms in 5-6 rings
#ATOMTYPE NR6 = connected to 3 non-hydrogen atoms in 6 atoms ring
#ATOMTYPE NR66 = between two atoms in 6-6 rings
#HEADER N Nitrogen SP3
# N with four bonds
#ATOMTYPE N = without hydrogen
Expand Down Expand Up @@ -165,13 +173,15 @@ _lib_atom.sp
NSP 14.00670 A 1.550 1.600 1.32 N 3 1
NS1 14.00670 D 1.550 1.600 1.32 N 3 1
NSP1 14.00670 D 1.550 1.600 1.32 N 3 1
N 14.00670 B 1.550 1.600 1.32 N 3 2
N 14.00670 N 1.550 1.600 1.32 N 3 2
NC1 14.00670 D 1.550 1.600 1.32 N 3 2
NH0 14.00670 N 1.550 1.600 1.32 N 3 2
NH1 14.00670 D 1.550 1.600 1.32 N 3 2
NC2 14.00670 D 1.550 1.600 1.32 N 3 2
NH2 14.00670 D 1.550 1.600 1.32 N 3 2
NC3 14.00670 D 1.550 1.600 1.32 N 3 2
N20 14.00670 A 1.550 1.600 1.32 N 3 2
N21 14.00670 B 1.550 1.600 1.32 N 3 2
NT 14.00670 N 1.550 1.600 1.32 N 3 3
NT1 14.00670 D 1.550 1.600 1.32 N 3 3
NT2 14.00670 D 1.550 1.600 1.32 N 3 3
Expand All @@ -186,8 +196,8 @@ _lib_atom.sp
NR5 14.00670 A 1.550 1.600 1.32 N 3 2
NR15 14.00670 D 1.550 1.600 1.32 N 3 2
NRD5 14.00670 A 1.550 1.600 1.32 N 3 2
NR56 14.00670 A 1.550 1.600 1.32 N 3 2
NR55 14.00670 A 1.550 1.600 1.32 N 3 2
NR56 14.00670 N 1.550 1.600 1.32 N 3 2
NR55 14.00670 N 1.550 1.600 1.32 N 3 2
NR6 14.00670 A 1.550 1.600 1.32 N 3 2
NR66 14.00670 N 1.550 1.600 1.32 N 3 2
NR16 14.00670 D 1.550 1.600 1.32 N 3 2
Expand Down