Skip to content

fix 180-degree ideal angles #65

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
keitaroyam merged 2 commits into from
Oct 8, 2025
Merged

fix 180-degree ideal angles #65

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
77ca36a
fix 180-degree ideal angles
keitaroyam Sep 17, 2025
0de54c8
overlooked triple bond cases
keitaroyam Sep 17, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
The table of contents is too big for display.
Diff view
Diff view
  •  
  •  
  •  
711 changes: 405 additions & 306 deletions 0/051.cif
View file
Open in desktop

Large diffs are not rendered by default.

650 changes: 367 additions & 283 deletions 0/06U.cif
View file
Open in desktop

Large diffs are not rendered by default.

680 changes: 384 additions & 296 deletions 0/06V.cif
View file
Open in desktop

Large diffs are not rendered by default.

650 changes: 367 additions & 283 deletions 0/06W.cif
View file
Open in desktop

Large diffs are not rendered by default.

465 changes: 266 additions & 199 deletions 0/07M.cif
View file
Open in desktop

Large diffs are not rendered by default.

596 changes: 341 additions & 255 deletions 0/09B.cif
View file
Open in desktop

Large diffs are not rendered by default.

610 changes: 350 additions & 260 deletions 0/09F.cif
View file
Open in desktop

Large diffs are not rendered by default.

596 changes: 341 additions & 255 deletions 0/09G.cif
View file
Open in desktop

Large diffs are not rendered by default.

587 changes: 332 additions & 255 deletions 0/0B6.cif
View file
Open in desktop

Large diffs are not rendered by default.

524 changes: 297 additions & 227 deletions 0/0C5.cif
View file
Open in desktop

Large diffs are not rendered by default.

183 changes: 103 additions & 80 deletions 0/0CG.cif
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@
#
data_comp_list
loop_
_chem_comp.id
Expand All @@ -8,87 +7,110 @@ _chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
0CG 0CG "prop-2-yn-1-yl trihydrogen diphosphate" NON-POLYMER 15 12 .
#
0CG 0CG "prop-2-yn-1-yl trihydrogen diphosphate" NON-POLYMER 15 12 .

data_comp_0CG
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
0CG O20 O O 0 -24.166 0.752 -17.317
0CG P17 P P 0 -25.082 0.979 -16.140
0CG O18 O OP -1 -24.561 0.358 -14.867
0CG O19 O OP -1 -25.463 2.429 -15.967
0CG O16 O O2 0 -26.452 0.198 -16.486
0CG P13 P P 0 -26.788 -1.353 -16.719
0CG O14 O O 0 -28.193 -1.482 -17.209
0CG O15 O OP -1 -25.688 -1.978 -17.512
0CG O29 O O2 0 -26.712 -1.920 -15.219
0CG C28 C CH2 0 -27.640 -1.571 -14.226
0CG C27 C CSP 0 -28.785 -2.479 -14.227
0CG C30 C CSP 0 -29.694 -3.215 -14.278
0CG H4 H H 0 -27.948 -0.655 -14.379
0CG H5 H H 0 -27.199 -1.604 -13.353
0CG H6 H H 0 -30.425 -3.821 -14.324
0CG O20 O20 O O 0 -3.769 0.604 -0.675
0CG P17 P17 P P 0 -2.805 1.653 -0.157
0CG O18 O18 O OP -1 -2.171 2.465 -1.270
0CG O19 O19 O OP -1 -3.414 2.523 0.925
0CG O16 O16 O O2 0 -1.595 0.840 0.549
0CG P13 P13 P P 0 -0.561 -0.255 0.005
0CG O14 O14 O O 0 -1.285 -1.528 -0.239
0CG O15 O15 O OP -1 0.241 0.339 -1.095
0CG O29 O29 O O2 0 0.375 -0.427 1.294
0CG C28 C28 C CH2 0 1.475 -1.327 1.329
0CG C27 C27 C CSP 0 2.670 -0.749 0.709
0CG C30 C30 C CSP 0 3.630 -0.285 0.212
0CG H4 H4 H H 0 1.228 -2.151 0.860
0CG H5 H5 H H 0 1.668 -1.554 2.263
0CG H6 H6 H H 0 4.409 0.091 -0.191

loop_
_chem_comp_acedrg.comp_id
_chem_comp_acedrg.atom_id
_chem_comp_acedrg.atom_type
0CG O20 O(PO3)
0CG P17 P(OP)(O)3
0CG O18 O(PO3)
0CG O19 O(PO3)
0CG O16 O(PO3)2
0CG P13 P(OC)(OP)(O)2
0CG O14 O(PO3)
0CG O15 O(PO3)
0CG O29 O(CCHH)(PO3)
0CG C28 C(CC)(OP)(H)2
0CG C27 C(CHHO)(CH)
0CG C30 C(CC)(H)
0CG H4 H(CCHO)
0CG H5 H(CCHO)
0CG H6 H(CC)

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.aromatic
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.value_dist_nucleus
_chem_comp_bond.value_dist_nucleus_esd
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
0CG O20 P17 DOUBLE n 1.509 0.0200 1.509 0.0200
0CG P13 O14 DOUBLE n 1.493 0.0122 1.493 0.0122
0CG P13 O15 SINGLE n 1.493 0.0122 1.493 0.0122
0CG P17 O16 SINGLE n 1.614 0.0178 1.614 0.0178
0CG P17 O19 SINGLE n 1.509 0.0200 1.509 0.0200
0CG P17 O18 SINGLE n 1.509 0.0200 1.509 0.0200
0CG O16 P13 SINGLE n 1.604 0.0133 1.604 0.0133
0CG P13 O29 SINGLE n 1.604 0.0133 1.604 0.0133
0CG O29 C28 SINGLE n 1.400 0.0187 1.400 0.0187
0CG C27 C30 TRIPLE n 1.171 0.0134 1.171 0.0134
0CG C28 C27 SINGLE n 1.461 0.0100 1.461 0.0100
0CG C28 H4 SINGLE n 1.089 0.0100 0.978 0.0131
0CG C28 H5 SINGLE n 1.089 0.0100 0.978 0.0131
0CG C30 H6 SINGLE n 1.048 0.0100 0.950 0.0200
0CG O20 P17 DOUBLE n 1.516 0.0200 1.516 0.0200
0CG P13 O14 DOUBLE n 1.485 0.0100 1.485 0.0100
0CG P13 O15 SINGLE n 1.485 0.0100 1.485 0.0100
0CG P17 O16 SINGLE n 1.620 0.0143 1.620 0.0143
0CG P17 O19 SINGLE n 1.516 0.0200 1.516 0.0200
0CG P17 O18 SINGLE n 1.516 0.0200 1.516 0.0200
0CG O16 P13 SINGLE n 1.601 0.0120 1.601 0.0120
0CG P13 O29 SINGLE n 1.601 0.0120 1.601 0.0120
0CG O29 C28 SINGLE n 1.421 0.0111 1.421 0.0111
0CG C27 C30 TRIPLE n 1.177 0.0139 1.177 0.0139
0CG C28 C27 SINGLE n 1.465 0.0100 1.465 0.0100
0CG C28 H4 SINGLE n 1.092 0.0100 0.980 0.0185
0CG C28 H5 SINGLE n 1.092 0.0100 0.980 0.0185
0CG C30 H6 SINGLE n 1.044 0.0220 0.953 0.0200

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
0CG O20 P17 O16 105.965 2.38
0CG O20 P17 O19 112.716 1.50
0CG O20 P17 O18 112.716 1.50
0CG O16 P17 O19 105.965 2.38
0CG O16 P17 O18 105.965 2.38
0CG O19 P17 O18 112.716 1.50
0CG P17 O16 P13 132.584 3.00
0CG O14 P13 O15 118.411 2.35
0CG O14 P13 O16 108.816 2.14
0CG O14 P13 O29 107.912 2.57
0CG O15 P13 O16 108.816 2.14
0CG O15 P13 O29 107.912 2.57
0CG O16 P13 O29 101.065 1.97
0CG P13 O29 C28 121.496 2.55
0CG O29 C28 C27 111.252 1.52
0CG O29 C28 H4 108.980 1.50
0CG O29 C28 H5 108.980 1.50
0CG C27 C28 H4 109.475 1.50
0CG C27 C28 H5 109.475 1.50
0CG H4 C28 H5 108.291 1.50
0CG C30 C27 C28 177.445 1.50
0CG C27 C30 H6 179.396 1.50
0CG O20 P17 O16 106.004 3.00
0CG O20 P17 O19 112.609 3.00
0CG O20 P17 O18 112.609 3.00
0CG O16 P17 O19 106.004 3.00
0CG O16 P17 O18 106.004 3.00
0CG O19 P17 O18 112.609 3.00
0CG P17 O16 P13 132.613 3.00
0CG O14 P13 O15 118.805 3.00
0CG O14 P13 O16 109.053 3.00
0CG O14 P13 O29 108.662 3.00
0CG O15 P13 O16 109.053 3.00
0CG O15 P13 O29 108.662 3.00
0CG O16 P13 O29 100.260 3.00
0CG P13 O29 C28 121.760 3.00
0CG O29 C28 C27 111.971 2.72
0CG O29 C28 H4 109.004 1.50
0CG O29 C28 H5 109.004 1.50
0CG C27 C28 H4 109.639 1.50
0CG C27 C28 H5 109.639 1.50
0CG H4 C28 H5 108.240 1.50
0CG C30 C27 C28 180.000 3.00
0CG C27 C30 H6 180.000 3.00

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
Expand All @@ -99,12 +121,11 @@ _chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
0CG other_tor_1 C28 C27 C30 H6 180.000 10.0 1
0CG sp3_sp3_3 P13 O16 P17 O20 60.000 10.0 3
0CG sp3_sp3_6 P17 O16 P13 O14 60.000 10.0 3
0CG sp3_sp3_9 C28 O29 P13 O14 60.000 10.0 3
0CG sp3_sp3_10 C27 C28 O29 P13 180.000 10.0 3
0CG sp3_sp3_13 C30 C27 C28 O29 180.000 10.0 3
0CG sp3_sp3_1 P13 O16 P17 O20 60.000 10.0 3
0CG sp3_sp3_2 P17 O16 P13 O14 60.000 10.0 3
0CG sp3_sp3_3 C28 O29 P13 O14 60.000 10.0 3
0CG sp3_sp3_4 C27 C28 O29 P13 180.000 10.0 3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
Expand All @@ -113,27 +134,29 @@ _chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
0CG chir_1 P17 O16 O19 O18 both
0CG chir_2 P13 O16 O29 O15 both
0CG chir_1 P13 O16 O29 O15 both
0CG chir_2 P17 O16 O19 O18 both

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
0CG SMILES ACDLabs 12.01 O=P(O)(O)OP(=O)(OCC#C)O
0CG InChI InChI 1.03 InChI=1S/C3H6O7P2/c1-2-3-9-12(7,8)10-11(4,5)6/h1H,3H2,(H,7,8)(H2,4,5,6)
0CG InChIKey InChI 1.03 CEUAGVILADDFJF-UHFFFAOYSA-N
0CG SMILES_CANONICAL CACTVS 3.370 O[P](O)(=O)O[P](O)(=O)OCC#C
0CG SMILES CACTVS 3.370 O[P](O)(=O)O[P](O)(=O)OCC#C
0CG SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 C#CCOP(=O)(O)OP(=O)(O)O
0CG SMILES "OpenEye OEToolkits" 1.7.6 C#CCOP(=O)(O)OP(=O)(O)O
0CG SMILES ACDLabs 12.01 "O=P(O)(O)OP(=O)(OCC#C)O"
0CG InChI InChI 1.03 "InChI=1S/C3H6O7P2/c1-2-3-9-12(7,8)10-11(4,5)6/h1H,3H2,(H,7,8)(H2,4,5,6)"
0CG InChIKey InChI 1.03 CEUAGVILADDFJF-UHFFFAOYSA-N
0CG SMILES_CANONICAL CACTVS 3.370 "O[P](O)(=O)O[P](O)(=O)OCC#C"
0CG SMILES CACTVS 3.370 "O[P](O)(=O)O[P](O)(=O)OCC#C"
0CG SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C#CCOP(=O)(O)OP(=O)(O)O"
0CG SMILES "OpenEye OEToolkits" 1.7.6 "C#CCOP(=O)(O)OP(=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
0CG acedrg 243 "dictionary generator"
0CG acedrg_database 11 "data source"
0CG rdkit 2017.03.2 "Chemoinformatics tool"
0CG refmac5 5.8.0238 "optimization tool"
_acedrg_chem_comp_descriptor.comp_id
_acedrg_chem_comp_descriptor.program_name
_acedrg_chem_comp_descriptor.program_version
_acedrg_chem_comp_descriptor.type
0CG acedrg 326 "dictionary generator"
0CG acedrg_database 12 "data source"
0CG rdkit 2023.03.3 "Chemoinformatics tool"
0CG servalcat 0.4.120 'optimization tool'
Loading