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Fix hydrides #52

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merged 4 commits into from
May 7, 2024
Merged

Fix hydrides #52

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32ead4f
Fix hydrides (X-H_n) using acedrg 285
keitaroyam Apr 8, 2024
f21f378
Merge branch 'master' into fix-hydrides
keitaroyam Apr 25, 2024
46da83d
pep-NH2 link updated using acedrg 289
keitaroyam Apr 25, 2024
c7d6bc0
pep-NH2 further corrected using acedrg 290
keitaroyam Apr 26, 2024
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52 changes: 43 additions & 9 deletions d/D3O.cif
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,30 +13,40 @@ data_comp_D3O
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
D3O O O OH2 1 1.489 37.691 -2.079
D3O D1 H H 0 1.558 37.731 -1.092
D3O D2 H H 0 1.558 38.635 -2.371
D3O D3 H H 0 2.341 37.279 -2.371
D3O O O O O 1 1.511 37.691 -2.079
D3O D1 D1 H H 0 2.440 37.691 -2.079
D3O D2 D2 H H 0 1.047 38.496 -2.079
D3O D3 D3 H H 0 1.047 36.886 -2.079

loop_
_chem_comp_acedrg.comp_id
_chem_comp_acedrg.atom_id
_chem_comp_acedrg.atom_type
D3O O O(H)3
D3O D1 H(OHH)
D3O D2 H(OHH)
D3O D3 H(OHH)

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
D3O O D1 SINGLE n 0.970 0.0120 0.929 0.0200
D3O O D2 SINGLE n 0.970 0.0120 0.929 0.0200
D3O O D3 SINGLE n 0.970 0.0120 0.929 0.0200
D3O O D1 SINGLE n 0.972 0.0180 0.929 0.0200
D3O O D2 SINGLE n 0.972 0.0180 0.929 0.0200
D3O O D3 SINGLE n 0.972 0.0180 0.929 0.0200

loop_
_chem_comp_angle.comp_id
Expand All @@ -48,3 +58,27 @@ _chem_comp_angle.value_angle_esd
D3O D1 O D2 112.905 3.00
D3O D1 O D3 112.905 3.00
D3O D2 O D3 112.905 3.00

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
D3O SMILES ACDLabs 12.01 "[2H][O+]([2H])[2H]"
D3O InChI InChI 1.03 InChI=1S/H2O/h1H2/p+1/i/hD3
D3O InChIKey InChI 1.03 XLYOFNOQVPJJNP-ZRLBSURWSA-O
D3O SMILES_CANONICAL CACTVS 3.385 "[O+]([2H])([2H])[2H]"
D3O SMILES CACTVS 3.385 "[O+]([2H])([2H])[2H]"
D3O SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "[2H][O+]([2H])[2H]"
D3O SMILES "OpenEye OEToolkits" 1.9.2 "[2H][O+]([2H])[2H]"

loop_
_acedrg_chem_comp_descriptor.comp_id
_acedrg_chem_comp_descriptor.program_name
_acedrg_chem_comp_descriptor.program_version
_acedrg_chem_comp_descriptor.type
D3O acedrg 285 "dictionary generator"
D3O acedrg_database 12 "data source"
D3O rdkit 2019.09.1 "Chemoinformatics tool"
D3O servalcat 0.4.57 'optimization tool'
57 changes: 40 additions & 17 deletions h/H2S.cif
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Original file line number Diff line number Diff line change
Expand Up @@ -7,43 +7,43 @@ _chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
H2S H2S 'HYDROSULFURIC ACID ' NON-POLYMER 3 1 .
H2S H2S "HYDROSULFURIC ACID" NON-POLYMER 3 1 .

data_comp_H2S
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.partial_charge
_chem_comp_atom.charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
H2S HS2 H H 0.000 0.000 0.000 0.000
H2S S S S2 0.000 -1.260 0.000 -0.469
H2S HS1 H H 0.000 -1.018 0.000 -1.791
H2S S S S SH1 0 27.069 73.238 42.929
H2S HS1 HS1 H HSH1 0 28.282 73.238 42.929
H2S HS2 HS2 H HSH1 0 26.864 74.434 42.929

loop_
_chem_comp_tree.comp_id
_chem_comp_tree.atom_id
_chem_comp_tree.atom_back
_chem_comp_tree.atom_forward
_chem_comp_tree.connect_type
H2S HS2 n/a S START
H2S S HS2 HS1 .
H2S HS1 S . END
_chem_comp_acedrg.comp_id
_chem_comp_acedrg.atom_id
_chem_comp_acedrg.atom_type
H2S S S(H)2
H2S HS1 H(SH)
H2S HS2 H(SH)

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.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
H2S HS1 S single 1.338 0.010 1.171 0.208
H2S S HS2 single 1.338 0.010 1.171 0.208
H2S S HS1 SINGLE n 1.338 0.0100 1.213 0.0200
H2S S HS2 SINGLE n 1.338 0.0100 1.213 0.0200

loop_
_chem_comp_angle.comp_id
Expand All @@ -52,4 +52,27 @@ _chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
H2S HS2 S HS1 100.018 3.000
H2S HS1 S HS2 99.729 3.00

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
H2S SMILES_CANONICAL CACTVS 3.341 S
H2S SMILES CACTVS 3.341 S
H2S SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 S
H2S SMILES "OpenEye OEToolkits" 1.5.0 S
H2S InChI InChI 1.03 InChI=1S/H2S/h1H2
H2S InChIKey InChI 1.03 RWSOTUBLDIXVET-UHFFFAOYSA-N

loop_
_acedrg_chem_comp_descriptor.comp_id
_acedrg_chem_comp_descriptor.program_name
_acedrg_chem_comp_descriptor.program_version
_acedrg_chem_comp_descriptor.type
H2S acedrg 285 "dictionary generator"
H2S acedrg_database 12 "data source"
H2S rdkit 2019.09.1 "Chemoinformatics tool"
H2S servalcat 0.4.57 'optimization tool'
58 changes: 41 additions & 17 deletions h/HOH.cif
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Original file line number Diff line number Diff line change
Expand Up @@ -7,43 +7,43 @@ _chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
HOH HOH 'WATER ' NON-POLYMER 3 1 .
HOH HOH WATER NON-POLYMER 3 1 .

data_comp_HOH
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.partial_charge
_chem_comp_atom.charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
HOH H2 H H 0.000 0.000 0.000 0.000
HOH O O OH2 0.000 -0.867 0.000 -0.427
HOH H1 H H 0.000 -0.709 0.000 -1.381
HOH O O O OH2 0 -23.107 18.382 -21.639
HOH H1 H1 H H 0 -22.244 18.382 -21.639
HOH H2 H2 H H 0 -23.365 19.206 -21.639

loop_
_chem_comp_tree.comp_id
_chem_comp_tree.atom_id
_chem_comp_tree.atom_back
_chem_comp_tree.atom_forward
_chem_comp_tree.connect_type
HOH H2 n/a O START
HOH O H2 H1 .
HOH H1 O . END
_chem_comp_acedrg.comp_id
_chem_comp_acedrg.atom_id
_chem_comp_acedrg.atom_type
HOH O O(H)2
HOH H1 H(OH)
HOH H2 H(OH)

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.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
HOH H1 O single 0.970 0.012 0.839 0.014
HOH O H2 single 0.970 0.012 0.839 0.014
HOH O H1 SINGLE n 0.972 0.0180 0.863 0.0200
HOH O H2 SINGLE n 0.972 0.0180 0.863 0.0200

loop_
_chem_comp_angle.comp_id
Expand All @@ -52,4 +52,28 @@ _chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
HOH H2 O H1 120.000 3.000
HOH H1 O H2 107.391 3.00

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
HOH SMILES ACDLabs 10.04 O
HOH SMILES_CANONICAL CACTVS 3.341 O
HOH SMILES CACTVS 3.341 O
HOH SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 O
HOH SMILES "OpenEye OEToolkits" 1.5.0 O
HOH InChI InChI 1.03 InChI=1S/H2O/h1H2
HOH InChIKey InChI 1.03 XLYOFNOQVPJJNP-UHFFFAOYSA-N

loop_
_acedrg_chem_comp_descriptor.comp_id
_acedrg_chem_comp_descriptor.program_name
_acedrg_chem_comp_descriptor.program_version
_acedrg_chem_comp_descriptor.type
HOH acedrg 285 "dictionary generator"
HOH acedrg_database 12 "data source"
HOH rdkit 2019.09.1 "Chemoinformatics tool"
HOH servalcat 0.4.57 'optimization tool'
26 changes: 12 additions & 14 deletions links_and_mods.cif
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Original file line number Diff line number Diff line change
Expand Up @@ -5305,7 +5305,7 @@ _chem_link_bond.atom_id_2
_chem_link_bond.type
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
pep-NH2 1 C 2 N SINGLE 1.324 0.0100
pep-NH2 1 C 2 N SINGLE 1.324 0.0120

loop_
_chem_link_angle.link_id
Expand All @@ -5317,10 +5317,10 @@ _chem_link_angle.atom_3_comp_id
_chem_link_angle.atom_id_3
_chem_link_angle.value_angle
_chem_link_angle.value_angle_esd
pep-NH2 1 CA 1 C 2 N 114.873 1.50
pep-NH2 1 O 1 C 2 N 123.611 1.50
pep-NH2 1 C 2 N 2 HN1 119.954 1.50
pep-NH2 1 C 2 N 2 HN 119.954 1.50
pep-NH2 1 CA 1 C 2 N 116.005 1.50
pep-NH2 1 O 1 C 2 N 123.568 1.50
pep-NH2 1 C 2 N 2 HN1 119.943 3.00
pep-NH2 1 C 2 N 2 HN2 119.943 3.00

loop_
_chem_link_tor.link_id
Expand All @@ -5336,7 +5336,7 @@ _chem_link_tor.atom_id_4
_chem_link_tor.value_angle
_chem_link_tor.value_angle_esd
_chem_link_tor.period
pep-NH2 sp2_sp2_1 1 CA 1 C 2 N 2 HN1 180.000 5.00 2
pep-NH2 sp2_sp2_1 1 CA 1 C 2 N 2 HN1 180.000 5.0 2

loop_
_chem_link_plane.link_id
Expand All @@ -5349,8 +5349,8 @@ pep-NH2 plan-1 1 C 0.020
pep-NH2 plan-1 2 N 0.020
pep-NH2 plan-1 1 O 0.020
pep-NH2 plan-2 1 C 0.020
pep-NH2 plan-2 2 HN 0.020
pep-NH2 plan-2 2 HN1 0.020
pep-NH2 plan-2 2 HN2 0.020
pep-NH2 plan-2 2 N 0.020

data_link_pept-CR8
Expand Down Expand Up @@ -11406,7 +11406,7 @@ _chem_mod_atom.new_atom_id
_chem_mod_atom.new_type_symbol
_chem_mod_atom.new_type_energy
_chem_mod_atom.new_charge
NH2mod1 delete HN2 . H H .
NH2mod1 delete H . H H 0
NH2mod1 change N . N NH2 0

loop_
Expand All @@ -11419,9 +11419,7 @@ _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
NH2mod1 delete HN2 N single . . . .
NH2mod1 change N HN1 single 0.914 0.010 1.036 0.016
NH2mod1 change N HN single 0.914 0.010 1.036 0.016
NH2mod1 delete N H single . . . .

loop_
_chem_mod_angle.mod_id
Expand All @@ -11431,9 +11429,9 @@ _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
NH2mod1 delete HN N HN2 . .
NH2mod1 delete HN2 N HN1 . .
NH2mod1 change HN1 N HN 120.093 2.38
NH2mod1 delete HN1 N H . .
NH2mod1 delete HN2 N H . .
NH2mod1 change HN1 N HN2 120.114 3.00

data_mod_CR8mod2
loop_
Expand Down
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