From 32ead4f2fdd3d4337a8046d310d3bc60f6c35229 Mon Sep 17 00:00:00 2001 From: Keitaro Yamashita Date: Mon, 8 Apr 2024 20:23:56 +0900 Subject: [PATCH 1/3] Fix hydrides (X-H_n) using acedrg 285 --- d/D3O.cif | 52 +++++++++++++++++++++++++++++------- h/H2S.cif | 57 +++++++++++++++++++++++++++------------ h/HOH.cif | 58 ++++++++++++++++++++++++++++------------ n/NH2.cif | 68 +++++++++++++++++++++++++++++++--------------- n/NH3.cif | 68 +++++++++++++++++++++++++++++++--------------- n/NH4.cif | 80 ++++++++++++++++++++++++++++++++++++------------------- o/OH.cif | 50 +++++++++++++++++++++++++--------- 7 files changed, 305 insertions(+), 128 deletions(-) diff --git a/d/D3O.cif b/d/D3O.cif index efc5f01b33..9d96f91fb3 100644 --- a/d/D3O.cif +++ b/d/D3O.cif @@ -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 @@ -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' diff --git a/h/H2S.cif b/h/H2S.cif index e07f1a5e5e..0268f3e49c 100644 --- a/h/H2S.cif +++ b/h/H2S.cif @@ -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 @@ -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' diff --git a/h/HOH.cif b/h/HOH.cif index b633b7ea04..9b16b4d268 100644 --- a/h/HOH.cif +++ b/h/HOH.cif @@ -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 @@ -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' diff --git a/n/NH2.cif b/n/NH2.cif index 401cd9673a..d625320347 100644 --- a/n/NH2.cif +++ b/n/NH2.cif @@ -7,46 +7,46 @@ _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level -NH2 NH2 'AMINO GROUP ' NON-POLYMER 4 1 . +NH2 NH2 "AMINO GROUP" NON-POLYMER 4 1 . data_comp_NH2 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 -NH2 HN H H 0.000 0.000 0.000 0.000 -NH2 N N N 0.000 0.674 0.674 0.000 -NH2 HN2 H H 0.000 1.595 0.427 0.000 -NH2 HN1 H H 0.000 0.427 1.595 0.000 +NH2 N N N N33 0 10.097 8.960 -7.822 +NH2 HN1 HN1 H H 0 10.995 8.960 -7.822 +NH2 HN2 HN2 H H 0 9.648 9.738 -7.822 +NH2 H H H H 0 9.648 8.182 -7.822 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 -NH2 HN n/a N START -NH2 N HN HN1 . -NH2 HN2 N . . -NH2 HN1 N . END +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +NH2 N N(H)3 +NH2 HN1 H(NHH) +NH2 HN2 H(NHH) +NH2 H H(NHH) 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 -NH2 HN1 N single 1.036 0.016 0.954 0.020 -NH2 HN2 N single 1.036 0.016 0.954 0.020 -NH2 N HN single 1.036 0.016 0.954 0.020 +NH2 N HN1 SINGLE n 1.018 0.0520 0.898 0.0200 +NH2 N HN2 SINGLE n 1.018 0.0520 0.898 0.0200 +NH2 N H SINGLE n 1.018 0.0520 0.898 0.0200 loop_ _chem_comp_angle.comp_id @@ -55,6 +55,30 @@ _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd -NH2 HN N HN2 120.000 3.000 -NH2 HN N HN1 120.000 3.000 -NH2 HN2 N HN1 120.000 3.000 +NH2 HN1 N HN2 107.512 3.00 +NH2 HN1 N H 107.512 3.00 +NH2 HN2 N H 107.512 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 +NH2 SMILES ACDLabs 10.04 N +NH2 InChI InChI 1.06 InChI=1S/H3N/h1H3 +NH2 InChIKey InChI 1.06 QGZKDVFQNNGYKY-UHFFFAOYSA-N +NH2 SMILES_CANONICAL CACTVS 3.385 "[NH2]" +NH2 SMILES CACTVS 3.385 "[NH2]" +NH2 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[NH2]" +NH2 SMILES "OpenEye OEToolkits" 2.0.7 "[NH2]" + +loop_ +_acedrg_chem_comp_descriptor.comp_id +_acedrg_chem_comp_descriptor.program_name +_acedrg_chem_comp_descriptor.program_version +_acedrg_chem_comp_descriptor.type +NH2 acedrg 285 "dictionary generator" +NH2 acedrg_database 12 "data source" +NH2 rdkit 2019.09.1 "Chemoinformatics tool" +NH2 servalcat 0.4.57 'optimization tool' diff --git a/n/NH3.cif b/n/NH3.cif index 6a77df836c..5a3b6a219e 100644 --- a/n/NH3.cif +++ b/n/NH3.cif @@ -7,46 +7,46 @@ _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level -NH3 NH3 'AMMONIA ' NON-POLYMER 4 1 . +NH3 NH3 AMMONIA NON-POLYMER 4 1 . data_comp_NH3 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 -NH3 HN3 H H 0.000 0.000 0.000 0.000 -NH3 N N N 0.000 -0.180 0.886 0.447 -NH3 HN2 H H 0.000 0.372 1.574 -0.040 -NH3 HN1 H H 0.000 0.194 0.821 1.381 +NH3 N N N N33 0 52.010 -12.715 -42.848 +NH3 HN1 HN1 H H 0 52.908 -12.715 -42.848 +NH3 HN2 HN2 H H 0 51.561 -11.937 -42.848 +NH3 HN3 HN3 H H 0 51.561 -13.493 -42.848 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 -NH3 HN3 n/a N START -NH3 N HN3 HN1 . -NH3 HN2 N . . -NH3 HN1 N . END +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +NH3 N N(H)3 +NH3 HN1 H(NHH) +NH3 HN2 H(NHH) +NH3 HN3 H(NHH) 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 -NH3 HN1 N single 1.036 0.016 0.954 0.020 -NH3 HN2 N single 1.036 0.016 0.954 0.020 -NH3 N HN3 single 1.036 0.016 0.954 0.020 +NH3 N HN1 SINGLE n 1.018 0.0520 0.898 0.0200 +NH3 N HN2 SINGLE n 1.018 0.0520 0.898 0.0200 +NH3 N HN3 SINGLE n 1.018 0.0520 0.898 0.0200 loop_ _chem_comp_angle.comp_id @@ -55,6 +55,30 @@ _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd -NH3 HN3 N HN2 120.000 3.000 -NH3 HN3 N HN1 120.000 3.000 -NH3 HN2 N HN1 120.000 3.000 +NH3 HN1 N HN2 107.512 3.00 +NH3 HN1 N HN3 107.512 3.00 +NH3 HN2 N HN3 107.512 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 +NH3 SMILES ACDLabs 10.04 N +NH3 SMILES_CANONICAL CACTVS 3.341 N +NH3 SMILES CACTVS 3.341 N +NH3 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 N +NH3 SMILES "OpenEye OEToolkits" 1.5.0 N +NH3 InChI InChI 1.03 InChI=1S/H3N/h1H3 +NH3 InChIKey InChI 1.03 QGZKDVFQNNGYKY-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 +NH3 acedrg 285 "dictionary generator" +NH3 acedrg_database 12 "data source" +NH3 rdkit 2019.09.1 "Chemoinformatics tool" +NH3 servalcat 0.4.57 'optimization tool' diff --git a/n/NH4.cif b/n/NH4.cif index 31ec73aa10..dda1fb6333 100644 --- a/n/NH4.cif +++ b/n/NH4.cif @@ -7,49 +7,49 @@ _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level -NH4 NH4 'AMMONIUM ION ' NON-POLYMER 5 1 . +NH4 NH4 "AMMONIUM ION" NON-POLYMER 5 1 . data_comp_NH4 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 -NH4 HN4 H H 0.000 0.000 0.000 0.000 -NH4 N N NT 1.000 -0.581 0.302 -0.782 -NH4 HN3 H H 0.000 -1.232 1.041 -0.516 -NH4 HN2 H H 0.000 -0.024 0.609 -1.579 -NH4 HN1 H H 0.000 -1.055 -0.583 -0.962 +NH4 N N N NT4 1 11.106 19.172 34.702 +NH4 HN1 HN1 H H 0 12.007 19.171 34.702 +NH4 HN2 HN2 H H 0 10.807 20.021 34.702 +NH4 HN3 HN3 H H 0 10.806 18.747 35.438 +NH4 HN4 HN4 H H 0 10.806 18.747 33.966 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 -NH4 N . HN1 START -NH4 HN4 N . . -NH4 HN3 N . . -NH4 HN2 N . . -NH4 HN1 N . END +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +NH4 N N(H)4 +NH4 HN1 H(NH3) +NH4 HN2 H(NH3) +NH4 HN3 H(NH3) +NH4 HN4 H(NH3) 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 -NH4 HN1 N single 1.036 0.016 0.914 0.007 -NH4 HN2 N single 1.036 0.016 0.914 0.007 -NH4 HN3 N single 1.036 0.016 0.914 0.007 -NH4 N HN4 single 1.036 0.016 0.914 0.007 +NH4 N HN1 SINGLE n 1.018 0.0520 0.901 0.0200 +NH4 N HN2 SINGLE n 1.018 0.0520 0.901 0.0200 +NH4 N HN3 SINGLE n 1.018 0.0520 0.901 0.0200 +NH4 N HN4 SINGLE n 1.018 0.0520 0.901 0.0200 loop_ _chem_comp_angle.comp_id @@ -58,9 +58,33 @@ _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd -NH4 HN4 N HN3 109.500 3.000 -NH4 HN4 N HN2 109.500 3.000 -NH4 HN4 N HN1 109.500 3.000 -NH4 HN3 N HN2 109.500 3.000 -NH4 HN3 N HN1 109.500 3.000 -NH4 HN2 N HN1 109.500 3.000 +NH4 HN1 N HN2 109.370 3.00 +NH4 HN1 N HN3 109.370 3.00 +NH4 HN1 N HN4 109.370 3.00 +NH4 HN2 N HN3 109.370 3.00 +NH4 HN2 N HN4 109.370 3.00 +NH4 HN3 N HN4 109.370 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 +NH4 SMILES ACDLabs 10.04 "[NH4+]" +NH4 SMILES_CANONICAL CACTVS 3.341 "[NH4+]" +NH4 SMILES CACTVS 3.341 "[NH4+]" +NH4 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "[NH4+]" +NH4 SMILES "OpenEye OEToolkits" 1.5.0 "[NH4+]" +NH4 InChI InChI 1.03 InChI=1S/H3N/h1H3/p+1 +NH4 InChIKey InChI 1.03 QGZKDVFQNNGYKY-UHFFFAOYSA-O + +loop_ +_acedrg_chem_comp_descriptor.comp_id +_acedrg_chem_comp_descriptor.program_name +_acedrg_chem_comp_descriptor.program_version +_acedrg_chem_comp_descriptor.type +NH4 acedrg 285 "dictionary generator" +NH4 acedrg_database 12 "data source" +NH4 rdkit 2019.09.1 "Chemoinformatics tool" +NH4 servalcat 0.4.57 'optimization tool' diff --git a/o/OH.cif b/o/OH.cif index dd5c082549..124aba64cf 100644 --- a/o/OH.cif +++ b/o/OH.cif @@ -7,37 +7,61 @@ _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level -OH OH 'HYDROXIDE ION ' NON-POLYMER 2 1 . +OH OH "HYDROXIDE ION" NON-POLYMER 2 1 . data_comp_OH 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 -OH HO H H 0.000 0.000 0.000 0.000 -OH O O O -1.000 -0.650 0.000 -0.715 +OH O O O OC -1 14.860 37.830 7.076 +OH HO HO H H 0 15.874 37.830 7.076 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 -OH HO n/a O START -OH O HO . END +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +OH O O(H) +OH HO H(O) 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 -OH O HO single 1.040 0.020 1.040 0.020 +OH O HO SINGLE n 0.966 0.0059 1.014 0.0200 + +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 +OH SMILES ACDLabs 10.04 "[OH-]" +OH SMILES_CANONICAL CACTVS 3.341 "[OH-]" +OH SMILES CACTVS 3.341 "[OH-]" +OH SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "[OH-]" +OH SMILES "OpenEye OEToolkits" 1.5.0 "[OH-]" +OH InChI InChI 1.03 InChI=1S/H2O/h1H2/p-1 +OH InChIKey InChI 1.03 XLYOFNOQVPJJNP-UHFFFAOYSA-M + +loop_ +_acedrg_chem_comp_descriptor.comp_id +_acedrg_chem_comp_descriptor.program_name +_acedrg_chem_comp_descriptor.program_version +_acedrg_chem_comp_descriptor.type +OH acedrg 285 "dictionary generator" +OH acedrg_database 12 "data source" +OH rdkit 2019.09.1 "Chemoinformatics tool" +OH servalcat 0.4.57 'optimization tool' From 46da83da2d145c7f1c7982933b6520764ae1f154 Mon Sep 17 00:00:00 2001 From: Keitaro Yamashita Date: Thu, 25 Apr 2024 10:17:20 +0900 Subject: [PATCH 2/3] pep-NH2 link updated using acedrg 289 --- links_and_mods.cif | 45 ++++++++++++------------------------------- list/mon_lib_list.cif | 45 ++++++++++++------------------------------- 2 files changed, 24 insertions(+), 66 deletions(-) diff --git a/links_and_mods.cif b/links_and_mods.cif index 0fa509a806..6d0e66e1eb 100644 --- a/links_and_mods.cif +++ b/links_and_mods.cif @@ -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 1.317 0.0154 loop_ _chem_link_angle.link_id @@ -5317,26 +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 - -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 -pep-NH2 sp2_sp2_1 1 CA 1 C 2 N 2 HN1 180.000 5.00 2 +pep-NH2 1 CA 1 C 2 N 116.444 3.00 +pep-NH2 1 O 1 C 2 N 123.225 1.50 +pep-NH2 1 C 2 N 2 HN1 114.198 3.00 +pep-NH2 1 C 2 N 2 HN2 114.198 3.00 loop_ _chem_link_plane.link_id @@ -5348,10 +5332,6 @@ pep-NH2 plan-1 1 CA 0.020 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 N 0.020 data_link_pept-CR8 loop_ @@ -11406,8 +11386,8 @@ _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 change N . N NH2 0 +NH2mod1 delete H . H H 0 +NH2mod1 change N . N N32 0 loop_ _chem_mod_bond.mod_id @@ -11419,9 +11399,9 @@ _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 . . . . +NH2mod1 change N HN1 single 0.922 0.0200 1.013 0.0120 +NH2mod1 change N HN2 single 0.922 0.0200 1.013 0.0120 loop_ _chem_mod_angle.mod_id @@ -11431,9 +11411,8 @@ _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 . . data_mod_CR8mod2 loop_ diff --git a/list/mon_lib_list.cif b/list/mon_lib_list.cif index 44670ed380..8e3608ed63 100644 --- a/list/mon_lib_list.cif +++ b/list/mon_lib_list.cif @@ -41205,7 +41205,7 @@ _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 1.317 0.0154 loop_ _chem_link_angle.link_id @@ -41217,26 +41217,10 @@ _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 - -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 -pep-NH2 sp2_sp2_1 1 CA 1 C 2 N 2 HN1 180.000 5.00 2 +pep-NH2 1 CA 1 C 2 N 116.444 3.00 +pep-NH2 1 O 1 C 2 N 123.225 1.50 +pep-NH2 1 C 2 N 2 HN1 114.198 3.00 +pep-NH2 1 C 2 N 2 HN2 114.198 3.00 loop_ _chem_link_plane.link_id @@ -41248,10 +41232,6 @@ pep-NH2 plan-1 1 CA 0.020 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 N 0.020 data_link_pept-CR8 loop_ @@ -47306,8 +47286,8 @@ _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 change N . N NH2 0 +NH2mod1 delete H . H H 0 +NH2mod1 change N . N N32 0 loop_ _chem_mod_bond.mod_id @@ -47319,9 +47299,9 @@ _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 . . . . +NH2mod1 change N HN1 single 0.922 0.0200 1.013 0.0120 +NH2mod1 change N HN2 single 0.922 0.0200 1.013 0.0120 loop_ _chem_mod_angle.mod_id @@ -47331,9 +47311,8 @@ _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 . . data_mod_CR8mod2 loop_ From c7d6bc0245edae027a5bd7da458b06af7e08ccff Mon Sep 17 00:00:00 2001 From: Keitaro Yamashita Date: Fri, 26 Apr 2024 22:18:56 +0900 Subject: [PATCH 3/3] pep-NH2 further corrected using acedrg 290 --- links_and_mods.cif | 35 +++++++++++++++++++++++++++-------- list/mon_lib_list.cif | 35 +++++++++++++++++++++++++++-------- 2 files changed, 54 insertions(+), 16 deletions(-) diff --git a/links_and_mods.cif b/links_and_mods.cif index 6d0e66e1eb..61a65497a1 100644 --- a/links_and_mods.cif +++ b/links_and_mods.cif @@ -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 1.317 0.0154 +pep-NH2 1 C 2 N SINGLE 1.324 0.0120 loop_ _chem_link_angle.link_id @@ -5317,10 +5317,26 @@ _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 116.444 3.00 -pep-NH2 1 O 1 C 2 N 123.225 1.50 -pep-NH2 1 C 2 N 2 HN1 114.198 3.00 -pep-NH2 1 C 2 N 2 HN2 114.198 3.00 +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 +_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 +pep-NH2 sp2_sp2_1 1 CA 1 C 2 N 2 HN1 180.000 5.0 2 loop_ _chem_link_plane.link_id @@ -5332,6 +5348,10 @@ pep-NH2 plan-1 1 CA 0.020 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 HN1 0.020 +pep-NH2 plan-2 2 HN2 0.020 +pep-NH2 plan-2 2 N 0.020 data_link_pept-CR8 loop_ @@ -11387,7 +11407,7 @@ _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_charge NH2mod1 delete H . H H 0 -NH2mod1 change N . N N32 0 +NH2mod1 change N . N NH2 0 loop_ _chem_mod_bond.mod_id @@ -11400,8 +11420,6 @@ _chem_mod_bond.new_value_dist_esd _chem_mod_bond.new_value_dist_nucleus _chem_mod_bond.new_value_dist_nucleus_esd NH2mod1 delete N H single . . . . -NH2mod1 change N HN1 single 0.922 0.0200 1.013 0.0120 -NH2mod1 change N HN2 single 0.922 0.0200 1.013 0.0120 loop_ _chem_mod_angle.mod_id @@ -11413,6 +11431,7 @@ _chem_mod_angle.new_value_angle _chem_mod_angle.new_value_angle_esd NH2mod1 delete HN1 N H . . NH2mod1 delete HN2 N H . . +NH2mod1 change HN1 N HN2 120.114 3.00 data_mod_CR8mod2 loop_ diff --git a/list/mon_lib_list.cif b/list/mon_lib_list.cif index 8e3608ed63..ae7b9d49f0 100644 --- a/list/mon_lib_list.cif +++ b/list/mon_lib_list.cif @@ -41205,7 +41205,7 @@ _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 1.317 0.0154 +pep-NH2 1 C 2 N SINGLE 1.324 0.0120 loop_ _chem_link_angle.link_id @@ -41217,10 +41217,26 @@ _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 116.444 3.00 -pep-NH2 1 O 1 C 2 N 123.225 1.50 -pep-NH2 1 C 2 N 2 HN1 114.198 3.00 -pep-NH2 1 C 2 N 2 HN2 114.198 3.00 +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 +_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 +pep-NH2 sp2_sp2_1 1 CA 1 C 2 N 2 HN1 180.000 5.0 2 loop_ _chem_link_plane.link_id @@ -41232,6 +41248,10 @@ pep-NH2 plan-1 1 CA 0.020 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 HN1 0.020 +pep-NH2 plan-2 2 HN2 0.020 +pep-NH2 plan-2 2 N 0.020 data_link_pept-CR8 loop_ @@ -47287,7 +47307,7 @@ _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_charge NH2mod1 delete H . H H 0 -NH2mod1 change N . N N32 0 +NH2mod1 change N . N NH2 0 loop_ _chem_mod_bond.mod_id @@ -47300,8 +47320,6 @@ _chem_mod_bond.new_value_dist_esd _chem_mod_bond.new_value_dist_nucleus _chem_mod_bond.new_value_dist_nucleus_esd NH2mod1 delete N H single . . . . -NH2mod1 change N HN1 single 0.922 0.0200 1.013 0.0120 -NH2mod1 change N HN2 single 0.922 0.0200 1.013 0.0120 loop_ _chem_mod_angle.mod_id @@ -47313,6 +47331,7 @@ _chem_mod_angle.new_value_angle _chem_mod_angle.new_value_angle_esd NH2mod1 delete HN1 N H . . NH2mod1 delete HN2 N H . . +NH2mod1 change HN1 N HN2 120.114 3.00 data_mod_CR8mod2 loop_