# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 13:25:29 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 4-[2-amino-5-(3,4,5-trimethoxyphenyl)pyridin-3-yl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(cc(OC)c1OC)c2cnc(N)c(c2)c3ccc(cc3)C(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 VGK  VGK  '4-[2-amino-5-(3,4,5-trimethoxyphenyl)pyridin-3-yl]benzoic acid'  ligand  47  28  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VGK
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 VGK  C01   C  CH3    0  -0.439   5.6080   2.2195  -1.1795
 VGK  O02   O  O2     0  -0.464   5.5733   0.8438  -0.8558
 VGK  C03   C  CR6    0   0.356   4.4170   0.3166  -0.4193
 VGK  C04   C  CR16   0  -0.498   3.2301   1.0318  -0.2828
 VGK  C05   C  CR6    0   0.137   2.0788   0.3938   0.1753
 VGK  C06   C  CR6    0  -0.007   0.8236   1.1504   0.3229
 VGK  C07   C  CR16   0  -0.111   0.8076   2.4784   0.7282
 VGK  N08   N  N      0  -0.446  -0.2915   3.2055   0.8586
 VGK  C09   C  CR6    0   0.398  -1.4755   2.6528   0.6085
 VGK  N10   N  NH2    0  -0.827  -2.5651   3.4559   0.7636
 VGK  C11   C  CR6    0  -0.034  -1.5963   1.2952   0.2241
 VGK  C12   C  CR6    0   0.035  -2.9017   0.6583  -0.0457
 VGK  C13   C  CR16   0  -0.290  -3.9403   0.6987   0.8868
 VGK  C14   C  CR16   0  -0.273  -5.1430   0.0570   0.6351
 VGK  C15   C  CR6    0  -0.107  -5.3540  -0.6399  -0.5520
 VGK  C16   C  C      0   0.395  -6.6786  -1.3407  -0.8256
 VGK  O17   O  O      0  -0.593  -7.5390  -1.2792   0.0734
 VGK  O18   O  OC    -1  -0.593  -6.7873  -1.9166  -1.9249
 VGK  C19   C  CR16   0  -0.275  -4.3178  -0.6790  -1.4812
 VGK  C20   C  CR16   0  -0.290  -3.1113  -0.0423  -1.2340
 VGK  C21   C  CR16   0  -0.248  -0.4261   0.5760   0.0773
 VGK  C22   C  CR16   0  -0.502   2.1144  -0.9638   0.4868
 VGK  C23   C  CR6    0   0.358   3.2965  -1.6842   0.3387
 VGK  O24   O  O2     0  -0.465   3.4259  -2.9934   0.6124
 VGK  C25   C  CH3    0  -0.439   2.2801  -3.7159   1.0179
 VGK  C26   C  CR6    0   0.162   4.4525  -1.0479  -0.1206
 VGK  O27   O  O2     0  -0.481   5.5980  -1.7572  -0.2971
 VGK  C28   C  CH3    0  -0.409   6.4490  -1.7880   0.8412
 VGK  H011  H  HCH3   0   0.262   6.6243   2.4337  -1.5008
 VGK  H012  H  HCH3   0   0.229   4.9227   2.4667  -1.9941
 VGK  H013  H  HCH3   0   0.229   5.3718   2.8486  -0.3176
 VGK  H04   H  HCR6   0   0.274   3.1862   2.0774  -0.5549
 VGK  H22   H  HCR6   0   0.275   1.2251  -1.4419   0.8729
 VGK  H07   H  HCR6   0   0.254   1.7361   2.9842   0.9748
 VGK  H21   H  HCR6   0   0.259  -0.4917  -0.4588  -0.2394
 VGK  H101  H  HNH2   0   0.386  -2.3762   4.4451   0.7815
 VGK  H102  H  HNH2   0   0.394  -3.4114   3.2069   0.2785
 VGK  H13   H  HCR6   0   0.253  -3.8034   1.2193   1.8270
 VGK  H20   H  HCR6   0   0.248  -2.3256  -0.0790  -1.9790
 VGK  H14   H  HCR6   0   0.245  -5.9291   0.0943   1.3773
 VGK  H19   H  HCR6   0   0.244  -4.4572  -1.2118  -2.4127
 VGK  H251  H  HCH3   0   0.229   1.4824  -3.6689   0.2724
 VGK  H252  H  HCH3   0   0.262   2.5939  -4.7506   1.1311
 VGK  H253  H  HCH3   0   0.230   1.8882  -3.3623   1.9751
 VGK  H281  H  HCH3   0   0.236   7.3115  -2.3990   0.5806
 VGK  H282  H  HCH3   0   0.221   6.7981  -0.7890   1.1128
 VGK  H283  H  HCH3   0   0.221   5.9530  -2.2347   1.7062

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_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 VGK  C01  O02   single    1.414  0.020  1.414
 VGK  O02  C03   single    1.344  0.020  1.344
 VGK  C03  C04   aromatic  1.392  0.020  1.392
 VGK  C03  C26   aromatic  1.397  0.020  1.397
 VGK  C04  C05   aromatic  1.394  0.020  1.394
 VGK  C05  C06   single    1.473  0.020  1.473
 VGK  C05  C22   aromatic  1.393  0.020  1.393
 VGK  C06  C07   aromatic  1.389  0.020  1.389
 VGK  C06  C21   aromatic  1.397  0.020  1.397
 VGK  C07  N08   aromatic  1.324  0.020  1.324
 VGK  N08  C09   aromatic  1.330  0.020  1.330
 VGK  C09  N10   single    1.362  0.020  1.362
 VGK  C09  C11   aromatic  1.416  0.020  1.416
 VGK  C11  C12   single    1.477  0.020  1.477
 VGK  C11  C21   aromatic  1.381  0.020  1.381
 VGK  C12  C13   aromatic  1.396  0.020  1.396
 VGK  C12  C20   aromatic  1.395  0.020  1.395
 VGK  C13  C14   aromatic  1.386  0.020  1.386
 VGK  C14  C15   aromatic  1.393  0.020  1.393
 VGK  C15  C16   single    1.523  0.020  1.523
 VGK  C15  C19   aromatic  1.392  0.020  1.392
 VGK  C16  O17   deloc     1.246  0.020  1.246
 VGK  C16  O18   deloc     1.246  0.020  1.246
 VGK  C19  C20   aromatic  1.386  0.020  1.386
 VGK  C22  C23   aromatic  1.392  0.020  1.392
 VGK  C23  O24   single    1.344  0.020  1.344
 VGK  C23  C26   aromatic  1.397  0.020  1.397
 VGK  O24  C25   single    1.414  0.020  1.414
 VGK  C26  O27   single    1.359  0.020  1.359
 VGK  O27  C28   single    1.422  0.020  1.422
 VGK  C01  H011  single    0.970  0.020  1.090
 VGK  C01  H012  single    0.970  0.020  1.090
 VGK  C01  H013  single    0.970  0.020  1.090
 VGK  C04  H04   single    0.930  0.020  1.080
 VGK  C22  H22   single    0.930  0.020  1.080
 VGK  C07  H07   single    0.930  0.020  1.080
 VGK  C21  H21   single    0.930  0.020  1.080
 VGK  N10  H101  single    0.890  0.020  1.040
 VGK  N10  H102  single    0.890  0.020  1.040
 VGK  C13  H13   single    0.930  0.020  1.080
 VGK  C20  H20   single    0.930  0.020  1.080
 VGK  C14  H14   single    0.930  0.020  1.080
 VGK  C19  H19   single    0.930  0.020  1.080
 VGK  C25  H251  single    0.970  0.020  1.090
 VGK  C25  H252  single    0.970  0.020  1.090
 VGK  C25  H253  single    0.970  0.020  1.090
 VGK  C28  H281  single    0.970  0.020  1.090
 VGK  C28  H282  single    0.970  0.020  1.090
 VGK  C28  H283  single    0.970  0.020  1.090

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
 VGK  H013  C01  H012  108.79  3.000
 VGK  H013  C01  H011  108.77  3.000
 VGK  H012  C01  H011  108.74  3.000
 VGK  H013  C01  O02   111.98  3.000
 VGK  H012  C01  O02   112.05  3.000
 VGK  H011  C01  O02   106.40  3.000
 VGK  C03   O02  C01   118.51  3.000
 VGK  C26   C03  C04   120.16  3.000
 VGK  C26   C03  O02   115.51  3.000
 VGK  C04   C03  O02   124.32  3.000
 VGK  H04   C04  C05   119.46  3.000
 VGK  H04   C04  C03   120.44  3.000
 VGK  C05   C04  C03   120.08  3.000
 VGK  C22   C05  C06   119.99  3.000
 VGK  C22   C05  C04   119.89  3.000
 VGK  C06   C05  C04   120.11  3.000
 VGK  C21   C06  C07   115.73  3.000
 VGK  C21   C06  C05   122.24  3.000
 VGK  C07   C06  C05   122.03  3.000
 VGK  H07   C07  N08   115.57  3.000
 VGK  H07   C07  C06   120.13  3.000
 VGK  N08   C07  C06   124.29  3.000
 VGK  C09   N08  C07   119.47  3.000
 VGK  C11   C09  N10   121.86  3.000
 VGK  C11   C09  N08   121.68  3.000
 VGK  N10   C09  N08   116.45  3.000
 VGK  H102  N10  H101  114.15  3.000
 VGK  H102  N10  C09   118.14  3.000
 VGK  H101  N10  C09   115.53  3.000
 VGK  C21   C11  C12   120.31  3.000
 VGK  C21   C11  C09   117.11  3.000
 VGK  C12   C11  C09   122.56  3.000
 VGK  C20   C12  C13   118.13  3.000
 VGK  C20   C12  C11   120.32  3.000
 VGK  C13   C12  C11   121.52  3.000
 VGK  H13   C13  C14   119.32  3.000
 VGK  H13   C13  C12   119.96  3.000
 VGK  C14   C13  C12   120.70  3.000
 VGK  H14   C14  C15   119.48  3.000
 VGK  H14   C14  C13   119.33  3.000
 VGK  C15   C14  C13   121.19  3.000
 VGK  C19   C15  C16   120.96  3.000
 VGK  C19   C15  C14   118.04  3.000
 VGK  C16   C15  C14   121.00  3.000
 VGK  O18   C16  O17   126.82  3.000
 VGK  O18   C16  C15   116.55  3.000
 VGK  O17   C16  C15   116.63  3.000
 VGK  H19   C19  C20   119.45  3.000
 VGK  H19   C19  C15   119.49  3.000
 VGK  C20   C19  C15   121.05  3.000
 VGK  H20   C20  C19   119.54  3.000
 VGK  H20   C20  C12   119.58  3.000
 VGK  C19   C20  C12   120.87  3.000
 VGK  H21   C21  C11   118.48  3.000
 VGK  H21   C21  C06   119.86  3.000
 VGK  C11   C21  C06   121.67  3.000
 VGK  H22   C22  C23   120.51  3.000
 VGK  H22   C22  C05   119.32  3.000
 VGK  C23   C22  C05   120.14  3.000
 VGK  C26   C23  O24   115.53  3.000
 VGK  C26   C23  C22   120.12  3.000
 VGK  O24   C23  C22   124.35  3.000
 VGK  C25   O24  C23   118.57  3.000
 VGK  H253  C25  H252  108.68  3.000
 VGK  H253  C25  H251  108.77  3.000
 VGK  H252  C25  H251  108.82  3.000
 VGK  H253  C25  O24   112.11  3.000
 VGK  H252  C25  O24   106.40  3.000
 VGK  H251  C25  O24   111.95  3.000
 VGK  O27   C26  C23   120.16  3.000
 VGK  O27   C26  C03   120.23  3.000
 VGK  C23   C26  C03   119.60  3.000
 VGK  C28   O27  C26   114.33  3.000
 VGK  H283  C28  H282  108.79  3.000
 VGK  H283  C28  H281  108.65  3.000
 VGK  H282  C28  H281  108.64  3.000
 VGK  H283  C28  O27   111.78  3.000
 VGK  H282  C28  O27   111.75  3.000
 VGK  H281  C28  O27   107.14  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 VGK  CONST_01  C06   C05  C04  C03   180.00   0.0  0
 VGK  CONST_02  C22   C05  C04  C03     0.00   0.0  0
 VGK  CONST_03  C22   C23  C26  C03     0.00   0.0  0
 VGK  CONST_04  C23   C26  C03  C04     0.00   0.0  0
 VGK  CONST_07  C23   C22  C05  C04     0.00   0.0  0
 VGK  CONST_08  C26   C03  C04  C05     0.00   0.0  0
 VGK  CONST_09  N08   C07  C06  C05   180.00   0.0  0
 VGK  CONST_10  C11   C21  C06  C05   180.00   0.0  0
 VGK  CONST_11  C26   C23  C22  C05     0.00   0.0  0
 VGK  CONST_12  C23   C22  C05  C06   180.00   0.0  0
 VGK  CONST_13  C09   N08  C07  C06     0.00   0.0  0
 VGK  CONST_14  C09   C11  C21  C06     0.00   0.0  0
 VGK  CONST_15  C12   C11  C21  C06   180.00   0.0  0
 VGK  CONST_17  C11   C21  C06  C07     0.00   0.0  0
 VGK  CONST_18  C11   C09  N08  C07     0.00   0.0  0
 VGK  CONST_19  C21   C06  C07  N08     0.00   0.0  0
 VGK  CONST_20  C12   C11  C09  N08   180.00   0.0  0
 VGK  CONST_21  C21   C11  C09  N08     0.00   0.0  0
 VGK  CONST_24  C14   C13  C12  C11   180.00   0.0  0
 VGK  CONST_25  C19   C20  C12  C11   180.00   0.0  0
 VGK  CONST_26  C15   C14  C13  C12     0.00   0.0  0
 VGK  CONST_27  C15   C19  C20  C12     0.00   0.0  0
 VGK  CONST_29  C19   C20  C12  C13     0.00   0.0  0
 VGK  CONST_30  C19   C15  C14  C13     0.00   0.0  0
 VGK  CONST_31  C20   C12  C13  C14     0.00   0.0  0
 VGK  CONST_32  C20   C19  C15  C14     0.00   0.0  0
 VGK  CONST_35  C05   C04  C03  O02   180.00   0.0  0
 VGK  CONST_36  C23   C26  C03  O02   180.00   0.0  0
 VGK  CONST_37  O24   C23  C26  C03   180.00   0.0  0
 VGK  CONST_38  O27   C26  C03  C04   180.00   0.0  0
 VGK  CONST_39  O24   C23  C22  C05   180.00   0.0  0
 VGK  CONST_40  N10   C09  N08  C07   180.00   0.0  0
 VGK  CONST_41  C12   C11  C09  N10     0.00   0.0  0
 VGK  CONST_42  C21   C11  C09  N10   180.00   0.0  0
 VGK  CONST_43  C16   C15  C14  C13   180.00   0.0  0
 VGK  CONST_44  C20   C19  C15  C16   180.00   0.0  0
 VGK  CONST_45  O27   C26  C23  C22   180.00   0.0  0
 VGK  CONST_46  H22   C22  C05  C04   180.00   0.0  0
 VGK  CONST_47  H07   C07  C06  C05     0.00   0.0  0
 VGK  CONST_48  H21   C21  C06  C05     0.00   0.0  0
 VGK  CONST_49  H04   C04  C05  C06     0.00   0.0  0
 VGK  CONST_50  H13   C13  C12  C11     0.00   0.0  0
 VGK  CONST_51  H20   C20  C12  C11     0.00   0.0  0
 VGK  CONST_52  H14   C14  C13  C12   180.00   0.0  0
 VGK  CONST_53  H19   C19  C20  C12   180.00   0.0  0
 VGK  Var_01    C04   C03  O02  C01     1.16  30.0  2
 VGK  Var_02    O17   C16  C15  C14    -1.47  30.0  2
 VGK  Var_03    C26   C23  O24  C25  -176.90  30.0  2
 VGK  Var_04    H011  C01  O02  C03   179.72  30.0  3
 VGK  Var_05    H251  C25  O24  C23    58.14  30.0  3
 VGK  Var_06    H281  C28  O27  C26   178.77  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 VGK  plan-1  O02   0.020
 VGK  plan-1  C03   0.020
 VGK  plan-1  C04   0.020
 VGK  plan-1  C05   0.020
 VGK  plan-1  C06   0.020
 VGK  plan-1  C22   0.020
 VGK  plan-1  C23   0.020
 VGK  plan-1  O24   0.020
 VGK  plan-1  C26   0.020
 VGK  plan-1  O27   0.020
 VGK  plan-1  H04   0.020
 VGK  plan-1  H22   0.020
 VGK  plan-2  C05   0.020
 VGK  plan-2  C06   0.020
 VGK  plan-2  C07   0.020
 VGK  plan-2  N08   0.020
 VGK  plan-2  C09   0.020
 VGK  plan-2  N10   0.020
 VGK  plan-2  C11   0.020
 VGK  plan-2  C12   0.020
 VGK  plan-2  C21   0.020
 VGK  plan-2  H07   0.020
 VGK  plan-2  H21   0.020
 VGK  plan-3  C11   0.020
 VGK  plan-3  C12   0.020
 VGK  plan-3  C13   0.020
 VGK  plan-3  C14   0.020
 VGK  plan-3  C15   0.020
 VGK  plan-3  C16   0.020
 VGK  plan-3  C19   0.020
 VGK  plan-3  C20   0.020
 VGK  plan-3  H13   0.020
 VGK  plan-3  H20   0.020
 VGK  plan-3  H14   0.020
 VGK  plan-3  H19   0.020
 VGK  plan-4  C09   0.020
 VGK  plan-4  N10   0.020
 VGK  plan-4  H101  0.020
 VGK  plan-4  H102  0.020
 VGK  plan-5  C15   0.020
 VGK  plan-5  C16   0.020
 VGK  plan-5  O17   0.020
 VGK  plan-5  O18   0.020

