# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 11:07:37 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: 4-(pyridin-3-yl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(cc1)c2cccnc2
#
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
 PQM  PQM  '4-(pyridin-3-yl)benzoic acid'  ligand  23  15  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PQM
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
 PQM  C01  C  CR16   0  -0.315  -4.0848  -1.0639   0.3567
 PQM  C02  C  CR16   0  -0.198  -2.7022  -1.1213   0.3992
 PQM  C03  C  CR6    0  -0.003  -1.9568  -0.0282  -0.0383
 PQM  C04  C  CR16   0  -0.104  -2.6726   1.0748  -0.5070
 PQM  C06  C  CR16   0  -0.073  -4.6871   0.0905  -0.1202
 PQM  C07  C  CR6    0   0.077  -0.4837  -0.0278  -0.0157
 PQM  C08  C  CR16   0  -0.300   0.2364  -1.1891  -0.2996
 PQM  C09  C  CR16   0  -0.273   1.6218  -1.1877  -0.2773
 PQM  C10  C  CR6    0  -0.107   2.3351  -0.0301   0.0234
 PQM  C11  C  CR16   0  -0.275   1.6158   1.1282   0.3062
 PQM  C12  C  CR16   0  -0.299   0.2300   1.1321   0.2904
 PQM  C13  C  C      0   0.396   3.8586  -0.0317   0.0423
 PQM  N05  N  N      0  -0.398  -3.9956   1.1409  -0.5475
 PQM  O14  O  O      0  -0.592   4.4169  -1.1263  -0.1631
 PQM  O15  O  OC    -1  -0.592   4.4144   1.0615   0.2610
 PQM  H1   H  HCR6   0   0.273  -4.6868  -1.8954   0.6966
 PQM  H2   H  HCR6   0   0.270  -2.2079  -2.0028   0.7875
 PQM  H3   H  HCR6   0   0.260  -2.1397   1.9422  -0.8828
 PQM  H4   H  HCR6   0   0.265  -5.7676   0.1706  -0.1590
 PQM  H5   H  HCR6   0   0.249  -0.2887  -2.1000  -0.5615
 PQM  H6   H  HCR6   0   0.245   2.1588  -2.0983  -0.5075
 PQM  H7   H  HCR6   0   0.245   2.1479   2.0373   0.5533
 PQM  H8   H  HCR6   0   0.249  -0.3003   2.0432   0.5405

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
 PQM  O14  C13  deloc     1.246  0.020  1.246
 PQM  C09  C08  aromatic  1.386  0.020  1.386
 PQM  C09  C10  aromatic  1.393  0.020  1.393
 PQM  C04  N05  aromatic  1.325  0.020  1.325
 PQM  C04  C03  aromatic  1.396  0.020  1.396
 PQM  C08  C07  aromatic  1.396  0.020  1.396
 PQM  N05  C06  aromatic  1.328  0.020  1.328
 PQM  C13  O15  deloc     1.246  0.020  1.246
 PQM  C13  C10  single    1.524  0.020  1.524
 PQM  C10  C11  aromatic  1.392  0.020  1.392
 PQM  C07  C03  single    1.473  0.020  1.473
 PQM  C07  C12  aromatic  1.396  0.020  1.396
 PQM  C03  C02  aromatic  1.394  0.020  1.394
 PQM  C06  C01  aromatic  1.387  0.020  1.387
 PQM  C11  C12  aromatic  1.386  0.020  1.386
 PQM  C02  C01  aromatic  1.384  0.020  1.384
 PQM  C01  H1   single    0.930  0.020  1.080
 PQM  C02  H2   single    0.930  0.020  1.080
 PQM  C04  H3   single    0.930  0.020  1.080
 PQM  C06  H4   single    0.930  0.020  1.080
 PQM  C08  H5   single    0.930  0.020  1.080
 PQM  C09  H6   single    0.930  0.020  1.080
 PQM  C11  H7   single    0.930  0.020  1.080
 PQM  C12  H8   single    0.930  0.020  1.080

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
 PQM  H1   C01  C06  120.43  3.000
 PQM  H1   C01  C02  120.96  3.000
 PQM  C06  C01  C02  118.61  3.000
 PQM  H2   C02  C03  120.47  3.000
 PQM  H2   C02  C01  120.04  3.000
 PQM  C03  C02  C01  119.48  3.000
 PQM  C07  C03  C04  121.17  3.000
 PQM  C07  C03  C02  122.02  3.000
 PQM  C04  C03  C02  116.80  3.000
 PQM  H3   C04  N05  116.10  3.000
 PQM  H3   C04  C03  119.73  3.000
 PQM  N05  C04  C03  124.16  3.000
 PQM  H4   C06  N05  116.68  3.000
 PQM  H4   C06  C01  120.44  3.000
 PQM  N05  C06  C01  122.88  3.000
 PQM  C12  C07  C08  118.18  3.000
 PQM  C12  C07  C03  120.99  3.000
 PQM  C08  C07  C03  120.83  3.000
 PQM  H5   C08  C09  119.29  3.000
 PQM  H5   C08  C07  119.92  3.000
 PQM  C09  C08  C07  120.78  3.000
 PQM  H6   C09  C10  119.43  3.000
 PQM  H6   C09  C08  119.47  3.000
 PQM  C10  C09  C08  121.10  3.000
 PQM  C13  C10  C11  120.99  3.000
 PQM  C11  C10  C09  118.08  3.000
 PQM  C13  C10  C09  120.93  3.000
 PQM  H7   C11  C12  119.47  3.000
 PQM  H7   C11  C10  119.42  3.000
 PQM  C12  C11  C10  121.10  3.000
 PQM  H8   C12  C11  119.29  3.000
 PQM  H8   C12  C07  119.94  3.000
 PQM  C11  C12  C07  120.76  3.000
 PQM  O15  C13  O14  126.88  3.000
 PQM  O15  C13  C10  116.57  3.000
 PQM  O14  C13  C10  116.55  3.000
 PQM  C06  N05  C04  118.07  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
 PQM  CONST_01  C04  N05  C06  C01    0.00   0.0  0
 PQM  CONST_02  C04  C03  C02  C01    0.00   0.0  0
 PQM  CONST_03  C07  C03  C02  C01  180.00   0.0  0
 PQM  CONST_04  N05  C04  C03  C02    0.00   0.0  0
 PQM  CONST_07  N05  C06  C01  C02    0.00   0.0  0
 PQM  CONST_08  C06  N05  C04  C03    0.00   0.0  0
 PQM  CONST_09  C09  C08  C07  C03  180.00   0.0  0
 PQM  CONST_10  C11  C12  C07  C03  180.00   0.0  0
 PQM  CONST_11  C06  C01  C02  C03    0.00   0.0  0
 PQM  CONST_14  C10  C09  C08  C07    0.00   0.0  0
 PQM  CONST_15  N05  C04  C03  C07  180.00   0.0  0
 PQM  CONST_16  C10  C11  C12  C07    0.00   0.0  0
 PQM  CONST_17  C11  C10  C09  C08    0.00   0.0  0
 PQM  CONST_18  C11  C12  C07  C08    0.00   0.0  0
 PQM  CONST_19  C12  C07  C08  C09    0.00   0.0  0
 PQM  CONST_20  C12  C11  C10  C09    0.00   0.0  0
 PQM  CONST_21  C13  C10  C09  C08  180.00   0.0  0
 PQM  CONST_22  C13  C10  C11  C12  180.00   0.0  0
 PQM  CONST_23  H3   C04  C03  C02  180.00   0.0  0
 PQM  CONST_24  H4   C06  C01  C02  180.00   0.0  0
 PQM  CONST_25  H5   C08  C07  C03    0.00   0.0  0
 PQM  CONST_26  H8   C12  C07  C03    0.00   0.0  0
 PQM  CONST_27  H1   C01  C02  C03  180.00   0.0  0
 PQM  CONST_28  H2   C02  C03  C04  180.00   0.0  0
 PQM  CONST_29  H6   C09  C08  C07  180.00   0.0  0
 PQM  CONST_30  H7   C11  C12  C07  180.00   0.0  0
 PQM  Var_01    O14  C13  C10  C09   -3.16  30.0  2

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
 PQM  plan-1  C01  0.020
 PQM  plan-1  C02  0.020
 PQM  plan-1  C03  0.020
 PQM  plan-1  C04  0.020
 PQM  plan-1  C06  0.020
 PQM  plan-1  C07  0.020
 PQM  plan-1  N05  0.020
 PQM  plan-1  H1   0.020
 PQM  plan-1  H2   0.020
 PQM  plan-1  H3   0.020
 PQM  plan-1  H4   0.020
 PQM  plan-2  C03  0.020
 PQM  plan-2  C07  0.020
 PQM  plan-2  C08  0.020
 PQM  plan-2  C09  0.020
 PQM  plan-2  C10  0.020
 PQM  plan-2  C11  0.020
 PQM  plan-2  C12  0.020
 PQM  plan-2  C13  0.020
 PQM  plan-2  H5   0.020
 PQM  plan-2  H6   0.020
 PQM  plan-2  H7   0.020
 PQM  plan-2  H8   0.020
 PQM  plan-3  C10  0.020
 PQM  plan-3  C13  0.020
 PQM  plan-3  O14  0.020
 PQM  plan-3  O15  0.020

