# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 23 14:09:35 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  24  15  .  2021-08-19  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -4.0537  -1.0792  -0.3634
 PQM  C02  C  CR16  0  -0.192  -2.6710  -1.1352  -0.3881
 PQM  C03  C  CR6   0  -0.006  -1.9358  -0.0341   0.0457
 PQM  C04  C  CR16  0  -0.096  -2.6564   1.0736   0.4942
 PQM  C06  C  CR16  0  -0.067  -4.6629   0.0794   0.0951
 PQM  C07  C  CR6   0   0.093  -0.4633  -0.0301   0.0413
 PQM  C08  C  CR16  0  -0.296   0.2536  -1.1859   0.3568
 PQM  C09  C  CR16  0  -0.239   1.6360  -1.1825   0.3555
 PQM  C10  C  CR6   0  -0.093   2.3392  -0.0214   0.0413
 PQM  C11  C  CR16  0  -0.242   1.6310   1.1361  -0.2766
 PQM  C12  C  CR16  0  -0.294   0.2470   1.1279  -0.2780
 PQM  C13  C  C     0   0.533   3.8212  -0.0664   0.0585
 PQM  N05  N  N     0  -0.397  -3.9795   1.1359   0.5200
 PQM  O14  O  O     0  -0.438   4.4597  -1.0660   0.2884
 PQM  O15  O  OH1   0  -0.593   4.3793   1.1072  -0.2020
 PQM  H1   H  HCR6  0   0.276  -4.6507  -1.9147  -0.7017
 PQM  H2   H  HCR6  0   0.274  -2.1699  -2.0197  -0.7603
 PQM  H3   H  HCR6  0   0.264  -2.1294   1.9455   0.8677
 PQM  H4   H  HCR6  0   0.269  -5.7439   0.1570   0.1204
 PQM  H5   H  HCR6  0   0.265  -0.2709  -2.0933   0.6274
 PQM  H6   H  HCR6  0   0.269   2.1694  -2.0876   0.6123
 PQM  H7   H  HCR6  0   0.271   2.1473   2.0495  -0.5371
 PQM  H8   H  HCR6  0   0.265  -0.2823   2.0310  -0.5532
 PQM  H9   H  HOH1  0   0.488   5.3443   1.0271  -0.1755

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  double    1.208  0.020  1.208
 PQM  C09  C08  aromatic  1.382  0.020  1.382
 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  single    1.325  0.020  1.325
 PQM  C13  C10  single    1.483  0.020  1.483
 PQM  C10  C11  aromatic  1.394  0.020  1.394
 PQM  C07  C03  single    1.472  0.020  1.472
 PQM  C07  C12  aromatic  1.396  0.020  1.396
 PQM  C03  C02  aromatic  1.393  0.020  1.393
 PQM  C06  C01  aromatic  1.387  0.020  1.387
 PQM  C11  C12  aromatic  1.384  0.020  1.384
 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
 PQM  O15  H9   single    0.850  0.020  0.980

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  120.98  3.000
 PQM  C06  C01  C02  118.59  3.000
 PQM  H2   C02  C03  120.57  3.000
 PQM  H2   C02  C01  120.10  3.000
 PQM  C03  C02  C01  119.32  3.000
 PQM  C07  C03  C04  121.01  3.000
 PQM  C07  C03  C02  121.93  3.000
 PQM  C04  C03  C02  117.06  3.000
 PQM  H3   C04  N05  116.14  3.000
 PQM  H3   C04  C03  119.84  3.000
 PQM  N05  C04  C03  124.01  3.000
 PQM  H4   C06  N05  116.66  3.000
 PQM  H4   C06  C01  120.37  3.000
 PQM  N05  C06  C01  122.97  3.000
 PQM  C12  C07  C08  118.50  3.000
 PQM  C12  C07  C03  120.79  3.000
 PQM  C08  C07  C03  120.70  3.000
 PQM  H5   C08  C09  119.13  3.000
 PQM  H5   C08  C07  120.11  3.000
 PQM  C09  C08  C07  120.75  3.000
 PQM  H6   C09  C10  120.14  3.000
 PQM  H6   C09  C08  119.40  3.000
 PQM  C10  C09  C08  120.46  3.000
 PQM  C13  C10  C11  122.39  3.000
 PQM  C11  C10  C09  119.15  3.000
 PQM  C13  C10  C09  118.45  3.000
 PQM  H7   C11  C12  118.83  3.000
 PQM  H7   C11  C10  120.93  3.000
 PQM  C12  C11  C10  120.23  3.000
 PQM  H8   C12  C11  118.97  3.000
 PQM  H8   C12  C07  120.10  3.000
 PQM  C11  C12  C07  120.91  3.000
 PQM  O15  C13  O14  123.20  3.000
 PQM  O15  C13  C10  113.06  3.000
 PQM  O14  C13  C10  123.75  3.000
 PQM  C06  N05  C04  118.05  3.000
 PQM  H9   O15  C13  109.92  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  CONST_31  H9   O15  C13  C10  180.00   0.0  0
 PQM  Var_01    O14  C13  C10  C09    2.47  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
 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
 PQM  plan-3  H9   0.020

