# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 15:49:01 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: 2-(pyridin-3-yl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccccc1c2cccnc2
#
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
 61O  61O  '2-(pyridin-3-yl)benzoic acid'  ligand  23  15  .  2021-08-05  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_61O
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
 61O  C10   C  CR6    0   0.013   0.9299   0.4582  -0.0647
 61O  C13   C  CR16   0  -0.077   3.6537   0.2691  -0.1099
 61O  C15   C  CR16   0  -0.107   1.7693   1.1745   0.7841
 61O  C01   C  CR16   0  -0.253  -2.3645   2.2541  -0.1416
 61O  C02   C  CR16   0  -0.298  -1.0059   1.9778  -0.1231
 61O  C03   C  CR6    0   0.050  -0.5326   0.6675  -0.0304
 61O  C04   C  CR6    0  -0.102  -1.4499  -0.3912   0.0287
 61O  C05   C  CR16   0  -0.283  -2.8113  -0.0991  -0.0270
 61O  C06   C  CR16   0  -0.255  -3.2735   1.2070  -0.0949
 61O  C07   C  C      0   0.350  -1.0310  -1.8449   0.2229
 61O  O08   O  O      0  -0.582  -0.0697  -2.0462   0.9846
 61O  O09   O  OC    -1  -0.596  -1.7129  -2.6972  -0.3776
 61O  C11   C  CR16   0  -0.175   1.5374  -0.3917  -0.9846
 61O  C12   C  CR16   0  -0.327   2.9170  -0.4884  -1.0105
 61O  N14   N  N      0  -0.404   3.0943   1.0864   0.7728
 61O  H131  H  HCR6   0   0.260   4.7369   0.2150  -0.1066
 61O  H151  H  HCR6   0   0.254   1.3391   1.8487   1.5187
 61O  H051  H  HCR6   0   0.249  -3.5235  -0.9133   0.0019
 61O  H061  H  HCR6   0   0.251  -4.3378   1.4044  -0.1162
 61O  H111  H  HCR6   0   0.261   0.9362  -0.9542  -1.6879
 61O  H121  H  HCR6   0   0.267   3.4194  -1.1330  -1.7190
 61O  H011  H  HCR6   0   0.254  -2.7069   3.2789  -0.2069
 61O  H021  H  HCR6   0   0.251  -0.2964   2.7929  -0.1993

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
 61O  C06  C05   aromatic  1.387  0.020  1.387
 61O  C06  C01   aromatic  1.387  0.020  1.387
 61O  C05  C04   aromatic  1.393  0.020  1.393
 61O  O08  C07   deloc     1.243  0.020  1.243
 61O  C01  C02   aromatic  1.386  0.020  1.386
 61O  C04  C07   single    1.525  0.020  1.525
 61O  C04  C03   aromatic  1.402  0.020  1.402
 61O  C07  O09   deloc     1.246  0.020  1.246
 61O  C02  C03   aromatic  1.396  0.020  1.396
 61O  C03  C10   single    1.478  0.020  1.478
 61O  C10  C15   aromatic  1.392  0.020  1.392
 61O  C10  C11   aromatic  1.392  0.020  1.392
 61O  C15  N14   aromatic  1.328  0.020  1.328
 61O  C11  C12   aromatic  1.383  0.020  1.383
 61O  N14  C13   aromatic  1.327  0.020  1.327
 61O  C12  C13   aromatic  1.388  0.020  1.388
 61O  C13  H131  single    0.930  0.020  1.080
 61O  C15  H151  single    0.930  0.020  1.080
 61O  C01  H011  single    0.930  0.020  1.080
 61O  C02  H021  single    0.930  0.020  1.080
 61O  C05  H051  single    0.930  0.020  1.080
 61O  C06  H061  single    0.930  0.020  1.080
 61O  C11  H111  single    0.930  0.020  1.080
 61O  C12  H121  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
 61O  C11   C10  C03  122.26  3.000
 61O  C11   C10  C15  116.99  3.000
 61O  C03   C10  C15  120.64  3.000
 61O  H131  C13  N14  116.73  3.000
 61O  H131  C13  C12  120.32  3.000
 61O  N14   C13  C12  122.96  3.000
 61O  H151  C15  N14  116.24  3.000
 61O  H151  C15  C10  119.54  3.000
 61O  N14   C15  C10  124.22  3.000
 61O  H011  C01  C06  120.61  3.000
 61O  H011  C01  C02  119.97  3.000
 61O  C06   C01  C02  119.41  3.000
 61O  H021  C02  C03  119.26  3.000
 61O  H021  C02  C01  119.39  3.000
 61O  C03   C02  C01  121.34  3.000
 61O  C04   C03  C02  119.32  3.000
 61O  C02   C03  C10  117.83  3.000
 61O  C04   C03  C10  122.79  3.000
 61O  C07   C04  C05  118.24  3.000
 61O  C07   C04  C03  123.05  3.000
 61O  C05   C04  C03  118.63  3.000
 61O  H051  C05  C06  119.37  3.000
 61O  H051  C05  C04  118.96  3.000
 61O  C06   C05  C04  121.66  3.000
 61O  H061  C06  C05  120.01  3.000
 61O  H061  C06  C01  120.39  3.000
 61O  C05   C06  C01  119.60  3.000
 61O  O09   C07  O08  127.44  3.000
 61O  O09   C07  C04  116.13  3.000
 61O  O08   C07  C04  116.41  3.000
 61O  H111  C11  C12  120.35  3.000
 61O  H111  C11  C10  120.27  3.000
 61O  C12   C11  C10  119.37  3.000
 61O  H121  C12  C11  121.15  3.000
 61O  H121  C12  C13  120.23  3.000
 61O  C11   C12  C13  118.61  3.000
 61O  C15   N14  C13  117.85  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
 61O  CONST_01  C05   C04  C03  C10  180.00   0.0  0
 61O  CONST_02  C01   C02  C03  C10  180.00   0.0  0
 61O  CONST_03  C13   N14  C15  C10    0.00   0.0  0
 61O  CONST_04  C13   C12  C11  C10    0.00   0.0  0
 61O  CONST_07  C12   C11  C10  C15    0.00   0.0  0
 61O  CONST_08  C12   C13  N14  C15    0.00   0.0  0
 61O  CONST_09  C04   C05  C06  C01    0.00   0.0  0
 61O  CONST_10  C04   C03  C02  C01    0.00   0.0  0
 61O  CONST_11  C05   C06  C01  C02    0.00   0.0  0
 61O  CONST_12  C05   C04  C03  C02    0.00   0.0  0
 61O  CONST_14  C06   C05  C04  C03    0.00   0.0  0
 61O  CONST_15  C06   C01  C02  C03    0.00   0.0  0
 61O  CONST_16  N14   C15  C10  C03  180.00   0.0  0
 61O  CONST_17  C12   C11  C10  C03  180.00   0.0  0
 61O  CONST_19  N14   C15  C10  C11    0.00   0.0  0
 61O  CONST_20  N14   C13  C12  C11    0.00   0.0  0
 61O  CONST_21  C07   C04  C03  C10    0.00   0.0  0
 61O  CONST_22  C07   C04  C03  C02  180.00   0.0  0
 61O  CONST_23  C07   C04  C05  C06  180.00   0.0  0
 61O  CONST_24  H021  C02  C03  C10    0.00   0.0  0
 61O  CONST_25  H121  C12  C11  C10  180.00   0.0  0
 61O  CONST_26  H151  C15  N14  C13  180.00   0.0  0
 61O  CONST_27  H111  C11  C12  C13  180.00   0.0  0
 61O  CONST_28  H131  C13  N14  C15  180.00   0.0  0
 61O  CONST_29  H051  C05  C06  C01  180.00   0.0  0
 61O  CONST_30  H061  C06  C01  C02  180.00   0.0  0
 61O  CONST_31  H011  C01  C02  C03  180.00   0.0  0
 61O  Var_01    O08   C07  C04  C03   36.88  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
 61O  plan-1  C10   0.020
 61O  plan-1  C13   0.020
 61O  plan-1  C15   0.020
 61O  plan-1  C03   0.020
 61O  plan-1  C11   0.020
 61O  plan-1  C12   0.020
 61O  plan-1  N14   0.020
 61O  plan-1  H131  0.020
 61O  plan-1  H151  0.020
 61O  plan-1  H111  0.020
 61O  plan-1  H121  0.020
 61O  plan-2  C10   0.020
 61O  plan-2  C01   0.020
 61O  plan-2  C02   0.020
 61O  plan-2  C03   0.020
 61O  plan-2  C04   0.020
 61O  plan-2  C05   0.020
 61O  plan-2  C06   0.020
 61O  plan-2  C07   0.020
 61O  plan-2  H051  0.020
 61O  plan-2  H061  0.020
 61O  plan-2  H011  0.020
 61O  plan-2  H021  0.020
 61O  plan-3  C04   0.020
 61O  plan-3  C07   0.020
 61O  plan-3  O08   0.020
 61O  plan-3  O09   0.020

