# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 18:14:53 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: 3-(pyridin-3-yl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cccc(c1)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
 5F8  5F8  '3-(pyridin-3-yl)benzoic acid'  ligand  23  15  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5F8
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
 5F8  O1   O  OC    -1  -0.592  -4.3388   0.4639  -0.3610
 5F8  C    C  C      0   0.400  -3.1745   0.9024  -0.4148
 5F8  O    O  O      0  -0.591  -2.8264   2.0706  -0.6721
 5F8  C1   C  C      0  -0.080  -2.0575  -0.0987  -0.1374
 5F8  C6   C  C1     0  -0.302  -2.3459  -1.4360   0.1223
 5F8  C5   C  C1     0  -0.229  -1.3229  -2.3427   0.3616
 5F8  C4   C  C1     0  -0.320  -0.0006  -1.9255   0.3495
 5F8  C3   C  C      0   0.105   0.3126  -0.5895   0.0950
 5F8  C2   C  C1     0  -0.358  -0.7274   0.3071  -0.1483
 5F8  C7   C  CR6    0  -0.005   1.7152  -0.1351   0.0858
 5F8  C11  C  CR16   0  -0.103   2.0718   1.1105   0.6061
 5F8  N    N  N      0  -0.399   3.3103   1.5815   0.6269
 5F8  C10  C  CR16   0  -0.074   4.2764   0.8205   0.1252
 5F8  C9   C  CR16   0  -0.315   4.0430  -0.4366  -0.4115
 5F8  C8   C  CR16   0  -0.198   2.7448  -0.9181  -0.4326
 5F8  H3   H  H      0   0.246  -3.3758  -1.7670   0.1372
 5F8  H2   H  H      0   0.252  -1.5547  -3.3801   0.5666
 5F8  H1   H  H      0   0.253   0.7870  -2.6392   0.5587
 5F8  H    H  H      0   0.243  -0.5040   1.3424  -0.3726
 5F8  H7   H  HCR6   0   0.259   1.3102   1.7496   1.0419
 5F8  H6   H  HCR6   0   0.265   5.2809   1.2275   0.1524
 5F8  H5   H  HCR6   0   0.272   4.8609  -1.0201  -0.8115
 5F8  H4   H  HCR6   0   0.269   2.5320  -1.8873  -0.8663

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
 5F8  N    C11  aromatic  1.325  0.020  1.325
 5F8  N    C10  aromatic  1.328  0.020  1.328
 5F8  C11  C7   aromatic  1.396  0.020  1.396
 5F8  O    C    deloc     1.246  0.020  1.246
 5F8  C10  C9   aromatic  1.387  0.020  1.387
 5F8  C7   C3   single    1.474  0.020  1.474
 5F8  C7   C8   aromatic  1.394  0.020  1.394
 5F8  C3   C2   aromatic  1.395  0.020  1.395
 5F8  C3   C4   aromatic  1.396  0.020  1.396
 5F8  C2   C1   aromatic  1.391  0.020  1.391
 5F8  C4   C5   aromatic  1.387  0.020  1.387
 5F8  C1   C    single    1.525  0.020  1.525
 5F8  C1   C6   aromatic  1.392  0.020  1.392
 5F8  C5   C6   aromatic  1.388  0.020  1.388
 5F8  C    O1   deloc     1.245  0.020  1.245
 5F8  C9   C8   aromatic  1.385  0.020  1.385
 5F8  C6   H3   single    0.930  0.020  1.080
 5F8  C5   H2   single    0.930  0.020  1.080
 5F8  C4   H1   single    0.930  0.020  1.080
 5F8  C2   H    single    0.930  0.020  1.080
 5F8  C11  H7   single    0.930  0.020  1.080
 5F8  C10  H6   single    0.930  0.020  1.080
 5F8  C9   H5   single    0.930  0.020  1.080
 5F8  C8   H4   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
 5F8  C1   C    O    116.64  3.000
 5F8  C1   C    O1   116.47  3.000
 5F8  O    C    O1   126.89  3.000
 5F8  C2   C1   C6   118.67  3.000
 5F8  C6   C1   C    120.83  3.000
 5F8  C2   C1   C    120.49  3.000
 5F8  H3   C6   C5   119.96  3.000
 5F8  H3   C6   C1   119.58  3.000
 5F8  C5   C6   C1   120.46  3.000
 5F8  H2   C5   C4   119.61  3.000
 5F8  H2   C5   C6   120.06  3.000
 5F8  C4   C5   C6   120.32  3.000
 5F8  H1   C4   C3   120.18  3.000
 5F8  H1   C4   C5   119.57  3.000
 5F8  C3   C4   C5   120.24  3.000
 5F8  C7   C3   C2   120.68  3.000
 5F8  C2   C3   C4   118.68  3.000
 5F8  C7   C3   C4   120.64  3.000
 5F8  H    C2   C3   119.81  3.000
 5F8  H    C2   C1   118.56  3.000
 5F8  C3   C2   C1   121.62  3.000
 5F8  C8   C7   C11  116.82  3.000
 5F8  C8   C7   C3   122.14  3.000
 5F8  C11  C7   C3   121.04  3.000
 5F8  H7   C11  N    116.11  3.000
 5F8  H7   C11  C7   119.71  3.000
 5F8  N    C11  C7   124.17  3.000
 5F8  C10  N    C11  118.05  3.000
 5F8  H6   C10  C9   120.40  3.000
 5F8  H6   C10  N    116.70  3.000
 5F8  C9   C10  N    122.90  3.000
 5F8  H5   C9   C8   121.05  3.000
 5F8  H5   C9   C10  120.33  3.000
 5F8  C8   C9   C10  118.61  3.000
 5F8  H4   C8   C9   120.10  3.000
 5F8  H4   C8   C7   120.44  3.000
 5F8  C9   C8   C7   119.45  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
 5F8  CONST_01  C7   C3   C2   C1    180.00   0.0  0
 5F8  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 5F8  CONST_03  C4   C5   C6   C1      0.00   0.0  0
 5F8  CONST_04  C3   C2   C1   C6      0.00   0.0  0
 5F8  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 5F8  CONST_06  C7   C3   C4   C5    180.00   0.0  0
 5F8  CONST_07  C2   C3   C4   C5      0.00   0.0  0
 5F8  CONST_08  C2   C1   C6   C5      0.00   0.0  0
 5F8  CONST_11  N    C11  C7   C3    180.00   0.0  0
 5F8  CONST_12  C9   C8   C7   C3    180.00   0.0  0
 5F8  CONST_15  C10  N    C11  C7      0.00   0.0  0
 5F8  CONST_16  C10  C9   C8   C7      0.00   0.0  0
 5F8  CONST_17  C9   C10  N    C11     0.00   0.0  0
 5F8  CONST_18  C9   C8   C7   C11     0.00   0.0  0
 5F8  CONST_19  C8   C7   C11  N       0.00   0.0  0
 5F8  CONST_20  C8   C9   C10  N       0.00   0.0  0
 5F8  CONST_21  C3   C2   C1   C     180.00   0.0  0
 5F8  CONST_22  C5   C6   C1   C     180.00   0.0  0
 5F8  CONST_23  H2   C5   C6   C1    180.00   0.0  0
 5F8  CONST_24  H    C2   C1   C6    180.00   0.0  0
 5F8  CONST_25  H1   C4   C5   C6    180.00   0.0  0
 5F8  CONST_26  H3   C6   C5   C4    180.00   0.0  0
 5F8  CONST_27  H7   C11  C7   C3      0.00   0.0  0
 5F8  CONST_28  H4   C8   C7   C3      0.00   0.0  0
 5F8  CONST_29  H5   C9   C8   C7    180.00   0.0  0
 5F8  CONST_30  H6   C10  N    C11   180.00   0.0  0
 5F8  Var_01    C2   C1   C    O1   -178.67  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
 5F8  plan-1  C    0.020
 5F8  plan-1  C1   0.020
 5F8  plan-1  C6   0.020
 5F8  plan-1  C5   0.020
 5F8  plan-1  C4   0.020
 5F8  plan-1  C3   0.020
 5F8  plan-1  C2   0.020
 5F8  plan-1  C7   0.020
 5F8  plan-1  H3   0.020
 5F8  plan-1  H2   0.020
 5F8  plan-1  H1   0.020
 5F8  plan-1  H    0.020
 5F8  plan-2  C3   0.020
 5F8  plan-2  C7   0.020
 5F8  plan-2  C11  0.020
 5F8  plan-2  N    0.020
 5F8  plan-2  C10  0.020
 5F8  plan-2  C9   0.020
 5F8  plan-2  C8   0.020
 5F8  plan-2  H7   0.020
 5F8  plan-2  H6   0.020
 5F8  plan-2  H5   0.020
 5F8  plan-2  H4   0.020
 5F8  plan-3  O1   0.020
 5F8  plan-3  C    0.020
 5F8  plan-3  O    0.020
 5F8  plan-3  C1   0.020

