# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 14:27:17 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  24  15  .  2021-08-04  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  OH1   0  -0.593  -4.3538   0.3838   0.2880
 5F8  C    C  C     0   0.536  -3.1299   0.8877   0.3379
 5F8  O    O  O     0  -0.436  -2.9017   2.0534   0.5564
 5F8  C1   C  CR6   0  -0.061  -2.0741  -0.1288   0.0967
 5F8  C6   C  CR16  0  -0.271  -2.3735  -1.4684  -0.1426
 5F8  C5   C  CR16  0  -0.224  -1.3431  -2.3720  -0.3511
 5F8  C4   C  CR16  0  -0.297  -0.0235  -1.9494  -0.3264
 5F8  C3   C  CR6   0   0.106   0.2920  -0.6106  -0.0887
 5F8  C2   C  CR16  0  -0.324  -0.7472   0.2898   0.1239
 5F8  C7   C  CR6   0  -0.006   1.6947  -0.1589  -0.0653
 5F8  C11  C  CR16  0  -0.098   2.0630   1.0699  -0.6148
 5F8  N    N  N     0  -0.398   3.3033   1.5355  -0.6246
 5F8  C10  C  CR16  0  -0.070   4.2560   0.7861  -0.0818
 5F8  C9   C  CR16  0  -0.315   4.0085  -0.4545   0.4862
 5F8  C8   C  CR16  0  -0.194   2.7089  -0.9318   0.4954
 5F8  H8   H  HOH1  0   0.489  -5.0067   1.0808   0.4506
 5F8  H3   H  HCR6  0   0.272  -3.3969  -1.8153  -0.1695
 5F8  H2   H  HCR6  0   0.270  -1.5699  -3.4120  -0.5422
 5F8  H1   H  HCR6  0   0.268   0.7663  -2.6664  -0.5124
 5F8  H    H  HCR6  0   0.266  -0.5245   1.3281   0.3336
 5F8  H7   H  HCR6  0   0.263   1.3127   1.6979  -1.0852
 5F8  H6   H  HCR6  0   0.268   5.2623   1.1890  -0.1003
 5F8  H5   H  HCR6  0   0.275   4.8162  -1.0291   0.9185
 5F8  H4   H  HCR6  0   0.273   2.4838  -1.8879   0.9514

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    double    1.208  0.020  1.208
 5F8  C10  C9   aromatic  1.387  0.020  1.387
 5F8  C7   C3   single    1.474  0.020  1.474
 5F8  C7   C8   aromatic  1.393  0.020  1.393
 5F8  C3   C2   aromatic  1.391  0.020  1.391
 5F8  C3   C4   aromatic  1.396  0.020  1.396
 5F8  C2   C1   aromatic  1.392  0.020  1.392
 5F8  C4   C5   aromatic  1.386  0.020  1.386
 5F8  C1   C    single    1.485  0.020  1.485
 5F8  C1   C6   aromatic  1.393  0.020  1.393
 5F8  C5   C6   aromatic  1.386  0.020  1.386
 5F8  C    O1   single    1.325  0.020  1.325
 5F8  C9   C8   aromatic  1.385  0.020  1.385
 5F8  O1   H8   single    0.850  0.020  0.980
 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  H8   O1   C    110.04  3.000
 5F8  C1   C    O    123.75  3.000
 5F8  C1   C    O1   112.97  3.000
 5F8  O    C    O1   123.27  3.000
 5F8  C2   C1   C6   119.83  3.000
 5F8  C6   C1   C    122.22  3.000
 5F8  C2   C1   C    117.95  3.000
 5F8  H3   C6   C5   119.39  3.000
 5F8  H3   C6   C1   121.08  3.000
 5F8  C5   C6   C1   119.53  3.000
 5F8  H2   C5   C4   119.74  3.000
 5F8  H2   C5   C6   119.84  3.000
 5F8  C4   C5   C6   120.42  3.000
 5F8  H1   C4   C3   119.96  3.000
 5F8  H1   C4   C5   119.31  3.000
 5F8  C3   C4   C5   120.72  3.000
 5F8  C7   C3   C2   120.67  3.000
 5F8  C2   C3   C4   118.55  3.000
 5F8  C7   C3   C4   120.79  3.000
 5F8  H    C2   C3   119.78  3.000
 5F8  H    C2   C1   119.25  3.000
 5F8  C3   C2   C1   120.96  3.000
 5F8  C8   C7   C11  117.06  3.000
 5F8  C8   C7   C3   121.95  3.000
 5F8  C11  C7   C3   120.99  3.000
 5F8  H7   C11  N    116.14  3.000
 5F8  H7   C11  C7   119.84  3.000
 5F8  N    C11  C7   124.02  3.000
 5F8  C10  N    C11  118.05  3.000
 5F8  H6   C10  C9   120.34  3.000
 5F8  H6   C10  N    116.69  3.000
 5F8  C9   C10  N    122.97  3.000
 5F8  H5   C9   C8   121.01  3.000
 5F8  H5   C9   C10  120.39  3.000
 5F8  C8   C9   C10  118.60  3.000
 5F8  H4   C8   C9   120.15  3.000
 5F8  H4   C8   C7   120.53  3.000
 5F8  C9   C8   C7   119.30  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  CONST_31  H8   O1   C    C1   180.00   0.0  0
 5F8  Var_01    C2   C1   C    O1   179.91  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
 5F8  plan-3  H8   0.020

