# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 18:48:34 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: 3-(pyridin-4-yl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cccc(c1)c2ccncc2
#
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
 5FL  5FL  '3-(pyridin-4-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_5FL
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
 5FL  C1   C  CR16   0  -0.382   2.7300   0.9066   0.4461
 5FL  C2   C  CR6    0   0.176   1.6932   0.0966  -0.0158
 5FL  C3   C  CR16   0  -0.380   2.0414  -1.1854  -0.4402
 5FL  C4   C  CR16   0  -0.062   3.3671  -1.5831  -0.3856
 5FL  C5   C  CR6    0   0.116   0.2965   0.5688  -0.0525
 5FL  C6   C  CR16   0  -0.357  -0.7569  -0.3143   0.1818
 5FL  C7   C  CR6    0  -0.079  -2.0811   0.1082   0.1552
 5FL  C8   C  CR16   0  -0.299  -2.3497   1.4462  -0.1212
 5FL  O    O  O      0  -0.591  -2.8818  -2.0512   0.6807
 5FL  C11  C  C      0   0.402  -3.2129  -0.8764   0.4315
 5FL  O1   O  OC    -1  -0.592  -4.3701  -0.4190   0.3848
 5FL  C9   C  CR16   0  -0.228  -1.3134   2.3382  -0.3588
 5FL  C10  C  CR16   0  -0.317   0.0035   1.9064  -0.3222
 5FL  C    C  CR16   0  -0.061   4.0243   0.4129   0.4593
 5FL  N    N  N      0  -0.409   4.3530  -0.8085   0.0534
 5FL  H1   H  HCR6   0   0.267   2.5399   1.9062   0.8139
 5FL  H2   H  HCR6   0   0.267   1.2973  -1.8690  -0.8275
 5FL  H3   H  HCR6   0   0.264   3.6434  -2.5772  -0.7194
 5FL  H4   H  HCR6   0   0.245  -0.5509  -1.3517   0.4122
 5FL  H5   H  HCR6   0   0.248  -3.3755   1.7885  -0.1511
 5FL  H6   H  HCR6   0   0.254  -1.5305   3.3757  -0.5783
 5FL  H7   H  HCR6   0   0.255   0.8011   2.6102  -0.5258
 5FL  H    H  HCR6   0   0.264   4.8334   1.0378   0.8213

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
 5FL  N    C4   aromatic  1.328  0.020  1.328
 5FL  N    C    aromatic  1.328  0.020  1.328
 5FL  C4   C3   aromatic  1.385  0.020  1.385
 5FL  C    C1   aromatic  1.385  0.020  1.385
 5FL  C3   C2   aromatic  1.395  0.020  1.395
 5FL  C1   C2   aromatic  1.394  0.020  1.394
 5FL  C2   C5   single    1.475  0.020  1.475
 5FL  C5   C10  aromatic  1.396  0.020  1.396
 5FL  C5   C6   aromatic  1.394  0.020  1.394
 5FL  C10  C9   aromatic  1.386  0.020  1.386
 5FL  C6   C7   aromatic  1.390  0.020  1.390
 5FL  C9   C8   aromatic  1.388  0.020  1.388
 5FL  C7   C8   aromatic  1.392  0.020  1.392
 5FL  C7   C11  single    1.525  0.020  1.525
 5FL  O    C11  deloc     1.246  0.020  1.246
 5FL  C11  O1   deloc     1.245  0.020  1.245
 5FL  C1   H1   single    0.930  0.020  1.080
 5FL  C3   H2   single    0.930  0.020  1.080
 5FL  C4   H3   single    0.930  0.020  1.080
 5FL  C6   H4   single    0.930  0.020  1.080
 5FL  C8   H5   single    0.930  0.020  1.080
 5FL  C9   H6   single    0.930  0.020  1.080
 5FL  C10  H7   single    0.930  0.020  1.080
 5FL  C    H    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
 5FL  H1   C1   C    119.35  3.000
 5FL  H1   C1   C2   121.24  3.000
 5FL  C    C1   C2   119.39  3.000
 5FL  C5   C2   C3   121.55  3.000
 5FL  C5   C2   C1   121.76  3.000
 5FL  C3   C2   C1   116.69  3.000
 5FL  H2   C3   C4   119.39  3.000
 5FL  H2   C3   C2   121.20  3.000
 5FL  C4   C3   C2   119.40  3.000
 5FL  H3   C4   N    116.56  3.000
 5FL  H3   C4   C3   119.66  3.000
 5FL  N    C4   C3   123.77  3.000
 5FL  C10  C5   C6   118.74  3.000
 5FL  C6   C5   C2   120.56  3.000
 5FL  C10  C5   C2   120.69  3.000
 5FL  H4   C6   C7   118.47  3.000
 5FL  H4   C6   C5   119.93  3.000
 5FL  C7   C6   C5   121.59  3.000
 5FL  C11  C7   C8   120.87  3.000
 5FL  C11  C7   C6   120.47  3.000
 5FL  C8   C7   C6   118.66  3.000
 5FL  H5   C8   C9   119.99  3.000
 5FL  H5   C8   C7   119.50  3.000
 5FL  C9   C8   C7   120.50  3.000
 5FL  O1   C11  O    126.94  3.000
 5FL  O1   C11  C7   116.46  3.000
 5FL  O    C11  C7   116.60  3.000
 5FL  H6   C9   C10  119.63  3.000
 5FL  H6   C9   C8   120.07  3.000
 5FL  C10  C9   C8   120.30  3.000
 5FL  H7   C10  C9   119.48  3.000
 5FL  H7   C10  C5   120.31  3.000
 5FL  C9   C10  C5   120.20  3.000
 5FL  H    C    N    116.56  3.000
 5FL  H    C    C1   119.66  3.000
 5FL  N    C    C1   123.77  3.000
 5FL  C    N    C4   116.97  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
 5FL  CONST_01  C4   N    C    C1     0.00   0.0  0
 5FL  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 5FL  CONST_05  N    C4   C3   C2     0.00   0.0  0
 5FL  CONST_06  N    C    C1   C2     0.00   0.0  0
 5FL  CONST_07  C9   C10  C5   C2   180.00   0.0  0
 5FL  CONST_08  C7   C6   C5   C2   180.00   0.0  0
 5FL  CONST_09  C    N    C4   C3     0.00   0.0  0
 5FL  CONST_10  C    C1   C2   C3     0.00   0.0  0
 5FL  CONST_13  C5   C2   C3   C4   180.00   0.0  0
 5FL  CONST_14  C    C1   C2   C5   180.00   0.0  0
 5FL  CONST_15  C8   C9   C10  C5     0.00   0.0  0
 5FL  CONST_16  C8   C7   C6   C5     0.00   0.0  0
 5FL  CONST_17  C9   C10  C5   C6     0.00   0.0  0
 5FL  CONST_18  C9   C8   C7   C6     0.00   0.0  0
 5FL  CONST_19  C10  C5   C6   C7     0.00   0.0  0
 5FL  CONST_20  C10  C9   C8   C7     0.00   0.0  0
 5FL  CONST_21  C11  C7   C6   C5   180.00   0.0  0
 5FL  CONST_22  C9   C8   C7   C11  180.00   0.0  0
 5FL  CONST_23  H2   C3   C2   C1   180.00   0.0  0
 5FL  CONST_24  H3   C4   C3   C2   180.00   0.0  0
 5FL  CONST_25  H    C    C1   C2   180.00   0.0  0
 5FL  CONST_26  H7   C10  C5   C2     0.00   0.0  0
 5FL  CONST_27  H4   C6   C5   C2     0.00   0.0  0
 5FL  CONST_28  H1   C1   C2   C3   180.00   0.0  0
 5FL  CONST_29  H6   C9   C10  C5   180.00   0.0  0
 5FL  CONST_30  H5   C8   C7   C6   180.00   0.0  0
 5FL  Var_01    O    C11  C7   C6     0.26  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
 5FL  plan-1  C2   0.020
 5FL  plan-1  C5   0.020
 5FL  plan-1  C6   0.020
 5FL  plan-1  C7   0.020
 5FL  plan-1  C8   0.020
 5FL  plan-1  C11  0.020
 5FL  plan-1  C9   0.020
 5FL  plan-1  C10  0.020
 5FL  plan-1  H4   0.020
 5FL  plan-1  H5   0.020
 5FL  plan-1  H6   0.020
 5FL  plan-1  H7   0.020
 5FL  plan-2  C1   0.020
 5FL  plan-2  C2   0.020
 5FL  plan-2  C3   0.020
 5FL  plan-2  C4   0.020
 5FL  plan-2  C5   0.020
 5FL  plan-2  C    0.020
 5FL  plan-2  N    0.020
 5FL  plan-2  H1   0.020
 5FL  plan-2  H2   0.020
 5FL  plan-2  H3   0.020
 5FL  plan-2  H    0.020
 5FL  plan-3  C7   0.020
 5FL  plan-3  O    0.020
 5FL  plan-3  C11  0.020
 5FL  plan-3  O1   0.020

