# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 12:45:29 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 3-(4-hydroxyphenyl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cccc(c1)c2ccc(O)cc2
#
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
 JSX  JSX  '3-(4-hydroxyphenyl)benzoic acid'  ligand  25  16  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JSX
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
 JSX  C    C  CR6    0   0.343   4.0334   0.3873   0.0393
 JSX  O    O  OH1    0  -0.631   5.3511   0.6672   0.0125
 JSX  C1   C  CR16   0  -0.323   3.6200  -0.8550  -0.4372
 JSX  C10  C  CR6    0  -0.080  -2.4635  -0.0377  -0.1774
 JSX  C11  C  C      0   0.398  -3.5136   1.0310  -0.4621
 JSX  C12  C  CR16   0  -0.366  -1.1102   0.2831  -0.1856
 JSX  C2   C  CR16   0  -0.300   2.2770  -1.1884  -0.4265
 JSX  C3   C  CR16   0  -0.370   3.0808   1.2815   0.5204
 JSX  C4   C  CR16   0  -0.298   1.7396   0.9328   0.5237
 JSX  C5   C  CR6    0   0.067   1.3055  -0.3069   0.0540
 JSX  C6   C  CR6    0   0.116  -0.1248  -0.6728   0.0638
 JSX  C7   C  CR16   0  -0.327  -0.5267  -1.9846   0.3235
 JSX  C8   C  CR16   0  -0.229  -1.8726  -2.3195   0.3304
 JSX  C9   C  CR16   0  -0.308  -2.8377  -1.3534   0.0841
 JSX  O1   O  O      0  -0.592  -3.0929   2.1767  -0.7133
 JSX  O2   O  OC    -1  -0.594  -4.7039   0.6661  -0.4205
 JSX  H    H  HOH1   0   0.474   5.5152   1.5521   0.3572
 JSX  H1   H  HCR6   0   0.263   4.3519  -1.5540  -0.8229
 JSX  H8   H  HCR6   0   0.238  -0.8225   1.3015  -0.4142
 JSX  H2   H  HCR6   0   0.253   1.9820  -2.1522  -0.8227
 JSX  H3   H  HCR6   0   0.271   3.3837   2.2494   0.9035
 JSX  H4   H  HCR6   0   0.256   1.0225   1.6409   0.9208
 JSX  H5   H  HCR6   0   0.248   0.2126  -2.7463   0.5398
 JSX  H6   H  HCR6   0   0.249  -2.1682  -3.3399   0.5399
 JSX  H7   H  HCR6   0   0.243  -3.8863  -1.6198   0.0966

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
 JSX  O    C    single    1.347  0.020  1.347
 JSX  C1   C    aromatic  1.393  0.020  1.393
 JSX  C1   C2   aromatic  1.384  0.020  1.384
 JSX  C    C3   aromatic  1.392  0.020  1.392
 JSX  C2   C5   aromatic  1.397  0.020  1.397
 JSX  C3   C4   aromatic  1.386  0.020  1.386
 JSX  C5   C4   aromatic  1.395  0.020  1.395
 JSX  C5   C6   single    1.476  0.020  1.476
 JSX  C7   C6   aromatic  1.396  0.020  1.396
 JSX  C7   C8   aromatic  1.387  0.020  1.387
 JSX  C6   C12  aromatic  1.395  0.020  1.395
 JSX  C8   C9   aromatic  1.388  0.020  1.388
 JSX  C12  C10  aromatic  1.391  0.020  1.391
 JSX  C9   C10  aromatic  1.393  0.020  1.393
 JSX  C10  C11  single    1.525  0.020  1.525
 JSX  C11  O1   deloc     1.246  0.020  1.246
 JSX  C11  O2   deloc     1.246  0.020  1.246
 JSX  O    H    single    0.850  0.020  0.980
 JSX  C1   H1   single    0.930  0.020  1.080
 JSX  C12  H8   single    0.930  0.020  1.080
 JSX  C2   H2   single    0.930  0.020  1.080
 JSX  C3   H3   single    0.930  0.020  1.080
 JSX  C4   H4   single    0.930  0.020  1.080
 JSX  C7   H5   single    0.930  0.020  1.080
 JSX  C8   H6   single    0.930  0.020  1.080
 JSX  C9   H7   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
 JSX  C3   C    C1   119.20  3.000
 JSX  C3   C    O    122.86  3.000
 JSX  C1   C    O    117.94  3.000
 JSX  H    O    C    110.50  3.000
 JSX  H1   C1   C2   120.21  3.000
 JSX  H1   C1   C    119.78  3.000
 JSX  C2   C1   C    120.00  3.000
 JSX  C9   C10  C12  118.71  3.000
 JSX  C9   C10  C11  120.80  3.000
 JSX  C12  C10  C11  120.48  3.000
 JSX  O2   C11  O1   126.77  3.000
 JSX  O2   C11  C10  116.52  3.000
 JSX  O1   C11  C10  116.71  3.000
 JSX  H8   C12  C6   119.63  3.000
 JSX  H8   C12  C10  118.48  3.000
 JSX  C6   C12  C10  121.88  3.000
 JSX  H2   C2   C5   119.87  3.000
 JSX  H2   C2   C1   118.41  3.000
 JSX  C5   C2   C1   121.71  3.000
 JSX  H3   C3   C4   119.61  3.000
 JSX  H3   C3   C    120.29  3.000
 JSX  C4   C3   C    120.09  3.000
 JSX  H4   C4   C5   119.90  3.000
 JSX  H4   C4   C3   118.49  3.000
 JSX  C5   C4   C3   121.60  3.000
 JSX  C6   C5   C4   121.29  3.000
 JSX  C6   C5   C2   121.31  3.000
 JSX  C4   C5   C2   117.40  3.000
 JSX  C7   C6   C5   120.85  3.000
 JSX  C7   C6   C12  118.27  3.000
 JSX  C5   C6   C12  120.88  3.000
 JSX  H5   C7   C8   119.44  3.000
 JSX  H5   C7   C6   120.08  3.000
 JSX  C8   C7   C6   120.47  3.000
 JSX  H6   C8   C9   120.04  3.000
 JSX  H6   C8   C7   119.56  3.000
 JSX  C9   C8   C7   120.40  3.000
 JSX  H7   C9   C8   120.04  3.000
 JSX  H7   C9   C10  119.68  3.000
 JSX  C8   C9   C10  120.28  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
 JSX  CONST_01  C5  C2   C1   C      0.00   0.0  0
 JSX  CONST_02  C5  C4   C3   C      0.00   0.0  0
 JSX  CONST_03  C4  C3   C    C1     0.00   0.0  0
 JSX  CONST_04  C4  C5   C2   C1     0.00   0.0  0
 JSX  CONST_05  C6  C5   C2   C1   180.00   0.0  0
 JSX  CONST_06  C5  C6   C12  C10  180.00   0.0  0
 JSX  CONST_07  C7  C6   C12  C10    0.00   0.0  0
 JSX  CONST_08  C7  C8   C9   C10    0.00   0.0  0
 JSX  CONST_11  C8  C7   C6   C12    0.00   0.0  0
 JSX  CONST_12  C8  C9   C10  C12    0.00   0.0  0
 JSX  CONST_13  C3  C    C1   C2     0.00   0.0  0
 JSX  CONST_14  C3  C4   C5   C2     0.00   0.0  0
 JSX  CONST_16  C6  C5   C4   C3   180.00   0.0  0
 JSX  CONST_18  C8  C7   C6   C5   180.00   0.0  0
 JSX  CONST_19  C9  C8   C7   C6     0.00   0.0  0
 JSX  CONST_20  C9  C10  C12  C6     0.00   0.0  0
 JSX  CONST_21  C2  C1   C    O    180.00   0.0  0
 JSX  CONST_22  C4  C3   C    O    180.00   0.0  0
 JSX  CONST_23  C6  C12  C10  C11  180.00   0.0  0
 JSX  CONST_24  C8  C9   C10  C11  180.00   0.0  0
 JSX  CONST_25  H2  C2   C1   C    180.00   0.0  0
 JSX  CONST_26  H4  C4   C3   C    180.00   0.0  0
 JSX  CONST_27  H3  C3   C    C1   180.00   0.0  0
 JSX  CONST_28  H6  C8   C9   C10  180.00   0.0  0
 JSX  CONST_29  H5  C7   C6   C12  180.00   0.0  0
 JSX  CONST_30  H7  C9   C10  C12  180.00   0.0  0
 JSX  CONST_31  H1  C1   C    C3   180.00   0.0  0
 JSX  CONST_32  H8  C12  C6   C5     0.00   0.0  0
 JSX  Var_01    O1  C11  C10  C12    0.88  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
 JSX  plan-1  C    0.020
 JSX  plan-1  O    0.020
 JSX  plan-1  C1   0.020
 JSX  plan-1  C2   0.020
 JSX  plan-1  C3   0.020
 JSX  plan-1  C4   0.020
 JSX  plan-1  C5   0.020
 JSX  plan-1  C6   0.020
 JSX  plan-1  H1   0.020
 JSX  plan-1  H2   0.020
 JSX  plan-1  H3   0.020
 JSX  plan-1  H4   0.020
 JSX  plan-2  C10  0.020
 JSX  plan-2  C11  0.020
 JSX  plan-2  C12  0.020
 JSX  plan-2  C5   0.020
 JSX  plan-2  C6   0.020
 JSX  plan-2  C7   0.020
 JSX  plan-2  C8   0.020
 JSX  plan-2  C9   0.020
 JSX  plan-2  H8   0.020
 JSX  plan-2  H5   0.020
 JSX  plan-2  H6   0.020
 JSX  plan-2  H7   0.020
 JSX  plan-3  C10  0.020
 JSX  plan-3  C11  0.020
 JSX  plan-3  O1   0.020
 JSX  plan-3  O2   0.020

