# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 18:15:25 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: 3-[3-(hydroxymethyl)phenyl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCc1cccc(c1)c2cccc(c2)C(O)=O
#
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
 QKU  QKU  '3-[3-(hydroxymethyl)phenyl]benzoic acid'  ligand  28  17  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_QKU
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
 QKU  C    C  C      0   0.399  -3.9899  -0.5851  -0.7158
 QKU  O    O  O      0  -0.592  -3.7756  -1.7725  -1.0264
 QKU  C1   C  CR6    0  -0.080  -2.7779   0.2393  -0.2945
 QKU  C10  C  CR6    0   0.110   3.3448  -0.1070  -0.3069
 QKU  C11  C  CH2    0  -0.228   4.5449   0.6650  -0.7768
 QKU  C12  C  CR16   0  -0.371   2.0810   0.4675  -0.3175
 QKU  C13  C  CR16   0  -0.359  -1.5102  -0.3323  -0.2727
 QKU  C2   C  CR16   0  -0.304  -2.9141   1.5764   0.0692
 QKU  C3   C  CR16   0  -0.231  -1.8031   2.3198   0.4418
 QKU  C4   C  CR16   0  -0.320  -0.5437   1.7383   0.4558
 QKU  C5   C  CR6    0   0.103  -0.3822   0.3989   0.0986
 QKU  C6   C  CR6    0   0.108   0.9536  -0.2331   0.1179
 QKU  C7   C  CR16   0  -0.324   1.1217  -1.5385   0.5762
 QKU  C8   C  CR16   0  -0.229   2.3821  -2.1205   0.5992
 QKU  C9   C  CR16   0  -0.296   3.4897  -1.4107   0.1633
 QKU  O1   O  OH1    0  -0.668   5.3773   0.9191   0.3362
 QKU  O2   O  OC    -1  -0.593  -5.0895  -0.0001  -0.7131
 QKU  H6   H  HCH2   0   0.212   5.0734   0.0824  -1.5413
 QKU  H7   H  HCH2   0   0.210   4.2151   1.5944  -1.2575
 QKU  H9   H  HCR6   0   0.249   1.9669   1.4790  -0.6915
 QKU  H10  H  HCR6   0   0.241  -1.4027  -1.3679  -0.5695
 QKU  H    H  HCR6   0   0.244  -3.8943   2.0342   0.0624
 QKU  H1   H  HCR6   0   0.250  -1.9177   3.3573   0.7298
 QKU  H2   H  HCR6   0   0.251   0.3131   2.3238   0.7667
 QKU  H3   H  HCR6   0   0.254   0.2681  -2.0989   0.9374
 QKU  H4   H  HCR6   0   0.256   2.4991  -3.1325   0.9651
 QKU  H5   H  HCR6   0   0.252   4.4685  -1.8749   0.1819
 QKU  H8   H  HOH1   0   0.456   6.1981   1.3005   0.0099

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
 QKU  C9   C8   aromatic  1.386  0.020  1.386
 QKU  C9   C10  aromatic  1.393  0.020  1.393
 QKU  C8   C7   aromatic  1.389  0.020  1.389
 QKU  C11  C10  single    1.502  0.020  1.502
 QKU  C11  O1   single    1.413  0.020  1.413
 QKU  C10  C12  aromatic  1.388  0.020  1.388
 QKU  O    C    deloc     1.246  0.020  1.246
 QKU  C7   C6   aromatic  1.394  0.020  1.394
 QKU  C12  C6   aromatic  1.397  0.020  1.397
 QKU  C6   C5   single    1.478  0.020  1.478
 QKU  C13  C5   aromatic  1.395  0.020  1.395
 QKU  C13  C1   aromatic  1.391  0.020  1.391
 QKU  C    O2   deloc     1.246  0.020  1.246
 QKU  C    C1   single    1.525  0.020  1.525
 QKU  C5   C4   aromatic  1.396  0.020  1.396
 QKU  C1   C2   aromatic  1.392  0.020  1.392
 QKU  C4   C3   aromatic  1.387  0.020  1.387
 QKU  C2   C3   aromatic  1.388  0.020  1.388
 QKU  C11  H6   single    0.970  0.020  1.090
 QKU  C11  H7   single    0.970  0.020  1.090
 QKU  C12  H9   single    0.930  0.020  1.080
 QKU  C13  H10  single    0.930  0.020  1.080
 QKU  C2   H    single    0.930  0.020  1.080
 QKU  C3   H1   single    0.930  0.020  1.080
 QKU  C4   H2   single    0.930  0.020  1.080
 QKU  C7   H3   single    0.930  0.020  1.080
 QKU  C8   H4   single    0.930  0.020  1.080
 QKU  C9   H5   single    0.930  0.020  1.080
 QKU  O1   H8   single    0.850  0.020  0.980

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
 QKU  O2   C    C1   116.56  3.000
 QKU  C1   C    O    116.57  3.000
 QKU  O2   C    O    126.87  3.000
 QKU  C2   C1   C13  118.67  3.000
 QKU  C2   C1   C    120.90  3.000
 QKU  C13  C1   C    120.43  3.000
 QKU  C9   C10  C12  118.98  3.000
 QKU  C12  C10  C11  120.81  3.000
 QKU  C9   C10  C11  120.21  3.000
 QKU  H7   C11  H6   106.82  3.000
 QKU  H7   C11  O1   111.71  3.000
 QKU  H6   C11  O1   111.15  3.000
 QKU  H7   C11  C10  109.40  3.000
 QKU  H6   C11  C10  109.26  3.000
 QKU  O1   C11  C10  108.46  3.000
 QKU  H9   C12  C6   119.36  3.000
 QKU  H9   C12  C10  118.97  3.000
 QKU  C6   C12  C10  121.65  3.000
 QKU  H10  C13  C5   119.62  3.000
 QKU  H10  C13  C1   118.64  3.000
 QKU  C5   C13  C1   121.73  3.000
 QKU  H    C2   C3   120.02  3.000
 QKU  H    C2   C1   119.57  3.000
 QKU  C3   C2   C1   120.41  3.000
 QKU  H1   C3   C4   119.67  3.000
 QKU  H1   C3   C2   120.00  3.000
 QKU  C4   C3   C2   120.33  3.000
 QKU  H2   C4   C5   120.04  3.000
 QKU  H2   C4   C3   119.63  3.000
 QKU  C5   C4   C3   120.31  3.000
 QKU  C6   C5   C4   120.77  3.000
 QKU  C4   C5   C13  118.54  3.000
 QKU  C6   C5   C13  120.68  3.000
 QKU  C7   C6   C5   120.92  3.000
 QKU  C5   C6   C12  120.73  3.000
 QKU  C7   C6   C12  118.35  3.000
 QKU  H3   C7   C8   119.54  3.000
 QKU  H3   C7   C6   119.95  3.000
 QKU  C8   C7   C6   120.50  3.000
 QKU  H4   C8   C9   119.92  3.000
 QKU  H4   C8   C7   119.71  3.000
 QKU  C9   C8   C7   120.37  3.000
 QKU  H5   C9   C8   119.81  3.000
 QKU  H5   C9   C10  120.05  3.000
 QKU  C8   C9   C10  120.14  3.000
 QKU  H8   O1   C11  107.86  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
 QKU  CONST_01  C6   C5   C13  C1   180.00   0.0  0
 QKU  CONST_02  C4   C5   C13  C1     0.00   0.0  0
 QKU  CONST_03  C4   C3   C2   C1     0.00   0.0  0
 QKU  CONST_04  C7   C8   C9   C10    0.00   0.0  0
 QKU  CONST_05  C7   C6   C12  C10    0.00   0.0  0
 QKU  CONST_06  C5   C6   C12  C10  180.00   0.0  0
 QKU  CONST_07  C8   C9   C10  C12    0.00   0.0  0
 QKU  CONST_08  C8   C7   C6   C12    0.00   0.0  0
 QKU  CONST_12  C3   C4   C5   C13    0.00   0.0  0
 QKU  CONST_13  C3   C2   C1   C13    0.00   0.0  0
 QKU  CONST_14  C5   C13  C1   C2     0.00   0.0  0
 QKU  CONST_15  C5   C4   C3   C2     0.00   0.0  0
 QKU  CONST_16  C6   C5   C4   C3   180.00   0.0  0
 QKU  CONST_18  C8   C7   C6   C5   180.00   0.0  0
 QKU  CONST_19  C9   C8   C7   C6     0.00   0.0  0
 QKU  CONST_20  C9   C10  C12  C6     0.00   0.0  0
 QKU  CONST_21  C5   C13  C1   C    180.00   0.0  0
 QKU  CONST_22  C3   C2   C1   C    180.00   0.0  0
 QKU  CONST_23  C8   C9   C10  C11  180.00   0.0  0
 QKU  CONST_24  C6   C12  C10  C11  180.00   0.0  0
 QKU  CONST_25  H1   C3   C2   C1   180.00   0.0  0
 QKU  CONST_26  H4   C8   C9   C10  180.00   0.0  0
 QKU  CONST_27  H5   C9   C10  C12  180.00   0.0  0
 QKU  CONST_28  H3   C7   C6   C12  180.00   0.0  0
 QKU  CONST_29  H2   C4   C5   C13  180.00   0.0  0
 QKU  CONST_30  H    C2   C1   C13  180.00   0.0  0
 QKU  CONST_31  H10  C13  C1   C2   180.00   0.0  0
 QKU  CONST_32  H9   C12  C6   C5     0.00   0.0  0
 QKU  Var_01    C13  C1   C    O      0.21  30.0  2
 QKU  Var_02    O1   C11  C10  C12  112.04  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
 QKU  plan-1  C    0.020
 QKU  plan-1  C1   0.020
 QKU  plan-1  C13  0.020
 QKU  plan-1  C2   0.020
 QKU  plan-1  C3   0.020
 QKU  plan-1  C4   0.020
 QKU  plan-1  C5   0.020
 QKU  plan-1  C6   0.020
 QKU  plan-1  H10  0.020
 QKU  plan-1  H    0.020
 QKU  plan-1  H1   0.020
 QKU  plan-1  H2   0.020
 QKU  plan-2  C10  0.020
 QKU  plan-2  C11  0.020
 QKU  plan-2  C12  0.020
 QKU  plan-2  C5   0.020
 QKU  plan-2  C6   0.020
 QKU  plan-2  C7   0.020
 QKU  plan-2  C8   0.020
 QKU  plan-2  C9   0.020
 QKU  plan-2  H9   0.020
 QKU  plan-2  H3   0.020
 QKU  plan-2  H4   0.020
 QKU  plan-2  H5   0.020
 QKU  plan-3  C    0.020
 QKU  plan-3  O    0.020
 QKU  plan-3  C1   0.020
 QKU  plan-3  O2   0.020

