# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 10:20:58 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 3-(3-methylphenyl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(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
 L5D  L5D  '3-(3-methylphenyl)benzoic acid'  ligand  28  16  .  2021-08-13  2021-08-13  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_L5D
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
 L5D  C    C  C     0   0.535   3.4727  -0.7150  -0.5925
 L5D  O    O  OH1   0  -0.593   4.6592  -0.1265  -0.5515
 L5D  C1   C  CR6   0  -0.061   2.3653   0.1785  -0.1679
 L5D  C10  C  CR16  0  -0.364  -2.4664   0.6619  -0.2010
 L5D  C11  C  CR16  0  -0.299   0.2218   1.7626   0.5982
 L5D  C12  C  CR16  0  -0.226   1.5068   2.2825   0.6054
 L5D  C13  C  CR16  0  -0.275   2.5840   1.4975   0.2251
 L5D  C2   C  CR16  0  -0.327   1.0727  -0.3374  -0.1731
 L5D  C3   C  CR6   0   0.106  -0.0148   0.4427   0.2091
 L5D  C4   C  CR6   0   0.108  -1.3825  -0.1155   0.2095
 L5D  C5   C  CR16  0  -0.329  -1.6169  -1.4264   0.6225
 L5D  C6   C  CR16  0  -0.226  -2.9067  -1.9365   0.6224
 L5D  C7   C  CR16  0  -0.308  -3.9732  -1.1497   0.2131
 L5D  C8   C  CR6   0   0.119  -3.7652   0.1641  -0.2034
 L5D  C9   C  CH3   0  -0.724  -4.9181   1.0273  -0.6264
 L5D  O1   O  O     0  -0.438   3.3159  -1.8616  -0.9385
 L5D  H11  H  HOH1  0   0.488   5.3468  -0.7522  -0.8239
 L5D  H8   H  HCR6  0   0.265  -0.6035   2.3861   0.9191
 L5D  H9   H  HCR6  0   0.268   1.6720   3.3047   0.9181
 L5D  H10  H  HCR6  0   0.270   3.5798   1.9175   0.2418
 L5D  H    H  HCR6  0   0.264   0.9119  -1.3580  -0.4960
 L5D  H1   H  HCR6  0   0.254  -0.7960  -2.0452   0.9635
 L5D  H2   H  HCR6  0   0.256  -3.0829  -2.9534   0.9488
 L5D  H3   H  HCR6  0   0.250  -4.9765  -1.5593   0.2174
 L5D  H6   H  HCH3  0   0.250  -5.4368   1.4355   0.2433
 L5D  H4   H  HCH3  0   0.244  -4.5872   1.8702  -1.2321
 L5D  H5   H  HCH3  0   0.245  -5.6508   0.4626  -1.2024
 L5D  H7   H  HCR6  0   0.248  -2.2944   1.6750  -0.5474

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
 L5D  C7   C6   aromatic  1.387  0.020  1.387
 L5D  C7   C8   aromatic  1.394  0.020  1.394
 L5D  C6   C5   aromatic  1.387  0.020  1.387
 L5D  C9   C8   single    1.501  0.020  1.501
 L5D  C8   C10  aromatic  1.391  0.020  1.391
 L5D  C5   C4   aromatic  1.394  0.020  1.394
 L5D  C10  C4   aromatic  1.396  0.020  1.396
 L5D  O1   C    double    1.208  0.020  1.208
 L5D  C4   C3   single    1.477  0.020  1.477
 L5D  C2   C3   aromatic  1.392  0.020  1.392
 L5D  C2   C1   aromatic  1.392  0.020  1.392
 L5D  C3   C11  aromatic  1.396  0.020  1.396
 L5D  C    C1   single    1.485  0.020  1.485
 L5D  C    O    single    1.325  0.020  1.325
 L5D  C1   C13  aromatic  1.394  0.020  1.394
 L5D  C11  C12  aromatic  1.386  0.020  1.386
 L5D  C13  C12  aromatic  1.386  0.020  1.386
 L5D  O    H11  single    0.850  0.020  0.980
 L5D  C10  H7   single    0.930  0.020  1.080
 L5D  C11  H8   single    0.930  0.020  1.080
 L5D  C12  H9   single    0.930  0.020  1.080
 L5D  C13  H10  single    0.930  0.020  1.080
 L5D  C2   H    single    0.930  0.020  1.080
 L5D  C5   H1   single    0.930  0.020  1.080
 L5D  C6   H2   single    0.930  0.020  1.080
 L5D  C7   H3   single    0.930  0.020  1.080
 L5D  C9   H6   single    0.970  0.020  1.090
 L5D  C9   H4   single    0.970  0.020  1.090
 L5D  C9   H5   single    0.970  0.020  1.090

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
 L5D  O1   C    C1   123.80  3.000
 L5D  C1   C    O    113.06  3.000
 L5D  O1   C    O    123.14  3.000
 L5D  H11  O    C    109.87  3.000
 L5D  C2   C1   C13  119.85  3.000
 L5D  C13  C1   C    122.22  3.000
 L5D  C2   C1   C    117.93  3.000
 L5D  H7   C10  C8   118.81  3.000
 L5D  H7   C10  C4   119.42  3.000
 L5D  C8   C10  C4   121.76  3.000
 L5D  H8   C11  C3   119.85  3.000
 L5D  H8   C11  C12  119.27  3.000
 L5D  C3   C11  C12  120.87  3.000
 L5D  H9   C12  C13  119.72  3.000
 L5D  H9   C12  C11  119.84  3.000
 L5D  C13  C12  C11  120.44  3.000
 L5D  H10  C13  C12  119.45  3.000
 L5D  H10  C13  C1   121.11  3.000
 L5D  C12  C13  C1   119.43  3.000
 L5D  H    C2   C3   119.62  3.000
 L5D  H    C2   C1   119.25  3.000
 L5D  C3   C2   C1   121.12  3.000
 L5D  C4   C3   C2   120.78  3.000
 L5D  C2   C3   C11  118.29  3.000
 L5D  C4   C3   C11  120.93  3.000
 L5D  C5   C4   C3   120.73  3.000
 L5D  C3   C4   C10  120.56  3.000
 L5D  C5   C4   C10  118.71  3.000
 L5D  H1   C5   C6   119.65  3.000
 L5D  H1   C5   C4   120.20  3.000
 L5D  C6   C5   C4   120.14  3.000
 L5D  H2   C6   C7   119.79  3.000
 L5D  H2   C6   C5   119.79  3.000
 L5D  C7   C6   C5   120.42  3.000
 L5D  H3   C7   C8   119.71  3.000
 L5D  H3   C7   C6   119.75  3.000
 L5D  C8   C7   C6   120.54  3.000
 L5D  C9   C8   C7   120.77  3.000
 L5D  C9   C8   C10  120.79  3.000
 L5D  C7   C8   C10  118.43  3.000
 L5D  H5   C9   H4   108.14  3.000
 L5D  H5   C9   H6   107.17  3.000
 L5D  H4   C9   H6   107.33  3.000
 L5D  H5   C9   C8   111.55  3.000
 L5D  H4   C9   C8   111.61  3.000
 L5D  H6   C9   C8   110.82  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
 L5D  CONST_01  C4   C3   C2   C1   180.00   0.0  0
 L5D  CONST_02  C11  C3   C2   C1     0.00   0.0  0
 L5D  CONST_03  C11  C12  C13  C1     0.00   0.0  0
 L5D  CONST_04  C6   C7   C8   C10    0.00   0.0  0
 L5D  CONST_05  C6   C5   C4   C10    0.00   0.0  0
 L5D  CONST_09  C4   C3   C11  C12  180.00   0.0  0
 L5D  CONST_10  C2   C3   C11  C12    0.00   0.0  0
 L5D  CONST_11  C2   C1   C13  C12    0.00   0.0  0
 L5D  CONST_12  C3   C2   C1   C13    0.00   0.0  0
 L5D  CONST_13  C3   C11  C12  C13    0.00   0.0  0
 L5D  CONST_15  C6   C5   C4   C3   180.00   0.0  0
 L5D  CONST_16  C8   C10  C4   C3   180.00   0.0  0
 L5D  CONST_17  C7   C6   C5   C4     0.00   0.0  0
 L5D  CONST_18  C7   C8   C10  C4     0.00   0.0  0
 L5D  CONST_19  C8   C7   C6   C5     0.00   0.0  0
 L5D  CONST_20  C8   C10  C4   C5     0.00   0.0  0
 L5D  CONST_21  C3   C2   C1   C    180.00   0.0  0
 L5D  CONST_22  C12  C13  C1   C    180.00   0.0  0
 L5D  CONST_23  C9   C8   C10  C4   180.00   0.0  0
 L5D  CONST_24  C9   C8   C7   C6   180.00   0.0  0
 L5D  CONST_25  H9   C12  C13  C1   180.00   0.0  0
 L5D  CONST_26  H3   C7   C8   C10  180.00   0.0  0
 L5D  CONST_27  H1   C5   C4   C10  180.00   0.0  0
 L5D  CONST_28  H    C2   C3   C11  180.00   0.0  0
 L5D  CONST_29  H10  C13  C12  C11  180.00   0.0  0
 L5D  CONST_30  H8   C11  C12  C13  180.00   0.0  0
 L5D  CONST_31  H7   C10  C4   C3     0.00   0.0  0
 L5D  CONST_32  H2   C6   C5   C4   180.00   0.0  0
 L5D  CONST_33  H11  O    C    C1   180.00   0.0  0
 L5D  Var_01    C2   C1   C    O    179.97  30.0  2
 L5D  Var_02    H6   C9   C8   C10  -99.07  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
 L5D  plan-1  C    0.020
 L5D  plan-1  C1   0.020
 L5D  plan-1  C11  0.020
 L5D  plan-1  C12  0.020
 L5D  plan-1  C13  0.020
 L5D  plan-1  C2   0.020
 L5D  plan-1  C3   0.020
 L5D  plan-1  C4   0.020
 L5D  plan-1  H8   0.020
 L5D  plan-1  H9   0.020
 L5D  plan-1  H10  0.020
 L5D  plan-1  H    0.020
 L5D  plan-2  C10  0.020
 L5D  plan-2  C3   0.020
 L5D  plan-2  C4   0.020
 L5D  plan-2  C5   0.020
 L5D  plan-2  C6   0.020
 L5D  plan-2  C7   0.020
 L5D  plan-2  C8   0.020
 L5D  plan-2  C9   0.020
 L5D  plan-2  H1   0.020
 L5D  plan-2  H2   0.020
 L5D  plan-2  H3   0.020
 L5D  plan-2  H7   0.020
 L5D  plan-3  C    0.020
 L5D  plan-3  O    0.020
 L5D  plan-3  C1   0.020
 L5D  plan-3  O1   0.020
 L5D  plan-3  H11  0.020

