# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 04:19:09 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  27  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_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   0.399   3.5342  -0.6333  -0.7499
 L5D  O    O  OC    -1  -0.593   4.6607  -0.1023  -0.7259
 L5D  C1   C  CR6    0  -0.080   2.3670   0.2204  -0.2653
 L5D  C10  C  CR16   0  -0.361  -2.4776   0.6650  -0.1683
 L5D  C11  C  CR16   0  -0.321   0.2147   1.7719   0.6062
 L5D  C12  C  CR16   0  -0.230   1.4981   2.2982   0.5992
 L5D  C13  C  CR16   0  -0.305   2.5689   1.5287   0.1668
 L5D  C2   C  CR16   0  -0.359   1.0754  -0.2953  -0.2514
 L5D  C3   C  CR6    0   0.103  -0.0133   0.4625   0.1800
 L5D  C4   C  CR6    0   0.108  -1.3760  -0.1101   0.1907
 L5D  C5   C  CR16   0  -0.331  -1.5894  -1.4391   0.5641
 L5D  C6   C  CR16   0  -0.226  -2.8714  -1.9638   0.5765
 L5D  C7   C  CR16   0  -0.319  -3.9576  -1.1752   0.2176
 L5D  C8   C  CR6    0   0.118  -3.7726   0.1513  -0.1599
 L5D  C9   C  CH3    0  -0.726  -4.9345   1.0194  -0.5487
 L5D  O1   O  O      0  -0.592   3.2614  -1.7893  -1.1267
 L5D  H8   H  HCR6   0   0.250  -0.6091   2.3767   0.9659
 L5D  H9   H  HCR6   0   0.250   1.6639   3.3119   0.9417
 L5D  H10  H  HCR6   0   0.244   3.5685   1.9428   0.1670
 L5D  H    H  HCR6   0   0.240   0.9174  -1.3070  -0.6030
 L5D  H1   H  HCR6   0   0.250  -0.7539  -2.0587   0.8657
 L5D  H2   H  HCR6   0   0.253  -3.0290  -2.9927   0.8740
 L5D  H3   H  HCR6   0   0.247  -4.9565  -1.5947   0.2336
 L5D  H6   H  HCH3   0   0.247  -5.0668   1.8392   0.1593
 L5D  H4   H  HCH3   0   0.246  -4.7859   1.4673  -1.5322
 L5D  H5   H  HCH3   0   0.244  -5.8643   0.4526  -0.5766
 L5D  H7   H  HCR6   0   0.244  -2.3246   1.6924  -0.4806

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  1.389  0.020  1.389
 L5D  C7   C8   aromatic  1.392  0.020  1.392
 L5D  C6   C5   aromatic  1.385  0.020  1.385
 L5D  C9   C8   single    1.502  0.020  1.502
 L5D  C8   C10  aromatic  1.393  0.020  1.393
 L5D  C5   C4   aromatic  1.397  0.020  1.397
 L5D  C10  C4   aromatic  1.394  0.020  1.394
 L5D  O1   C    deloc     1.246  0.020  1.246
 L5D  C4   C3   single    1.478  0.020  1.478
 L5D  C2   C3   aromatic  1.395  0.020  1.395
 L5D  C2   C1   aromatic  1.391  0.020  1.391
 L5D  C3   C11  aromatic  1.396  0.020  1.396
 L5D  C    C1   single    1.525  0.020  1.525
 L5D  C    O    deloc     1.246  0.020  1.246
 L5D  C1   C13  aromatic  1.393  0.020  1.393
 L5D  C11  C12  aromatic  1.387  0.020  1.387
 L5D  C13  C12  aromatic  1.388  0.020  1.388
 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   116.61  3.000
 L5D  C1   C    O    116.57  3.000
 L5D  O1   C    O    126.82  3.000
 L5D  C2   C1   C13  118.68  3.000
 L5D  C13  C1   C    120.90  3.000
 L5D  C2   C1   C    120.42  3.000
 L5D  H7   C10  C8   118.82  3.000
 L5D  H7   C10  C4   119.30  3.000
 L5D  C8   C10  C4   121.87  3.000
 L5D  H8   C11  C3   120.06  3.000
 L5D  H8   C11  C12  119.56  3.000
 L5D  C3   C11  C12  120.36  3.000
 L5D  H9   C12  C13  119.97  3.000
 L5D  H9   C12  C11  119.68  3.000
 L5D  C13  C12  C11  120.34  3.000
 L5D  H10  C13  C12  120.04  3.000
 L5D  H10  C13  C1   119.58  3.000
 L5D  C12  C13  C1   120.38  3.000
 L5D  H    C2   C3   119.62  3.000
 L5D  H    C2   C1   118.60  3.000
 L5D  C3   C2   C1   121.77  3.000
 L5D  C4   C3   C2   120.75  3.000
 L5D  C2   C3   C11  118.47  3.000
 L5D  C4   C3   C11  120.78  3.000
 L5D  C5   C4   C3   120.75  3.000
 L5D  C3   C4   C10  120.75  3.000
 L5D  C5   C4   C10  118.49  3.000
 L5D  H1   C5   C6   119.65  3.000
 L5D  H1   C5   C4   120.06  3.000
 L5D  C6   C5   C4   120.28  3.000
 L5D  H2   C6   C7   119.77  3.000
 L5D  H2   C6   C5   119.82  3.000
 L5D  C7   C6   C5   120.41  3.000
 L5D  H3   C7   C8   119.71  3.000
 L5D  H3   C7   C6   119.82  3.000
 L5D  C8   C7   C6   120.48  3.000
 L5D  C9   C8   C7   121.23  3.000
 L5D  C9   C8   C10  120.30  3.000
 L5D  C7   C8   C10  118.46  3.000
 L5D  H5   C9   H4   107.87  3.000
 L5D  H5   C9   H6   107.70  3.000
 L5D  H4   C9   H6   107.03  3.000
 L5D  H5   C9   C8   111.49  3.000
 L5D  H4   C9   C8   111.43  3.000
 L5D  H6   C9   C8   111.11  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  Var_01    C2   C1   C    O    -179.66  30.0  2
 L5D  Var_02    H6   C9   C8   C10   -64.86  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

