# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 09:10:08 2022
#   Inital geometry file: a 81 line input string
#   Ligand name: [1,1'-biphenyl]-3,4'-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(cc1)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
 VAJ  VAJ  "[1,1'-biphenyl]-3,4'-dicarboxylic acid"  ligand  26  18  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_VAJ
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
 VAJ  C1   C  CR6    0  -0.108  39.2101  -41.5838  11.1721
 VAJ  C2   C  CR16   0  -0.277  38.8244  -41.6437  12.5090
 VAJ  C3   C  CR16   0  -0.300  38.3087  -40.5326  13.1580
 VAJ  C4   C  CR6    0   0.077  38.1673  -39.3131  12.4934
 VAJ  C7   C  CR6    0   0.110  37.6051  -38.1313  13.1780
 VAJ  C9   C  CR16   0  -0.228  37.5699  -35.7517  13.5816
 VAJ  C10  C  CR16   0  -0.307  36.5137  -35.9069  14.4685
 VAJ  C    C  C      0   0.391  39.7607  -42.8116  10.4532
 VAJ  O    O  O      0  -0.587  40.0244  -42.6751   9.2430
 VAJ  C11  C  CR6    0  -0.077  35.9877  -37.1708  14.7253
 VAJ  C12  C  CR16   0  -0.363  36.5452  -38.2665  14.0749
 VAJ  C5   C  CR16   0  -0.300  38.5638  -39.2503  11.1565
 VAJ  C6   C  CR16   0  -0.275  39.0715  -40.3663  10.5102
 VAJ  C8   C  CR16   0  -0.322  38.1137  -36.8535  12.9380
 VAJ  O1   O  OC    -1  -0.588  39.8977  -43.8427  11.1396
 VAJ  O2   O  O      0  -0.587  34.3778  -36.3225  16.2316
 VAJ  O3   O  OC    -1  -0.586  34.4075  -38.5208  15.8515
 VAJ  H1   H  HCR6   0   0.238  38.9305  -42.5739  13.0516
 VAJ  H2   H  HCR6   0   0.242  38.0293  -40.6114  14.2020
 VAJ  H3   H  HCR6   0   0.245  37.9782  -34.7666  13.3927
 VAJ  H4   H  HCR6   0   0.240  36.0933  -35.0424  14.9649
 VAJ  H5   H  HCR6   0   0.236  36.1243  -39.2470  14.2576
 VAJ  H6   H  HCR6   0   0.242  38.4509  -38.3248  10.6045
 VAJ  H7   H  HCR6   0   0.238  39.3567  -40.2922   9.4690
 VAJ  H8   H  HCR6   0   0.247  38.9483  -36.7211  12.2602
 VAJ  C13  C  C      0   0.395  34.8170  -37.3550  15.6908

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
 VAJ  O    C    deloc     1.246  0.020  1.246
 VAJ  C    O1   deloc     1.246  0.020  1.246
 VAJ  C    C1   single    1.526  0.020  1.526
 VAJ  C6   C1   aromatic  1.393  0.020  1.393
 VAJ  C6   C5   aromatic  1.386  0.020  1.386
 VAJ  C1   C2   aromatic  1.393  0.020  1.393
 VAJ  C5   C4   aromatic  1.396  0.020  1.396
 VAJ  C2   C3   aromatic  1.386  0.020  1.386
 VAJ  C4   C3   aromatic  1.396  0.020  1.396
 VAJ  C4   C7   single    1.477  0.020  1.477
 VAJ  C8   C7   aromatic  1.396  0.020  1.396
 VAJ  C8   C9   aromatic  1.387  0.020  1.387
 VAJ  C7   C12  aromatic  1.395  0.020  1.395
 VAJ  C9   C10  aromatic  1.388  0.020  1.388
 VAJ  C12  C11  aromatic  1.391  0.020  1.391
 VAJ  C10  C11  aromatic  1.393  0.020  1.393
 VAJ  C11  C13  single    1.529  0.020  1.529
 VAJ  C13  O2   deloc     1.246  0.020  1.246
 VAJ  C13  O3   deloc     1.246  0.020  1.246
 VAJ  C2   H1   single    0.930  0.020  1.080
 VAJ  C3   H2   single    0.930  0.020  1.080
 VAJ  C9   H3   single    0.930  0.020  1.080
 VAJ  C10  H4   single    0.930  0.020  1.080
 VAJ  C12  H5   single    0.930  0.020  1.080
 VAJ  C5   H6   single    0.930  0.020  1.080
 VAJ  C6   H7   single    0.930  0.020  1.080
 VAJ  C8   H8   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
 VAJ  C6   C1   C    121.03  3.000
 VAJ  C6   C1   C2   117.79  3.000
 VAJ  C    C1   C2   121.18  3.000
 VAJ  H1   C2   C3   119.39  3.000
 VAJ  H1   C2   C1   119.42  3.000
 VAJ  C3   C2   C1   121.20  3.000
 VAJ  H2   C3   C4   119.74  3.000
 VAJ  H2   C3   C2   119.26  3.000
 VAJ  C4   C3   C2   120.99  3.000
 VAJ  C5   C4   C7   121.08  3.000
 VAJ  C7   C4   C3   121.12  3.000
 VAJ  C5   C4   C3   117.80  3.000
 VAJ  C8   C7   C12  118.42  3.000
 VAJ  C12  C7   C4   120.65  3.000
 VAJ  C8   C7   C4   120.93  3.000
 VAJ  H3   C9   C8   119.59  3.000
 VAJ  H3   C9   C10  120.01  3.000
 VAJ  C8   C9   C10  120.40  3.000
 VAJ  H4   C10  C11  119.58  3.000
 VAJ  H4   C10  C9   119.97  3.000
 VAJ  C11  C10  C9   120.45  3.000
 VAJ  O1   C    O    127.04  3.000
 VAJ  O1   C    C1   116.49  3.000
 VAJ  O    C    C1   116.48  3.000
 VAJ  C12  C11  C13  120.49  3.000
 VAJ  C13  C11  C10  121.00  3.000
 VAJ  C12  C11  C10  118.50  3.000
 VAJ  H5   C12  C11  118.60  3.000
 VAJ  H5   C12  C7   119.45  3.000
 VAJ  C11  C12  C7   121.93  3.000
 VAJ  H6   C5   C6   119.23  3.000
 VAJ  H6   C5   C4   119.78  3.000
 VAJ  C6   C5   C4   120.97  3.000
 VAJ  H7   C6   C5   119.35  3.000
 VAJ  H7   C6   C1   119.40  3.000
 VAJ  C5   C6   C1   121.24  3.000
 VAJ  H8   C8   C9   119.69  3.000
 VAJ  H8   C8   C7   120.01  3.000
 VAJ  C9   C8   C7   120.29  3.000
 VAJ  O3   C13  O2   127.13  3.000
 VAJ  O3   C13  C11  116.48  3.000
 VAJ  O2   C13  C11  116.39  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
 VAJ  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 VAJ  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 VAJ  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 VAJ  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 VAJ  CONST_05  C7   C4   C3   C2   180.00   0.0  0
 VAJ  CONST_06  C6   C1   C2   C3     0.00   0.0  0
 VAJ  CONST_07  C6   C5   C4   C3     0.00   0.0  0
 VAJ  CONST_10  C9   C8   C7   C4   180.00   0.0  0
 VAJ  CONST_11  C11  C12  C7   C4   180.00   0.0  0
 VAJ  CONST_12  C6   C5   C4   C7   180.00   0.0  0
 VAJ  CONST_13  C10  C9   C8   C7     0.00   0.0  0
 VAJ  CONST_14  C10  C11  C12  C7     0.00   0.0  0
 VAJ  CONST_15  C12  C7   C8   C9     0.00   0.0  0
 VAJ  CONST_16  C12  C11  C10  C9     0.00   0.0  0
 VAJ  CONST_17  C8   C7   C12  C11    0.00   0.0  0
 VAJ  CONST_18  C8   C9   C10  C11    0.00   0.0  0
 VAJ  CONST_21  C    C1   C2   C3   180.00   0.0  0
 VAJ  CONST_22  C13  C11  C12  C7   180.00   0.0  0
 VAJ  CONST_23  C13  C11  C10  C9   180.00   0.0  0
 VAJ  CONST_24  C5   C6   C1   C    180.00   0.0  0
 VAJ  CONST_25  H6   C5   C6   C1   180.00   0.0  0
 VAJ  CONST_26  H2   C3   C2   C1   180.00   0.0  0
 VAJ  CONST_27  H7   C6   C1   C2   180.00   0.0  0
 VAJ  CONST_28  H6   C5   C4   C3   180.00   0.0  0
 VAJ  CONST_29  H7   C6   C5   C4   180.00   0.0  0
 VAJ  CONST_30  H1   C2   C3   C4   180.00   0.0  0
 VAJ  CONST_31  H8   C8   C7   C4     0.00   0.0  0
 VAJ  CONST_32  H5   C12  C7   C4     0.00   0.0  0
 VAJ  CONST_33  H6   C5   C4   C7     0.00   0.0  0
 VAJ  CONST_34  H2   C3   C4   C7     0.00   0.0  0
 VAJ  CONST_35  H3   C9   C8   C7   180.00   0.0  0
 VAJ  CONST_36  H8   C8   C9   C10  180.00   0.0  0
 VAJ  CONST_37  H5   C12  C11  C10  180.00   0.0  0
 VAJ  CONST_38  H3   C9   C10  C11  180.00   0.0  0
 VAJ  CONST_39  H8   C8   C7   C12  180.00   0.0  0
 VAJ  CONST_40  H4   C10  C11  C12  180.00   0.0  0
 VAJ  CONST_41  H2   C3   C4   C5   180.00   0.0  0
 VAJ  CONST_42  H1   C2   C1   C6   180.00   0.0  0
 VAJ  CONST_43  H5   C12  C7   C8   180.00   0.0  0
 VAJ  CONST_44  H4   C10  C9   C8   180.00   0.0  0
 VAJ  Var_01    O    C    C1   C2   177.00  30.0  3
 VAJ  Var_02    O1   C    C1   C2    -2.98  30.0  3
 VAJ  Var_03    O2   C13  C11  C10   -0.52  30.0  2
 VAJ  Var_04    O3   C13  C11  C10  179.53  30.0  2
 VAJ  Var_05    C6   C1   C    O     -2.74  30.0  2
 VAJ  Var_06    O2   C13  C11  C12  179.96  30.0  2
 VAJ  Var_07    O3   C13  C11  C12    0.01  30.0  2
 VAJ  Var_08    O1   C    C1   C6   177.29  30.0  3

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
 VAJ  plan-1  C1   0.020
 VAJ  plan-1  C2   0.020
 VAJ  plan-1  C3   0.020
 VAJ  plan-1  C4   0.020
 VAJ  plan-1  C7   0.020
 VAJ  plan-1  C    0.020
 VAJ  plan-1  C5   0.020
 VAJ  plan-1  C6   0.020
 VAJ  plan-1  H1   0.020
 VAJ  plan-1  H2   0.020
 VAJ  plan-1  H6   0.020
 VAJ  plan-1  H7   0.020
 VAJ  plan-2  C4   0.020
 VAJ  plan-2  C7   0.020
 VAJ  plan-2  C9   0.020
 VAJ  plan-2  C10  0.020
 VAJ  plan-2  C11  0.020
 VAJ  plan-2  C12  0.020
 VAJ  plan-2  C8   0.020
 VAJ  plan-2  H3   0.020
 VAJ  plan-2  H4   0.020
 VAJ  plan-2  H5   0.020
 VAJ  plan-2  H8   0.020
 VAJ  plan-2  C13  0.020
 VAJ  plan-3  C1   0.020
 VAJ  plan-3  C    0.020
 VAJ  plan-3  O    0.020
 VAJ  plan-3  O1   0.020
 VAJ  plan-4  C11  0.020
 VAJ  plan-4  O2   0.020
 VAJ  plan-4  O3   0.020
 VAJ  plan-4  C13  0.020

