# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 22:04:08 2022
#   Inital geometry file: a 72 line input string
#   Ligand name: biphenyl-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(cc1)c2ccccc2
#
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
 Z7Z  Z7Z  "biphenyl-4-carboxylic acid"  ligand  24  15  .  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_Z7Z
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
 Z7Z  O1    O  OC    -1  -0.586  66.3234  38.1428  28.9318
 Z7Z  C1    C  C      0   0.393  67.4501  38.5117  29.3141
 Z7Z  O2    O  O      0  -0.587  68.2226  37.9033  30.0791
 Z7Z  C2    C  CR6    0  -0.108  67.9394  39.8583  28.7880
 Z7Z  C3    C  CR16   0  -0.276  67.1531  40.6268  27.9334
 Z7Z  C4    C  CR16   0  -0.299  67.5973  41.8495  27.4545
 Z7Z  C5    C  CR16   0  -0.275  69.1877  40.3580  29.1497
 Z7Z  C6    C  CR16   0  -0.299  69.6369  41.5802  28.6748
 Z7Z  C7    C  CR6    0   0.077  68.8493  42.3495  27.8164
 Z7Z  C8    C  CR6    0   0.090  69.3248  43.6518  27.3070
 Z7Z  C9    C  CR16   0  -0.311  69.0432  44.0560  26.0003
 Z7Z  C10   C  CR16   0  -0.310  70.0674  44.5112  28.1195
 Z7Z  C11   C  CR16   0  -0.238  69.4868  45.2804  25.5222
 Z7Z  C12   C  CR16   0  -0.239  70.5107  45.7360  27.6425
 Z7Z  C13   C  CR16   0  -0.266  70.2218  46.1268  26.3417
 Z7Z  H31   H  HCR6   0   0.240  66.1749  40.2667  27.6432
 Z7Z  H41   H  HCR6   0   0.244  66.9511  42.4311  26.8079
 Z7Z  H51   H  HCR6   0   0.240  69.8213  39.7777  29.8073
 Z7Z  H61   H  HCR6   0   0.244  70.6222  41.9294  28.9599
 Z7Z  H91   H  HCR6   0   0.251  68.4878  43.3993  25.3420
 Z7Z  H101  H  HCR6   0   0.251  70.2843  44.2314  29.1431
 Z7Z  H111  H  HCR6   0   0.255  69.2626  45.5697  24.5034
 Z7Z  H121  H  HCR6   0   0.255  71.0774  46.3900  28.2926
 Z7Z  H131  H  HCR6   0   0.255  70.5678  47.0823  25.9694

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
 Z7Z  O1   C1    deloc     1.246  0.020  1.246
 Z7Z  C1   O2    deloc     1.246  0.020  1.246
 Z7Z  C1   C2    single    1.526  0.020  1.526
 Z7Z  C2   C3    aromatic  1.393  0.020  1.393
 Z7Z  C2   C5    aromatic  1.392  0.020  1.392
 Z7Z  C3   C4    aromatic  1.386  0.020  1.386
 Z7Z  C3   H31   single    0.930  0.020  1.080
 Z7Z  C4   C7    aromatic  1.396  0.020  1.396
 Z7Z  C4   H41   single    0.930  0.020  1.080
 Z7Z  C5   C6    aromatic  1.386  0.020  1.386
 Z7Z  C5   H51   single    0.930  0.020  1.080
 Z7Z  C6   C7    aromatic  1.396  0.020  1.396
 Z7Z  C6   H61   single    0.930  0.020  1.080
 Z7Z  C7   C8    single    1.477  0.020  1.477
 Z7Z  C8   C9    aromatic  1.397  0.020  1.397
 Z7Z  C8   C10   aromatic  1.397  0.020  1.397
 Z7Z  C9   C11   aromatic  1.387  0.020  1.387
 Z7Z  C9   H91   single    0.930  0.020  1.080
 Z7Z  C10  C12   aromatic  1.387  0.020  1.387
 Z7Z  C10  H101  single    0.930  0.020  1.080
 Z7Z  C11  C13   aromatic  1.389  0.020  1.389
 Z7Z  C11  H111  single    0.930  0.020  1.080
 Z7Z  C12  C13   aromatic  1.389  0.020  1.389
 Z7Z  C12  H121  single    0.930  0.020  1.080
 Z7Z  C13  H131  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
 Z7Z  C2    C1   O2   116.35  3.000
 Z7Z  C2    C1   O1   116.45  3.000
 Z7Z  O2    C1   O1   127.20  3.000
 Z7Z  C5    C2   C3   117.87  3.000
 Z7Z  C5    C2   C1   120.96  3.000
 Z7Z  C3    C2   C1   121.16  3.000
 Z7Z  H31   C3   C4   119.38  3.000
 Z7Z  H31   C3   C2   119.43  3.000
 Z7Z  C4    C3   C2   121.19  3.000
 Z7Z  H41   C4   C7   119.82  3.000
 Z7Z  H41   C4   C3   119.25  3.000
 Z7Z  C7    C4   C3   120.92  3.000
 Z7Z  H51   C5   C6   119.43  3.000
 Z7Z  H51   C5   C2   119.36  3.000
 Z7Z  C6    C5   C2   121.20  3.000
 Z7Z  H61   C6   C7   119.82  3.000
 Z7Z  H61   C6   C5   119.26  3.000
 Z7Z  C7    C6   C5   120.91  3.000
 Z7Z  C8    C7   C6   121.08  3.000
 Z7Z  C8    C7   C4   121.01  3.000
 Z7Z  C6    C7   C4   117.91  3.000
 Z7Z  C10   C8   C9   118.26  3.000
 Z7Z  C10   C8   C7   120.87  3.000
 Z7Z  C9    C8   C7   120.87  3.000
 Z7Z  H91   C9   C11  119.32  3.000
 Z7Z  H91   C9   C8   119.77  3.000
 Z7Z  C11   C9   C8   120.90  3.000
 Z7Z  H101  C10  C12  119.28  3.000
 Z7Z  H101  C10  C8   119.83  3.000
 Z7Z  C12   C10  C8   120.87  3.000
 Z7Z  H111  C11  C13  120.15  3.000
 Z7Z  H111  C11  C9   119.60  3.000
 Z7Z  C13   C11  C9   120.25  3.000
 Z7Z  H121  C12  C13  120.10  3.000
 Z7Z  H121  C12  C10  119.62  3.000
 Z7Z  C13   C12  C10  120.28  3.000
 Z7Z  H131  C13  C12  120.28  3.000
 Z7Z  H131  C13  C11  120.29  3.000
 Z7Z  C12   C13  C11  119.44  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
 Z7Z  CONST_01  C7    C4   C3   C2      0.00   0.0  0
 Z7Z  CONST_02  C7    C6   C5   C2      0.00   0.0  0
 Z7Z  CONST_03  C6    C5   C2   C3      0.00   0.0  0
 Z7Z  CONST_04  C6    C7   C4   C3      0.00   0.0  0
 Z7Z  CONST_05  C8    C7   C4   C3    180.00   0.0  0
 Z7Z  CONST_06  C5    C2   C3   C4      0.00   0.0  0
 Z7Z  CONST_07  C5    C6   C7   C4      0.00   0.0  0
 Z7Z  CONST_10  C8    C7   C6   C5    180.00   0.0  0
 Z7Z  CONST_13  C11   C9   C8   C7    180.00   0.0  0
 Z7Z  CONST_14  C12   C10  C8   C7    180.00   0.0  0
 Z7Z  CONST_15  C13   C11  C9   C8      0.00   0.0  0
 Z7Z  CONST_16  C13   C12  C10  C8      0.00   0.0  0
 Z7Z  CONST_17  C12   C10  C8   C9      0.00   0.0  0
 Z7Z  CONST_18  C12   C13  C11  C9      0.00   0.0  0
 Z7Z  CONST_19  C11   C9   C8   C10     0.00   0.0  0
 Z7Z  CONST_20  C11   C13  C12  C10     0.00   0.0  0
 Z7Z  CONST_21  C4    C3   C2   C1    180.00   0.0  0
 Z7Z  CONST_22  C6    C5   C2   C1    180.00   0.0  0
 Z7Z  CONST_23  H41   C4   C3   C2    180.00   0.0  0
 Z7Z  CONST_24  H61   C6   C5   C2    180.00   0.0  0
 Z7Z  CONST_25  H51   C5   C2   C3    180.00   0.0  0
 Z7Z  CONST_26  H61   C6   C7   C4    180.00   0.0  0
 Z7Z  CONST_27  H31   C3   C2   C5    180.00   0.0  0
 Z7Z  CONST_28  H41   C4   C7   C6    180.00   0.0  0
 Z7Z  CONST_29  H31   C3   C4   C7    180.00   0.0  0
 Z7Z  CONST_30  H51   C5   C6   C7    180.00   0.0  0
 Z7Z  CONST_31  H91   C9   C8   C7      0.00   0.0  0
 Z7Z  CONST_32  H101  C10  C8   C7      0.00   0.0  0
 Z7Z  CONST_33  H41   C4   C7   C8      0.00   0.0  0
 Z7Z  CONST_34  H61   C6   C7   C8      0.00   0.0  0
 Z7Z  CONST_35  H111  C11  C9   C8    180.00   0.0  0
 Z7Z  CONST_36  H121  C12  C10  C8    180.00   0.0  0
 Z7Z  CONST_37  H101  C10  C8   C9    180.00   0.0  0
 Z7Z  CONST_38  H131  C13  C11  C9    180.00   0.0  0
 Z7Z  CONST_39  H91   C9   C8   C10   180.00   0.0  0
 Z7Z  CONST_40  H131  C13  C12  C10   180.00   0.0  0
 Z7Z  CONST_41  H121  C12  C13  C11   180.00   0.0  0
 Z7Z  CONST_42  H111  C11  C13  C12   180.00   0.0  0
 Z7Z  CONST_43  H91   C9   C11  C13   180.00   0.0  0
 Z7Z  CONST_44  H101  C10  C12  C13   180.00   0.0  0
 Z7Z  Var_01    C3    C2   C1   O1      0.41  30.0  2
 Z7Z  Var_02    C5    C2   C1   O1   -179.67  30.0  2
 Z7Z  Var_03    C3    C2   C1   O2   -179.57  30.0  2
 Z7Z  Var_04    C5    C2   C1   O2      0.35  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
 Z7Z  plan-1  C1    0.020
 Z7Z  plan-1  C2    0.020
 Z7Z  plan-1  C3    0.020
 Z7Z  plan-1  C4    0.020
 Z7Z  plan-1  C5    0.020
 Z7Z  plan-1  C6    0.020
 Z7Z  plan-1  C7    0.020
 Z7Z  plan-1  C8    0.020
 Z7Z  plan-1  H31   0.020
 Z7Z  plan-1  H41   0.020
 Z7Z  plan-1  H51   0.020
 Z7Z  plan-1  H61   0.020
 Z7Z  plan-2  C7    0.020
 Z7Z  plan-2  C8    0.020
 Z7Z  plan-2  C9    0.020
 Z7Z  plan-2  C10   0.020
 Z7Z  plan-2  C11   0.020
 Z7Z  plan-2  C12   0.020
 Z7Z  plan-2  C13   0.020
 Z7Z  plan-2  H91   0.020
 Z7Z  plan-2  H101  0.020
 Z7Z  plan-2  H111  0.020
 Z7Z  plan-2  H121  0.020
 Z7Z  plan-2  H131  0.020
 Z7Z  plan-3  O1    0.020
 Z7Z  plan-3  C1    0.020
 Z7Z  plan-3  O2    0.020
 Z7Z  plan-3  C2    0.020

