# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 11:28:02 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 4-(2,4-dichlorophenoxy)-2'-methylbiphenyl-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccccc1c2ccc(Oc3ccc(Cl)cc3Cl)c(O)c2
#
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
 JPA  JPA  4-(2,4-dichlorophenoxy)-2'-methylbiphenyl-3-ol  ligand  37  23  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JPA
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
 JPA  CLL2  CL  CL    0  -0.122  -5.6939  -2.2212  -0.8478
 JPA  C4    C   CR6   0  -0.066  -4.3734  -1.1769  -0.4445
 JPA  C3    C   CR16  0  -0.166  -4.6250   0.1582  -0.1719
 JPA  C5    C   CR16  0  -0.200  -3.0853  -1.6809  -0.3955
 JPA  C6    C   CR16  0  -0.350  -2.0321  -0.8398  -0.0711
 JPA  C1    C   CR6   0   0.460  -2.2590   0.5027   0.2015
 JPA  C2    C   CR6   0  -0.147  -3.5649   0.9880   0.1474
 JPA  CLL1  CL  CL    0  -0.094  -3.8570   2.6532   0.4882
 JPA  O1    O   O2    0  -0.489  -1.2945   1.3847   0.5450
 JPA  C9    C   CR6   0   0.224   0.0212   1.0068   0.4339
 JPA  C8    C   CR6   0   0.338   0.6190   0.9703  -0.8269
 JPA  O2    O   OH1   0  -0.615  -0.1531   1.2556  -1.8873
 JPA  C7    C   CR16  0  -0.430   1.9635   0.6325  -0.9200
 JPA  C12   C   CR6   0   0.058   2.7117   0.3366   0.2178
 JPA  C11   C   CR16  0  -0.320   2.0974   0.3881   1.4662
 JPA  C10   C   CR16  0  -0.292   0.7545   0.7191   1.5690
 JPA  C17   C   CR6   0   0.039   4.1527   0.0167   0.0816
 JPA  C18   C   CR6   0   0.069   4.6879  -1.1975   0.5376
 JPA  C23   C   CH3   0  -0.742   3.8344  -2.2641   1.1637
 JPA  C19   C   CR16  0  -0.294   6.0538  -1.4217   0.3759
 JPA  C20   C   CR16  0  -0.250   6.8826  -0.4817  -0.2197
 JPA  C21   C   CR16  0  -0.260   6.3468   0.7123  -0.6786
 JPA  C22   C   CR16  0  -0.283   4.9892   0.9511  -0.5281
 JPA  H3    H   HCR6  0   0.303  -5.6304   0.5541  -0.2085
 JPA  H5    H   HCR6  0   0.291  -2.8921  -2.7236  -0.6056
 JPA  H6    H   HCR6  0   0.295  -1.0309  -1.2475  -0.0274
 JPA  HO2   H   HOH1  0   0.482   0.3559   1.1858  -2.7032
 JPA  H7    H   HCR6  0   0.275   2.4335   0.5904  -1.8969
 JPA  H11   H   HCR6  0   0.259   2.6641   0.1842   2.3647
 JPA  H10   H   HCR6  0   0.275   0.2731   0.7674   2.5377
 JPA  H231  H   HCH3  0   0.249   3.5357  -2.0046   2.1798
 JPA  H232  H   HCH3  0   0.244   2.9182  -2.4369   0.5984
 JPA  H233  H   HCH3  0   0.250   4.3779  -3.2066   1.2180
 JPA  H19   H   HCR6  0   0.249   6.4745  -2.3590   0.7205
 JPA  H20   H   HCR6  0   0.254   7.9397  -0.6863  -0.3299
 JPA  H21   H   HCR6  0   0.255   6.9782   1.4551  -1.1486
 JPA  H22   H   HCR6  0   0.252   4.5691   1.8859  -0.8790

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
 JPA  CLL2  C4    single    1.731  0.020  1.731
 JPA  C4    C3    aromatic  1.386  0.020  1.386
 JPA  C4    C5    aromatic  1.384  0.020  1.384
 JPA  C3    C2    aromatic  1.384  0.020  1.384
 JPA  C3    H3    single    0.930  0.020  1.080
 JPA  C5    C6    aromatic  1.386  0.020  1.386
 JPA  C5    H5    single    0.930  0.020  1.080
 JPA  C6    C1    aromatic  1.389  0.020  1.389
 JPA  C6    H6    single    0.930  0.020  1.080
 JPA  C1    C2    aromatic  1.394  0.020  1.394
 JPA  C1    O1    single    1.351  0.020  1.351
 JPA  C2    CLL1  single    1.725  0.020  1.725
 JPA  O1    C9    single    1.373  0.020  1.373
 JPA  C9    C8    aromatic  1.396  0.020  1.396
 JPA  C9    C10   aromatic  1.382  0.020  1.382
 JPA  C8    O2    single    1.342  0.020  1.342
 JPA  C8    C7    aromatic  1.389  0.020  1.389
 JPA  O2    HO2   single    0.850  0.020  0.980
 JPA  C7    C12   aromatic  1.394  0.020  1.394
 JPA  C7    H7    single    0.930  0.020  1.080
 JPA  C12   C11   aromatic  1.392  0.020  1.392
 JPA  C12   C17   single    1.482  0.020  1.482
 JPA  C11   C10   aromatic  1.387  0.020  1.387
 JPA  C11   H11   single    0.930  0.020  1.080
 JPA  C10   H10   single    0.930  0.020  1.080
 JPA  C17   C18   aromatic  1.403  0.020  1.403
 JPA  C17   C22   aromatic  1.394  0.020  1.394
 JPA  C18   C23   single    1.503  0.020  1.503
 JPA  C18   C19   aromatic  1.394  0.020  1.394
 JPA  C23   H231  single    0.970  0.020  1.090
 JPA  C23   H232  single    0.970  0.020  1.090
 JPA  C23   H233  single    0.970  0.020  1.090
 JPA  C19   C20   aromatic  1.388  0.020  1.388
 JPA  C19   H19   single    0.930  0.020  1.080
 JPA  C20   C21   aromatic  1.387  0.020  1.387
 JPA  C20   H20   single    0.930  0.020  1.080
 JPA  C21   C22   aromatic  1.387  0.020  1.387
 JPA  C21   H21   single    0.930  0.020  1.080
 JPA  C22   H22   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
 JPA  C5    C4   C3    120.85  3.000
 JPA  C5    C4   CLL2  119.90  3.000
 JPA  C3    C4   CLL2  119.24  3.000
 JPA  H3    C3   C2    120.05  3.000
 JPA  H3    C3   C4    120.99  3.000
 JPA  C2    C3   C4    118.96  3.000
 JPA  H5    C5   C6    119.66  3.000
 JPA  H5    C5   C4    120.71  3.000
 JPA  C6    C5   C4    119.63  3.000
 JPA  H6    C6   C1    120.50  3.000
 JPA  H6    C6   C5    118.94  3.000
 JPA  C1    C6   C5    120.56  3.000
 JPA  O1    C1   C2    116.82  3.000
 JPA  O1    C1   C6    124.35  3.000
 JPA  C2    C1   C6    118.81  3.000
 JPA  CLL1  C2   C1    119.15  3.000
 JPA  CLL1  C2   C3    119.66  3.000
 JPA  C1    C2   C3    121.19  3.000
 JPA  C9    O1   C1    118.92  3.000
 JPA  C10   C9   C8    120.62  3.000
 JPA  C10   C9   O1    119.95  3.000
 JPA  C8    C9   O1    119.38  3.000
 JPA  C7    C8   O2    123.73  3.000
 JPA  C7    C8   C9    118.77  3.000
 JPA  O2    C8   C9    117.50  3.000
 JPA  HO2   O2   C8    110.45  3.000
 JPA  H7    C7   C12   119.63  3.000
 JPA  H7    C7   C8    119.27  3.000
 JPA  C12   C7   C8    121.09  3.000
 JPA  C17   C12  C11   121.29  3.000
 JPA  C17   C12  C7    119.52  3.000
 JPA  C11   C12  C7    119.17  3.000
 JPA  H11   C11  C10   119.39  3.000
 JPA  H11   C11  C12   120.44  3.000
 JPA  C10   C11  C12   120.17  3.000
 JPA  H10   C10  C11   120.49  3.000
 JPA  H10   C10  C9    119.33  3.000
 JPA  C11   C10  C9    120.17  3.000
 JPA  C22   C17  C18   119.55  3.000
 JPA  C22   C17  C12   118.60  3.000
 JPA  C18   C17  C12   121.85  3.000
 JPA  C19   C18  C23   119.40  3.000
 JPA  C19   C18  C17   118.38  3.000
 JPA  C23   C18  C17   122.21  3.000
 JPA  H233  C23  H232  107.94  3.000
 JPA  H233  C23  H231  107.23  3.000
 JPA  H232  C23  H231  106.89  3.000
 JPA  H233  C23  C18   110.58  3.000
 JPA  H232  C23  C18   111.95  3.000
 JPA  H231  C23  C18   112.01  3.000
 JPA  H19   C19  C20   119.38  3.000
 JPA  H19   C19  C18   118.87  3.000
 JPA  C20   C19  C18   121.75  3.000
 JPA  H20   C20  C21   120.42  3.000
 JPA  H20   C20  C19   119.93  3.000
 JPA  C21   C20  C19   119.64  3.000
 JPA  H21   C21  C22   120.01  3.000
 JPA  H21   C21  C20   120.62  3.000
 JPA  C22   C21  C20   119.38  3.000
 JPA  H22   C22  C21   119.54  3.000
 JPA  H22   C22  C17   119.16  3.000
 JPA  C21   C22  C17   121.29  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
 JPA  CONST_01  C1    C2   C3   C4      0.00   0.0  0
 JPA  CONST_02  C1    C6   C5   C4      0.00   0.0  0
 JPA  CONST_03  C6    C5   C4   C3      0.00   0.0  0
 JPA  CONST_04  C6    C1   C2   C3      0.00   0.0  0
 JPA  CONST_05  C2    C3   C4   C5      0.00   0.0  0
 JPA  CONST_06  C2    C1   C6   C5      0.00   0.0  0
 JPA  CONST_07  C12   C7   C8   C9      0.00   0.0  0
 JPA  CONST_08  C12   C11  C10  C9      0.00   0.0  0
 JPA  CONST_09  C11   C10  C9   C8      0.00   0.0  0
 JPA  CONST_10  C11   C12  C7   C8      0.00   0.0  0
 JPA  CONST_11  C17   C12  C7   C8    180.00   0.0  0
 JPA  CONST_12  C10   C9   C8   C7      0.00   0.0  0
 JPA  CONST_13  C10   C11  C12  C7      0.00   0.0  0
 JPA  CONST_16  C19   C18  C17  C12   180.00   0.0  0
 JPA  CONST_17  C21   C22  C17  C12   180.00   0.0  0
 JPA  CONST_20  C17   C12  C11  C10   180.00   0.0  0
 JPA  CONST_21  C20   C19  C18  C17     0.00   0.0  0
 JPA  CONST_22  C20   C21  C22  C17     0.00   0.0  0
 JPA  CONST_23  C21   C22  C17  C18     0.00   0.0  0
 JPA  CONST_24  C21   C20  C19  C18     0.00   0.0  0
 JPA  CONST_25  C22   C17  C18  C19     0.00   0.0  0
 JPA  CONST_26  C22   C21  C20  C19     0.00   0.0  0
 JPA  CONST_27  C2    C3   C4   CLL2  180.00   0.0  0
 JPA  CONST_28  C6    C5   C4   CLL2  180.00   0.0  0
 JPA  CONST_29  CLL1  C2   C3   C4    180.00   0.0  0
 JPA  CONST_30  O1    C1   C2   C3    180.00   0.0  0
 JPA  CONST_31  O1    C1   C6   C5    180.00   0.0  0
 JPA  CONST_32  CLL1  C2   C1   C6    180.00   0.0  0
 JPA  CONST_33  C7    C8   C9   O1    180.00   0.0  0
 JPA  CONST_34  C11   C10  C9   O1    180.00   0.0  0
 JPA  CONST_35  C10   C9   C8   O2    180.00   0.0  0
 JPA  CONST_36  C12   C7   C8   O2    180.00   0.0  0
 JPA  CONST_37  C23   C18  C17  C12     0.00   0.0  0
 JPA  CONST_38  C22   C17  C18  C23   180.00   0.0  0
 JPA  CONST_39  C20   C19  C18  C23   180.00   0.0  0
 JPA  CONST_40  H6    C6   C5   C4    180.00   0.0  0
 JPA  CONST_41  H5    C5   C4   C3    180.00   0.0  0
 JPA  CONST_42  H3    C3   C4   C5    180.00   0.0  0
 JPA  CONST_43  H7    C7   C8   C9    180.00   0.0  0
 JPA  CONST_44  H11   C11  C10  C9    180.00   0.0  0
 JPA  CONST_45  H10   C10  C9   C8    180.00   0.0  0
 JPA  CONST_46  H22   C22  C17  C12     0.00   0.0  0
 JPA  CONST_47  H19   C19  C18  C17   180.00   0.0  0
 JPA  CONST_48  H21   C21  C22  C17   180.00   0.0  0
 JPA  CONST_49  H20   C20  C19  C18   180.00   0.0  0
 JPA  Var_01    C8    C9   O1   C1     76.48  30.0  2
 JPA  Var_02    H231  C23  C18  C17   -74.67  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
 JPA  plan-1  CLL2  0.020
 JPA  plan-1  C4    0.020
 JPA  plan-1  C3    0.020
 JPA  plan-1  C5    0.020
 JPA  plan-1  C6    0.020
 JPA  plan-1  C1    0.020
 JPA  plan-1  C2    0.020
 JPA  plan-1  CLL1  0.020
 JPA  plan-1  O1    0.020
 JPA  plan-1  H3    0.020
 JPA  plan-1  H5    0.020
 JPA  plan-1  H6    0.020
 JPA  plan-2  O1    0.020
 JPA  plan-2  C9    0.020
 JPA  plan-2  C8    0.020
 JPA  plan-2  O2    0.020
 JPA  plan-2  C7    0.020
 JPA  plan-2  C12   0.020
 JPA  plan-2  C11   0.020
 JPA  plan-2  C10   0.020
 JPA  plan-2  C17   0.020
 JPA  plan-2  H7    0.020
 JPA  plan-2  H11   0.020
 JPA  plan-2  H10   0.020
 JPA  plan-3  C12   0.020
 JPA  plan-3  C17   0.020
 JPA  plan-3  C18   0.020
 JPA  plan-3  C23   0.020
 JPA  plan-3  C19   0.020
 JPA  plan-3  C20   0.020
 JPA  plan-3  C21   0.020
 JPA  plan-3  C22   0.020
 JPA  plan-3  H19   0.020
 JPA  plan-3  H20   0.020
 JPA  plan-3  H21   0.020
 JPA  plan-3  H22   0.020

