# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 09:22:04 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 2-(2,4-dichlorophenoxy)-5-(2-phenylethyl)phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc(CCc2ccccc2)ccc1Oc3ccc(Cl)cc3Cl
#
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
 JPJ  JPJ  2-(2,4-dichlorophenoxy)-5-(2-phenylethyl)phenol  ligand  40  24  .  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_JPJ
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
 JPJ  CL20  CL  CL    0  -0.095  -6.1816  -5.0286  2.1498
 JPJ  C15   C   CR6   0  -0.148  -5.9472  -3.3367  2.3910
 JPJ  C16   C   CR16  0  -0.167  -7.0236  -2.4740  2.2855
 JPJ  C17   C   CR6   0  -0.066  -6.8184  -1.1178  2.4828
 JPJ  CL21  CL  CL    0  -0.122  -8.1607  -0.0318  2.3556
 JPJ  C22   C   CR16  0  -0.200  -5.5582  -0.6267  2.7768
 JPJ  C19   C   CR16  0  -0.353  -4.4872  -1.5014  2.8774
 JPJ  C14   C   CR6   0   0.460  -4.6688  -2.8647  2.6873
 JPJ  O13   O   O2    0  -0.489  -3.6801  -3.7824  2.7433
 JPJ  C2    C   CR6   0   0.221  -2.4447  -3.4080  3.2160
 JPJ  C1    C   CR6   0   0.333  -2.2528  -3.2683  4.5922
 JPJ  O22   O   OH1   0  -0.615  -3.3217  -3.4436  5.3865
 JPJ  C3    C   CR16  0  -0.292  -1.3924  -3.2369  2.3385
 JPJ  C4    C   CR16  0  -0.342  -0.1272  -2.9316  2.8220
 JPJ  C5    C   CR6   0   0.144   0.0884  -2.7895  4.1884
 JPJ  C6    C   CR16  0  -0.437  -0.9830  -2.9580  5.0626
 JPJ  C7    C   CH2   0  -0.509   1.4436  -2.4161  4.7180
 JPJ  C18   C   CH2   0  -0.508   1.5569  -0.9095  4.9986
 JPJ  C28   C   CR6   0   0.133   2.9256  -0.5420  5.4974
 JPJ  C27   C   CR16  0  -0.311   3.2044  -0.5134  6.8620
 JPJ  C26   C   CR16  0  -0.241   4.4817  -0.2217  7.3232
 JPJ  C25   C   CR16  0  -0.273   5.5039   0.0454  6.4218
 JPJ  C24   C   CR16  0  -0.241   5.2382   0.0200  5.0584
 JPJ  C23   C   CR16  0  -0.309   3.9595  -0.2718  4.6030
 JPJ  H16   H   HCR6  0   0.303  -8.0063  -2.8609  2.0546
 JPJ  H22   H   HCR6  0   0.290  -5.3987   0.4320  2.9256
 JPJ  H19   H   HCR6  0   0.297  -3.5056  -1.1041  3.1000
 JPJ  HO22  H   HOH1  0   0.481  -3.0780  -3.3096  6.3095
 JPJ  H3    H   HCR6  0   0.273  -1.5637  -3.3533  1.2757
 JPJ  H4    H   HCR6  0   0.252   0.6938  -2.8077  2.1274
 JPJ  H6    H   HCR6  0   0.271  -0.8254  -2.8546  6.1320
 JPJ  H71   H   HCH2  0   0.253   1.6569  -2.9670  5.6373
 JPJ  H72   H   HCH2  0   0.253   2.2111  -2.7029  3.9956
 JPJ  H181  H   HCH2  0   0.251   0.8019  -0.6235  5.7349
 JPJ  H182  H   HCH2  0   0.252   1.3278  -0.3591  4.0829
 JPJ  H27   H   HCR6  0   0.246   2.4118  -0.7166  7.5733
 JPJ  H26   H   HCR6  0   0.253   4.6772  -0.2004  8.3878
 JPJ  H25   H   HCR6  0   0.253   6.4994   0.2758  6.7788
 JPJ  H24   H   HCR6  0   0.253   6.0275   0.2303  4.3478
 JPJ  H23   H   HCR6  0   0.246   3.7610  -0.2876  3.5371

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
 JPJ  CL20  C15   single    1.725  0.020  1.725
 JPJ  C15   C16   aromatic  1.383  0.020  1.383
 JPJ  C15   C14   aromatic  1.395  0.020  1.395
 JPJ  C16   C17   aromatic  1.386  0.020  1.386
 JPJ  C16   H16   single    0.930  0.020  1.080
 JPJ  C17   CL21  single    1.731  0.020  1.731
 JPJ  C17   C22   aromatic  1.384  0.020  1.384
 JPJ  C22   C19   aromatic  1.386  0.020  1.386
 JPJ  C22   H22   single    0.930  0.020  1.080
 JPJ  C19   C14   aromatic  1.388  0.020  1.388
 JPJ  C19   H19   single    0.930  0.020  1.080
 JPJ  C14   O13   single    1.350  0.020  1.350
 JPJ  O13   C2    single    1.375  0.020  1.375
 JPJ  C2    C1    aromatic  1.396  0.020  1.396
 JPJ  C2    C3    aromatic  1.381  0.020  1.381
 JPJ  C1    O22   single    1.343  0.020  1.343
 JPJ  C1    C6    aromatic  1.389  0.020  1.389
 JPJ  O22   HO22  single    0.850  0.020  0.980
 JPJ  C3    C4    aromatic  1.388  0.020  1.388
 JPJ  C3    H3    single    0.930  0.020  1.080
 JPJ  C4    C5    aromatic  1.391  0.020  1.391
 JPJ  C4    H4    single    0.930  0.020  1.080
 JPJ  C5    C6    aromatic  1.393  0.020  1.393
 JPJ  C5    C7    single    1.502  0.020  1.502
 JPJ  C6    H6    single    0.930  0.020  1.080
 JPJ  C7    C18   single    1.537  0.020  1.537
 JPJ  C7    H71   single    0.970  0.020  1.090
 JPJ  C7    H72   single    0.970  0.020  1.090
 JPJ  C18   C28   single    1.502  0.020  1.502
 JPJ  C18   H181  single    0.970  0.020  1.090
 JPJ  C18   H182  single    0.970  0.020  1.090
 JPJ  C28   C27   aromatic  1.393  0.020  1.393
 JPJ  C28   C23   aromatic  1.394  0.020  1.394
 JPJ  C27   C26   aromatic  1.389  0.020  1.389
 JPJ  C27   H27   single    0.930  0.020  1.080
 JPJ  C26   C25   aromatic  1.389  0.020  1.389
 JPJ  C26   H26   single    0.930  0.020  1.080
 JPJ  C25   C24   aromatic  1.389  0.020  1.389
 JPJ  C25   H25   single    0.930  0.020  1.080
 JPJ  C24   C23   aromatic  1.388  0.020  1.388
 JPJ  C24   H24   single    0.930  0.020  1.080
 JPJ  C23   H23   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
 JPJ  C14   C15  C16   121.23  3.000
 JPJ  C14   C15  CL20  119.09  3.000
 JPJ  C16   C15  CL20  119.68  3.000
 JPJ  H16   C16  C17   121.01  3.000
 JPJ  H16   C16  C15   120.03  3.000
 JPJ  C17   C16  C15   118.96  3.000
 JPJ  C22   C17  CL21  119.93  3.000
 JPJ  C22   C17  C16   120.82  3.000
 JPJ  CL21  C17  C16   119.25  3.000
 JPJ  H22   C22  C19   119.60  3.000
 JPJ  H22   C22  C17   120.74  3.000
 JPJ  C19   C22  C17   119.66  3.000
 JPJ  H19   C19  C14   120.49  3.000
 JPJ  H19   C19  C22   118.95  3.000
 JPJ  C14   C19  C22   120.57  3.000
 JPJ  O13   C14  C19   124.47  3.000
 JPJ  O13   C14  C15   116.75  3.000
 JPJ  C19   C14  C15   118.77  3.000
 JPJ  C2    O13  C14   119.15  3.000
 JPJ  C3    C2   C1    120.61  3.000
 JPJ  C3    C2   O13   120.00  3.000
 JPJ  C1    C2   O13   119.32  3.000
 JPJ  C6    C1   O22   123.80  3.000
 JPJ  C6    C1   C2    118.79  3.000
 JPJ  O22   C1   C2    117.41  3.000
 JPJ  HO22  O22  C1    110.29  3.000
 JPJ  H3    C3   C4    120.64  3.000
 JPJ  H3    C3   C2    119.33  3.000
 JPJ  C4    C3   C2    120.03  3.000
 JPJ  H4    C4   C5    120.08  3.000
 JPJ  H4    C4   C3    119.53  3.000
 JPJ  C5    C4   C3    120.39  3.000
 JPJ  C7    C5   C6    120.18  3.000
 JPJ  C7    C5   C4    120.78  3.000
 JPJ  C6    C5   C4    119.02  3.000
 JPJ  H6    C6   C5    119.66  3.000
 JPJ  H6    C6   C1    119.17  3.000
 JPJ  C5    C6   C1    121.16  3.000
 JPJ  H72   C7   H71   106.67  3.000
 JPJ  H72   C7   C18   109.05  3.000
 JPJ  H71   C7   C18   109.04  3.000
 JPJ  H72   C7   C5    109.60  3.000
 JPJ  H71   C7   C5    110.33  3.000
 JPJ  C18   C7   C5    112.00  3.000
 JPJ  H182  C18  H181  106.74  3.000
 JPJ  H182  C18  C28   110.24  3.000
 JPJ  H181  C18  C28   109.98  3.000
 JPJ  H182  C18  C7    108.99  3.000
 JPJ  H181  C18  C7    109.19  3.000
 JPJ  C28   C18  C7    111.57  3.000
 JPJ  C23   C28  C27   118.44  3.000
 JPJ  C23   C28  C18   120.68  3.000
 JPJ  C27   C28  C18   120.84  3.000
 JPJ  H27   C27  C26   119.60  3.000
 JPJ  H27   C27  C28   119.50  3.000
 JPJ  C26   C27  C28   120.90  3.000
 JPJ  H26   C26  C25   120.10  3.000
 JPJ  H26   C26  C27   119.78  3.000
 JPJ  C25   C26  C27   120.12  3.000
 JPJ  H25   C25  C24   120.23  3.000
 JPJ  H25   C25  C26   120.25  3.000
 JPJ  C24   C25  C26   119.51  3.000
 JPJ  H24   C24  C23   119.80  3.000
 JPJ  H24   C24  C25   120.08  3.000
 JPJ  C23   C24  C25   120.13  3.000
 JPJ  H23   C23  C24   119.61  3.000
 JPJ  H23   C23  C28   119.49  3.000
 JPJ  C24   C23  C28   120.90  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
 JPJ  CONST_01  C22   C17  C16  C15      0.00   0.0  0
 JPJ  CONST_02  C22   C19  C14  C15      0.00   0.0  0
 JPJ  CONST_03  C19   C14  C15  C16      0.00   0.0  0
 JPJ  CONST_04  C19   C22  C17  C16      0.00   0.0  0
 JPJ  CONST_05  C14   C15  C16  C17      0.00   0.0  0
 JPJ  CONST_06  C14   C19  C22  C17      0.00   0.0  0
 JPJ  CONST_07  C5    C6   C1   C2       0.00   0.0  0
 JPJ  CONST_08  C5    C4   C3   C2       0.00   0.0  0
 JPJ  CONST_09  C4    C3   C2   C1       0.00   0.0  0
 JPJ  CONST_10  C4    C5   C6   C1       0.00   0.0  0
 JPJ  CONST_11  C6    C1   C2   C3       0.00   0.0  0
 JPJ  CONST_12  C6    C5   C4   C3       0.00   0.0  0
 JPJ  CONST_13  C25   C26  C27  C28      0.00   0.0  0
 JPJ  CONST_14  C25   C24  C23  C28      0.00   0.0  0
 JPJ  CONST_15  C24   C23  C28  C27      0.00   0.0  0
 JPJ  CONST_16  C24   C25  C26  C27      0.00   0.0  0
 JPJ  CONST_17  C23   C28  C27  C26      0.00   0.0  0
 JPJ  CONST_18  C23   C24  C25  C26      0.00   0.0  0
 JPJ  CONST_19  C17   C16  C15  CL20   180.00   0.0  0
 JPJ  CONST_20  C19   C14  C15  CL20   180.00   0.0  0
 JPJ  CONST_21  CL21  C17  C16  C15    180.00   0.0  0
 JPJ  CONST_22  O13   C14  C15  C16    180.00   0.0  0
 JPJ  CONST_23  C19   C22  C17  CL21   180.00   0.0  0
 JPJ  CONST_24  O13   C14  C19  C22    180.00   0.0  0
 JPJ  CONST_25  C6    C1   C2   O13    180.00   0.0  0
 JPJ  CONST_26  C4    C3   C2   O13    180.00   0.0  0
 JPJ  CONST_27  C7    C5   C6   C1     180.00   0.0  0
 JPJ  CONST_28  C3    C2   C1   O22    180.00   0.0  0
 JPJ  CONST_29  C5    C6   C1   O22    180.00   0.0  0
 JPJ  CONST_30  C7    C5   C4   C3     180.00   0.0  0
 JPJ  CONST_31  C26   C27  C28  C18    180.00   0.0  0
 JPJ  CONST_32  C24   C23  C28  C18    180.00   0.0  0
 JPJ  CONST_33  H19   C19  C14  C15    180.00   0.0  0
 JPJ  CONST_34  H22   C22  C17  C16    180.00   0.0  0
 JPJ  CONST_35  H16   C16  C17  C22    180.00   0.0  0
 JPJ  CONST_36  H6    C6   C1   C2     180.00   0.0  0
 JPJ  CONST_37  H4    C4   C3   C2     180.00   0.0  0
 JPJ  CONST_38  H3    C3   C2   C1     180.00   0.0  0
 JPJ  CONST_39  H26   C26  C27  C28    180.00   0.0  0
 JPJ  CONST_40  H24   C24  C23  C28    180.00   0.0  0
 JPJ  CONST_41  H23   C23  C28  C27    180.00   0.0  0
 JPJ  CONST_42  H25   C25  C26  C27    180.00   0.0  0
 JPJ  CONST_43  H27   C27  C26  C25    180.00   0.0  0
 JPJ  Var_01    C1    C2   O13  C14     77.48  30.0  2
 JPJ  Var_02    C18   C7   C5   C4      97.17  30.0  2
 JPJ  Var_03    C28   C18  C7   C5    -178.68  30.0  3
 JPJ  Var_04    C27   C28  C18  C7     -91.81  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
 JPJ  plan-1  CL20  0.020
 JPJ  plan-1  C15   0.020
 JPJ  plan-1  C16   0.020
 JPJ  plan-1  C17   0.020
 JPJ  plan-1  CL21  0.020
 JPJ  plan-1  C22   0.020
 JPJ  plan-1  C19   0.020
 JPJ  plan-1  C14   0.020
 JPJ  plan-1  O13   0.020
 JPJ  plan-1  H16   0.020
 JPJ  plan-1  H22   0.020
 JPJ  plan-1  H19   0.020
 JPJ  plan-2  O13   0.020
 JPJ  plan-2  C2    0.020
 JPJ  plan-2  C1    0.020
 JPJ  plan-2  O22   0.020
 JPJ  plan-2  C3    0.020
 JPJ  plan-2  C4    0.020
 JPJ  plan-2  C5    0.020
 JPJ  plan-2  C6    0.020
 JPJ  plan-2  C7    0.020
 JPJ  plan-2  H3    0.020
 JPJ  plan-2  H4    0.020
 JPJ  plan-2  H6    0.020
 JPJ  plan-3  C18   0.020
 JPJ  plan-3  C28   0.020
 JPJ  plan-3  C27   0.020
 JPJ  plan-3  C26   0.020
 JPJ  plan-3  C25   0.020
 JPJ  plan-3  C24   0.020
 JPJ  plan-3  C23   0.020
 JPJ  plan-3  H27   0.020
 JPJ  plan-3  H26   0.020
 JPJ  plan-3  H25   0.020
 JPJ  plan-3  H24   0.020
 JPJ  plan-3  H23   0.020

