# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 15:44:26 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 2-(2,4-dichlorophenoxy)-5-(3-phenylpropyl)phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc(CCCc2ccccc2)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
 JPN  JPN  2-(2,4-dichlorophenoxy)-5-(3-phenylpropyl)phenol  ligand  43  25  .  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_JPN
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
 JPN  CL24  CL  CL    0  -0.095   5.3362   3.2844  -2.8500
 JPN  C18   C   CR6   0  -0.148   6.5700   3.0664  -1.6647
 JPN  C19   C   CR16  0  -0.167   7.8717   3.4344  -1.9555
 JPN  C17   C   CR6   0   0.460   6.2335   2.5184  -0.4275
 JPN  C22   C   CR16  0  -0.352   7.2333   2.3429   0.5200
 JPN  C21   C   CR16  0  -0.200   8.5409   2.7094   0.2422
 JPN  C20   C   CR6   0  -0.067   8.8513   3.2531  -0.9923
 JPN  CL25  CL  CL    0  -0.122  10.4823   3.7127  -1.3478
 JPN  O16   O   O2    0  -0.489   4.9419   2.1687  -0.2452
 JPN  C13   C   CR6   0   0.218   4.5142   1.8397   1.0196
 JPN  C14   C   CR16  0  -0.291   4.2616   0.5216   1.3437
 JPN  C15   C   CR16  0  -0.347   3.7666   0.1975   2.6004
 JPN  C10   C   CR6   0   0.147   3.5275   1.1928   3.5413
 JPN  C11   C   CR16  0  -0.438   3.7892   2.5188   3.2018
 JPN  C12   C   CR6   0   0.335   4.2815   2.8570   1.9481
 JPN  O23   O   OH1   0  -0.615   4.5555   4.1157   1.5671
 JPN  C9    C   CH2   0  -0.511   3.0375   0.8507   4.9199
 JPN  C8    C   CH2   0  -0.412   4.1617   0.8884   5.9553
 JPN  C7    C   CH2   0  -0.510   3.6789   0.4959   7.3521
 JPN  C3    C   CR6   0   0.137   4.7849   0.5695   8.3666
 JPN  C4    C   CR16  0  -0.314   5.5905  -0.5368   8.6286
 JPN  C5    C   CR16  0  -0.240   6.6437  -0.4547   9.5305
 JPN  C6    C   CR16  0  -0.275   6.9088   0.7406  10.1865
 JPN  C1    C   CR16  0  -0.240   6.1121   1.8504   9.9349
 JPN  C2    C   CR16  0  -0.312   5.0609   1.7628   9.0319
 JPN  H19   H   HCR6  0   0.302   8.1117   3.8593  -2.9203
 JPN  H22   H   HCR6  0   0.297   7.0021   1.9116   1.4851
 JPN  H21   H   HCR6  0   0.290   9.3076   2.5655   0.9907
 JPN  H14   H   HCR6  0   0.272   4.4444  -0.2506   0.6070
 JPN  H15   H   HCR6  0   0.251   3.5699  -0.8380   2.8472
 JPN  H11   H   HCR6  0   0.269   3.6049   3.3046   3.9280
 JPN  HO23  H   HOH1  0   0.480   4.3608   4.7326   2.2820
 JPN  H91   H   HCH2  0   0.244   2.5880  -0.1457   4.9095
 JPN  H92   H   HCH2  0   0.244   2.2482   1.5454   5.2212
 JPN  H81   H   HCH2  0   0.234   4.9670   0.2161   5.6450
 JPN  H82   H   HCH2  0   0.233   4.5942   1.8926   5.9898
 JPN  H71   H   HCH2  0   0.241   2.8590   1.1564   7.6484
 JPN  H72   H   HCH2  0   0.241   3.2689  -0.5173   7.3197
 JPN  H4    H   HCR6  0   0.245   5.3888  -1.4751   8.1241
 JPN  H5    H   HCR6  0   0.252   7.2562  -1.3264   9.7234
 JPN  H6    H   HCR6  0   0.253   7.7277   0.8055  10.8911
 JPN  H1    H   HCR6  0   0.252   6.3068   2.7854  10.4453
 JPN  H2    H   HCR6  0   0.245   4.4424   2.6331   8.8425

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
 JPN  CL24  C18   single    1.725  0.020  1.725
 JPN  C18   C17   aromatic  1.394  0.020  1.394
 JPN  C18   C19   aromatic  1.384  0.020  1.384
 JPN  C19   C20   aromatic  1.386  0.020  1.386
 JPN  C19   H19   single    0.930  0.020  1.080
 JPN  C17   C22   aromatic  1.389  0.020  1.389
 JPN  C17   O16   single    1.350  0.020  1.350
 JPN  C22   C21   aromatic  1.386  0.020  1.386
 JPN  C22   H22   single    0.930  0.020  1.080
 JPN  C21   C20   aromatic  1.384  0.020  1.384
 JPN  C21   H21   single    0.930  0.020  1.080
 JPN  C20   CL25  single    1.731  0.020  1.731
 JPN  O16   C13   single    1.375  0.020  1.375
 JPN  C13   C12   aromatic  1.397  0.020  1.397
 JPN  C13   C14   aromatic  1.381  0.020  1.381
 JPN  C14   C15   aromatic  1.389  0.020  1.389
 JPN  C14   H14   single    0.930  0.020  1.080
 JPN  C15   C10   aromatic  1.390  0.020  1.390
 JPN  C15   H15   single    0.930  0.020  1.080
 JPN  C10   C9    single    1.503  0.020  1.503
 JPN  C10   C11   aromatic  1.394  0.020  1.394
 JPN  C11   C12   aromatic  1.389  0.020  1.389
 JPN  C11   H11   single    0.930  0.020  1.080
 JPN  C12   O23   single    1.343  0.020  1.343
 JPN  O23   HO23  single    0.850  0.020  0.980
 JPN  C9    C8    single    1.529  0.020  1.529
 JPN  C9    H91   single    0.970  0.020  1.090
 JPN  C9    H92   single    0.970  0.020  1.090
 JPN  C8    C7    single    1.529  0.020  1.529
 JPN  C8    H81   single    0.970  0.020  1.090
 JPN  C8    H82   single    0.970  0.020  1.090
 JPN  C7    C3    single    1.503  0.020  1.503
 JPN  C7    H71   single    0.970  0.020  1.090
 JPN  C7    H72   single    0.970  0.020  1.090
 JPN  C3    C4    aromatic  1.393  0.020  1.393
 JPN  C3    C2    aromatic  1.394  0.020  1.394
 JPN  C4    C5    aromatic  1.389  0.020  1.389
 JPN  C4    H4    single    0.930  0.020  1.080
 JPN  C5    C6    aromatic  1.389  0.020  1.389
 JPN  C5    H5    single    0.930  0.020  1.080
 JPN  C6    C1    aromatic  1.389  0.020  1.389
 JPN  C6    H6    single    0.930  0.020  1.080
 JPN  C1    C2    aromatic  1.389  0.020  1.389
 JPN  C1    H1    single    0.930  0.020  1.080
 JPN  C2    H2    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
 JPN  C17   C18  C19   121.20  3.000
 JPN  C19   C18  CL24  119.66  3.000
 JPN  C17   C18  CL24  119.13  3.000
 JPN  H19   C19  C20   120.98  3.000
 JPN  H19   C19  C18   120.06  3.000
 JPN  C20   C19  C18   118.96  3.000
 JPN  O16   C17  C22   124.32  3.000
 JPN  O16   C17  C18   116.89  3.000
 JPN  C22   C17  C18   118.77  3.000
 JPN  H22   C22  C21   119.06  3.000
 JPN  H22   C22  C17   120.34  3.000
 JPN  C21   C22  C17   120.60  3.000
 JPN  H21   C21  C20   120.71  3.000
 JPN  H21   C21  C22   119.67  3.000
 JPN  C20   C21  C22   119.61  3.000
 JPN  CL25  C20  C21   119.91  3.000
 JPN  CL25  C20  C19   119.24  3.000
 JPN  C21   C20  C19   120.85  3.000
 JPN  C13   O16  C17   118.92  3.000
 JPN  C12   C13  C14   120.58  3.000
 JPN  C14   C13  O16   120.08  3.000
 JPN  C12   C13  O16   119.27  3.000
 JPN  H14   C14  C15   120.62  3.000
 JPN  H14   C14  C13   119.36  3.000
 JPN  C15   C14  C13   120.02  3.000
 JPN  H15   C15  C10   119.95  3.000
 JPN  H15   C15  C14   119.62  3.000
 JPN  C10   C15  C14   120.43  3.000
 JPN  C9    C10  C11   120.09  3.000
 JPN  C11   C10  C15   118.95  3.000
 JPN  C9    C10  C15   120.93  3.000
 JPN  H11   C11  C12   119.19  3.000
 JPN  H11   C11  C10   119.59  3.000
 JPN  C12   C11  C10   121.21  3.000
 JPN  O23   C12  C11   123.82  3.000
 JPN  O23   C12  C13   117.38  3.000
 JPN  C11   C12  C13   118.80  3.000
 JPN  HO23  O23  C12   110.37  3.000
 JPN  H92   C9   H91   106.55  3.000
 JPN  H92   C9   C8    109.17  3.000
 JPN  H91   C9   C8    109.35  3.000
 JPN  H92   C9   C10   110.08  3.000
 JPN  H91   C9   C10   109.45  3.000
 JPN  C8    C9   C10   112.09  3.000
 JPN  H82   C8   H81   106.38  3.000
 JPN  H82   C8   C7    109.37  3.000
 JPN  H81   C8   C7    109.50  3.000
 JPN  H82   C8   C9    109.55  3.000
 JPN  H81   C8   C9    109.51  3.000
 JPN  C7    C8   C9    112.35  3.000
 JPN  H72   C7   H71   106.65  3.000
 JPN  H72   C7   C3    109.96  3.000
 JPN  H71   C7   C3    109.83  3.000
 JPN  H72   C7   C8    109.22  3.000
 JPN  H71   C7   C8    109.22  3.000
 JPN  C3    C7   C8    111.82  3.000
 JPN  C2    C3   C4    118.39  3.000
 JPN  C2    C3   C7    120.66  3.000
 JPN  C4    C3   C7    120.91  3.000
 JPN  H4    C4   C5    119.62  3.000
 JPN  H4    C4   C3    119.47  3.000
 JPN  C5    C4   C3    120.90  3.000
 JPN  H5    C5   C6    120.04  3.000
 JPN  H5    C5   C4    119.81  3.000
 JPN  C6    C5   C4    120.15  3.000
 JPN  H6    C6   C1    120.26  3.000
 JPN  H6    C6   C5    120.23  3.000
 JPN  C1    C6   C5    119.51  3.000
 JPN  H1    C1   C2    119.81  3.000
 JPN  H1    C1   C6    120.09  3.000
 JPN  C2    C1   C6    120.10  3.000
 JPN  H2    C2   C1    119.65  3.000
 JPN  H2    C2   C3    119.39  3.000
 JPN  C1    C2   C3    120.95  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
 JPN  CONST_01  C21   C22  C17  C18      0.00   0.0  0
 JPN  CONST_02  C21   C20  C19  C18      0.00   0.0  0
 JPN  CONST_03  C22   C17  C18  C19      0.00   0.0  0
 JPN  CONST_04  C22   C21  C20  C19      0.00   0.0  0
 JPN  CONST_05  C20   C19  C18  C17      0.00   0.0  0
 JPN  CONST_06  C20   C21  C22  C17      0.00   0.0  0
 JPN  CONST_07  C10   C11  C12  C13      0.00   0.0  0
 JPN  CONST_08  C10   C15  C14  C13      0.00   0.0  0
 JPN  CONST_09  C11   C12  C13  C14      0.00   0.0  0
 JPN  CONST_10  C11   C10  C15  C14      0.00   0.0  0
 JPN  CONST_11  C12   C13  C14  C15      0.00   0.0  0
 JPN  CONST_12  C12   C11  C10  C15      0.00   0.0  0
 JPN  CONST_13  C6    C5   C4   C3       0.00   0.0  0
 JPN  CONST_14  C6    C1   C2   C3       0.00   0.0  0
 JPN  CONST_15  C1    C2   C3   C4       0.00   0.0  0
 JPN  CONST_16  C1    C6   C5   C4       0.00   0.0  0
 JPN  CONST_17  C2    C3   C4   C5       0.00   0.0  0
 JPN  CONST_18  C2    C1   C6   C5       0.00   0.0  0
 JPN  CONST_19  C22   C17  C18  CL24   180.00   0.0  0
 JPN  CONST_20  C20   C19  C18  CL24   180.00   0.0  0
 JPN  CONST_21  CL25  C20  C19  C18    180.00   0.0  0
 JPN  CONST_22  O16   C17  C18  C19    180.00   0.0  0
 JPN  CONST_23  CL25  C20  C21  C22    180.00   0.0  0
 JPN  CONST_24  O16   C17  C22  C21    180.00   0.0  0
 JPN  CONST_25  C11   C12  C13  O16    180.00   0.0  0
 JPN  CONST_26  C15   C14  C13  O16    180.00   0.0  0
 JPN  CONST_27  O23   C12  C13  C14    180.00   0.0  0
 JPN  CONST_28  C9    C10  C15  C14    180.00   0.0  0
 JPN  CONST_29  O23   C12  C11  C10    180.00   0.0  0
 JPN  CONST_30  C9    C10  C11  C12    180.00   0.0  0
 JPN  CONST_31  C5    C4   C3   C7     180.00   0.0  0
 JPN  CONST_32  C1    C2   C3   C7     180.00   0.0  0
 JPN  CONST_33  H22   C22  C17  C18    180.00   0.0  0
 JPN  CONST_34  H21   C21  C20  C19    180.00   0.0  0
 JPN  CONST_35  H19   C19  C18  C17    180.00   0.0  0
 JPN  CONST_36  H11   C11  C12  C13    180.00   0.0  0
 JPN  CONST_37  H15   C15  C14  C13    180.00   0.0  0
 JPN  CONST_38  H14   C14  C15  C10    180.00   0.0  0
 JPN  CONST_39  H5    C5   C4   C3     180.00   0.0  0
 JPN  CONST_40  H1    C1   C2   C3     180.00   0.0  0
 JPN  CONST_41  H2    C2   C3   C4     180.00   0.0  0
 JPN  CONST_42  H6    C6   C5   C4     180.00   0.0  0
 JPN  CONST_43  H4    C4   C5   C6     180.00   0.0  0
 JPN  Var_01    C12   C13  O16  C17     76.67  30.0  2
 JPN  Var_02    C8    C9   C10  C15    101.33  30.0  2
 JPN  Var_03    C4    C3   C7   C8     -90.15  30.0  2
 JPN  Var_04    C7    C8   C9   C10   -178.10  30.0  3
 JPN  Var_05    C3    C7   C8   C9    -178.60  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
 JPN  plan-1  CL24  0.020
 JPN  plan-1  C18   0.020
 JPN  plan-1  C19   0.020
 JPN  plan-1  C17   0.020
 JPN  plan-1  C22   0.020
 JPN  plan-1  C21   0.020
 JPN  plan-1  C20   0.020
 JPN  plan-1  CL25  0.020
 JPN  plan-1  O16   0.020
 JPN  plan-1  H19   0.020
 JPN  plan-1  H22   0.020
 JPN  plan-1  H21   0.020
 JPN  plan-2  O16   0.020
 JPN  plan-2  C13   0.020
 JPN  plan-2  C14   0.020
 JPN  plan-2  C15   0.020
 JPN  plan-2  C10   0.020
 JPN  plan-2  C11   0.020
 JPN  plan-2  C12   0.020
 JPN  plan-2  O23   0.020
 JPN  plan-2  C9    0.020
 JPN  plan-2  H14   0.020
 JPN  plan-2  H15   0.020
 JPN  plan-2  H11   0.020
 JPN  plan-3  C7    0.020
 JPN  plan-3  C3    0.020
 JPN  plan-3  C4    0.020
 JPN  plan-3  C5    0.020
 JPN  plan-3  C6    0.020
 JPN  plan-3  C1    0.020
 JPN  plan-3  C2    0.020
 JPN  plan-3  H4    0.020
 JPN  plan-3  H5    0.020
 JPN  plan-3  H6    0.020
 JPN  plan-3  H1    0.020
 JPN  plan-3  H2    0.020

