# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 08:16:18 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 5-(cyclohexylmethyl)-2-(2,4-dichlorophenoxy)phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc(CC2CCCCC2)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
 JPL  JPL  5-(cyclohexylmethyl)-2-(2,4-dichlorophenoxy)phenol  ligand  43  23  .  2021-08-12  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JPL
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
 JPL  C2   C   CR6   0   0.330  -0.4367   1.7635   1.1175
 JPL  C3   C   CR6   0   0.172   0.2522   1.6531  -0.0872
 JPL  C4   C   CR16  0  -0.281  -0.4288   1.5126  -1.2845
 JPL  C5   C   CR16  0  -0.332  -1.8120   1.4649  -1.2886
 JPL  C7   C   CR6   0  -0.139   3.7140   0.6618  -0.2356
 JPL  C8   C   CR6   0   0.443   2.3297   0.5556  -0.1101
 JPL  C9   C   CR16  0  -0.342   1.7578  -0.7067  -0.0296
 JPL  C10  C   CR16  0  -0.197   2.5514  -1.8428  -0.0737
 JPL  C11  C   CR6   0  -0.064   3.9234  -1.7147  -0.2001
 JPL  C12  C   CR16  0  -0.167   4.5161  -0.4644  -0.2805
 JPL  C15  C   CH2   0  -0.429  -6.1126  -2.3837   0.2770
 JPL  C16  C   CH2   0  -0.428  -4.5920  -2.3780   0.3892
 JPL  C19  C   CH2   0  -0.418  -6.0528   0.0127  -0.4927
 JPL  O2   O   OH1   0  -0.622   0.1871   1.9059   2.3007
 JPL  C1   C   CR16  0  -0.411  -1.8280   1.7160   1.0970
 JPL  C6   C   CR6   0   0.156  -2.5259   1.5558  -0.0928
 JPL  C13  C   CH1   0  -0.224  -4.5283   0.0286  -0.3850
 JPL  C14  C   CH2   0  -0.431  -6.5892  -1.3874  -0.7747
 JPL  C17  C   CH2   0  -0.411  -4.0576  -0.9756   0.6655
 JPL  O1   O   O2    0  -0.505   1.6305   1.7163  -0.0606
 JPL  CL5  CL  CL    0  -0.119   4.9198  -3.1283  -0.2596
 JPL  H1   H   HCR6  0   0.278   0.1302   1.4380  -2.2094
 JPL  H2   H   HCR6  0   0.251  -2.3400   1.3527  -2.2275
 JPL  H3   H   HCR6  0   0.298   0.6866  -0.8205   0.0682
 JPL  H4   H   HCR6  0   0.292   2.0911  -2.8185  -0.0061
 JPL  H5   H   HCR6  0   0.304   5.5878  -0.3614  -0.3777
 JPL  H6   H   HCH2  0   0.225  -6.4733  -3.3879   0.0404
 JPL  H7   H   HCH2  0   0.207  -6.5466  -2.1170   1.2474
 JPL  H8   H   HCH2  0   0.225  -4.2660  -3.0643   1.1748
 JPL  H9   H   HCH2  0   0.207  -4.1575  -2.7495  -0.5457
 JPL  H12  H   HCH2  0   0.206  -6.4835   0.3823   0.4462
 JPL  H13  H   HCH2  0   0.224  -6.3757   0.7065  -1.2746
 JPL  H14  H   HOH1  0   0.475   1.1322   2.0534   2.1763
 JPL  H15  H   HCR6  0   0.261  -2.3666   1.8012   2.0339
 JPL  H16  H   HCH2  0   0.208  -6.2496  -1.7132  -1.7642
 JPL  H17  H   HCH2  0   0.225  -7.6813  -1.3702  -0.8130
 JPL  H18  H   HCH2  0   0.203  -4.3959  -0.6416   1.6549
 JPL  H19  H   HCH1  0   0.214  -4.1203  -0.2828  -1.3570
 JPL  H20  H   HCH2  0   0.229  -2.9657  -0.9955   0.7065
 JPL  C18  C   CH2   0  -0.501  -4.0250   1.4489  -0.0963
 JPL  CL1  CL  CL    0  -0.090   4.4314   2.2267  -0.3297
 JPL  H10  H   HCH2  0   0.236  -4.4233   1.7804   0.8673
 JPL  H11  H   HCH2  0   0.245  -4.4358   2.1246  -0.8526

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
 JPL  C14  C15  single    1.525  0.020  1.525
 JPL  C14  C19  single    1.526  0.020  1.526
 JPL  C15  C16  single    1.525  0.020  1.525
 JPL  C16  C17  single    1.526  0.020  1.526
 JPL  C19  C13  single    1.528  0.020  1.528
 JPL  C13  C17  single    1.528  0.020  1.528
 JPL  C13  C18  single    1.534  0.020  1.534
 JPL  C18  C6   single    1.503  0.020  1.503
 JPL  C5   C4   aromatic  1.384  0.020  1.384
 JPL  C5   C6   aromatic  1.396  0.020  1.396
 JPL  C4   C3   aromatic  1.385  0.020  1.385
 JPL  C6   C1   aromatic  1.389  0.020  1.389
 JPL  C10  C9   aromatic  1.387  0.020  1.387
 JPL  C10  C11  aromatic  1.384  0.020  1.384
 JPL  C9   C8   aromatic  1.388  0.020  1.388
 JPL  CL5  C11  single    1.731  0.020  1.731
 JPL  C11  C12  aromatic  1.386  0.020  1.386
 JPL  C3   O1   single    1.380  0.020  1.380
 JPL  C3   C2   aromatic  1.392  0.020  1.392
 JPL  C1   C2   aromatic  1.392  0.020  1.392
 JPL  C8   O1   single    1.356  0.020  1.356
 JPL  C8   C7   aromatic  1.394  0.020  1.394
 JPL  C2   O2   single    1.345  0.020  1.345
 JPL  C12  C7   aromatic  1.383  0.020  1.383
 JPL  C7   CL1  single    1.724  0.020  1.724
 JPL  C4   H1   single    0.930  0.020  1.080
 JPL  C5   H2   single    0.930  0.020  1.080
 JPL  C9   H3   single    0.930  0.020  1.080
 JPL  C10  H4   single    0.930  0.020  1.080
 JPL  C12  H5   single    0.930  0.020  1.080
 JPL  C15  H6   single    0.970  0.020  1.090
 JPL  C15  H7   single    0.970  0.020  1.090
 JPL  C16  H8   single    0.970  0.020  1.090
 JPL  C16  H9   single    0.970  0.020  1.090
 JPL  C18  H10  single    0.970  0.020  1.090
 JPL  C18  H11  single    0.970  0.020  1.090
 JPL  C19  H12  single    0.970  0.020  1.090
 JPL  C19  H13  single    0.970  0.020  1.090
 JPL  O2   H14  single    0.850  0.020  0.980
 JPL  C1   H15  single    0.930  0.020  1.080
 JPL  C14  H16  single    0.970  0.020  1.090
 JPL  C14  H17  single    0.970  0.020  1.090
 JPL  C17  H18  single    0.970  0.020  1.090
 JPL  C13  H19  single    0.970  0.020  1.090
 JPL  C17  H20  single    0.970  0.020  1.090

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
 JPL  C1   C2   O2   118.68  3.000
 JPL  O2   C2   C3   122.69  3.000
 JPL  C1   C2   C3   118.63  3.000
 JPL  O1   C3   C4   120.84  3.000
 JPL  O1   C3   C2   118.29  3.000
 JPL  C4   C3   C2   120.86  3.000
 JPL  H1   C4   C5   120.72  3.000
 JPL  H1   C4   C3   119.44  3.000
 JPL  C5   C4   C3   119.84  3.000
 JPL  H2   C5   C6   120.01  3.000
 JPL  H2   C5   C4   119.56  3.000
 JPL  C6   C5   C4   120.42  3.000
 JPL  CL1  C7   C12  119.73  3.000
 JPL  CL1  C7   C8   119.16  3.000
 JPL  C12  C7   C8   121.11  3.000
 JPL  O1   C8   C9   124.32  3.000
 JPL  O1   C8   C7   116.75  3.000
 JPL  C9   C8   C7   118.92  3.000
 JPL  H3   C9   C10  118.92  3.000
 JPL  H3   C9   C8   120.59  3.000
 JPL  C10  C9   C8   120.49  3.000
 JPL  H4   C10  C11  120.77  3.000
 JPL  H4   C10  C9   119.59  3.000
 JPL  C11  C10  C9   119.64  3.000
 JPL  CL5  C11  C12  119.25  3.000
 JPL  C12  C11  C10  120.86  3.000
 JPL  CL5  C11  C10  119.90  3.000
 JPL  H5   C12  C11  121.01  3.000
 JPL  H5   C12  C7   120.01  3.000
 JPL  C11  C12  C7   118.98  3.000
 JPL  H7   C15  H6   106.54  3.000
 JPL  H7   C15  C14  109.14  3.000
 JPL  H6   C15  C14  110.35  3.000
 JPL  H7   C15  C16  109.20  3.000
 JPL  H6   C15  C16  110.40  3.000
 JPL  C14  C15  C16  111.09  3.000
 JPL  H9   C16  H8   106.39  3.000
 JPL  H9   C16  C17  109.10  3.000
 JPL  H8   C16  C17  110.03  3.000
 JPL  H9   C16  C15  109.35  3.000
 JPL  H8   C16  C15  110.36  3.000
 JPL  C17  C16  C15  111.47  3.000
 JPL  H13  C19  H12  106.38  3.000
 JPL  H13  C19  C14  110.25  3.000
 JPL  H12  C19  C14  109.23  3.000
 JPL  H13  C19  C13  109.76  3.000
 JPL  H12  C19  C13  109.14  3.000
 JPL  C14  C19  C13  111.92  3.000
 JPL  H14  O2   C2   110.92  3.000
 JPL  H15  C1   C6   120.00  3.000
 JPL  H15  C1   C2   118.75  3.000
 JPL  C6   C1   C2   121.25  3.000
 JPL  C1   C6   C18  120.76  3.000
 JPL  C1   C6   C5   118.99  3.000
 JPL  C18  C6   C5   120.24  3.000
 JPL  H19  C13  C17  107.91  3.000
 JPL  H19  C13  C19  107.76  3.000
 JPL  C17  C13  C19  110.42  3.000
 JPL  H19  C13  C18  107.88  3.000
 JPL  C17  C13  C18  112.21  3.000
 JPL  C19  C13  C18  110.50  3.000
 JPL  H17  C14  H16  106.42  3.000
 JPL  H17  C14  C19  110.09  3.000
 JPL  H16  C14  C19  109.32  3.000
 JPL  H17  C14  C15  110.29  3.000
 JPL  H16  C14  C15  109.37  3.000
 JPL  C19  C14  C15  111.24  3.000
 JPL  H20  C17  H18  106.24  3.000
 JPL  H20  C17  C13  110.22  3.000
 JPL  H18  C17  C13  108.96  3.000
 JPL  H20  C17  C16  109.87  3.000
 JPL  H18  C17  C16  109.58  3.000
 JPL  C13  C17  C16  111.82  3.000
 JPL  C8   O1   C3   118.37  3.000
 JPL  H11  C18  H10  106.55  3.000
 JPL  H11  C18  C13  108.57  3.000
 JPL  H10  C18  C13  109.08  3.000
 JPL  H11  C18  C6   109.40  3.000
 JPL  H10  C18  C6   109.84  3.000
 JPL  C13  C18  C6   113.17  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
 JPL  CONST_01  C5   C4   C3   C2     0.00   0.0  0
 JPL  CONST_02  C5   C6   C1   C2     0.00   0.0  0
 JPL  CONST_03  C6   C5   C4   C3     0.00   0.0  0
 JPL  CONST_04  C6   C1   C2   C3     0.00   0.0  0
 JPL  CONST_05  C1   C6   C5   C4     0.00   0.0  0
 JPL  CONST_06  C1   C2   C3   C4     0.00   0.0  0
 JPL  CONST_07  C10  C9   C8   C7     0.00   0.0  0
 JPL  CONST_08  C10  C11  C12  C7     0.00   0.0  0
 JPL  CONST_09  C11  C10  C9   C8     0.00   0.0  0
 JPL  CONST_10  C11  C12  C7   C8     0.00   0.0  0
 JPL  CONST_11  C12  C11  C10  C9     0.00   0.0  0
 JPL  CONST_12  C12  C7   C8   C9     0.00   0.0  0
 JPL  CONST_13  C18  C6   C1   C2   180.00   0.0  0
 JPL  CONST_14  C18  C6   C5   C4   180.00   0.0  0
 JPL  CONST_15  O2   C2   C3   C4   180.00   0.0  0
 JPL  CONST_16  O1   C3   C4   C5   180.00   0.0  0
 JPL  CONST_17  CL5  C11  C12  C7   180.00   0.0  0
 JPL  CONST_18  CL5  C11  C10  C9   180.00   0.0  0
 JPL  CONST_19  CL1  C7   C8   C9   180.00   0.0  0
 JPL  CONST_20  O1   C8   C9   C10  180.00   0.0  0
 JPL  CONST_21  CL1  C7   C12  C11  180.00   0.0  0
 JPL  CONST_22  O1   C8   C7   C12  180.00   0.0  0
 JPL  CONST_23  C6   C1   C2   O2   180.00   0.0  0
 JPL  CONST_24  O1   C3   C2   C1   180.00   0.0  0
 JPL  CONST_25  H1   C4   C3   C2   180.00   0.0  0
 JPL  CONST_26  H2   C5   C4   C3   180.00   0.0  0
 JPL  CONST_27  H15  C1   C2   C3   180.00   0.0  0
 JPL  CONST_28  H3   C9   C8   C7   180.00   0.0  0
 JPL  CONST_29  H4   C10  C9   C8   180.00   0.0  0
 JPL  CONST_30  H5   C12  C7   C8   180.00   0.0  0
 JPL  Var_01    C13  C19  C14  C15   55.59  30.0  1
 JPL  Var_02    C13  C17  C16  C15  -55.34  30.0  1
 JPL  Var_03    C19  C14  C15  C16  -55.06  30.0  1
 JPL  Var_04    C17  C16  C15  C14   55.02  30.0  1
 JPL  Var_05    C9   C8   O1   C3    -7.85  30.0  2
 JPL  Var_06    C13  C18  C6   C5    71.51  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 JPL  chir_01  C13  C19  C17  C18  positiv

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
 JPL  plan-1  C2   0.020
 JPL  plan-1  C3   0.020
 JPL  plan-1  C4   0.020
 JPL  plan-1  C5   0.020
 JPL  plan-1  O2   0.020
 JPL  plan-1  C1   0.020
 JPL  plan-1  C6   0.020
 JPL  plan-1  O1   0.020
 JPL  plan-1  H1   0.020
 JPL  plan-1  H2   0.020
 JPL  plan-1  H15  0.020
 JPL  plan-1  C18  0.020
 JPL  plan-2  C7   0.020
 JPL  plan-2  C8   0.020
 JPL  plan-2  C9   0.020
 JPL  plan-2  C10  0.020
 JPL  plan-2  C11  0.020
 JPL  plan-2  C12  0.020
 JPL  plan-2  O1   0.020
 JPL  plan-2  CL5  0.020
 JPL  plan-2  H3   0.020
 JPL  plan-2  H4   0.020
 JPL  plan-2  H5   0.020
 JPL  plan-2  CL1  0.020

