# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 13:28:20 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 5-benzyl-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
 JPM  JPM  5-benzyl-2-(2,4-dichlorophenoxy)phenol  ligand  37  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_JPM
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
 JPM  C2    C   CR6   0   0.332  -0.7556  -1.4131  -1.1703
 JPM  C3    C   CR6   0   0.180   0.0310  -1.5840  -0.0302
 JPM  C4    C   CR16  0  -0.282  -0.5481  -1.7461   1.2136
 JPM  C5    C   CR16  0  -0.349  -1.9297  -1.7267   1.3390
 JPM  C7    C   CR6   0  -0.138   3.5080  -0.6235  -0.0509
 JPM  C8    C   CR6   0   0.442   2.1226  -0.5071   0.0520
 JPM  C9    C   CR16  0  -0.345   1.5738   0.7252   0.3780
 JPM  C10   C   CR16  0  -0.197   2.3932   1.8219   0.5999
 JPM  C11   C   CR6   0  -0.064   3.7658   1.6846   0.4937
 JPM  C12   C   CR16  0  -0.167   4.3350   0.4635   0.1677
 JPM  C15   C   CR16  0  -0.272  -5.6443   2.5336  -0.3090
 JPM  C16   C   CR16  0  -0.240  -5.0193   2.1924   0.8853
 JPM  C19   C   CR16  0  -0.322  -5.3820   0.2664  -1.0733
 JPM  O2    O   OH1   0  -0.620  -0.2259  -1.2593  -2.3965
 JPM  O1    O   O2    0  -0.505   1.3999  -1.6291  -0.1879
 JPM  CL5   CL  CL    0  -0.119   4.7928   3.0499   0.7691
 JPM  C1    C   CR16  0  -0.383  -2.1374  -1.3979  -1.0302
 JPM  C6    C   CR6   0   0.161  -2.7333  -1.5442   0.2178
 JPM  C13   C   CR6   0   0.150  -4.7532  -0.0843   0.1171
 JPM  C17   C   CR16  0  -0.291  -4.5780   0.8943   1.0943
 JPM  C14   C   CR16  0  -0.239  -5.8252   1.5666  -1.2873
 JPM  H4    H   HCR6  0   0.281   0.0823  -1.8875   2.0828
 JPM  H5    H   HCR6  0   0.255  -2.3792  -1.8574   2.3150
 JPM  H9    H   HCR6  0   0.301   0.5027   0.8467   0.4659
 JPM  H10   H   HCR6  0   0.292   1.9512   2.7751   0.8539
 JPM  H12   H   HCR6  0   0.304   5.4071   0.3530   0.0837
 JPM  H15   H   HCR6  0   0.255  -5.9899   3.5462  -0.4730
 JPM  H16   H   HCR6  0   0.254  -4.8770   2.9403   1.6550
 JPM  H18   H   HCH2  0   0.271  -4.6920  -2.1640  -0.3805
 JPM  H18A  H   HCH2  0   0.271  -4.5301  -1.8340   1.3325
 JPM  H19   H   HCR6  0   0.248  -5.5292  -0.4828  -1.8427
 JPM  HO2   H   HOH1  0   0.476   0.7235  -1.4303  -2.3855
 JPM  H1    H   HCR6  0   0.263  -2.7496  -1.2630  -1.9148
 JPM  H17   H   HCR6  0   0.247  -4.0912   0.6357   2.0279
 JPM  H14   H   HCR6  0   0.254  -6.3141   1.8221  -2.2188
 JPM  C18   C   CH2   0  -0.614  -4.2354  -1.4833   0.3412
 JPM  CL1   CL  CL    0  -0.089   4.1940  -2.1502  -0.4638

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
 JPM  C2   C3    aromatic  1.396  0.020  1.396
 JPM  C2   O2    single    1.345  0.020  1.345
 JPM  C2   C1    aromatic  1.389  0.020  1.389
 JPM  C3   C4    aromatic  1.382  0.020  1.382
 JPM  C3   O1    single    1.379  0.020  1.379
 JPM  C4   C5    aromatic  1.387  0.020  1.387
 JPM  C5   C6    aromatic  1.391  0.020  1.391
 JPM  C7   C8    aromatic  1.394  0.020  1.394
 JPM  C7   C12   aromatic  1.383  0.020  1.383
 JPM  C7   CL1   single    1.724  0.020  1.724
 JPM  C8   C9    aromatic  1.388  0.020  1.388
 JPM  C8   O1    single    1.356  0.020  1.356
 JPM  C9   C10   aromatic  1.387  0.020  1.387
 JPM  C10  C11   aromatic  1.384  0.020  1.384
 JPM  C11  C12   aromatic  1.386  0.020  1.386
 JPM  C11  CL5   single    1.730  0.020  1.730
 JPM  C15  C16   aromatic  1.390  0.020  1.390
 JPM  C15  C14   aromatic  1.387  0.020  1.387
 JPM  C16  C17   aromatic  1.387  0.020  1.387
 JPM  C18  C6    single    1.508  0.020  1.508
 JPM  C18  C13   single    1.508  0.020  1.508
 JPM  C19  C13   aromatic  1.391  0.020  1.391
 JPM  C19  C14   aromatic  1.390  0.020  1.390
 JPM  C1   C6    aromatic  1.391  0.020  1.391
 JPM  C13  C17   aromatic  1.394  0.020  1.394
 JPM  C4   H4    single    0.930  0.020  1.080
 JPM  C5   H5    single    0.930  0.020  1.080
 JPM  C9   H9    single    0.930  0.020  1.080
 JPM  C10  H10   single    0.930  0.020  1.080
 JPM  C12  H12   single    0.930  0.020  1.080
 JPM  C15  H15   single    0.930  0.020  1.080
 JPM  C16  H16   single    0.930  0.020  1.080
 JPM  C18  H18   single    0.970  0.020  1.090
 JPM  C18  H18A  single    0.970  0.020  1.090
 JPM  C19  H19   single    0.930  0.020  1.080
 JPM  O2   HO2   single    0.850  0.020  0.980
 JPM  C1   H1    single    0.930  0.020  1.080
 JPM  C17  H17   single    0.930  0.020  1.080
 JPM  C14  H14   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
 JPM  C1    C2   O2   118.86  3.000
 JPM  C1    C2   C3   118.66  3.000
 JPM  O2    C2   C3   122.47  3.000
 JPM  O1    C3   C4   121.02  3.000
 JPM  O1    C3   C2   118.05  3.000
 JPM  C4    C3   C2   120.90  3.000
 JPM  H4    C4   C5   120.59  3.000
 JPM  H4    C4   C3   119.60  3.000
 JPM  C5    C4   C3   119.81  3.000
 JPM  H5    C5   C6   120.17  3.000
 JPM  H5    C5   C4   119.56  3.000
 JPM  C6    C5   C4   120.27  3.000
 JPM  CL1   C7   C12  119.73  3.000
 JPM  CL1   C7   C8   119.15  3.000
 JPM  C12   C7   C8   121.12  3.000
 JPM  O1    C8   C9   124.44  3.000
 JPM  O1    C8   C7   116.58  3.000
 JPM  C9    C8   C7   118.98  3.000
 JPM  H9    C9   C10  118.90  3.000
 JPM  H9    C9   C8   120.69  3.000
 JPM  C10   C9   C8   120.41  3.000
 JPM  H10   C10  C11  120.74  3.000
 JPM  H10   C10  C9   119.56  3.000
 JPM  C11   C10  C9   119.69  3.000
 JPM  CL5   C11  C12  119.26  3.000
 JPM  CL5   C11  C10  119.88  3.000
 JPM  C12   C11  C10  120.85  3.000
 JPM  H12   C12  C11  121.03  3.000
 JPM  H12   C12  C7   120.02  3.000
 JPM  C11   C12  C7   118.95  3.000
 JPM  H15   C15  C14  120.23  3.000
 JPM  H15   C15  C16  120.21  3.000
 JPM  C14   C15  C16  119.55  3.000
 JPM  H16   C16  C17  119.84  3.000
 JPM  H16   C16  C15  120.02  3.000
 JPM  C17   C16  C15  120.14  3.000
 JPM  H19   C19  C14  119.60  3.000
 JPM  H19   C19  C13  119.63  3.000
 JPM  C14   C19  C13  120.77  3.000
 JPM  HO2   O2   C2   110.92  3.000
 JPM  C8    O1   C3   118.81  3.000
 JPM  H1    C1   C6   120.22  3.000
 JPM  H1    C1   C2   118.74  3.000
 JPM  C6    C1   C2   121.04  3.000
 JPM  C1    C6   C18  119.73  3.000
 JPM  C1    C6   C5   119.30  3.000
 JPM  C18   C6   C5   120.96  3.000
 JPM  C17   C13  C19  118.66  3.000
 JPM  C17   C13  C18  120.25  3.000
 JPM  C19   C13  C18  121.07  3.000
 JPM  H17   C17  C13  119.51  3.000
 JPM  H17   C17  C16  119.72  3.000
 JPM  C13   C17  C16  120.76  3.000
 JPM  H14   C14  C19  119.81  3.000
 JPM  H14   C14  C15  120.07  3.000
 JPM  C19   C14  C15  120.12  3.000
 JPM  H18A  C18  H18  106.67  3.000
 JPM  H18A  C18  C13  109.88  3.000
 JPM  H18   C18  C13  109.66  3.000
 JPM  H18A  C18  C6   109.27  3.000
 JPM  H18   C18  C6   109.70  3.000
 JPM  C13   C18  C6   111.54  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
 JPM  CONST_01  C5   C4   C3   C2     0.00   0.0  0
 JPM  CONST_02  C5   C6   C1   C2     0.00   0.0  0
 JPM  CONST_03  C6   C1   C2   C3     0.00   0.0  0
 JPM  CONST_04  C6   C5   C4   C3     0.00   0.0  0
 JPM  CONST_05  C1   C2   C3   C4     0.00   0.0  0
 JPM  CONST_06  C1   C6   C5   C4     0.00   0.0  0
 JPM  CONST_07  C10  C9   C8   C7     0.00   0.0  0
 JPM  CONST_08  C10  C11  C12  C7     0.00   0.0  0
 JPM  CONST_09  C11  C12  C7   C8     0.00   0.0  0
 JPM  CONST_10  C11  C10  C9   C8     0.00   0.0  0
 JPM  CONST_11  C12  C7   C8   C9     0.00   0.0  0
 JPM  CONST_12  C12  C11  C10  C9     0.00   0.0  0
 JPM  CONST_13  C13  C17  C16  C15    0.00   0.0  0
 JPM  CONST_14  C13  C19  C14  C15    0.00   0.0  0
 JPM  CONST_15  C19  C14  C15  C16    0.00   0.0  0
 JPM  CONST_16  C19  C13  C17  C16    0.00   0.0  0
 JPM  CONST_17  C14  C15  C16  C17    0.00   0.0  0
 JPM  CONST_18  C14  C19  C13  C17    0.00   0.0  0
 JPM  CONST_19  C18  C6   C1   C2   180.00   0.0  0
 JPM  CONST_20  O2   C2   C3   C4   180.00   0.0  0
 JPM  CONST_21  C18  C6   C5   C4   180.00   0.0  0
 JPM  CONST_22  O1   C3   C4   C5   180.00   0.0  0
 JPM  CONST_23  CL5  C11  C12  C7   180.00   0.0  0
 JPM  CONST_24  CL1  C7   C8   C9   180.00   0.0  0
 JPM  CONST_25  CL5  C11  C10  C9   180.00   0.0  0
 JPM  CONST_26  O1   C8   C9   C10  180.00   0.0  0
 JPM  CONST_27  CL1  C7   C12  C11  180.00   0.0  0
 JPM  CONST_28  O1   C8   C7   C12  180.00   0.0  0
 JPM  CONST_29  C18  C13  C17  C16  180.00   0.0  0
 JPM  CONST_30  C14  C19  C13  C18  180.00   0.0  0
 JPM  CONST_31  C6   C1   C2   O2   180.00   0.0  0
 JPM  CONST_32  C1   C2   C3   O1   180.00   0.0  0
 JPM  CONST_33  H4   C4   C3   C2   180.00   0.0  0
 JPM  CONST_34  H1   C1   C2   C3   180.00   0.0  0
 JPM  CONST_35  H5   C5   C4   C3   180.00   0.0  0
 JPM  CONST_36  H9   C9   C8   C7   180.00   0.0  0
 JPM  CONST_37  H12  C12  C7   C8   180.00   0.0  0
 JPM  CONST_38  H10  C10  C9   C8   180.00   0.0  0
 JPM  CONST_39  H17  C17  C16  C15  180.00   0.0  0
 JPM  CONST_40  H19  C19  C14  C15  180.00   0.0  0
 JPM  CONST_41  H14  C14  C15  C16  180.00   0.0  0
 JPM  CONST_42  H15  C15  C14  C19  180.00   0.0  0
 JPM  CONST_43  H16  C16  C17  C13  180.00   0.0  0
 JPM  Var_01    C7   C8   O1   C3   176.63  30.0  3
 JPM  Var_02    C13  C18  C6   C5   108.32  30.0  2
 JPM  Var_03    C6   C18  C13  C19  104.60  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
 JPM  plan-1  C2   0.020
 JPM  plan-1  C3   0.020
 JPM  plan-1  C4   0.020
 JPM  plan-1  C5   0.020
 JPM  plan-1  O2   0.020
 JPM  plan-1  O1   0.020
 JPM  plan-1  C1   0.020
 JPM  plan-1  C6   0.020
 JPM  plan-1  H4   0.020
 JPM  plan-1  H5   0.020
 JPM  plan-1  H1   0.020
 JPM  plan-1  C18  0.020
 JPM  plan-2  C7   0.020
 JPM  plan-2  C8   0.020
 JPM  plan-2  C9   0.020
 JPM  plan-2  C10  0.020
 JPM  plan-2  C11  0.020
 JPM  plan-2  C12  0.020
 JPM  plan-2  O1   0.020
 JPM  plan-2  CL5  0.020
 JPM  plan-2  H9   0.020
 JPM  plan-2  H10  0.020
 JPM  plan-2  H12  0.020
 JPM  plan-2  CL1  0.020
 JPM  plan-3  C15  0.020
 JPM  plan-3  C16  0.020
 JPM  plan-3  C19  0.020
 JPM  plan-3  C13  0.020
 JPM  plan-3  C17  0.020
 JPM  plan-3  C14  0.020
 JPM  plan-3  H15  0.020
 JPM  plan-3  H16  0.020
 JPM  plan-3  H19  0.020
 JPM  plan-3  H17  0.020
 JPM  plan-3  H14  0.020
 JPM  plan-3  C18  0.020

