# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 16:11:10 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 4-nitro-2-({4-[3-(trifluoromethyl)phenyl]piperazin-1-yl}methyl)phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(cc1CN2CCN(CC2)c3cccc(c3)C(F)(F)F)[N+]([O-])=O
#
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
 WDV  WDV  4-nitro-2-({4-[3-(trifluoromethyl)phenyl]piperazin-1-yl}methyl)phenol  ligand  45  27  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WDV
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
 WDV  C8   C  CR16   0  -0.229   4.8886  -2.2982   0.4733
 WDV  C11  C  CR16   0  -0.316   5.5827  -1.1001   0.4824
 WDV  C4   C  CR16   0  -0.348   3.5292  -2.3403   0.2027
 WDV  C24  C  CR16   0  -0.267  -5.6729   0.4367   1.3195
 WDV  C22  C  CR16   0  -0.341  -4.7054  -0.4068   1.8194
 WDV  C3   C  CR16   0  -0.362   3.5284   0.0396  -0.0842
 WDV  C19  C  CR16   0  -0.326  -4.6422   0.3031  -0.8653
 WDV  C7   C  CR6    0  -0.178   4.8843   0.0685   0.1991
 WDV  C18  C  CR6    0  -0.041  -3.6802  -0.5579  -0.3791
 WDV  C1   C  CR6    0   0.398   2.8196  -1.1688  -0.0861
 WDV  C21  C  CR6    0   0.241  -5.6347   0.7946  -0.0238
 WDV  C20  C  CR6    0   0.364  -3.7011  -0.9090   0.9865
 WDV  C5   C  CH2    0  -0.323   0.8066  -2.4456  -0.6133
 WDV  C6   C  CH2    0  -0.312   0.6019  -0.2208   0.2746
 WDV  C9   C  CH2    0  -0.277  -0.4942  -2.2461  -1.3673
 WDV  C10  C  CH2    0  -0.292  -0.6909  -0.0347  -0.4896
 WDV  C17  C  CH2    0  -0.319  -2.6667  -1.1798  -1.3037
 WDV  C12  C  CT     0   1.049   5.5838   1.3918   0.2324
 WDV  N2   N  NT     0  -0.522   1.4662  -1.1726  -0.4079
 WDV  N13  N  NT     0  -0.508  -1.3646  -1.3172  -0.6603
 WDV  N25  N  N      1   0.323  -6.6350   1.6862  -0.5518
 WDV  O27  O  O     -1  -0.395  -6.5686   1.9998  -1.7209
 WDV  O26  O  O      0  -0.395  -7.5020   2.0847   0.1954
 WDV  O23  O  OH1    0  -0.624  -2.7798  -1.7123   1.5033
 WDV  F14  F  F      0  -0.306   6.9065   1.2755   0.0742
 WDV  F15  F  F      0  -0.310   5.1483   2.2240  -0.7227
 WDV  F16  F  F      0  -0.316   5.3893   2.0227   1.4020
 WDV  H1   H  HCR6   0   0.266   5.4102  -3.2200   0.6947
 WDV  H2   H  HCR6   0   0.266   6.6409  -1.0903   0.7019
 WDV  H3   H  HCR6   0   0.278   3.0286  -3.2980   0.2302
 WDV  H5   H  HCR6   0   0.279  -4.7155  -0.6849   2.8650
 WDV  H6   H  HCR6   0   0.278   3.0116   0.9565  -0.3350
 WDV  H7   H  HCR6   0   0.291  -4.6186   0.5802  -1.9107
 WDV  H8   H  HCH2   0   0.225   0.6054  -2.9627   0.3368
 WDV  H9   H  HCH2   0   0.265   1.4421  -3.0963  -1.2141
 WDV  H10  H  HCH2   0   0.268   1.0905   0.7471   0.3616
 WDV  H11  H  HCH2   0   0.228   0.3787  -0.5641   1.2955
 WDV  H12  H  HCH2   0   0.227  -0.2783  -1.8841  -2.3825
 WDV  H13  H  HCH2   0   0.261  -1.0011  -3.2078  -1.4596
 WDV  H14  H  HCH2   0   0.262  -1.3359   0.6476   0.0668
 WDV  H15  H  HCH2   0   0.235  -0.4834   0.4270  -1.4653
 WDV  H16  H  HCH2   0   0.283  -3.0080  -2.1837  -1.5739
 WDV  H17  H  HCH2   0   0.255  -2.6054  -0.6065  -2.2381
 WDV  H19  H  HOH1   0   0.470  -2.0458  -1.7915   0.8219
 WDV  H4   H  HCR6   0   0.295  -6.4399   0.8171   1.9781

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
 WDV  O26  N25  double    1.212  0.020  1.212
 WDV  O27  N25  single    1.212  0.020  1.212
 WDV  N25  C21  single    1.440  0.020  1.440
 WDV  C21  C19  aromatic  1.391  0.020  1.391
 WDV  C21  C24  aromatic  1.391  0.020  1.391
 WDV  C19  C18  aromatic  1.380  0.020  1.380
 WDV  C24  C22  aromatic  1.378  0.020  1.378
 WDV  F15  C12  single    1.340  0.020  1.340
 WDV  C18  C17  single    1.506  0.020  1.506
 WDV  C18  C20  aromatic  1.410  0.020  1.410
 WDV  C9   C5   single    1.517  0.020  1.517
 WDV  C9   N13  single    1.456  0.020  1.456
 WDV  C22  C20  aromatic  1.398  0.020  1.398
 WDV  C17  N13  single    1.459  0.020  1.459
 WDV  C5   N2   single    1.448  0.020  1.448
 WDV  C20  O23  single    1.327  0.020  1.327
 WDV  N13  C10  single    1.459  0.020  1.459
 WDV  C12  F16  single    1.343  0.020  1.343
 WDV  C12  F14  single    1.337  0.020  1.337
 WDV  C12  C7   single    1.497  0.020  1.497
 WDV  C3   C7   aromatic  1.385  0.020  1.385
 WDV  C3   C1   aromatic  1.401  0.020  1.401
 WDV  N2   C1   single    1.391  0.020  1.391
 WDV  N2   C6   single    1.455  0.020  1.455
 WDV  C7   C11  aromatic  1.391  0.020  1.391
 WDV  C10  C6   single    1.513  0.020  1.513
 WDV  C1   C4   aromatic  1.400  0.020  1.400
 WDV  C11  C8   aromatic  1.385  0.020  1.385
 WDV  C4   C8   aromatic  1.387  0.020  1.387
 WDV  C8   H1   single    0.930  0.020  1.080
 WDV  C11  H2   single    0.930  0.020  1.080
 WDV  C4   H3   single    0.930  0.020  1.080
 WDV  C24  H4   single    0.930  0.020  1.080
 WDV  C22  H5   single    0.930  0.020  1.080
 WDV  C3   H6   single    0.930  0.020  1.080
 WDV  C19  H7   single    0.930  0.020  1.080
 WDV  C5   H8   single    0.970  0.020  1.090
 WDV  C5   H9   single    0.970  0.020  1.090
 WDV  C6   H10  single    0.970  0.020  1.090
 WDV  C6   H11  single    0.970  0.020  1.090
 WDV  C9   H12  single    0.970  0.020  1.090
 WDV  C9   H13  single    0.970  0.020  1.090
 WDV  C10  H14  single    0.970  0.020  1.090
 WDV  C10  H15  single    0.970  0.020  1.090
 WDV  C17  H16  single    0.970  0.020  1.090
 WDV  C17  H17  single    0.970  0.020  1.090
 WDV  O23  H19  single    0.850  0.020  0.980

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
 WDV  H1   C8   C4   119.13  3.000
 WDV  H1   C8   C11  119.61  3.000
 WDV  C4   C8   C11  121.26  3.000
 WDV  H2   C11  C7   121.70  3.000
 WDV  H2   C11  C8   120.01  3.000
 WDV  C7   C11  C8   118.29  3.000
 WDV  H3   C4   C1   120.79  3.000
 WDV  H3   C4   C8   118.42  3.000
 WDV  C1   C4   C8   120.79  3.000
 WDV  H4   C24  C21  121.19  3.000
 WDV  H4   C24  C22  119.55  3.000
 WDV  C21  C24  C22  119.26  3.000
 WDV  H5   C22  C20  119.35  3.000
 WDV  H5   C22  C24  120.10  3.000
 WDV  C20  C22  C24  120.55  3.000
 WDV  H6   C3   C1   119.27  3.000
 WDV  H6   C3   C7   119.82  3.000
 WDV  C1   C3   C7   120.89  3.000
 WDV  H7   C19  C21  120.65  3.000
 WDV  H7   C19  C18  119.03  3.000
 WDV  C21  C19  C18  120.32  3.000
 WDV  C12  C7   C3   118.70  3.000
 WDV  C3   C7   C11  121.04  3.000
 WDV  C12  C7   C11  120.23  3.000
 WDV  C17  C18  C20  120.11  3.000
 WDV  C20  C18  C19  119.10  3.000
 WDV  C17  C18  C19  120.70  3.000
 WDV  N2   C1   C3   119.66  3.000
 WDV  N2   C1   C4   122.60  3.000
 WDV  C3   C1   C4   117.71  3.000
 WDV  N25  C21  C19  119.50  3.000
 WDV  C19  C21  C24  120.87  3.000
 WDV  N25  C21  C24  119.63  3.000
 WDV  O23  C20  C18  121.17  3.000
 WDV  O23  C20  C22  118.95  3.000
 WDV  C18  C20  C22  119.88  3.000
 WDV  H9   C5   H8   107.58  3.000
 WDV  H9   C5   N2   109.72  3.000
 WDV  H8   C5   N2   111.95  3.000
 WDV  H9   C5   C9   107.73  3.000
 WDV  H8   C5   C9   109.53  3.000
 WDV  N2   C5   C9   110.21  3.000
 WDV  H11  C6   H10  107.13  3.000
 WDV  H11  C6   N2   110.58  3.000
 WDV  H10  C6   N2   110.65  3.000
 WDV  H11  C6   C10  109.49  3.000
 WDV  H10  C6   C10  108.35  3.000
 WDV  N2   C6   C10  110.55  3.000
 WDV  H13  C9   H12  107.66  3.000
 WDV  H13  C9   N13  109.00  3.000
 WDV  H12  C9   N13  110.84  3.000
 WDV  H13  C9   C5   108.94  3.000
 WDV  H12  C9   C5   109.51  3.000
 WDV  N13  C9   C5   110.81  3.000
 WDV  H15  C10  H14  107.55  3.000
 WDV  H15  C10  N13  110.65  3.000
 WDV  H14  C10  N13  109.66  3.000
 WDV  H15  C10  C6   109.79  3.000
 WDV  H14  C10  C6   108.92  3.000
 WDV  N13  C10  C6   110.22  3.000
 WDV  H17  C17  H16  106.64  3.000
 WDV  H17  C17  N13  112.00  3.000
 WDV  H16  C17  N13  107.51  3.000
 WDV  H17  C17  C18  110.15  3.000
 WDV  H16  C17  C18  108.69  3.000
 WDV  N13  C17  C18  111.64  3.000
 WDV  F16  C12  F15  106.38  3.000
 WDV  F16  C12  F14  106.69  3.000
 WDV  F15  C12  F14  106.94  3.000
 WDV  F14  C12  C7   112.50  3.000
 WDV  F16  C12  C7   111.52  3.000
 WDV  F15  C12  C7   112.41  3.000
 WDV  C6   N2   C5   111.77  3.000
 WDV  C6   N2   C1   117.87  3.000
 WDV  C5   N2   C1   118.57  3.000
 WDV  C17  N13  C10  112.40  3.000
 WDV  C10  N13  C9   109.97  3.000
 WDV  C17  N13  C9   112.30  3.000
 WDV  O26  N25  O27  123.28  3.000
 WDV  O27  N25  C21  118.40  3.000
 WDV  O26  N25  C21  118.31  3.000
 WDV  H19  O23  C20  106.90  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
 WDV  CONST_01  C3   C7   C11  C8      0.00   0.0  0
 WDV  CONST_02  C3   C1   C4   C8      0.00   0.0  0
 WDV  CONST_03  C1   C3   C7   C11     0.00   0.0  0
 WDV  CONST_04  C1   C4   C8   C11     0.00   0.0  0
 WDV  CONST_05  C7   C3   C1   C4      0.00   0.0  0
 WDV  CONST_06  C7   C11  C8   C4      0.00   0.0  0
 WDV  CONST_07  C18  C19  C21  C24     0.00   0.0  0
 WDV  CONST_08  C18  C20  C22  C24     0.00   0.0  0
 WDV  CONST_09  C19  C21  C24  C22     0.00   0.0  0
 WDV  CONST_10  C19  C18  C20  C22     0.00   0.0  0
 WDV  CONST_11  C20  C18  C19  C21     0.00   0.0  0
 WDV  CONST_12  C20  C22  C24  C21     0.00   0.0  0
 WDV  CONST_13  N2   C1   C4   C8    180.00   0.0  0
 WDV  CONST_14  N2   C1   C3   C7    180.00   0.0  0
 WDV  CONST_15  C12  C7   C11  C8    180.00   0.0  0
 WDV  CONST_16  O23  C20  C22  C24   180.00   0.0  0
 WDV  CONST_17  N25  C21  C24  C22   180.00   0.0  0
 WDV  CONST_18  C17  C18  C20  C22   180.00   0.0  0
 WDV  CONST_19  O23  C20  C18  C19   180.00   0.0  0
 WDV  CONST_20  N25  C21  C19  C18   180.00   0.0  0
 WDV  CONST_21  C12  C7   C3   C1    180.00   0.0  0
 WDV  CONST_22  C17  C18  C19  C21   180.00   0.0  0
 WDV  CONST_23  H6   C3   C7   C11   180.00   0.0  0
 WDV  CONST_24  H3   C4   C8   C11   180.00   0.0  0
 WDV  CONST_25  H2   C11  C8   C4    180.00   0.0  0
 WDV  CONST_26  H7   C19  C21  C24   180.00   0.0  0
 WDV  CONST_27  H4   C24  C21  C19   180.00   0.0  0
 WDV  CONST_28  H1   C8   C11  C7    180.00   0.0  0
 WDV  CONST_29  H5   C22  C20  C18   180.00   0.0  0
 WDV  CONST_30  O26  N25  C21  C24     0.00   0.0  0
 WDV  CONST_31  O27  N25  C21  C24   180.00   0.0  0
 WDV  CONST_32  O26  N25  C21  C19   180.00   0.0  0
 WDV  CONST_33  O27  N25  C21  C19     0.00   0.0  0
 WDV  Var_01    C5   N2   C1   C4     -7.82  30.0  1
 WDV  Var_02    C9   C5   N2   C1   -161.99  30.0  1
 WDV  Var_03    C10  C6   N2   C1    161.19  30.0  1
 WDV  Var_04    C10  N13  C9   C5     58.43  30.0  1
 WDV  Var_05    C9   N13  C10  C6    -58.41  30.0  1
 WDV  Var_06    N13  C9   C5   N2    -56.82  30.0  1
 WDV  Var_07    N13  C10  C6   N2     57.14  30.0  1
 WDV  Var_08    N13  C17  C18  C19   144.21  30.0  2
 WDV  Var_09    F15  C12  C7   C11   143.09  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
 WDV  plan-1  C8   0.020
 WDV  plan-1  C11  0.020
 WDV  plan-1  C4   0.020
 WDV  plan-1  C3   0.020
 WDV  plan-1  C7   0.020
 WDV  plan-1  C1   0.020
 WDV  plan-1  C12  0.020
 WDV  plan-1  N2   0.020
 WDV  plan-1  H1   0.020
 WDV  plan-1  H2   0.020
 WDV  plan-1  H3   0.020
 WDV  plan-1  H6   0.020
 WDV  plan-2  C24  0.020
 WDV  plan-2  C22  0.020
 WDV  plan-2  C19  0.020
 WDV  plan-2  C18  0.020
 WDV  plan-2  C21  0.020
 WDV  plan-2  C20  0.020
 WDV  plan-2  C17  0.020
 WDV  plan-2  N25  0.020
 WDV  plan-2  O23  0.020
 WDV  plan-2  H5   0.020
 WDV  plan-2  H7   0.020
 WDV  plan-2  H4   0.020
 WDV  plan-3  C21  0.020
 WDV  plan-3  N25  0.020
 WDV  plan-3  O27  0.020
 WDV  plan-3  O26  0.020

