# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 17:29:50 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: N-(1-benzylpiperidin-4-yl)-N'-[3-(trifluoromethyl)phenyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1cccc(NC(=O)NC2CCN(CC2)Cc3ccccc3)c1
#
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
 8Z7  8Z7  N-(1-benzylpiperidin-4-yl)-N'-[3-(trifluoromethyl)phenyl]urea  ligand  49  27  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8Z7
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
 8Z7  C4   C  CH2   0  -0.448   2.3730   0.6541   0.9916
 8Z7  C14  C  CH2   0  -0.316   5.1069  -1.4503  -0.4744
 8Z7  C5   C  CH1   0  -0.060   1.1670   0.0131   0.3185
 8Z7  C11  C  CR6   0  -0.172  -5.6071   0.3299  -0.3587
 8Z7  C7   C  CR6   0   0.399  -3.5349   1.4381   0.1689
 8Z7  C8   C  CR16  0  -0.339  -4.2762   2.5527   0.5774
 8Z7  C9   C  CR16  0  -0.229  -5.6553   2.5492   0.5093
 8Z7  C10  C  CR16  0  -0.315  -6.3409   1.4337   0.0459
 8Z7  C12  C  CR16  0  -0.341  -4.2165   0.3199  -0.3072
 8Z7  N1   N  NT    0  -0.412   3.8878  -0.6750  -0.4079
 8Z7  N2   N  NH1   0  -0.690   0.0472   0.9318   0.3325
 8Z7  C3   C  CH2   0  -0.280   3.5663  -0.2869   0.9520
 8Z7  N3   N  NH1   0  -0.794  -2.1504   1.5393   0.2253
 8Z7  F3   F  F     0  -0.315  -5.8457  -1.2463  -2.0888
 8Z7  F1   F  F     0  -0.316  -6.0602  -1.9604  -0.0751
 8Z7  F2   F  F     0  -0.303  -7.6121  -0.7631  -0.9608
 8Z7  O    O  O     0  -0.519  -1.5565  -0.6701   0.2534
 8Z7  C1   C  CH2   0  -0.432   1.5507  -0.4375  -1.0886
 8Z7  C2   C  CH2   0  -0.285   2.7702  -1.3457  -1.0442
 8Z7  C15  C  CR6   0   0.084   6.3333  -0.6251  -0.1747
 8Z7  C20  C  CR16  0  -0.283   6.4701   0.6584  -0.7002
 8Z7  C19  C  CR16  0  -0.242   7.6139   1.4042  -0.4550
 8Z7  C18  C  CR16  0  -0.271   8.6412   0.8776   0.3200
 8Z7  C17  C  CR16  0  -0.242   8.5127  -0.3986   0.8495
 8Z7  C16  C  CR16  0  -0.314   7.3631  -1.1408   0.6051
 8Z7  H1   H  HCH2  0   0.226   2.6323   1.5853   0.4773
 8Z7  H2   H  HCH2  0   0.244   2.1398   0.9053   2.0285
 8Z7  H3   H  HCH2  0   0.210   5.0866  -2.3258   0.1968
 8Z7  H4   H  HCH2  0   0.251   5.1949  -1.8504  -1.4895
 8Z7  H5   H  HCH1  0   0.237   0.8765  -0.8663   0.9007
 8Z7  H6   H  HCR6  0   0.277  -3.7612   3.4293   0.9517
 8Z7  H7   H  HCR6  0   0.270  -6.2051   3.4233   0.8310
 8Z7  H8   H  HCR6  0   0.268  -7.4206   1.4448   0.0071
 8Z7  H9   H  HCR6  0   0.287  -3.6669  -0.5450  -0.6439
 8Z7  H11  H  HNH1  0   0.394   0.2535   1.9082   0.1871
 8Z7  H12  H  HCH2  0   0.245   4.4316   0.2102   1.3942
 8Z7  H13  H  HCH2  0   0.192   3.3540  -1.1705   1.5809
 8Z7  H14  H  HNH1  0   0.410  -1.7999   2.4697   0.3960
 8Z7  H15  H  HCH2  0   0.240   0.7190  -0.9646  -1.5594
 8Z7  H16  H  HCH2  0   0.219   1.7756   0.4405  -1.7019
 8Z7  H17  H  HCH2  0   0.240   3.0607  -1.6214  -2.0605
 8Z7  H18  H  HCH2  0   0.189   2.5078  -2.2851  -0.5254
 8Z7  H19  H  HCR6  0   0.243   5.6652   1.0750  -1.2924
 8Z7  H20  H  HCR6  0   0.251   7.7062   2.4009  -0.8678
 8Z7  H21  H  HCR6  0   0.252   9.5320   1.4618   0.5131
 8Z7  H22  H  HCR6  0   0.252   9.3025  -0.8159   1.4609
 8Z7  H23  H  HCR6  0   0.246   7.2642  -2.1333   1.0302
 8Z7  C6   C  C     0   0.742  -1.2355   0.5093   0.2621
 8Z7  C13  C  CT    0   1.047  -6.2866  -0.9028  -0.8691

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
 8Z7  C14  C15  single    1.508  0.020  1.508
 8Z7  C14  N1   single    1.446  0.020  1.446
 8Z7  C20  C15  aromatic  1.394  0.020  1.394
 8Z7  C20  C19  aromatic  1.387  0.020  1.387
 8Z7  C15  C16  aromatic  1.391  0.020  1.391
 8Z7  C16  C17  aromatic  1.390  0.020  1.390
 8Z7  C19  C18  aromatic  1.390  0.020  1.390
 8Z7  C17  C18  aromatic  1.388  0.020  1.388
 8Z7  N1   C2   single    1.450  0.020  1.450
 8Z7  N1   C3   single    1.450  0.020  1.450
 8Z7  C2   C1   single    1.521  0.020  1.521
 8Z7  C3   C4   single    1.520  0.020  1.520
 8Z7  C1   C5   single    1.527  0.020  1.527
 8Z7  C4   C5   single    1.523  0.020  1.523
 8Z7  C5   N2   single    1.448  0.020  1.448
 8Z7  N2   C6   single    1.352  0.020  1.352
 8Z7  C6   O    double    1.222  0.020  1.222
 8Z7  C6   N3   single    1.378  0.020  1.378
 8Z7  N3   C7   single    1.389  0.020  1.389
 8Z7  C7   C12  aromatic  1.393  0.020  1.393
 8Z7  C7   C8   aromatic  1.399  0.020  1.399
 8Z7  C12  C11  aromatic  1.392  0.020  1.392
 8Z7  C8   C9   aromatic  1.381  0.020  1.381
 8Z7  F3   C13  single    1.342  0.020  1.342
 8Z7  C11  C13  single    1.497  0.020  1.497
 8Z7  C11  C10  aromatic  1.386  0.020  1.386
 8Z7  F1   C13  single    1.342  0.020  1.342
 8Z7  C13  F2   single    1.336  0.020  1.336
 8Z7  C9   C10  aromatic  1.389  0.020  1.389
 8Z7  C4   H1   single    0.970  0.020  1.090
 8Z7  C4   H2   single    0.970  0.020  1.090
 8Z7  C14  H3   single    0.970  0.020  1.090
 8Z7  C14  H4   single    0.970  0.020  1.090
 8Z7  C5   H5   single    0.970  0.020  1.090
 8Z7  C8   H6   single    0.930  0.020  1.080
 8Z7  C9   H7   single    0.930  0.020  1.080
 8Z7  C10  H8   single    0.930  0.020  1.080
 8Z7  C12  H9   single    0.930  0.020  1.080
 8Z7  N2   H11  single    0.860  0.020  1.020
 8Z7  C3   H12  single    0.970  0.020  1.090
 8Z7  C3   H13  single    0.970  0.020  1.090
 8Z7  N3   H14  single    0.860  0.020  1.020
 8Z7  C1   H15  single    0.970  0.020  1.090
 8Z7  C1   H16  single    0.970  0.020  1.090
 8Z7  C2   H17  single    0.970  0.020  1.090
 8Z7  C2   H18  single    0.970  0.020  1.090
 8Z7  C20  H19  single    0.930  0.020  1.080
 8Z7  C19  H20  single    0.930  0.020  1.080
 8Z7  C18  H21  single    0.930  0.020  1.080
 8Z7  C17  H22  single    0.930  0.020  1.080
 8Z7  C16  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
 8Z7  H2   C4   H1   107.52  3.000
 8Z7  H2   C4   C3   109.56  3.000
 8Z7  H1   C4   C3   109.17  3.000
 8Z7  H2   C4   C5   110.33  3.000
 8Z7  H1   C4   C5   109.75  3.000
 8Z7  C3   C4   C5   110.46  3.000
 8Z7  H4   C14  H3   106.00  3.000
 8Z7  H4   C14  C15  108.60  3.000
 8Z7  H3   C14  C15  109.16  3.000
 8Z7  H4   C14  N1   107.84  3.000
 8Z7  H3   C14  N1   112.45  3.000
 8Z7  C15  C14  N1   112.52  3.000
 8Z7  H5   C5   C1   108.67  3.000
 8Z7  H5   C5   N2   107.43  3.000
 8Z7  C1   C5   N2   112.98  3.000
 8Z7  H5   C5   C4   108.27  3.000
 8Z7  N2   C5   C4   109.94  3.000
 8Z7  C1   C5   C4   109.43  3.000
 8Z7  C13  C11  C12  117.40  3.000
 8Z7  C13  C11  C10  121.00  3.000
 8Z7  C12  C11  C10  121.60  3.000
 8Z7  N3   C7   C12  124.04  3.000
 8Z7  C12  C7   C8   118.67  3.000
 8Z7  N3   C7   C8   117.26  3.000
 8Z7  H6   C8   C9   119.60  3.000
 8Z7  H6   C8   C7   119.57  3.000
 8Z7  C9   C8   C7   120.84  3.000
 8Z7  H7   C9   C10  119.83  3.000
 8Z7  H7   C9   C8   119.41  3.000
 8Z7  C10  C9   C8   120.76  3.000
 8Z7  H8   C10  C9   119.80  3.000
 8Z7  H8   C10  C11  121.79  3.000
 8Z7  C9   C10  C11  118.41  3.000
 8Z7  H9   C12  C7   120.06  3.000
 8Z7  H9   C12  C11  120.22  3.000
 8Z7  C7   C12  C11  119.71  3.000
 8Z7  C2   N1   C3   111.36  3.000
 8Z7  C3   N1   C14  111.93  3.000
 8Z7  C2   N1   C14  112.43  3.000
 8Z7  H11  N2   C6   119.27  3.000
 8Z7  H11  N2   C5   117.04  3.000
 8Z7  C6   N2   C5   122.32  3.000
 8Z7  H13  C3   H12  106.61  3.000
 8Z7  H13  C3   N1   111.24  3.000
 8Z7  H12  C3   N1   109.03  3.000
 8Z7  H13  C3   C4   109.22  3.000
 8Z7  H12  C3   C4   109.25  3.000
 8Z7  N1   C3   C4   111.35  3.000
 8Z7  H14  N3   C7   114.85  3.000
 8Z7  H14  N3   C6   117.01  3.000
 8Z7  C7   N3   C6   127.46  3.000
 8Z7  H16  C1   H15  107.60  3.000
 8Z7  H16  C1   C2   109.31  3.000
 8Z7  H15  C1   C2   109.58  3.000
 8Z7  H16  C1   C5   109.36  3.000
 8Z7  H15  C1   C5   110.40  3.000
 8Z7  C2   C1   C5   110.54  3.000
 8Z7  H18  C2   H17  106.58  3.000
 8Z7  H18  C2   C1   109.33  3.000
 8Z7  H17  C2   C1   109.68  3.000
 8Z7  H18  C2   N1   111.73  3.000
 8Z7  H17  C2   N1   108.65  3.000
 8Z7  C1   C2   N1   110.76  3.000
 8Z7  C16  C15  C20  118.70  3.000
 8Z7  C16  C15  C14  120.70  3.000
 8Z7  C20  C15  C14  120.58  3.000
 8Z7  H19  C20  C19  120.19  3.000
 8Z7  H19  C20  C15  119.18  3.000
 8Z7  C19  C20  C15  120.62  3.000
 8Z7  H20  C19  C18  119.87  3.000
 8Z7  H20  C19  C20  119.85  3.000
 8Z7  C18  C19  C20  120.27  3.000
 8Z7  H21  C18  C17  120.29  3.000
 8Z7  H21  C18  C19  120.20  3.000
 8Z7  C17  C18  C19  119.51  3.000
 8Z7  H22  C17  C16  119.79  3.000
 8Z7  H22  C17  C18  120.17  3.000
 8Z7  C16  C17  C18  120.04  3.000
 8Z7  H23  C16  C17  119.69  3.000
 8Z7  H23  C16  C15  119.45  3.000
 8Z7  C17  C16  C15  120.86  3.000
 8Z7  O    C6   N3   123.14  3.000
 8Z7  N3   C6   N2   113.42  3.000
 8Z7  O    C6   N2   123.43  3.000
 8Z7  F2   C13  F1   106.88  3.000
 8Z7  F2   C13  F3   106.88  3.000
 8Z7  F1   C13  F3   106.30  3.000
 8Z7  F2   C13  C11  112.81  3.000
 8Z7  F1   C13  C11  111.75  3.000
 8Z7  F3   C13  C11  111.82  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
 8Z7  CONST_01  C8   C7   C12  C11    0.00   0.0  0
 8Z7  CONST_02  C8   C9   C10  C11    0.00   0.0  0
 8Z7  CONST_03  C10  C11  C12  C7     0.00   0.0  0
 8Z7  CONST_04  C10  C9   C8   C7     0.00   0.0  0
 8Z7  CONST_05  C12  C7   C8   C9     0.00   0.0  0
 8Z7  CONST_06  C12  C11  C10  C9     0.00   0.0  0
 8Z7  CONST_07  C18  C19  C20  C15    0.00   0.0  0
 8Z7  CONST_08  C18  C17  C16  C15    0.00   0.0  0
 8Z7  CONST_09  C17  C16  C15  C20    0.00   0.0  0
 8Z7  CONST_10  C17  C18  C19  C20    0.00   0.0  0
 8Z7  CONST_11  C16  C15  C20  C19    0.00   0.0  0
 8Z7  CONST_12  C16  C17  C18  C19    0.00   0.0  0
 8Z7  CONST_13  C19  C20  C15  C14  180.00   0.0  0
 8Z7  CONST_14  C17  C16  C15  C14  180.00   0.0  0
 8Z7  CONST_15  N3   C7   C12  C11  180.00   0.0  0
 8Z7  CONST_16  C13  C11  C12  C7   180.00   0.0  0
 8Z7  CONST_17  N3   C7   C8   C9   180.00   0.0  0
 8Z7  CONST_18  C13  C11  C10  C9   180.00   0.0  0
 8Z7  CONST_19  H7   C9   C10  C11  180.00   0.0  0
 8Z7  CONST_20  H9   C12  C7   C8   180.00   0.0  0
 8Z7  CONST_21  H8   C10  C9   C8   180.00   0.0  0
 8Z7  CONST_22  H6   C8   C9   C10  180.00   0.0  0
 8Z7  CONST_23  H20  C19  C20  C15  180.00   0.0  0
 8Z7  CONST_24  H22  C17  C16  C15  180.00   0.0  0
 8Z7  CONST_25  H23  C16  C15  C20  180.00   0.0  0
 8Z7  CONST_26  H21  C18  C19  C20  180.00   0.0  0
 8Z7  CONST_27  H19  C20  C19  C18  180.00   0.0  0
 8Z7  CONST_30  H14  N3   C7   C8     0.00   0.0  0
 8Z7  CONST_31  O    C6   N2   C5     0.00   0.0  0
 8Z7  CONST_32  O    C6   N3   C7     0.00   0.0  0
 8Z7  CONST_33  N2   C6   N3   C7   180.00   0.0  0
 8Z7  CONST_34  N3   C6   N2   C5   180.00   0.0  0
 8Z7  CONST_35  H11  N2   C6   O    180.00   0.0  0
 8Z7  Var_01    C2   N1   C3   C4   -59.53  30.0  1
 8Z7  Var_02    N1   C2   C1   C5   -57.42  30.0  1
 8Z7  Var_03    N1   C3   C4   C5    56.71  30.0  1
 8Z7  Var_04    C1   C2   N1   C3    59.71  30.0  1
 8Z7  Var_05    C20  C15  C14  N1   -42.28  30.0  2
 8Z7  Var_06    C15  C14  N1   C3   -69.82  30.0  2
 8Z7  Var_07    F3   C13  C11  C10  124.61  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
 8Z7  chir_01  C5  C1  C4  N2  negativ

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
 8Z7  plan-1  C11  0.020
 8Z7  plan-1  C7   0.020
 8Z7  plan-1  C8   0.020
 8Z7  plan-1  C9   0.020
 8Z7  plan-1  C10  0.020
 8Z7  plan-1  C12  0.020
 8Z7  plan-1  N3   0.020
 8Z7  plan-1  H6   0.020
 8Z7  plan-1  H7   0.020
 8Z7  plan-1  H8   0.020
 8Z7  plan-1  H9   0.020
 8Z7  plan-1  C13  0.020
 8Z7  plan-2  C14  0.020
 8Z7  plan-2  C15  0.020
 8Z7  plan-2  C20  0.020
 8Z7  plan-2  C19  0.020
 8Z7  plan-2  C18  0.020
 8Z7  plan-2  C17  0.020
 8Z7  plan-2  C16  0.020
 8Z7  plan-2  H19  0.020
 8Z7  plan-2  H20  0.020
 8Z7  plan-2  H21  0.020
 8Z7  plan-2  H22  0.020
 8Z7  plan-2  H23  0.020
 8Z7  plan-3  C5   0.020
 8Z7  plan-3  C7   0.020
 8Z7  plan-3  N2   0.020
 8Z7  plan-3  N3   0.020
 8Z7  plan-3  O    0.020
 8Z7  plan-3  H11  0.020
 8Z7  plan-3  H14  0.020
 8Z7  plan-3  C6   0.020

