# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 19:45:33 2021
#   Inital geometry file: a 118 line input string
#   Ligand name: ~{N}-[(3-chlorophenyl)methyl]-1-(1~{H}-indol-3-ylmethyl)piperidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cccc(CNC2CCN(CC2)Cc3c[nH]c4ccccc34)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
 LEZ  LEZ  ~{N}-[(3-chlorophenyl)methyl]-1-(1~{H}-indol-3-ylmethyl)piperidin-4-amine  ligand  49  25  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LEZ
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
 LEZ  C1   C   CR16  0  -0.286  17.1017  19.2759  -15.1433
 LEZ  C2   C   CR16  0  -0.270  15.9787  18.9307  -14.3724
 LEZ  C3   C   CR16  0  -0.373  15.4501  17.6553  -14.4153
 LEZ  C11  C   CH2   0  -0.487  13.0008  11.2860  -15.9019
 LEZ  C12  C   CH2   0  -0.265  13.6455  12.3279  -14.9838
 LEZ  C14  C   CH2   0  -0.292  13.6445  13.6719  -16.9628
 LEZ  C15  C   CH2   0  -0.462  13.7073  12.4966  -17.9416
 LEZ  C16  C   CH1   0  -0.024  13.7845  11.1570  -17.2021
 LEZ  C18  C   CH2   0  -0.325  13.6542   8.7664  -17.6529
 LEZ  C19  C   CR6   0   0.084  12.8723   7.7061  -18.3838
 LEZ  C20  C   CR16  0  -0.308  13.4951   6.5626  -18.8716
 LEZ  C21  C   CR16  0  -0.246  12.7577   5.5714  -19.5065
 LEZ  C22  C   CR16  0  -0.233  11.3872   5.7054  -19.6678
 LEZ  C23  C   CR6   0  -0.020  10.7760   6.8526  -19.1828
 LEZ  C24  C   CR16  0  -0.250  11.4965   7.8506  -18.5506
 LEZ  C4   C   CR56  0   0.029  16.0502  16.6990  -15.2438
 LEZ  C5   C   CR56  0   0.348  17.1801  17.0675  -16.0099
 LEZ  C6   C   CR16  0  -0.305  17.7162  18.3542  -15.9692
 LEZ  C7   C   CR5   0  -0.031  15.7766  15.3231  -15.5313
 LEZ  C8   C   CR15  0  -0.069  16.7238  14.9270  -16.4322
 LEZ  N9   N   NR15  0  -0.688  17.5635  15.9688  -16.7193
 LEZ  C10  C   CH2   0  -0.337  14.6910  14.4860  -14.9353
 LEZ  N13  N   NT    0  -0.428  14.3657  13.3368  -15.7496
 LEZ  N17  N   NH1   0  -0.609  13.2431  10.0991  -18.0431
 LEZ  CL   CL  CL    0  -0.137   9.0595   7.0418  -19.3745
 LEZ  H1   H   HCR6  0   0.248  17.4925  20.2838  -15.0892
 LEZ  H2   H   HCR6  0   0.244  15.5246  19.6780  -13.7345
 LEZ  H3   H   HCR6  0   0.240  14.5832  17.4028  -13.8167
 LEZ  H4   H   HCH2  0   0.223  11.9747  11.5713  -16.1504
 LEZ  H5   H   HCH2  0   0.243  12.9345  10.3341  -15.3708
 LEZ  H6   H   HCH2  0   0.198  12.8629  12.7826  -14.3545
 LEZ  H7   H   HCH2  0   0.226  14.3531  11.8455  -14.3028
 LEZ  H8   H   HCH2  0   0.244  14.0941  14.5551  -17.4169
 LEZ  H9   H   HCH2  0   0.202  12.5968  13.9396  -16.7436
 LEZ  H10  H   HCH2  0   0.231  14.5690  12.5990  -18.6056
 LEZ  H11  H   HCH2  0   0.223  12.8132  12.5056  -18.5713
 LEZ  H12  H   HCH1  0   0.199  14.8397  10.9622  -16.9516
 LEZ  H13  H   HCH2  0   0.246  13.4683   8.6494  -16.5814
 LEZ  H14  H   HCH2  0   0.224  14.7304   8.5874  -17.7920
 LEZ  H15  H   HCR6  0   0.254  14.5658   6.4438  -18.7575
 LEZ  H16  H   HCR6  0   0.266  13.2528   4.6872  -19.8857
 LEZ  H17  H   HCR6  0   0.277  10.8098   4.9366  -20.1627
 LEZ  H18  H   HCR6  0   0.268  11.0040   8.7431  -18.1880
 LEZ  H19  H   HCR6  0   0.257  18.5823  18.6231  -16.5608
 LEZ  H20  H   HCR5  0   0.276  16.8551  13.9669  -16.9052
 LEZ  H21  H   HNR5  0   0.406  18.3306  15.9287  -17.3685
 LEZ  H22  H   HCH2  0   0.199  13.8039  15.1145  -14.7373
 LEZ  H23  H   HCH2  0   0.242  15.0108  14.1208  -13.9529
 LEZ  H25  H   HNH1  0   0.347  13.5289  10.2556  -19.0027

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
 LEZ  C21  C22  aromatic  1.386  0.020  1.386
 LEZ  C21  C20  aromatic  1.389  0.020  1.389
 LEZ  C22  C23  aromatic  1.387  0.020  1.387
 LEZ  C20  C19  aromatic  1.391  0.020  1.391
 LEZ  C23  C24  aromatic  1.384  0.020  1.384
 LEZ  C23  CL   single    1.738  0.020  1.738
 LEZ  C19  C24  aromatic  1.393  0.020  1.393
 LEZ  C19  C18  single    1.507  0.020  1.507
 LEZ  N17  C18  single    1.448  0.020  1.448
 LEZ  N17  C16  single    1.456  0.020  1.456
 LEZ  C15  C16  single    1.532  0.020  1.532
 LEZ  C15  C14  single    1.531  0.020  1.531
 LEZ  C16  C11  single    1.524  0.020  1.524
 LEZ  C14  N13  single    1.451  0.020  1.451
 LEZ  C1   C2   aromatic  1.405  0.020  1.405
 LEZ  C1   C6   aromatic  1.382  0.020  1.382
 LEZ  C2   C3   aromatic  1.381  0.020  1.381
 LEZ  C6   C5   aromatic  1.394  0.020  1.394
 LEZ  C11  C12  single    1.531  0.020  1.531
 LEZ  C3   C4   aromatic  1.400  0.020  1.400
 LEZ  C5   C4   aromatic  1.414  0.020  1.414
 LEZ  C5   N9   aromatic  1.363  0.020  1.363
 LEZ  N13  C12  single    1.457  0.020  1.457
 LEZ  N13  C10  single    1.445  0.020  1.445
 LEZ  C4   C7   aromatic  1.432  0.020  1.432
 LEZ  N9   C8   aromatic  1.369  0.020  1.369
 LEZ  C7   C8   aromatic  1.366  0.020  1.366
 LEZ  C7   C10  single    1.495  0.020  1.495
 LEZ  C1   H1   single    0.930  0.020  1.080
 LEZ  C2   H2   single    0.930  0.020  1.080
 LEZ  C3   H3   single    0.930  0.020  1.080
 LEZ  C11  H4   single    0.970  0.020  1.090
 LEZ  C11  H5   single    0.970  0.020  1.090
 LEZ  C12  H6   single    0.970  0.020  1.090
 LEZ  C12  H7   single    0.970  0.020  1.090
 LEZ  C14  H8   single    0.970  0.020  1.090
 LEZ  C14  H9   single    0.970  0.020  1.090
 LEZ  C15  H10  single    0.970  0.020  1.090
 LEZ  C15  H11  single    0.970  0.020  1.090
 LEZ  C16  H12  single    0.970  0.020  1.090
 LEZ  C18  H13  single    0.970  0.020  1.090
 LEZ  C18  H14  single    0.970  0.020  1.090
 LEZ  C20  H15  single    0.930  0.020  1.080
 LEZ  C21  H16  single    0.930  0.020  1.080
 LEZ  C22  H17  single    0.930  0.020  1.080
 LEZ  C24  H18  single    0.930  0.020  1.080
 LEZ  C6   H19  single    0.930  0.020  1.080
 LEZ  C8   H20  single    0.930  0.020  1.080
 LEZ  N9   H21  single    0.860  0.020  1.020
 LEZ  C10  H22  single    0.970  0.020  1.090
 LEZ  C10  H23  single    0.970  0.020  1.090
 LEZ  N17  H25  single    0.890  0.020  1.040

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
 LEZ  H1   C1   C6   119.37  3.000
 LEZ  H1   C1   C2   119.34  3.000
 LEZ  C6   C1   C2   121.29  3.000
 LEZ  H2   C2   C3   119.69  3.000
 LEZ  H2   C2   C1   119.27  3.000
 LEZ  C3   C2   C1   121.04  3.000
 LEZ  H3   C3   C4   120.71  3.000
 LEZ  H3   C3   C2   120.29  3.000
 LEZ  C4   C3   C2   119.01  3.000
 LEZ  H5   C11  H4   106.31  3.000
 LEZ  H5   C11  C16  111.87  3.000
 LEZ  H4   C11  C16  108.11  3.000
 LEZ  H5   C11  C12  109.09  3.000
 LEZ  H4   C11  C12  110.72  3.000
 LEZ  C16  C11  C12  110.66  3.000
 LEZ  H7   C12  H6   106.60  3.000
 LEZ  H7   C12  N13  108.23  3.000
 LEZ  H6   C12  N13  111.43  3.000
 LEZ  H7   C12  C11  110.21  3.000
 LEZ  H6   C12  C11  108.91  3.000
 LEZ  N13  C12  C11  111.36  3.000
 LEZ  H9   C14  H8   106.13  3.000
 LEZ  H9   C14  N13  111.22  3.000
 LEZ  H8   C14  N13  109.30  3.000
 LEZ  H9   C14  C15  110.63  3.000
 LEZ  H8   C14  C15  109.80  3.000
 LEZ  N13  C14  C15  109.70  3.000
 LEZ  H11  C15  H10  107.10  3.000
 LEZ  H11  C15  C16  109.04  3.000
 LEZ  H10  C15  C16  109.61  3.000
 LEZ  H11  C15  C14  109.17  3.000
 LEZ  H10  C15  C14  110.42  3.000
 LEZ  C16  C15  C14  111.39  3.000
 LEZ  H12  C16  N17  111.04  3.000
 LEZ  H12  C16  C15  108.21  3.000
 LEZ  N17  C16  C15  109.74  3.000
 LEZ  H12  C16  C11  108.27  3.000
 LEZ  C15  C16  C11  108.18  3.000
 LEZ  N17  C16  C11  111.30  3.000
 LEZ  H14  C18  H13  105.83  3.000
 LEZ  H14  C18  N17  113.16  3.000
 LEZ  H13  C18  N17  108.31  3.000
 LEZ  H14  C18  C19  109.39  3.000
 LEZ  H13  C18  C19  108.17  3.000
 LEZ  N17  C18  C19  111.69  3.000
 LEZ  C24  C19  C20  119.05  3.000
 LEZ  C24  C19  C18  119.84  3.000
 LEZ  C20  C19  C18  121.10  3.000
 LEZ  H15  C20  C21  119.64  3.000
 LEZ  H15  C20  C19  119.73  3.000
 LEZ  C21  C20  C19  120.63  3.000
 LEZ  H16  C21  C22  119.37  3.000
 LEZ  H16  C21  C20  120.03  3.000
 LEZ  C22  C21  C20  120.59  3.000
 LEZ  H17  C22  C23  120.84  3.000
 LEZ  H17  C22  C21  120.82  3.000
 LEZ  C23  C22  C21  118.34  3.000
 LEZ  CL   C23  C24  119.09  3.000
 LEZ  CL   C23  C22  119.13  3.000
 LEZ  C24  C23  C22  121.78  3.000
 LEZ  H18  C24  C23  120.73  3.000
 LEZ  H18  C24  C19  119.66  3.000
 LEZ  C23  C24  C19  119.61  3.000
 LEZ  C7   C4   C5   107.12  3.000
 LEZ  C7   C4   C3   133.87  3.000
 LEZ  C5   C4   C3   119.01  3.000
 LEZ  N9   C5   C6   130.61  3.000
 LEZ  N9   C5   C4   107.26  3.000
 LEZ  C6   C5   C4   122.13  3.000
 LEZ  H19  C6   C5   121.38  3.000
 LEZ  H19  C6   C1   121.11  3.000
 LEZ  C5   C6   C1   117.52  3.000
 LEZ  C10  C7   C8   127.17  3.000
 LEZ  C10  C7   C4   126.64  3.000
 LEZ  C8   C7   C4   106.17  3.000
 LEZ  H20  C8   N9   120.73  3.000
 LEZ  H20  C8   C7   129.20  3.000
 LEZ  N9   C8   C7   110.07  3.000
 LEZ  H21  N9   C8   124.96  3.000
 LEZ  H21  N9   C5   125.65  3.000
 LEZ  C8   N9   C5   109.38  3.000
 LEZ  H23  C10  H22  105.26  3.000
 LEZ  H23  C10  N13  107.80  3.000
 LEZ  H22  C10  N13  111.87  3.000
 LEZ  H23  C10  C7   109.39  3.000
 LEZ  H22  C10  C7   109.63  3.000
 LEZ  N13  C10  C7   112.58  3.000
 LEZ  C10  N13  C14  113.54  3.000
 LEZ  C10  N13  C12  111.45  3.000
 LEZ  C14  N13  C12  110.72  3.000
 LEZ  H25  N17  C18  108.50  3.000
 LEZ  H25  N17  C16  109.26  3.000
 LEZ  C18  N17  C16  114.05  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
 LEZ  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 LEZ  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 LEZ  CONST_03  N9   C5   C6   C1   180.00   0.0  0
 LEZ  CONST_04  C5   C6   C1   C2     0.00   0.0  0
 LEZ  CONST_05  C5   C4   C3   C2     0.00   0.0  0
 LEZ  CONST_06  C7   C4   C3   C2   180.00   0.0  0
 LEZ  CONST_07  C6   C1   C2   C3     0.00   0.0  0
 LEZ  CONST_08  C6   C5   C4   C3     0.00   0.0  0
 LEZ  CONST_09  N9   C5   C4   C3   180.00   0.0  0
 LEZ  CONST_10  C8   C7   C4   C3   180.00   0.0  0
 LEZ  CONST_11  C22  C21  C20  C19    0.00   0.0  0
 LEZ  CONST_12  C22  C23  C24  C19    0.00   0.0  0
 LEZ  CONST_13  C23  C22  C21  C20    0.00   0.0  0
 LEZ  CONST_14  C23  C24  C19  C20    0.00   0.0  0
 LEZ  CONST_15  C24  C23  C22  C21    0.00   0.0  0
 LEZ  CONST_16  C24  C19  C20  C21    0.00   0.0  0
 LEZ  CONST_17  C8   N9   C5   C4     0.00   0.0  0
 LEZ  CONST_18  N9   C8   C7   C4     0.00   0.0  0
 LEZ  CONST_19  C8   C7   C4   C5     0.00   0.0  0
 LEZ  CONST_20  C7   C8   N9   C5     0.00   0.0  0
 LEZ  CONST_21  C7   C4   C5   C6   180.00   0.0  0
 LEZ  CONST_22  C8   N9   C5   C6   180.00   0.0  0
 LEZ  CONST_23  N9   C5   C4   C7     0.00   0.0  0
 LEZ  CONST_24  C10  C7   C4   C3     0.00   0.0  0
 LEZ  CONST_25  C21  C20  C19  C18  180.00   0.0  0
 LEZ  CONST_26  C23  C24  C19  C18  180.00   0.0  0
 LEZ  CONST_27  CL   C23  C24  C19  180.00   0.0  0
 LEZ  CONST_28  CL   C23  C22  C21  180.00   0.0  0
 LEZ  CONST_29  C10  C7   C4   C5   180.00   0.0  0
 LEZ  CONST_30  C10  C7   C8   N9   180.00   0.0  0
 LEZ  CONST_31  H3   C3   C2   C1   180.00   0.0  0
 LEZ  CONST_32  H19  C6   C1   C2   180.00   0.0  0
 LEZ  CONST_33  H1   C1   C2   C3   180.00   0.0  0
 LEZ  CONST_34  H16  C21  C20  C19  180.00   0.0  0
 LEZ  CONST_35  H17  C22  C21  C20  180.00   0.0  0
 LEZ  CONST_36  H18  C24  C19  C20  180.00   0.0  0
 LEZ  CONST_37  H15  C20  C21  C22  180.00   0.0  0
 LEZ  CONST_38  H2   C2   C3   C4   180.00   0.0  0
 LEZ  CONST_39  H21  N9   C5   C4   180.00   0.0  0
 LEZ  CONST_40  H20  C8   C7   C4   180.00   0.0  0
 LEZ  Var_01    C14  N13  C12  C11   38.41  30.0  1
 LEZ  Var_02    C15  C14  N13  C12  -70.46  30.0  1
 LEZ  Var_03    N13  C14  C15  C16   30.72  30.0  1
 LEZ  Var_04    N13  C12  C11  C16   27.56  30.0  1
 LEZ  Var_05    C7   C10  N13  C12  161.68  30.0  3
 LEZ  Var_06    N13  C10  C7   C4   158.80  30.0  2
 LEZ  Var_07    C19  C18  N17  C16  169.38  30.0  3
 LEZ  Var_08    N17  C18  C19  C20  138.78  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
 LEZ  chir_01  C16  N17  C15  C11  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
 LEZ  plan-1  C18  0.020
 LEZ  plan-1  C19  0.020
 LEZ  plan-1  C20  0.020
 LEZ  plan-1  C21  0.020
 LEZ  plan-1  C22  0.020
 LEZ  plan-1  C23  0.020
 LEZ  plan-1  C24  0.020
 LEZ  plan-1  CL   0.020
 LEZ  plan-1  H15  0.020
 LEZ  plan-1  H16  0.020
 LEZ  plan-1  H17  0.020
 LEZ  plan-1  H18  0.020
 LEZ  plan-2  C1   0.020
 LEZ  plan-2  C2   0.020
 LEZ  plan-2  C3   0.020
 LEZ  plan-2  C4   0.020
 LEZ  plan-2  C5   0.020
 LEZ  plan-2  C6   0.020
 LEZ  plan-2  C7   0.020
 LEZ  plan-2  C8   0.020
 LEZ  plan-2  N9   0.020
 LEZ  plan-2  C10  0.020
 LEZ  plan-2  H1   0.020
 LEZ  plan-2  H2   0.020
 LEZ  plan-2  H3   0.020
 LEZ  plan-2  H19  0.020
 LEZ  plan-2  H20  0.020
 LEZ  plan-2  H21  0.020

