# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 07:01:20 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: 3-[4-[4-(4-cyanophenyl)piperazin-1-yl]butyl]-6-oxidanyl-1~{H}-indole-5-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc2[nH]cc(CCCCN3CCN(CC3)c4ccc(cc4)C#N)c2cc1C#N
#
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
 70M  70M  3-[4-[4-(4-cyanophenyl)piperazin-1-yl]butyl]-6-oxidanyl-1~{H}-indole-5-carbonitrile  ligand  55  30  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_70M
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
 70M  C1   C  CR56  0   0.029  -5.3345   0.7197   0.2744
 70M  C2   C  CR56  0   0.403  -6.5291   1.3190  -0.2015
 70M  C3   C  CR5   0   0.043  -4.3658   1.7682   0.4452
 70M  C7   C  CR15  0  -0.093  -4.9970   2.9152   0.0750
 70M  C8   C  CH2   0  -0.536  -2.9553   1.6065   0.9034
 70M  C9   C  CR6   0  -0.107  -6.4685  -1.3887   0.2314
 70M  C10  C  CR6   0   0.353  -7.6532  -0.7721  -0.2499
 70M  C11  C  CH2   0  -0.415  -2.0411   1.0055  -0.1660
 70M  C12  C  CSP   0   0.018  -6.4694  -2.7898   0.4563
 70M  C14  C  CH2   0  -0.454  -0.6136   0.8166   0.3319
 70M  C16  C  CH2   0  -0.252   0.3116   0.3378  -0.7772
 70M  C19  C  CH2   0  -0.286   2.3994  -0.6427  -1.3939
 70M  C20  C  CH2   0  -0.311   3.7385   0.6251   0.7510
 70M  C21  C  CH2   0  -0.310   3.7423  -1.1438  -0.9039
 70M  C24  C  CR16  0  -0.344   6.6357  -0.8613  -1.1145
 70M  C27  C  CR16  0  -0.226   7.9449   0.3836   0.9839
 70M  C4   C  CR16  0  -0.377  -5.3161  -0.6470   0.4899
 70M  N5   N  NR15  0  -0.694  -6.2904   2.6458  -0.3144
 70M  C6   C  CR16  0  -0.400  -7.6858   0.5914  -0.4682
 70M  O13  O  OH1   0  -0.613  -8.7728  -1.4709  -0.5035
 70M  N15  N  NS    0  -0.254  -6.4995  -3.9309   0.6308
 70M  N17  N  NT    0  -0.425   1.6367  -0.0438  -0.3187
 70M  C18  C  CH2   0  -0.290   2.3909   1.0710   0.2143
 70M  N22  N  NT    0  -0.518   4.5033  -0.0827  -0.2594
 70M  C23  C  CR6   0   0.419   5.8655  -0.1732  -0.1509
 70M  C25  C  CR16  0  -0.359   6.5697   0.4352   0.9100
 70M  C26  C  CR16  0  -0.226   8.0079  -0.9112  -1.0372
 70M  C28  C  CR6   0  -0.040   8.6882  -0.2874   0.0125
 70M  C29  C  CSP   0   0.039  10.1050  -0.3389   0.0895
 70M  N30  N  NS    0  -0.272  11.2571  -0.3799   0.1487
 70M  H1   H  HCR5  0   0.285  -4.6253   3.9279   0.0577
 70M  H2   H  HCH2  0   0.242  -2.5578   2.5777   1.2097
 70M  H3   H  HCH2  0   0.231  -2.9322   0.9704   1.7948
 70M  H4   H  HCH2  0   0.223  -2.4446   0.0442  -0.4994
 70M  H5   H  HCH2  0   0.222  -2.0445   1.6610  -1.0423
 70M  H6   H  HCH2  0   0.224  -0.2597   1.7659   0.7450
 70M  H7   H  HCH2  0   0.221  -0.5984   0.0929   1.1527
 70M  H8   H  HCH2  0   0.227  -0.1342  -0.5432  -1.2492
 70M  H9   H  HCH2  0   0.189   0.3698   1.1122  -1.5623
 70M  H10  H  HCH2  0   0.199   2.5575   0.0690  -2.2228
 70M  H11  H  HCH2  0   0.247   1.8486  -1.4942  -1.7995
 70M  H12  H  HCH2  0   0.259   4.2715   1.5230   1.0576
 70M  H13  H  HCH2  0   0.230   3.5971   0.0009   1.6435
 70M  H14  H  HCH2  0   0.233   3.5924  -1.9735  -0.2011
 70M  H15  H  HCH2  0   0.263   4.2795  -1.5356  -1.7625
 70M  H16  H  HCR6  0   0.276   6.1657  -1.3452  -1.9570
 70M  H17  H  HCR6  0   0.275   8.4455   0.8585   1.8171
 70M  H18  H  HCR6  0   0.272  -4.4294  -1.1473   0.8587
 70M  H19  H  HNR5  0   0.414  -6.9553   3.3381  -0.6175
 70M  H20  H  HCR6  0   0.281  -8.5882   1.0657  -0.8327
 70M  H21  H  HOH1  0   0.479  -8.6589  -2.4172  -0.3564
 70M  H23  H  HCH2  0   0.252   1.8509   1.5307   1.0425
 70M  H24  H  HCH2  0   0.198   2.5453   1.8534  -0.5498
 70M  H25  H  HCR6  0   0.279   6.0472   0.9441   1.7053
 70M  H26  H  HCR6  0   0.275   8.5607  -1.4360  -1.8051

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
 70M  N15  C12  triple    1.155  0.020  1.155
 70M  C27  C25  aromatic  1.378  0.020  1.378
 70M  C27  C28  aromatic  1.395  0.020  1.395
 70M  C25  C23  aromatic  1.411  0.020  1.411
 70M  C20  C18  single    1.518  0.020  1.518
 70M  C20  N22  single    1.451  0.020  1.451
 70M  C18  N17  single    1.448  0.020  1.448
 70M  C12  C9   single    1.419  0.020  1.419
 70M  N30  C29  triple    1.154  0.020  1.154
 70M  C29  C28  single    1.420  0.020  1.420
 70M  C28  C26  aromatic  1.398  0.020  1.398
 70M  C23  N22  single    1.370  0.020  1.370
 70M  C23  C24  aromatic  1.412  0.020  1.412
 70M  N22  C21  single    1.456  0.020  1.456
 70M  C9   C4   aromatic  1.395  0.020  1.395
 70M  C9   C10  aromatic  1.420  0.020  1.420
 70M  N17  C16  single    1.453  0.020  1.453
 70M  N17  C19  single    1.448  0.020  1.448
 70M  C16  C14  single    1.522  0.020  1.522
 70M  O13  C10  single    1.344  0.020  1.344
 70M  C4   C1   aromatic  1.384  0.020  1.384
 70M  C26  C24  aromatic  1.375  0.020  1.375
 70M  C10  C6   aromatic  1.381  0.020  1.381
 70M  C19  C21  single    1.515  0.020  1.515
 70M  C11  C14  single    1.524  0.020  1.524
 70M  C11  C8   single    1.530  0.020  1.530
 70M  C1   C2   aromatic  1.419  0.020  1.419
 70M  C1   C3   aromatic  1.438  0.020  1.438
 70M  C6   C2   aromatic  1.392  0.020  1.392
 70M  C8   C3   single    1.492  0.020  1.492
 70M  C2   N5   aromatic  1.353  0.020  1.353
 70M  C3   C7   aromatic  1.361  0.020  1.361
 70M  N5   C7   aromatic  1.377  0.020  1.377
 70M  C7   H1   single    0.930  0.020  1.080
 70M  C8   H2   single    0.970  0.020  1.090
 70M  C8   H3   single    0.970  0.020  1.090
 70M  C11  H4   single    0.970  0.020  1.090
 70M  C11  H5   single    0.970  0.020  1.090
 70M  C14  H6   single    0.970  0.020  1.090
 70M  C14  H7   single    0.970  0.020  1.090
 70M  C16  H8   single    0.970  0.020  1.090
 70M  C16  H9   single    0.970  0.020  1.090
 70M  C19  H10  single    0.970  0.020  1.090
 70M  C19  H11  single    0.970  0.020  1.090
 70M  C20  H12  single    0.970  0.020  1.090
 70M  C20  H13  single    0.970  0.020  1.090
 70M  C21  H14  single    0.970  0.020  1.090
 70M  C21  H15  single    0.970  0.020  1.090
 70M  C24  H16  single    0.930  0.020  1.080
 70M  C27  H17  single    0.930  0.020  1.080
 70M  C4   H18  single    0.930  0.020  1.080
 70M  N5   H19  single    0.860  0.020  1.020
 70M  C6   H20  single    0.930  0.020  1.080
 70M  O13  H21  single    0.850  0.020  0.980
 70M  C18  H23  single    0.970  0.020  1.090
 70M  C18  H24  single    0.970  0.020  1.090
 70M  C25  H25  single    0.930  0.020  1.080
 70M  C26  H26  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
 70M  C4   C1   C3   133.85  3.000
 70M  C3   C1   C2   107.41  3.000
 70M  C4   C1   C2   118.73  3.000
 70M  C6   C2   N5   130.03  3.000
 70M  N5   C2   C1   107.08  3.000
 70M  C6   C2   C1   122.89  3.000
 70M  C8   C3   C7   127.85  3.000
 70M  C7   C3   C1   105.65  3.000
 70M  C8   C3   C1   126.48  3.000
 70M  H1   C7   N5   120.18  3.000
 70M  H1   C7   C3   129.48  3.000
 70M  N5   C7   C3   110.34  3.000
 70M  H3   C8   H2   106.28  3.000
 70M  H3   C8   C11  109.15  3.000
 70M  H2   C8   C11  109.12  3.000
 70M  H3   C8   C3   109.44  3.000
 70M  H2   C8   C3   109.49  3.000
 70M  C11  C8   C3   113.13  3.000
 70M  C4   C9   C12  119.75  3.000
 70M  C4   C9   C10  121.43  3.000
 70M  C12  C9   C10  118.82  3.000
 70M  O13  C10  C6   117.63  3.000
 70M  C6   C10  C9   120.13  3.000
 70M  O13  C10  C9   122.23  3.000
 70M  H5   C11  H4   106.32  3.000
 70M  H5   C11  C14  109.80  3.000
 70M  H4   C11  C14  109.64  3.000
 70M  H5   C11  C8   108.82  3.000
 70M  H4   C11  C8   109.73  3.000
 70M  C14  C11  C8   112.35  3.000
 70M  N15  C12  C9   180.00  3.000
 70M  H7   C14  H6   106.62  3.000
 70M  H7   C14  C16  109.28  3.000
 70M  H6   C14  C16  110.59  3.000
 70M  H7   C14  C11  109.88  3.000
 70M  H6   C14  C11  108.59  3.000
 70M  C16  C14  C11  111.75  3.000
 70M  H9   C16  H8   106.22  3.000
 70M  H9   C16  N17  111.12  3.000
 70M  H8   C16  N17  107.22  3.000
 70M  H9   C16  C14  109.25  3.000
 70M  H8   C16  C14  108.66  3.000
 70M  N17  C16  C14  114.02  3.000
 70M  H11  C19  H10  107.22  3.000
 70M  H11  C19  N17  109.43  3.000
 70M  H10  C19  N17  111.49  3.000
 70M  H11  C19  C21  108.02  3.000
 70M  H10  C19  C21  109.22  3.000
 70M  N17  C19  C21  111.32  3.000
 70M  H13  C20  H12  107.64  3.000
 70M  H13  C20  N22  110.88  3.000
 70M  H12  C20  N22  109.90  3.000
 70M  H13  C20  C18  109.88  3.000
 70M  H12  C20  C18  106.98  3.000
 70M  N22  C20  C18  111.41  3.000
 70M  H15  C21  H14  107.52  3.000
 70M  H15  C21  N22  110.75  3.000
 70M  H14  C21  N22  109.80  3.000
 70M  H15  C21  C19  107.59  3.000
 70M  H14  C21  C19  109.64  3.000
 70M  N22  C21  C19  111.43  3.000
 70M  H16  C24  C26  117.52  3.000
 70M  H16  C24  C23  120.89  3.000
 70M  C26  C24  C23  121.56  3.000
 70M  H17  C27  C28  120.05  3.000
 70M  H17  C27  C25  119.12  3.000
 70M  C28  C27  C25  120.82  3.000
 70M  H18  C4   C9   119.61  3.000
 70M  H18  C4   C1   121.35  3.000
 70M  C9   C4   C1   119.04  3.000
 70M  H19  N5   C7   124.81  3.000
 70M  H19  N5   C2   125.67  3.000
 70M  C7   N5   C2   109.51  3.000
 70M  H20  C6   C10  120.35  3.000
 70M  H20  C6   C2   121.87  3.000
 70M  C10  C6   C2   117.77  3.000
 70M  H21  O13  C10  112.52  3.000
 70M  C18  N17  C19  108.51  3.000
 70M  C19  N17  C16  110.77  3.000
 70M  C18  N17  C16  112.89  3.000
 70M  H24  C18  H23  107.21  3.000
 70M  H24  C18  N17  111.32  3.000
 70M  H23  C18  N17  110.26  3.000
 70M  H24  C18  C20  109.19  3.000
 70M  H23  C18  C20  107.17  3.000
 70M  N17  C18  C20  111.51  3.000
 70M  C23  N22  C21  120.44  3.000
 70M  C21  N22  C20  112.84  3.000
 70M  C23  N22  C20  120.08  3.000
 70M  C25  C23  N22  121.83  3.000
 70M  N22  C23  C24  121.37  3.000
 70M  C25  C23  C24  116.79  3.000
 70M  H25  C25  C23  121.05  3.000
 70M  H25  C25  C27  117.47  3.000
 70M  C23  C25  C27  121.47  3.000
 70M  H26  C26  C28  120.06  3.000
 70M  H26  C26  C24  119.17  3.000
 70M  C28  C26  C24  120.77  3.000
 70M  C29  C28  C26  120.68  3.000
 70M  C26  C28  C27  118.57  3.000
 70M  C29  C28  C27  120.75  3.000
 70M  N30  C29  C28  180.00  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
 70M  CONST_01  C10  C9   C4   C1      0.00   0.0  0
 70M  CONST_02  C10  C6   C2   C1      0.00   0.0  0
 70M  CONST_03  C7   N5   C2   C1      0.00   0.0  0
 70M  CONST_04  N5   C7   C3   C1      0.00   0.0  0
 70M  CONST_05  C9   C4   C1   C2      0.00   0.0  0
 70M  CONST_06  C7   C3   C1   C2      0.00   0.0  0
 70M  CONST_07  C9   C10  C6   C2      0.00   0.0  0
 70M  CONST_08  C3   C7   N5   C2      0.00   0.0  0
 70M  CONST_09  C9   C4   C1   C3    180.00   0.0  0
 70M  CONST_10  C6   C2   C1   C3    180.00   0.0  0
 70M  CONST_11  N5   C2   C1   C3      0.00   0.0  0
 70M  CONST_12  C4   C1   C3   C7    180.00   0.0  0
 70M  CONST_13  C6   C2   N5   C7    180.00   0.0  0
 70M  CONST_14  N5   C2   C6   C10   180.00   0.0  0
 70M  CONST_15  C27  C25  C23  C24     0.00   0.0  0
 70M  CONST_16  C27  C28  C26  C24     0.00   0.0  0
 70M  CONST_17  C6   C10  C9   C4      0.00   0.0  0
 70M  CONST_18  C6   C2   C1   C4      0.00   0.0  0
 70M  CONST_19  N5   C2   C1   C4    180.00   0.0  0
 70M  CONST_20  C28  C27  C25  C23     0.00   0.0  0
 70M  CONST_21  C28  C26  C24  C23     0.00   0.0  0
 70M  CONST_22  C26  C28  C27  C25     0.00   0.0  0
 70M  CONST_23  C26  C24  C23  C25     0.00   0.0  0
 70M  CONST_24  N22  C23  C25  C27   180.00   0.0  0
 70M  CONST_25  C26  C24  C23  N22   180.00   0.0  0
 70M  CONST_26  C12  C9   C4   C1    180.00   0.0  0
 70M  CONST_27  C8   C3   C1   C2    180.00   0.0  0
 70M  CONST_28  O13  C10  C6   C2    180.00   0.0  0
 70M  CONST_29  C4   C1   C3   C8      0.00   0.0  0
 70M  CONST_30  N5   C7   C3   C8    180.00   0.0  0
 70M  CONST_31  C6   C10  C9   C12   180.00   0.0  0
 70M  CONST_32  C29  C28  C26  C24   180.00   0.0  0
 70M  CONST_33  O13  C10  C9   C4    180.00   0.0  0
 70M  CONST_34  C29  C28  C27  C25   180.00   0.0  0
 70M  CONST_35  H20  C6   C2   C1    180.00   0.0  0
 70M  CONST_36  H19  N5   C2   C1    180.00   0.0  0
 70M  CONST_37  H1   C7   C3   C1    180.00   0.0  0
 70M  CONST_38  H18  C4   C1   C2    180.00   0.0  0
 70M  CONST_39  H25  C25  C23  C24   180.00   0.0  0
 70M  CONST_40  H26  C26  C28  C27   180.00   0.0  0
 70M  CONST_41  H16  C24  C23  N22     0.00   0.0  0
 70M  CONST_42  H17  C27  C25  C23   180.00   0.0  0
 70M  Var_01    C20  C18  N17  C19   -59.85  30.0  1
 70M  Var_02    C20  N22  C21  C19    50.55  30.0  1
 70M  Var_03    C25  C23  N22  C20    -1.59  30.0  3
 70M  Var_04    C18  C20  N22  C21   -50.30  30.0  1
 70M  Var_05    C18  N17  C19  C21    60.00  30.0  1
 70M  Var_06    N22  C20  C18  N17    55.46  30.0  1
 70M  Var_07    N22  C21  C19  N17   -55.78  30.0  1
 70M  Var_08    C11  C8   C3   C1     74.27  30.0  2
 70M  Var_09    C14  C11  C8   C3   -178.60  30.0  2
 70M  Var_10    N17  C16  C14  C11  -171.55  30.0  1
 70M  Var_11    C16  C14  C11  C8   -174.82  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
 70M  plan-1  C24  0.020
 70M  plan-1  C27  0.020
 70M  plan-1  N22  0.020
 70M  plan-1  C23  0.020
 70M  plan-1  C25  0.020
 70M  plan-1  C26  0.020
 70M  plan-1  C28  0.020
 70M  plan-1  C29  0.020
 70M  plan-1  N30  0.020
 70M  plan-1  H16  0.020
 70M  plan-1  H17  0.020
 70M  plan-1  H25  0.020
 70M  plan-1  H26  0.020
 70M  plan-2  C1   0.020
 70M  plan-2  C2   0.020
 70M  plan-2  C3   0.020
 70M  plan-2  C7   0.020
 70M  plan-2  C8   0.020
 70M  plan-2  C9   0.020
 70M  plan-2  C10  0.020
 70M  plan-2  C12  0.020
 70M  plan-2  C4   0.020
 70M  plan-2  N5   0.020
 70M  plan-2  C6   0.020
 70M  plan-2  O13  0.020
 70M  plan-2  N15  0.020
 70M  plan-2  H1   0.020
 70M  plan-2  H18  0.020
 70M  plan-2  H19  0.020
 70M  plan-2  H20  0.020

