# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 23:00:48 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: 2-[5-[2-[4-(4-cyanophenyl)piperazin-1-yl]-2-oxidanylidene-ethoxy]-1~{H}-indol-3-yl]ethylazanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+]CCc1c[nH]c2ccc(OCC(=O)N3CCN(CC3)c4ccc(cc4)C#N)cc12
#
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
 EP5  EP5  2-[5-[2-[4-(4-cyanophenyl)piperazin-1-yl]-2-oxidanylidene-ethoxy]-1~{H}-indol-3-yl]ethylazanium  ligand  56  30  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EP5
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
 EP5  N2   N  NS    0  -0.270  -10.2318   1.1626  -1.7645
 EP5  C10  C  CSP   0   0.041   -9.1714   0.8953  -1.3956
 EP5  C7   C  CR6   0  -0.038   -7.8666   0.5643  -0.9419
 EP5  C8   C  CR16  0  -0.225   -7.5342  -0.7568  -0.6316
 EP5  C9   C  CR16  0  -0.341   -6.2700  -1.0793  -0.1952
 EP5  C6   C  CR16  0  -0.225   -6.8898   1.5497  -0.8036
 EP5  C5   C  CR16  0  -0.358   -5.6207   1.2286  -0.3704
 EP5  C4   C  CR6   0   0.421   -5.2698  -0.0963  -0.0410
 EP5  N1   N  NT    0  -0.526   -4.0206  -0.4196   0.4328
 EP5  C    C  CH2   0  -0.304   -3.4573  -1.7339   0.1472
 EP5  C1   C  CH2   0  -0.317   -2.3716  -2.1025   1.1412
 EP5  C3   C  CH2   0  -0.297   -3.0145   0.6196   0.5587
 EP5  C2   C  CH2   0  -0.330   -1.9281   0.2179   1.5440
 EP5  N    N  NT    0  -0.461   -1.3622  -1.0672   1.1968
 EP5  C11  C  C     0   0.529   -0.0789  -1.3114   0.8651
 EP5  O    O  O     0  -0.480    0.3244  -2.4103   0.5268
 EP5  C12  C  CH2   0  -0.321    0.8707  -0.1222   0.9498
 EP5  O1   O  O2    0  -0.475    2.1417  -0.5831   0.5960
 EP5  C13  C  CR6   0   0.391    3.1751   0.2996   0.5900
 EP5  C14  C  CR16  0  -0.493    4.3993  -0.2115   0.1907
 EP5  C15  C  CR56  0   0.059    5.5094   0.6349   0.1656
 EP5  C16  C  CR56  0   0.343    5.3669   1.9864   0.5480
 EP5  C17  C  CR16  0  -0.289    4.1398   2.4998   0.9451
 EP5  C18  C  CR16  0  -0.398    3.0464   1.6505   0.9619
 EP5  C20  C  CR5   0  -0.011    6.8857   0.4417  -0.1808
 EP5  C19  C  CR15  0  -0.066    7.4979   1.6514   0.0019
 EP5  N3   N  NR15  0  -0.688    6.5965   2.5753   0.4369
 EP5  C21  C  CH2   0  -0.565    7.5067  -0.8150  -0.6917
 EP5  C22  C  CH2   0  -0.302    7.1538  -1.0249  -2.1565
 EP5  N4   N  NT3   1  -0.780    7.6985  -2.3128  -2.6637
 EP5  H1   H  HCR6  0   0.277   -8.2749  -1.5393  -0.7282
 EP5  H2   H  HCR6  0   0.279   -6.0751  -2.1132   0.0456
 EP5  H3   H  HCR6  0   0.278   -7.1184   2.5780  -1.0499
 EP5  H4   H  HCR6  0   0.281   -4.8998   2.0293  -0.3108
 EP5  H5   H  HCH2  0   0.273   -4.2223  -2.5023   0.2057
 EP5  H6   H  HCH2  0   0.242   -3.0466  -1.7549  -0.8706
 EP5  H7   H  HCH2  0   0.257   -2.8069  -2.2289   2.1370
 EP5  H8   H  HCH2  0   0.278   -1.9232  -3.0479   0.8489
 EP5  H9   H  HCH2  0   0.239   -2.5647   0.8595  -0.4145
 EP5  H10  H  HCH2  0   0.271   -3.4660   1.5298   0.9485
 EP5  H11  H  HCH2  0   0.284   -1.1764   1.0020   1.5636
 EP5  H12  H  HCH2  0   0.264   -2.3534   0.1570   2.5499
 EP5  H13  H  HCH2  0   0.257    0.5334   0.6746   0.2743
 EP5  H14  H  HCH2  0   0.261    0.8597   0.2867   1.9683
 EP5  H15  H  HCR6  0   0.246    4.4820  -1.2550  -0.0906
 EP5  H16  H  HCR6  0   0.267    4.0261   3.5361   1.2359
 EP5  H17  H  HCR6  0   0.275    2.0926   2.0553   1.2706
 EP5  H18  H  HCR5  0   0.286    8.5319   1.9198  -0.1497
 EP5  H19  H  HNR5  0   0.410    6.8119   3.5339   0.6525
 EP5  H20  H  HCH2  0   0.274    8.5924  -0.7708  -0.5798
 EP5  H21  H  HCH2  0   0.263    7.1627  -1.6735  -0.1064
 EP5  H22  H  HCH2  0   0.296    6.0780  -1.0606  -2.3122
 EP5  H23  H  HCH2  0   0.297    7.5695  -0.2377  -2.7806
 EP5  H24  H  HNT3  0   0.470    8.7142  -2.3563  -2.5848
 EP5  H25  H  HNT3  0   0.469    7.3219  -3.1129  -2.1561
 EP5  H26  H  HNT3  0   0.479    7.4709  -2.4515  -3.6476

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
 EP5  O    C11  double    1.218  0.020  1.218
 EP5  C    C1   single    1.517  0.020  1.517
 EP5  C    N1   single    1.458  0.020  1.458
 EP5  C9   C8   aromatic  1.376  0.020  1.376
 EP5  C9   C4   aromatic  1.411  0.020  1.411
 EP5  C8   C7   aromatic  1.397  0.020  1.397
 EP5  C1   N    single    1.447  0.020  1.447
 EP5  C11  N    single    1.348  0.020  1.348
 EP5  C11  C12  single    1.524  0.020  1.524
 EP5  N1   C4   single    1.375  0.020  1.375
 EP5  N1   C3   single    1.452  0.020  1.452
 EP5  C4   C5   aromatic  1.410  0.020  1.410
 EP5  N    C2   single    1.446  0.020  1.446
 EP5  C7   C10  single    1.421  0.020  1.421
 EP5  C7   C6   aromatic  1.394  0.020  1.394
 EP5  C10  N2   triple    1.154  0.020  1.154
 EP5  O1   C12  single    1.397  0.020  1.397
 EP5  O1   C13  single    1.359  0.020  1.359
 EP5  C3   C2   single    1.521  0.020  1.521
 EP5  C13  C14  aromatic  1.385  0.020  1.385
 EP5  C13  C18  aromatic  1.407  0.020  1.407
 EP5  C14  C15  aromatic  1.396  0.020  1.396
 EP5  C5   C6   aromatic  1.379  0.020  1.379
 EP5  C18  C17  aromatic  1.385  0.020  1.385
 EP5  C15  C16  aromatic  1.412  0.020  1.412
 EP5  C15  C20  aromatic  1.432  0.020  1.432
 EP5  C17  C16  aromatic  1.388  0.020  1.388
 EP5  C21  C20  single    1.492  0.020  1.492
 EP5  C21  C22  single    1.521  0.020  1.521
 EP5  C16  N3   aromatic  1.368  0.020  1.368
 EP5  C20  C19  aromatic  1.368  0.020  1.368
 EP5  C22  N4   single    1.488  0.020  1.488
 EP5  N3   C19  aromatic  1.362  0.020  1.362
 EP5  C8   H1   single    0.930  0.020  1.080
 EP5  C9   H2   single    0.930  0.020  1.080
 EP5  C6   H3   single    0.930  0.020  1.080
 EP5  C5   H4   single    0.930  0.020  1.080
 EP5  C    H5   single    0.970  0.020  1.090
 EP5  C    H6   single    0.970  0.020  1.090
 EP5  C1   H7   single    0.970  0.020  1.090
 EP5  C1   H8   single    0.970  0.020  1.090
 EP5  C3   H9   single    0.970  0.020  1.090
 EP5  C3   H10  single    0.970  0.020  1.090
 EP5  C2   H11  single    0.970  0.020  1.090
 EP5  C2   H12  single    0.970  0.020  1.090
 EP5  C12  H13  single    0.970  0.020  1.090
 EP5  C12  H14  single    0.970  0.020  1.090
 EP5  C14  H15  single    0.930  0.020  1.080
 EP5  C17  H16  single    0.930  0.020  1.080
 EP5  C18  H17  single    0.930  0.020  1.080
 EP5  C19  H18  single    0.930  0.020  1.080
 EP5  N3   H19  single    0.860  0.020  1.020
 EP5  C21  H20  single    0.970  0.020  1.090
 EP5  C21  H21  single    0.970  0.020  1.090
 EP5  C22  H22  single    0.970  0.020  1.090
 EP5  C22  H23  single    0.970  0.020  1.090
 EP5  N4   H24  single    0.890  0.020  1.040
 EP5  N4   H25  single    0.890  0.020  1.040
 EP5  N4   H26  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
 EP5  C7   C10  N2   180.00  3.000
 EP5  C6   C7   C8   118.66  3.000
 EP5  C6   C7   C10  120.70  3.000
 EP5  C8   C7   C10  120.64  3.000
 EP5  H1   C8   C9   119.21  3.000
 EP5  H1   C8   C7   120.08  3.000
 EP5  C9   C8   C7   120.71  3.000
 EP5  H2   C9   C4   121.00  3.000
 EP5  H2   C9   C8   117.46  3.000
 EP5  C4   C9   C8   121.52  3.000
 EP5  H3   C6   C5   119.17  3.000
 EP5  H3   C6   C7   120.07  3.000
 EP5  C5   C6   C7   120.75  3.000
 EP5  H4   C5   C4   121.21  3.000
 EP5  H4   C5   C6   117.35  3.000
 EP5  C4   C5   C6   121.43  3.000
 EP5  N1   C4   C5   121.86  3.000
 EP5  C5   C4   C9   116.93  3.000
 EP5  N1   C4   C9   121.20  3.000
 EP5  C3   N1   C    113.23  3.000
 EP5  C3   N1   C4   119.42  3.000
 EP5  C    N1   C4   119.71  3.000
 EP5  H6   C    H5   107.46  3.000
 EP5  H6   C    C1   109.57  3.000
 EP5  H5   C    C1   107.28  3.000
 EP5  H6   C    N1   110.08  3.000
 EP5  H5   C    N1   110.80  3.000
 EP5  C1   C    N1   111.53  3.000
 EP5  H8   C1   H7   107.97  3.000
 EP5  H8   C1   N    110.18  3.000
 EP5  H7   C1   N    108.98  3.000
 EP5  H8   C1   C    109.30  3.000
 EP5  H7   C1   C    109.85  3.000
 EP5  N    C1   C    110.52  3.000
 EP5  H10  C3   H9   107.73  3.000
 EP5  H10  C3   C2   106.57  3.000
 EP5  H9   C3   C2   109.83  3.000
 EP5  H10  C3   N1   110.01  3.000
 EP5  H9   C3   N1   111.30  3.000
 EP5  C2   C3   N1   111.23  3.000
 EP5  H12  C2   H11  107.02  3.000
 EP5  H12  C2   N    108.87  3.000
 EP5  H11  C2   N    112.01  3.000
 EP5  H12  C2   C3   109.44  3.000
 EP5  H11  C2   C3   108.39  3.000
 EP5  N    C2   C3   111.02  3.000
 EP5  C11  N    C2   126.34  3.000
 EP5  C2   N    C1   111.83  3.000
 EP5  C11  N    C1   121.67  3.000
 EP5  C12  C11  O    120.86  3.000
 EP5  C12  C11  N    115.98  3.000
 EP5  O    C11  N    123.15  3.000
 EP5  H14  C12  H13  107.31  3.000
 EP5  H14  C12  O1   111.52  3.000
 EP5  H13  C12  O1   111.29  3.000
 EP5  H14  C12  C11  109.63  3.000
 EP5  H13  C12  C11  109.92  3.000
 EP5  O1   C12  C11  107.17  3.000
 EP5  C13  O1   C12  118.58  3.000
 EP5  C18  C13  C14  120.74  3.000
 EP5  C18  C13  O1   123.56  3.000
 EP5  C14  C13  O1   115.69  3.000
 EP5  H15  C14  C15  121.22  3.000
 EP5  H15  C14  C13  119.83  3.000
 EP5  C15  C14  C13  118.95  3.000
 EP5  C20  C15  C16  106.95  3.000
 EP5  C20  C15  C14  133.36  3.000
 EP5  C16  C15  C14  119.69  3.000
 EP5  N3   C16  C17  131.19  3.000
 EP5  N3   C16  C15  107.43  3.000
 EP5  C17  C16  C15  121.38  3.000
 EP5  H16  C17  C18  120.07  3.000
 EP5  H16  C17  C16  121.59  3.000
 EP5  C18  C17  C16  118.34  3.000
 EP5  H17  C18  C17  118.07  3.000
 EP5  H17  C18  C13  121.04  3.000
 EP5  C17  C18  C13  120.89  3.000
 EP5  C21  C20  C19  127.18  3.000
 EP5  C19  C20  C15  106.16  3.000
 EP5  C21  C20  C15  126.61  3.000
 EP5  H18  C19  N3   120.68  3.000
 EP5  H18  C19  C20  129.06  3.000
 EP5  N3   C19  C20  110.26  3.000
 EP5  H19  N3   C19  124.97  3.000
 EP5  H19  N3   C16  125.83  3.000
 EP5  C19  N3   C16  109.19  3.000
 EP5  H21  C21  H20  106.82  3.000
 EP5  H21  C21  C22  109.50  3.000
 EP5  H20  C21  C22  109.56  3.000
 EP5  H21  C21  C20  110.29  3.000
 EP5  H20  C21  C20  110.15  3.000
 EP5  C22  C21  C20  110.45  3.000
 EP5  H23  C22  H22  108.65  3.000
 EP5  H23  C22  N4   106.92  3.000
 EP5  H22  C22  N4   106.56  3.000
 EP5  H23  C22  C21  111.36  3.000
 EP5  H22  C22  C21  111.83  3.000
 EP5  N4   C22  C21  111.27  3.000
 EP5  H26  N4   H25  106.93  3.000
 EP5  H26  N4   H24  106.94  3.000
 EP5  H25  N4   H24  107.21  3.000
 EP5  H26  N4   C22  111.42  3.000
 EP5  H25  N4   C22  111.98  3.000
 EP5  H24  N4   C22  112.04  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
 EP5  CONST_01  C4   C9   C8   C7      0.00   0.0  0
 EP5  CONST_02  C4   C5   C6   C7      0.00   0.0  0
 EP5  CONST_03  C5   C4   C9   C8      0.00   0.0  0
 EP5  CONST_04  C5   C6   C7   C8      0.00   0.0  0
 EP5  CONST_05  C6   C7   C8   C9      0.00   0.0  0
 EP5  CONST_06  C6   C5   C4   C9      0.00   0.0  0
 EP5  CONST_07  C16  C15  C14  C13     0.00   0.0  0
 EP5  CONST_08  C20  C15  C14  C13   180.00   0.0  0
 EP5  CONST_09  C16  C17  C18  C13     0.00   0.0  0
 EP5  CONST_10  C17  C18  C13  C14     0.00   0.0  0
 EP5  CONST_11  C17  C16  C15  C14     0.00   0.0  0
 EP5  CONST_12  N3   C16  C15  C14   180.00   0.0  0
 EP5  CONST_13  C19  C20  C15  C14   180.00   0.0  0
 EP5  CONST_14  C18  C13  C14  C15     0.00   0.0  0
 EP5  CONST_15  C18  C17  C16  C15     0.00   0.0  0
 EP5  CONST_16  C19  N3   C16  C15     0.00   0.0  0
 EP5  CONST_17  N3   C19  C20  C15     0.00   0.0  0
 EP5  CONST_18  C19  C20  C15  C16     0.00   0.0  0
 EP5  CONST_19  C20  C19  N3   C16     0.00   0.0  0
 EP5  CONST_20  C20  C15  C16  C17   180.00   0.0  0
 EP5  CONST_21  C19  N3   C16  C17   180.00   0.0  0
 EP5  CONST_22  N3   C16  C17  C18   180.00   0.0  0
 EP5  CONST_23  N3   C16  C15  C20     0.00   0.0  0
 EP5  CONST_24  N1   C4   C9   C8    180.00   0.0  0
 EP5  CONST_25  N1   C4   C5   C6    180.00   0.0  0
 EP5  CONST_26  C9   C8   C7   C10   180.00   0.0  0
 EP5  CONST_27  C5   C6   C7   C10   180.00   0.0  0
 EP5  CONST_28  C15  C14  C13  O1    180.00   0.0  0
 EP5  CONST_29  C17  C18  C13  O1    180.00   0.0  0
 EP5  CONST_30  C21  C20  C15  C14     0.00   0.0  0
 EP5  CONST_31  C21  C20  C15  C16   180.00   0.0  0
 EP5  CONST_32  C21  C20  C19  N3    180.00   0.0  0
 EP5  CONST_33  H2   C9   C8   C7    180.00   0.0  0
 EP5  CONST_34  H4   C5   C6   C7    180.00   0.0  0
 EP5  CONST_35  H3   C6   C7   C8    180.00   0.0  0
 EP5  CONST_36  H1   C8   C7   C6    180.00   0.0  0
 EP5  CONST_37  H16  C17  C18  C13   180.00   0.0  0
 EP5  CONST_38  H17  C18  C13  C14   180.00   0.0  0
 EP5  CONST_39  H19  N3   C16  C15   180.00   0.0  0
 EP5  CONST_40  H18  C19  C20  C15   180.00   0.0  0
 EP5  CONST_41  H15  C14  C15  C16   180.00   0.0  0
 EP5  CONST_42  O    C11  N    C1      0.00   0.0  0
 EP5  CONST_43  C12  C11  N    C1    180.00   0.0  0
 EP5  CONST_44  O    C11  N    C2    180.00   0.0  0
 EP5  CONST_45  C12  C11  N    C2      0.00   0.0  0
 EP5  Var_01    C    N1   C4   C9     31.68  30.0  2
 EP5  Var_02    C1   C    N1   C4   -158.41  30.0  1
 EP5  Var_03    C2   C3   N1   C4    158.77  30.0  1
 EP5  Var_04    N    C1   C    N1    -54.04  30.0  1
 EP5  Var_05    N    C2   C3   N1     53.67  30.0  1
 EP5  Var_06    C2   N    C1   C      57.36  30.0  1
 EP5  Var_07    C3   C2   N    C1    -57.33  30.0  1
 EP5  Var_08    C14  C13  O1   C12  -178.09  30.0  2
 EP5  Var_09    C22  C21  C20  C15    76.17  30.0  3
 EP5  Var_10    O1   C12  C11  N     178.87  30.0  3
 EP5  Var_11    N4   C22  C21  C20  -176.73  30.0  3
 EP5  Var_12    H24  N4   C22  C21   -59.69  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
 EP5  plan-1  N2   0.020
 EP5  plan-1  C10  0.020
 EP5  plan-1  C7   0.020
 EP5  plan-1  C8   0.020
 EP5  plan-1  C9   0.020
 EP5  plan-1  C6   0.020
 EP5  plan-1  C5   0.020
 EP5  plan-1  C4   0.020
 EP5  plan-1  N1   0.020
 EP5  plan-1  H1   0.020
 EP5  plan-1  H2   0.020
 EP5  plan-1  H3   0.020
 EP5  plan-1  H4   0.020
 EP5  plan-2  O1   0.020
 EP5  plan-2  C13  0.020
 EP5  plan-2  C14  0.020
 EP5  plan-2  C15  0.020
 EP5  plan-2  C16  0.020
 EP5  plan-2  C17  0.020
 EP5  plan-2  C18  0.020
 EP5  plan-2  C20  0.020
 EP5  plan-2  C19  0.020
 EP5  plan-2  N3   0.020
 EP5  plan-2  C21  0.020
 EP5  plan-2  H15  0.020
 EP5  plan-2  H16  0.020
 EP5  plan-2  H17  0.020
 EP5  plan-2  H18  0.020
 EP5  plan-2  H19  0.020
 EP5  plan-3  C1   0.020
 EP5  plan-3  C2   0.020
 EP5  plan-3  N    0.020
 EP5  plan-3  C11  0.020
 EP5  plan-3  O    0.020
 EP5  plan-3  C12  0.020

