# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 04:34:44 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: 5-azanyl-3-[1-[[4-(piperidin-1-ylmethyl)phenyl]methyl]indol-6-yl]-1~{H}-pyrazole-4-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1[nH]nc(c2ccc3ccn(Cc4ccc(CN5CCCCC5)cc4)c3c2)c1C#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
 JEK  JEK  5-azanyl-3-[1-[[4-(piperidin-1-ylmethyl)phenyl]methyl]indol-6-yl]-1~{H}-pyrazole-4-carbonitrile  ligand  57  31  .  2021-08-12  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JEK
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
 JEK  C10  C  CR16  0  -0.328   3.6680   2.4417   1.3032
 JEK  C13  C  CR15  0  -0.022   0.9771   4.2791  -0.2813
 JEK  C15  C  CH2   0  -0.422  -0.2270   2.5512  -1.6388
 JEK  C17  C  CR16  0  -0.272  -1.9997   2.4217   0.1430
 JEK  C20  C  CH2   0  -0.316  -4.3073  -0.3487   1.3414
 JEK  C22  C  C     0  -0.274  -6.0100  -0.3195  -0.3527
 JEK  C24  C  C     0  -0.441  -7.7269  -2.1404  -0.4775
 JEK  C26  C  C     0  -0.277  -5.9865  -2.0491   1.3192
 JEK  C28  C  CR16  0  -0.299  -1.5793   0.4704  -1.1732
 JEK  C02  C  CR5   0   0.623   4.4704  -3.0937  -0.2149
 JEK  N03  N  NR15  0  -0.491   3.1507  -3.1505  -0.4146
 JEK  N04  N  N     0  -0.298   2.5302  -1.9627  -0.2693
 JEK  C05  C  CR5   0   0.323   3.4702  -1.1021   0.0297
 JEK  C06  C  CR6   0   0.042   3.1645   0.3162   0.2296
 JEK  C07  C  CR16  0  -0.345   2.0855   0.8753  -0.4422
 JEK  C08  C  CR56  0   0.410   1.8151   2.2221  -0.2357
 JEK  C09  C  CR56  0   0.049   2.5913   3.0266   0.6291
 JEK  C11  C  CR16  0  -0.336   3.9430   1.1055   1.1012
 JEK  C12  C  CR15  0  -0.430   2.0318   4.3385   0.5829
 JEK  N14  N  NR5   0  -0.518   0.8449   3.0136  -0.7855
 JEK  C16  C  CR6   0   0.114  -1.2879   1.7973  -0.8757
 JEK  C18  C  CR16  0  -0.297  -2.9784   1.7335   0.8440
 JEK  C19  C  CR6   0   0.072  -3.2682   0.4040   0.5516
 JEK  N21  N  NR6   0  -0.413  -5.1828  -1.1478   0.5100
 JEK  C23  C  C     0  -0.438  -6.8704  -1.1680  -1.2767
 JEK  C25  C  C     0  -0.439  -6.8430  -2.9601   0.4530
 JEK  C27  C  CR16  0  -0.268  -2.5574  -0.2187  -0.4696
 JEK  C29  C  CR5   0  -0.289   4.7390  -1.7531   0.0843
 JEK  C30  C  CSP   0  -0.037   6.0167  -1.2194   0.2956
 JEK  N31  N  NS    0  -0.267   7.0812  -0.8010   0.4669
 JEK  H1   H  HCR6  0   0.251   4.2770   3.0259   1.9815
 JEK  H2   H  HCR5  0   0.289   0.2956   5.0572  -0.5900
 JEK  H3   H  HCH2  0   0.290  -0.6539   3.4276  -2.1278
 JEK  H4   H  HCH2  0   0.280   0.1903   1.9237  -2.4286
 JEK  H5   H  HCR6  0   0.250  -1.7992   3.4578   0.3902
 JEK  H6   H  HCH2  0   0.250  -3.7954  -1.0247   2.0344
 JEK  H7   H  HCH2  0   0.208  -4.8685   0.3640   1.9709
 JEK  H8   H  H     0   0.184  -6.6602   0.3476   0.2432
 JEK  H9   H  H     0   0.238  -5.3612   0.3255  -0.9483
 JEK  H10  H  H     0   0.210  -8.4569  -1.5791   0.1162
 JEK  H11  H  H     0   0.231  -8.2977  -2.7918  -1.1429
 JEK  H12  H  H     0   0.233  -5.3141  -2.6484   1.9381
 JEK  H13  H  H     0   0.182  -6.6415  -1.4911   2.0134
 JEK  H14  H  HCR6  0   0.250  -1.0377  -0.0339  -1.9655
 JEK  H15  H  HNH2  0   0.409   4.9157  -5.0653  -0.3315
 JEK  H16  H  HNH2  0   0.409   6.2061  -4.0698   0.0881
 JEK  H17  H  HNR5  0   0.429   2.6082  -3.9698  -0.6404
 JEK  H18  H  HCR6  0   0.255   1.4899   0.2707  -1.1137
 JEK  H19  H  HCR6  0   0.247   4.7621   0.6554   1.6460
 JEK  H20  H  HCR5  0   0.250   2.3692   5.2133   1.1152
 JEK  H21  H  HCR6  0   0.248  -3.5321   2.2427   1.6241
 JEK  H23  H  H     0   0.230  -7.4924  -0.5123  -1.8897
 JEK  H24  H  H     0   0.215  -6.2198  -1.7230  -1.9598
 JEK  H25  H  H     0   0.230  -7.4452  -3.6049   1.0967
 JEK  H26  H  H     0   0.215  -6.1911  -3.6132  -0.1352
 JEK  H27  H  HCR6  0   0.245  -2.7789  -1.2482  -0.7215
 JEK  N01  N  NH2   0  -0.843   5.3099  -4.1387  -0.3661

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
 JEK  C25  C24  single    1.523  0.020  1.523
 JEK  C25  C26  single    1.521  0.020  1.521
 JEK  C24  C23  single    1.522  0.020  1.522
 JEK  C26  N21  single    1.454  0.020  1.454
 JEK  C23  C22  single    1.521  0.020  1.521
 JEK  N21  C20  single    1.448  0.020  1.448
 JEK  N21  C22  single    1.454  0.020  1.454
 JEK  C20  C19  single    1.507  0.020  1.507
 JEK  C18  C19  aromatic  1.392  0.020  1.392
 JEK  C18  C17  aromatic  1.387  0.020  1.387
 JEK  C19  C27  aromatic  1.391  0.020  1.391
 JEK  C17  C16  aromatic  1.391  0.020  1.391
 JEK  C27  C28  aromatic  1.388  0.020  1.388
 JEK  C16  C28  aromatic  1.391  0.020  1.391
 JEK  C16  C15  single    1.509  0.020  1.509
 JEK  C13  C12  aromatic  1.365  0.020  1.365
 JEK  C13  N14  aromatic  1.369  0.020  1.369
 JEK  C12  C09  aromatic  1.427  0.020  1.427
 JEK  N14  C15  single    1.446  0.020  1.446
 JEK  N14  C08  aromatic  1.367  0.020  1.367
 JEK  C09  C08  aromatic  1.413  0.020  1.413
 JEK  C09  C10  aromatic  1.398  0.020  1.398
 JEK  C08  C07  aromatic  1.389  0.020  1.389
 JEK  C10  C11  aromatic  1.379  0.020  1.379
 JEK  C07  C06  aromatic  1.389  0.020  1.389
 JEK  C11  C06  aromatic  1.410  0.020  1.410
 JEK  C06  C05  single    1.465  0.020  1.465
 JEK  C05  N04  aromatic  1.309  0.020  1.309
 JEK  C05  C29  aromatic  1.427  0.020  1.427
 JEK  N04  N03  aromatic  1.348  0.020  1.348
 JEK  C29  C30  single    1.401  0.020  1.401
 JEK  C29  C02  aromatic  1.400  0.020  1.400
 JEK  C30  N31  triple    1.156  0.020  1.156
 JEK  N03  C02  aromatic  1.336  0.020  1.336
 JEK  C02  N01  single    1.349  0.020  1.349
 JEK  C10  H1   single    0.930  0.020  1.080
 JEK  C13  H2   single    0.930  0.020  1.080
 JEK  C15  H3   single    0.970  0.020  1.090
 JEK  C15  H4   single    0.970  0.020  1.090
 JEK  C17  H5   single    0.930  0.020  1.080
 JEK  C20  H6   single    0.970  0.020  1.090
 JEK  C20  H7   single    0.970  0.020  1.090
 JEK  C22  H8   single    0.970  0.020  1.090
 JEK  C22  H9   single    0.970  0.020  1.090
 JEK  C24  H10  single    0.970  0.020  1.090
 JEK  C24  H11  single    0.970  0.020  1.090
 JEK  C26  H12  single    0.970  0.020  1.090
 JEK  C26  H13  single    0.970  0.020  1.090
 JEK  C28  H14  single    0.930  0.020  1.080
 JEK  N01  H15  single    0.890  0.020  1.040
 JEK  N01  H16  single    0.890  0.020  1.040
 JEK  N03  H17  single    0.860  0.020  1.020
 JEK  C07  H18  single    0.930  0.020  1.080
 JEK  C11  H19  single    0.930  0.020  1.080
 JEK  C12  H20  single    0.930  0.020  1.080
 JEK  C18  H21  single    0.930  0.020  1.080
 JEK  C23  H23  single    0.970  0.020  1.090
 JEK  C23  H24  single    0.970  0.020  1.090
 JEK  C25  H25  single    0.970  0.020  1.090
 JEK  C25  H26  single    0.970  0.020  1.090
 JEK  C27  H27  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
 JEK  H1   C10  C11  120.16  3.000
 JEK  H1   C10  C09  120.62  3.000
 JEK  C11  C10  C09  119.22  3.000
 JEK  H2   C13  N14  120.01  3.000
 JEK  H2   C13  C12  129.62  3.000
 JEK  N14  C13  C12  110.37  3.000
 JEK  H4   C15  H3   106.69  3.000
 JEK  H4   C15  C16  110.33  3.000
 JEK  H3   C15  C16  110.68  3.000
 JEK  H4   C15  N14  109.11  3.000
 JEK  H3   C15  N14  107.32  3.000
 JEK  C16  C15  N14  112.50  3.000
 JEK  H5   C17  C18  119.33  3.000
 JEK  H5   C17  C16  120.09  3.000
 JEK  C18  C17  C16  120.58  3.000
 JEK  H7   C20  H6   105.98  3.000
 JEK  H7   C20  N21  112.10  3.000
 JEK  H6   C20  N21  107.78  3.000
 JEK  H7   C20  C19  109.09  3.000
 JEK  H6   C20  C19  108.53  3.000
 JEK  N21  C20  C19  113.06  3.000
 JEK  H9   C22  H8   106.68  3.000
 JEK  H9   C22  C23  109.54  3.000
 JEK  H8   C22  C23  109.35  3.000
 JEK  H9   C22  N21  108.79  3.000
 JEK  H8   C22  N21  111.00  3.000
 JEK  C23  C22  N21  111.37  3.000
 JEK  H11  C24  H10  106.71  3.000
 JEK  H11  C24  C25  110.77  3.000
 JEK  H10  C24  C25  109.35  3.000
 JEK  H11  C24  C23  110.80  3.000
 JEK  H10  C24  C23  109.39  3.000
 JEK  C25  C24  C23  109.76  3.000
 JEK  H13  C26  H12  106.60  3.000
 JEK  H13  C26  C25  109.04  3.000
 JEK  H12  C26  C25  109.91  3.000
 JEK  H13  C26  N21  111.35  3.000
 JEK  H12  C26  N21  108.36  3.000
 JEK  C25  C26  N21  111.45  3.000
 JEK  H14  C28  C27  119.44  3.000
 JEK  H14  C28  C16  119.70  3.000
 JEK  C27  C28  C16  120.85  3.000
 JEK  C29  C02  N03  105.20  3.000
 JEK  N03  C02  N01  124.41  3.000
 JEK  C29  C02  N01  130.28  3.000
 JEK  H17  N03  N04  119.51  3.000
 JEK  H17  N03  C02  126.84  3.000
 JEK  N04  N03  C02  113.65  3.000
 JEK  C05  N04  N03  105.87  3.000
 JEK  C29  C05  C06  128.47  3.000
 JEK  C29  C05  N04  110.32  3.000
 JEK  C06  C05  N04  121.20  3.000
 JEK  C11  C06  C07  120.17  3.000
 JEK  C11  C06  C05  120.74  3.000
 JEK  C07  C06  C05  119.08  3.000
 JEK  H18  C07  C08  121.79  3.000
 JEK  H18  C07  C06  120.19  3.000
 JEK  C08  C07  C06  118.02  3.000
 JEK  N14  C08  C09  107.83  3.000
 JEK  C09  C08  C07  122.41  3.000
 JEK  N14  C08  C07  129.76  3.000
 JEK  C12  C09  C08  106.75  3.000
 JEK  C08  C09  C10  118.67  3.000
 JEK  C12  C09  C10  134.59  3.000
 JEK  H19  C11  C06  119.76  3.000
 JEK  H19  C11  C10  118.71  3.000
 JEK  C06  C11  C10  121.52  3.000
 JEK  H20  C12  C09  127.39  3.000
 JEK  H20  C12  C13  126.14  3.000
 JEK  C09  C12  C13  106.47  3.000
 JEK  C08  N14  C15  125.31  3.000
 JEK  C08  N14  C13  108.58  3.000
 JEK  C15  N14  C13  125.78  3.000
 JEK  C28  C16  C17  118.54  3.000
 JEK  C28  C16  C15  121.06  3.000
 JEK  C17  C16  C15  120.40  3.000
 JEK  H21  C18  C19  119.59  3.000
 JEK  H21  C18  C17  119.42  3.000
 JEK  C19  C18  C17  120.99  3.000
 JEK  C27  C19  C18  118.38  3.000
 JEK  C27  C19  C20  120.90  3.000
 JEK  C18  C19  C20  120.71  3.000
 JEK  C26  N21  C22  111.64  3.000
 JEK  C22  N21  C20  111.73  3.000
 JEK  C26  N21  C20  110.91  3.000
 JEK  H24  C23  H23  107.01  3.000
 JEK  H24  C23  C24  109.76  3.000
 JEK  H23  C23  C24  110.96  3.000
 JEK  H24  C23  C22  109.01  3.000
 JEK  H23  C23  C22  109.16  3.000
 JEK  C24  C23  C22  110.83  3.000
 JEK  H26  C25  H25  107.03  3.000
 JEK  H26  C25  C26  109.15  3.000
 JEK  H25  C25  C26  109.18  3.000
 JEK  H26  C25  C24  109.78  3.000
 JEK  H25  C25  C24  110.97  3.000
 JEK  C26  C25  C24  110.64  3.000
 JEK  H27  C27  C19  119.46  3.000
 JEK  H27  C27  C28  119.88  3.000
 JEK  C19  C27  C28  120.66  3.000
 JEK  C30  C29  C05  130.01  3.000
 JEK  C30  C29  C02  124.91  3.000
 JEK  C05  C29  C02  104.96  3.000
 JEK  N31  C30  C29  180.00  3.000
 JEK  H16  N01  H15  113.30  3.000
 JEK  H16  N01  C02  116.76  3.000
 JEK  H15  N01  C02  117.72  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
 JEK  CONST_01  C13  C12  C09  C10  180.00   0.0  0
 JEK  CONST_02  N14  C08  C09  C10  180.00   0.0  0
 JEK  CONST_03  C07  C08  C09  C10    0.00   0.0  0
 JEK  CONST_04  C07  C06  C11  C10    0.00   0.0  0
 JEK  CONST_05  C05  C06  C11  C10  180.00   0.0  0
 JEK  CONST_06  C08  C09  C12  C13    0.00   0.0  0
 JEK  CONST_07  C09  C08  N14  C13    0.00   0.0  0
 JEK  CONST_08  C07  C08  N14  C13  180.00   0.0  0
 JEK  CONST_09  C27  C19  C18  C17    0.00   0.0  0
 JEK  CONST_10  C27  C28  C16  C17    0.00   0.0  0
 JEK  CONST_11  C18  C19  C27  C28    0.00   0.0  0
 JEK  CONST_12  C18  C17  C16  C28    0.00   0.0  0
 JEK  CONST_13  C06  C05  C29  C02  180.00   0.0  0
 JEK  CONST_14  N04  C05  C29  C02    0.00   0.0  0
 JEK  CONST_15  C05  N04  N03  C02    0.00   0.0  0
 JEK  CONST_16  C06  C05  N04  N03  180.00   0.0  0
 JEK  CONST_17  C29  C05  N04  N03    0.00   0.0  0
 JEK  CONST_18  C05  C29  C02  N03    0.00   0.0  0
 JEK  CONST_21  C29  C02  N03  N04    0.00   0.0  0
 JEK  CONST_22  C08  C07  C06  C05  180.00   0.0  0
 JEK  CONST_23  N14  C08  C07  C06  180.00   0.0  0
 JEK  CONST_24  C09  C08  C07  C06    0.00   0.0  0
 JEK  CONST_25  C09  C10  C11  C06    0.00   0.0  0
 JEK  CONST_26  C12  C09  C08  C07  180.00   0.0  0
 JEK  CONST_28  C12  C13  N14  C08    0.00   0.0  0
 JEK  CONST_29  C11  C10  C09  C08    0.00   0.0  0
 JEK  CONST_30  C11  C06  C07  C08    0.00   0.0  0
 JEK  CONST_31  N14  C13  C12  C09    0.00   0.0  0
 JEK  CONST_32  C12  C09  C10  C11  180.00   0.0  0
 JEK  CONST_34  N14  C08  C09  C12    0.00   0.0  0
 JEK  CONST_35  C19  C18  C17  C16    0.00   0.0  0
 JEK  CONST_36  C19  C27  C28  C16    0.00   0.0  0
 JEK  CONST_37  C18  C17  C16  C15  180.00   0.0  0
 JEK  CONST_38  C27  C28  C16  C15  180.00   0.0  0
 JEK  CONST_39  C12  C13  N14  C15  180.00   0.0  0
 JEK  CONST_40  C09  C08  N14  C15  180.00   0.0  0
 JEK  CONST_41  C07  C08  N14  C15    0.00   0.0  0
 JEK  CONST_42  C20  C19  C18  C17  180.00   0.0  0
 JEK  CONST_43  C28  C27  C19  C20  180.00   0.0  0
 JEK  CONST_44  C05  C29  C02  N01  180.00   0.0  0
 JEK  CONST_45  N04  N03  C02  N01  180.00   0.0  0
 JEK  CONST_46  C30  C29  C02  N03  180.00   0.0  0
 JEK  CONST_47  C30  C29  C05  N04  180.00   0.0  0
 JEK  CONST_48  C30  C29  C05  C06    0.00   0.0  0
 JEK  CONST_49  H20  C12  C09  C10    0.00   0.0  0
 JEK  CONST_50  H14  C28  C16  C17  180.00   0.0  0
 JEK  CONST_51  H5   C17  C16  C28  180.00   0.0  0
 JEK  CONST_52  H18  C07  C06  C05    0.00   0.0  0
 JEK  CONST_53  H19  C11  C06  C05    0.00   0.0  0
 JEK  CONST_54  H17  N03  N04  C05  180.00   0.0  0
 JEK  CONST_55  H1   C10  C11  C06  180.00   0.0  0
 JEK  CONST_56  H2   C13  N14  C08  180.00   0.0  0
 JEK  CONST_57  H21  C18  C17  C16  180.00   0.0  0
 JEK  CONST_58  H27  C27  C28  C16  180.00   0.0  0
 JEK  Var_01    C25  C24  C23  C22  -53.80  30.0  1
 JEK  Var_02    C25  C26  N21  C22   58.51  30.0  1
 JEK  Var_03    N21  C26  C25  C24  -56.41  30.0  1
 JEK  Var_04    N21  C22  C23  C24   56.15  30.0  1
 JEK  Var_05    C23  C24  C25  C26   53.85  30.0  1
 JEK  Var_06    C23  C22  N21  C26  -58.29  30.0  1
 JEK  Var_07    C16  C15  N14  C13  -99.21  30.0  2
 JEK  Var_08    N14  C15  C16  C17   60.70  30.0  2
 JEK  Var_09    C19  C20  N21  C22  -65.95  30.0  3
 JEK  Var_10    N21  C20  C19  C18  136.49  30.0  1

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
 JEK  plan-1  C02  0.020
 JEK  plan-1  N03  0.020
 JEK  plan-1  N04  0.020
 JEK  plan-1  C05  0.020
 JEK  plan-1  C06  0.020
 JEK  plan-1  C29  0.020
 JEK  plan-1  C30  0.020
 JEK  plan-1  N31  0.020
 JEK  plan-1  H17  0.020
 JEK  plan-1  N01  0.020
 JEK  plan-2  C15  0.020
 JEK  plan-2  C17  0.020
 JEK  plan-2  C20  0.020
 JEK  plan-2  C28  0.020
 JEK  plan-2  C16  0.020
 JEK  plan-2  C18  0.020
 JEK  plan-2  C19  0.020
 JEK  plan-2  C27  0.020
 JEK  plan-2  H5   0.020
 JEK  plan-2  H14  0.020
 JEK  plan-2  H21  0.020
 JEK  plan-2  H27  0.020
 JEK  plan-3  C10  0.020
 JEK  plan-3  C13  0.020
 JEK  plan-3  C15  0.020
 JEK  plan-3  C05  0.020
 JEK  plan-3  C06  0.020
 JEK  plan-3  C07  0.020
 JEK  plan-3  C08  0.020
 JEK  plan-3  C09  0.020
 JEK  plan-3  C11  0.020
 JEK  plan-3  C12  0.020
 JEK  plan-3  N14  0.020
 JEK  plan-3  H1   0.020
 JEK  plan-3  H2   0.020
 JEK  plan-3  H18  0.020
 JEK  plan-3  H19  0.020
 JEK  plan-3  H20  0.020
 JEK  plan-4  C02  0.020
 JEK  plan-4  H15  0.020
 JEK  plan-4  H16  0.020
 JEK  plan-4  N01  0.020

