# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 12:05:37 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: 5-azanyl-3-[1-[[4-(pyrrolidin-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(CN5CCCC5)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
 JCK  JCK  5-azanyl-3-[1-[[4-(pyrrolidin-1-ylmethyl)phenyl]methyl]indol-6-yl]-1~{H}-pyrazole-4-carbonitrile  ligand  54  30  .  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_JCK
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
 JCK  C10  C  CR16  0  -0.329   3.0936   2.7205   1.1526
 JCK  C13  C  CR15  0  -0.021   0.3256   3.9694  -0.8237
 JCK  C15  C  CH2   0  -0.418  -0.4832   1.9564  -2.0819
 JCK  C17  C  CR16  0  -0.274  -2.3149   1.5500  -0.3990
 JCK  C22  C  CH2   0  -0.277  -6.4130  -1.8614   1.5427
 JCK  C24  C  CH2   0  -0.464  -7.5587  -1.0251  -0.4248
 JCK  C26  C  CR16  0  -0.301  -2.3137  -1.1647  -0.9159
 JCK  C28  C  CR5   0  -0.289   4.8185  -1.3901   0.5579
 JCK  C02  C  CR5   0   0.622   4.7585  -2.7783   0.3924
 JCK  N03  N  NR15  0  -0.491   3.4909  -3.0373   0.0598
 JCK  N04  N  N     0  -0.298   2.7132  -1.9383  -0.0031
 JCK  C05  C  CR5   0   0.323   3.4942  -0.9295   0.2915
 JCK  C06  C  CR6   0   0.043   2.9867   0.4443   0.2962
 JCK  C07  C  CR16  0  -0.342   1.9083   0.7689  -0.5165
 JCK  C08  C  CR56  0   0.408   1.4363   2.0752  -0.4855
 JCK  C09  C  CR56  0   0.049   2.0117   3.0692   0.3382
 JCK  C11  C  CR16  0  -0.338   3.5668   1.4254   1.1266
 JCK  C12  C  CR15  0  -0.431   1.2810   4.2719   0.1029
 JCK  N14  N  NR5   0  -0.519   0.4162   2.6539  -1.1897
 JCK  C16  C  CR6   0   0.111  -1.4292   1.0396  -1.3478
 JCK  C18  C  CR16  0  -0.269  -3.1833   0.7136   0.2792
 JCK  C19  C  CR6   0   0.095  -3.1907  -0.6600   0.0333
 JCK  N21  N  NT    0  -0.421  -5.4981  -1.1231   0.6903
 JCK  C23  C  CH2   0  -0.466  -7.7943  -1.4312   1.0469
 JCK  C25  C  CH2   0  -0.272  -6.0615  -1.2480  -0.6429
 JCK  C27  C  CR16  0  -0.295  -1.4396  -0.3245  -1.5983
 JCK  N30  N  NS    0  -0.267   6.9630  -0.0983   1.0784
 JCK  H1   H  HCR6  0   0.251   3.5538   3.4519   1.8047
 JCK  H2   H  HCR5  0   0.289  -0.4257   4.6039  -1.2681
 JCK  H3   H  HCH2  0   0.289  -1.0375   2.7121  -2.6400
 JCK  H4   H  HCH2  0   0.279   0.1009   1.3933  -2.8134
 JCK  H5   H  HCR6  0   0.249  -2.3272   2.6132  -0.1872
 JCK  H6   H  HCH2  0   0.209  -4.0007  -2.6009   0.4448
 JCK  H7   H  HCH2  0   0.249  -3.8466  -1.5560   1.8517
 JCK  H9   H  HCH2  0   0.233  -6.2394  -1.6307   2.5960
 JCK  H10  H  HCH2  0   0.233  -8.1529  -1.6141  -1.1226
 JCK  H11  H  HCH2  0   0.234  -7.8208   0.0210  -0.5843
 JCK  H12  H  HCR6  0   0.248  -2.3070  -2.2269  -1.1305
 JCK  H15  H  HNR5  0   0.429   3.0862  -3.9429  -0.1200
 JCK  H16  H  HCR6  0   0.257   1.4625   0.0196  -1.1570
 JCK  H17  H  HCR6  0   0.247   4.3888   1.1611   1.7785
 JCK  H18  H  HCR5  0   0.250   1.4444   5.2367   0.5559
 JCK  H19  H  HCR6  0   0.245  -3.8718   1.1292   1.0049
 JCK  H21  H  HCH2  0   0.234  -8.5206  -2.2368   1.1478
 JCK  H22  H  HCH2  0   0.234  -8.1674  -0.5864   1.6265
 JCK  H23  H  HCH2  0   0.190  -5.8790  -2.2546  -1.0581
 JCK  H24  H  HCH2  0   0.234  -5.6150  -0.5293  -1.3323
 JCK  H25  H  HCR6  0   0.251  -0.7658  -0.7444  -2.3367
 JCK  C29  C  CSP   0  -0.038   5.9855  -0.6696   0.8431
 JCK  C20  C  CH2   0  -0.335  -4.1273  -1.5609   0.7934
 JCK  N01  N  NH2   0  -0.842   5.7352  -3.7071   0.4593
 JCK  H8   H  HCH2  0   0.191  -6.2896  -2.9510   1.4198
 JCK  H13  H  HNH2  0   0.408   6.5474  -3.4691   1.0054
 JCK  H14  H  HNH2  0   0.409   5.4567  -4.6701   0.5607

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
 JCK  C22  C23  single    1.529  0.020  1.529
 JCK  C22  N21  single    1.452  0.020  1.452
 JCK  C23  C24  single    1.545  0.020  1.545
 JCK  N21  C20  single    1.443  0.020  1.443
 JCK  N21  C25  single    1.453  0.020  1.453
 JCK  C20  C19  single    1.505  0.020  1.505
 JCK  C24  C25  single    1.529  0.020  1.529
 JCK  C18  C19  aromatic  1.395  0.020  1.395
 JCK  C18  C17  aromatic  1.383  0.020  1.383
 JCK  C19  C26  aromatic  1.387  0.020  1.387
 JCK  C17  C16  aromatic  1.395  0.020  1.395
 JCK  C26  C27  aromatic  1.391  0.020  1.391
 JCK  C16  C27  aromatic  1.387  0.020  1.387
 JCK  C16  C15  single    1.508  0.020  1.508
 JCK  C13  C12  aromatic  1.365  0.020  1.365
 JCK  C13  N14  aromatic  1.368  0.020  1.368
 JCK  C12  C09  aromatic  1.427  0.020  1.427
 JCK  N14  C15  single    1.446  0.020  1.446
 JCK  N14  C08  aromatic  1.368  0.020  1.368
 JCK  C09  C08  aromatic  1.413  0.020  1.413
 JCK  C09  C10  aromatic  1.398  0.020  1.398
 JCK  C08  C07  aromatic  1.389  0.020  1.389
 JCK  C10  C11  aromatic  1.379  0.020  1.379
 JCK  C07  C06  aromatic  1.389  0.020  1.389
 JCK  C11  C06  aromatic  1.410  0.020  1.410
 JCK  C06  C05  single    1.465  0.020  1.465
 JCK  C05  N04  aromatic  1.309  0.020  1.309
 JCK  C05  C28  aromatic  1.427  0.020  1.427
 JCK  N04  N03  aromatic  1.348  0.020  1.348
 JCK  C28  C29  single    1.401  0.020  1.401
 JCK  C28  C02  aromatic  1.399  0.020  1.399
 JCK  C29  N30  triple    1.156  0.020  1.156
 JCK  N03  C02  aromatic  1.336  0.020  1.336
 JCK  C02  N01  single    1.350  0.020  1.350
 JCK  C10  H1   single    0.930  0.020  1.080
 JCK  C13  H2   single    0.930  0.020  1.080
 JCK  C15  H3   single    0.970  0.020  1.090
 JCK  C15  H4   single    0.970  0.020  1.090
 JCK  C17  H5   single    0.930  0.020  1.080
 JCK  C20  H6   single    0.970  0.020  1.090
 JCK  C20  H7   single    0.970  0.020  1.090
 JCK  C22  H8   single    0.970  0.020  1.090
 JCK  C22  H9   single    0.970  0.020  1.090
 JCK  C24  H10  single    0.970  0.020  1.090
 JCK  C24  H11  single    0.970  0.020  1.090
 JCK  C26  H12  single    0.930  0.020  1.080
 JCK  N01  H13  single    0.890  0.020  1.040
 JCK  N01  H14  single    0.890  0.020  1.040
 JCK  N03  H15  single    0.860  0.020  1.020
 JCK  C07  H16  single    0.930  0.020  1.080
 JCK  C11  H17  single    0.930  0.020  1.080
 JCK  C12  H18  single    0.930  0.020  1.080
 JCK  C18  H19  single    0.930  0.020  1.080
 JCK  C23  H21  single    0.970  0.020  1.090
 JCK  C23  H22  single    0.970  0.020  1.090
 JCK  C25  H23  single    0.970  0.020  1.090
 JCK  C25  H24  single    0.970  0.020  1.090
 JCK  C27  H25  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
 JCK  H1   C10  C11  120.00  3.000
 JCK  H1   C10  C09  120.75  3.000
 JCK  C11  C10  C09  119.25  3.000
 JCK  H2   C13  N14  120.08  3.000
 JCK  H2   C13  C12  129.53  3.000
 JCK  N14  C13  C12  110.39  3.000
 JCK  H4   C15  H3   106.63  3.000
 JCK  H4   C15  C16  110.37  3.000
 JCK  H3   C15  C16  110.57  3.000
 JCK  H4   C15  N14  109.22  3.000
 JCK  H3   C15  N14  107.31  3.000
 JCK  C16  C15  N14  112.52  3.000
 JCK  H5   C17  C18  119.35  3.000
 JCK  H5   C17  C16  119.94  3.000
 JCK  C18  C17  C16  120.72  3.000
 JCK  H9   C22  H8   107.35  3.000
 JCK  H9   C22  C23  113.38  3.000
 JCK  H8   C22  C23  110.05  3.000
 JCK  H9   C22  N21  111.01  3.000
 JCK  H8   C22  N21  111.48  3.000
 JCK  C23  C22  N21  103.64  3.000
 JCK  H11  C24  H10  107.09  3.000
 JCK  H11  C24  C25  110.75  3.000
 JCK  H10  C24  C25  111.34  3.000
 JCK  H11  C24  C23  110.79  3.000
 JCK  H10  C24  C23  112.64  3.000
 JCK  C25  C24  C23  104.29  3.000
 JCK  H12  C26  C27  119.40  3.000
 JCK  H12  C26  C19  119.73  3.000
 JCK  C27  C26  C19  120.87  3.000
 JCK  C29  C28  C05  130.17  3.000
 JCK  C29  C28  C02  124.75  3.000
 JCK  C05  C28  C02  104.97  3.000
 JCK  N03  C02  N01  124.45  3.000
 JCK  N01  C02  C28  130.23  3.000
 JCK  N03  C02  C28  105.22  3.000
 JCK  H15  N03  N04  119.50  3.000
 JCK  H15  N03  C02  126.84  3.000
 JCK  N04  N03  C02  113.65  3.000
 JCK  C05  N04  N03  105.87  3.000
 JCK  C06  C05  N04  121.12  3.000
 JCK  N04  C05  C28  110.29  3.000
 JCK  C06  C05  C28  128.58  3.000
 JCK  C11  C06  C07  120.09  3.000
 JCK  C11  C06  C05  120.80  3.000
 JCK  C07  C06  C05  119.10  3.000
 JCK  H16  C07  C08  121.63  3.000
 JCK  H16  C07  C06  120.30  3.000
 JCK  C08  C07  C06  118.07  3.000
 JCK  N14  C08  C09  107.83  3.000
 JCK  C09  C08  C07  122.41  3.000
 JCK  N14  C08  C07  129.76  3.000
 JCK  C12  C09  C08  106.75  3.000
 JCK  C08  C09  C10  118.62  3.000
 JCK  C12  C09  C10  134.62  3.000
 JCK  H17  C11  C06  119.83  3.000
 JCK  H17  C11  C10  118.61  3.000
 JCK  C06  C11  C10  121.55  3.000
 JCK  H18  C12  C09  127.40  3.000
 JCK  H18  C12  C13  126.13  3.000
 JCK  C09  C12  C13  106.47  3.000
 JCK  C08  N14  C15  125.26  3.000
 JCK  C08  N14  C13  108.56  3.000
 JCK  C15  N14  C13  125.98  3.000
 JCK  C27  C16  C17  118.56  3.000
 JCK  C27  C16  C15  120.98  3.000
 JCK  C17  C16  C15  120.46  3.000
 JCK  H19  C18  C19  119.49  3.000
 JCK  H19  C18  C17  119.70  3.000
 JCK  C19  C18  C17  120.81  3.000
 JCK  C18  C19  C26  118.38  3.000
 JCK  C26  C19  C20  121.40  3.000
 JCK  C18  C19  C20  120.22  3.000
 JCK  C25  N21  C22  104.52  3.000
 JCK  C25  N21  C20  114.07  3.000
 JCK  C22  N21  C20  113.73  3.000
 JCK  H22  C23  H21  107.19  3.000
 JCK  H22  C23  C24  110.79  3.000
 JCK  H21  C23  C24  112.60  3.000
 JCK  H22  C23  C22  110.78  3.000
 JCK  H21  C23  C22  111.36  3.000
 JCK  C24  C23  C22  104.18  3.000
 JCK  H24  C25  H23  107.17  3.000
 JCK  H24  C25  N21  111.37  3.000
 JCK  H23  C25  N21  111.07  3.000
 JCK  H24  C25  C24  113.24  3.000
 JCK  H23  C25  C24  110.38  3.000
 JCK  N21  C25  C24  103.66  3.000
 JCK  H25  C27  C16  119.95  3.000
 JCK  H25  C27  C26  119.38  3.000
 JCK  C16  C27  C26  120.67  3.000
 JCK  N30  C29  C28  180.00  3.000
 JCK  H7   C20  H6   106.26  3.000
 JCK  H7   C20  N21  108.14  3.000
 JCK  H6   C20  N21  111.85  3.000
 JCK  H7   C20  C19  109.02  3.000
 JCK  H6   C20  C19  109.45  3.000
 JCK  N21  C20  C19  111.93  3.000
 JCK  H14  N01  H13  113.22  3.000
 JCK  H14  N01  C02  117.56  3.000
 JCK  H13  N01  C02  116.61  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
 JCK  CONST_01  C13  C12  C09  C10   180.00   0.0  0
 JCK  CONST_02  N14  C08  C09  C10   180.00   0.0  0
 JCK  CONST_03  C07  C08  C09  C10     0.00   0.0  0
 JCK  CONST_04  C07  C06  C11  C10     0.00   0.0  0
 JCK  CONST_05  C05  C06  C11  C10   180.00   0.0  0
 JCK  CONST_06  C08  C09  C12  C13     0.00   0.0  0
 JCK  CONST_07  C09  C08  N14  C13     0.00   0.0  0
 JCK  CONST_08  C07  C08  N14  C13   180.00   0.0  0
 JCK  CONST_09  C26  C19  C18  C17     0.00   0.0  0
 JCK  CONST_10  C26  C27  C16  C17     0.00   0.0  0
 JCK  CONST_13  N03  N04  C05  C28     0.00   0.0  0
 JCK  CONST_14  N04  N03  C02  C28     0.00   0.0  0
 JCK  CONST_15  C06  C05  C28  C02   180.00   0.0  0
 JCK  CONST_16  N04  C05  C28  C02     0.00   0.0  0
 JCK  CONST_17  C05  N04  N03  C02     0.00   0.0  0
 JCK  CONST_18  C06  C05  N04  N03   180.00   0.0  0
 JCK  CONST_19  C05  C28  C02  N03     0.00   0.0  0
 JCK  CONST_22  C08  C07  C06  C05   180.00   0.0  0
 JCK  CONST_23  N14  C08  C07  C06   180.00   0.0  0
 JCK  CONST_24  C09  C08  C07  C06     0.00   0.0  0
 JCK  CONST_25  C09  C10  C11  C06     0.00   0.0  0
 JCK  CONST_26  C12  C09  C08  C07   180.00   0.0  0
 JCK  CONST_27  C12  C13  N14  C08     0.00   0.0  0
 JCK  CONST_28  C11  C10  C09  C08     0.00   0.0  0
 JCK  CONST_29  C11  C06  C07  C08     0.00   0.0  0
 JCK  CONST_30  N14  C13  C12  C09     0.00   0.0  0
 JCK  CONST_31  C12  C09  C10  C11   180.00   0.0  0
 JCK  CONST_32  N14  C08  C09  C12     0.00   0.0  0
 JCK  CONST_33  C19  C18  C17  C16     0.00   0.0  0
 JCK  CONST_34  C19  C26  C27  C16     0.00   0.0  0
 JCK  CONST_35  C27  C26  C19  C18     0.00   0.0  0
 JCK  CONST_36  C27  C16  C17  C18     0.00   0.0  0
 JCK  CONST_37  C18  C17  C16  C15   180.00   0.0  0
 JCK  CONST_38  C26  C27  C16  C15   180.00   0.0  0
 JCK  CONST_39  C12  C13  N14  C15   180.00   0.0  0
 JCK  CONST_40  C09  C08  N14  C15   180.00   0.0  0
 JCK  CONST_41  C07  C08  N14  C15     0.00   0.0  0
 JCK  CONST_42  C20  C19  C18  C17   180.00   0.0  0
 JCK  CONST_43  C27  C26  C19  C20   180.00   0.0  0
 JCK  CONST_44  C05  C28  C02  N01   180.00   0.0  0
 JCK  CONST_45  N04  N03  C02  N01   180.00   0.0  0
 JCK  CONST_46  C29  C28  C02  N03   180.00   0.0  0
 JCK  CONST_47  C29  C28  C05  N04   180.00   0.0  0
 JCK  CONST_48  C29  C28  C05  C06     0.00   0.0  0
 JCK  CONST_49  H18  C12  C09  C10     0.00   0.0  0
 JCK  CONST_50  H25  C27  C16  C17   180.00   0.0  0
 JCK  CONST_51  H19  C18  C19  C26   180.00   0.0  0
 JCK  CONST_52  H15  N03  C02  C28   180.00   0.0  0
 JCK  CONST_53  H16  C07  C06  C05     0.00   0.0  0
 JCK  CONST_54  H17  C11  C06  C05     0.00   0.0  0
 JCK  CONST_55  H1   C10  C11  C06   180.00   0.0  0
 JCK  CONST_56  H2   C13  N14  C08   180.00   0.0  0
 JCK  CONST_57  H12  C26  C27  C16   180.00   0.0  0
 JCK  CONST_58  H5   C17  C18  C19   180.00   0.0  0
 JCK  Var_01    C25  C24  C23  C22    -0.39  30.0  1
 JCK  Var_02    C24  C25  N21  C22    43.21  30.0  1
 JCK  Var_03    N21  C22  C23  C24    26.02  30.0  1
 JCK  Var_04    C23  C24  C25  N21   -25.36  30.0  1
 JCK  Var_05    C25  N21  C22  C23   -43.48  30.0  1
 JCK  Var_06    C16  C15  N14  C13  -104.54  30.0  2
 JCK  Var_07    N14  C15  C16  C17    60.22  30.0  2
 JCK  Var_08    C19  C20  N21  C22  -172.66  30.0  3
 JCK  Var_09    N21  C20  C19  C26  -126.19  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
 JCK  plan-1  C28  0.020
 JCK  plan-1  C02  0.020
 JCK  plan-1  N03  0.020
 JCK  plan-1  N04  0.020
 JCK  plan-1  C05  0.020
 JCK  plan-1  C06  0.020
 JCK  plan-1  N30  0.020
 JCK  plan-1  H15  0.020
 JCK  plan-1  C29  0.020
 JCK  plan-1  N01  0.020
 JCK  plan-2  C15  0.020
 JCK  plan-2  C17  0.020
 JCK  plan-2  C26  0.020
 JCK  plan-2  C16  0.020
 JCK  plan-2  C18  0.020
 JCK  plan-2  C19  0.020
 JCK  plan-2  C27  0.020
 JCK  plan-2  H5   0.020
 JCK  plan-2  H12  0.020
 JCK  plan-2  H19  0.020
 JCK  plan-2  H25  0.020
 JCK  plan-2  C20  0.020
 JCK  plan-3  C10  0.020
 JCK  plan-3  C13  0.020
 JCK  plan-3  C15  0.020
 JCK  plan-3  C05  0.020
 JCK  plan-3  C06  0.020
 JCK  plan-3  C07  0.020
 JCK  plan-3  C08  0.020
 JCK  plan-3  C09  0.020
 JCK  plan-3  C11  0.020
 JCK  plan-3  C12  0.020
 JCK  plan-3  N14  0.020
 JCK  plan-3  H1   0.020
 JCK  plan-3  H2   0.020
 JCK  plan-3  H16  0.020
 JCK  plan-3  H17  0.020
 JCK  plan-3  H18  0.020
 JCK  plan-4  C02  0.020
 JCK  plan-4  N01  0.020
 JCK  plan-4  H13  0.020
 JCK  plan-4  H14  0.020

