# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 07:53:53 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 3-[1-[[4-(piperidin-1-ylmethyl)phenyl]methyl]indol-6-yl]-1~{H}-pyrazol-5-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1[nH]nc(c1)c2ccc3ccn(Cc4ccc(CN5CCCCC5)cc4)c3c2
#
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
 JDK  JDK  3-[1-[[4-(piperidin-1-ylmethyl)phenyl]methyl]indol-6-yl]-1~{H}-pyrazol-5-amine  ligand  56  29  .  2021-08-12  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JDK
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
 JDK  C10  C  CR16  0  -0.326   3.8918   2.5506   1.1786
 JDK  C13  C  CR15  0  -0.026   1.1752   3.8462  -0.8395
 JDK  C15  C  CH2   0  -0.420   0.3519   1.8496  -2.1087
 JDK  C17  C  CR16  0  -0.275  -1.5646   1.5544  -0.4947
 JDK  C20  C  CH2   0  -0.320  -3.5617  -1.4600   0.6604
 JDK  C22  C  C     0  -0.276  -5.8030  -1.6190   1.4830
 JDK  C24  C  C     0  -0.439  -7.7663  -0.9585   0.0709
 JDK  C26  C  C     0  -0.272  -5.4136  -0.9547  -0.7889
 JDK  C28  C  CR16  0  -0.298  -0.7113  -0.3792  -1.6127
 JDK  C02  C  CR5   0   0.549   5.3494  -2.9776   0.8052
 JDK  N03  N  NR15  0  -0.481   4.4999  -3.1246  -0.2281
 JDK  N04  N  N     0  -0.329   3.8336  -2.0004  -0.5287
 JDK  C05  C  CR5   0   0.279   4.2710  -1.1038   0.3367
 JDK  C06  C  CR6   0   0.045   3.7586   0.2704   0.3247
 JDK  C07  C  CR16  0  -0.361   2.7007   0.6170  -0.5056
 JDK  C08  C  CR56  0   0.416   2.2518   1.9328  -0.4845
 JDK  C09  C  CR56  0   0.042   2.8270   2.9174   0.3495
 JDK  C11  C  CR16  0  -0.349   4.3419   1.2475   1.1586
 JDK  C12  C  CR15  0  -0.432   2.1185   4.1324   0.1036
 JDK  N14  N  NR5   0  -0.519   1.2527   2.5286  -1.2054
 JDK  C16  C  CR6   0   0.115  -0.6578   0.9891  -1.3907
 JDK  C18  C  CR16  0  -0.267  -2.4970   0.7680   0.1590
 JDK  C19  C  CR6   0   0.077  -2.5537  -0.6082  -0.0652
 JDK  N21  N  NR6   0  -0.411  -4.9055  -0.9282   0.5725
 JDK  C23  C  C     0  -0.437  -7.1876  -0.9889   1.4795
 JDK  C25  C  C     0  -0.435  -6.7797  -0.2923  -0.8791
 JDK  C27  C  CR16  0  -0.298  -1.6535  -1.1678  -0.9608
 JDK  C29  C  CR15  0  -0.585   5.2325  -1.6610   1.2094
 JDK  H1   H  HCR6  0   0.246   4.3612   3.2770   1.8301
 JDK  H2   H  HCR5  0   0.286   0.4424   4.4924  -1.2978
 JDK  H3   H  HCH2  0   0.287  -0.1514   2.6156  -2.7006
 JDK  H4   H  HCH2  0   0.278   0.9319   1.2436  -2.8082
 JDK  H5   H  HCR6  0   0.249  -1.5443   2.6218  -0.3063
 JDK  H6   H  HCH2  0   0.207  -3.4961  -2.4972   0.2882
 JDK  H7   H  HCH2  0   0.248  -3.2895  -1.5011   1.7202
 JDK  H8   H  H     0   0.182  -5.8927  -2.6899   1.2234
 JDK  H9   H  H     0   0.232  -5.3787  -1.5752   2.4894
 JDK  H10  H  H     0   0.210  -7.9575  -1.9830  -0.2663
 JDK  H11  H  H     0   0.229  -8.7271  -0.4389   0.0604
 JDK  H12  H  H     0   0.237  -4.7096  -0.4330  -1.4400
 JDK  H13  H  H     0   0.182  -5.4859  -1.9924  -1.1643
 JDK  H14  H  HCR6  0   0.251  -0.0209  -0.8412  -2.3094
 JDK  H15  H  HNH2  0   0.387   5.7873  -4.9170   1.1586
 JDK  H16  H  HNH2  0   0.390   6.5470  -3.8359   2.1581
 JDK  H17  H  HNR5  0   0.413   4.3412  -3.9591  -0.7696
 JDK  H18  H  HCR6  0   0.249   2.2431  -0.1256  -1.1462
 JDK  H19  H  HCR6  0   0.242   5.1717   0.9735   1.7970
 JDK  H20  H  HCR5  0   0.247   2.2894   5.0942   0.5604
 JDK  H21  H  HCR6  0   0.244  -3.2041   1.2259   0.8399
 JDK  H23  H  H     0   0.229  -7.8384  -1.5475   2.1559
 JDK  H24  H  H     0   0.214  -7.1170   0.0304   1.8708
 JDK  H25  H  H     0   0.228  -7.1367  -0.3429  -1.9102
 JDK  H26  H  H     0   0.214  -6.6795   0.7673  -0.6251
 JDK  H27  H  HCR6  0   0.248  -1.6845  -2.2330  -1.1579
 JDK  H28  H  HCR5  0   0.261   5.7570  -1.1911   2.0248
 JDK  N01  N  NH2   0  -0.857   6.1743  -3.9880   1.2342

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
 JDK  C23  C22  single    1.521  0.020  1.521
 JDK  C23  C24  single    1.523  0.020  1.523
 JDK  C22  N21  single    1.453  0.020  1.453
 JDK  C24  C25  single    1.523  0.020  1.523
 JDK  N21  C20  single    1.448  0.020  1.448
 JDK  N21  C26  single    1.453  0.020  1.453
 JDK  C20  C19  single    1.506  0.020  1.506
 JDK  C25  C26  single    1.521  0.020  1.521
 JDK  C19  C18  aromatic  1.395  0.020  1.395
 JDK  C19  C27  aromatic  1.388  0.020  1.388
 JDK  C18  C17  aromatic  1.384  0.020  1.384
 JDK  C17  C16  aromatic  1.395  0.020  1.395
 JDK  C27  C28  aromatic  1.391  0.020  1.391
 JDK  C28  C16  aromatic  1.387  0.020  1.387
 JDK  C16  C15  single    1.508  0.020  1.508
 JDK  C13  C12  aromatic  1.364  0.020  1.364
 JDK  C13  N14  aromatic  1.370  0.020  1.370
 JDK  C12  C09  aromatic  1.428  0.020  1.428
 JDK  N14  C15  single    1.445  0.020  1.445
 JDK  N14  C08  aromatic  1.369  0.020  1.369
 JDK  C09  C08  aromatic  1.413  0.020  1.413
 JDK  C09  C10  aromatic  1.398  0.020  1.398
 JDK  C08  C07  aromatic  1.390  0.020  1.390
 JDK  C10  C11  aromatic  1.379  0.020  1.379
 JDK  C07  C06  aromatic  1.389  0.020  1.389
 JDK  C11  C06  aromatic  1.411  0.020  1.411
 JDK  C06  C05  single    1.467  0.020  1.467
 JDK  C29  C05  aromatic  1.413  0.020  1.413
 JDK  C29  C02  aromatic  1.382  0.020  1.382
 JDK  C05  N04  aromatic  1.321  0.020  1.321
 JDK  C02  N01  single    1.373  0.020  1.373
 JDK  C02  N03  aromatic  1.346  0.020  1.346
 JDK  N04  N03  aromatic  1.341  0.020  1.341
 JDK  C10  H1   single    0.930  0.020  1.080
 JDK  C13  H2   single    0.930  0.020  1.080
 JDK  C15  H3   single    0.970  0.020  1.090
 JDK  C15  H4   single    0.970  0.020  1.090
 JDK  C17  H5   single    0.930  0.020  1.080
 JDK  C20  H6   single    0.970  0.020  1.090
 JDK  C20  H7   single    0.970  0.020  1.090
 JDK  C22  H8   single    0.970  0.020  1.090
 JDK  C22  H9   single    0.970  0.020  1.090
 JDK  C24  H10  single    0.970  0.020  1.090
 JDK  C24  H11  single    0.970  0.020  1.090
 JDK  C26  H12  single    0.970  0.020  1.090
 JDK  C26  H13  single    0.970  0.020  1.090
 JDK  C28  H14  single    0.930  0.020  1.080
 JDK  N01  H15  single    0.890  0.020  1.040
 JDK  N01  H16  single    0.890  0.020  1.040
 JDK  N03  H17  single    0.860  0.020  1.020
 JDK  C07  H18  single    0.930  0.020  1.080
 JDK  C11  H19  single    0.930  0.020  1.080
 JDK  C12  H20  single    0.930  0.020  1.080
 JDK  C18  H21  single    0.930  0.020  1.080
 JDK  C23  H23  single    0.970  0.020  1.090
 JDK  C23  H24  single    0.970  0.020  1.090
 JDK  C25  H25  single    0.970  0.020  1.090
 JDK  C25  H26  single    0.970  0.020  1.090
 JDK  C27  H27  single    0.930  0.020  1.080
 JDK  C29  H28  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
 JDK  H1   C10  C11  120.08  3.000
 JDK  H1   C10  C09  120.72  3.000
 JDK  C11  C10  C09  119.20  3.000
 JDK  H2   C13  N14  120.06  3.000
 JDK  H2   C13  C12  129.60  3.000
 JDK  N14  C13  C12  110.33  3.000
 JDK  H4   C15  H3   106.68  3.000
 JDK  H4   C15  C16  110.10  3.000
 JDK  H3   C15  C16  110.48  3.000
 JDK  H4   C15  N14  109.27  3.000
 JDK  H3   C15  N14  107.27  3.000
 JDK  C16  C15  N14  112.82  3.000
 JDK  H5   C17  C18  119.34  3.000
 JDK  H5   C17  C16  119.91  3.000
 JDK  C18  C17  C16  120.75  3.000
 JDK  H7   C20  H6   106.04  3.000
 JDK  H7   C20  N21  107.65  3.000
 JDK  H6   C20  N21  112.32  3.000
 JDK  H7   C20  C19  108.73  3.000
 JDK  H6   C20  C19  109.22  3.000
 JDK  N21  C20  C19  112.59  3.000
 JDK  H9   C22  H8   106.65  3.000
 JDK  H9   C22  C23  109.81  3.000
 JDK  H8   C22  C23  109.08  3.000
 JDK  H9   C22  N21  108.55  3.000
 JDK  H8   C22  N21  111.31  3.000
 JDK  C23  C22  N21  111.33  3.000
 JDK  H11  C24  H10  106.77  3.000
 JDK  H11  C24  C25  110.84  3.000
 JDK  H10  C24  C25  109.28  3.000
 JDK  H11  C24  C23  110.64  3.000
 JDK  H10  C24  C23  109.41  3.000
 JDK  C25  C24  C23  109.84  3.000
 JDK  H13  C26  H12  106.75  3.000
 JDK  H13  C26  C25  109.26  3.000
 JDK  H12  C26  C25  109.62  3.000
 JDK  H13  C26  N21  110.97  3.000
 JDK  H12  C26  N21  108.93  3.000
 JDK  C25  C26  N21  111.20  3.000
 JDK  H14  C28  C27  119.41  3.000
 JDK  H14  C28  C16  119.90  3.000
 JDK  C27  C28  C16  120.68  3.000
 JDK  C29  C02  N03  105.98  3.000
 JDK  N03  C02  N01  122.60  3.000
 JDK  C29  C02  N01  131.32  3.000
 JDK  H17  N03  N04  119.72  3.000
 JDK  H17  N03  C02  127.06  3.000
 JDK  N04  N03  C02  113.21  3.000
 JDK  C05  N04  N03  104.94  3.000
 JDK  C29  C05  C06  127.75  3.000
 JDK  C29  C05  N04  111.25  3.000
 JDK  C06  C05  N04  121.00  3.000
 JDK  C11  C06  C07  119.70  3.000
 JDK  C11  C06  C05  119.98  3.000
 JDK  C07  C06  C05  120.32  3.000
 JDK  H18  C07  C08  121.46  3.000
 JDK  H18  C07  C06  120.31  3.000
 JDK  C08  C07  C06  118.23  3.000
 JDK  N14  C08  C09  107.74  3.000
 JDK  C09  C08  C07  122.49  3.000
 JDK  N14  C08  C07  129.77  3.000
 JDK  C12  C09  C08  106.83  3.000
 JDK  C08  C09  C10  118.50  3.000
 JDK  C12  C09  C10  134.68  3.000
 JDK  H19  C11  C06  119.37  3.000
 JDK  H19  C11  C10  118.75  3.000
 JDK  C06  C11  C10  121.88  3.000
 JDK  H20  C12  C09  127.40  3.000
 JDK  H20  C12  C13  126.12  3.000
 JDK  C09  C12  C13  106.47  3.000
 JDK  C08  N14  C15  125.44  3.000
 JDK  C08  N14  C13  108.62  3.000
 JDK  C15  N14  C13  125.71  3.000
 JDK  C28  C16  C17  118.53  3.000
 JDK  C28  C16  C15  120.82  3.000
 JDK  C17  C16  C15  120.65  3.000
 JDK  H21  C18  C19  119.43  3.000
 JDK  H21  C18  C17  119.77  3.000
 JDK  C19  C18  C17  120.79  3.000
 JDK  C27  C19  C18  118.36  3.000
 JDK  C27  C19  C20  121.13  3.000
 JDK  C18  C19  C20  120.51  3.000
 JDK  C26  N21  C22  111.24  3.000
 JDK  C26  N21  C20  112.00  3.000
 JDK  C22  N21  C20  111.14  3.000
 JDK  H24  C23  H23  107.06  3.000
 JDK  H24  C23  C24  109.68  3.000
 JDK  H23  C23  C24  110.88  3.000
 JDK  H24  C23  C22  109.04  3.000
 JDK  H23  C23  C22  109.21  3.000
 JDK  C24  C23  C22  110.87  3.000
 JDK  H26  C25  H25  107.09  3.000
 JDK  H26  C25  C26  109.01  3.000
 JDK  H25  C25  C26  109.23  3.000
 JDK  H26  C25  C24  109.76  3.000
 JDK  H25  C25  C24  110.91  3.000
 JDK  C26  C25  C24  110.75  3.000
 JDK  H27  C27  C19  119.69  3.000
 JDK  H27  C27  C28  119.43  3.000
 JDK  C19  C27  C28  120.88  3.000
 JDK  H28  C29  C05  128.81  3.000
 JDK  H28  C29  C02  126.56  3.000
 JDK  C05  C29  C02  104.62  3.000
 JDK  H16  N01  H15  110.45  3.000
 JDK  H16  N01  C02  113.43  3.000
 JDK  H15  N01  C02  115.06  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
 JDK  CONST_01  C13  C12  C09  C10   180.00   0.0  0
 JDK  CONST_02  N14  C08  C09  C10   180.00   0.0  0
 JDK  CONST_03  C07  C08  C09  C10     0.00   0.0  0
 JDK  CONST_04  C07  C06  C11  C10     0.00   0.0  0
 JDK  CONST_05  C05  C06  C11  C10   180.00   0.0  0
 JDK  CONST_06  C08  C09  C12  C13     0.00   0.0  0
 JDK  CONST_07  C09  C08  N14  C13     0.00   0.0  0
 JDK  CONST_08  C07  C08  N14  C13   180.00   0.0  0
 JDK  CONST_09  C27  C19  C18  C17     0.00   0.0  0
 JDK  CONST_10  C27  C28  C16  C17     0.00   0.0  0
 JDK  CONST_11  C18  C19  C27  C28     0.00   0.0  0
 JDK  CONST_12  C18  C17  C16  C28     0.00   0.0  0
 JDK  CONST_13  C06  C05  C29  C02   180.00   0.0  0
 JDK  CONST_14  N04  C05  C29  C02     0.00   0.0  0
 JDK  CONST_15  C05  N04  N03  C02     0.00   0.0  0
 JDK  CONST_16  C05  C29  C02  N03     0.00   0.0  0
 JDK  CONST_17  C06  C05  N04  N03   180.00   0.0  0
 JDK  CONST_18  C29  C05  N04  N03     0.00   0.0  0
 JDK  CONST_19  C07  C06  C05  N04     0.00   0.0  0
 JDK  CONST_20  C11  C06  C05  N04   180.00   0.0  0
 JDK  CONST_21  C29  C02  N03  N04     0.00   0.0  0
 JDK  CONST_22  C08  C07  C06  C05   180.00   0.0  0
 JDK  CONST_23  N14  C08  C07  C06   180.00   0.0  0
 JDK  CONST_24  C09  C08  C07  C06     0.00   0.0  0
 JDK  CONST_25  C09  C10  C11  C06     0.00   0.0  0
 JDK  CONST_26  C12  C09  C08  C07   180.00   0.0  0
 JDK  CONST_27  C29  C05  C06  C07   180.00   0.0  0
 JDK  CONST_28  C12  C13  N14  C08     0.00   0.0  0
 JDK  CONST_29  C11  C10  C09  C08     0.00   0.0  0
 JDK  CONST_30  C11  C06  C07  C08     0.00   0.0  0
 JDK  CONST_31  N14  C13  C12  C09     0.00   0.0  0
 JDK  CONST_32  C12  C09  C10  C11   180.00   0.0  0
 JDK  CONST_33  C29  C05  C06  C11     0.00   0.0  0
 JDK  CONST_34  N14  C08  C09  C12     0.00   0.0  0
 JDK  CONST_35  C19  C18  C17  C16     0.00   0.0  0
 JDK  CONST_36  C19  C27  C28  C16     0.00   0.0  0
 JDK  CONST_37  C18  C17  C16  C15   180.00   0.0  0
 JDK  CONST_38  C27  C28  C16  C15   180.00   0.0  0
 JDK  CONST_39  C12  C13  N14  C15   180.00   0.0  0
 JDK  CONST_40  C09  C08  N14  C15   180.00   0.0  0
 JDK  CONST_41  C07  C08  N14  C15     0.00   0.0  0
 JDK  CONST_42  C20  C19  C18  C17   180.00   0.0  0
 JDK  CONST_43  C28  C27  C19  C20   180.00   0.0  0
 JDK  CONST_44  C05  C29  C02  N01   180.00   0.0  0
 JDK  CONST_45  N04  N03  C02  N01   180.00   0.0  0
 JDK  CONST_46  H20  C12  C09  C10     0.00   0.0  0
 JDK  CONST_47  H14  C28  C16  C17   180.00   0.0  0
 JDK  CONST_48  H5   C17  C16  C28   180.00   0.0  0
 JDK  CONST_49  H28  C29  C02  N03   180.00   0.0  0
 JDK  CONST_50  H18  C07  C06  C05     0.00   0.0  0
 JDK  CONST_51  H19  C11  C06  C05     0.00   0.0  0
 JDK  CONST_52  H17  N03  N04  C05   180.00   0.0  0
 JDK  CONST_53  H1   C10  C11  C06   180.00   0.0  0
 JDK  CONST_54  H2   C13  N14  C08   180.00   0.0  0
 JDK  CONST_55  H21  C18  C17  C16   180.00   0.0  0
 JDK  CONST_56  H27  C27  C28  C16   180.00   0.0  0
 JDK  Var_01    C25  C24  C23  C22   -53.09  30.0  1
 JDK  Var_02    C25  C26  N21  C22    59.46  30.0  1
 JDK  Var_03    N21  C22  C23  C24    56.23  30.0  1
 JDK  Var_04    N21  C26  C25  C24   -56.75  30.0  1
 JDK  Var_05    C23  C22  N21  C26   -59.19  30.0  1
 JDK  Var_06    C23  C24  C25  C26    53.35  30.0  1
 JDK  Var_07    C16  C15  N14  C13  -102.14  30.0  2
 JDK  Var_08    N14  C15  C16  C17    61.00  30.0  2
 JDK  Var_09    C19  C20  N21  C22  -169.09  30.0  3
 JDK  Var_10    N21  C20  C19  C18    50.14  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
 JDK  plan-1  C02  0.020
 JDK  plan-1  N03  0.020
 JDK  plan-1  N04  0.020
 JDK  plan-1  C05  0.020
 JDK  plan-1  C06  0.020
 JDK  plan-1  C29  0.020
 JDK  plan-1  H17  0.020
 JDK  plan-1  H28  0.020
 JDK  plan-1  N01  0.020
 JDK  plan-2  C15  0.020
 JDK  plan-2  C17  0.020
 JDK  plan-2  C20  0.020
 JDK  plan-2  C28  0.020
 JDK  plan-2  C16  0.020
 JDK  plan-2  C18  0.020
 JDK  plan-2  C19  0.020
 JDK  plan-2  C27  0.020
 JDK  plan-2  H5   0.020
 JDK  plan-2  H14  0.020
 JDK  plan-2  H21  0.020
 JDK  plan-2  H27  0.020
 JDK  plan-3  C10  0.020
 JDK  plan-3  C13  0.020
 JDK  plan-3  C15  0.020
 JDK  plan-3  C05  0.020
 JDK  plan-3  C06  0.020
 JDK  plan-3  C07  0.020
 JDK  plan-3  C08  0.020
 JDK  plan-3  C09  0.020
 JDK  plan-3  C11  0.020
 JDK  plan-3  C12  0.020
 JDK  plan-3  N14  0.020
 JDK  plan-3  H1   0.020
 JDK  plan-3  H2   0.020
 JDK  plan-3  H18  0.020
 JDK  plan-3  H19  0.020
 JDK  plan-3  H20  0.020
 JDK  plan-4  C02  0.020
 JDK  plan-4  H15  0.020
 JDK  plan-4  H16  0.020
 JDK  plan-4  N01  0.020

