# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 08:09:32 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 5-azanyl-3-[1-[[4-(morpholin-4-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(CN5CCOCC5)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
 JEE  JEE  5-azanyl-3-[1-[[4-(morpholin-4-ylmethyl)phenyl]methyl]indol-6-yl]-1~{H}-pyrazole-4-carbonitrile  ligand  55  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_JEE
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
 JEE  C10  C  CR16  0  -0.331   3.6972   2.4322   1.2547
 JEE  C13  C  CR15  0  -0.020   0.7596   3.7586  -0.4012
 JEE  C15  C  CH2   0  -0.450  -0.1214   1.8412  -1.7433
 JEE  C17  C  CR16  0  -0.296  -2.4334   1.9766  -0.7596
 JEE  C20  C  CH2   0  -0.337  -4.5108  -0.3634   1.3852
 JEE  C22  C  CH2   0  -0.299  -5.6273  -1.4405  -0.4588
 JEE  C26  C  CH2   0  -0.305  -6.8844  -0.7476   1.4338
 JEE  C28  C  CR16  0  -0.279  -1.1631  -0.0145  -0.3846
 JEE  C02  C  CR5   0   0.619   5.4204  -2.9332  -0.1190
 JEE  N03  N  NR15  0  -0.490   4.1303  -3.2027  -0.3379
 JEE  N04  N  N     0  -0.299   3.3274  -2.1260  -0.2315
 JEE  C05  C  CR5   0   0.321   4.1138  -1.1201   0.0597
 JEE  C06  C  CR6   0   0.045   3.5813   0.2352   0.2154
 JEE  C07  C  CR16  0  -0.361   2.4412   0.5953  -0.4894
 JEE  C08  C  CR56  0   0.411   1.9394   1.8788  -0.3119
 JEE  C09  C  CR56  0   0.053   2.5491   2.8151   0.5531
 JEE  C11  C  CR16  0  -0.335   4.1976   1.1587   1.0845
 JEE  C12  C  CR15  0  -0.423   1.7718   4.0096   0.4794
 JEE  N14  N  NR5   0  -0.515   0.8600   2.4865  -0.8930
 JEE  C16  C  CR6   0   0.137  -1.2624   1.2488  -0.9561
 JEE  C18  C  CR16  0  -0.270  -3.4768   1.4563  -0.0116
 JEE  C19  C  CR6   0   0.091  -3.3734   0.1964   0.5737
 JEE  N21  N  NT    0  -0.417  -5.7280  -0.4603   0.6058
 JEE  C23  C  CH2   0  -0.186  -6.9063  -1.4597  -1.2718
 JEE  O24  O  O2    0  -0.485  -8.0312  -1.7271  -0.4638
 JEE  C25  C  CH2   0  -0.187  -8.1363  -0.7827   0.5779
 JEE  C27  C  CR16  0  -0.294  -2.2072  -0.5314   0.3717
 JEE  C29  C  CR5   0  -0.286   5.4685  -1.5601   0.1501
 JEE  C30  C  CSP   0  -0.037   6.6406  -0.8267   0.3733
 JEE  N31  N  NS    0  -0.267   7.6230  -0.2435   0.5518
 JEE  H1   H  HCR6  0   0.251   4.1864   3.1210   1.9318
 JEE  H2   H  HCR5  0   0.284  -0.0386   4.4074  -0.7304
 JEE  H3   H  HCH2  0   0.291  -0.4936   2.5841  -2.4501
 JEE  H4   H  HCH2  0   0.286   0.3844   1.0780  -2.3363
 JEE  H5   H  HCR6  0   0.251  -2.5399   2.9563  -1.2117
 JEE  H6   H  HCH2  0   0.214  -4.2113  -1.3362   1.8109
 JEE  H7   H  HCH2  0   0.252  -4.7096   0.2975   2.2342
 JEE  H8   H  HCH2  0   0.246  -4.7980  -1.1854  -1.1228
 JEE  H9   H  HCH2  0   0.196  -5.4237  -2.4509  -0.0621
 JEE  H10  H  HCH2  0   0.197  -6.7797  -1.7043   1.9745
 JEE  H11  H  HCH2  0   0.242  -6.9952   0.0359   2.1879
 JEE  H12  H  HCR6  0   0.248  -0.2788  -0.6205  -0.5409
 JEE  H13  H  HNH2  0   0.409   6.2416  -4.7066  -0.6433
 JEE  H14  H  HNH2  0   0.409   7.3466  -3.5204  -0.1925
 JEE  H15  H  HNR5  0   0.429   3.7277  -4.1046  -0.5399
 JEE  H16  H  HCR6  0   0.261   1.9772  -0.1051  -1.1717
 JEE  H17  H  HCR6  0   0.248   5.0719   0.8631   1.6491
 JEE  H18  H  HCR5  0   0.250   1.9468   4.9373   1.0006
 JEE  H19  H  HCR6  0   0.247  -4.3857   2.0329   0.1112
 JEE  H21  H  HCH2  0   0.199  -7.0212  -0.4959  -1.7882
 JEE  H22  H  HCH2  0   0.236  -6.8545  -2.2424  -2.0303
 JEE  H23  H  HCH2  0   0.236  -8.9982  -1.0608   1.1866
 JEE  H24  H  HCH2  0   0.199  -8.3230   0.2211   0.1696
 JEE  H25  H  HCR6  0   0.251  -2.1139  -1.5235   0.7978
 JEE  N01  N  NH2   0  -0.842   6.4007  -3.8600  -0.1211

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
 JEE  C25  O24  single    1.410  0.020  1.410
 JEE  C25  C26  single    1.517  0.020  1.517
 JEE  O24  C23  single    1.411  0.020  1.411
 JEE  C26  N21  single    1.451  0.020  1.451
 JEE  C23  C22  single    1.516  0.020  1.516
 JEE  C20  N21  single    1.449  0.020  1.449
 JEE  C20  C19  single    1.505  0.020  1.505
 JEE  N21  C22  single    1.451  0.020  1.451
 JEE  C18  C19  aromatic  1.393  0.020  1.393
 JEE  C18  C17  aromatic  1.385  0.020  1.385
 JEE  C19  C27  aromatic  1.389  0.020  1.389
 JEE  C17  C16  aromatic  1.393  0.020  1.393
 JEE  C27  C28  aromatic  1.389  0.020  1.389
 JEE  C16  C28  aromatic  1.390  0.020  1.390
 JEE  C16  C15  single    1.507  0.020  1.507
 JEE  C13  C12  aromatic  1.365  0.020  1.365
 JEE  C13  N14  aromatic  1.368  0.020  1.368
 JEE  C12  C09  aromatic  1.427  0.020  1.427
 JEE  N14  C15  single    1.450  0.020  1.450
 JEE  N14  C08  aromatic  1.368  0.020  1.368
 JEE  C09  C08  aromatic  1.413  0.020  1.413
 JEE  C09  C10  aromatic  1.399  0.020  1.399
 JEE  C08  C07  aromatic  1.389  0.020  1.389
 JEE  C10  C11  aromatic  1.379  0.020  1.379
 JEE  C07  C06  aromatic  1.388  0.020  1.388
 JEE  C11  C06  aromatic  1.410  0.020  1.410
 JEE  C06  C05  single    1.464  0.020  1.464
 JEE  C05  N04  aromatic  1.310  0.020  1.310
 JEE  C05  C29  aromatic  1.427  0.020  1.427
 JEE  N04  N03  aromatic  1.347  0.020  1.347
 JEE  N31  C30  triple    1.156  0.020  1.156
 JEE  C30  C29  single    1.401  0.020  1.401
 JEE  C29  C02  aromatic  1.400  0.020  1.400
 JEE  N03  C02  aromatic  1.336  0.020  1.336
 JEE  C02  N01  single    1.349  0.020  1.349
 JEE  C10  H1   single    0.930  0.020  1.080
 JEE  C13  H2   single    0.930  0.020  1.080
 JEE  C15  H3   single    0.970  0.020  1.090
 JEE  C15  H4   single    0.970  0.020  1.090
 JEE  C17  H5   single    0.930  0.020  1.080
 JEE  C20  H6   single    0.970  0.020  1.090
 JEE  C20  H7   single    0.970  0.020  1.090
 JEE  C22  H8   single    0.970  0.020  1.090
 JEE  C22  H9   single    0.970  0.020  1.090
 JEE  C26  H10  single    0.970  0.020  1.090
 JEE  C26  H11  single    0.970  0.020  1.090
 JEE  C28  H12  single    0.930  0.020  1.080
 JEE  N01  H13  single    0.890  0.020  1.040
 JEE  N01  H14  single    0.890  0.020  1.040
 JEE  N03  H15  single    0.860  0.020  1.020
 JEE  C07  H16  single    0.930  0.020  1.080
 JEE  C11  H17  single    0.930  0.020  1.080
 JEE  C12  H18  single    0.930  0.020  1.080
 JEE  C18  H19  single    0.930  0.020  1.080
 JEE  C23  H21  single    0.970  0.020  1.090
 JEE  C23  H22  single    0.970  0.020  1.090
 JEE  C25  H23  single    0.970  0.020  1.090
 JEE  C25  H24  single    0.970  0.020  1.090
 JEE  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
 JEE  H1   C10  C11  120.05  3.000
 JEE  H1   C10  C09  120.69  3.000
 JEE  C11  C10  C09  119.26  3.000
 JEE  H2   C13  N14  120.23  3.000
 JEE  H2   C13  C12  129.37  3.000
 JEE  N14  C13  C12  110.40  3.000
 JEE  H4   C15  H3   106.41  3.000
 JEE  H4   C15  C16  111.09  3.000
 JEE  H3   C15  C16  110.35  3.000
 JEE  H4   C15  N14  108.44  3.000
 JEE  H3   C15  N14  107.93  3.000
 JEE  C16  C15  N14  112.39  3.000
 JEE  H5   C17  C18  119.38  3.000
 JEE  H5   C17  C16  119.73  3.000
 JEE  C18  C17  C16  120.87  3.000
 JEE  H7   C20  H6   106.41  3.000
 JEE  H7   C20  N21  107.77  3.000
 JEE  H6   C20  N21  112.13  3.000
 JEE  H7   C20  C19  109.33  3.000
 JEE  H6   C20  C19  109.32  3.000
 JEE  N21  C20  C19  111.70  3.000
 JEE  H9   C22  H8   106.98  3.000
 JEE  H9   C22  C23  109.67  3.000
 JEE  H8   C22  C23  108.51  3.000
 JEE  H9   C22  N21  111.56  3.000
 JEE  H8   C22  N21  109.93  3.000
 JEE  C23  C22  N21  110.10  3.000
 JEE  H11  C26  H10  107.03  3.000
 JEE  H11  C26  C25  108.79  3.000
 JEE  H10  C26  C25  109.55  3.000
 JEE  H11  C26  N21  109.43  3.000
 JEE  H10  C26  N21  112.05  3.000
 JEE  C25  C26  N21  109.90  3.000
 JEE  H12  C28  C27  118.95  3.000
 JEE  H12  C28  C16  120.48  3.000
 JEE  C27  C28  C16  120.56  3.000
 JEE  C29  C02  N03  105.22  3.000
 JEE  N03  C02  N01  124.25  3.000
 JEE  C29  C02  N01  130.48  3.000
 JEE  H15  N03  N04  119.53  3.000
 JEE  H15  N03  C02  126.79  3.000
 JEE  N04  N03  C02  113.66  3.000
 JEE  C05  N04  N03  105.87  3.000
 JEE  C29  C05  C06  128.59  3.000
 JEE  C29  C05  N04  110.32  3.000
 JEE  C06  C05  N04  121.07  3.000
 JEE  C11  C06  C07  120.14  3.000
 JEE  C11  C06  C05  120.85  3.000
 JEE  C07  C06  C05  119.00  3.000
 JEE  H16  C07  C08  121.57  3.000
 JEE  H16  C07  C06  120.29  3.000
 JEE  C08  C07  C06  118.13  3.000
 JEE  N14  C08  C09  107.82  3.000
 JEE  C09  C08  C07  122.30  3.000
 JEE  N14  C08  C07  129.86  3.000
 JEE  C12  C09  C08  106.74  3.000
 JEE  C08  C09  C10  118.67  3.000
 JEE  C12  C09  C10  134.59  3.000
 JEE  H17  C11  C06  119.73  3.000
 JEE  H17  C11  C10  118.76  3.000
 JEE  C06  C11  C10  121.49  3.000
 JEE  H18  C12  C09  127.36  3.000
 JEE  H18  C12  C13  126.18  3.000
 JEE  C09  C12  C13  106.46  3.000
 JEE  C08  N14  C15  125.83  3.000
 JEE  C08  N14  C13  108.57  3.000
 JEE  C15  N14  C13  125.11  3.000
 JEE  C28  C16  C17  118.49  3.000
 JEE  C28  C16  C15  121.19  3.000
 JEE  C17  C16  C15  120.31  3.000
 JEE  H19  C18  C19  119.73  3.000
 JEE  H19  C18  C17  119.55  3.000
 JEE  C19  C18  C17  120.71  3.000
 JEE  C27  C19  C18  118.35  3.000
 JEE  C27  C19  C20  121.18  3.000
 JEE  C18  C19  C20  120.46  3.000
 JEE  C26  N21  C22  109.90  3.000
 JEE  C22  N21  C20  112.44  3.000
 JEE  C26  N21  C20  112.08  3.000
 JEE  H22  C23  H21  107.89  3.000
 JEE  H22  C23  O24  107.46  3.000
 JEE  H21  C23  O24  110.60  3.000
 JEE  H22  C23  C22  109.99  3.000
 JEE  H21  C23  C22  109.22  3.000
 JEE  O24  C23  C22  111.60  3.000
 JEE  C25  O24  C23  110.83  3.000
 JEE  H24  C25  H23  107.81  3.000
 JEE  H24  C25  O24  110.47  3.000
 JEE  H23  C25  O24  107.47  3.000
 JEE  H24  C25  C26  109.18  3.000
 JEE  H23  C25  C26  110.06  3.000
 JEE  O24  C25  C26  111.77  3.000
 JEE  H25  C27  C19  119.64  3.000
 JEE  H25  C27  C28  119.35  3.000
 JEE  C19  C27  C28  121.01  3.000
 JEE  C30  C29  C05  130.02  3.000
 JEE  C30  C29  C02  124.95  3.000
 JEE  C05  C29  C02  104.93  3.000
 JEE  N31  C30  C29  180.00  3.000
 JEE  H14  N01  H13  113.26  3.000
 JEE  H14  N01  C02  116.79  3.000
 JEE  H13  N01  C02  117.60  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
 JEE  CONST_01  C13  C12  C09  C10  180.00   0.0  0
 JEE  CONST_02  N14  C08  C09  C10  180.00   0.0  0
 JEE  CONST_03  C07  C08  C09  C10    0.00   0.0  0
 JEE  CONST_04  C07  C06  C11  C10    0.00   0.0  0
 JEE  CONST_05  C05  C06  C11  C10  180.00   0.0  0
 JEE  CONST_06  C08  C09  C12  C13    0.00   0.0  0
 JEE  CONST_07  C09  C08  N14  C13    0.00   0.0  0
 JEE  CONST_08  C07  C08  N14  C13  180.00   0.0  0
 JEE  CONST_09  C27  C19  C18  C17    0.00   0.0  0
 JEE  CONST_10  C27  C28  C16  C17    0.00   0.0  0
 JEE  CONST_11  C18  C19  C27  C28    0.00   0.0  0
 JEE  CONST_12  C18  C17  C16  C28    0.00   0.0  0
 JEE  CONST_13  C06  C05  C29  C02  180.00   0.0  0
 JEE  CONST_14  N04  C05  C29  C02    0.00   0.0  0
 JEE  CONST_15  C05  N04  N03  C02    0.00   0.0  0
 JEE  CONST_16  C06  C05  N04  N03  180.00   0.0  0
 JEE  CONST_17  C29  C05  N04  N03    0.00   0.0  0
 JEE  CONST_18  C05  C29  C02  N03    0.00   0.0  0
 JEE  CONST_21  C29  C02  N03  N04    0.00   0.0  0
 JEE  CONST_22  C08  C07  C06  C05  180.00   0.0  0
 JEE  CONST_23  N14  C08  C07  C06  180.00   0.0  0
 JEE  CONST_24  C09  C08  C07  C06    0.00   0.0  0
 JEE  CONST_25  C09  C10  C11  C06    0.00   0.0  0
 JEE  CONST_26  C12  C09  C08  C07  180.00   0.0  0
 JEE  CONST_28  C12  C13  N14  C08    0.00   0.0  0
 JEE  CONST_29  C11  C10  C09  C08    0.00   0.0  0
 JEE  CONST_30  C11  C06  C07  C08    0.00   0.0  0
 JEE  CONST_31  N14  C13  C12  C09    0.00   0.0  0
 JEE  CONST_32  C12  C09  C10  C11  180.00   0.0  0
 JEE  CONST_34  N14  C08  C09  C12    0.00   0.0  0
 JEE  CONST_35  C19  C18  C17  C16    0.00   0.0  0
 JEE  CONST_36  C19  C27  C28  C16    0.00   0.0  0
 JEE  CONST_37  C18  C17  C16  C15  180.00   0.0  0
 JEE  CONST_38  C27  C28  C16  C15  180.00   0.0  0
 JEE  CONST_39  C12  C13  N14  C15  180.00   0.0  0
 JEE  CONST_40  C09  C08  N14  C15  180.00   0.0  0
 JEE  CONST_41  C07  C08  N14  C15    0.00   0.0  0
 JEE  CONST_42  C20  C19  C18  C17  180.00   0.0  0
 JEE  CONST_43  C28  C27  C19  C20  180.00   0.0  0
 JEE  CONST_44  C05  C29  C02  N01  180.00   0.0  0
 JEE  CONST_45  N04  N03  C02  N01  180.00   0.0  0
 JEE  CONST_46  C30  C29  C02  N03  180.00   0.0  0
 JEE  CONST_47  C30  C29  C05  N04  180.00   0.0  0
 JEE  CONST_48  C30  C29  C05  C06    0.00   0.0  0
 JEE  CONST_49  H18  C12  C09  C10    0.00   0.0  0
 JEE  CONST_50  H12  C28  C16  C17  180.00   0.0  0
 JEE  CONST_51  H5   C17  C16  C28  180.00   0.0  0
 JEE  CONST_52  H16  C07  C06  C05    0.00   0.0  0
 JEE  CONST_53  H17  C11  C06  C05    0.00   0.0  0
 JEE  CONST_54  H15  N03  N04  C05  180.00   0.0  0
 JEE  CONST_55  H1   C10  C11  C06  180.00   0.0  0
 JEE  CONST_56  H2   C13  N14  C08  180.00   0.0  0
 JEE  CONST_57  H19  C18  C17  C16  180.00   0.0  0
 JEE  CONST_58  H25  C27  C28  C16  180.00   0.0  0
 JEE  Var_01    C25  C26  N21  C22  -56.48  30.0  1
 JEE  Var_02    C23  C22  N21  C26   56.61  30.0  1
 JEE  Var_03    O24  C25  C26  N21   57.07  30.0  1
 JEE  Var_04    O24  C23  C22  N21  -57.11  30.0  1
 JEE  Var_05    C16  C15  N14  C13  -82.64  30.0  2
 JEE  Var_06    N14  C15  C16  C17   94.42  30.0  2
 JEE  Var_07    C19  C20  N21  C22   66.83  30.0  1
 JEE  Var_08    N21  C20  C19  C18   58.77  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
 JEE  plan-1  C02  0.020
 JEE  plan-1  N03  0.020
 JEE  plan-1  N04  0.020
 JEE  plan-1  C05  0.020
 JEE  plan-1  C06  0.020
 JEE  plan-1  C29  0.020
 JEE  plan-1  C30  0.020
 JEE  plan-1  N31  0.020
 JEE  plan-1  H15  0.020
 JEE  plan-1  N01  0.020
 JEE  plan-2  C15  0.020
 JEE  plan-2  C17  0.020
 JEE  plan-2  C20  0.020
 JEE  plan-2  C28  0.020
 JEE  plan-2  C16  0.020
 JEE  plan-2  C18  0.020
 JEE  plan-2  C19  0.020
 JEE  plan-2  C27  0.020
 JEE  plan-2  H5   0.020
 JEE  plan-2  H12  0.020
 JEE  plan-2  H19  0.020
 JEE  plan-2  H25  0.020
 JEE  plan-3  C10  0.020
 JEE  plan-3  C13  0.020
 JEE  plan-3  C15  0.020
 JEE  plan-3  C05  0.020
 JEE  plan-3  C06  0.020
 JEE  plan-3  C07  0.020
 JEE  plan-3  C08  0.020
 JEE  plan-3  C09  0.020
 JEE  plan-3  C11  0.020
 JEE  plan-3  C12  0.020
 JEE  plan-3  N14  0.020
 JEE  plan-3  H1   0.020
 JEE  plan-3  H2   0.020
 JEE  plan-3  H16  0.020
 JEE  plan-3  H17  0.020
 JEE  plan-3  H18  0.020
 JEE  plan-4  C02  0.020
 JEE  plan-4  H13  0.020
 JEE  plan-4  H14  0.020
 JEE  plan-4  N01  0.020

