# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 03:26:02 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 6-[7-methoxy-6-(1-methyl-1H-pyrazol-4-yl)imidazo[1,2-a]pyridin-3-yl]-N-[(3R)-pyrrolidin-3-yl]pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2ncc(n2cc1c3cnn(C)c3)c4cccc(N[C@@H]5CCNC5)n4
#
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
 JX4  JX4  6-[7-methoxy-6-(1-methyl-1H-pyrazol-4-yl)imidazo[1,2-a]pyridin-3-yl]-N-[(3R)-pyrrolidin-3-yl]pyridin-2-amine  ligand  52  29  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_JX4
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
 JX4  C10  C  CR16  0  -0.024  -1.7738  -0.1622  -0.2532
 JX4  C13  C  CR15  0   0.027  -3.4831   2.1164   0.8373
 JX4  C15  C  CH3   0  -0.506  -4.5469   4.3340   1.2649
 JX4  C17  C  CR15  0  -0.075  -5.2030   1.2457  -0.2092
 JX4  C20  C  CR16  0  -0.151   2.0261   1.7127  -1.8428
 JX4  C21  C  CR16  0  -0.408   3.3134   1.4459  -1.4332
 JX4  C22  C  CR6   0   0.492   3.5554   0.2152  -0.7895
 JX4  C24  C  CH1   0  -0.112   5.9826   0.6540  -0.4619
 JX4  C26  C  CH2   0  -0.302   7.2966   0.0291   1.4901
 JX4  C28  C  CH2   0  -0.321   5.9909   1.7480   0.6185
 JX4  C01  C  CH3   0  -0.443  -5.6076  -2.8474   0.6553
 JX4  C03  C  CR6   0   0.464  -3.6690  -1.5731   0.1990
 JX4  C04  C  CR16  0  -0.544  -2.8805  -2.6852   0.0849
 JX4  C05  C  CR56  0   0.535  -1.5108  -2.5367  -0.2013
 JX4  C07  C  CR15  0  -0.222   0.5660  -2.7809  -0.5709
 JX4  C08  C  CR5   0   0.242   0.3624  -1.4234  -0.6382
 JX4  C11  C  CR6   0  -0.150  -3.0982  -0.2650   0.0410
 JX4  C12  C  CR5   0  -0.148  -3.8942   0.9488   0.2226
 JX4  C18  C  CR6   0   0.217   1.3291  -0.3722  -0.9301
 JX4  C19  C  CR16  0  -0.390   1.0029   0.8006  -1.6062
 JX4  C25  C  CH2   0  -0.511   7.1990  -0.1727  -0.0438
 JX4  N06  N  N     0  -0.480  -0.5727  -3.4606  -0.3167
 JX4  N09  N  N     0  -0.596  -0.9935  -1.2704  -0.3905
 JX4  N14  N  NR5   0  -0.265  -4.4957   2.9901   0.7412
 JX4  N16  N  N     0  -0.282  -5.5469   2.4780   0.1092
 JX4  N23  N  NH1   0  -0.669   4.7929  -0.1656  -0.3959
 JX4  N27  N  NH1   0  -0.586   6.3239   1.0636   1.8580
 JX4  N29  N  N     0  -0.498   2.5734  -0.6508  -0.5402
 JX4  O02  O  O2    0  -0.455  -4.9742  -1.5935   0.4769
 JX4  H1   H  HCR6  0   0.307  -1.2954   0.7961  -0.3798
 JX4  H2   H  HCR5  0   0.294  -2.5608   2.3665   1.3376
 JX4  H3   H  HCH3  0   0.262  -4.8196   5.0313   0.4758
 JX4  H4   H  HCH3  0   0.260  -5.2736   4.4040   2.0723
 JX4  H5   H  HCH3  0   0.259  -3.5664   4.6010   1.6475
 JX4  H6   H  HCR5  0   0.257  -5.8905   0.6129  -0.7479
 JX4  H7   H  HCR6  0   0.266   1.8109   2.6369  -2.3638
 JX4  H8   H  HCR6  0   0.272   4.1073   2.1559  -1.6167
 JX4  H9   H  HCH1  0   0.250   6.0980   1.0621  -1.4703
 JX4  H10  H  HCH2  0   0.236   7.0931  -0.8880   2.0429
 JX4  H11  H  HCH2  0   0.225   8.3062   0.3473   1.7584
 JX4  H12  H  HCH2  0   0.229   6.7652   2.4837   0.3771
 JX4  H13  H  HCH2  0   0.246   5.0455   2.2840   0.7100
 JX4  H14  H  HCH3  0   0.236  -5.5251  -3.4718  -0.2374
 JX4  H15  H  HCH3  0   0.235  -5.1922  -3.3894   1.5082
 JX4  H16  H  HCH3  0   0.267  -6.6564  -2.6373   0.8461
 JX4  H17  H  HCR6  0   0.298  -3.2557  -3.6887   0.2240
 JX4  H18  H  HCR5  0   0.261   1.5076  -3.2869  -0.7231
 JX4  H19  H  HCR6  0   0.262   0.0087   0.9906  -1.9827
 JX4  H20  H  HCH2  0   0.253   7.1071  -1.2203  -0.3336
 JX4  H21  H  HCH2  0   0.257   8.0864   0.2200  -0.5404
 JX4  H22  H  HNH1  0   0.382   4.8468  -1.0624   0.0603
 JX4  H23  H  HNH1  0   0.346   5.4863   0.6154   2.2058

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
 JX4  C20  C21  aromatic  1.377  0.020  1.377
 JX4  C20  C19  aromatic  1.391  0.020  1.391
 JX4  C21  C22  aromatic  1.410  0.020  1.410
 JX4  C19  C18  aromatic  1.392  0.020  1.392
 JX4  C22  N23  single    1.353  0.020  1.353
 JX4  C22  N29  aromatic  1.333  0.020  1.333
 JX4  N23  C24  single    1.446  0.020  1.446
 JX4  C18  N29  aromatic  1.333  0.020  1.333
 JX4  C18  C08  single    1.458  0.020  1.458
 JX4  C07  C08  aromatic  1.374  0.020  1.374
 JX4  C07  N06  aromatic  1.350  0.020  1.350
 JX4  C08  N09  aromatic  1.387  0.020  1.387
 JX4  C25  C24  single    1.529  0.020  1.529
 JX4  C25  C26  single    1.550  0.020  1.550
 JX4  C24  C28  single    1.538  0.020  1.538
 JX4  N06  C05  aromatic  1.322  0.020  1.322
 JX4  N09  C05  aromatic  1.381  0.020  1.381
 JX4  N09  C10  aromatic  1.362  0.020  1.362
 JX4  C26  N27  single    1.467  0.020  1.467
 JX4  N27  C28  single    1.455  0.020  1.455
 JX4  C05  C04  aromatic  1.407  0.020  1.407
 JX4  C10  C11  aromatic  1.361  0.020  1.361
 JX4  C17  N16  aromatic  1.318  0.020  1.318
 JX4  C17  C12  aromatic  1.410  0.020  1.410
 JX4  C04  C03  aromatic  1.368  0.020  1.368
 JX4  C11  C03  aromatic  1.436  0.020  1.436
 JX4  C11  C12  single    1.463  0.020  1.463
 JX4  N16  N14  aromatic  1.329  0.020  1.329
 JX4  C03  O02  single    1.335  0.020  1.335
 JX4  C12  C13  aromatic  1.382  0.020  1.382
 JX4  O02  C01  single    1.416  0.020  1.416
 JX4  N14  C13  aromatic  1.341  0.020  1.341
 JX4  N14  C15  single    1.443  0.020  1.443
 JX4  C10  H1   single    0.930  0.020  1.080
 JX4  C13  H2   single    0.930  0.020  1.080
 JX4  C15  H3   single    0.970  0.020  1.090
 JX4  C15  H4   single    0.970  0.020  1.090
 JX4  C15  H5   single    0.970  0.020  1.090
 JX4  C17  H6   single    0.930  0.020  1.080
 JX4  C20  H7   single    0.930  0.020  1.080
 JX4  C21  H8   single    0.930  0.020  1.080
 JX4  C24  H9   single    0.970  0.020  1.090
 JX4  C26  H10  single    0.970  0.020  1.090
 JX4  C26  H11  single    0.970  0.020  1.090
 JX4  C28  H12  single    0.970  0.020  1.090
 JX4  C28  H13  single    0.970  0.020  1.090
 JX4  C01  H14  single    0.970  0.020  1.090
 JX4  C01  H15  single    0.970  0.020  1.090
 JX4  C01  H16  single    0.970  0.020  1.090
 JX4  C04  H17  single    0.930  0.020  1.080
 JX4  C07  H18  single    0.930  0.020  1.080
 JX4  C19  H19  single    0.930  0.020  1.080
 JX4  C25  H20  single    0.970  0.020  1.090
 JX4  C25  H21  single    0.970  0.020  1.090
 JX4  N23  H22  single    0.860  0.020  1.020
 JX4  N27  H23  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
 JX4  H1   C10  N09  117.19  3.000
 JX4  H1   C10  C11  121.62  3.000
 JX4  N09  C10  C11  121.19  3.000
 JX4  H2   C13  N14  121.86  3.000
 JX4  H2   C13  C12  131.03  3.000
 JX4  N14  C13  C12  107.10  3.000
 JX4  H5   C15  H4   109.00  3.000
 JX4  H5   C15  H3   108.93  3.000
 JX4  H4   C15  H3   109.24  3.000
 JX4  H5   C15  N14  108.96  3.000
 JX4  H4   C15  N14  110.66  3.000
 JX4  H3   C15  N14  110.04  3.000
 JX4  H6   C17  N16  120.18  3.000
 JX4  H6   C17  C12  128.40  3.000
 JX4  N16  C17  C12  111.41  3.000
 JX4  H7   C20  C19  119.70  3.000
 JX4  H7   C20  C21  119.63  3.000
 JX4  C19  C20  C21  120.67  3.000
 JX4  H8   C21  C22  121.67  3.000
 JX4  H8   C21  C20  120.59  3.000
 JX4  C22  C21  C20  117.74  3.000
 JX4  N29  C22  N23  115.88  3.000
 JX4  N29  C22  C21  121.75  3.000
 JX4  N23  C22  C21  122.37  3.000
 JX4  H9   C24  N23  109.89  3.000
 JX4  H9   C24  C25  111.70  3.000
 JX4  N23  C24  C25  109.61  3.000
 JX4  H9   C24  C28  112.44  3.000
 JX4  C25  C24  C28  100.85  3.000
 JX4  N23  C24  C28  112.06  3.000
 JX4  H11  C26  H10  107.05  3.000
 JX4  H11  C26  N27  110.24  3.000
 JX4  H10  C26  N27  110.02  3.000
 JX4  H11  C26  C25  109.83  3.000
 JX4  H10  C26  C25  112.37  3.000
 JX4  N27  C26  C25  107.35  3.000
 JX4  H13  C28  H12  107.53  3.000
 JX4  H13  C28  N27  111.00  3.000
 JX4  H12  C28  N27  110.01  3.000
 JX4  H13  C28  C24  113.82  3.000
 JX4  H12  C28  C24  109.08  3.000
 JX4  N27  C28  C24  105.38  3.000
 JX4  H16  C01  H15  109.02  3.000
 JX4  H16  C01  H14  109.08  3.000
 JX4  H15  C01  H14  109.00  3.000
 JX4  H16  C01  O02  106.42  3.000
 JX4  H15  C01  O02  111.57  3.000
 JX4  H14  C01  O02  111.67  3.000
 JX4  O02  C03  C11  115.19  3.000
 JX4  O02  C03  C04  124.65  3.000
 JX4  C11  C03  C04  120.15  3.000
 JX4  H17  C04  C05  117.53  3.000
 JX4  H17  C04  C03  122.97  3.000
 JX4  C05  C04  C03  119.49  3.000
 JX4  N09  C05  N06  111.30  3.000
 JX4  N09  C05  C04  119.29  3.000
 JX4  N06  C05  C04  129.41  3.000
 JX4  H18  C07  N06  121.74  3.000
 JX4  H18  C07  C08  125.82  3.000
 JX4  N06  C07  C08  112.43  3.000
 JX4  N09  C08  C18  127.20  3.000
 JX4  N09  C08  C07  104.19  3.000
 JX4  C18  C08  C07  128.60  3.000
 JX4  C12  C11  C03  121.73  3.000
 JX4  C12  C11  C10  119.60  3.000
 JX4  C03  C11  C10  118.65  3.000
 JX4  C11  C12  C17  129.93  3.000
 JX4  C11  C12  C13  126.46  3.000
 JX4  C17  C12  C13  103.56  3.000
 JX4  N29  C18  C19  122.45  3.000
 JX4  N29  C18  C08  114.18  3.000
 JX4  C19  C18  C08  123.32  3.000
 JX4  H19  C19  C18  122.22  3.000
 JX4  H19  C19  C20  120.17  3.000
 JX4  C18  C19  C20  117.55  3.000
 JX4  H21  C25  H20  107.07  3.000
 JX4  H21  C25  C26  110.65  3.000
 JX4  H20  C25  C26  113.16  3.000
 JX4  H21  C25  C24  109.16  3.000
 JX4  H20  C25  C24  112.31  3.000
 JX4  C26  C25  C24  104.49  3.000
 JX4  C07  N06  C05  105.25  3.000
 JX4  C08  N09  C05  106.83  3.000
 JX4  C05  N09  C10  121.17  3.000
 JX4  C08  N09  C10  131.90  3.000
 JX4  N16  N14  C15  120.21  3.000
 JX4  C15  N14  C13  127.41  3.000
 JX4  N16  N14  C13  112.35  3.000
 JX4  N14  N16  C17  105.58  3.000
 JX4  H22  N23  C24  118.76  3.000
 JX4  H22  N23  C22  115.53  3.000
 JX4  C24  N23  C22  125.42  3.000
 JX4  H23  N27  C28  108.17  3.000
 JX4  H23  N27  C26  108.83  3.000
 JX4  C28  N27  C26  105.66  3.000
 JX4  C18  N29  C22  119.81  3.000
 JX4  C03  O02  C01  118.51  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
 JX4  CONST_01  C18  C08  N09  C10    0.00   0.0  0
 JX4  CONST_02  C07  C08  N09  C10  180.00   0.0  0
 JX4  CONST_03  N06  C05  N09  C10  180.00   0.0  0
 JX4  CONST_04  C04  C05  N09  C10    0.00   0.0  0
 JX4  CONST_05  C04  C03  C11  C10    0.00   0.0  0
 JX4  CONST_08  N16  C17  C12  C13    0.00   0.0  0
 JX4  CONST_10  C17  N16  N14  C13    0.00   0.0  0
 JX4  CONST_12  N14  C13  C12  C17    0.00   0.0  0
 JX4  CONST_13  N29  C22  C21  C20    0.00   0.0  0
 JX4  CONST_14  N29  C18  C19  C20    0.00   0.0  0
 JX4  CONST_15  C08  C18  C19  C20  180.00   0.0  0
 JX4  CONST_16  C18  C19  C20  C21    0.00   0.0  0
 JX4  CONST_17  C18  N29  C22  C21    0.00   0.0  0
 JX4  CONST_18  C19  C20  C21  C22    0.00   0.0  0
 JX4  CONST_19  C19  C18  N29  C22    0.00   0.0  0
 JX4  CONST_20  C08  C18  N29  C22  180.00   0.0  0
 JX4  CONST_21  N06  C05  C04  C03  180.00   0.0  0
 JX4  CONST_22  N09  C05  C04  C03    0.00   0.0  0
 JX4  CONST_23  N09  C10  C11  C03    0.00   0.0  0
 JX4  CONST_24  C07  N06  C05  C04  180.00   0.0  0
 JX4  CONST_25  C08  N09  C05  C04  180.00   0.0  0
 JX4  CONST_26  C12  C11  C03  C04  180.00   0.0  0
 JX4  CONST_27  C08  C07  N06  C05    0.00   0.0  0
 JX4  CONST_28  C18  C08  N09  C05  180.00   0.0  0
 JX4  CONST_29  C07  C08  N09  C05    0.00   0.0  0
 JX4  CONST_30  C11  C10  N09  C05    0.00   0.0  0
 JX4  CONST_31  C11  C03  C04  C05    0.00   0.0  0
 JX4  CONST_34  N09  C05  N06  C07    0.00   0.0  0
 JX4  CONST_35  N06  C05  N09  C08    0.00   0.0  0
 JX4  CONST_36  C11  C10  N09  C08  180.00   0.0  0
 JX4  CONST_37  N16  C17  C12  C11  180.00   0.0  0
 JX4  CONST_38  N14  C13  C12  C11  180.00   0.0  0
 JX4  CONST_39  N14  N16  C17  C12    0.00   0.0  0
 JX4  CONST_40  N09  C10  C11  C12  180.00   0.0  0
 JX4  CONST_41  N16  N14  C13  C12    0.00   0.0  0
 JX4  CONST_42  N06  C07  C08  C18  180.00   0.0  0
 JX4  CONST_44  N09  C08  C07  N06    0.00   0.0  0
 JX4  CONST_46  O02  C03  C11  C10  180.00   0.0  0
 JX4  CONST_47  C17  N16  N14  C15  180.00   0.0  0
 JX4  CONST_48  C12  C13  N14  C15  180.00   0.0  0
 JX4  CONST_49  N23  C22  C21  C20  180.00   0.0  0
 JX4  CONST_50  O02  C03  C04  C05  180.00   0.0  0
 JX4  CONST_51  O02  C03  C11  C12    0.00   0.0  0
 JX4  CONST_52  N23  C22  N29  C18  180.00   0.0  0
 JX4  CONST_53  C24  N23  C22  C21    0.00   0.0  0
 JX4  CONST_54  N29  C22  N23  C24  180.00   0.0  0
 JX4  CONST_55  H6   C17  C12  C13  180.00   0.0  0
 JX4  CONST_56  H2   C13  C12  C17  180.00   0.0  0
 JX4  CONST_57  H19  C19  C20  C21  180.00   0.0  0
 JX4  CONST_58  H7   C20  C21  C22  180.00   0.0  0
 JX4  CONST_59  H1   C10  C11  C03  180.00   0.0  0
 JX4  CONST_60  H18  C07  N06  C05  180.00   0.0  0
 JX4  CONST_61  H17  C04  C03  C11  180.00   0.0  0
 JX4  CONST_62  H8   C21  C20  C19  180.00   0.0  0
 JX4  CONST_63  H22  N23  C22  C21  180.00   0.0  0
 JX4  Var_01    N27  C26  C25  C24   -8.10  30.0  1
 JX4  Var_02    C26  N27  C28  C24   36.53  30.0  1
 JX4  Var_03    C25  C26  N27  C28  -17.43  30.0  1
 JX4  Var_04    C04  C03  O02  C01   -0.72  30.0  1
 JX4  Var_05    H3   C15  N14  C13  127.17  30.0  2
 JX4  Var_06    H14  C01  O02  C03  -59.74  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 JX4  chir_01  C24  N23  C25  C28  positiv

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
 JX4  plan-1  C13  0.020
 JX4  plan-1  C15  0.020
 JX4  plan-1  C17  0.020
 JX4  plan-1  C11  0.020
 JX4  plan-1  C12  0.020
 JX4  plan-1  N14  0.020
 JX4  plan-1  N16  0.020
 JX4  plan-1  H2   0.020
 JX4  plan-1  H6   0.020
 JX4  plan-2  C20  0.020
 JX4  plan-2  C21  0.020
 JX4  plan-2  C22  0.020
 JX4  plan-2  C08  0.020
 JX4  plan-2  C18  0.020
 JX4  plan-2  C19  0.020
 JX4  plan-2  N23  0.020
 JX4  plan-2  N29  0.020
 JX4  plan-2  H7   0.020
 JX4  plan-2  H8   0.020
 JX4  plan-2  H19  0.020
 JX4  plan-3  C10  0.020
 JX4  plan-3  C03  0.020
 JX4  plan-3  C04  0.020
 JX4  plan-3  C05  0.020
 JX4  plan-3  C07  0.020
 JX4  plan-3  C08  0.020
 JX4  plan-3  C11  0.020
 JX4  plan-3  C12  0.020
 JX4  plan-3  C18  0.020
 JX4  plan-3  N06  0.020
 JX4  plan-3  N09  0.020
 JX4  plan-3  O02  0.020
 JX4  plan-3  H1   0.020
 JX4  plan-3  H17  0.020
 JX4  plan-3  H18  0.020
 JX4  plan-4  C22  0.020
 JX4  plan-4  C24  0.020
 JX4  plan-4  N23  0.020
 JX4  plan-4  H22  0.020

