# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 19:12:48 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: N-[(1S)-1-(5-fluoropyridin-2-yl)ethyl]-1-(5-methyl-1H-pyrazol-3-yl)-3-[(oxetan-3-yl)sulfonyl]-1H-pyrrolo[2,3-b]pyridin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](Nc1ccc2c(n1)n(cc2[S](=O)(=O)C3COC3)c4cc(C)[nH]n4)c5ccc(F)cn5
#
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
 HKJ  HKJ  N-[(1S)-1-(5-fluoropyridin-2-yl)ethyl]-1-(5-methyl-1H-pyrazol-3-yl)-3-[(oxetan-3-yl)sulfonyl]-1H-pyrrolo[2,3-b]pyridin-6-amine  ligand  53  32  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_HKJ
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
 HKJ  C5   C  CR6   0   0.492  -1.2523   0.5712   0.2294
 HKJ  C6   C  CR16  0  -0.407  -0.7249   1.8754   0.4330
 HKJ  C7   C  CR16  0  -0.232   0.6208   2.0476   0.6471
 HKJ  C8   C  CR56  0   0.077   1.4378   0.9154   0.6577
 HKJ  C10  C  CR15  0   0.028   2.9846  -0.7318   0.7060
 HKJ  C13  C  CR15  0  -0.542   2.3027  -3.5380  -0.4941
 HKJ  C15  C  CH3   0  -0.731   2.0625  -6.1102  -0.8555
 HKJ  C24  C  C     0  -0.535   4.3465   2.4846  -0.5748
 HKJ  C28  C  CR6   0   0.269  -4.9297   0.8194  -0.1589
 HKJ  C1   C  CH3   0  -0.655  -3.3455   1.8991  -1.7452
 HKJ  C12  C  CR5   0   0.463   1.5637  -2.6822   0.3370
 HKJ  C14  C  CR5   0   0.408   1.7336  -4.7769  -0.2884
 HKJ  C19  C  CR56  0   0.479   0.7999  -0.3167   0.4621
 HKJ  C2   C  CH1   0  -0.151  -3.5340   1.3791  -0.3156
 HKJ  C25  C  C     0  -0.121   5.6750   3.2365  -0.7200
 HKJ  C27  C  C     0  -0.121   4.9246   1.5547  -1.6409
 HKJ  C29  C  CR16  0  -0.312  -5.9925   1.6493   0.1817
 HKJ  C30  C  CR16  0  -0.296  -7.2683   1.1177   0.2568
 HKJ  C31  C  CR6   0   0.429  -7.4121  -0.2279  -0.0135
 HKJ  C33  C  CR16  0  -0.205  -6.3130  -0.9974  -0.3419
 HKJ  C9   C  CR5   0  -0.382   2.8299   0.6216   0.8049
 HKJ  F32  F  F     0  -0.301  -8.6209  -0.7984   0.0443
 HKJ  N11  N  NR5   0  -0.625   1.7627  -1.3060   0.5074
 HKJ  N16  N  NR15  0  -0.471   0.7402  -4.5765   0.5971
 HKJ  N18  N  N     0  -0.270   0.6222  -3.3163   0.9995
 HKJ  N20  N  N     0  -0.480  -0.4844  -0.5164   0.2475
 HKJ  N34  N  N     0  -0.424  -5.0986  -0.4706  -0.4134
 HKJ  N4   N  NH1   0  -0.668  -2.5780   0.3578   0.0389
 HKJ  O22  O  OS    0  -0.661   5.3342   0.9851   1.3545
 HKJ  O23  O  OS    0  -0.664   3.6894   2.8008   1.9445
 HKJ  O26  O  O     0  -0.498   6.1703   2.2565  -1.6342
 HKJ  S21  S  S     0   1.190   4.1250   1.7429   1.0358
 HKJ  H1   H  HCR6  0   0.281  -1.3767   2.7367   0.4275
 HKJ  H2   H  HCR6  0   0.264   1.0217   3.0400   0.8053
 HKJ  H3   H  HCR5  0   0.328   3.8749  -1.3355   0.7807
 HKJ  H4   H  HCR5  0   0.279   3.1218  -3.2923  -1.1496
 HKJ  H5   H  HCH3  0   0.263   2.4934  -6.7664  -0.0983
 HKJ  H6   H  HCH3  0   0.261   1.1783  -6.6046  -1.2577
 HKJ  H7   H  HCH3  0   0.263   2.7871  -6.0050  -1.6593
 HKJ  H8   H  H     0   0.340   3.4370   3.0290  -0.8276
 HKJ  H10  H  HCH3  0   0.240  -4.0697   2.6815  -1.9728
 HKJ  H11  H  HCH3  0   0.243  -2.3479   2.3180  -1.8815
 HKJ  H12  H  HCH1  0   0.267  -3.4371   2.2159   0.3814
 HKJ  H13  H  H     0   0.249   5.5609   4.2229  -1.1745
 HKJ  H14  H  H     0   0.243   6.2905   3.3314   0.1776
 HKJ  H15  H  H     0   0.238   5.0278   0.5009  -1.3686
 HKJ  H16  H  H     0   0.249   4.4056   1.6208  -2.5996
 HKJ  H17  H  HCR6  0   0.282  -5.8267   2.6987   0.3870
 HKJ  H18  H  HCR6  0   0.301  -8.1205   1.7296   0.5217
 HKJ  H19  H  HCR6  0   0.286  -6.4187  -2.0566  -0.5490
 HKJ  H20  H  HNR5  0   0.424   0.1069  -5.2709   0.9620
 HKJ  H21  H  HNH1  0   0.382  -2.8364  -0.5843  -0.2164
 HKJ  H9   H  HCH3  0   0.235  -3.4783   1.0891  -2.4636

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
 HKJ  F32  C31  single    1.338  0.020  1.338
 HKJ  C31  C30  aromatic  1.380  0.020  1.380
 HKJ  C31  C33  aromatic  1.381  0.020  1.381
 HKJ  N16  C14  aromatic  1.346  0.020  1.346
 HKJ  N16  N18  aromatic  1.328  0.020  1.328
 HKJ  C15  C14  single    1.486  0.020  1.486
 HKJ  C30  C29  aromatic  1.384  0.020  1.384
 HKJ  C33  N34  aromatic  1.326  0.020  1.326
 HKJ  C14  C13  aromatic  1.379  0.020  1.379
 HKJ  N18  C12  aromatic  1.314  0.020  1.314
 HKJ  C12  C13  aromatic  1.403  0.020  1.403
 HKJ  C12  N11  single    1.401  0.020  1.401
 HKJ  C29  C28  aromatic  1.391  0.020  1.391
 HKJ  N34  C28  aromatic  1.326  0.020  1.326
 HKJ  N11  C10  aromatic  1.365  0.020  1.365
 HKJ  N11  C19  aromatic  1.381  0.020  1.381
 HKJ  C28  C2   single    1.512  0.020  1.512
 HKJ  C10  C9   aromatic  1.366  0.020  1.366
 HKJ  O23  S21  double    1.461  0.020  1.461
 HKJ  C19  N20  aromatic  1.317  0.020  1.317
 HKJ  C19  C8   aromatic  1.401  0.020  1.401
 HKJ  C9   S21  single    1.729  0.020  1.729
 HKJ  C9   C8   aromatic  1.430  0.020  1.430
 HKJ  N20  C5   aromatic  1.331  0.020  1.331
 HKJ  S21  C24  single    1.787  0.020  1.787
 HKJ  S21  O22  double    1.462  0.020  1.462
 HKJ  C8   C7   aromatic  1.396  0.020  1.396
 HKJ  C27  C24  single    1.528  0.020  1.528
 HKJ  C27  O26  single    1.430  0.020  1.430
 HKJ  C2   N4   single    1.443  0.020  1.443
 HKJ  C2   C1   single    1.533  0.020  1.533
 HKJ  C24  C25  single    1.533  0.020  1.533
 HKJ  C5   N4   single    1.356  0.020  1.356
 HKJ  C5   C6   aromatic  1.421  0.020  1.421
 HKJ  C7   C6   aromatic  1.373  0.020  1.373
 HKJ  O26  C25  single    1.429  0.020  1.429
 HKJ  C6   H1   single    0.930  0.020  1.080
 HKJ  C7   H2   single    0.930  0.020  1.080
 HKJ  C10  H3   single    0.930  0.020  1.080
 HKJ  C13  H4   single    0.930  0.020  1.080
 HKJ  C15  H5   single    0.970  0.020  1.090
 HKJ  C15  H6   single    0.970  0.020  1.090
 HKJ  C15  H7   single    0.970  0.020  1.090
 HKJ  C24  H8   single    0.970  0.020  1.090
 HKJ  C1   H9   single    0.970  0.020  1.090
 HKJ  C1   H10  single    0.970  0.020  1.090
 HKJ  C1   H11  single    0.970  0.020  1.090
 HKJ  C2   H12  single    0.970  0.020  1.090
 HKJ  C25  H13  single    0.970  0.020  1.090
 HKJ  C25  H14  single    0.970  0.020  1.090
 HKJ  C27  H15  single    0.970  0.020  1.090
 HKJ  C27  H16  single    0.970  0.020  1.090
 HKJ  C29  H17  single    0.930  0.020  1.080
 HKJ  C30  H18  single    0.930  0.020  1.080
 HKJ  C33  H19  single    0.930  0.020  1.080
 HKJ  N16  H20  single    0.860  0.020  1.020
 HKJ  N4   H21  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
 HKJ  N4   C5   N20  115.92  3.000
 HKJ  N4   C5   C6   121.81  3.000
 HKJ  N20  C5   C6   122.25  3.000
 HKJ  H1   C6   C7   119.48  3.000
 HKJ  H1   C6   C5   120.46  3.000
 HKJ  C7   C6   C5   120.06  3.000
 HKJ  H2   C7   C8   121.73  3.000
 HKJ  H2   C7   C6   120.05  3.000
 HKJ  C8   C7   C6   118.22  3.000
 HKJ  C9   C8   C19  106.06  3.000
 HKJ  C9   C8   C7   137.46  3.000
 HKJ  C19  C8   C7   116.47  3.000
 HKJ  H3   C10  N11  120.92  3.000
 HKJ  H3   C10  C9   130.04  3.000
 HKJ  N11  C10  C9   109.03  3.000
 HKJ  H4   C13  C14  127.55  3.000
 HKJ  H4   C13  C12  128.43  3.000
 HKJ  C14  C13  C12  104.02  3.000
 HKJ  H7   C15  H6   108.16  3.000
 HKJ  H7   C15  H5   107.95  3.000
 HKJ  H6   C15  H5   107.68  3.000
 HKJ  H7   C15  C14  110.05  3.000
 HKJ  H6   C15  C14  111.61  3.000
 HKJ  H5   C15  C14  111.25  3.000
 HKJ  H8   C24  S21  108.24  3.000
 HKJ  H8   C24  C27  117.25  3.000
 HKJ  S21  C24  C27  115.03  3.000
 HKJ  H8   C24  C25  117.14  3.000
 HKJ  C27  C24  C25   84.53  3.000
 HKJ  S21  C24  C25  113.35  3.000
 HKJ  N34  C28  C29  122.03  3.000
 HKJ  N34  C28  C2   117.26  3.000
 HKJ  C29  C28  C2   120.65  3.000
 HKJ  H11  C1   H10  107.81  3.000
 HKJ  H11  C1   H9   108.31  3.000
 HKJ  H10  C1   H9   108.34  3.000
 HKJ  H11  C1   C2   111.06  3.000
 HKJ  H10  C1   C2   110.89  3.000
 HKJ  H9   C1   C2   110.33  3.000
 HKJ  N18  C12  N11  120.96  3.000
 HKJ  N11  C12  C13  126.60  3.000
 HKJ  N18  C12  C13  112.43  3.000
 HKJ  N16  C14  C15  123.24  3.000
 HKJ  C15  C14  C13  131.15  3.000
 HKJ  N16  C14  C13  105.61  3.000
 HKJ  N20  C19  N11  125.20  3.000
 HKJ  N20  C19  C8   126.86  3.000
 HKJ  N11  C19  C8   107.94  3.000
 HKJ  H12  C2   N4   109.04  3.000
 HKJ  H12  C2   C1   108.91  3.000
 HKJ  N4   C2   C1   112.81  3.000
 HKJ  H12  C2   C28  107.40  3.000
 HKJ  C1   C2   C28  109.62  3.000
 HKJ  N4   C2   C28  108.91  3.000
 HKJ  H14  C25  H13  108.81  3.000
 HKJ  H14  C25  O26  112.95  3.000
 HKJ  H13  C25  O26  112.92  3.000
 HKJ  H14  C25  C24  116.93  3.000
 HKJ  H13  C25  C24  113.07  3.000
 HKJ  O26  C25  C24   91.41  3.000
 HKJ  H16  C27  H15  108.78  3.000
 HKJ  H16  C27  O26  112.86  3.000
 HKJ  H15  C27  O26  112.94  3.000
 HKJ  H16  C27  C24  113.31  3.000
 HKJ  H15  C27  C24  116.64  3.000
 HKJ  O26  C27  C24   91.58  3.000
 HKJ  H17  C29  C30  120.23  3.000
 HKJ  H17  C29  C28  120.54  3.000
 HKJ  C30  C29  C28  119.24  3.000
 HKJ  H18  C30  C31  121.15  3.000
 HKJ  H18  C30  C29  121.47  3.000
 HKJ  C31  C30  C29  117.38  3.000
 HKJ  F32  C31  C33  119.45  3.000
 HKJ  C33  C31  C30  120.45  3.000
 HKJ  F32  C31  C30  120.10  3.000
 HKJ  H19  C33  N34  117.85  3.000
 HKJ  H19  C33  C31  120.79  3.000
 HKJ  N34  C33  C31  121.36  3.000
 HKJ  S21  C9   C10  124.58  3.000
 HKJ  S21  C9   C8   127.56  3.000
 HKJ  C10  C9   C8   107.84  3.000
 HKJ  C19  N11  C12  126.91  3.000
 HKJ  C19  N11  C10  109.12  3.000
 HKJ  C12  N11  C10  123.94  3.000
 HKJ  H20  N16  N18  119.22  3.000
 HKJ  H20  N16  C14  126.82  3.000
 HKJ  N18  N16  C14  113.96  3.000
 HKJ  N16  N18  C12  103.97  3.000
 HKJ  C19  N20  C5   116.15  3.000
 HKJ  C33  N34  C28  119.54  3.000
 HKJ  H21  N4   C2   115.38  3.000
 HKJ  H21  N4   C5   115.62  3.000
 HKJ  C2   N4   C5   124.80  3.000
 HKJ  C27  O26  C25   92.15  3.000
 HKJ  O23  S21  O22  119.09  3.000
 HKJ  O22  S21  C9   108.21  3.000
 HKJ  O23  S21  C9   109.23  3.000
 HKJ  O22  S21  C24  108.00  3.000
 HKJ  C9   S21  C24  103.99  3.000
 HKJ  O23  S21  C24  107.28  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
 HKJ  CONST_01  N11  C19  N20  C5    180.00   0.0  0
 HKJ  CONST_02  C8   C19  N20  C5      0.00   0.0  0
 HKJ  CONST_03  C8   C7   C6   C5      0.00   0.0  0
 HKJ  CONST_04  C19  N20  C5   C6      0.00   0.0  0
 HKJ  CONST_05  C19  C8   C7   C6      0.00   0.0  0
 HKJ  CONST_06  C9   C8   C7   C6    180.00   0.0  0
 HKJ  CONST_07  N11  C19  C8   C7    180.00   0.0  0
 HKJ  CONST_08  N20  C19  C8   C7      0.00   0.0  0
 HKJ  CONST_09  C10  C9   C8   C7    180.00   0.0  0
 HKJ  CONST_10  N20  C5   C6   C7      0.00   0.0  0
 HKJ  CONST_11  C12  N11  C19  C8    180.00   0.0  0
 HKJ  CONST_12  C10  N11  C19  C8      0.00   0.0  0
 HKJ  CONST_13  N11  C10  C9   C8      0.00   0.0  0
 HKJ  CONST_16  N20  C19  N11  C10   180.00   0.0  0
 HKJ  CONST_17  C19  C8   C9   C10     0.00   0.0  0
 HKJ  CONST_18  N18  N16  C14  C13     0.00   0.0  0
 HKJ  CONST_19  N16  N18  C12  C13     0.00   0.0  0
 HKJ  CONST_21  C31  C30  C29  C28     0.00   0.0  0
 HKJ  CONST_22  C31  C33  N34  C28     0.00   0.0  0
 HKJ  CONST_23  C14  N16  N18  C12     0.00   0.0  0
 HKJ  CONST_24  N16  C14  C13  C12     0.00   0.0  0
 HKJ  CONST_25  C9   C10  N11  C12   180.00   0.0  0
 HKJ  CONST_26  N20  C19  N11  C12     0.00   0.0  0
 HKJ  CONST_27  N18  C12  C13  C14     0.00   0.0  0
 HKJ  CONST_28  N11  C12  C13  C14   180.00   0.0  0
 HKJ  CONST_30  C9   C10  N11  C19     0.00   0.0  0
 HKJ  CONST_31  C33  C31  C30  C29     0.00   0.0  0
 HKJ  CONST_32  C33  N34  C28  C29     0.00   0.0  0
 HKJ  CONST_33  N34  C33  C31  C30     0.00   0.0  0
 HKJ  CONST_34  N34  C28  C29  C30     0.00   0.0  0
 HKJ  CONST_35  N11  C19  C8   C9      0.00   0.0  0
 HKJ  CONST_36  N20  C19  C8   C9    180.00   0.0  0
 HKJ  CONST_37  N16  N18  C12  N11   180.00   0.0  0
 HKJ  CONST_38  S21  C9   C8   C7      0.00   0.0  0
 HKJ  CONST_39  N4   C5   C6   C7    180.00   0.0  0
 HKJ  CONST_40  N18  N16  C14  C15   180.00   0.0  0
 HKJ  CONST_41  C12  C13  C14  C15   180.00   0.0  0
 HKJ  CONST_42  N4   C5   N20  C19   180.00   0.0  0
 HKJ  CONST_43  S21  C9   C8   C19   180.00   0.0  0
 HKJ  CONST_44  C30  C29  C28  C2    180.00   0.0  0
 HKJ  CONST_45  C33  N34  C28  C2    180.00   0.0  0
 HKJ  CONST_46  F32  C31  C30  C29   180.00   0.0  0
 HKJ  CONST_47  N34  C33  C31  F32   180.00   0.0  0
 HKJ  CONST_48  S21  C9   C10  N11   180.00   0.0  0
 HKJ  CONST_49  H2   C7   C6   C5    180.00   0.0  0
 HKJ  CONST_50  H3   C10  C9   C8    180.00   0.0  0
 HKJ  CONST_51  H1   C6   C7   C8    180.00   0.0  0
 HKJ  CONST_52  H20  N16  C14  C13   180.00   0.0  0
 HKJ  CONST_53  H18  C30  C29  C28   180.00   0.0  0
 HKJ  CONST_54  H19  C33  N34  C28   180.00   0.0  0
 HKJ  CONST_55  H17  C29  C30  C31   180.00   0.0  0
 HKJ  CONST_56  H4   C13  C12  N11     0.00   0.0  0
 HKJ  CONST_58  N20  C5   N4   C2    180.00   0.0  0
 HKJ  CONST_59  H21  N4   C5   C6    180.00   0.0  0
 HKJ  Var_01    C24  S21  C9   C8    -74.56  30.0  2
 HKJ  Var_02    H15  C27  O26  C25  -124.39  30.0  1
 HKJ  Var_03    H13  C25  O26  C27  -111.39  30.0  1
 HKJ  Var_04    H5   C15  C14  C13   110.23  30.0  2

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
 HKJ  chir_01  C24  S21  C27  C25  positiv
 HKJ  chir_02  C2   C28  N4   C1   negativ

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
 HKJ  plan-1  C13  0.020
 HKJ  plan-1  C15  0.020
 HKJ  plan-1  C12  0.020
 HKJ  plan-1  C14  0.020
 HKJ  plan-1  N11  0.020
 HKJ  plan-1  N16  0.020
 HKJ  plan-1  N18  0.020
 HKJ  plan-1  H4   0.020
 HKJ  plan-1  H20  0.020
 HKJ  plan-2  C28  0.020
 HKJ  plan-2  C2   0.020
 HKJ  plan-2  C29  0.020
 HKJ  plan-2  C30  0.020
 HKJ  plan-2  C31  0.020
 HKJ  plan-2  C33  0.020
 HKJ  plan-2  F32  0.020
 HKJ  plan-2  N34  0.020
 HKJ  plan-2  H17  0.020
 HKJ  plan-2  H18  0.020
 HKJ  plan-2  H19  0.020
 HKJ  plan-3  C5   0.020
 HKJ  plan-3  C6   0.020
 HKJ  plan-3  C7   0.020
 HKJ  plan-3  C8   0.020
 HKJ  plan-3  C10  0.020
 HKJ  plan-3  C12  0.020
 HKJ  plan-3  C19  0.020
 HKJ  plan-3  C9   0.020
 HKJ  plan-3  N11  0.020
 HKJ  plan-3  N20  0.020
 HKJ  plan-3  N4   0.020
 HKJ  plan-3  S21  0.020
 HKJ  plan-3  H1   0.020
 HKJ  plan-3  H2   0.020
 HKJ  plan-3  H3   0.020
 HKJ  plan-4  C5   0.020
 HKJ  plan-4  C2   0.020
 HKJ  plan-4  N4   0.020
 HKJ  plan-4  H21  0.020

