# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 02:55:22 2022
#   Inital geometry file: a 133 line input string
#   Ligand name: ~{N}-methyl-~{N}-[3-[[[2-[(2-oxidanylidene-1,3-dihydroindol-5-yl)amino]pyrimidin-4-yl]amino]methyl]pyridin-2-yl]methanesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(c1ncccc1CNc2ccnc(Nc3ccc4NC(=O)Cc4c3)n2)[S](C)(=O)=O
#
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
 PKE  PKE  ~{N}-methyl-~{N}-[3-[[[2-[(2-oxidanylidene-1,3-dihydroindol-5-yl)amino]pyrimidin-4-yl]amino]methyl]pyridin-2-yl]methanesulfonamide  ligand  52  31  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_PKE
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
 PKE  C2   C  CR6   0   0.566  -1.2744  -3.6549  18.9622
 PKE  C9   C  CH2   0  -0.347   0.0711  -6.7651  21.2400
 PKE  C10  C  CR6   0   0.038  -1.2782  -7.4335  21.1784
 PKE  C11  C  CR16  0  -0.178  -1.7406  -8.0865  20.0441
 PKE  C12  C  CR16  0  -0.317  -2.9848  -8.6955  20.0640
 PKE  C13  C  CR16  0  -0.080  -3.7351  -8.6336  21.2279
 PKE  C15  C  CR6   0   0.395  -2.1179  -7.4404  22.2889
 PKE  C20  C  CH3   0  -0.794  -2.4359  -8.3253  25.5965
 PKE  C22  C  CR6   0   0.336  -3.3868  -3.4368  20.2556
 PKE  C24  C  CR16  0  -0.297  -4.8748  -5.1219  21.1643
 PKE  C27  C  CR56  0   0.014  -4.9625  -2.8397  21.9608
 PKE  N1   N  N     0  -0.505  -0.8905  -4.7221  19.6557
 PKE  N3   N  N     0  -0.492  -0.6383  -3.1101  17.9241
 PKE  C4   C  CR16  0  -0.032   0.4736  -3.7387  17.5464
 PKE  C5   C  CR16  0  -0.441   0.9587  -4.8701  18.1530
 PKE  C6   C  CR6   0   0.563   0.2204  -5.3364  19.2592
 PKE  N7   N  NH1   0  -0.673   0.6199  -6.4197  19.9554
 PKE  N8   N  NH1   0  -0.761  -2.4180  -3.0182  19.3326
 PKE  N14  N  N     0  -0.385  -3.3072  -8.0139  22.3190
 PKE  N16  N  N     0  -0.649  -1.6971  -6.7532  23.4632
 PKE  S17  S  S     0   1.330  -1.0566  -7.6849  24.6743
 PKE  C18  C  CH3   0  -0.536  -2.4394  -5.5460  23.8132
 PKE  O19  O  OS    0  -0.656  -0.2972  -6.8068  25.5487
 PKE  O21  O  OS    0  -0.659  -0.3815  -8.7919  24.0141
 PKE  C23  C  CR16  0  -0.392  -3.9470  -2.4752  21.1042
 PKE  C25  C  CR16  0  -0.286  -3.8599  -4.7478  20.2907
 PKE  C26  C  CR56  0   0.404  -5.4136  -4.1563  21.9905
 PKE  C28  C  CH2   0  -0.622  -5.7532  -2.0544  22.9582
 PKE  C29  C  CR5   0   0.509  -6.6961  -3.0908  23.5572
 PKE  N30  N  NR15  0  -0.743  -6.4267  -4.2735  22.9362
 PKE  O31  O  O     0  -0.450  -7.5306  -2.9147  24.4191
 PKE  H1   H  HCH2  0   0.281   0.7791  -7.4416  21.7209
 PKE  H2   H  HCH2  0   0.261   0.0096  -5.8814  21.8777
 PKE  H3   H  HCR6  0   0.270  -1.1326  -8.1119  19.1487
 PKE  H4   H  HCR6  0   0.273  -3.3693  -9.2087  19.1933
 PKE  H5   H  HCR6  0   0.268  -4.7136  -9.0963  21.2818
 PKE  H6   H  HCH3  0   0.303  -2.0443  -8.9491  26.3987
 PKE  H7   H  HCH3  0   0.292  -3.0022  -7.4975  26.0182
 PKE  H8   H  HCH3  0   0.291  -3.0666  -8.9118  24.9335
 PKE  H9   H  HCR6  0   0.268  -5.2359  -6.1410  21.1781
 PKE  H10  H  HCR6  0   0.261   1.0048  -3.3060  16.7049
 PKE  H11  H  HCR6  0   0.266   1.8646  -5.3562  17.8202
 PKE  H12  H  HNH1  0   0.404   1.4961  -6.8403  19.6951
 PKE  H13  H  HNH1  0   0.397  -2.5764  -2.1353  18.8726
 PKE  H14  H  HCH3  0   0.264  -1.9628  -5.0460  24.6528
 PKE  H15  H  HCH3  0   0.268  -2.4103  -4.8706  22.9598
 PKE  H16  H  HCH3  0   0.245  -3.4831  -5.7506  24.0590
 PKE  H17  H  HCR6  0   0.262  -3.5848  -1.4541  21.0764
 PKE  H18  H  HCR6  0   0.261  -3.4423  -5.4904  19.6256
 PKE  H19  H  HCH2  0   0.300  -5.1407  -1.6080  23.7454
 PKE  H20  H  HCH2  0   0.301  -6.3318  -1.2436  22.5083
 PKE  H21  H  HNR5  0   0.409  -6.9168  -5.1313  23.1423

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
 PKE  C4   N3   aromatic  1.332  0.020  1.332
 PKE  C4   C5   aromatic  1.372  0.020  1.372
 PKE  N3   C2   aromatic  1.334  0.020  1.334
 PKE  C5   C6   aromatic  1.409  0.020  1.409
 PKE  C2   N8   single    1.360  0.020  1.360
 PKE  C2   N1   aromatic  1.329  0.020  1.329
 PKE  N8   C22  single    1.402  0.020  1.402
 PKE  C6   N1   aromatic  1.330  0.020  1.330
 PKE  C6   N7   single    1.348  0.020  1.348
 PKE  C12  C11  aromatic  1.385  0.020  1.385
 PKE  C12  C13  aromatic  1.386  0.020  1.386
 PKE  C11  C10  aromatic  1.388  0.020  1.388
 PKE  N7   C9   single    1.439  0.020  1.439
 PKE  C22  C23  aromatic  1.399  0.020  1.399
 PKE  C22  C25  aromatic  1.394  0.020  1.394
 PKE  C23  C27  aromatic  1.378  0.020  1.378
 PKE  C13  N14  aromatic  1.326  0.020  1.326
 PKE  C10  C9   single    1.507  0.020  1.507
 PKE  C10  C15  aromatic  1.392  0.020  1.392
 PKE  C25  C24  aromatic  1.390  0.020  1.390
 PKE  C27  C28  single    1.496  0.020  1.496
 PKE  C27  C26  aromatic  1.392  0.020  1.392
 PKE  N14  C15  aromatic  1.321  0.020  1.321
 PKE  C15  N16  single    1.424  0.020  1.424
 PKE  C28  C29  single    1.524  0.020  1.524
 PKE  C24  C26  aromatic  1.380  0.020  1.380
 PKE  C26  N30  single    1.391  0.020  1.391
 PKE  N16  C18  single    1.460  0.020  1.460
 PKE  N16  S17  single    1.657  0.020  1.657
 PKE  C29  N30  single    1.363  0.020  1.363
 PKE  C29  O31  double    1.213  0.020  1.213
 PKE  O21  S17  double    1.455  0.020  1.455
 PKE  S17  C20  single    1.779  0.020  1.779
 PKE  S17  O19  double    1.453  0.020  1.453
 PKE  C9   H1   single    0.970  0.020  1.090
 PKE  C9   H2   single    0.970  0.020  1.090
 PKE  C11  H3   single    0.930  0.020  1.080
 PKE  C12  H4   single    0.930  0.020  1.080
 PKE  C13  H5   single    0.930  0.020  1.080
 PKE  C20  H6   single    0.970  0.020  1.090
 PKE  C20  H7   single    0.970  0.020  1.090
 PKE  C20  H8   single    0.970  0.020  1.090
 PKE  C24  H9   single    0.930  0.020  1.080
 PKE  C4   H10  single    0.930  0.020  1.080
 PKE  C5   H11  single    0.930  0.020  1.080
 PKE  N7   H12  single    0.860  0.020  1.020
 PKE  N8   H13  single    0.860  0.020  1.020
 PKE  C18  H14  single    0.970  0.020  1.090
 PKE  C18  H15  single    0.970  0.020  1.090
 PKE  C18  H16  single    0.970  0.020  1.090
 PKE  C23  H17  single    0.930  0.020  1.080
 PKE  C25  H18  single    0.930  0.020  1.080
 PKE  C28  H19  single    0.970  0.020  1.090
 PKE  C28  H20  single    0.970  0.020  1.090
 PKE  N30  H21  single    0.860  0.020  1.020

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
 PKE  N8   C2   N3   114.94  3.000
 PKE  N8   C2   N1   118.46  3.000
 PKE  N3   C2   N1   126.60  3.000
 PKE  H2   C9   H1   106.32  3.000
 PKE  H2   C9   N7   110.40  3.000
 PKE  H1   C9   N7   107.15  3.000
 PKE  H2   C9   C10  109.43  3.000
 PKE  H1   C9   C10  108.91  3.000
 PKE  N7   C9   C10  114.29  3.000
 PKE  C15  C10  C11  116.65  3.000
 PKE  C15  C10  C9   120.64  3.000
 PKE  C11  C10  C9   122.70  3.000
 PKE  H3   C11  C12  120.39  3.000
 PKE  H3   C11  C10  119.99  3.000
 PKE  C12  C11  C10  119.62  3.000
 PKE  H4   C12  C13  120.32  3.000
 PKE  H4   C12  C11  121.09  3.000
 PKE  C13  C12  C11  118.59  3.000
 PKE  H5   C13  N14  116.75  3.000
 PKE  H5   C13  C12  120.76  3.000
 PKE  N14  C13  C12  122.49  3.000
 PKE  N16  C15  N14  117.18  3.000
 PKE  N16  C15  C10  118.49  3.000
 PKE  N14  C15  C10  124.29  3.000
 PKE  H8   C20  H7   110.18  3.000
 PKE  H8   C20  H6   110.42  3.000
 PKE  H7   C20  H6   109.72  3.000
 PKE  H8   C20  S17  109.14  3.000
 PKE  H7   C20  S17  109.31  3.000
 PKE  H6   C20  S17  108.02  3.000
 PKE  C25  C22  C23  119.68  3.000
 PKE  C25  C22  N8   122.13  3.000
 PKE  C23  C22  N8   118.07  3.000
 PKE  H9   C24  C26  121.42  3.000
 PKE  H9   C24  C25  120.36  3.000
 PKE  C26  C24  C25  118.21  3.000
 PKE  C28  C27  C26  108.12  3.000
 PKE  C26  C27  C23  120.16  3.000
 PKE  C28  C27  C23  131.72  3.000
 PKE  C6   N1   C2   117.16  3.000
 PKE  C4   N3   C2   115.22  3.000
 PKE  H10  C4   C5   119.90  3.000
 PKE  H10  C4   N3   116.13  3.000
 PKE  C5   C4   N3   123.97  3.000
 PKE  H11  C5   C6   122.15  3.000
 PKE  H11  C5   C4   122.08  3.000
 PKE  C6   C5   C4   115.76  3.000
 PKE  N7   C6   C5   121.06  3.000
 PKE  N7   C6   N1   117.69  3.000
 PKE  C5   C6   N1   121.25  3.000
 PKE  H12  N7   C6   117.41  3.000
 PKE  H12  N7   C9   117.56  3.000
 PKE  C6   N7   C9   122.74  3.000
 PKE  H13  N8   C22  116.96  3.000
 PKE  H13  N8   C2   114.69  3.000
 PKE  C22  N8   C2   128.35  3.000
 PKE  C15  N14  C13  118.35  3.000
 PKE  C18  N16  S17  119.10  3.000
 PKE  S17  N16  C15  116.46  3.000
 PKE  C18  N16  C15  116.52  3.000
 PKE  O21  S17  O19  119.36  3.000
 PKE  O19  S17  N16  107.58  3.000
 PKE  O21  S17  N16  106.00  3.000
 PKE  O19  S17  C20  108.11  3.000
 PKE  O21  S17  C20  108.73  3.000
 PKE  N16  S17  C20  106.37  3.000
 PKE  H16  C18  H15  108.56  3.000
 PKE  H16  C18  H14  109.36  3.000
 PKE  H15  C18  H14  107.95  3.000
 PKE  H16  C18  N16  112.66  3.000
 PKE  H15  C18  N16  108.15  3.000
 PKE  H14  C18  N16  110.03  3.000
 PKE  H17  C23  C27  120.77  3.000
 PKE  H17  C23  C22  119.87  3.000
 PKE  C27  C23  C22  119.36  3.000
 PKE  H18  C25  C24  118.93  3.000
 PKE  H18  C25  C22  119.97  3.000
 PKE  C24  C25  C22  121.10  3.000
 PKE  N30  C26  C27  109.28  3.000
 PKE  N30  C26  C24  129.22  3.000
 PKE  C27  C26  C24  121.49  3.000
 PKE  H20  C28  H19  106.86  3.000
 PKE  H20  C28  C29  109.80  3.000
 PKE  H19  C28  C29  109.97  3.000
 PKE  H20  C28  C27  113.26  3.000
 PKE  H19  C28  C27  113.50  3.000
 PKE  C29  C28  C27  103.43  3.000
 PKE  O31  C29  N30  125.87  3.000
 PKE  O31  C29  C28  127.34  3.000
 PKE  N30  C29  C28  106.79  3.000
 PKE  H21  N30  C29  123.28  3.000
 PKE  H21  N30  C26  124.35  3.000
 PKE  C29  N30  C26  112.38  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
 PKE  CONST_01  C5   C4   N3   C2      0.00   0.0  0
 PKE  CONST_02  C5   C6   N1   C2      0.00   0.0  0
 PKE  CONST_03  C13  C12  C11  C10     0.00   0.0  0
 PKE  CONST_04  C13  N14  C15  C10     0.00   0.0  0
 PKE  CONST_05  N14  C13  C12  C11     0.00   0.0  0
 PKE  CONST_06  N14  C15  C10  C11     0.00   0.0  0
 PKE  CONST_07  C15  C10  C11  C12     0.00   0.0  0
 PKE  CONST_08  C15  N14  C13  C12     0.00   0.0  0
 PKE  CONST_09  C26  C27  C23  C22     0.00   0.0  0
 PKE  CONST_10  C26  C24  C25  C22     0.00   0.0  0
 PKE  CONST_11  C23  C22  C25  C24     0.00   0.0  0
 PKE  CONST_12  C23  C27  C26  C24     0.00   0.0  0
 PKE  CONST_13  C25  C22  C23  C27     0.00   0.0  0
 PKE  CONST_14  C25  C24  C26  C27     0.00   0.0  0
 PKE  CONST_15  C4   N3   C2   N1      0.00   0.0  0
 PKE  CONST_16  C4   C5   C6   N1      0.00   0.0  0
 PKE  CONST_17  C6   C5   C4   N3      0.00   0.0  0
 PKE  CONST_18  C6   N1   C2   N3      0.00   0.0  0
 PKE  CONST_19  C28  C29  N30  C26     0.00   0.0  0
 PKE  CONST_20  N7   C6   N1   C2    180.00   0.0  0
 PKE  CONST_21  C12  C11  C10  C9    180.00   0.0  0
 PKE  CONST_22  N14  C15  C10  C9    180.00   0.0  0
 PKE  CONST_23  N16  C15  C10  C11   180.00   0.0  0
 PKE  CONST_24  N16  C15  N14  C13   180.00   0.0  0
 PKE  CONST_25  N8   C22  C25  C24   180.00   0.0  0
 PKE  CONST_26  N8   C22  C23  C27   180.00   0.0  0
 PKE  CONST_27  N8   C2   N3   C4    180.00   0.0  0
 PKE  CONST_28  N7   C6   C5   C4    180.00   0.0  0
 PKE  CONST_29  N8   C2   N1   C6    180.00   0.0  0
 PKE  CONST_30  O31  C29  N30  C26   180.00   0.0  0
 PKE  CONST_31  H10  C4   N3   C2    180.00   0.0  0
 PKE  CONST_32  H4   C12  C11  C10   180.00   0.0  0
 PKE  CONST_33  H5   C13  C12  C11   180.00   0.0  0
 PKE  CONST_34  H3   C11  C12  C13   180.00   0.0  0
 PKE  CONST_35  H9   C24  C25  C22   180.00   0.0  0
 PKE  CONST_36  H11  C5   C6   N1    180.00   0.0  0
 PKE  CONST_37  H18  C25  C22  C23   180.00   0.0  0
 PKE  CONST_38  H17  C23  C22  C25   180.00   0.0  0
 PKE  CONST_39  H21  N30  C29  C28   180.00   0.0  0
 PKE  CONST_40  C5   C6   N7   C9    180.00   0.0  0
 PKE  CONST_41  N1   C6   N7   C9      0.00   0.0  0
 PKE  CONST_46  H12  N7   C6   N1    180.00   0.0  0
 PKE  Var_01    C23  C22  N8   C2    140.15  30.0  2
 PKE  Var_02    N3   C2   N8   C22   170.93  30.0  2
 PKE  Var_03    H19  C28  C27  C23   -60.35  30.0  1
 PKE  Var_04    C6   N7   C9   C10    78.52  30.0  1
 PKE  Var_05    N7   C9   C10  C11    21.86  30.0  2
 PKE  Var_06    O21  S17  N16  C15    32.36  30.0  3
 PKE  Var_07    H14  C18  N16  C15  -173.48  30.0  3
 PKE  Var_08    H6   C20  S17  N16   179.65  30.0  3

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
 PKE  plan-1  C9   0.020
 PKE  plan-1  C10  0.020
 PKE  plan-1  C11  0.020
 PKE  plan-1  C12  0.020
 PKE  plan-1  C13  0.020
 PKE  plan-1  C15  0.020
 PKE  plan-1  N14  0.020
 PKE  plan-1  N16  0.020
 PKE  plan-1  H3   0.020
 PKE  plan-1  H4   0.020
 PKE  plan-1  H5   0.020
 PKE  plan-2  C2   0.020
 PKE  plan-2  N1   0.020
 PKE  plan-2  N3   0.020
 PKE  plan-2  C4   0.020
 PKE  plan-2  C5   0.020
 PKE  plan-2  C6   0.020
 PKE  plan-2  N7   0.020
 PKE  plan-2  N8   0.020
 PKE  plan-2  H10  0.020
 PKE  plan-2  H11  0.020
 PKE  plan-3  C9   0.020
 PKE  plan-3  C6   0.020
 PKE  plan-3  N7   0.020
 PKE  plan-3  H12  0.020
 PKE  plan-4  C15  0.020
 PKE  plan-4  N16  0.020
 PKE  plan-4  S17  0.020
 PKE  plan-4  C18  0.020
 PKE  plan-5  C22  0.020
 PKE  plan-5  C24  0.020
 PKE  plan-5  C27  0.020
 PKE  plan-5  N8   0.020
 PKE  plan-5  C23  0.020
 PKE  plan-5  C25  0.020
 PKE  plan-5  C26  0.020
 PKE  plan-5  C28  0.020
 PKE  plan-5  C29  0.020
 PKE  plan-5  N30  0.020
 PKE  plan-5  O31  0.020
 PKE  plan-5  H9   0.020
 PKE  plan-5  H17  0.020
 PKE  plan-5  H18  0.020
 PKE  plan-5  H21  0.020

