# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 02:58:24 2020
#   Inital geometry file: a 155 line input string
#   Ligand name: N-{3-[(2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}-7H-pyrrolo[2,3-d]pyrimidin-4-yl)oxy]phenyl}propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)Nc1cccc(Oc2nc(Nc3ccc(cc3)N4CCN(C)CC4)nc5[nH]ccc25)c1
#
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
 633  633  N-{3-[(2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}-7H-pyrrolo[2,3-d]pyrimidin-4-yl)oxy]phenyl}propanamide  ligand  64  35  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_633
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
 633  C4   C  CR56  0  -0.116  -1.7402  -3.8664  -0.0913
 633  C5   C  CR56  0   0.537  -0.3580  -3.8168  -0.3231
 633  C8   C  CR15  0  -0.020  -1.0738  -5.8725  -0.7912
 633  C13  C  CR16  0  -0.249  -4.7919  -0.0418   2.8934
 633  C15  C  CR6   0   0.385  -5.2984   0.6231   0.6386
 633  C20  C  CH3   0  -0.659  -7.2818   4.7217  -1.4357
 633  C24  C  CR16  0  -0.304   2.8060  -1.0281  -0.0847
 633  C26  C  CR6   0   0.338   4.4504   0.7725   0.0010
 633  C28  C  CR16  0  -0.345   2.1185   1.1750   0.5291
 633  C1   C  CR6   0   0.593  -0.2153  -1.6821   0.2641
 633  N2   N  N     0  -0.514  -1.5373  -1.5951   0.5306
 633  C3   C  CR6   0   0.485  -2.2744  -2.6572   0.3580
 633  N6   N  N     0  -0.511   0.4289  -2.7537  -0.1573
 633  N7   N  NR15  0  -0.667   0.0244  -5.0408  -0.7447
 633  C9   C  CR15  0  -0.430  -2.1832  -5.1892  -0.3962
 633  O10  O  O2    0  -0.509  -3.5887  -2.6080   0.6108
 633  C11  C  CR6   0   0.382  -4.1325  -1.4317   1.0871
 633  C12  C  CR16  0  -0.322  -4.1754  -1.2011   2.4510
 633  C14  C  CR16  0  -0.322  -5.3509   0.8732   2.0114
 633  C16  C  CR16  0  -0.415  -4.6795  -0.5443   0.1838
 633  C18  C  C     0   0.552  -6.4499   2.6692  -0.2073
 633  C19  C  CH2   0  -0.586  -6.9188   3.2506  -1.5249
 633  O21  O  O     0  -0.465  -6.6327   3.2217   0.8607
 633  N22  N  NH1   0  -0.772   0.4446  -0.5107   0.4739
 633  C23  C  CR6   0   0.337   1.7806  -0.1585   0.2971
 633  C25  C  CR16  0  -0.312   4.1040  -0.5646  -0.2200
 633  C27  C  CR16  0  -0.342   3.4162   1.6341   0.3773
 633  N29  N  NT    0  -0.512   5.7821   1.1886  -0.1265
 633  C30  C  CH2   0  -0.314   6.0979   2.5397   0.2893
 633  C31  C  CH2   0  -0.279   7.6005   2.7310   0.3774
 633  N32  N  NT    0  -0.412   8.2394   2.4269  -0.8851
 633  C33  C  CH2   0  -0.283   7.9410   1.0636  -1.2686
 633  C34  C  CH2   0  -0.307   6.4447   0.8524  -1.3797
 633  C35  C  CH3   0  -0.517   9.6624   2.6724  -0.8385
 633  H1   H  HCR5  0   0.287  -0.9672  -6.8965  -1.1082
 633  H2   H  HCR6  0   0.266  -4.8412   0.1620   3.9550
 633  H3   H  HCH3  0   0.231  -8.0836   4.8968  -0.7204
 633  H4   H  HCH3  0   0.230  -6.4265   5.3274  -1.1371
 633  H5   H  HCH3  0   0.237  -7.6190   5.0802  -2.4073
 633  H6   H  HCR6  0   0.280   2.6000  -2.0702  -0.2661
 633  H7   H  HCR6  0   0.262   1.3484   1.8804   0.8218
 633  H8   H  HNR5  0   0.413   0.9658  -5.3072  -0.9832
 633  H9   H  HCR5  0   0.257  -3.1849  -5.5817  -0.3342
 633  H10  H  HCR6  0   0.270  -3.7447  -1.9088   3.1470
 633  H11  H  HCR6  0   0.283  -5.8199   1.7627   2.3957
 633  H12  H  HCR6  0   0.282  -4.6297  -0.7604  -0.8772
 633  H13  H  HNH1  0   0.418  -5.7236   1.1292  -1.2862
 633  H14  H  HCH2  0   0.279  -7.7847   2.6659  -1.8525
 633  H15  H  HCH2  0   0.264  -6.1504   3.0930  -2.2861
 633  H16  H  HNH1  0   0.406  -0.1619   0.2338   0.7817
 633  H17  H  HCR6  0   0.257   4.8689  -1.2821  -0.4903
 633  H18  H  HCR6  0   0.267   3.6008   2.6848   0.5526
 633  H19  H  HCH2  0   0.207   5.6768   3.2909  -0.3976
 633  H20  H  HCH2  0   0.249   5.6714   2.7259   1.2765
 633  H21  H  HCH2  0   0.240   7.8032   3.7714   0.6426
 633  H22  H  HCH2  0   0.192   7.9972   2.1055   1.1965
 633  H24  H  HCH2  0   0.239   8.3967   0.8534  -2.2391
 633  H25  H  HCH2  0   0.192   8.3575   0.3361  -0.5497
 633  H26  H  HCH2  0   0.252   6.2630  -0.1902  -1.6337
 633  H27  H  HCH2  0   0.211   6.0496   1.4630  -2.2061
 633  H28  H  HCH3  0   0.192  10.1860   2.0445  -0.1006
 633  H29  H  HCH3  0   0.233  10.1073   2.4796  -1.8159
 633  H30  H  HCH3  0   0.233   9.8529   3.7155  -0.5822
 633  N17  N  NH1   0  -0.751  -5.8252   1.4661  -0.3406

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
 633  N7   C8   aromatic  1.378  0.020  1.378
 633  N7   C5   aromatic  1.350  0.020  1.350
 633  C8   C9   aromatic  1.362  0.020  1.362
 633  N6   C5   aromatic  1.333  0.020  1.333
 633  N6   C1   aromatic  1.319  0.020  1.319
 633  C5   C4   aromatic  1.402  0.020  1.402
 633  C12  C13  aromatic  1.386  0.020  1.386
 633  C12  C11  aromatic  1.384  0.020  1.384
 633  C9   C4   aromatic  1.428  0.020  1.428
 633  N22  C1   single    1.361  0.020  1.361
 633  N22  C23  single    1.393  0.020  1.393
 633  C1   N2   aromatic  1.351  0.020  1.351
 633  C4   C3   aromatic  1.396  0.020  1.396
 633  C28  C23  aromatic  1.395  0.020  1.395
 633  C28  C27  aromatic  1.385  0.020  1.385
 633  N2   C3   aromatic  1.304  0.020  1.304
 633  C23  C24  aromatic  1.398  0.020  1.398
 633  C3   O10  single    1.339  0.020  1.339
 633  C27  C26  aromatic  1.398  0.020  1.398
 633  C13  C14  aromatic  1.388  0.020  1.388
 633  O10  C11  single    1.381  0.020  1.381
 633  C24  C25  aromatic  1.385  0.020  1.385
 633  C26  C25  aromatic  1.399  0.020  1.399
 633  C26  N29  single    1.401  0.020  1.401
 633  C11  C16  aromatic  1.379  0.020  1.379
 633  N29  C30  single    1.448  0.020  1.448
 633  N29  C34  single    1.457  0.020  1.457
 633  C30  C31  single    1.517  0.020  1.517
 633  C31  N32  single    1.447  0.020  1.447
 633  C14  C15  aromatic  1.396  0.020  1.396
 633  C34  C33  single    1.515  0.020  1.515
 633  N32  C33  single    1.447  0.020  1.447
 633  N32  C35  single    1.445  0.020  1.445
 633  C16  C15  aromatic  1.397  0.020  1.397
 633  C15  N17  single    1.395  0.020  1.395
 633  N17  C18  single    1.362  0.020  1.362
 633  O21  C18  double    1.216  0.020  1.216
 633  C18  C19  single    1.514  0.020  1.514
 633  C19  C20  single    1.518  0.020  1.518
 633  C8   H1   single    0.930  0.020  1.080
 633  C13  H2   single    0.930  0.020  1.080
 633  C20  H3   single    0.970  0.020  1.090
 633  C20  H4   single    0.970  0.020  1.090
 633  C20  H5   single    0.970  0.020  1.090
 633  C24  H6   single    0.930  0.020  1.080
 633  C28  H7   single    0.930  0.020  1.080
 633  N7   H8   single    0.860  0.020  1.020
 633  C9   H9   single    0.930  0.020  1.080
 633  C12  H10  single    0.930  0.020  1.080
 633  C14  H11  single    0.930  0.020  1.080
 633  C16  H12  single    0.930  0.020  1.080
 633  N17  H13  single    0.860  0.020  1.020
 633  C19  H14  single    0.970  0.020  1.090
 633  C19  H15  single    0.970  0.020  1.090
 633  N22  H16  single    0.860  0.020  1.020
 633  C25  H17  single    0.930  0.020  1.080
 633  C27  H18  single    0.930  0.020  1.080
 633  C30  H19  single    0.970  0.020  1.090
 633  C30  H20  single    0.970  0.020  1.090
 633  C31  H21  single    0.970  0.020  1.090
 633  C31  H22  single    0.970  0.020  1.090
 633  C33  H24  single    0.970  0.020  1.090
 633  C33  H25  single    0.970  0.020  1.090
 633  C34  H26  single    0.970  0.020  1.090
 633  C34  H27  single    0.970  0.020  1.090
 633  C35  H28  single    0.970  0.020  1.090
 633  C35  H29  single    0.970  0.020  1.090
 633  C35  H30  single    0.970  0.020  1.090

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
 633  C9   C4   C3   138.79  3.000
 633  C3   C4   C5   113.55  3.000
 633  C9   C4   C5   107.65  3.000
 633  N7   C5   N6   126.50  3.000
 633  N6   C5   C4   126.12  3.000
 633  N7   C5   C4   107.38  3.000
 633  H1   C8   C9   130.02  3.000
 633  H1   C8   N7   120.31  3.000
 633  C9   C8   N7   109.67  3.000
 633  H2   C13  C14  118.73  3.000
 633  H2   C13  C12  119.41  3.000
 633  C14  C13  C12  121.85  3.000
 633  N17  C15  C16  116.33  3.000
 633  N17  C15  C14  124.58  3.000
 633  C16  C15  C14  119.10  3.000
 633  H5   C20  H4   107.73  3.000
 633  H5   C20  H3   107.77  3.000
 633  H4   C20  H3   107.97  3.000
 633  H5   C20  C19  109.92  3.000
 633  H4   C20  C19  111.53  3.000
 633  H3   C20  C19  111.75  3.000
 633  H6   C24  C25  119.10  3.000
 633  H6   C24  C23  120.49  3.000
 633  C25  C24  C23  120.40  3.000
 633  N29  C26  C27  123.01  3.000
 633  N29  C26  C25  120.33  3.000
 633  C27  C26  C25  116.65  3.000
 633  H7   C28  C27  118.64  3.000
 633  H7   C28  C23  119.64  3.000
 633  C27  C28  C23  121.71  3.000
 633  N22  C1   N6   120.77  3.000
 633  N22  C1   N2   112.87  3.000
 633  N6   C1   N2   126.36  3.000
 633  C3   N2   C1   118.31  3.000
 633  O10  C3   N2   119.98  3.000
 633  O10  C3   C4   117.91  3.000
 633  N2   C3   C4   122.12  3.000
 633  C1   N6   C5   113.53  3.000
 633  H8   N7   C8   125.25  3.000
 633  H8   N7   C5   125.36  3.000
 633  C8   N7   C5   109.39  3.000
 633  H9   C9   C8   126.26  3.000
 633  H9   C9   C4   127.84  3.000
 633  C8   C9   C4   105.90  3.000
 633  C11  O10  C3   118.88  3.000
 633  C16  C11  C12  121.73  3.000
 633  C16  C11  O10  118.58  3.000
 633  C12  C11  O10  119.61  3.000
 633  H10  C12  C11  120.84  3.000
 633  H10  C12  C13  121.27  3.000
 633  C11  C12  C13  117.89  3.000
 633  H11  C14  C15  121.02  3.000
 633  H11  C14  C13  119.55  3.000
 633  C15  C14  C13  119.43  3.000
 633  H12  C16  C11  119.64  3.000
 633  H12  C16  C15  120.37  3.000
 633  C11  C16  C15  119.99  3.000
 633  O21  C18  C19  122.89  3.000
 633  C19  C18  N17  113.33  3.000
 633  O21  C18  N17  123.78  3.000
 633  H15  C19  H14  105.69  3.000
 633  H15  C19  C18  109.45  3.000
 633  H14  C19  C18  107.47  3.000
 633  H15  C19  C20  110.41  3.000
 633  H14  C19  C20  110.24  3.000
 633  C18  C19  C20  113.27  3.000
 633  H16  N22  C23  115.40  3.000
 633  H16  N22  C1   113.01  3.000
 633  C23  N22  C1   131.55  3.000
 633  N22  C23  C28  116.93  3.000
 633  C28  C23  C24  117.54  3.000
 633  N22  C23  C24  125.53  3.000
 633  H17  C25  C26  119.86  3.000
 633  H17  C25  C24  117.68  3.000
 633  C26  C25  C24  122.45  3.000
 633  H18  C27  C28  117.67  3.000
 633  H18  C27  C26  121.10  3.000
 633  C28  C27  C26  121.23  3.000
 633  C34  N29  C30  111.28  3.000
 633  C34  N29  C26  116.24  3.000
 633  C30  N29  C26  117.26  3.000
 633  H20  C30  H19  107.36  3.000
 633  H20  C30  C31  108.24  3.000
 633  H19  C30  C31  109.19  3.000
 633  H20  C30  N29  109.49  3.000
 633  H19  C30  N29  111.95  3.000
 633  C31  C30  N29  110.50  3.000
 633  H22  C31  H21  107.01  3.000
 633  H22  C31  N32  111.68  3.000
 633  H21  C31  N32  109.26  3.000
 633  H22  C31  C30  109.11  3.000
 633  H21  C31  C30  108.53  3.000
 633  N32  C31  C30  111.11  3.000
 633  C35  N32  C33  111.82  3.000
 633  C35  N32  C31  111.78  3.000
 633  C33  N32  C31  109.75  3.000
 633  H25  C33  H24  107.11  3.000
 633  H25  C33  C34  109.17  3.000
 633  H24  C33  C34  108.66  3.000
 633  H25  C33  N32  111.73  3.000
 633  H24  C33  N32  109.31  3.000
 633  C34  C33  N32  110.75  3.000
 633  H27  C34  H26  107.23  3.000
 633  H27  C34  C33  109.40  3.000
 633  H26  C34  C33  108.39  3.000
 633  H27  C34  N29  110.77  3.000
 633  H26  C34  N29  110.23  3.000
 633  C33  C34  N29  110.72  3.000
 633  H30  C35  H29  107.95  3.000
 633  H30  C35  H28  107.74  3.000
 633  H29  C35  H28  107.79  3.000
 633  H30  C35  N32  110.00  3.000
 633  H29  C35  N32  110.04  3.000
 633  H28  C35  N32  113.14  3.000
 633  H13  N17  C18  115.64  3.000
 633  H13  N17  C15  114.71  3.000
 633  C18  N17  C15  129.65  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
 633  CONST_01  C8   N7   C5   C4      0.00   0.0  0
 633  CONST_02  C1   N6   C5   C4      0.00   0.0  0
 633  CONST_03  N7   C8   C9   C4      0.00   0.0  0
 633  CONST_04  C1   N2   C3   C4      0.00   0.0  0
 633  CONST_05  C9   C8   N7   C5      0.00   0.0  0
 633  CONST_06  N2   C1   N6   C5      0.00   0.0  0
 633  CONST_07  C8   C9   C4   C5      0.00   0.0  0
 633  CONST_08  N2   C3   C4   C5      0.00   0.0  0
 633  CONST_09  N6   C5   N7   C8    180.00   0.0  0
 633  CONST_10  C3   C4   C9   C8    180.00   0.0  0
 633  CONST_11  C16  C11  C12  C13     0.00   0.0  0
 633  CONST_12  C16  C15  C14  C13     0.00   0.0  0
 633  CONST_13  C12  C13  C14  C15     0.00   0.0  0
 633  CONST_14  C12  C11  C16  C15     0.00   0.0  0
 633  CONST_15  C27  C28  C23  C24     0.00   0.0  0
 633  CONST_16  C27  C26  C25  C24     0.00   0.0  0
 633  CONST_17  C23  C28  C27  C26     0.00   0.0  0
 633  CONST_18  C23  C24  C25  C26     0.00   0.0  0
 633  CONST_19  C25  C24  C23  C28     0.00   0.0  0
 633  CONST_20  C25  C26  C27  C28     0.00   0.0  0
 633  CONST_21  N7   C5   N6   C1    180.00   0.0  0
 633  CONST_22  C9   C4   C3   N2    180.00   0.0  0
 633  CONST_23  N7   C5   C4   C3    180.00   0.0  0
 633  CONST_24  N6   C5   C4   C3      0.00   0.0  0
 633  CONST_25  N6   C1   N2   C3      0.00   0.0  0
 633  CONST_26  C9   C4   C5   N6    180.00   0.0  0
 633  CONST_27  C9   C4   C5   N7      0.00   0.0  0
 633  CONST_28  C14  C13  C12  C11     0.00   0.0  0
 633  CONST_29  C14  C15  C16  C11     0.00   0.0  0
 633  CONST_30  N29  C26  C25  C24   180.00   0.0  0
 633  CONST_31  N29  C26  C27  C28   180.00   0.0  0
 633  CONST_32  N22  C1   N6   C5    180.00   0.0  0
 633  CONST_33  O10  C3   C4   C5    180.00   0.0  0
 633  CONST_34  O10  C11  C12  C13   180.00   0.0  0
 633  CONST_35  N17  C15  C14  C13   180.00   0.0  0
 633  CONST_36  O10  C11  C16  C15   180.00   0.0  0
 633  CONST_37  O10  C3   N2   C1    180.00   0.0  0
 633  CONST_38  N22  C1   N2   C3    180.00   0.0  0
 633  CONST_39  O10  C3   C4   C9      0.00   0.0  0
 633  CONST_40  N17  C15  C16  C11   180.00   0.0  0
 633  CONST_41  C27  C28  C23  N22   180.00   0.0  0
 633  CONST_42  C25  C24  C23  N22   180.00   0.0  0
 633  CONST_43  H8   N7   C5   C4    180.00   0.0  0
 633  CONST_44  H1   C8   C9   C4    180.00   0.0  0
 633  CONST_45  H9   C9   C4   C5    180.00   0.0  0
 633  CONST_46  H2   C13  C14  C15   180.00   0.0  0
 633  CONST_47  H7   C28  C23  C24   180.00   0.0  0
 633  CONST_48  H6   C24  C25  C26   180.00   0.0  0
 633  CONST_49  H11  C14  C13  C12   180.00   0.0  0
 633  CONST_50  H12  C16  C11  C12   180.00   0.0  0
 633  CONST_51  H10  C12  C13  C14   180.00   0.0  0
 633  CONST_52  H18  C27  C28  C23   180.00   0.0  0
 633  CONST_53  H17  C25  C24  C23   180.00   0.0  0
 633  CONST_54  C18  N17  C15  C14     0.00   0.0  0
 633  CONST_55  C18  N17  C15  C16   180.00   0.0  0
 633  CONST_56  H13  N17  C15  C14   180.00   0.0  0
 633  CONST_57  O21  C18  N17  C15     0.00   0.0  0
 633  CONST_58  C19  C18  N17  C15   180.00   0.0  0
 633  Var_01    C31  C30  N29  C26   167.56  30.0  1
 633  Var_02    C33  C34  N29  C26  -166.85  30.0  1
 633  Var_03    C30  N29  C26  C25  -171.93  30.0  2
 633  Var_04    N32  C31  C30  N29    56.98  30.0  1
 633  Var_05    N32  C33  C34  N29   -56.96  30.0  1
 633  Var_06    C33  N32  C31  C30   -58.40  30.0  1
 633  Var_07    C34  C33  N32  C31    58.30  30.0  1
 633  Var_08    C1   N22  C23  C24    -4.43  30.0  1
 633  Var_09    C23  N22  C1   N2   -178.35  30.0  1
 633  Var_10    C12  C11  O10  C3    -88.79  30.0  2
 633  Var_11    H28  C35  N32  C31    62.02  30.0  3
 633  Var_12    N17  C18  C19  C20  -165.06  30.0  1
 633  Var_13    H3   C20  C19  C18   -59.87  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
 633  plan-1  C24  0.020
 633  plan-1  C26  0.020
 633  plan-1  C28  0.020
 633  plan-1  N22  0.020
 633  plan-1  C23  0.020
 633  plan-1  C25  0.020
 633  plan-1  C27  0.020
 633  plan-1  N29  0.020
 633  plan-1  H6   0.020
 633  plan-1  H7   0.020
 633  plan-1  H17  0.020
 633  plan-1  H18  0.020
 633  plan-2  C13  0.020
 633  plan-2  C15  0.020
 633  plan-2  O10  0.020
 633  plan-2  C11  0.020
 633  plan-2  C12  0.020
 633  plan-2  C14  0.020
 633  plan-2  C16  0.020
 633  plan-2  H2   0.020
 633  plan-2  H10  0.020
 633  plan-2  H11  0.020
 633  plan-2  H12  0.020
 633  plan-2  N17  0.020
 633  plan-3  C4   0.020
 633  plan-3  C5   0.020
 633  plan-3  C8   0.020
 633  plan-3  C1   0.020
 633  plan-3  N2   0.020
 633  plan-3  C3   0.020
 633  plan-3  N6   0.020
 633  plan-3  N7   0.020
 633  plan-3  C9   0.020
 633  plan-3  O10  0.020
 633  plan-3  N22  0.020
 633  plan-3  H1   0.020
 633  plan-3  H8   0.020
 633  plan-3  H9   0.020
 633  plan-4  C15  0.020
 633  plan-4  C18  0.020
 633  plan-4  C19  0.020
 633  plan-4  O21  0.020
 633  plan-4  H13  0.020
 633  plan-4  N17  0.020

