# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 12:05:35 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: 2-[2-[[4-(4-methylpiperazin-1-yl)phenyl]amino]pyrimidin-4-yl]-1,5,6,7-tetrahydropyrrolo[3,2-c]pyridin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)c2ccc(Nc3nccc(n3)c4[nH]c5CCNC(=O)c5c4)cc2
#
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
 8X2  8X2  2-[2-[[4-(4-methylpiperazin-1-yl)phenyl]amino]pyrimidin-4-yl]-1,5,6,7-tetrahydropyrrolo[3,2-c]pyridin-4-one  ligand  55  30  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8X2
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
 8X2  C1   C  CH2   0  -0.278   8.0687  -0.9624  -0.8751
 8X2  C2   C  CH2   0  -0.313   6.6206  -1.2996  -0.5714
 8X2  C3   C  CH2   0  -0.307   6.6278   0.3888   1.1401
 8X2  N6   N  NH1   0  -0.649  -8.3068  -1.4131  -0.1688
 8X2  C7   C  CR16  0  -0.337   2.4096  -1.2840  -0.3504
 8X2  C8   C  CR6   0   0.331   1.6952  -0.1594   0.0549
 8X2  C9   C  CR16  0  -0.291   2.4272   0.9598   0.4574
 8X2  C10  C  CR16  0  -0.322   3.8106   0.9427   0.4303
 8X2  C11  C  CR6   0   0.588  -0.6551   0.7103   0.0659
 8X2  C12  C  CR16  0  -0.001  -1.3000   2.8668   0.0872
 8X2  C13  C  CR16  0  -0.398  -2.6301   2.5046   0.0521
 8X2  C14  C  CR6   0   0.256  -2.8945   1.1305   0.0266
 8X2  C15  C  CR5   0   0.309  -4.2378   0.5887  -0.0039
 8X2  C16  C  CR15  0  -0.382  -4.6445  -0.7260  -0.0579
 8X2  C19  C  CH2   0  -0.529  -7.8899   1.0114   0.0267
 8X2  C20  C  CH2   0  -0.286  -8.7026  -0.0941  -0.6389
 8X2  C21  C  C     0   0.476  -7.0167  -1.8155  -0.0628
 8X2  O    O  O     0  -0.492  -6.6944  -2.9899   0.0777
 8X2  C17  C  CR5   0  -0.143  -6.0542  -0.7157  -0.0794
 8X2  C18  C  CR5   0   0.369  -6.4650   0.6029  -0.0302
 8X2  N5   N  NR15  0  -0.716  -5.3704   1.3752   0.0158
 8X2  N3   N  N     0  -0.469  -0.3014   1.9943   0.0969
 8X2  N4   N  N     0  -0.503  -1.9053   0.2454   0.0321
 8X2  N2   N  NH1   0  -0.768   0.3014  -0.2535   0.0644
 8X2  C6   C  CR16  0  -0.348   3.7951  -1.3052  -0.3530
 8X2  C5   C  CR6   0   0.350   4.5392  -0.1831   0.0259
 8X2  N1   N  NT    0  -0.516   5.9353  -0.1476  -0.0231
 8X2  C4   C  CH2   0  -0.283   8.0718   0.7048   0.8055
 8X2  N    N  NT    0  -0.411   8.7512  -0.4699   0.3021
 8X2  C    C  CH3   0  -0.519  10.1465  -0.2068   0.0369
 8X2  H1   H  HCH2  0   0.240   8.5695  -1.8666  -1.2288
 8X2  H2   H  HCH2  0   0.192   8.1010  -0.2286  -1.7003
 8X2  H3   H  HCH2  0   0.249   6.1432  -1.5971  -1.5058
 8X2  H4   H  HCH2  0   0.210   6.5798  -2.1644   0.1096
 8X2  H5   H  HCH2  0   0.253   6.1465   1.3052   1.4746
 8X2  H6   H  HCH2  0   0.213   6.5940  -0.3243   1.9776
 8X2  H8   H  HCR6  0   0.263   1.8759  -2.1741  -0.6641
 8X2  H9   H  HCR6  0   0.273   1.9233   1.8569   0.7783
 8X2  H10  H  HCR6  0   0.259   4.3263   1.8475   0.7238
 8X2  H11  H  HCR6  0   0.273  -1.0221   3.9149   0.1082
 8X2  H12  H  HCR6  0   0.263  -3.4013   3.2597   0.0453
 8X2  H13  H  HCR5  0   0.259  -3.9913  -1.5829  -0.0848
 8X2  H14  H  HCH2  0   0.277  -8.0705   1.9562  -0.4871
 8X2  H15  H  HCH2  0   0.272  -8.1979   1.1452   1.0684
 8X2  H16  H  HCH2  0   0.243  -8.5823  -0.0222  -1.7251
 8X2  H17  H  HCH2  0   0.266  -9.7604   0.0354  -0.4199
 8X2  H18  H  HNR5  0   0.422  -5.3879   2.3822   0.0581
 8X2  H19  H  HNH1  0   0.403  -0.0707  -1.1859  -0.0348
 8X2  H20  H  HCR6  0   0.267   4.2804  -2.2204  -0.6610
 8X2  H21  H  HCH2  0   0.193   8.1015   1.5363   0.0788
 8X2  H22  H  HCH2  0   0.240   8.5742   1.0500   1.7122
 8X2  H24  H  HCH3  0   0.192  10.3029   0.5647  -0.7335
 8X2  H25  H  HCH3  0   0.234  10.6448   0.1271   0.9483
 8X2  H26  H  HCH3  0   0.234  10.6429  -1.1184  -0.2993
 8X2  H7   H  HNH1  0   0.397  -8.9985  -2.1445  -0.2336

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
 8X2  O    C21  double    1.226  0.020  1.226
 8X2  C12  C13  aromatic  1.379  0.020  1.379
 8X2  C12  N3   aromatic  1.326  0.020  1.326
 8X2  C13  C14  aromatic  1.400  0.020  1.400
 8X2  C16  C17  aromatic  1.410  0.020  1.410
 8X2  C16  C15  aromatic  1.377  0.020  1.377
 8X2  C21  C17  single    1.462  0.020  1.462
 8X2  C21  N6   single    1.356  0.020  1.356
 8X2  N3   C11  aromatic  1.332  0.020  1.332
 8X2  C17  C18  aromatic  1.382  0.020  1.382
 8X2  C14  C15  single    1.449  0.020  1.449
 8X2  C14  N4   aromatic  1.327  0.020  1.327
 8X2  C15  N5   aromatic  1.379  0.020  1.379
 8X2  N6   C20  single    1.455  0.020  1.455
 8X2  C11  N4   aromatic  1.334  0.020  1.334
 8X2  C11  N2   single    1.358  0.020  1.358
 8X2  C18  N5   aromatic  1.340  0.020  1.340
 8X2  C18  C19  single    1.483  0.020  1.483
 8X2  N2   C8   single    1.397  0.020  1.397
 8X2  C19  C20  single    1.525  0.020  1.525
 8X2  C8   C9   aromatic  1.397  0.020  1.397
 8X2  C8   C7   aromatic  1.393  0.020  1.393
 8X2  C9   C10  aromatic  1.384  0.020  1.384
 8X2  C7   C6   aromatic  1.386  0.020  1.386
 8X2  C10  C5   aromatic  1.401  0.020  1.401
 8X2  C6   C5   aromatic  1.399  0.020  1.399
 8X2  C5   N1   single    1.397  0.020  1.397
 8X2  C2   N1   single    1.448  0.020  1.448
 8X2  C2   C1   single    1.518  0.020  1.518
 8X2  C3   N1   single    1.456  0.020  1.456
 8X2  C3   C4   single    1.516  0.020  1.516
 8X2  N    C1   single    1.447  0.020  1.447
 8X2  N    C4   single    1.447  0.020  1.447
 8X2  N    C    single    1.444  0.020  1.444
 8X2  C1   H1   single    0.970  0.020  1.090
 8X2  C1   H2   single    0.970  0.020  1.090
 8X2  C2   H3   single    0.970  0.020  1.090
 8X2  C2   H4   single    0.970  0.020  1.090
 8X2  C3   H5   single    0.970  0.020  1.090
 8X2  C3   H6   single    0.970  0.020  1.090
 8X2  N6   H7   single    0.890  0.020  1.040
 8X2  C7   H8   single    0.930  0.020  1.080
 8X2  C9   H9   single    0.930  0.020  1.080
 8X2  C10  H10  single    0.930  0.020  1.080
 8X2  C12  H11  single    0.930  0.020  1.080
 8X2  C13  H12  single    0.930  0.020  1.080
 8X2  C16  H13  single    0.930  0.020  1.080
 8X2  C19  H14  single    0.970  0.020  1.090
 8X2  C19  H15  single    0.970  0.020  1.090
 8X2  C20  H16  single    0.970  0.020  1.090
 8X2  C20  H17  single    0.970  0.020  1.090
 8X2  N5   H18  single    0.860  0.020  1.020
 8X2  N2   H19  single    0.860  0.020  1.020
 8X2  C6   H20  single    0.930  0.020  1.080
 8X2  C4   H21  single    0.970  0.020  1.090
 8X2  C4   H22  single    0.970  0.020  1.090
 8X2  C    H24  single    0.970  0.020  1.090
 8X2  C    H25  single    0.970  0.020  1.090
 8X2  C    H26  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
 8X2  H2   C1   H1   107.13  3.000
 8X2  H2   C1   N    111.58  3.000
 8X2  H1   C1   N    109.20  3.000
 8X2  H2   C1   C2   108.97  3.000
 8X2  H1   C1   C2   108.56  3.000
 8X2  N    C1   C2   111.27  3.000
 8X2  H4   C2   H3   107.42  3.000
 8X2  H4   C2   N1   111.90  3.000
 8X2  H3   C2   N1   109.52  3.000
 8X2  H4   C2   C1   109.48  3.000
 8X2  H3   C2   C1   107.87  3.000
 8X2  N1   C2   C1   110.52  3.000
 8X2  H6   C3   H5   107.35  3.000
 8X2  H6   C3   C4   109.42  3.000
 8X2  H5   C3   C4   108.29  3.000
 8X2  H6   C3   N1   110.77  3.000
 8X2  H5   C3   N1   110.21  3.000
 8X2  C4   C3   N1   110.71  3.000
 8X2  H7   N6   C21  116.25  3.000
 8X2  H7   N6   C20  116.74  3.000
 8X2  C21  N6   C20  123.59  3.000
 8X2  H8   C7   C6   118.62  3.000
 8X2  H8   C7   C8   119.65  3.000
 8X2  C6   C7   C8   121.72  3.000
 8X2  N2   C8   C9   125.10  3.000
 8X2  C9   C8   C7   117.53  3.000
 8X2  N2   C8   C7   117.34  3.000
 8X2  H9   C9   C10  118.91  3.000
 8X2  H9   C9   C8   120.52  3.000
 8X2  C10  C9   C8   120.56  3.000
 8X2  H10  C10  C5   120.17  3.000
 8X2  H10  C10  C9   117.44  3.000
 8X2  C5   C10  C9   122.39  3.000
 8X2  N2   C11  N4   114.38  3.000
 8X2  N2   C11  N3   119.81  3.000
 8X2  N4   C11  N3   125.81  3.000
 8X2  H11  C12  N3   116.28  3.000
 8X2  H11  C12  C13  120.10  3.000
 8X2  N3   C12  C13  123.62  3.000
 8X2  H12  C13  C14  123.49  3.000
 8X2  H12  C13  C12  120.37  3.000
 8X2  C14  C13  C12  116.14  3.000
 8X2  N4   C14  C15  116.21  3.000
 8X2  N4   C14  C13  120.92  3.000
 8X2  C15  C14  C13  122.87  3.000
 8X2  N5   C15  C16  107.60  3.000
 8X2  N5   C15  C14  123.23  3.000
 8X2  C16  C15  C14  129.17  3.000
 8X2  H13  C16  C17  127.69  3.000
 8X2  H13  C16  C15  125.51  3.000
 8X2  C17  C16  C15  106.79  3.000
 8X2  H15  C19  H14  107.21  3.000
 8X2  H15  C19  C18  109.91  3.000
 8X2  H14  C19  C18  112.31  3.000
 8X2  H15  C19  C20  110.74  3.000
 8X2  H14  C19  C20  109.52  3.000
 8X2  C18  C19  C20  107.19  3.000
 8X2  H17  C20  H16  107.38  3.000
 8X2  H17  C20  C19  110.12  3.000
 8X2  H16  C20  C19  109.07  3.000
 8X2  H17  C20  N6   107.90  3.000
 8X2  H16  C20  N6   110.49  3.000
 8X2  C19  C20  N6   111.78  3.000
 8X2  C17  C21  O    123.29  3.000
 8X2  C17  C21  N6   113.73  3.000
 8X2  O    C21  N6   122.93  3.000
 8X2  C18  C17  C21  121.45  3.000
 8X2  C18  C17  C16  107.68  3.000
 8X2  C21  C17  C16  130.75  3.000
 8X2  N5   C18  C17  107.95  3.000
 8X2  N5   C18  C19  128.64  3.000
 8X2  C17  C18  C19  123.34  3.000
 8X2  H18  N5   C18  124.25  3.000
 8X2  H18  N5   C15  125.77  3.000
 8X2  C18  N5   C15  109.98  3.000
 8X2  C12  N3   C11  115.73  3.000
 8X2  C14  N4   C11  117.78  3.000
 8X2  H19  N2   C11  113.34  3.000
 8X2  H19  N2   C8   115.45  3.000
 8X2  C11  N2   C8   130.92  3.000
 8X2  H20  C6   C5   121.18  3.000
 8X2  H20  C6   C7   117.55  3.000
 8X2  C5   C6   C7   121.27  3.000
 8X2  N1   C5   C6   122.84  3.000
 8X2  N1   C5   C10  120.62  3.000
 8X2  C6   C5   C10  116.51  3.000
 8X2  C5   N1   C3   117.16  3.000
 8X2  C3   N1   C2   111.74  3.000
 8X2  C5   N1   C2   117.77  3.000
 8X2  H22  C4   H21  107.20  3.000
 8X2  H22  C4   N    109.22  3.000
 8X2  H21  C4   N    111.68  3.000
 8X2  H22  C4   C3   108.71  3.000
 8X2  H21  C4   C3   109.14  3.000
 8X2  N    C4   C3   110.78  3.000
 8X2  C    N    C4   111.68  3.000
 8X2  C    N    C1   111.60  3.000
 8X2  C4   N    C1   109.74  3.000
 8X2  H26  C    H25  107.77  3.000
 8X2  H26  C    H24  107.76  3.000
 8X2  H25  C    H24  107.76  3.000
 8X2  H26  C    N    110.11  3.000
 8X2  H25  C    N    110.09  3.000
 8X2  H24  C    N    113.16  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
 8X2  CONST_01  C10  C9   C8   C7      0.00   0.0  0
 8X2  CONST_02  C10  C5   C6   C7      0.00   0.0  0
 8X2  CONST_03  C5   C10  C9   C8      0.00   0.0  0
 8X2  CONST_04  C5   C6   C7   C8      0.00   0.0  0
 8X2  CONST_05  C6   C7   C8   C9      0.00   0.0  0
 8X2  CONST_06  C6   C5   C10  C9      0.00   0.0  0
 8X2  CONST_07  C13  C12  N3   C11     0.00   0.0  0
 8X2  CONST_08  C13  C14  N4   C11     0.00   0.0  0
 8X2  CONST_09  C15  C14  N4   C11   180.00   0.0  0
 8X2  CONST_10  C15  C14  C13  C12   180.00   0.0  0
 8X2  CONST_11  N4   C14  C13  C12     0.00   0.0  0
 8X2  CONST_12  N4   C11  N3   C12     0.00   0.0  0
 8X2  CONST_13  C16  C15  C14  C13   180.00   0.0  0
 8X2  CONST_14  N5   C15  C14  C13     0.00   0.0  0
 8X2  CONST_15  N3   C12  C13  C14     0.00   0.0  0
 8X2  CONST_16  C17  C16  C15  C14   180.00   0.0  0
 8X2  CONST_17  C18  N5   C15  C14   180.00   0.0  0
 8X2  CONST_18  N3   C11  N4   C14     0.00   0.0  0
 8X2  CONST_19  C18  C17  C16  C15     0.00   0.0  0
 8X2  CONST_20  C17  C18  N5   C15     0.00   0.0  0
 8X2  CONST_21  N5   C18  C17  C16     0.00   0.0  0
 8X2  CONST_22  N4   C14  C15  C16     0.00   0.0  0
 8X2  CONST_23  C18  N5   C15  C16     0.00   0.0  0
 8X2  CONST_24  N5   C15  C16  C17     0.00   0.0  0
 8X2  CONST_25  N4   C14  C15  N5    180.00   0.0  0
 8X2  CONST_26  N1   C5   C6   C7    180.00   0.0  0
 8X2  CONST_27  N1   C5   C10  C9    180.00   0.0  0
 8X2  CONST_29  N2   C8   C9   C10   180.00   0.0  0
 8X2  CONST_30  N2   C11  N3   C12   180.00   0.0  0
 8X2  CONST_31  N2   C11  N4   C14   180.00   0.0  0
 8X2  CONST_32  C6   C7   C8   N2    180.00   0.0  0
 8X2  CONST_33  O    C21  N6   C20   180.00   0.0  0
 8X2  CONST_34  H9   C9   C8   C7    180.00   0.0  0
 8X2  CONST_35  H10  C10  C9   C8    180.00   0.0  0
 8X2  CONST_36  H20  C6   C7   C8    180.00   0.0  0
 8X2  CONST_37  H8   C7   C8   C9    180.00   0.0  0
 8X2  CONST_38  H11  C12  N3   C11   180.00   0.0  0
 8X2  CONST_39  H13  C16  C15  C14     0.00   0.0  0
 8X2  CONST_40  H18  N5   C15  C14     0.00   0.0  0
 8X2  CONST_41  H12  C13  C14  C15     0.00   0.0  0
 8X2  CONST_42  H7   N6   C21  C17   180.00   0.0  0
 8X2  Var_01    C5   N1   C2   C1    165.60  30.0  1
 8X2  Var_02    C3   C4   N    C1     58.44  30.0  1
 8X2  Var_03    C10  C5   N1   C2   -174.17  30.0  2
 8X2  Var_04    C4   C3   N1   C2     54.90  30.0  1
 8X2  Var_05    C4   N    C1   C2    -58.39  30.0  1
 8X2  Var_06    C16  C17  C21  N6   -176.52  30.0  1
 8X2  Var_07    C18  C19  C20  N6     46.72  30.0  1
 8X2  Var_08    C21  N6   C20  C19   -46.61  30.0  1
 8X2  Var_09    C17  C18  C19  C20   -26.99  30.0  1
 8X2  Var_10    N    C1   C2   N1     56.42  30.0  1
 8X2  Var_11    N    C4   C3   N1    -56.79  30.0  1
 8X2  Var_12    C11  N2   C8   C7   -160.83  30.0  3
 8X2  Var_13    N3   C11  N2   C8     -1.95  30.0  1
 8X2  Var_14    H24  C    N    C1     61.45  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
 8X2  plan-1  C7   0.020
 8X2  plan-1  C8   0.020
 8X2  plan-1  C9   0.020
 8X2  plan-1  C10  0.020
 8X2  plan-1  N2   0.020
 8X2  plan-1  C6   0.020
 8X2  plan-1  C5   0.020
 8X2  plan-1  N1   0.020
 8X2  plan-1  H8   0.020
 8X2  plan-1  H9   0.020
 8X2  plan-1  H10  0.020
 8X2  plan-1  H20  0.020
 8X2  plan-2  C14  0.020
 8X2  plan-2  C15  0.020
 8X2  plan-2  C16  0.020
 8X2  plan-2  C19  0.020
 8X2  plan-2  C21  0.020
 8X2  plan-2  C17  0.020
 8X2  plan-2  C18  0.020
 8X2  plan-2  N5   0.020
 8X2  plan-2  H13  0.020
 8X2  plan-2  H18  0.020
 8X2  plan-3  C11  0.020
 8X2  plan-3  C12  0.020
 8X2  plan-3  C13  0.020
 8X2  plan-3  C14  0.020
 8X2  plan-3  C15  0.020
 8X2  plan-3  N3   0.020
 8X2  plan-3  N4   0.020
 8X2  plan-3  N2   0.020
 8X2  plan-3  H11  0.020
 8X2  plan-3  H12  0.020
 8X2  plan-4  N6   0.020
 8X2  plan-4  C20  0.020
 8X2  plan-4  C21  0.020
 8X2  plan-4  O    0.020
 8X2  plan-4  C17  0.020
 8X2  plan-4  H7   0.020

