# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 02:58:07 2022
#   Inital geometry file: a 130 line input string
#   Ligand name: 7-[[4-[4-[(dimethylamino)methyl]pyrazol-1-yl]pyrimidin-2-yl]amino]-~{N},3-dimethyl-imidazo[1,5-a]pyridine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1nc(C)n2ccc(Nc3nccc(n3)n4cc(CN(C)C)cn4)cc12
#
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
 QFK  QFK  7-[[4-[4-[(dimethylamino)methyl]pyrazol-1-yl]pyrimidin-2-yl]amino]-~{N},3-dimethyl-imidazo[1,5-a]pyridine-1-carboxamide  ligand  53  30  .  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_QFK
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
 QFK  C1   C  CR5   0   0.421  -2.8157  -2.0488  13.7249
 QFK  C2   C  CR5   0  -0.086  -1.6725  -0.2512  13.3900
 QFK  C3   C  CR56  0   0.460  -0.8342  -1.0919  14.1070
 QFK  N6   N  N     0  -0.273   5.1547   2.5366  13.9481
 QFK  C7   C  CR16  0  -0.484   0.4834  -1.0283  14.6046
 QFK  C8   C  CR6   0   0.618   3.3443  -1.3521  15.6855
 QFK  C9   C  CR16  0  -0.015   5.4823  -0.9406  16.2589
 QFK  C10  C  CR16  0  -0.416   5.4995   0.2225  15.5075
 QFK  C11  C  CR6   0   0.607   4.3120   0.5072  14.8490
 QFK  C12  C  CR15  0   0.034   3.0871   1.9700  13.2926
 QFK  C13  C  CR5   0  -0.171   3.3887   3.1480  12.6743
 QFK  C14  C  CR15  0  -0.031   4.6969   3.4515  13.1303
 QFK  C15  C  CH2   0  -0.363   2.5289   3.9361  11.7451
 QFK  C16  C  CH3   0  -0.522   1.5360   6.0473  11.2660
 QFK  C19  C  CH3   0  -0.514  -2.1832   3.0126  11.6438
 QFK  O    O  O     0  -0.507  -0.2813   1.6344  13.1283
 QFK  C18  C  C     0   0.481  -1.3654   1.0917  12.9055
 QFK  N8   N  NH1   0  -0.638  -2.3384   1.6933  12.2027
 QFK  N    N  N     0  -0.454  -2.8709  -0.8704  13.1765
 QFK  C6   C  CR6   0   0.479   1.0011  -2.1067  15.2722
 QFK  C5   C  CR16  0  -0.453   0.1753  -3.2655  15.4680
 QFK  C4   C  CR16  0   0.038  -1.0839  -3.3092  14.9907
 QFK  N1   N  N     0  -0.583  -1.5848  -2.2349  14.3101
 QFK  C    C  CH3   0  -0.761  -3.8787  -3.0809  13.7485
 QFK  N2   N  NH1   0  -0.771   2.2748  -2.1906  15.8032
 QFK  N4   N  N     0  -0.513   3.2434  -0.2648  14.9365
 QFK  N3   N  N     0  -0.463   4.4296  -1.7350  16.3609
 QFK  N5   N  NR5   0  -0.399   4.1699   1.6326  14.0464
 QFK  N7   N  NT    0  -0.399   2.2036   5.2503  12.2728
 QFK  C17  C  CH3   0  -0.522   1.4053   5.1698  13.4773
 QFK  H1   H  HCR6  0   0.313   1.0500  -0.1310  14.4449
 QFK  H2   H  HCR6  0   0.283   6.3689  -1.2438  16.8040
 QFK  H3   H  HCR6  0   0.290   6.3743   0.8486  15.4419
 QFK  H4   H  HCR5  0   0.318   2.1982   1.3648  13.2508
 QFK  H5   H  HCR5  0   0.269   5.3037   4.3090  12.8790
 QFK  H6   H  HCH2  0   0.249   3.0579   4.0781  10.7983
 QFK  H7   H  HCH2  0   0.210   1.6230   3.3525  11.5083
 QFK  H8   H  HCH3  0   0.235   1.3451   7.0503  11.6496
 QFK  H9   H  HCH3  0   0.233   2.1665   6.1409  10.3807
 QFK  H10  H  HCH3  0   0.192   0.5705   5.6218  10.9483
 QFK  H11  H  HCH3  0   0.248  -3.0970   3.2731  11.1170
 QFK  H12  H  HCH3  0   0.235  -2.0081   3.7644  12.4154
 QFK  H13  H  HCH3  0   0.233  -1.3547   3.0603  10.9350
 QFK  H14  H  HNH1  0   0.399  -3.2010   1.1948  12.0566
 QFK  H15  H  HCR6  0   0.296   0.5581  -4.1260  16.0002
 QFK  H16  H  HCR6  0   0.321  -1.7331  -4.1633  15.1146
 QFK  H17  H  HCH3  0   0.274  -4.7597  -2.7015  13.2370
 QFK  H18  H  HCH3  0   0.261  -3.5634  -3.9983  13.2474
 QFK  H19  H  HCH3  0   0.261  -4.1648  -3.3451  14.7685
 QFK  H20  H  HNH1  0   0.418   2.4750  -3.0118  16.3550
 QFK  H22  H  HCH3  0   0.238   1.9370   4.6255  14.2576
 QFK  H23  H  HCH3  0   0.233   1.2034   6.1736  13.8528
 QFK  H24  H  HCH3  0   0.191   0.4365   4.6684  13.3203

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
 QFK  C19  N8   single    1.441  0.020  1.441
 QFK  N8   C18  single    1.343  0.020  1.343
 QFK  C16  N7   single    1.447  0.020  1.447
 QFK  C15  C13  single    1.491  0.020  1.491
 QFK  C15  N7   single    1.453  0.020  1.453
 QFK  C18  O    double    1.233  0.020  1.233
 QFK  C18  C2   single    1.460  0.020  1.460
 QFK  C13  C14  aromatic  1.418  0.020  1.418
 QFK  C13  C12  aromatic  1.364  0.020  1.364
 QFK  N7   C17  single    1.447  0.020  1.447
 QFK  C14  N6   aromatic  1.310  0.020  1.310
 QFK  N    C2   aromatic  1.366  0.020  1.366
 QFK  N    C1   aromatic  1.301  0.020  1.301
 QFK  C2   C3   aromatic  1.387  0.020  1.387
 QFK  C12  N5   aromatic  1.362  0.020  1.362
 QFK  N6   N5   aromatic  1.340  0.020  1.340
 QFK  C1   C    single    1.482  0.020  1.482
 QFK  C1   N1   aromatic  1.376  0.020  1.376
 QFK  N5   C11  single    1.390  0.020  1.390
 QFK  C3   N1   aromatic  1.382  0.020  1.382
 QFK  C3   C7   aromatic  1.410  0.020  1.410
 QFK  N1   C4   aromatic  1.367  0.020  1.367
 QFK  C7   C6   aromatic  1.370  0.020  1.370
 QFK  C11  N4   aromatic  1.321  0.020  1.321
 QFK  C11  C10  aromatic  1.387  0.020  1.387
 QFK  N4   C8   aromatic  1.324  0.020  1.324
 QFK  C4   C5   aromatic  1.347  0.020  1.347
 QFK  C6   C5   aromatic  1.436  0.020  1.436
 QFK  C6   N2   single    1.382  0.020  1.382
 QFK  C10  C9   aromatic  1.385  0.020  1.385
 QFK  C8   N2   single    1.364  0.020  1.364
 QFK  C8   N3   aromatic  1.334  0.020  1.334
 QFK  C9   N3   aromatic  1.323  0.020  1.323
 QFK  C7   H1   single    0.930  0.020  1.080
 QFK  C9   H2   single    0.930  0.020  1.080
 QFK  C10  H3   single    0.930  0.020  1.080
 QFK  C12  H4   single    0.930  0.020  1.080
 QFK  C14  H5   single    0.930  0.020  1.080
 QFK  C15  H6   single    0.970  0.020  1.090
 QFK  C15  H7   single    0.970  0.020  1.090
 QFK  C16  H8   single    0.970  0.020  1.090
 QFK  C16  H9   single    0.970  0.020  1.090
 QFK  C16  H10  single    0.970  0.020  1.090
 QFK  C19  H11  single    0.970  0.020  1.090
 QFK  C19  H12  single    0.970  0.020  1.090
 QFK  C19  H13  single    0.970  0.020  1.090
 QFK  N8   H14  single    0.860  0.020  1.020
 QFK  C5   H15  single    0.930  0.020  1.080
 QFK  C4   H16  single    0.930  0.020  1.080
 QFK  C    H17  single    0.970  0.020  1.090
 QFK  C    H18  single    0.970  0.020  1.090
 QFK  C    H19  single    0.970  0.020  1.090
 QFK  N2   H20  single    0.860  0.020  1.020
 QFK  C17  H22  single    0.970  0.020  1.090
 QFK  C17  H23  single    0.970  0.020  1.090
 QFK  C17  H24  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
 QFK  C    C1   N1   122.75  3.000
 QFK  N1   C1   N    109.87  3.000
 QFK  C    C1   N    127.38  3.000
 QFK  N    C2   C18  123.35  3.000
 QFK  N    C2   C3   109.65  3.000
 QFK  C18  C2   C3   127.00  3.000
 QFK  N1   C3   C7   119.53  3.000
 QFK  C7   C3   C2   136.05  3.000
 QFK  N1   C3   C2   104.42  3.000
 QFK  N5   N6   C14  105.07  3.000
 QFK  H1   C7   C6   122.09  3.000
 QFK  H1   C7   C3   118.60  3.000
 QFK  C6   C7   C3   119.32  3.000
 QFK  N3   C8   N4   125.73  3.000
 QFK  N3   C8   N2   114.68  3.000
 QFK  N4   C8   N2   119.59  3.000
 QFK  H2   C9   N3   116.36  3.000
 QFK  H2   C9   C10  119.85  3.000
 QFK  N3   C9   C10  123.79  3.000
 QFK  H3   C10  C11  123.14  3.000
 QFK  H3   C10  C9   122.07  3.000
 QFK  C11  C10  C9   114.79  3.000
 QFK  N5   C11  N4   115.39  3.000
 QFK  N4   C11  C10  122.75  3.000
 QFK  N5   C11  C10  121.86  3.000
 QFK  H4   C12  N5   122.61  3.000
 QFK  H4   C12  C13  130.59  3.000
 QFK  N5   C12  C13  106.80  3.000
 QFK  C15  C13  C14  128.25  3.000
 QFK  C14  C13  C12  104.07  3.000
 QFK  C15  C13  C12  127.68  3.000
 QFK  H5   C14  C13  127.83  3.000
 QFK  H5   C14  N6   120.22  3.000
 QFK  C13  C14  N6   111.94  3.000
 QFK  H7   C15  H6   106.25  3.000
 QFK  H7   C15  N7   111.88  3.000
 QFK  H6   C15  N7   107.77  3.000
 QFK  H7   C15  C13  109.13  3.000
 QFK  H6   C15  C13  109.21  3.000
 QFK  N7   C15  C13  112.38  3.000
 QFK  H10  C16  H9   107.80  3.000
 QFK  H10  C16  H8   107.65  3.000
 QFK  H9   C16  H8   107.92  3.000
 QFK  H10  C16  N7   113.09  3.000
 QFK  H9   C16  N7   110.19  3.000
 QFK  H8   C16  N7   110.02  3.000
 QFK  H13  C19  H12  107.89  3.000
 QFK  H13  C19  H11  108.24  3.000
 QFK  H12  C19  H11  108.21  3.000
 QFK  H13  C19  N8   111.94  3.000
 QFK  H12  C19  N8   111.94  3.000
 QFK  H11  C19  N8   108.48  3.000
 QFK  N8   C18  O    122.32  3.000
 QFK  O    C18  C2   122.00  3.000
 QFK  N8   C18  C2   115.67  3.000
 QFK  H14  N8   C18  118.36  3.000
 QFK  H14  N8   C19  119.29  3.000
 QFK  C18  N8   C19  122.35  3.000
 QFK  C2   N    C1   107.91  3.000
 QFK  N2   C6   C5   115.36  3.000
 QFK  N2   C6   C7   125.67  3.000
 QFK  C5   C6   C7   118.96  3.000
 QFK  H15  C5   C4   118.64  3.000
 QFK  H15  C5   C6   120.35  3.000
 QFK  C4   C5   C6   121.01  3.000
 QFK  H16  C4   N1   117.29  3.000
 QFK  H16  C4   C5   123.15  3.000
 QFK  N1   C4   C5   119.56  3.000
 QFK  C4   N1   C3   121.60  3.000
 QFK  C4   N1   C1   130.25  3.000
 QFK  C3   N1   C1   108.15  3.000
 QFK  H19  C    H18  107.53  3.000
 QFK  H19  C    H17  108.16  3.000
 QFK  H18  C    H17  108.14  3.000
 QFK  H19  C    C1   111.80  3.000
 QFK  H18  C    C1   111.76  3.000
 QFK  H17  C    C1   109.31  3.000
 QFK  H20  N2   C6   116.24  3.000
 QFK  H20  N2   C8   113.06  3.000
 QFK  C6   N2   C8   130.68  3.000
 QFK  C11  N4   C8   117.10  3.000
 QFK  C9   N3   C8   115.84  3.000
 QFK  C12  N5   C11  126.99  3.000
 QFK  C11  N5   N6   120.89  3.000
 QFK  C12  N5   N6   112.12  3.000
 QFK  C17  N7   C16  110.80  3.000
 QFK  C17  N7   C15  112.05  3.000
 QFK  C16  N7   C15  110.41  3.000
 QFK  H24  C17  H23  107.76  3.000
 QFK  H24  C17  H22  107.68  3.000
 QFK  H23  C17  H22  107.66  3.000
 QFK  H24  C17  N7   113.06  3.000
 QFK  H23  C17  N7   109.72  3.000
 QFK  H22  C17  N7   110.77  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
 QFK  CONST_01  C3   C2   N    C1      0.00   0.0  0
 QFK  CONST_02  C2   C3   N1   C1      0.00   0.0  0
 QFK  CONST_03  C7   C3   N1   C1    180.00   0.0  0
 QFK  CONST_04  C5   C4   N1   C1    180.00   0.0  0
 QFK  CONST_05  N1   C1   N    C2      0.00   0.0  0
 QFK  CONST_06  C4   N1   C3   C2    180.00   0.0  0
 QFK  CONST_07  C6   C7   C3   C2    180.00   0.0  0
 QFK  CONST_08  N    C1   N1   C3      0.00   0.0  0
 QFK  CONST_09  C5   C4   N1   C3      0.00   0.0  0
 QFK  CONST_10  C5   C6   C7   C3      0.00   0.0  0
 QFK  CONST_11  C12  C13  C14  N6      0.00   0.0  0
 QFK  CONST_12  C13  C12  N5   N6      0.00   0.0  0
 QFK  CONST_13  N4   C11  N5   N6    180.00   0.0  0
 QFK  CONST_14  C10  C11  N5   N6      0.00   0.0  0
 QFK  CONST_15  N    C2   C3   C7    180.00   0.0  0
 QFK  CONST_16  C4   N1   C3   C7      0.00   0.0  0
 QFK  CONST_17  C4   C5   C6   C7      0.00   0.0  0
 QFK  CONST_18  N5   C11  N4   C8    180.00   0.0  0
 QFK  CONST_19  C10  C11  N4   C8      0.00   0.0  0
 QFK  CONST_20  C10  C9   N3   C8      0.00   0.0  0
 QFK  CONST_21  N5   C11  C10  C9    180.00   0.0  0
 QFK  CONST_22  N4   C11  C10  C9      0.00   0.0  0
 QFK  CONST_23  N4   C8   N3   C9      0.00   0.0  0
 QFK  CONST_24  C12  N5   C11  C10   180.00   0.0  0
 QFK  CONST_25  C13  C12  N5   C11   180.00   0.0  0
 QFK  CONST_26  C14  N6   N5   C11   180.00   0.0  0
 QFK  CONST_27  N3   C8   N4   C11     0.00   0.0  0
 QFK  CONST_28  N3   C9   C10  C11     0.00   0.0  0
 QFK  CONST_29  C14  N6   N5   C12     0.00   0.0  0
 QFK  CONST_30  N4   C11  N5   C12     0.00   0.0  0
 QFK  CONST_31  N5   N6   C14  C13     0.00   0.0  0
 QFK  CONST_32  N5   C12  C13  C14     0.00   0.0  0
 QFK  CONST_33  N1   C3   C2   N       0.00   0.0  0
 QFK  CONST_34  C4   N1   C1   N     180.00   0.0  0
 QFK  CONST_35  N1   C3   C7   C6      0.00   0.0  0
 QFK  CONST_36  N1   C4   C5   C6      0.00   0.0  0
 QFK  CONST_37  C18  C2   N    C1    180.00   0.0  0
 QFK  CONST_38  C    C1   N    C2    180.00   0.0  0
 QFK  CONST_39  C    C1   N1   C3    180.00   0.0  0
 QFK  CONST_40  N2   C6   C7   C3    180.00   0.0  0
 QFK  CONST_41  C15  C13  C14  N6    180.00   0.0  0
 QFK  CONST_42  C18  C2   C3   C7      0.00   0.0  0
 QFK  CONST_43  N2   C8   N3   C9    180.00   0.0  0
 QFK  CONST_44  N2   C8   N4   C11   180.00   0.0  0
 QFK  CONST_45  N5   C12  C13  C15   180.00   0.0  0
 QFK  CONST_46  N1   C3   C2   C18   180.00   0.0  0
 QFK  CONST_47  C    C1   N1   C4      0.00   0.0  0
 QFK  CONST_48  N2   C6   C5   C4    180.00   0.0  0
 QFK  CONST_49  H16  C4   N1   C1      0.00   0.0  0
 QFK  CONST_50  H1   C7   C3   C2      0.00   0.0  0
 QFK  CONST_51  H4   C12  N5   N6    180.00   0.0  0
 QFK  CONST_52  H15  C5   C6   C7    180.00   0.0  0
 QFK  CONST_53  H2   C9   N3   C8    180.00   0.0  0
 QFK  CONST_54  H5   C14  C13  C12   180.00   0.0  0
 QFK  CONST_55  H3   C10  C11  N4    180.00   0.0  0
 QFK  CONST_56  C19  N8   C18  C2    180.00   0.0  0
 QFK  CONST_57  H14  N8   C18  C2      0.00   0.0  0
 QFK  CONST_58  O    C18  N8   C19     0.00   0.0  0
 QFK  Var_01    C8   N2   C6   C7     -8.17  30.0  2
 QFK  Var_02    N4   C8   N2   C6     -1.49  30.0  2
 QFK  Var_03    N8   C18  C2   C3    178.38  30.0  1
 QFK  Var_04    N7   C15  C13  C12   117.17  30.0  3
 QFK  Var_05    H17  C    C1   N      -0.95  30.0  2
 QFK  Var_06    C16  N7   C15  C13   171.77  30.0  3
 QFK  Var_07    H8   C16  N7   C15  -176.83  30.0  3
 QFK  Var_08    H22  C17  N7   C15    59.95  30.0  3
 QFK  Var_09    H11  C19  N8   C18   179.47  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
 QFK  plan-1  N6   0.020
 QFK  plan-1  C11  0.020
 QFK  plan-1  C12  0.020
 QFK  plan-1  C13  0.020
 QFK  plan-1  C14  0.020
 QFK  plan-1  C15  0.020
 QFK  plan-1  N5   0.020
 QFK  plan-1  H4   0.020
 QFK  plan-1  H5   0.020
 QFK  plan-2  C8   0.020
 QFK  plan-2  C9   0.020
 QFK  plan-2  C10  0.020
 QFK  plan-2  C11  0.020
 QFK  plan-2  N2   0.020
 QFK  plan-2  N4   0.020
 QFK  plan-2  N3   0.020
 QFK  plan-2  N5   0.020
 QFK  plan-2  H2   0.020
 QFK  plan-2  H3   0.020
 QFK  plan-3  C1   0.020
 QFK  plan-3  C2   0.020
 QFK  plan-3  C3   0.020
 QFK  plan-3  C7   0.020
 QFK  plan-3  C18  0.020
 QFK  plan-3  N    0.020
 QFK  plan-3  C6   0.020
 QFK  plan-3  C5   0.020
 QFK  plan-3  C4   0.020
 QFK  plan-3  N1   0.020
 QFK  plan-3  C    0.020
 QFK  plan-3  N2   0.020
 QFK  plan-3  H1   0.020
 QFK  plan-3  H15  0.020
 QFK  plan-3  H16  0.020
 QFK  plan-4  C2   0.020
 QFK  plan-4  C19  0.020
 QFK  plan-4  O    0.020
 QFK  plan-4  C18  0.020
 QFK  plan-4  N8   0.020
 QFK  plan-4  H14  0.020

