# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 13:55:51 2021
#   Inital geometry file: a 117 line input string
#   Ligand name: ~{N}-[1-[3-cyano-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]indol-6-yl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1ccc2ccn(c3cc(NC4CC4)n5ncc(C#N)c5n3)c2c1
#
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
 QB8  QB8  ~{N}-[1-[3-cyano-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]indol-6-yl]ethanamide  ligand  45  28  .  2022-07-22  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_QB8
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
 QB8  N1   N  N     0  -0.511  -4.7632  -44.3548   3.3339
 QB8  C2   C  CR56  0   0.687  -5.3490  -43.2451   3.7534
 QB8  N3   N  N     0  -0.299  -6.5968  -41.3532   3.5626
 QB8  C4   C  CR16  0  -0.547  -5.6026  -43.8366   1.1418
 QB8  C5   C  CR6   0   0.734  -6.2197  -42.6851   1.6039
 QB8  C6   C  CR15  0   0.038  -6.2042  -41.4776   4.8065
 QB8  O    O  O     0  -0.484  -0.8486  -46.8615   7.3343
 QB8  C16  C  C     0   0.475  -1.5790  -47.0023   6.3654
 QB8  C17  C  CH3   0  -0.803  -3.0793  -47.0407   6.5018
 QB8  C15  C  CR6   0   0.314  -1.7324  -47.2883   3.8954
 QB8  C18  C  CR16  0  -0.302  -1.4039  -48.3809   3.0793
 QB8  C19  C  CR16  0  -0.336  -2.0157  -48.5524   1.8554
 QB8  C12  C  CR56  0   0.031  -2.9872  -47.6387   1.4484
 QB8  C11  C  CR15  0  -0.388  -3.7881  -47.5329   0.2659
 QB8  C10  C  CR15  0  -0.012  -4.5465  -46.4239   0.3982
 QB8  C14  C  CR16  0  -0.306  -2.6724  -46.3502   3.4979
 QB8  C13  C  CR56  0   0.357  -3.3158  -46.5512   2.2800
 QB8  N5   N  NR5   0  -0.667  -4.2816  -45.8016   1.6131
 QB8  C3   C  CR6   0   0.575  -4.8943  -44.6369   2.0521
 QB8  N4   N  NH1   0  -0.668  -6.9170  -41.8173   0.8792
 QB8  C7   C  CH1   0  -0.113  -7.1895  -42.0197  -0.5065
 QB8  C9   C  CH2   0  -0.506  -7.1506  -40.8267  -1.4004
 QB8  C8   C  CH2   0  -0.488  -6.0717  -41.8586  -1.4930
 QB8  N2   N  N     0  -0.463  -6.0752  -42.4252   2.9343
 QB8  C1   C  CR5   0  -0.322  -5.4203  -42.6318   5.0088
 QB8  C    C  CSP   0   0.001  -4.8200  -43.0934   6.1896
 QB8  N    N  NS    0  -0.269  -4.3205  -43.4785   7.1572
 QB8  H1   H  HCR6  0   0.315  -5.6589  -44.0650   0.0910
 QB8  H2   H  HCR5  0   0.299  -6.4855  -40.7436   5.5458
 QB8  H3   H  HCH3  0   0.272  -3.3318  -47.3030   7.5264
 QB8  H4   H  HCH3  0   0.271  -3.5101  -46.0596   6.2972
 QB8  H5   H  HCH3  0   0.263  -3.5491  -47.7510   5.8239
 QB8  H6   H  HNH1  0   0.399  -0.0434  -47.2015   5.0894
 QB8  H7   H  HCR6  0   0.266  -0.6640  -49.0933   3.4212
 QB8  H8   H  HCR6  0   0.259  -1.7491  -49.3894   1.2232
 QB8  H9   H  HCR5  0   0.263  -3.7983  -48.2087  -0.5741
 QB8  H10  H  HCR5  0   0.304  -5.2884  -46.0335  -0.2763
 QB8  H11  H  HCR6  0   0.290  -2.8909  -45.4946   4.1143
 QB8  H12  H  HNH1  0   0.423  -7.3621  -41.0503   1.3627
 QB8  H13  H  HCH1  0   0.288  -7.9355  -42.7810  -0.7140
 QB8  H14  H  HCH2  0   0.267  -6.8958  -39.8745  -0.9526
 QB8  H15  H  HCH2  0   0.269  -7.8909  -40.7720  -2.1867
 QB8  H16  H  HCH2  0   0.268  -6.0572  -42.5264  -2.3440
 QB8  H17  H  HCH2  0   0.268  -5.0960  -41.5984  -1.1029
 QB8  N6   N  NH1   0  -0.709  -1.0516  -47.1346   5.1210

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
 QB8  C8   C9   single    1.496  0.020  1.496
 QB8  C8   C7   single    1.499  0.020  1.499
 QB8  C9   C7   single    1.491  0.020  1.491
 QB8  C7   N4   single    1.427  0.020  1.427
 QB8  C11  C10  aromatic  1.350  0.020  1.350
 QB8  C11  C12  aromatic  1.432  0.020  1.432
 QB8  C10  N5   aromatic  1.390  0.020  1.390
 QB8  N4   C5   single    1.328  0.020  1.328
 QB8  C4   C5   aromatic  1.386  0.020  1.386
 QB8  C4   C3   aromatic  1.404  0.020  1.404
 QB8  C12  C19  aromatic  1.394  0.020  1.394
 QB8  C12  C13  aromatic  1.408  0.020  1.408
 QB8  N5   C3   single    1.387  0.020  1.387
 QB8  N5   C13  aromatic  1.393  0.020  1.393
 QB8  C5   N2   aromatic  1.363  0.020  1.363
 QB8  C19  C18  aromatic  1.379  0.020  1.379
 QB8  C3   N1   aromatic  1.319  0.020  1.319
 QB8  C13  C14  aromatic  1.392  0.020  1.392
 QB8  N2   N3   aromatic  1.348  0.020  1.348
 QB8  N2   C2   aromatic  1.368  0.020  1.368
 QB8  C18  C15  aromatic  1.403  0.020  1.403
 QB8  N1   C2   aromatic  1.323  0.020  1.323
 QB8  C14  C15  aromatic  1.386  0.020  1.386
 QB8  N3   C6   aromatic  1.310  0.020  1.310
 QB8  C2   C1   aromatic  1.399  0.020  1.399
 QB8  C15  N6   single    1.410  0.020  1.410
 QB8  C6   C1   aromatic  1.410  0.020  1.410
 QB8  C1   C    single    1.403  0.020  1.403
 QB8  N6   C16  single    1.358  0.020  1.358
 QB8  C    N    triple    1.155  0.020  1.155
 QB8  C16  C17  single    1.507  0.020  1.507
 QB8  C16  O    double    1.222  0.020  1.222
 QB8  C4   H1   single    0.930  0.020  1.080
 QB8  C6   H2   single    0.930  0.020  1.080
 QB8  C17  H3   single    0.970  0.020  1.090
 QB8  C17  H4   single    0.970  0.020  1.090
 QB8  C17  H5   single    0.970  0.020  1.090
 QB8  N6   H6   single    0.860  0.020  1.020
 QB8  C18  H7   single    0.930  0.020  1.080
 QB8  C19  H8   single    0.930  0.020  1.080
 QB8  C11  H9   single    0.930  0.020  1.080
 QB8  C10  H10  single    0.930  0.020  1.080
 QB8  C14  H11  single    0.930  0.020  1.080
 QB8  N4   H12  single    0.860  0.020  1.020
 QB8  C7   H13  single    0.970  0.020  1.090
 QB8  C9   H14  single    0.970  0.020  1.090
 QB8  C9   H15  single    0.970  0.020  1.090
 QB8  C8   H16  single    0.970  0.020  1.090
 QB8  C8   H17  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
 QB8  C3   N1   C2   116.33  3.000
 QB8  C1   C2   N2   104.34  3.000
 QB8  C1   C2   N1   132.44  3.000
 QB8  N2   C2   N1   123.23  3.000
 QB8  N2   N3   C6   104.55  3.000
 QB8  H1   C4   C3   122.56  3.000
 QB8  H1   C4   C5   118.58  3.000
 QB8  C3   C4   C5   118.83  3.000
 QB8  N2   C5   N4   117.62  3.000
 QB8  N2   C5   C4   115.89  3.000
 QB8  N4   C5   C4   126.49  3.000
 QB8  H2   C6   C1   127.12  3.000
 QB8  H2   C6   N3   120.51  3.000
 QB8  C1   C6   N3   112.37  3.000
 QB8  N6   C16  C17  117.85  3.000
 QB8  C17  C16  O    121.76  3.000
 QB8  N6   C16  O    120.39  3.000
 QB8  H5   C17  H4   107.44  3.000
 QB8  H5   C17  H3   109.22  3.000
 QB8  H4   C17  H3   107.58  3.000
 QB8  H5   C17  C16  112.95  3.000
 QB8  H4   C17  C16  110.69  3.000
 QB8  H3   C17  C16  108.82  3.000
 QB8  C14  C15  C18  121.27  3.000
 QB8  C14  C15  N6   120.18  3.000
 QB8  C18  C15  N6   118.51  3.000
 QB8  H7   C18  C19  120.11  3.000
 QB8  H7   C18  C15  119.27  3.000
 QB8  C19  C18  C15  120.62  3.000
 QB8  H8   C19  C12  120.52  3.000
 QB8  H8   C19  C18  120.36  3.000
 QB8  C12  C19  C18  119.12  3.000
 QB8  C13  C12  C11  107.47  3.000
 QB8  C13  C12  C19  119.76  3.000
 QB8  C11  C12  C19  132.77  3.000
 QB8  H9   C11  C10  125.88  3.000
 QB8  H9   C11  C12  127.03  3.000
 QB8  C10  C11  C12  107.09  3.000
 QB8  H10  C10  N5   121.11  3.000
 QB8  H10  C10  C11  128.60  3.000
 QB8  N5   C10  C11  110.26  3.000
 QB8  H11  C14  C13  121.45  3.000
 QB8  H11  C14  C15  120.74  3.000
 QB8  C13  C14  C15  117.81  3.000
 QB8  N5   C13  C14  131.44  3.000
 QB8  C14  C13  C12  121.36  3.000
 QB8  N5   C13  C12  107.14  3.000
 QB8  C3   N5   C13  127.35  3.000
 QB8  C13  N5   C10  108.04  3.000
 QB8  C3   N5   C10  124.61  3.000
 QB8  N5   C3   C4   119.75  3.000
 QB8  N5   C3   N1   116.31  3.000
 QB8  C4   C3   N1   123.94  3.000
 QB8  H12  N4   C7   119.24  3.000
 QB8  H12  N4   C5   117.79  3.000
 QB8  C7   N4   C5   122.51  3.000
 QB8  H13  C7   C8   117.50  3.000
 QB8  H13  C7   C9   117.66  3.000
 QB8  C8   C7   C9    60.02  3.000
 QB8  H13  C7   N4   114.60  3.000
 QB8  C9   C7   N4   117.63  3.000
 QB8  C8   C7   N4   118.78  3.000
 QB8  H15  C9   H14  114.67  3.000
 QB8  H15  C9   C8   118.93  3.000
 QB8  H14  C9   C8   117.56  3.000
 QB8  H15  C9   C7   117.29  3.000
 QB8  H14  C9   C7   117.50  3.000
 QB8  C8   C9   C7    60.26  3.000
 QB8  H17  C8   H16  114.82  3.000
 QB8  H17  C8   C9   117.51  3.000
 QB8  H16  C8   C9   118.96  3.000
 QB8  H17  C8   C7   117.43  3.000
 QB8  H16  C8   C7   117.47  3.000
 QB8  C9   C8   C7    59.72  3.000
 QB8  C5   N2   N3   124.45  3.000
 QB8  N3   N2   C2   113.77  3.000
 QB8  C5   N2   C2   121.77  3.000
 QB8  C    C1   C6   128.91  3.000
 QB8  C    C1   C2   126.11  3.000
 QB8  C6   C1   C2   104.98  3.000
 QB8  N    C    C1   180.00  3.000
 QB8  H6   N6   C15  116.56  3.000
 QB8  H6   N6   C16  114.99  3.000
 QB8  C15  N6   C16  128.27  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
 QB8  CONST_01  C5   C4   C3   N1      0.00   0.0  0
 QB8  CONST_04  C5   N2   C2   N1      0.00   0.0  0
 QB8  CONST_05  N3   N2   C2   N1    180.00   0.0  0
 QB8  CONST_06  C6   C1   C2   N1    180.00   0.0  0
 QB8  CONST_07  C4   C5   N2   C2      0.00   0.0  0
 QB8  CONST_08  C6   N3   N2   C2      0.00   0.0  0
 QB8  CONST_09  C4   C3   N1   C2      0.00   0.0  0
 QB8  CONST_10  N5   C3   N1   C2    180.00   0.0  0
 QB8  CONST_11  N3   C6   C1   C2      0.00   0.0  0
 QB8  CONST_12  C4   C5   N2   N3    180.00   0.0  0
 QB8  CONST_13  C1   C2   N2   N3      0.00   0.0  0
 QB8  CONST_16  N5   C3   C4   C5    180.00   0.0  0
 QB8  CONST_17  C6   N3   N2   C5    180.00   0.0  0
 QB8  CONST_18  C1   C2   N2   C5    180.00   0.0  0
 QB8  CONST_19  N2   C2   C1   C6      0.00   0.0  0
 QB8  CONST_20  C12  C19  C18  C15     0.00   0.0  0
 QB8  CONST_21  C12  C13  C14  C15     0.00   0.0  0
 QB8  CONST_22  N5   C13  C14  C15   180.00   0.0  0
 QB8  CONST_23  C11  C12  C19  C18   180.00   0.0  0
 QB8  CONST_24  C13  C12  C19  C18     0.00   0.0  0
 QB8  CONST_25  C13  C14  C15  C18     0.00   0.0  0
 QB8  CONST_26  C10  C11  C12  C19   180.00   0.0  0
 QB8  CONST_27  N5   C13  C12  C19   180.00   0.0  0
 QB8  CONST_28  C14  C13  C12  C19     0.00   0.0  0
 QB8  CONST_29  C14  C15  C18  C19     0.00   0.0  0
 QB8  CONST_30  N5   C10  C11  C12     0.00   0.0  0
 QB8  CONST_31  C10  N5   C13  C12     0.00   0.0  0
 QB8  CONST_32  C3   N5   C13  C12   180.00   0.0  0
 QB8  CONST_33  C3   N5   C10  C11   180.00   0.0  0
 QB8  CONST_34  C13  N5   C10  C11     0.00   0.0  0
 QB8  CONST_35  N5   C13  C12  C11     0.00   0.0  0
 QB8  CONST_36  C14  C13  C12  C11   180.00   0.0  0
 QB8  CONST_37  C13  C12  C11  C10     0.00   0.0  0
 QB8  CONST_38  C14  C13  N5   C10   180.00   0.0  0
 QB8  CONST_39  C3   N5   C13  C14     0.00   0.0  0
 QB8  CONST_40  N2   C5   C4   C3      0.00   0.0  0
 QB8  CONST_41  N2   C2   N1   C3      0.00   0.0  0
 QB8  CONST_42  C1   C2   N1   C3    180.00   0.0  0
 QB8  CONST_43  C1   C6   N3   N2      0.00   0.0  0
 QB8  CONST_44  C    C1   C2   N1      0.00   0.0  0
 QB8  CONST_45  N4   C5   N2   C2    180.00   0.0  0
 QB8  CONST_46  N4   C5   N2   N3      0.00   0.0  0
 QB8  CONST_47  C    C1   C6   N3    180.00   0.0  0
 QB8  CONST_48  C19  C18  C15  N6    180.00   0.0  0
 QB8  CONST_49  C13  C14  C15  N6    180.00   0.0  0
 QB8  CONST_50  N4   C5   C4   C3    180.00   0.0  0
 QB8  CONST_51  C    C1   C2   N2    180.00   0.0  0
 QB8  CONST_52  C7   N4   C5   C4      0.00   0.0  0
 QB8  CONST_53  N2   C5   N4   C7    180.00   0.0  0
 QB8  CONST_54  H1   C4   C3   N1    180.00   0.0  0
 QB8  CONST_55  H2   C6   C1   C2    180.00   0.0  0
 QB8  CONST_56  H8   C19  C18  C15   180.00   0.0  0
 QB8  CONST_57  H11  C14  C15  C18   180.00   0.0  0
 QB8  CONST_58  H9   C11  C12  C19     0.00   0.0  0
 QB8  CONST_59  H10  C10  C11  C12   180.00   0.0  0
 QB8  CONST_60  H7   C18  C19  C12   180.00   0.0  0
 QB8  CONST_63  H12  N4   C5   C4    180.00   0.0  0
 QB8  CONST_65  C15  N6   C16  O     180.00   0.0  0
 QB8  CONST_66  C15  N6   C16  C17     0.00   0.0  0
 QB8  Var_01    C8   C7   N4   C5    -72.61  30.0  1
 QB8  Var_02    C9   C8   C7   N4   -107.10  30.0  1
 QB8  Var_03    H14  C9   C8   C7    107.56  30.0  1
 QB8  Var_04    H3   C17  C16  O     -21.14  30.0  3

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
 QB8  chir_01  C7  C8  C9  N4  both

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
 QB8  plan-1  C15  0.020
 QB8  plan-1  C18  0.020
 QB8  plan-1  C19  0.020
 QB8  plan-1  C12  0.020
 QB8  plan-1  C11  0.020
 QB8  plan-1  C10  0.020
 QB8  plan-1  C14  0.020
 QB8  plan-1  C13  0.020
 QB8  plan-1  N5   0.020
 QB8  plan-1  C3   0.020
 QB8  plan-1  H7   0.020
 QB8  plan-1  H8   0.020
 QB8  plan-1  H9   0.020
 QB8  plan-1  H10  0.020
 QB8  plan-1  H11  0.020
 QB8  plan-1  N6   0.020
 QB8  plan-2  N1   0.020
 QB8  plan-2  C2   0.020
 QB8  plan-2  N3   0.020
 QB8  plan-2  C4   0.020
 QB8  plan-2  C5   0.020
 QB8  plan-2  C6   0.020
 QB8  plan-2  N5   0.020
 QB8  plan-2  C3   0.020
 QB8  plan-2  N4   0.020
 QB8  plan-2  N2   0.020
 QB8  plan-2  C1   0.020
 QB8  plan-2  C    0.020
 QB8  plan-2  N    0.020
 QB8  plan-2  H1   0.020
 QB8  plan-2  H2   0.020
 QB8  plan-3  C5   0.020
 QB8  plan-3  N4   0.020
 QB8  plan-3  C7   0.020
 QB8  plan-3  H12  0.020
 QB8  plan-4  O    0.020
 QB8  plan-4  C16  0.020
 QB8  plan-4  C17  0.020
 QB8  plan-4  C15  0.020
 QB8  plan-4  H6   0.020
 QB8  plan-4  N6   0.020

