# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 17:45:15 2021
#   Inital geometry file: a 124 line input string
#   Ligand name: ~{N}-[5-[[3-cyano-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]amino]-2-methyl-phenyl]propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)Nc1cc(Nc2cc(NC3CC3)n4ncc(C#N)c4n2)ccc1C
#
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
 QBE  QBE  ~{N}-[5-[[3-cyano-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]amino]-2-methyl-phenyl]propanamide  ligand  49  28  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_QBE
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
 QBE  C11  C  CR56  0   0.694  -4.6181  -42.9974   3.6979
 QBE  C2   C  CR6   0   0.283  -1.5023  -47.4494   3.6523
 QBE  C3   C  C     0   0.496  -2.0453  -47.6636   6.0697
 QBE  C4   C  CH2   0  -0.571  -3.5078  -47.9122   5.7743
 QBE  C5   C  CH3   0  -0.662  -4.3936  -46.7405   6.1932
 QBE  C6   C  CR16  0  -0.329  -2.3156  -46.4095   3.2161
 QBE  C7   C  CR16  0  -0.299  -1.3080  -48.2529   1.4259
 QBE  C8   C  CR16  0  -0.350  -2.1463  -47.2488   0.9789
 QBE  N    N  NH1   0  -0.712  -1.1866  -47.5333   5.0265
 QBE  O    O  O     0  -0.488  -1.6377  -47.6098   7.2205
 QBE  N1   N  NH1   0  -0.799  -3.5140  -45.3389   1.3387
 QBE  C1   C  CR6   0   0.054  -0.9684  -48.3880   2.7693
 QBE  N6   N  NS    0  -0.268  -3.3373  -43.2025   7.0281
 QBE  C19  C  CSP   0  -0.007  -3.9289  -42.8515   6.1001
 QBE  C12  C  CR5   0  -0.333  -4.6520  -42.4257   4.9764
 QBE  C13  C  CR15  0   0.032  -5.5474  -41.3404   4.8685
 QBE  N3   N  N     0  -0.303  -6.0392  -41.2189   3.6617
 QBE  N4   N  N     0  -0.469  -5.4708  -42.2236   2.9620
 QBE  N2   N  N     0  -0.536  -3.9586  -44.0333   3.2036
 QBE  C14  C  CR6   0   0.719  -5.6988  -42.4646   1.6352
 QBE  N5   N  NH1   0  -0.674  -6.5575  -41.6594   1.0095
 QBE  C15  C  CH1   0  -0.109  -6.8140  -41.7542  -0.3891
 QBE  C17  C  CH2   0  -0.485  -7.6325  -42.9039  -0.8948
 QBE  C16  C  CH2   0  -0.506  -8.2155  -41.5270  -0.8476
 QBE  C18  C  CR16  0  -0.566  -5.0140  -43.5287   1.0918
 QBE  C10  C  CR6   0   0.582  -4.1572  -44.2944   1.9189
 QBE  C9   C  CR6   0   0.347  -2.6694  -46.3102   1.8723
 QBE  H1   H  HCH2  0   0.256  -3.6821  -48.1573   4.7277
 QBE  H2   H  HCH2  0   0.271  -3.7860  -48.7948   6.3552
 QBE  H3   H  HCH3  0   0.239  -5.4432  -47.0197   6.1091
 QBE  H4   H  HCH3  0   0.232  -4.2059  -46.4471   7.2253
 QBE  H5   H  HCH3  0   0.232  -4.2337  -45.8660   5.5621
 QBE  H6   H  HCR6  0   0.303  -2.6651  -45.6787   3.9252
 QBE  H7   H  HCR6  0   0.256  -0.9181  -48.9641   0.7079
 QBE  H8   H  HCR6  0   0.270  -2.3973  -47.1940  -0.0738
 QBE  H9   H  HNH1  0   0.396  -0.2076  -47.4831   5.2779
 QBE  H10  H  HCH3  0   0.247   0.8713  -49.1198   3.6310
 QBE  H11  H  HCH3  0   0.246  -0.5441  -50.0694   4.0488
 QBE  H12  H  HCH3  0   0.249   0.1510  -50.1834   2.4324
 QBE  H13  H  HNH1  0   0.421  -3.7060  -45.4558   0.3558
 QBE  H15  H  HCR5  0   0.294  -5.8353  -40.6540   5.6499
 QBE  H16  H  HNH1  0   0.418  -6.9057  -40.8601   1.5183
 QBE  H17  H  HCH1  0   0.282  -6.0125  -41.3942  -1.0281
 QBE  H18  H  HCH2  0   0.265  -7.9837  -43.6237  -0.1667
 QBE  H19  H  HCH2  0   0.265  -7.3635  -43.3236  -1.8550
 QBE  H20  H  HCH2  0   0.266  -8.3533  -40.9869  -1.7744
 QBE  H21  H  HCH2  0   0.265  -8.9619  -41.3235  -0.0902
 QBE  H22  H  HCR6  0   0.307  -5.1430  -43.7756   0.0487
 QBE  C    C  CH3   0  -0.723  -0.0788  -49.4961   3.2452

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
 QBE  C16  C17  single    1.496  0.020  1.496
 QBE  C16  C15  single    1.492  0.020  1.492
 QBE  C17  C15  single    1.499  0.020  1.499
 QBE  C15  N5   single    1.425  0.020  1.425
 QBE  N5   C14  single    1.333  0.020  1.333
 QBE  C8   C7   aromatic  1.382  0.020  1.382
 QBE  C8   C9   aromatic  1.397  0.020  1.397
 QBE  C18  C14  aromatic  1.377  0.020  1.377
 QBE  C18  C10  aromatic  1.416  0.020  1.416
 QBE  N1   C9   single    1.393  0.020  1.393
 QBE  N1   C10  single    1.357  0.020  1.357
 QBE  C7   C1   aromatic  1.392  0.020  1.392
 QBE  C14  N4   aromatic  1.368  0.020  1.368
 QBE  C9   C6   aromatic  1.393  0.020  1.393
 QBE  C10  N2   aromatic  1.326  0.020  1.326
 QBE  C1   C    single    1.499  0.020  1.499
 QBE  C1   C2   aromatic  1.395  0.020  1.395
 QBE  N4   N3   aromatic  1.350  0.020  1.350
 QBE  N4   C11  aromatic  1.367  0.020  1.367
 QBE  C6   C2   aromatic  1.390  0.020  1.390
 QBE  N2   C11  aromatic  1.324  0.020  1.324
 QBE  C2   N    single    1.413  0.020  1.413
 QBE  N3   C13  aromatic  1.309  0.020  1.309
 QBE  C11  C12  aromatic  1.401  0.020  1.401
 QBE  N    C3   single    1.357  0.020  1.357
 QBE  C13  C12  aromatic  1.411  0.020  1.411
 QBE  C12  C19  single    1.402  0.020  1.402
 QBE  C4   C3   single    1.513  0.020  1.513
 QBE  C4   C5   single    1.527  0.020  1.527
 QBE  C3   O    double    1.222  0.020  1.222
 QBE  C19  N6   triple    1.155  0.020  1.155
 QBE  C4   H1   single    0.970  0.020  1.090
 QBE  C4   H2   single    0.970  0.020  1.090
 QBE  C5   H3   single    0.970  0.020  1.090
 QBE  C5   H4   single    0.970  0.020  1.090
 QBE  C5   H5   single    0.970  0.020  1.090
 QBE  C6   H6   single    0.930  0.020  1.080
 QBE  C7   H7   single    0.930  0.020  1.080
 QBE  C8   H8   single    0.930  0.020  1.080
 QBE  N    H9   single    0.860  0.020  1.020
 QBE  C    H10  single    0.970  0.020  1.090
 QBE  C    H11  single    0.970  0.020  1.090
 QBE  C    H12  single    0.970  0.020  1.090
 QBE  N1   H13  single    0.860  0.020  1.020
 QBE  C13  H15  single    0.930  0.020  1.080
 QBE  N5   H16  single    0.860  0.020  1.020
 QBE  C15  H17  single    0.970  0.020  1.090
 QBE  C17  H18  single    0.970  0.020  1.090
 QBE  C17  H19  single    0.970  0.020  1.090
 QBE  C16  H20  single    0.970  0.020  1.090
 QBE  C16  H21  single    0.970  0.020  1.090
 QBE  C18  H22  single    0.930  0.020  1.080

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
 QBE  N2   C11  N4   123.56  3.000
 QBE  N2   C11  C12  132.24  3.000
 QBE  N4   C11  C12  104.20  3.000
 QBE  C1   C2   N    119.36  3.000
 QBE  N    C2   C6   118.71  3.000
 QBE  C1   C2   C6   121.91  3.000
 QBE  O    C3   N    120.56  3.000
 QBE  O    C3   C4   120.91  3.000
 QBE  N    C3   C4   118.51  3.000
 QBE  H2   C4   H1   106.76  3.000
 QBE  H2   C4   C5   109.04  3.000
 QBE  H1   C4   C5   110.08  3.000
 QBE  H2   C4   C3   105.97  3.000
 QBE  H1   C4   C3   112.30  3.000
 QBE  C5   C4   C3   112.40  3.000
 QBE  H5   C5   H4   107.89  3.000
 QBE  H5   C5   H3   107.59  3.000
 QBE  H4   C5   H3   107.95  3.000
 QBE  H5   C5   C4   111.81  3.000
 QBE  H4   C5   C4   111.50  3.000
 QBE  H3   C5   C4   109.94  3.000
 QBE  H6   C6   C9   120.30  3.000
 QBE  H6   C6   C2   119.40  3.000
 QBE  C9   C6   C2   120.30  3.000
 QBE  H7   C7   C1   119.22  3.000
 QBE  H7   C7   C8   118.74  3.000
 QBE  C1   C7   C8   122.04  3.000
 QBE  H8   C8   C9   120.02  3.000
 QBE  H8   C8   C7   119.43  3.000
 QBE  C9   C8   C7   120.54  3.000
 QBE  H9   N    C3   115.20  3.000
 QBE  H9   N    C2   117.06  3.000
 QBE  C3   N    C2   127.73  3.000
 QBE  H13  N1   C9   114.07  3.000
 QBE  H13  N1   C10  114.57  3.000
 QBE  C9   N1   C10  131.31  3.000
 QBE  C    C1   C7   121.53  3.000
 QBE  C    C1   C2   121.59  3.000
 QBE  C7   C1   C2   116.88  3.000
 QBE  C12  C19  N6   180.00  3.000
 QBE  C13  C12  C19  128.46  3.000
 QBE  C19  C12  C11  126.50  3.000
 QBE  C13  C12  C11  105.04  3.000
 QBE  H15  C13  N3   120.55  3.000
 QBE  H15  C13  C12  127.10  3.000
 QBE  N3   C13  C12  112.36  3.000
 QBE  N4   N3   C13  104.52  3.000
 QBE  C14  N4   N3   124.32  3.000
 QBE  N3   N4   C11  113.89  3.000
 QBE  C14  N4   C11  121.78  3.000
 QBE  C10  N2   C11  116.19  3.000
 QBE  C18  C14  N5   127.00  3.000
 QBE  C18  C14  N4   115.85  3.000
 QBE  N5   C14  N4   117.15  3.000
 QBE  H16  N5   C15  119.03  3.000
 QBE  H16  N5   C14  117.64  3.000
 QBE  C15  N5   C14  122.44  3.000
 QBE  H17  C15  C16  117.50  3.000
 QBE  H17  C15  C17  117.29  3.000
 QBE  C16  C15  C17   60.01  3.000
 QBE  H17  C15  N5   114.99  3.000
 QBE  C17  C15  N5   118.71  3.000
 QBE  C16  C15  N5   117.42  3.000
 QBE  H19  C17  H18  114.82  3.000
 QBE  H19  C17  C16  118.82  3.000
 QBE  H18  C17  C16  117.67  3.000
 QBE  H19  C17  C15  117.46  3.000
 QBE  H18  C17  C15  117.40  3.000
 QBE  C16  C17  C15   59.75  3.000
 QBE  H21  C16  H20  114.69  3.000
 QBE  H21  C16  C17  117.63  3.000
 QBE  H20  C16  C17  118.83  3.000
 QBE  H21  C16  C15  117.47  3.000
 QBE  H20  C16  C15  117.32  3.000
 QBE  C17  C16  C15   60.23  3.000
 QBE  H22  C18  C10  120.86  3.000
 QBE  H22  C18  C14  119.90  3.000
 QBE  C10  C18  C14  119.23  3.000
 QBE  C18  C10  N2   123.38  3.000
 QBE  N2   C10  N1   119.66  3.000
 QBE  C18  C10  N1   116.96  3.000
 QBE  N1   C9   C8   116.76  3.000
 QBE  N1   C9   C6   124.96  3.000
 QBE  C8   C9   C6   118.28  3.000
 QBE  H12  C    H11  107.94  3.000
 QBE  H12  C    H10  107.31  3.000
 QBE  H11  C    H10  106.96  3.000
 QBE  H12  C    C1   110.79  3.000
 QBE  H11  C    C1   111.66  3.000
 QBE  H10  C    C1   111.95  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
 QBE  CONST_01  C18  C14  N4   C11     0.00   0.0  0
 QBE  CONST_02  C13  N3   N4   C11     0.00   0.0  0
 QBE  CONST_03  C18  C10  N2   C11     0.00   0.0  0
 QBE  CONST_04  N3   C13  C12  C11     0.00   0.0  0
 QBE  CONST_05  C8   C7   C1   C2      0.00   0.0  0
 QBE  CONST_06  C8   C9   C6   C2      0.00   0.0  0
 QBE  CONST_07  C7   C8   C9   C6      0.00   0.0  0
 QBE  CONST_08  C7   C1   C2   C6      0.00   0.0  0
 QBE  CONST_09  C9   C8   C7   C1      0.00   0.0  0
 QBE  CONST_10  C9   C6   C2   C1      0.00   0.0  0
 QBE  CONST_11  C14  N4   C11  C12   180.00   0.0  0
 QBE  CONST_12  N3   N4   C11  C12     0.00   0.0  0
 QBE  CONST_13  C10  N2   C11  C12   180.00   0.0  0
 QBE  CONST_14  N4   N3   C13  C12     0.00   0.0  0
 QBE  CONST_15  C14  N4   N3   C13   180.00   0.0  0
 QBE  CONST_16  N4   C11  C12  C13     0.00   0.0  0
 QBE  CONST_17  N2   C11  C12  C13   180.00   0.0  0
 QBE  CONST_18  C18  C14  N4   N3    180.00   0.0  0
 QBE  CONST_19  N2   C11  N4   N3    180.00   0.0  0
 QBE  CONST_20  C10  C18  C14  N4      0.00   0.0  0
 QBE  CONST_21  C10  N2   C11  N4      0.00   0.0  0
 QBE  CONST_22  C14  C18  C10  N2      0.00   0.0  0
 QBE  CONST_23  C14  N4   C11  N2      0.00   0.0  0
 QBE  CONST_24  N5   C14  N4   C11   180.00   0.0  0
 QBE  CONST_25  N1   C10  N2   C11   180.00   0.0  0
 QBE  CONST_26  N1   C9   C6   C2    180.00   0.0  0
 QBE  CONST_27  C    C1   C2   C6    180.00   0.0  0
 QBE  CONST_28  N1   C9   C8   C7    180.00   0.0  0
 QBE  CONST_29  N    C2   C1   C7    180.00   0.0  0
 QBE  CONST_30  C    C1   C7   C8    180.00   0.0  0
 QBE  CONST_31  C9   C6   C2   N     180.00   0.0  0
 QBE  CONST_32  C14  C18  C10  N1    180.00   0.0  0
 QBE  CONST_33  N4   C11  C12  C19   180.00   0.0  0
 QBE  CONST_34  N2   C11  C12  C19     0.00   0.0  0
 QBE  CONST_35  N3   C13  C12  C19   180.00   0.0  0
 QBE  CONST_36  N5   C14  N4   N3      0.00   0.0  0
 QBE  CONST_37  C10  C18  C14  N5    180.00   0.0  0
 QBE  CONST_38  C15  N5   C14  N4    180.00   0.0  0
 QBE  CONST_39  C18  C14  N5   C15     0.00   0.0  0
 QBE  CONST_40  H15  C13  C12  C11   180.00   0.0  0
 QBE  CONST_41  H7   C7   C1   C2    180.00   0.0  0
 QBE  CONST_42  H8   C8   C9   C6    180.00   0.0  0
 QBE  CONST_43  H6   C6   C9   C8    180.00   0.0  0
 QBE  CONST_44  H22  C18  C14  N4    180.00   0.0  0
 QBE  CONST_48  H16  N5   C14  N4      0.00   0.0  0
 QBE  CONST_49  C4   C3   N    C2      0.00   0.0  0
 QBE  CONST_50  O    C3   N    C2    180.00   0.0  0
 QBE  Var_01    C10  N1   C9   C6      1.13  30.0  1
 QBE  Var_02    C9   N1   C10  N2      3.84  30.0  3
 QBE  Var_03    C16  C15  N5   C14   142.48  30.0  1
 QBE  Var_04    C17  C16  C15  N5   -108.99  30.0  1
 QBE  Var_05    H18  C17  C16  C15   107.20  30.0  1
 QBE  Var_06    H10  C    C1   C2    -66.25  30.0  2
 QBE  Var_07    N    C3   C4   C5   -113.36  30.0  3
 QBE  Var_08    H3   C5   C4   C3   -171.18  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
 QBE  chir_01  C15  C16  C17  N5  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
 QBE  plan-1  C2   0.020
 QBE  plan-1  C6   0.020
 QBE  plan-1  C7   0.020
 QBE  plan-1  C8   0.020
 QBE  plan-1  N    0.020
 QBE  plan-1  N1   0.020
 QBE  plan-1  C1   0.020
 QBE  plan-1  C9   0.020
 QBE  plan-1  H6   0.020
 QBE  plan-1  H7   0.020
 QBE  plan-1  H8   0.020
 QBE  plan-1  C    0.020
 QBE  plan-2  C11  0.020
 QBE  plan-2  N1   0.020
 QBE  plan-2  N6   0.020
 QBE  plan-2  C19  0.020
 QBE  plan-2  C12  0.020
 QBE  plan-2  C13  0.020
 QBE  plan-2  N3   0.020
 QBE  plan-2  N4   0.020
 QBE  plan-2  N2   0.020
 QBE  plan-2  C14  0.020
 QBE  plan-2  N5   0.020
 QBE  plan-2  C18  0.020
 QBE  plan-2  C10  0.020
 QBE  plan-2  H15  0.020
 QBE  plan-2  H22  0.020
 QBE  plan-3  C14  0.020
 QBE  plan-3  N5   0.020
 QBE  plan-3  C15  0.020
 QBE  plan-3  H16  0.020
 QBE  plan-4  C2   0.020
 QBE  plan-4  C3   0.020
 QBE  plan-4  C4   0.020
 QBE  plan-4  N    0.020
 QBE  plan-4  O    0.020
 QBE  plan-4  H9   0.020

