# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 20:17:44 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: ~{N}-[5-[[7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]amino]-2-methyl-phenyl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1cc(Nc2cc(NC3CC3)n4nccc4n2)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
 6XT  6XT  ~{N}-[5-[[7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]amino]-2-methyl-phenyl]ethanamide  ligand  45  25  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_6XT
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
 6XT  C1   C  CH3   0  -0.752   5.6478  -1.6786  -0.4388
 6XT  C2   C  CR6   0   0.032   4.1571  -1.5849  -0.2921
 6XT  C3   C  CR16  0  -0.292   3.3618  -2.7247  -0.3300
 6XT  C7   C  CR6   0   0.335   3.5099  -0.3571  -0.1089
 6XT  C9   C  C     0   0.505   4.1251   1.9101   0.6831
 6XT  C11  C  CH3   0  -0.786   5.2249   2.9341   0.5571
 6XT  C13  C  CR6   0   0.555  -0.9609  -0.4627   0.0803
 6XT  C14  C  CR16  0  -0.575  -2.3129  -0.8523   0.2753
 6XT  C15  C  CR6   0   0.702  -3.2955   0.1086   0.2372
 6XT  N18  N  N     0  -0.538  -0.5812   0.7797  -0.1293
 6XT  C19  C  CR15  0  -0.590  -1.5296   3.0807  -0.3456
 6XT  C20  C  CR15  0  -0.010  -2.8723   3.4675  -0.2649
 6XT  C24  C  CH2   0  -0.508  -6.4803  -1.7136   0.1273
 6XT  C4   C  CR16  0  -0.363   1.9881  -2.6663  -0.1931
 6XT  C5   C  CR6   0   0.359   1.3514  -1.4344  -0.0232
 6XT  C6   C  CR16  0  -0.374   2.1246  -0.2747   0.0147
 6XT  N8   N  NH1   0  -0.738   4.3019   0.8034  -0.0866
 6XT  O10  O  O     0  -0.472   3.1816   2.0654   1.4370
 6XT  N12  N  NH1   0  -0.797  -0.0333  -1.4623   0.1162
 6XT  N16  N  N     0  -0.452  -2.8765   1.3900   0.0183
 6XT  C17  C  CR56  0   0.601  -1.5484   1.7059  -0.1563
 6XT  N21  N  N     0  -0.334  -3.6927   2.4544  -0.0453
 6XT  N22  N  NH1   0  -0.674  -4.6110  -0.0838   0.3866
 6XT  C23  C  CH1   0  -0.106  -5.1552  -1.3581   0.7134
 6XT  C25  C  CH2   0  -0.483  -5.2436  -2.3980  -0.3635
 6XT  H1   H  HCH3  0   0.248   6.1713  -1.2252   0.4056
 6XT  H2   H  HCH3  0   0.259   5.9626  -2.7190  -0.5011
 6XT  H3   H  HCH3  0   0.245   6.0071  -1.1836  -1.3453
 6XT  H4   H  HCR6  0   0.251   3.8327  -3.6904  -0.4692
 6XT  H5   H  HCH3  0   0.275   5.8739   2.8666   1.4317
 6XT  H6   H  HCH3  0   0.254   5.8411   2.8079  -0.3311
 6XT  H7   H  HCH3  0   0.268   4.7948   3.9338   0.5452
 6XT  H8   H  HCR6  0   0.296  -2.5719  -1.8850   0.4552
 6XT  H9   H  HCR5  0   0.262  -0.6663   3.7009  -0.5164
 6XT  H10  H  HCR5  0   0.268  -3.2743   4.4652  -0.3606
 6XT  H12  H  HCH2  0   0.263  -6.9490  -0.9894  -0.5268
 6XT  H13  H  HCR6  0   0.264   1.4049  -3.5791  -0.2226
 6XT  H14  H  HCR6  0   0.301   1.6441   0.6803   0.1265
 6XT  H15  H  HNH1  0   0.413   5.1597   0.7640  -0.6145
 6XT  H16  H  HNH1  0   0.413  -0.4186  -2.3884   0.2133
 6XT  H17  H  HNH1  0   0.412  -5.1936   0.7363   0.4669
 6XT  H18  H  HCH1  0   0.277  -4.9443  -1.7071   1.7208
 6XT  H19  H  HCH2  0   0.262  -5.0704  -3.4279  -0.0811
 6XT  H20  H  HCH2  0   0.262  -4.8755  -2.1275  -1.3447
 6XT  H11  H  HCH2  0   0.264  -7.1681  -2.2665   0.7526

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
 6XT  C25  C24  single    1.496  0.020  1.496
 6XT  C25  C23  single    1.500  0.020  1.500
 6XT  C24  C23  single    1.492  0.020  1.492
 6XT  C23  N22  single    1.424  0.020  1.424
 6XT  N22  C15  single    1.338  0.020  1.338
 6XT  C14  C15  aromatic  1.375  0.020  1.375
 6XT  C14  C13  aromatic  1.420  0.020  1.420
 6XT  C4   C3   aromatic  1.382  0.020  1.382
 6XT  C4   C5   aromatic  1.397  0.020  1.397
 6XT  N12  C13  single    1.364  0.020  1.364
 6XT  N12  C5   single    1.392  0.020  1.392
 6XT  C15  N16  aromatic  1.366  0.020  1.366
 6XT  C3   C2   aromatic  1.390  0.020  1.390
 6XT  C13  N18  aromatic  1.316  0.020  1.316
 6XT  C5   C6   aromatic  1.394  0.020  1.394
 6XT  N16  N21  aromatic  1.343  0.020  1.343
 6XT  N16  C17  aromatic  1.376  0.020  1.376
 6XT  C2   C1   single    1.501  0.020  1.501
 6XT  C2   C7   aromatic  1.400  0.020  1.400
 6XT  N18  C17  aromatic  1.339  0.020  1.339
 6XT  C6   C7   aromatic  1.393  0.020  1.393
 6XT  N21  C20  aromatic  1.322  0.020  1.322
 6XT  C17  C19  aromatic  1.388  0.020  1.388
 6XT  C7   N8   single    1.405  0.020  1.405
 6XT  C20  C19  aromatic  1.400  0.020  1.400
 6XT  N8   C9   single    1.360  0.020  1.360
 6XT  C9   O10  double    1.218  0.020  1.218
 6XT  C9   C11  single    1.508  0.020  1.508
 6XT  C1   H1   single    0.970  0.020  1.090
 6XT  C1   H2   single    0.970  0.020  1.090
 6XT  C1   H3   single    0.970  0.020  1.090
 6XT  C3   H4   single    0.930  0.020  1.080
 6XT  C11  H5   single    0.970  0.020  1.090
 6XT  C11  H6   single    0.970  0.020  1.090
 6XT  C11  H7   single    0.970  0.020  1.090
 6XT  C14  H8   single    0.930  0.020  1.080
 6XT  C19  H9   single    0.930  0.020  1.080
 6XT  C20  H10  single    0.930  0.020  1.080
 6XT  C24  H11  single    0.970  0.020  1.090
 6XT  C24  H12  single    0.970  0.020  1.090
 6XT  C4   H13  single    0.930  0.020  1.080
 6XT  C6   H14  single    0.930  0.020  1.080
 6XT  N8   H15  single    0.860  0.020  1.020
 6XT  N12  H16  single    0.860  0.020  1.020
 6XT  N22  H17  single    0.860  0.020  1.020
 6XT  C23  H18  single    0.970  0.020  1.090
 6XT  C25  H19  single    0.970  0.020  1.090
 6XT  C25  H20  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
 6XT  H3   C1   H2   106.87  3.000
 6XT  H3   C1   H1   107.19  3.000
 6XT  H2   C1   H1   107.60  3.000
 6XT  H3   C1   C2   112.28  3.000
 6XT  H2   C1   C2   110.63  3.000
 6XT  H1   C1   C2   112.00  3.000
 6XT  C7   C2   C3   117.26  3.000
 6XT  C7   C2   C1   121.78  3.000
 6XT  C3   C2   C1   120.95  3.000
 6XT  H4   C3   C4   118.85  3.000
 6XT  H4   C3   C2   119.05  3.000
 6XT  C4   C3   C2   122.09  3.000
 6XT  N8   C7   C6   120.68  3.000
 6XT  N8   C7   C2   117.76  3.000
 6XT  C6   C7   C2   121.54  3.000
 6XT  O10  C9   N8   123.71  3.000
 6XT  O10  C9   C11  122.02  3.000
 6XT  N8   C9   C11  114.25  3.000
 6XT  H7   C11  H6   108.74  3.000
 6XT  H7   C11  H5   107.50  3.000
 6XT  H6   C11  H5   108.07  3.000
 6XT  H7   C11  C9   109.66  3.000
 6XT  H6   C11  C9   113.73  3.000
 6XT  H5   C11  C9   108.96  3.000
 6XT  N12  C13  N18  119.99  3.000
 6XT  N18  C13  C14  123.75  3.000
 6XT  N12  C13  C14  116.27  3.000
 6XT  H8   C14  C15  120.11  3.000
 6XT  H8   C14  C13  120.90  3.000
 6XT  C15  C14  C13  118.99  3.000
 6XT  N22  C15  N16  117.03  3.000
 6XT  N16  C15  C14  116.16  3.000
 6XT  N22  C15  C14  126.80  3.000
 6XT  C17  N18  C13  116.59  3.000
 6XT  H9   C19  C17  127.10  3.000
 6XT  H9   C19  C20  128.26  3.000
 6XT  C17  C19  C20  104.65  3.000
 6XT  H10  C20  N21  119.45  3.000
 6XT  H10  C20  C19  127.39  3.000
 6XT  N21  C20  C19  113.16  3.000
 6XT  H12  C24  H11  114.58  3.000
 6XT  H12  C24  C25  117.76  3.000
 6XT  H11  C24  C25  118.78  3.000
 6XT  H12  C24  C23  117.55  3.000
 6XT  H11  C24  C23  117.36  3.000
 6XT  C25  C24  C23   60.25  3.000
 6XT  H13  C4   C5   120.05  3.000
 6XT  H13  C4   C3   119.78  3.000
 6XT  C5   C4   C3   120.16  3.000
 6XT  N12  C5   C6   124.45  3.000
 6XT  C6   C5   C4   118.94  3.000
 6XT  N12  C5   C4   116.61  3.000
 6XT  H14  C6   C5   119.59  3.000
 6XT  H14  C6   C7   120.41  3.000
 6XT  C5   C6   C7   119.99  3.000
 6XT  H15  N8   C9   116.04  3.000
 6XT  H15  N8   C7   116.04  3.000
 6XT  C9   N8   C7   127.44  3.000
 6XT  H16  N12  C5   114.10  3.000
 6XT  H16  N12  C13  114.58  3.000
 6XT  C5   N12  C13  131.23  3.000
 6XT  N21  N16  C17  113.48  3.000
 6XT  C17  N16  C15  122.12  3.000
 6XT  N21  N16  C15  124.39  3.000
 6XT  N16  C17  C19  104.94  3.000
 6XT  C19  C17  N18  132.68  3.000
 6XT  N16  C17  N18  122.38  3.000
 6XT  N16  N21  C20  103.78  3.000
 6XT  H17  N22  C23  119.24  3.000
 6XT  H17  N22  C15  117.36  3.000
 6XT  C23  N22  C15  122.02  3.000
 6XT  H18  C23  C25  117.03  3.000
 6XT  H18  C23  N22  115.21  3.000
 6XT  C25  C23  N22  118.58  3.000
 6XT  H18  C23  C24  117.39  3.000
 6XT  N22  C23  C24  117.56  3.000
 6XT  C25  C23  C24   60.02  3.000
 6XT  H20  C25  H19  114.84  3.000
 6XT  H20  C25  C23  117.24  3.000
 6XT  H19  C25  C23  117.60  3.000
 6XT  H20  C25  C24  117.65  3.000
 6XT  H19  C25  C24  118.82  3.000
 6XT  C23  C25  C24   59.73  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
 6XT  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 6XT  CONST_02  C5   C6   C7   C2      0.00   0.0  0
 6XT  CONST_03  C6   C5   C4   C3      0.00   0.0  0
 6XT  CONST_04  C6   C7   C2   C3      0.00   0.0  0
 6XT  CONST_05  C4   C3   C2   C7      0.00   0.0  0
 6XT  CONST_06  C4   C5   C6   C7      0.00   0.0  0
 6XT  CONST_07  N16  C15  C14  C13     0.00   0.0  0
 6XT  CONST_08  N16  C17  N18  C13     0.00   0.0  0
 6XT  CONST_09  C19  C17  N18  C13   180.00   0.0  0
 6XT  CONST_10  N21  N16  C15  C14   180.00   0.0  0
 6XT  CONST_11  C17  N16  C15  C14     0.00   0.0  0
 6XT  CONST_12  C17  N18  C13  C14     0.00   0.0  0
 6XT  CONST_13  N18  C13  C14  C15     0.00   0.0  0
 6XT  CONST_14  C20  N21  N16  C15   180.00   0.0  0
 6XT  CONST_15  N18  C17  N16  C15     0.00   0.0  0
 6XT  CONST_16  C19  C17  N16  C15   180.00   0.0  0
 6XT  CONST_17  N21  N16  C17  N18   180.00   0.0  0
 6XT  CONST_18  C20  C19  C17  N18   180.00   0.0  0
 6XT  CONST_19  N21  N16  C17  C19     0.00   0.0  0
 6XT  CONST_20  N16  N21  C20  C19     0.00   0.0  0
 6XT  CONST_21  C17  N16  N21  C20     0.00   0.0  0
 6XT  CONST_22  N16  C17  C19  C20     0.00   0.0  0
 6XT  CONST_23  N21  C20  C19  C17     0.00   0.0  0
 6XT  CONST_24  C4   C3   C2   C1    180.00   0.0  0
 6XT  CONST_25  C6   C7   C2   C1    180.00   0.0  0
 6XT  CONST_26  N12  C5   C4   C3    180.00   0.0  0
 6XT  CONST_27  N8   C7   C2   C3    180.00   0.0  0
 6XT  CONST_28  N12  C5   C6   C7    180.00   0.0  0
 6XT  CONST_29  N22  C15  C14  C13   180.00   0.0  0
 6XT  CONST_30  N12  C13  C14  C15   180.00   0.0  0
 6XT  CONST_31  N8   C7   C6   C5    180.00   0.0  0
 6XT  CONST_32  C17  N18  C13  N12   180.00   0.0  0
 6XT  CONST_33  N22  C15  N16  C17   180.00   0.0  0
 6XT  CONST_34  N22  C15  N16  N21     0.00   0.0  0
 6XT  CONST_35  C23  N22  C15  C14     0.00   0.0  0
 6XT  CONST_36  C23  N22  C15  N16   180.00   0.0  0
 6XT  CONST_37  H13  C4   C3   C2    180.00   0.0  0
 6XT  CONST_38  H14  C6   C7   C2    180.00   0.0  0
 6XT  CONST_39  H4   C3   C2   C7    180.00   0.0  0
 6XT  CONST_40  H8   C14  C13  N18   180.00   0.0  0
 6XT  CONST_41  H9   C19  C17  N18     0.00   0.0  0
 6XT  CONST_42  H10  C20  N21  N16   180.00   0.0  0
 6XT  CONST_46  H17  N22  C15  C14   180.00   0.0  0
 6XT  CONST_47  O10  C9   N8   C7      0.00   0.0  0
 6XT  CONST_48  C11  C9   N8   C7    180.00   0.0  0
 6XT  Var_01    C4   C5   N12  C13  -167.96  30.0  2
 6XT  Var_02    C5   N12  C13  C14  -179.42  30.0  2
 6XT  Var_03    C25  C23  N22  C15   -76.31  30.0  2
 6XT  Var_04    N22  C23  C25  C24  -107.09  30.0  1
 6XT  Var_05    H11  C24  C25  C23  -106.85  30.0  1
 6XT  Var_06    H1   C1   C2   C3   -123.86  30.0  2
 6XT  Var_07    H5   C11  C9   N8   -102.91  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
 6XT  chir_01  C23  C25  C24  N22  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
 6XT  plan-1  C1   0.020
 6XT  plan-1  C2   0.020
 6XT  plan-1  C3   0.020
 6XT  plan-1  C7   0.020
 6XT  plan-1  C4   0.020
 6XT  plan-1  C5   0.020
 6XT  plan-1  C6   0.020
 6XT  plan-1  N8   0.020
 6XT  plan-1  N12  0.020
 6XT  plan-1  H4   0.020
 6XT  plan-1  H13  0.020
 6XT  plan-1  H14  0.020
 6XT  plan-2  C13  0.020
 6XT  plan-2  C14  0.020
 6XT  plan-2  C15  0.020
 6XT  plan-2  N18  0.020
 6XT  plan-2  C19  0.020
 6XT  plan-2  C20  0.020
 6XT  plan-2  N12  0.020
 6XT  plan-2  N16  0.020
 6XT  plan-2  C17  0.020
 6XT  plan-2  N21  0.020
 6XT  plan-2  N22  0.020
 6XT  plan-2  H8   0.020
 6XT  plan-2  H9   0.020
 6XT  plan-2  H10  0.020
 6XT  plan-3  C15  0.020
 6XT  plan-3  N22  0.020
 6XT  plan-3  C23  0.020
 6XT  plan-3  H17  0.020
 6XT  plan-4  C7   0.020
 6XT  plan-4  C9   0.020
 6XT  plan-4  C11  0.020
 6XT  plan-4  N8   0.020
 6XT  plan-4  O10  0.020
 6XT  plan-4  H15  0.020

