# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 20:12:53 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: N-{2-(3,3-difluoropyrrolidin-1-yl)-6-[(3R)-pyrrolidin-3-yl]pyrimidin-4-yl}-1-(propan-2-yl)-1H-pyrazolo[4,3-c]pyridin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)n1ncc2cnc(Nc3cc(nc(n3)N4CCC(F)(F)C4)[C@@H]5CCNC5)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
 F97  F97  N-{2-(3,3-difluoropyrrolidin-1-yl)-6-[(3R)-pyrrolidin-3-yl]pyrimidin-4-yl}-1-(propan-2-yl)-1H-pyrazolo[4,3-c]pyridin-6-amine  ligand  57  31  .  2021-08-09  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_F97
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
 F97  C5   C  CR56  0   0.582   4.1214  -1.2238  -0.3170
 F97  C6   C  CR16  0  -0.450   2.7537  -0.9494  -0.3859
 F97  C7   C  CR6   0   0.479   1.9270  -1.9155   0.1590
 F97  C10  C  CR56  0  -0.216   4.5946  -2.4274   0.2319
 F97  N12  N  N     0  -0.238   6.3427  -1.2067  -0.4444
 F97  C15  C  CR16  0  -0.491   0.1579   0.6004   0.3780
 F97  C21  C  CH2   0  -0.260  -4.7810   0.7072  -0.0343
 F97  C22  C  CH2   0  -0.596  -6.0274  -0.0863  -0.4138
 F97  C24  C  CH2   0  -0.349  -4.2192  -1.6546  -0.1685
 F97  C28  C  CH2   0  -0.436  -1.3558   3.7807   1.5410
 F97  C1   C  CH3   0  -0.645   5.9022   1.7792  -0.3115
 F97  C3   C  CH3   0  -0.648   5.9990   0.7725  -2.6294
 F97  N4   N  NR5   0  -0.405   5.2094  -0.5337  -0.7121
 F97  N8   N  N     0  -0.460   2.3664  -3.0856   0.6717
 F97  C9   C  CR16  0  -0.098   3.6529  -3.3423   0.7001
 F97  C11  C  CR15  0  -0.103   6.0060  -2.3374   0.1128
 F97  N13  N  NH1   0  -0.733   0.5461  -1.8129   0.1871
 F97  C14  C  CR6   0   0.529  -0.2727  -0.7197   0.1938
 F97  C16  C  CR6   0   0.319  -0.8259   1.5753   0.3698
 F97  N17  N  N     0  -0.478  -2.1140   1.2916   0.2143
 F97  C18  C  CR6   0   0.619  -2.4220   0.0026   0.0759
 F97  N19  N  N     0  -0.525  -1.5602  -1.0143   0.0464
 F97  N20  N  NT    0  -0.528  -3.7282  -0.3001  -0.0557
 F97  C23  C  CT    0   0.712  -5.7041  -1.4722   0.0903
 F97  F25  F  F     0  -0.337  -6.4527  -2.4522  -0.4782
 F97  F26  F  F     0  -0.348  -5.9508  -1.5514   1.4353
 F97  C27  C  CR15  0  -0.343  -0.4719   3.0255   0.5189
 F97  C29  C  CH2   0  -0.284  -2.1692   4.7478   0.6883
 F97  N30  N  NR15  0  -0.612  -1.2405   5.0707  -0.3830
 F97  C31  C  CH2   0  -0.272  -0.7012   3.7891  -0.8076
 F97  H1   H  HCR6  0   0.294   2.3701  -0.0633  -0.8682
 F97  H2   H  HCR6  0   0.274   1.1867   0.8656   0.5598
 F97  H3   H  HCH2  0   0.257  -4.5767   1.5108  -0.7401
 F97  H4   H  HCH2  0   0.244  -4.8731   1.1576   0.9573
 F97  H5   H  HCH2  0   0.287  -6.9439   0.3186   0.0136
 F97  H6   H  HCH2  0   0.275  -6.1391  -0.1243  -1.4987
 F97  H7   H  HCH2  0   0.258  -4.0589  -2.0694  -1.1686
 F97  H8   H  HCH2  0   0.272  -3.7558  -2.3288   0.5531
 F97  H9   H  HCH2  0   0.239  -1.9883   3.1120   2.1224
 F97  H10  H  HCH2  0   0.237  -0.7207   4.3287   2.2381
 F97  H11  H  HCH3  0   0.239   5.3521   1.8051   0.6292
 F97  H12  H  HCH3  0   0.234   6.9368   1.5070  -0.1008
 F97  H13  H  HCH3  0   0.238   5.8960   2.7839  -0.7333
 F97  H14  H  HCH1  0   0.261   4.2356   1.0920  -1.4673
 F97  H15  H  HCH3  0   0.234   7.0425   0.4837  -2.5040
 F97  H16  H  HCH3  0   0.241   5.5275   0.0762  -3.3227
 F97  H17  H  HCH3  0   0.239   5.9756   1.7650  -3.0787
 F97  H18  H  HCR6  0   0.274   3.9550  -4.3006   1.1089
 F97  H19  H  HCR5  0   0.276   6.7572  -3.0519   0.4131
 F97  H20  H  HNH1  0   0.397   0.0632  -2.6948   0.2839
 F97  H21  H  HCR5  0   0.260   0.5785   3.0979   0.8053
 F97  H22  H  HCH2  0   0.202  -3.0813   4.2467   0.3332
 F97  H23  H  HCH2  0   0.222  -2.4714   5.6452   1.2322
 F97  H24  H  HNR5  0   0.348  -1.6997   5.5480  -1.1475
 F97  H26  H  HCH2  0   0.230   0.2264   3.9133  -1.3697
 F97  H27  H  HCH2  0   0.213  -1.4001   3.2247  -1.4399
 F97  C2   C  CH1   0  -0.124   5.2728   0.8000  -1.2929

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
 F97  C9   N8   aromatic  1.312  0.020  1.312
 F97  C9   C10  aromatic  1.394  0.020  1.394
 F97  N8   C7   aromatic  1.351  0.020  1.351
 F97  C10  C11  aromatic  1.419  0.020  1.419
 F97  C10  C5   aromatic  1.405  0.020  1.405
 F97  C11  N12  aromatic  1.305  0.020  1.305
 F97  N13  C7   single    1.385  0.020  1.385
 F97  N13  C14  single    1.366  0.020  1.366
 F97  C7   C6   aromatic  1.383  0.020  1.383
 F97  C15  C14  aromatic  1.401  0.020  1.401
 F97  C15  C16  aromatic  1.385  0.020  1.385
 F97  C5   C6   aromatic  1.397  0.020  1.397
 F97  C5   N4   aromatic  1.348  0.020  1.348
 F97  C28  C27  single    1.548  0.020  1.548
 F97  C28  C29  single    1.525  0.020  1.525
 F97  C14  N19  aromatic  1.329  0.020  1.329
 F97  N12  N4   aromatic  1.345  0.020  1.345
 F97  C27  C16  single    1.500  0.020  1.500
 F97  C27  C31  single    1.548  0.020  1.548
 F97  C29  N30  single    1.454  0.020  1.454
 F97  C16  N17  aromatic  1.328  0.020  1.328
 F97  N4   C2   single    1.456  0.020  1.456
 F97  N19  C18  aromatic  1.333  0.020  1.333
 F97  N17  C18  aromatic  1.332  0.020  1.332
 F97  C31  N30  single    1.454  0.020  1.454
 F97  C18  N20  single    1.347  0.020  1.347
 F97  C2   C1   single    1.523  0.020  1.523
 F97  C2   C3   single    1.521  0.020  1.521
 F97  N20  C24  single    1.445  0.020  1.445
 F97  N20  C21  single    1.457  0.020  1.457
 F97  C24  C23  single    1.518  0.020  1.518
 F97  C21  C22  single    1.526  0.020  1.526
 F97  C23  F26  single    1.370  0.020  1.370
 F97  C23  F25  single    1.358  0.020  1.358
 F97  C23  C22  single    1.510  0.020  1.510
 F97  C6   H1   single    0.930  0.020  1.080
 F97  C15  H2   single    0.930  0.020  1.080
 F97  C21  H3   single    0.970  0.020  1.090
 F97  C21  H4   single    0.970  0.020  1.090
 F97  C22  H5   single    0.970  0.020  1.090
 F97  C22  H6   single    0.970  0.020  1.090
 F97  C24  H7   single    0.970  0.020  1.090
 F97  C24  H8   single    0.970  0.020  1.090
 F97  C28  H9   single    0.970  0.020  1.090
 F97  C28  H10  single    0.970  0.020  1.090
 F97  C1   H11  single    0.970  0.020  1.090
 F97  C1   H12  single    0.970  0.020  1.090
 F97  C1   H13  single    0.970  0.020  1.090
 F97  C2   H14  single    0.970  0.020  1.090
 F97  C3   H15  single    0.970  0.020  1.090
 F97  C3   H16  single    0.970  0.020  1.090
 F97  C3   H17  single    0.970  0.020  1.090
 F97  C9   H18  single    0.930  0.020  1.080
 F97  C11  H19  single    0.930  0.020  1.080
 F97  N13  H20  single    0.860  0.020  1.020
 F97  C27  H21  single    0.970  0.020  1.090
 F97  C29  H22  single    0.970  0.020  1.090
 F97  C29  H23  single    0.970  0.020  1.090
 F97  N30  H24  single    0.890  0.020  1.040
 F97  C31  H26  single    0.970  0.020  1.090
 F97  C31  H27  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
 F97  N4   C5   C10  106.34  3.000
 F97  N4   C5   C6   132.49  3.000
 F97  C10  C5   C6   121.16  3.000
 F97  H1   C6   C7   122.47  3.000
 F97  H1   C6   C5   122.10  3.000
 F97  C7   C6   C5   115.38  3.000
 F97  N13  C7   N8   112.38  3.000
 F97  N13  C7   C6   123.51  3.000
 F97  N8   C7   C6   124.05  3.000
 F97  C11  C10  C9   137.87  3.000
 F97  C11  C10  C5   104.35  3.000
 F97  C9   C10  C5   117.77  3.000
 F97  C11  N12  N4   107.53  3.000
 F97  H2   C15  C16  120.38  3.000
 F97  H2   C15  C14  123.20  3.000
 F97  C16  C15  C14  116.37  3.000
 F97  H4   C21  H3   107.45  3.000
 F97  H4   C21  N20  111.04  3.000
 F97  H3   C21  N20  111.41  3.000
 F97  H4   C21  C22  111.79  3.000
 F97  H3   C21  C22  112.08  3.000
 F97  N20  C21  C22  103.12  3.000
 F97  H6   C22  H5   108.48  3.000
 F97  H6   C22  C23  108.78  3.000
 F97  H5   C22  C23  112.98  3.000
 F97  H6   C22  C21  110.43  3.000
 F97  H5   C22  C21  113.36  3.000
 F97  C23  C22  C21  102.68  3.000
 F97  H8   C24  H7   107.94  3.000
 F97  H8   C24  C23  112.14  3.000
 F97  H7   C24  C23  110.16  3.000
 F97  H8   C24  N20  112.54  3.000
 F97  H7   C24  N20  112.14  3.000
 F97  C23  C24  N20  101.91  3.000
 F97  H10  C28  H9   107.80  3.000
 F97  H10  C28  C29  110.45  3.000
 F97  H9   C28  C29  112.23  3.000
 F97  H10  C28  C27  109.55  3.000
 F97  H9   C28  C27  112.63  3.000
 F97  C29  C28  C27  104.17  3.000
 F97  H13  C1   H12  108.08  3.000
 F97  H13  C1   H11  108.01  3.000
 F97  H12  C1   H11  108.54  3.000
 F97  H13  C1   C2   109.95  3.000
 F97  H12  C1   C2   110.87  3.000
 F97  H11  C1   C2   111.28  3.000
 F97  H17  C3   H16  108.07  3.000
 F97  H17  C3   H15  108.02  3.000
 F97  H16  C3   H15  108.55  3.000
 F97  H17  C3   C2   109.61  3.000
 F97  H16  C3   C2   111.34  3.000
 F97  H15  C3   C2   111.15  3.000
 F97  C2   N4   N12  120.07  3.000
 F97  C2   N4   C5   128.40  3.000
 F97  N12  N4   C5   111.45  3.000
 F97  C9   N8   C7   119.77  3.000
 F97  H18  C9   N8   117.00  3.000
 F97  H18  C9   C10  121.22  3.000
 F97  N8   C9   C10  121.78  3.000
 F97  H19  C11  N12  120.86  3.000
 F97  H19  C11  C10  128.81  3.000
 F97  N12  C11  C10  110.33  3.000
 F97  H20  N13  C14  114.31  3.000
 F97  H20  N13  C7   114.45  3.000
 F97  C14  N13  C7   131.08  3.000
 F97  N19  C14  N13  113.75  3.000
 F97  N19  C14  C15  121.42  3.000
 F97  N13  C14  C15  124.80  3.000
 F97  C27  C16  N17  116.55  3.000
 F97  N17  C16  C15  122.63  3.000
 F97  C27  C16  C15  120.81  3.000
 F97  C18  N17  C16  116.29  3.000
 F97  N20  C18  N19  116.95  3.000
 F97  N20  C18  N17  116.84  3.000
 F97  N19  C18  N17  126.21  3.000
 F97  C18  N19  C14  117.04  3.000
 F97  C18  N20  C24  123.20  3.000
 F97  C24  N20  C21  113.80  3.000
 F97  C18  N20  C21  122.94  3.000
 F97  F26  C23  F25  105.67  3.000
 F97  F25  C23  C24  112.40  3.000
 F97  F26  C23  C24  109.67  3.000
 F97  F25  C23  C22  113.87  3.000
 F97  F26  C23  C22  110.02  3.000
 F97  C24  C23  C22  105.24  3.000
 F97  H21  C27  C31  109.57  3.000
 F97  H21  C27  C16  108.50  3.000
 F97  C31  C27  C16  110.90  3.000
 F97  H21  C27  C28  110.12  3.000
 F97  C31  C27  C28  103.93  3.000
 F97  C16  C27  C28  113.73  3.000
 F97  H23  C29  H22  107.81  3.000
 F97  H23  C29  N30  111.18  3.000
 F97  H22  C29  N30  113.14  3.000
 F97  H23  C29  C28  112.97  3.000
 F97  H22  C29  C28  109.51  3.000
 F97  N30  C29  C28  102.25  3.000
 F97  H24  N30  C31  111.33  3.000
 F97  H24  N30  C29  111.82  3.000
 F97  C31  N30  C29  104.85  3.000
 F97  H27  C31  H26  107.61  3.000
 F97  H27  C31  N30  112.65  3.000
 F97  H26  C31  N30  111.42  3.000
 F97  H27  C31  C27  109.52  3.000
 F97  H26  C31  C27  111.81  3.000
 F97  N30  C31  C27  103.86  3.000
 F97  H14  C2   N4   105.51  3.000
 F97  H14  C2   C3   108.55  3.000
 F97  N4   C2   C3   110.77  3.000
 F97  H14  C2   C1   108.89  3.000
 F97  C3   C2   C1   112.37  3.000
 F97  N4   C2   C1   110.48  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
 F97  CONST_01  N8   C9   C10  C5     0.00   0.0  0
 F97  CONST_02  N12  C11  C10  C5     0.00   0.0  0
 F97  CONST_03  N8   C7   C6   C5     0.00   0.0  0
 F97  CONST_04  C11  N12  N4   C5     0.00   0.0  0
 F97  CONST_05  C9   N8   C7   C6     0.00   0.0  0
 F97  CONST_06  C9   C10  C5   C6     0.00   0.0  0
 F97  CONST_07  C11  C10  C5   C6   180.00   0.0  0
 F97  CONST_08  N12  N4   C5   C6   180.00   0.0  0
 F97  CONST_09  C10  C9   N8   C7     0.00   0.0  0
 F97  CONST_10  C10  C5   C6   C7     0.00   0.0  0
 F97  CONST_11  N4   C5   C6   C7   180.00   0.0  0
 F97  CONST_12  N4   N12  C11  C10    0.00   0.0  0
 F97  CONST_13  N12  N4   C5   C10    0.00   0.0  0
 F97  CONST_14  C9   C10  C11  N12  180.00   0.0  0
 F97  CONST_15  C18  N19  C14  C15    0.00   0.0  0
 F97  CONST_16  C18  N17  C16  C15    0.00   0.0  0
 F97  CONST_17  C9   C10  C5   N4   180.00   0.0  0
 F97  CONST_18  C11  C10  C5   N4     0.00   0.0  0
 F97  CONST_19  C11  C10  C9   N8   180.00   0.0  0
 F97  CONST_20  N17  C16  C15  C14    0.00   0.0  0
 F97  CONST_21  N17  C18  N19  C14    0.00   0.0  0
 F97  CONST_22  N19  C14  C15  C16    0.00   0.0  0
 F97  CONST_23  N19  C18  N17  C16    0.00   0.0  0
 F97  CONST_24  C27  C16  C15  C14  180.00   0.0  0
 F97  CONST_25  N20  C18  N19  C14  180.00   0.0  0
 F97  CONST_26  N20  C18  N17  C16  180.00   0.0  0
 F97  CONST_27  C27  C16  N17  C18  180.00   0.0  0
 F97  CONST_28  N13  C7   C6   C5   180.00   0.0  0
 F97  CONST_29  C2   N4   C5   C6     0.00   0.0  0
 F97  CONST_30  C2   N4   C5   C10  180.00   0.0  0
 F97  CONST_31  C11  N12  N4   C2   180.00   0.0  0
 F97  CONST_32  N13  C7   N8   C9   180.00   0.0  0
 F97  CONST_33  C16  C15  C14  N13  180.00   0.0  0
 F97  CONST_34  C18  N19  C14  N13  180.00   0.0  0
 F97  CONST_35  H18  C9   C10  C5   180.00   0.0  0
 F97  CONST_36  H19  C11  C10  C5   180.00   0.0  0
 F97  CONST_37  H1   C6   C5   C10  180.00   0.0  0
 F97  CONST_38  H2   C15  C16  N17  180.00   0.0  0
 F97  Var_01    N19  C18  N20  C21  179.63  30.0  2
 F97  Var_02    C23  C24  N20  C21  -12.09  30.0  1
 F97  Var_03    C24  C23  C22  C21  -37.00  30.0  1
 F97  Var_04    C18  N20  C21  C22  172.23  30.0  1
 F97  Var_05    N20  C24  C23  C22   30.22  30.0  1
 F97  Var_06    C31  N30  C29  C28   46.67  30.0  1
 F97  Var_07    C23  C22  C21  N20   28.61  30.0  1
 F97  Var_08    N30  C29  C28  C27  -32.98  30.0  1
 F97  Var_09    C29  N30  C31  C27  -41.04  30.0  1
 F97  Var_10    C14  N13  C7   C6   -26.70  30.0  2
 F97  Var_11    C15  C14  N13  C7   -10.31  30.0  2
 F97  Var_12    C1   C2   N4   C5   110.47  30.0  2
 F97  Var_13    H11  C1   C2   N4   -57.31  30.0  3
 F97  Var_14    H15  C3   C2   N4   -64.54  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
 F97  chir_01  C27  C28  C16  C31  negativ

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
 F97  plan-1  C15  0.020
 F97  plan-1  N13  0.020
 F97  plan-1  C14  0.020
 F97  plan-1  C16  0.020
 F97  plan-1  N17  0.020
 F97  plan-1  C18  0.020
 F97  plan-1  N19  0.020
 F97  plan-1  N20  0.020
 F97  plan-1  C27  0.020
 F97  plan-1  H2   0.020
 F97  plan-2  C5   0.020
 F97  plan-2  C6   0.020
 F97  plan-2  C7   0.020
 F97  plan-2  C10  0.020
 F97  plan-2  N12  0.020
 F97  plan-2  N4   0.020
 F97  plan-2  N8   0.020
 F97  plan-2  C9   0.020
 F97  plan-2  C11  0.020
 F97  plan-2  N13  0.020
 F97  plan-2  H1   0.020
 F97  plan-2  H18  0.020
 F97  plan-2  H19  0.020
 F97  plan-2  C2   0.020

