# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 23:20:52 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 6-[(3~{R})-3-oxidanylpyrrolidin-1-yl]-5-pyrimidin-5-yl-~{N}-[4-(trifluoromethyloxy)phenyl]pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CCN(C1)c2ncc(cc2c3cncnc3)C(=O)Nc4ccc(OC(F)(F)F)cc4
#
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
 FYW  FYW  6-[(3~{R})-3-oxidanylpyrrolidin-1-yl]-5-pyrimidin-5-yl-~{N}-[4-(trifluoromethyloxy)phenyl]pyridine-3-carboxamide  ligand  50  32  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FYW
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
 FYW  C2   C  CT    0   1.071   7.9291   0.2807   0.7619
 FYW  C41  C  CR15  0  -0.017  -6.4208   2.7133  -0.3507
 FYW  C43  C  CH2   0  -0.503  -6.6185   1.5937  -1.3650
 FYW  C46  C  CH2   0  -0.282  -5.7455   0.4751  -0.8107
 FYW  C11  C  CR6   0   0.397   3.0445   0.5881  -0.0599
 FYW  C12  C  CR16  0  -0.315   3.7704  -0.4698  -0.6110
 FYW  C14  C  CR16  0  -0.288   5.1560  -0.4112  -0.6548
 FYW  C18  C  C     0   0.547   0.7382  -0.3096  -0.3107
 FYW  C20  C  CR6   0  -0.171  -0.6841   0.0838  -0.1763
 FYW  C21  C  CR16  0  -0.071  -1.1540   1.3822  -0.0160
 FYW  C24  C  CR6   0   0.503  -3.3681   0.7554  -0.0965
 FYW  C25  C  CR6   0  -0.038  -3.0022  -0.6219  -0.1219
 FYW  C26  C  CR16  0  -0.182  -1.6583  -0.9162  -0.2076
 FYW  C28  C  CR6   0  -0.096  -3.9493  -1.7378   0.0328
 FYW  C29  C  CR16  0  -0.043  -4.8329  -1.8271   1.1045
 FYW  F1   F  F     0  -0.278   9.2079   0.4681   0.4753
 FYW  F3   F  F     0  -0.300   7.7317  -1.0245   0.9602
 FYW  F4   F  F     0  -0.300   7.6653   0.8898   1.9199
 FYW  O5   O  O2    0  -0.523   7.2079   0.7658  -0.2550
 FYW  C6   C  CR6   0   0.295   5.8215   0.6917  -0.1554
 FYW  C7   C  CR16  0  -0.284   5.1194   1.7543   0.3868
 FYW  C9   C  CR16  0  -0.362   3.7395   1.6978   0.4304
 FYW  O19  O  O     0  -0.464   1.0454  -1.4248  -0.6998
 FYW  N23  N  N     0  -0.466  -2.4303   1.7044   0.0181
 FYW  N31  N  N     0  -0.382  -5.6341  -2.8672   1.2838
 FYW  C32  C  CR16  0   0.050  -5.5565  -3.8405   0.3890
 FYW  N34  N  N     0  -0.387  -4.7524  -3.8719  -0.6626
 FYW  C35  C  CR16  0  -0.030  -3.9568  -2.8260  -0.8334
 FYW  N37  N  NR5   0  -0.497  -4.6381   1.1970  -0.1883
 FYW  C38  C  CH2   0  -0.268  -4.9308   2.6251  -0.0775
 FYW  O49  O  OH1   0  -0.669  -7.1074   2.4605   0.8563
 FYW  H1   H  HCR5  0   0.239  -6.6832   3.6944  -0.7615
 FYW  H3   H  HCH2  0   0.249  -6.2490   1.9150  -2.3410
 FYW  H4   H  HCH2  0   0.246  -6.3020  -0.1215  -0.0846
 FYW  H5   H  HCH2  0   0.260  -5.3914  -0.1959  -1.5933
 FYW  H6   H  HCR6  0   0.291   3.2757  -1.3391  -1.0085
 FYW  H7   H  HCR6  0   0.282   5.7047  -1.2314  -1.0985
 FYW  H8   H  HCR6  0   0.256  -0.4780   2.2280   0.0656
 FYW  H9   H  HCR6  0   0.271  -1.3508  -1.9539  -0.2496
 FYW  H10  H  HCR6  0   0.283  -4.8852  -1.0352   1.8450
 FYW  H11  H  HCR6  0   0.284   5.6346   2.6286   0.7613
 FYW  H12  H  HCR6  0   0.282   3.1944   2.5329   0.8527
 FYW  H14  H  HCR6  0   0.269  -6.2103  -4.6929   0.5334
 FYW  H15  H  HCR6  0   0.279  -3.3011  -2.8425  -1.6983
 FYW  H16  H  HCH2  0   0.244  -4.3789   3.2012  -0.8243
 FYW  H17  H  HCH2  0   0.255  -4.6610   3.0149   0.9053
 FYW  H18  H  HOH1  0   0.452  -8.0485   2.4097   0.6612
 FYW  N16  N  NH1   0  -0.777   1.6529   0.6402   0.0243
 FYW  H2   H  HCH2  0   0.263  -7.6601   1.2926  -1.4841
 FYW  H13  H  HNH1  0   0.425   1.3009   1.4918   0.4318

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
 FYW  F4   C2   single    1.335  0.020  1.335
 FYW  O5   C2   single    1.338  0.020  1.338
 FYW  O5   C6   single    1.392  0.020  1.392
 FYW  C2   F3   single    1.335  0.020  1.335
 FYW  C2   F1   single    1.324  0.020  1.324
 FYW  C6   C7   aromatic  1.384  0.020  1.384
 FYW  C6   C14  aromatic  1.382  0.020  1.382
 FYW  C7   C9   aromatic  1.382  0.020  1.382
 FYW  C9   C11  aromatic  1.398  0.020  1.398
 FYW  C14  C12  aromatic  1.388  0.020  1.388
 FYW  C11  C12  aromatic  1.396  0.020  1.396
 FYW  C11  N16  single    1.395  0.020  1.395
 FYW  O19  C18  double    1.220  0.020  1.220
 FYW  N16  C18  single    1.361  0.020  1.361
 FYW  C18  C20  single    1.482  0.020  1.482
 FYW  C20  C21  aromatic  1.390  0.020  1.390
 FYW  C20  C26  aromatic  1.396  0.020  1.396
 FYW  C21  N23  aromatic  1.317  0.020  1.317
 FYW  C26  C25  aromatic  1.378  0.020  1.378
 FYW  N23  C24  aromatic  1.339  0.020  1.339
 FYW  C24  C25  aromatic  1.425  0.020  1.425
 FYW  C24  N37  single    1.348  0.020  1.348
 FYW  C25  C28  single    1.472  0.020  1.472
 FYW  C38  N37  single    1.462  0.020  1.462
 FYW  C38  C41  single    1.517  0.020  1.517
 FYW  N37  C46  single    1.461  0.020  1.461
 FYW  C28  C35  aromatic  1.391  0.020  1.391
 FYW  C28  C29  aromatic  1.392  0.020  1.392
 FYW  C35  N34  aromatic  1.325  0.020  1.325
 FYW  C29  N31  aromatic  1.325  0.020  1.325
 FYW  C46  C43  single    1.523  0.020  1.523
 FYW  C41  C43  single    1.524  0.020  1.524
 FYW  C41  O49  single    1.411  0.020  1.411
 FYW  N34  C32  aromatic  1.324  0.020  1.324
 FYW  N31  C32  aromatic  1.324  0.020  1.324
 FYW  C41  H1   single    0.970  0.020  1.090
 FYW  C43  H2   single    0.970  0.020  1.090
 FYW  C43  H3   single    0.970  0.020  1.090
 FYW  C46  H4   single    0.970  0.020  1.090
 FYW  C46  H5   single    0.970  0.020  1.090
 FYW  C12  H6   single    0.930  0.020  1.080
 FYW  C14  H7   single    0.930  0.020  1.080
 FYW  C21  H8   single    0.930  0.020  1.080
 FYW  C26  H9   single    0.930  0.020  1.080
 FYW  C29  H10  single    0.930  0.020  1.080
 FYW  C7   H11  single    0.930  0.020  1.080
 FYW  C9   H12  single    0.930  0.020  1.080
 FYW  N16  H13  single    0.860  0.020  1.020
 FYW  C32  H14  single    0.930  0.020  1.080
 FYW  C35  H15  single    0.930  0.020  1.080
 FYW  C38  H16  single    0.970  0.020  1.090
 FYW  C38  H17  single    0.970  0.020  1.090
 FYW  O49  H18  single    0.850  0.020  0.980

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
 FYW  O5   C2   F4   112.80  3.000
 FYW  O5   C2   F3   112.82  3.000
 FYW  F4   C2   F3   106.75  3.000
 FYW  F3   C2   F1   108.27  3.000
 FYW  O5   C2   F1   107.75  3.000
 FYW  F4   C2   F1   108.31  3.000
 FYW  H1   C41  O49  111.38  3.000
 FYW  H1   C41  C38  110.78  3.000
 FYW  O49  C41  C38  108.26  3.000
 FYW  H1   C41  C43  112.17  3.000
 FYW  O49  C41  C43  112.00  3.000
 FYW  C38  C41  C43  101.81  3.000
 FYW  H3   C43  H2   107.86  3.000
 FYW  H3   C43  C46  110.32  3.000
 FYW  H2   C43  C46  112.60  3.000
 FYW  H3   C43  C41  109.57  3.000
 FYW  H2   C43  C41  113.55  3.000
 FYW  C46  C43  C41  102.88  3.000
 FYW  H5   C46  H4   107.85  3.000
 FYW  H5   C46  N37  111.33  3.000
 FYW  H4   C46  N37  111.89  3.000
 FYW  H5   C46  C43  112.15  3.000
 FYW  H4   C46  C43  110.55  3.000
 FYW  N37  C46  C43  103.09  3.000
 FYW  N16  C11  C9   116.42  3.000
 FYW  N16  C11  C12  124.80  3.000
 FYW  C9   C11  C12  118.77  3.000
 FYW  H6   C12  C14  118.78  3.000
 FYW  H6   C12  C11  121.25  3.000
 FYW  C14  C12  C11  119.97  3.000
 FYW  H7   C14  C6   120.60  3.000
 FYW  H7   C14  C12  119.17  3.000
 FYW  C6   C14  C12  120.22  3.000
 FYW  O19  C18  N16  123.17  3.000
 FYW  N16  C18  C20  115.95  3.000
 FYW  O19  C18  C20  120.88  3.000
 FYW  C26  C20  C21  115.82  3.000
 FYW  C26  C20  C18  118.52  3.000
 FYW  C21  C20  C18  125.66  3.000
 FYW  H8   C21  N23  114.26  3.000
 FYW  H8   C21  C20  121.73  3.000
 FYW  N23  C21  C20  124.00  3.000
 FYW  N37  C24  N23  115.70  3.000
 FYW  N37  C24  C25  123.87  3.000
 FYW  N23  C24  C25  120.43  3.000
 FYW  C28  C25  C26  118.17  3.000
 FYW  C28  C25  C24  124.44  3.000
 FYW  C26  C25  C24  117.24  3.000
 FYW  H9   C26  C25  118.93  3.000
 FYW  H9   C26  C20  119.27  3.000
 FYW  C25  C26  C20  121.73  3.000
 FYW  C35  C28  C29  115.21  3.000
 FYW  C29  C28  C25  122.55  3.000
 FYW  C35  C28  C25  122.09  3.000
 FYW  H10  C29  N31  116.82  3.000
 FYW  H10  C29  C28  120.61  3.000
 FYW  N31  C29  C28  122.57  3.000
 FYW  C6   O5   C2   117.59  3.000
 FYW  C7   C6   O5   119.50  3.000
 FYW  C7   C6   C14  120.67  3.000
 FYW  O5   C6   C14  119.76  3.000
 FYW  H11  C7   C9   119.86  3.000
 FYW  H11  C7   C6   120.96  3.000
 FYW  C9   C7   C6   119.18  3.000
 FYW  H12  C9   C7   118.91  3.000
 FYW  H12  C9   C11  119.91  3.000
 FYW  C7   C9   C11  121.19  3.000
 FYW  C24  N23  C21  120.21  3.000
 FYW  C32  N31  C29  116.74  3.000
 FYW  H14  C32  N34  116.96  3.000
 FYW  H14  C32  N31  116.91  3.000
 FYW  N34  C32  N31  126.13  3.000
 FYW  C35  N34  C32  116.63  3.000
 FYW  H15  C35  N34  116.96  3.000
 FYW  H15  C35  C28  120.32  3.000
 FYW  N34  C35  C28  122.71  3.000
 FYW  C38  N37  C24  120.23  3.000
 FYW  C38  N37  C46  111.30  3.000
 FYW  C24  N37  C46  125.55  3.000
 FYW  H17  C38  H16  107.60  3.000
 FYW  H17  C38  N37  111.58  3.000
 FYW  H16  C38  N37  111.23  3.000
 FYW  H17  C38  C41  112.59  3.000
 FYW  H16  C38  C41  110.01  3.000
 FYW  N37  C38  C41  103.87  3.000
 FYW  H18  O49  C41  108.17  3.000
 FYW  H13  N16  C18  117.05  3.000
 FYW  H13  N16  C11  113.86  3.000
 FYW  C18  N16  C11  129.02  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
 FYW  CONST_01  C6   C7   C9   C11     0.00   0.0  0
 FYW  CONST_02  C6   C14  C12  C11     0.00   0.0  0
 FYW  CONST_03  C7   C6   C14  C12     0.00   0.0  0
 FYW  CONST_04  C7   C9   C11  C12     0.00   0.0  0
 FYW  CONST_05  C9   C7   C6   C14     0.00   0.0  0
 FYW  CONST_06  C9   C11  C12  C14     0.00   0.0  0
 FYW  CONST_07  C24  N23  C21  C20     0.00   0.0  0
 FYW  CONST_08  C24  C25  C26  C20     0.00   0.0  0
 FYW  CONST_09  C28  C25  C26  C20   180.00   0.0  0
 FYW  CONST_10  C25  C26  C20  C21     0.00   0.0  0
 FYW  CONST_11  C25  C24  N23  C21     0.00   0.0  0
 FYW  CONST_14  N34  C35  C28  C25   180.00   0.0  0
 FYW  CONST_15  N31  C29  C28  C25   180.00   0.0  0
 FYW  CONST_16  N23  C21  C20  C26     0.00   0.0  0
 FYW  CONST_17  N23  C24  C25  C26     0.00   0.0  0
 FYW  CONST_20  N23  C24  C25  C28   180.00   0.0  0
 FYW  CONST_21  C32  N34  C35  C28     0.00   0.0  0
 FYW  CONST_22  C32  N31  C29  C28     0.00   0.0  0
 FYW  CONST_23  N34  C35  C28  C29     0.00   0.0  0
 FYW  CONST_24  N34  C32  N31  C29     0.00   0.0  0
 FYW  CONST_25  C35  C28  C29  N31     0.00   0.0  0
 FYW  CONST_26  C35  N34  C32  N31     0.00   0.0  0
 FYW  CONST_27  N37  C24  N23  C21   180.00   0.0  0
 FYW  CONST_28  N37  C24  C25  C26   180.00   0.0  0
 FYW  CONST_29  N37  C24  C25  C28     0.00   0.0  0
 FYW  CONST_30  O5   C6   C14  C12   180.00   0.0  0
 FYW  CONST_31  N16  C11  C12  C14   180.00   0.0  0
 FYW  CONST_32  N23  C21  C20  C18   180.00   0.0  0
 FYW  CONST_33  C25  C26  C20  C18   180.00   0.0  0
 FYW  CONST_34  C9   C7   C6   O5    180.00   0.0  0
 FYW  CONST_35  N16  C11  C9   C7    180.00   0.0  0
 FYW  CONST_36  H11  C7   C9   C11   180.00   0.0  0
 FYW  CONST_37  H7   C14  C12  C11   180.00   0.0  0
 FYW  CONST_38  H12  C9   C11  C12   180.00   0.0  0
 FYW  CONST_39  H9   C26  C20  C21   180.00   0.0  0
 FYW  CONST_40  H8   C21  N23  C24   180.00   0.0  0
 FYW  CONST_41  H15  C35  C28  C25     0.00   0.0  0
 FYW  CONST_42  H10  C29  C28  C25     0.00   0.0  0
 FYW  CONST_43  H14  C32  N31  C29   180.00   0.0  0
 FYW  CONST_44  H6   C12  C14  C6    180.00   0.0  0
 FYW  CONST_45  C20  C18  N16  C11   180.00   0.0  0
 FYW  CONST_46  C18  N16  C11  C12     0.00   0.0  0
 FYW  CONST_47  C9   C11  N16  C18   180.00   0.0  0
 FYW  CONST_48  H13  N16  C11  C12   180.00   0.0  0
 FYW  CONST_49  O19  C18  N16  C11     0.00   0.0  0
 FYW  Var_01    C24  N37  C38  C41   175.27  30.0  1
 FYW  Var_02    N37  C46  C43  C41   -33.08  30.0  1
 FYW  Var_03    N23  C24  N37  C46   155.15  30.0  2
 FYW  Var_04    C7   C6   O5   C2     91.93  30.0  2
 FYW  Var_05    O19  C18  C20  C21  -165.85  30.0  2

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
 FYW  chir_01  C41  C38  C43  O49  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
 FYW  plan-1  C18  0.020
 FYW  plan-1  C20  0.020
 FYW  plan-1  C21  0.020
 FYW  plan-1  C24  0.020
 FYW  plan-1  C25  0.020
 FYW  plan-1  C26  0.020
 FYW  plan-1  C28  0.020
 FYW  plan-1  N23  0.020
 FYW  plan-1  N37  0.020
 FYW  plan-1  H8   0.020
 FYW  plan-1  H9   0.020
 FYW  plan-2  C25  0.020
 FYW  plan-2  C28  0.020
 FYW  plan-2  C29  0.020
 FYW  plan-2  N31  0.020
 FYW  plan-2  C32  0.020
 FYW  plan-2  N34  0.020
 FYW  plan-2  C35  0.020
 FYW  plan-2  H10  0.020
 FYW  plan-2  H14  0.020
 FYW  plan-2  H15  0.020
 FYW  plan-3  C11  0.020
 FYW  plan-3  C12  0.020
 FYW  plan-3  C14  0.020
 FYW  plan-3  O5   0.020
 FYW  plan-3  C6   0.020
 FYW  plan-3  C7   0.020
 FYW  plan-3  C9   0.020
 FYW  plan-3  H6   0.020
 FYW  plan-3  H7   0.020
 FYW  plan-3  H11  0.020
 FYW  plan-3  H12  0.020
 FYW  plan-3  N16  0.020
 FYW  plan-4  C11  0.020
 FYW  plan-4  C18  0.020
 FYW  plan-4  C20  0.020
 FYW  plan-4  O19  0.020
 FYW  plan-4  N16  0.020
 FYW  plan-4  H13  0.020

