# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 13:40:35 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: N-{3-[(4S,5R)-2-amino-5-fluoro-4-(fluoromethyl)-5,6-dihydro-4H-1,3-oxazin-4-yl]-4-fluorophenyl}-5-cyanopyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=N[C@@](CF)([C@@H](F)CO1)c2cc(NC(=O)c3ccc(cn3)C#N)ccc2F
#
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
 1H5  1H5  N-{3-[(4S,5R)-2-amino-5-fluoro-4-(fluoromethyl)-5,6-dihydro-4H-1,3-oxazin-4-yl]-4-fluorophenyl}-5-cyanopyridine-2-carboxamide  ligand  42  28  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_1H5
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
 1H5  C2   C  CR16  0  -0.303  -0.1214   2.5258   0.7498
 1H5  C3   C  CR16  0  -0.377  -1.4660   2.8478   0.8088
 1H5  C4   C  CR6   0   0.522  -2.4275   1.9475   0.3966
 1H5  C5   C  CR6   0  -0.080  -2.1030   0.6795  -0.0748
 1H5  C6   C  CR16  0  -0.391  -0.7473   0.3776  -0.1273
 1H5  C8   C  CT    0  -0.119  -3.1084  -0.3479  -0.6099
 1H5  C9   C  CH2   0   0.052  -3.5156   0.0588  -2.0291
 1H5  C10  C  CH1   0   0.130  -4.3168  -0.5071   0.3196
 1H5  C11  C  CH2   0  -0.185  -3.8717  -1.1625   1.5991
 1H5  C13  C  C     0   0.668  -2.5375  -2.4866   0.1607
 1H5  N14  N  N     0  -0.494  -2.4791  -1.6366  -0.7843
 1H5  C1   C  CR6   0   0.439   0.2446   1.2704   0.2713
 1H5  F7   F  F     0  -0.310  -3.7080   2.3449   0.4899
 1H5  O12  O  O2    0  -0.462  -3.1369  -2.3572   1.3472
 1H5  F15  F  F     0  -0.365  -5.2300  -1.3520  -0.3023
 1H5  N16  N  NH2   0  -0.808  -1.9093  -3.6900   0.0664
 1H5  N17  N  NH1   0  -0.768   1.5640   0.8289   0.1526
 1H5  C18  C  C     0   0.546   2.7067   1.4632   0.4838
 1H5  C19  C  CR6   0   0.137   3.9346   0.6400   0.1940
 1H5  O20  O  O     0  -0.411   2.8051   2.5729   0.9645
 1H5  N21  N  N     0  -0.429   3.7577  -0.5687  -0.3263
 1H5  C22  C  CR16  0  -0.014   4.8118  -1.3135  -0.5878
 1H5  C23  C  CR6   0  -0.063   6.1133  -0.8774  -0.3392
 1H5  C24  C  CR16  0  -0.113   6.2993   0.3908   0.2037
 1H5  C25  C  CR16  0  -0.271   5.1881   1.1650   0.4767
 1H5  C26  C  CSP   0   0.022   7.2202  -1.7252  -0.6367
 1H5  N27  N  NS    0  -0.168   8.1100  -2.4142  -0.8780
 1H5  F28  F  F     0  -0.354  -4.0971   1.3102  -2.0473
 1H5  H1   H  HCR6  0   0.295   0.6130   3.2464   1.0702
 1H5  H2   H  HCR6  0   0.263  -1.7731   3.8183   1.1746
 1H5  H3   H  HCR6  0   0.257  -0.4608  -0.5958  -0.5034
 1H5  H4   H  HCH2  0   0.205  -2.6211   0.0760  -2.6538
 1H5  H5   H  HCH2  0   0.215  -4.2193  -0.6625  -2.4445
 1H5  H6   H  HCH1  0   0.259  -4.8313   0.4242   0.5410
 1H5  H7   H  HCH2  0   0.245  -3.2570  -0.4738   2.1822
 1H5  H8   H  HCH2  0   0.264  -4.7279  -1.4462   2.2103
 1H5  H9   H  HNH2  0   0.369  -1.6377  -3.9553  -0.8636
 1H5  H10  H  HNH2  0   0.370  -2.2527  -4.4402   0.6410
 1H5  H11  H  HNH1  0   0.404   1.6980  -0.0958  -0.2348
 1H5  H12  H  HCR6  0   0.268   4.6330  -2.2950  -1.0100
 1H5  H13  H  HCR6  0   0.271   7.2956   0.7583   0.4076
 1H5  H14  H  HCR6  0   0.285   5.2810   2.1544   0.9000

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
 1H5  F7   C4   single    1.344  0.020  1.344
 1H5  F15  C10  single    1.391  0.020  1.391
 1H5  C10  C11  single    1.505  0.020  1.505
 1H5  C10  C8   single    1.533  0.020  1.533
 1H5  F28  C9   single    1.380  0.020  1.380
 1H5  C9   C8   single    1.531  0.020  1.531
 1H5  C4   C3   aromatic  1.380  0.020  1.380
 1H5  C4   C5   aromatic  1.391  0.020  1.391
 1H5  C11  O12  single    1.425  0.020  1.425
 1H5  C3   C2   aromatic  1.384  0.020  1.384
 1H5  C8   C5   single    1.534  0.020  1.534
 1H5  C8   N14  single    1.445  0.020  1.445
 1H5  C5   C6   aromatic  1.390  0.020  1.390
 1H5  O12  C13  single    1.336  0.020  1.336
 1H5  C2   C1   aromatic  1.392  0.020  1.392
 1H5  N14  C13  double    1.272  0.020  1.272
 1H5  C13  N16  single    1.361  0.020  1.361
 1H5  C6   C1   aromatic  1.393  0.020  1.393
 1H5  C1   N17  single    1.396  0.020  1.396
 1H5  O20  C18  double    1.213  0.020  1.213
 1H5  N17  C18  single    1.348  0.020  1.348
 1H5  C18  C19  single    1.506  0.020  1.506
 1H5  C19  C25  aromatic  1.388  0.020  1.388
 1H5  C19  N21  aromatic  1.328  0.020  1.328
 1H5  C25  C24  aromatic  1.382  0.020  1.382
 1H5  N21  C22  aromatic  1.317  0.020  1.317
 1H5  C24  C23  aromatic  1.392  0.020  1.392
 1H5  C22  C23  aromatic  1.395  0.020  1.395
 1H5  C23  C26  single    1.426  0.020  1.426
 1H5  C26  N27  triple    1.151  0.020  1.151
 1H5  C2   H1   single    0.930  0.020  1.080
 1H5  C3   H2   single    0.930  0.020  1.080
 1H5  C6   H3   single    0.930  0.020  1.080
 1H5  C9   H4   single    0.970  0.020  1.090
 1H5  C9   H5   single    0.970  0.020  1.090
 1H5  C10  H6   single    0.970  0.020  1.090
 1H5  C11  H7   single    0.970  0.020  1.090
 1H5  C11  H8   single    0.970  0.020  1.090
 1H5  N16  H9   single    0.890  0.020  1.040
 1H5  N16  H10  single    0.890  0.020  1.040
 1H5  N17  H11  single    0.860  0.020  1.020
 1H5  C22  H12  single    0.930  0.020  1.080
 1H5  C24  H13  single    0.930  0.020  1.080
 1H5  C25  H14  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
 1H5  H1   C2   C1   121.73  3.000
 1H5  H1   C2   C3   119.60  3.000
 1H5  C1   C2   C3   118.67  3.000
 1H5  H2   C3   C4   119.24  3.000
 1H5  H2   C3   C2   119.94  3.000
 1H5  C4   C3   C2   120.82  3.000
 1H5  F7   C4   C5   121.02  3.000
 1H5  C5   C4   C3   122.22  3.000
 1H5  F7   C4   C3   116.75  3.000
 1H5  C8   C5   C6   118.73  3.000
 1H5  C6   C5   C4   116.00  3.000
 1H5  C8   C5   C4   125.15  3.000
 1H5  H3   C6   C1   119.17  3.000
 1H5  H3   C6   C5   117.82  3.000
 1H5  C1   C6   C5   123.00  3.000
 1H5  N14  C8   C10  108.90  3.000
 1H5  N14  C8   C9   103.93  3.000
 1H5  C10  C8   C9   112.33  3.000
 1H5  N14  C8   C5   110.74  3.000
 1H5  C9   C8   C5   108.64  3.000
 1H5  C10  C8   C5   112.01  3.000
 1H5  H5   C9   H4   108.75  3.000
 1H5  H5   C9   F28  108.84  3.000
 1H5  H4   C9   F28  108.88  3.000
 1H5  H5   C9   C8   110.44  3.000
 1H5  H4   C9   C8   108.46  3.000
 1H5  F28  C9   C8   111.41  3.000
 1H5  H6   C10  F15  107.51  3.000
 1H5  H6   C10  C11  109.88  3.000
 1H5  F15  C10  C11  108.05  3.000
 1H5  H6   C10  C8   114.06  3.000
 1H5  C11  C10  C8   109.13  3.000
 1H5  F15  C10  C8   108.04  3.000
 1H5  H8   C11  H7   107.88  3.000
 1H5  H8   C11  O12  106.63  3.000
 1H5  H7   C11  O12  109.45  3.000
 1H5  H8   C11  C10  110.97  3.000
 1H5  H7   C11  C10  110.23  3.000
 1H5  O12  C11  C10  111.55  3.000
 1H5  N16  C13  O12  110.76  3.000
 1H5  N16  C13  N14  121.21  3.000
 1H5  O12  C13  N14  128.00  3.000
 1H5  C13  N14  C8   119.09  3.000
 1H5  N17  C1   C6   116.49  3.000
 1H5  N17  C1   C2   124.23  3.000
 1H5  C6   C1   C2   119.28  3.000
 1H5  C13  O12  C11  118.02  3.000
 1H5  H10  N16  H9   115.11  3.000
 1H5  H10  N16  C13  117.56  3.000
 1H5  H9   N16  C13  114.99  3.000
 1H5  H11  N17  C18  114.32  3.000
 1H5  H11  N17  C1   116.54  3.000
 1H5  C18  N17  C1   129.14  3.000
 1H5  O20  C18  C19  120.66  3.000
 1H5  C19  C18  N17  112.73  3.000
 1H5  O20  C18  N17  126.60  3.000
 1H5  C25  C19  N21  122.98  3.000
 1H5  N21  C19  C18  117.66  3.000
 1H5  C25  C19  C18  119.35  3.000
 1H5  C22  N21  C19  119.08  3.000
 1H5  H12  C22  C23  120.44  3.000
 1H5  H12  C22  N21  117.24  3.000
 1H5  C23  C22  N21  122.32  3.000
 1H5  C26  C23  C24  121.29  3.000
 1H5  C26  C23  C22  120.09  3.000
 1H5  C24  C23  C22  118.62  3.000
 1H5  H13  C24  C25  120.89  3.000
 1H5  H13  C24  C23  120.42  3.000
 1H5  C25  C24  C23  118.69  3.000
 1H5  H14  C25  C24  121.44  3.000
 1H5  H14  C25  C19  120.26  3.000
 1H5  C24  C25  C19  118.30  3.000
 1H5  N27  C26  C23  180.00  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
 1H5  CONST_01  C5   C4   C3   C2     0.00   0.0  0
 1H5  CONST_02  C5   C6   C1   C2     0.00   0.0  0
 1H5  CONST_03  C6   C5   C4   C3     0.00   0.0  0
 1H5  CONST_04  C6   C1   C2   C3     0.00   0.0  0
 1H5  CONST_05  C1   C2   C3   C4     0.00   0.0  0
 1H5  CONST_06  C1   C6   C5   C4     0.00   0.0  0
 1H5  CONST_07  C23  C24  C25  C19    0.00   0.0  0
 1H5  CONST_08  C23  C22  N21  C19    0.00   0.0  0
 1H5  CONST_09  C24  C25  C19  N21    0.00   0.0  0
 1H5  CONST_10  C24  C23  C22  N21    0.00   0.0  0
 1H5  CONST_11  C25  C19  N21  C22    0.00   0.0  0
 1H5  CONST_12  C25  C24  C23  C22    0.00   0.0  0
 1H5  CONST_13  C8   C5   C4   C3   180.00   0.0  0
 1H5  CONST_14  C1   C6   C5   C8   180.00   0.0  0
 1H5  CONST_15  O12  C13  N14  C8     0.00   0.0  0
 1H5  CONST_16  F7   C4   C3   C2   180.00   0.0  0
 1H5  CONST_17  N17  C1   C2   C3   180.00   0.0  0
 1H5  CONST_18  N17  C1   C6   C5   180.00   0.0  0
 1H5  CONST_19  F7   C4   C5   C6   180.00   0.0  0
 1H5  CONST_20  F7   C4   C5   C8     0.00   0.0  0
 1H5  CONST_21  C24  C25  C19  C18  180.00   0.0  0
 1H5  CONST_22  C22  N21  C19  C18  180.00   0.0  0
 1H5  CONST_23  C26  C23  C22  N21  180.00   0.0  0
 1H5  CONST_24  C26  C23  C24  C25  180.00   0.0  0
 1H5  CONST_25  N16  C13  N14  C8   180.00   0.0  0
 1H5  CONST_26  H3   C6   C1   C2   180.00   0.0  0
 1H5  CONST_27  H1   C2   C3   C4   180.00   0.0  0
 1H5  CONST_28  H2   C3   C4   C5   180.00   0.0  0
 1H5  CONST_29  H13  C24  C25  C19  180.00   0.0  0
 1H5  CONST_30  H12  C22  N21  C19  180.00   0.0  0
 1H5  CONST_31  H14  C25  C19  N21  180.00   0.0  0
 1H5  CONST_32  C19  C18  N17  C1   180.00   0.0  0
 1H5  CONST_33  C18  N17  C1   C2     0.00   0.0  0
 1H5  CONST_34  C18  N17  C1   C6   180.00   0.0  0
 1H5  CONST_35  H11  N17  C1   C2   180.00   0.0  0
 1H5  CONST_38  O20  C18  N17  C1     0.00   0.0  0
 1H5  Var_01    N14  C13  O12  C11    3.64  30.0  1
 1H5  Var_02    H7   C11  O12  C13  -98.74  30.0  1
 1H5  Var_03    C25  C19  C18  N17  179.68  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
 1H5  chir_01  C8   C10  C5  N14  negativ
 1H5  chir_02  C10  F15  C8  C11  positiv

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
 1H5  plan-1  C2   0.020
 1H5  plan-1  C3   0.020
 1H5  plan-1  C4   0.020
 1H5  plan-1  C5   0.020
 1H5  plan-1  C6   0.020
 1H5  plan-1  C8   0.020
 1H5  plan-1  C1   0.020
 1H5  plan-1  F7   0.020
 1H5  plan-1  N17  0.020
 1H5  plan-1  H1   0.020
 1H5  plan-1  H2   0.020
 1H5  plan-1  H3   0.020
 1H5  plan-2  C18  0.020
 1H5  plan-2  C19  0.020
 1H5  plan-2  N21  0.020
 1H5  plan-2  C22  0.020
 1H5  plan-2  C23  0.020
 1H5  plan-2  C24  0.020
 1H5  plan-2  C25  0.020
 1H5  plan-2  C26  0.020
 1H5  plan-2  N27  0.020
 1H5  plan-2  H12  0.020
 1H5  plan-2  H13  0.020
 1H5  plan-2  H14  0.020
 1H5  plan-3  C1   0.020
 1H5  plan-3  N17  0.020
 1H5  plan-3  C18  0.020
 1H5  plan-3  C19  0.020
 1H5  plan-3  O20  0.020
 1H5  plan-3  H11  0.020
 1H5  plan-4  C8   0.020
 1H5  plan-4  C13  0.020
 1H5  plan-4  N14  0.020
 1H5  plan-4  O12  0.020
 1H5  plan-4  N16  0.020
 1H5  plan-4  H9   0.020
 1H5  plan-4  H10  0.020

