# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 22:42:19 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: N-{3-[(4S)-2-amino-4-methyl-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: C[C@]1(CCOC(=N1)N)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
 1H8  1H8  N-{3-[(4S)-2-amino-4-methyl-5,6-dihydro-4H-1,3-oxazin-4-yl]-4-fluorophenyl}-5-cyanopyridine-2-carboxamide  ligand  42  26  .  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_1H8
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
 1H8  C1   C  CR6   0  -0.081  -5.6517   1.1438  -0.1217
 1H8  C2   C  CR16  0  -0.016  -4.3272   1.5614  -0.2627
 1H8  N3   N  N     0  -0.438  -3.3176   0.7216  -0.1644
 1H8  C4   C  CR6   0   0.145  -3.5642  -0.5619   0.0747
 1H8  C5   C  CR16  0  -0.283  -4.8457  -1.0708   0.2308
 1H8  C6   C  CR16  0  -0.112  -5.9142  -0.1989   0.1312
 1H8  C10  C  CSP   0   0.060  -6.7101   2.0907  -0.2403
 1H8  C14  C  CR16  0  -0.423   1.1329  -0.4833  -0.1650
 1H8  C15  C  CR16  0  -0.395   1.7138  -3.1409   0.2035
 1H8  C16  C  CR6   0   0.421   0.0910  -1.3930   0.0247
 1H8  C17  C  CR16  0  -0.315   0.3863  -2.7405   0.2125
 1H8  C19  C  CR6   0   0.034   3.5758   0.1702  -0.4007
 1H8  C23  C  C     0  -0.186   5.4067   1.3973   0.7610
 1H8  C25  C  CR6   0   0.628   3.4506   2.4908   0.0659
 1H8  C7   C  C     0   0.542  -2.3810  -1.4884   0.1725
 1H8  O8   O  O     0  -0.453  -2.5404  -2.6786   0.3809
 1H8  N9   N  NH1   0  -0.761  -1.2027  -0.8631   0.0069
 1H8  N11  N  NS    0  -0.233  -7.5616   2.8595  -0.3384
 1H8  C12  C  CR6   0  -0.059   2.4674  -0.8620  -0.1769
 1H8  C13  C  CR6   0   0.507   2.7189  -2.2176   0.0119
 1H8  F18  F  F     0  -0.316   3.9865  -2.6778   0.0142
 1H8  C20  C  CH3   0  -0.640   4.2733  -0.1360  -1.7362
 1H8  N21  N  N     0  -0.485   2.9598   1.4743  -0.5181
 1H8  C22  C  C     0  -0.505   4.5652   0.1427   0.7770
 1H8  O24  O  O     0  -0.464   4.5844   2.5618   0.7786
 1H8  N26  N  NH2   0  -0.829   2.8042   3.6907   0.0758
 1H8  H1   H  HCR6  0   0.302  -4.0936   2.6006  -0.4597
 1H8  H2   H  HCR6  0   0.295  -5.0069  -2.1208   0.4236
 1H8  H3   H  HCR6  0   0.305  -6.9297  -0.5511   0.2468
 1H8  H5   H  HCR6  0   0.278   1.9654  -4.1838   0.3473
 1H8  H6   H  HCR6  0   0.286  -0.3853  -3.4768   0.3619
 1H8  H7   H  H     0   0.259   6.0402   1.4588   1.6445
 1H8  H8   H  H     0   0.235   6.0557   1.4298  -0.1183
 1H8  H9   H  HNH1  0   0.426  -1.2724   0.1349  -0.1530
 1H8  H10  H  HCH3  0   0.237   3.5550  -0.0711  -2.5537
 1H8  H11  H  HCH3  0   0.233   5.0618   0.5915  -1.9324
 1H8  H12  H  HCH3  0   0.230   4.7224  -1.1276  -1.7529
 1H8  H13  H  H     0   0.255   4.0164   0.0866   1.7214
 1H8  H14  H  H     0   0.262   5.2291  -0.7188   0.7329
 1H8  H15  H  HNH2  0   0.387   2.0405   3.7675  -0.5756
 1H8  H16  H  HNH2  0   0.389   3.3715   4.5212   0.1385
 1H8  H4   H  HCR6  0   0.278   0.9098   0.5654  -0.3142

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
 1H8  F18  C13  single    1.349  0.020  1.349
 1H8  C22  C23  single    1.511  0.020  1.511
 1H8  C22  C19  single    1.538  0.020  1.538
 1H8  C13  C15  aromatic  1.378  0.020  1.378
 1H8  C13  C12  aromatic  1.392  0.020  1.392
 1H8  C23  O24  single    1.426  0.020  1.426
 1H8  C20  C19  single    1.537  0.020  1.537
 1H8  C15  C17  aromatic  1.387  0.020  1.387
 1H8  C19  C12  single    1.531  0.020  1.531
 1H8  C19  N21  single    1.447  0.020  1.447
 1H8  C12  C14  aromatic  1.387  0.020  1.387
 1H8  O24  C25  single    1.341  0.020  1.341
 1H8  C17  C16  aromatic  1.392  0.020  1.392
 1H8  N21  C25  double    1.271  0.020  1.271
 1H8  C25  N26  single    1.363  0.020  1.363
 1H8  C14  C16  aromatic  1.396  0.020  1.396
 1H8  C16  N9   single    1.398  0.020  1.398
 1H8  O8   C7   double    1.219  0.020  1.219
 1H8  N9   C7   single    1.344  0.020  1.344
 1H8  C7   C4   single    1.506  0.020  1.506
 1H8  C4   C5   aromatic  1.388  0.020  1.388
 1H8  C4   N3   aromatic  1.329  0.020  1.329
 1H8  C5   C6   aromatic  1.383  0.020  1.383
 1H8  N3   C2   aromatic  1.317  0.020  1.317
 1H8  C6   C1   aromatic  1.391  0.020  1.391
 1H8  C2   C1   aromatic  1.396  0.020  1.396
 1H8  C1   C10  single    1.425  0.020  1.425
 1H8  C10  N11  triple    1.151  0.020  1.151
 1H8  C2   H1   single    0.930  0.020  1.080
 1H8  C5   H2   single    0.930  0.020  1.080
 1H8  C6   H3   single    0.930  0.020  1.080
 1H8  C14  H4   single    0.930  0.020  1.080
 1H8  C15  H5   single    0.930  0.020  1.080
 1H8  C17  H6   single    0.930  0.020  1.080
 1H8  C23  H7   single    0.970  0.020  1.090
 1H8  C23  H8   single    0.970  0.020  1.090
 1H8  N9   H9   single    0.860  0.020  1.020
 1H8  C20  H10  single    0.970  0.020  1.090
 1H8  C20  H11  single    0.970  0.020  1.090
 1H8  C20  H12  single    0.970  0.020  1.090
 1H8  C22  H13  single    0.970  0.020  1.090
 1H8  C22  H14  single    0.970  0.020  1.090
 1H8  N26  H15  single    0.890  0.020  1.040
 1H8  N26  H16  single    0.890  0.020  1.040

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
 1H8  C10  C1   C6   121.08  3.000
 1H8  C10  C1   C2   119.83  3.000
 1H8  C6   C1   C2   119.08  3.000
 1H8  H1   C2   N3   117.40  3.000
 1H8  H1   C2   C1   120.66  3.000
 1H8  N3   C2   C1   121.95  3.000
 1H8  C4   N3   C2   119.16  3.000
 1H8  C7   C4   C5   119.52  3.000
 1H8  C5   C4   N3   123.08  3.000
 1H8  C7   C4   N3   117.40  3.000
 1H8  H2   C5   C6   120.71  3.000
 1H8  H2   C5   C4   120.97  3.000
 1H8  C6   C5   C4   118.32  3.000
 1H8  H3   C6   C5   120.85  3.000
 1H8  H3   C6   C1   120.74  3.000
 1H8  C5   C6   C1   118.41  3.000
 1H8  N11  C10  C1   180.00  3.000
 1H8  H4   C14  C12  117.48  3.000
 1H8  H4   C14  C16  119.75  3.000
 1H8  C12  C14  C16  122.76  3.000
 1H8  H5   C15  C13  119.63  3.000
 1H8  H5   C15  C17  120.00  3.000
 1H8  C13  C15  C17  120.37  3.000
 1H8  N9   C16  C17  124.39  3.000
 1H8  N9   C16  C14  116.22  3.000
 1H8  C17  C16  C14  119.39  3.000
 1H8  H6   C17  C16  121.91  3.000
 1H8  H6   C17  C15  119.30  3.000
 1H8  C16  C17  C15  118.79  3.000
 1H8  C22  C19  N21  110.61  3.000
 1H8  N21  C19  C20  107.59  3.000
 1H8  C22  C19  C20  111.70  3.000
 1H8  N21  C19  C12  108.13  3.000
 1H8  C20  C19  C12  108.73  3.000
 1H8  C22  C19  C12  109.98  3.000
 1H8  H8   C23  H7   107.78  3.000
 1H8  H8   C23  O24  109.15  3.000
 1H8  H7   C23  O24  106.22  3.000
 1H8  H8   C23  C22  111.34  3.000
 1H8  H7   C23  C22  111.25  3.000
 1H8  O24  C23  C22  110.91  3.000
 1H8  N26  C25  O24  110.52  3.000
 1H8  N26  C25  N21  121.62  3.000
 1H8  O24  C25  N21  127.81  3.000
 1H8  N9   C7   O8   126.16  3.000
 1H8  N9   C7   C4   113.24  3.000
 1H8  O8   C7   C4   120.61  3.000
 1H8  H9   N9   C7   114.67  3.000
 1H8  H9   N9   C16  116.04  3.000
 1H8  C7   N9   C16  129.29  3.000
 1H8  C13  C12  C19  123.08  3.000
 1H8  C19  C12  C14  120.91  3.000
 1H8  C13  C12  C14  116.01  3.000
 1H8  F18  C13  C12  120.16  3.000
 1H8  C12  C13  C15  122.66  3.000
 1H8  F18  C13  C15  117.17  3.000
 1H8  H12  C20  H11  107.85  3.000
 1H8  H12  C20  H10  108.33  3.000
 1H8  H11  C20  H10  107.57  3.000
 1H8  H12  C20  C19  112.45  3.000
 1H8  H11  C20  C19  110.57  3.000
 1H8  H10  C20  C19  109.92  3.000
 1H8  C25  N21  C19  121.27  3.000
 1H8  H14  C22  H13  107.49  3.000
 1H8  H14  C22  C23  108.49  3.000
 1H8  H13  C22  C23  109.34  3.000
 1H8  H14  C22  C19  112.05  3.000
 1H8  H13  C22  C19  109.83  3.000
 1H8  C23  C22  C19  109.59  3.000
 1H8  C25  O24  C23  115.97  3.000
 1H8  H16  N26  H15  113.86  3.000
 1H8  H16  N26  C25  117.32  3.000
 1H8  H15  N26  C25  114.97  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
 1H8  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 1H8  CONST_02  C4   N3   C2   C1      0.00   0.0  0
 1H8  CONST_03  C5   C4   N3   C2      0.00   0.0  0
 1H8  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 1H8  CONST_05  C6   C5   C4   N3      0.00   0.0  0
 1H8  CONST_06  C6   C1   C2   N3      0.00   0.0  0
 1H8  CONST_07  C15  C13  C12  C14     0.00   0.0  0
 1H8  CONST_08  C15  C17  C16  C14     0.00   0.0  0
 1H8  CONST_09  C13  C15  C17  C16     0.00   0.0  0
 1H8  CONST_10  C13  C12  C14  C16     0.00   0.0  0
 1H8  CONST_11  C12  C13  C15  C17     0.00   0.0  0
 1H8  CONST_12  C12  C14  C16  C17     0.00   0.0  0
 1H8  CONST_13  C19  C12  C13  C15   180.00   0.0  0
 1H8  CONST_14  C19  C12  C14  C16   180.00   0.0  0
 1H8  CONST_15  O24  C25  N21  C19     0.00   0.0  0
 1H8  CONST_16  C7   C4   N3   C2    180.00   0.0  0
 1H8  CONST_17  C10  C1   C2   N3    180.00   0.0  0
 1H8  CONST_18  C10  C1   C6   C5    180.00   0.0  0
 1H8  CONST_19  C7   C4   C5   C6    180.00   0.0  0
 1H8  CONST_20  F18  C13  C12  C14   180.00   0.0  0
 1H8  CONST_21  N9   C16  C17  C15   180.00   0.0  0
 1H8  CONST_22  F18  C13  C15  C17   180.00   0.0  0
 1H8  CONST_23  F18  C13  C12  C19     0.00   0.0  0
 1H8  CONST_24  C12  C14  C16  N9    180.00   0.0  0
 1H8  CONST_25  N26  C25  N21  C19   180.00   0.0  0
 1H8  CONST_26  H2   C5   C6   C1    180.00   0.0  0
 1H8  CONST_27  H3   C6   C1   C2    180.00   0.0  0
 1H8  CONST_28  H1   C2   N3   C4    180.00   0.0  0
 1H8  CONST_29  H6   C17  C16  C14   180.00   0.0  0
 1H8  CONST_30  H5   C15  C17  C16   180.00   0.0  0
 1H8  CONST_31  H4   C14  C16  C17   180.00   0.0  0
 1H8  CONST_32  C16  N9   C7   C4    180.00   0.0  0
 1H8  CONST_33  C7   N9   C16  C14   180.00   0.0  0
 1H8  CONST_34  C7   N9   C16  C17     0.00   0.0  0
 1H8  CONST_35  H9   N9   C16  C14     0.00   0.0  0
 1H8  CONST_36  H15  N26  C25  N21     0.00   0.0  0
 1H8  CONST_38  O8   C7   N9   C16     0.00   0.0  0
 1H8  Var_01    O24  C23  C22  C19    55.71  30.0  1
 1H8  Var_02    N21  C25  O24  C23     7.24  30.0  1
 1H8  Var_03    C22  C23  O24  C25   -37.59  30.0  1
 1H8  Var_04    O8   C7   C4   N3   -179.49  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
 1H8  chir_01  C19  C22  C12  N21  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
 1H8  plan-1  C1   0.020
 1H8  plan-1  C2   0.020
 1H8  plan-1  N3   0.020
 1H8  plan-1  C4   0.020
 1H8  plan-1  C5   0.020
 1H8  plan-1  C6   0.020
 1H8  plan-1  C10  0.020
 1H8  plan-1  C7   0.020
 1H8  plan-1  N11  0.020
 1H8  plan-1  H1   0.020
 1H8  plan-1  H2   0.020
 1H8  plan-1  H3   0.020
 1H8  plan-2  C14  0.020
 1H8  plan-2  C15  0.020
 1H8  plan-2  C16  0.020
 1H8  plan-2  C17  0.020
 1H8  plan-2  C19  0.020
 1H8  plan-2  N9   0.020
 1H8  plan-2  C12  0.020
 1H8  plan-2  C13  0.020
 1H8  plan-2  F18  0.020
 1H8  plan-2  H5   0.020
 1H8  plan-2  H6   0.020
 1H8  plan-2  H4   0.020
 1H8  plan-3  C4   0.020
 1H8  plan-3  C16  0.020
 1H8  plan-3  C7   0.020
 1H8  plan-3  O8   0.020
 1H8  plan-3  N9   0.020
 1H8  plan-3  H9   0.020
 1H8  plan-4  C19  0.020
 1H8  plan-4  C25  0.020
 1H8  plan-4  N21  0.020
 1H8  plan-4  O24  0.020
 1H8  plan-4  N26  0.020
 1H8  plan-4  H15  0.020
 1H8  plan-4  H16  0.020

