# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 11:53:51 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: N-{3-[(4S)-2-amino-4-(difluoromethyl)-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@](CCO1)(C(F)F)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
 1HQ  1HQ  N-{3-[(4S)-2-amino-4-(difluoromethyl)-5,6-dihydro-4H-1,3-oxazin-4-yl]-4-fluorophenyl}-5-cyanopyridine-2-carboxamide  ligand  42  28  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1HQ
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
 1HQ  C2   C  CR16  0  -0.112   6.3381   0.2569   0.1233
 1HQ  C3   C  CR16  0  -0.283   5.2708   1.1285   0.2375
 1HQ  C4   C  CR6   0   0.145   3.9866   0.6117   0.1412
 1HQ  N5   N  N     0  -0.439   3.7359  -0.6782  -0.0538
 1HQ  C6   C  CR16  0  -0.015   4.7445  -1.5177  -0.1647
 1HQ  N9   N  NH1   0  -0.762   1.6228   0.9030   0.1503
 1HQ  C15  C  CR6   0   0.516  -2.2989   2.2523   0.2629
 1HQ  C1   C  CR6   0  -0.080   6.0716  -1.0928  -0.0826
 1HQ  C7   C  C     0   0.544   2.8043   1.5368   0.2574
 1HQ  O8   O  O     0  -0.451   2.9654   2.7322   0.4298
 1HQ  C10  C  CSP   0   0.061   7.1287  -2.0401  -0.2113
 1HQ  N11  N  NS    0  -0.232   7.9780  -2.8101  -0.3186
 1HQ  C12  C  CR6   0   0.423   0.3296   1.4296   0.1998
 1HQ  C13  C  CR16  0  -0.310   0.0355   2.7768   0.3974
 1HQ  C14  C  CR16  0  -0.395  -1.2909   3.1778   0.4257
 1HQ  C16  C  CR6   0  -0.069  -2.0467   0.9000   0.0680
 1HQ  C17  C  CR16  0  -0.414  -0.7144   0.5188   0.0357
 1HQ  C19  C  CT    0  -0.085  -3.1535  -0.1489  -0.0837
 1HQ  C20  C  CH2   0  -0.524  -4.0662  -0.1153   1.1555
 1HQ  C21  C  CH2   0  -0.175  -4.8805  -1.3829   1.2805
 1HQ  O22  O  O2    0  -0.461  -4.0657  -2.5444   1.1433
 1HQ  C23  C  C     0   0.641  -3.0224  -2.4696   0.3123
 1HQ  N24  N  N     0  -0.493  -2.5505  -1.4378  -0.2697
 1HQ  C25  C  CH1   0   0.574  -3.9303   0.1847  -1.3658
 1HQ  F26  F  F     0  -0.336  -3.0750   0.2496  -2.4206
 1HQ  F27  F  F     0  -0.337  -4.8133  -0.8114  -1.6542
 1HQ  N28  N  NH2   0  -0.827  -2.4790  -3.6952   0.1052
 1HQ  H1   H  HCR6  0   0.305   7.3560   0.6149   0.1924
 1HQ  H2   H  HCR6  0   0.296   5.4346   2.1840   0.3965
 1HQ  H3   H  HCR6  0   0.302   4.5084  -2.5628  -0.3239
 1HQ  H4   H  HNH1  0   0.427   1.6917  -0.0978   0.0098
 1HQ  H5   H  HCR6  0   0.290   0.8102   3.5134   0.5272
 1HQ  H6   H  HCR6  0   0.283  -1.5392   4.2202   0.5763
 1HQ  H7   H  HCR6  0   0.284  -0.4983  -0.5297  -0.1242
 1HQ  H8   H  HCH2  0   0.271  -3.4317  -0.0105   2.0384
 1HQ  H9   H  HCH2  0   0.273  -4.7464   0.7352   1.1501
 1HQ  H10  H  HCH2  0   0.258  -5.3309  -1.4453   2.2698
 1HQ  H11  H  HCH2  0   0.243  -5.6867  -1.4300   0.5477
 1HQ  H12  H  HCH1  0   0.194  -4.4909   1.1184  -1.3164
 1HQ  H13  H  HNH2  0   0.395  -2.6715  -4.4206   0.7763
 1HQ  H14  H  HNH2  0   0.393  -1.5487  -3.7045  -0.2775
 1HQ  F18  F  F     0  -0.316  -3.5701   2.7031   0.2976

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
 1HQ  F18  C15  single    1.349  0.020  1.349
 1HQ  C20  C21  single    1.512  0.020  1.512
 1HQ  C20  C19  single    1.539  0.020  1.539
 1HQ  F27  C25  single    1.362  0.020  1.362
 1HQ  C25  C19  single    1.536  0.020  1.536
 1HQ  C25  F26  single    1.360  0.020  1.360
 1HQ  C15  C14  aromatic  1.378  0.020  1.378
 1HQ  C15  C16  aromatic  1.389  0.020  1.389
 1HQ  C21  O22  single    1.425  0.020  1.425
 1HQ  C14  C13  aromatic  1.386  0.020  1.386
 1HQ  C19  C16  single    1.532  0.020  1.532
 1HQ  C19  N24  single    1.435  0.020  1.435
 1HQ  C16  C17  aromatic  1.386  0.020  1.386
 1HQ  O22  C23  single    1.336  0.020  1.336
 1HQ  C13  C12  aromatic  1.393  0.020  1.393
 1HQ  N24  C23  double    1.275  0.020  1.275
 1HQ  C23  N28  single    1.357  0.020  1.357
 1HQ  C17  C12  aromatic  1.395  0.020  1.395
 1HQ  C12  N9   single    1.397  0.020  1.397
 1HQ  O8   C7   double    1.218  0.020  1.218
 1HQ  N9   C7   single    1.345  0.020  1.345
 1HQ  C7   C4   single    1.506  0.020  1.506
 1HQ  C4   C3   aromatic  1.388  0.020  1.388
 1HQ  C4   N5   aromatic  1.328  0.020  1.328
 1HQ  C3   C2   aromatic  1.383  0.020  1.383
 1HQ  N5   C6   aromatic  1.317  0.020  1.317
 1HQ  C2   C1   aromatic  1.391  0.020  1.391
 1HQ  C6   C1   aromatic  1.396  0.020  1.396
 1HQ  C1   C10  single    1.425  0.020  1.425
 1HQ  C10  N11  triple    1.151  0.020  1.151
 1HQ  C2   H1   single    0.930  0.020  1.080
 1HQ  C3   H2   single    0.930  0.020  1.080
 1HQ  C6   H3   single    0.930  0.020  1.080
 1HQ  N9   H4   single    0.860  0.020  1.020
 1HQ  C13  H5   single    0.930  0.020  1.080
 1HQ  C14  H6   single    0.930  0.020  1.080
 1HQ  C17  H7   single    0.930  0.020  1.080
 1HQ  C20  H8   single    0.970  0.020  1.090
 1HQ  C20  H9   single    0.970  0.020  1.090
 1HQ  C21  H10  single    0.970  0.020  1.090
 1HQ  C21  H11  single    0.970  0.020  1.090
 1HQ  C25  H12  single    0.970  0.020  1.090
 1HQ  N28  H13  single    0.890  0.020  1.040
 1HQ  N28  H14  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
 1HQ  H1   C2   C1   120.74  3.000
 1HQ  H1   C2   C3   120.84  3.000
 1HQ  C1   C2   C3   118.42  3.000
 1HQ  H2   C3   C4   120.97  3.000
 1HQ  H2   C3   C2   120.74  3.000
 1HQ  C4   C3   C2   118.29  3.000
 1HQ  C7   C4   N5   117.37  3.000
 1HQ  N5   C4   C3   123.12  3.000
 1HQ  C7   C4   C3   119.51  3.000
 1HQ  C6   N5   C4   119.13  3.000
 1HQ  H3   C6   C1   120.63  3.000
 1HQ  H3   C6   N5   117.42  3.000
 1HQ  C1   C6   N5   121.94  3.000
 1HQ  H4   N9   C12  116.12  3.000
 1HQ  H4   N9   C7   114.63  3.000
 1HQ  C12  N9   C7   129.25  3.000
 1HQ  F18  C15  C16  119.99  3.000
 1HQ  C16  C15  C14  122.51  3.000
 1HQ  F18  C15  C14  117.50  3.000
 1HQ  C10  C1   C6   119.83  3.000
 1HQ  C10  C1   C2   121.08  3.000
 1HQ  C6   C1   C2   119.09  3.000
 1HQ  O8   C7   N9   126.13  3.000
 1HQ  N9   C7   C4   113.21  3.000
 1HQ  O8   C7   C4   120.65  3.000
 1HQ  N11  C10  C1   180.00  3.000
 1HQ  C17  C12  C13  119.34  3.000
 1HQ  C17  C12  N9   116.26  3.000
 1HQ  C13  C12  N9   124.40  3.000
 1HQ  H5   C13  C14  119.22  3.000
 1HQ  H5   C13  C12  121.79  3.000
 1HQ  C14  C13  C12  118.99  3.000
 1HQ  H6   C14  C13  120.07  3.000
 1HQ  H6   C14  C15  119.70  3.000
 1HQ  C13  C14  C15  120.22  3.000
 1HQ  C19  C16  C17  120.24  3.000
 1HQ  C17  C16  C15  116.45  3.000
 1HQ  C19  C16  C15  123.30  3.000
 1HQ  H7   C17  C16  117.50  3.000
 1HQ  H7   C17  C12  120.03  3.000
 1HQ  C16  C17  C12  122.48  3.000
 1HQ  C25  C19  N24  107.43  3.000
 1HQ  N24  C19  C20  111.90  3.000
 1HQ  C25  C19  C20  111.56  3.000
 1HQ  N24  C19  C16  108.91  3.000
 1HQ  C25  C19  C16  107.41  3.000
 1HQ  C20  C19  C16  109.48  3.000
 1HQ  H9   C20  H8   106.97  3.000
 1HQ  H9   C20  C21  108.59  3.000
 1HQ  H8   C20  C21  109.05  3.000
 1HQ  H9   C20  C19  112.54  3.000
 1HQ  H8   C20  C19  107.96  3.000
 1HQ  C21  C20  C19  111.57  3.000
 1HQ  H11  C21  H10  107.59  3.000
 1HQ  H11  C21  O22  108.83  3.000
 1HQ  H10  C21  O22  106.09  3.000
 1HQ  H11  C21  C20  112.26  3.000
 1HQ  H10  C21  C20  110.25  3.000
 1HQ  O22  C21  C20  111.55  3.000
 1HQ  C23  O22  C21  117.43  3.000
 1HQ  N28  C23  N24  120.87  3.000
 1HQ  N28  C23  O22  110.93  3.000
 1HQ  N24  C23  O22  128.19  3.000
 1HQ  C23  N24  C19  120.80  3.000
 1HQ  H12  C25  F27  107.61  3.000
 1HQ  H12  C25  F26  108.53  3.000
 1HQ  F27  C25  F26  106.17  3.000
 1HQ  H12  C25  C19  114.10  3.000
 1HQ  F26  C25  C19  109.87  3.000
 1HQ  F27  C25  C19  110.23  3.000
 1HQ  H14  N28  H13  115.07  3.000
 1HQ  H14  N28  C23  115.90  3.000
 1HQ  H13  N28  C23  118.20  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
 1HQ  CONST_01  N5   C4   C3   C2     0.00   0.0  0
 1HQ  CONST_02  N5   C6   C1   C2     0.00   0.0  0
 1HQ  CONST_03  C6   N5   C4   C3     0.00   0.0  0
 1HQ  CONST_04  C6   C1   C2   C3     0.00   0.0  0
 1HQ  CONST_05  C1   C2   C3   C4     0.00   0.0  0
 1HQ  CONST_06  C1   C6   N5   C4     0.00   0.0  0
 1HQ  CONST_07  C12  C13  C14  C15    0.00   0.0  0
 1HQ  CONST_08  C12  C17  C16  C15    0.00   0.0  0
 1HQ  CONST_09  C16  C15  C14  C13    0.00   0.0  0
 1HQ  CONST_10  C16  C17  C12  C13    0.00   0.0  0
 1HQ  CONST_11  C17  C16  C15  C14    0.00   0.0  0
 1HQ  CONST_12  C17  C12  C13  C14    0.00   0.0  0
 1HQ  CONST_13  C19  C16  C17  C12  180.00   0.0  0
 1HQ  CONST_14  C19  C16  C15  C14  180.00   0.0  0
 1HQ  CONST_15  O22  C23  N24  C19    0.00   0.0  0
 1HQ  CONST_16  C7   C4   C3   C2   180.00   0.0  0
 1HQ  CONST_17  C10  C1   C2   C3   180.00   0.0  0
 1HQ  CONST_18  C10  C1   C6   N5   180.00   0.0  0
 1HQ  CONST_19  C7   C4   N5   C6   180.00   0.0  0
 1HQ  CONST_20  C14  C13  C12  N9   180.00   0.0  0
 1HQ  CONST_21  C16  C17  C12  N9   180.00   0.0  0
 1HQ  CONST_22  F18  C15  C14  C13  180.00   0.0  0
 1HQ  CONST_23  F18  C15  C16  C17  180.00   0.0  0
 1HQ  CONST_24  C19  C16  C15  F18    0.00   0.0  0
 1HQ  CONST_25  N28  C23  N24  C19  180.00   0.0  0
 1HQ  CONST_26  H3   C6   C1   C2   180.00   0.0  0
 1HQ  CONST_27  H1   C2   C3   C4   180.00   0.0  0
 1HQ  CONST_28  H2   C3   C4   N5   180.00   0.0  0
 1HQ  CONST_29  H5   C13  C14  C15  180.00   0.0  0
 1HQ  CONST_30  H7   C17  C16  C15  180.00   0.0  0
 1HQ  CONST_31  H6   C14  C13  C12  180.00   0.0  0
 1HQ  CONST_32  C12  N9   C7   C4   180.00   0.0  0
 1HQ  CONST_33  C13  C12  N9   C7     0.00   0.0  0
 1HQ  CONST_34  C17  C12  N9   C7   180.00   0.0  0
 1HQ  CONST_35  H4   N9   C12  C13  180.00   0.0  0
 1HQ  CONST_38  C12  N9   C7   O8     0.00   0.0  0
 1HQ  Var_01    O22  C21  C20  C19   48.85  30.0  1
 1HQ  Var_02    N24  C23  O22  C21    9.19  30.0  1
 1HQ  Var_03    O8   C7   C4   C3     0.27  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
 1HQ  chir_01  C19  C20  C16  N24  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
 1HQ  plan-1  C2   0.020
 1HQ  plan-1  C3   0.020
 1HQ  plan-1  C4   0.020
 1HQ  plan-1  N5   0.020
 1HQ  plan-1  C6   0.020
 1HQ  plan-1  C1   0.020
 1HQ  plan-1  C7   0.020
 1HQ  plan-1  C10  0.020
 1HQ  plan-1  N11  0.020
 1HQ  plan-1  H1   0.020
 1HQ  plan-1  H2   0.020
 1HQ  plan-1  H3   0.020
 1HQ  plan-2  N9   0.020
 1HQ  plan-2  C15  0.020
 1HQ  plan-2  C12  0.020
 1HQ  plan-2  C13  0.020
 1HQ  plan-2  C14  0.020
 1HQ  plan-2  C16  0.020
 1HQ  plan-2  C17  0.020
 1HQ  plan-2  C19  0.020
 1HQ  plan-2  H5   0.020
 1HQ  plan-2  H6   0.020
 1HQ  plan-2  H7   0.020
 1HQ  plan-2  F18  0.020
 1HQ  plan-3  C4   0.020
 1HQ  plan-3  N9   0.020
 1HQ  plan-3  C7   0.020
 1HQ  plan-3  O8   0.020
 1HQ  plan-3  C12  0.020
 1HQ  plan-3  H4   0.020
 1HQ  plan-4  C19  0.020
 1HQ  plan-4  O22  0.020
 1HQ  plan-4  C23  0.020
 1HQ  plan-4  N24  0.020
 1HQ  plan-4  N28  0.020
 1HQ  plan-4  H13  0.020
 1HQ  plan-4  H14  0.020

