# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 20:39:31 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: ~{N}-[3-[(4~{S})-2-azanyl-6-(fluoranylmethyl)-4-methyl-1,3-oxazin-4-yl]-4-fluoranyl-phenyl]-5-cyano-pyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]1(C=C(CF)OC(=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
 0B6  0B6  ~{N}-[3-[(4~{S})-2-azanyl-6-(fluoranylmethyl)-4-methyl-1,3-oxazin-4-yl]-4-fluoranyl-phenyl]-5-cyano-pyridine-2-carboxamide  ligand  43  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_0B6
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
 0B6  F2   F  F     0  -0.316  -3.4299   2.8652  -0.3563
 0B6  C19  C  CR6   0   0.514  -2.1808   2.3654  -0.2818
 0B6  C7   C  CR6   0  -0.026  -1.9510   1.0300  -0.5936
 0B6  C2   C  CT    0  -0.008  -3.0675   0.0770  -1.0437
 0B6  N2   N  N     0  -0.473  -2.5293  -1.2582  -1.2054
 0B6  C6   C  C     0   0.627  -2.7096  -2.1369  -0.3096
 0B6  N1   N  NH2   0  -0.829  -2.1026  -3.3448  -0.3229
 0B6  O1   O  O2    0  -0.476  -3.4805  -2.0036   0.7988
 0B6  C4   C  C     0   0.305  -4.3267  -0.9269   0.8143
 0B6  C5   C  CH2   0  -0.072  -5.3658  -1.0310   1.8689
 0B6  F1   F  F     0  -0.375  -6.1748  -2.1400   1.6325
 0B6  C3   C  C1    0  -0.325  -4.1858   0.0792  -0.0336
 0B6  C1   C  CH3   0  -0.635  -3.5927   0.5229  -2.4145
 0B6  C18  C  CR16  0  -0.394  -1.1734   3.2184   0.1122
 0B6  C17  C  CR16  0  -0.314   0.1323   2.7611   0.2091
 0B6  C9   C  CR6   0   0.420   0.4049   1.4308  -0.0989
 0B6  C8   C  CR16  0  -0.425  -0.6391   0.5923  -0.4950
 0B6  N3   N  NH1   0  -0.762   1.6745   0.8504  -0.0363
 0B6  C10  C  C     0   0.543   2.8554   1.4146   0.2725
 0B6  O2   O  O     0  -0.452   3.0399   2.5833   0.5630
 0B6  C11  C  CR6   0   0.146   4.0039   0.4414   0.2330
 0B6  C15  C  CR16  0  -0.283   5.2844   0.8804   0.5368
 0B6  C14  C  CR16  0  -0.112   6.3192  -0.0357   0.4928
 0B6  C13  C  CR6   0  -0.081   6.0256  -1.3505   0.1462
 0B6  C12  C  CR16  0  -0.015   4.7047  -1.6967  -0.1435
 0B6  N4   N  N     0  -0.439   3.7275  -0.8154  -0.0978
 0B6  C16  C  CSP   0   0.060   7.0481  -2.3414   0.0836
 0B6  N5   N  NS    0  -0.232   7.8680  -3.1480   0.0332
 0B6  H1   H  HNH2  0   0.399  -1.6307  -3.5905  -1.1771
 0B6  H2   H  HNH2  0   0.400  -2.5450  -4.1115   0.1575
 0B6  H3   H  HCH2  0   0.232  -4.9159  -1.1517   2.8562
 0B6  H4   H  HCH2  0   0.235  -5.9819  -0.1331   1.8670
 0B6  H5   H  H     0   0.276  -4.9042   0.8857  -0.0170
 0B6  H6   H  HCH3  0   0.239  -2.7863   0.5012  -3.1475
 0B6  H7   H  HCH3  0   0.239  -4.3777  -0.1569  -2.7473
 0B6  H8   H  HCH3  0   0.232  -4.0070   1.5290  -2.3875
 0B6  H9   H  HCR6  0   0.281  -1.4054   4.2488   0.3487
 0B6  H10  H  HCR6  0   0.287   0.9075   3.4413   0.5207
 0B6  H11  H  HCR6  0   0.280  -0.4245  -0.4396  -0.7422
 0B6  H12  H  HNH1  0   0.427   1.7256  -0.1373  -0.2551
 0B6  H13  H  HCR6  0   0.296   5.4717   1.9105   0.8010
 0B6  H14  H  HCR6  0   0.305   7.3327   0.2621   0.7222
 0B6  H15  H  HCR6  0   0.303   4.4476  -2.7127  -0.4165

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
 0B6  F1   C5   single    1.393  0.020  1.393
 0B6  F2   C19  single    1.347  0.020  1.347
 0B6  C5   C4   single    1.484  0.020  1.484
 0B6  C3   C4   double    1.323  0.020  1.323
 0B6  C3   C2   single    1.507  0.020  1.507
 0B6  C4   O1   single    1.370  0.020  1.370
 0B6  C1   C2   single    1.534  0.020  1.534
 0B6  C19  C18  aromatic  1.378  0.020  1.378
 0B6  C19  C7   aromatic  1.390  0.020  1.390
 0B6  C18  C17  aromatic  1.387  0.020  1.387
 0B6  C2   C7   single    1.535  0.020  1.535
 0B6  C2   N2   single    1.449  0.020  1.449
 0B6  C7   C8   aromatic  1.387  0.020  1.387
 0B6  O1   C6   single    1.357  0.020  1.357
 0B6  C17  C9   aromatic  1.392  0.020  1.392
 0B6  N2   C6   double    1.268  0.020  1.268
 0B6  C6   N1   single    1.352  0.020  1.352
 0B6  C8   C9   aromatic  1.396  0.020  1.396
 0B6  C9   N3   single    1.397  0.020  1.397
 0B6  O2   C10  double    1.218  0.020  1.218
 0B6  N3   C10  single    1.345  0.020  1.345
 0B6  C10  C11  single    1.506  0.020  1.506
 0B6  C11  C15  aromatic  1.387  0.020  1.387
 0B6  C11  N4   aromatic  1.329  0.020  1.329
 0B6  C15  C14  aromatic  1.383  0.020  1.383
 0B6  N4   C12  aromatic  1.317  0.020  1.317
 0B6  C14  C13  aromatic  1.391  0.020  1.391
 0B6  C12  C13  aromatic  1.396  0.020  1.396
 0B6  C13  C16  single    1.425  0.020  1.425
 0B6  C16  N5   triple    1.151  0.020  1.151
 0B6  N1   H1   single    0.890  0.020  1.040
 0B6  N1   H2   single    0.890  0.020  1.040
 0B6  C5   H3   single    0.970  0.020  1.090
 0B6  C5   H4   single    0.970  0.020  1.090
 0B6  C3   H5   single    0.930  0.020  1.080
 0B6  C1   H6   single    0.970  0.020  1.090
 0B6  C1   H7   single    0.970  0.020  1.090
 0B6  C1   H8   single    0.970  0.020  1.090
 0B6  C18  H9   single    0.930  0.020  1.080
 0B6  C17  H10  single    0.930  0.020  1.080
 0B6  C8   H11  single    0.930  0.020  1.080
 0B6  N3   H12  single    0.860  0.020  1.020
 0B6  C15  H13  single    0.930  0.020  1.080
 0B6  C14  H14  single    0.930  0.020  1.080
 0B6  C12  H15  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
 0B6  C18  C19  C7   122.55  3.000
 0B6  C7   C19  F2   119.80  3.000
 0B6  C18  C19  F2   117.65  3.000
 0B6  C8   C7   C2   120.86  3.000
 0B6  C8   C7   C19  116.34  3.000
 0B6  C2   C7   C19  122.80  3.000
 0B6  C1   C2   C3   110.15  3.000
 0B6  C1   C2   N2   107.18  3.000
 0B6  C3   C2   N2   110.60  3.000
 0B6  N2   C2   C7   109.55  3.000
 0B6  C1   C2   C7   109.30  3.000
 0B6  C3   C2   C7   110.01  3.000
 0B6  C6   N2   C2   120.48  3.000
 0B6  O1   C6   N1   110.55  3.000
 0B6  N1   C6   N2   123.26  3.000
 0B6  O1   C6   N2   126.16  3.000
 0B6  H2   N1   H1   115.15  3.000
 0B6  H2   N1   C6   118.57  3.000
 0B6  H1   N1   C6   115.92  3.000
 0B6  C4   O1   C6   115.95  3.000
 0B6  C3   C4   C5   125.67  3.000
 0B6  C3   C4   O1   121.65  3.000
 0B6  C5   C4   O1   112.68  3.000
 0B6  H4   C5   H3   109.02  3.000
 0B6  H4   C5   F1   109.12  3.000
 0B6  H3   C5   F1   107.75  3.000
 0B6  H4   C5   C4   109.70  3.000
 0B6  H3   C5   C4   111.22  3.000
 0B6  F1   C5   C4   109.99  3.000
 0B6  H5   C3   C4   119.15  3.000
 0B6  H5   C3   C2   120.33  3.000
 0B6  C4   C3   C2   120.49  3.000
 0B6  H8   C1   H7   108.05  3.000
 0B6  H8   C1   H6   108.46  3.000
 0B6  H7   C1   H6   108.36  3.000
 0B6  H8   C1   C2   112.13  3.000
 0B6  H7   C1   C2   109.75  3.000
 0B6  H6   C1   C2   109.99  3.000
 0B6  H9   C18  C17  120.03  3.000
 0B6  H9   C18  C19  119.68  3.000
 0B6  C17  C18  C19  120.28  3.000
 0B6  H10  C17  C9   121.76  3.000
 0B6  H10  C17  C18  119.30  3.000
 0B6  C9   C17  C18  118.94  3.000
 0B6  N3   C9   C8   116.27  3.000
 0B6  N3   C9   C17  124.38  3.000
 0B6  C8   C9   C17  119.35  3.000
 0B6  H11  C8   C9   119.27  3.000
 0B6  H11  C8   C7   118.18  3.000
 0B6  C9   C8   C7   122.55  3.000
 0B6  H12  N3   C10  114.48  3.000
 0B6  H12  N3   C9   116.18  3.000
 0B6  C10  N3   C9   129.34  3.000
 0B6  C11  C10  O2   120.71  3.000
 0B6  C11  C10  N3   113.11  3.000
 0B6  O2   C10  N3   126.18  3.000
 0B6  N4   C11  C15  123.08  3.000
 0B6  N4   C11  C10  117.33  3.000
 0B6  C15  C11  C10  119.58  3.000
 0B6  H13  C15  C14  120.67  3.000
 0B6  H13  C15  C11  121.03  3.000
 0B6  C14  C15  C11  118.30  3.000
 0B6  H14  C14  C13  120.74  3.000
 0B6  H14  C14  C15  120.83  3.000
 0B6  C13  C14  C15  118.44  3.000
 0B6  C16  C13  C12  119.82  3.000
 0B6  C16  C13  C14  121.11  3.000
 0B6  C12  C13  C14  119.07  3.000
 0B6  H15  C12  N4   117.42  3.000
 0B6  H15  C12  C13  120.64  3.000
 0B6  N4   C12  C13  121.95  3.000
 0B6  C12  N4   C11  119.16  3.000
 0B6  N5   C16  C13  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
 0B6  CONST_01  C9   C17  C18  C19     0.00   0.0  0
 0B6  CONST_02  C9   C8   C7   C19     0.00   0.0  0
 0B6  CONST_03  C17  C18  C19  C7      0.00   0.0  0
 0B6  CONST_04  C17  C9   C8   C7      0.00   0.0  0
 0B6  CONST_05  C8   C7   C19  C18     0.00   0.0  0
 0B6  CONST_06  C8   C9   C17  C18     0.00   0.0  0
 0B6  CONST_07  C13  C14  C15  C11     0.00   0.0  0
 0B6  CONST_08  C13  C12  N4   C11     0.00   0.0  0
 0B6  CONST_09  C12  N4   C11  C15     0.00   0.0  0
 0B6  CONST_10  C12  C13  C14  C15     0.00   0.0  0
 0B6  CONST_11  N4   C11  C15  C14     0.00   0.0  0
 0B6  CONST_12  N4   C12  C13  C14     0.00   0.0  0
 0B6  CONST_13  C18  C19  C7   C2    180.00   0.0  0
 0B6  CONST_14  C9   C8   C7   C2    180.00   0.0  0
 0B6  CONST_15  O1   C6   N2   C2      0.00   0.0  0
 0B6  CONST_16  C17  C18  C19  F2    180.00   0.0  0
 0B6  CONST_17  C2   C7   C19  F2      0.00   0.0  0
 0B6  CONST_18  C8   C7   C19  F2    180.00   0.0  0
 0B6  CONST_19  N3   C9   C8   C7    180.00   0.0  0
 0B6  CONST_20  N3   C9   C17  C18   180.00   0.0  0
 0B6  CONST_21  C14  C15  C11  C10   180.00   0.0  0
 0B6  CONST_22  C12  N4   C11  C10   180.00   0.0  0
 0B6  CONST_23  C16  C13  C14  C15   180.00   0.0  0
 0B6  CONST_24  C16  C13  C12  N4    180.00   0.0  0
 0B6  CONST_25  N1   C6   N2   C2    180.00   0.0  0
 0B6  CONST_26  H10  C17  C18  C19   180.00   0.0  0
 0B6  CONST_27  H11  C8   C7   C19   180.00   0.0  0
 0B6  CONST_28  H9   C18  C19  C7    180.00   0.0  0
 0B6  CONST_29  H14  C14  C15  C11   180.00   0.0  0
 0B6  CONST_30  H15  C12  N4   C11   180.00   0.0  0
 0B6  CONST_31  H13  C15  C14  C13   180.00   0.0  0
 0B6  CONST_32  C11  C10  N3   C9    180.00   0.0  0
 0B6  CONST_33  C10  N3   C9   C17     0.00   0.0  0
 0B6  CONST_34  C10  N3   C9   C8    180.00   0.0  0
 0B6  CONST_35  H12  N3   C9   C17   180.00   0.0  0
 0B6  CONST_36  H1   N1   C6   N2      0.00   0.0  0
 0B6  CONST_38  O2   C10  N3   C9      0.00   0.0  0
 0B6  Var_01    O1   C4   C3   C2     -0.66  30.0  1
 0B6  Var_02    C3   C4   O1   C6    -15.14  30.0  1
 0B6  Var_03    F1   C5   C4   O1    -62.47  30.0  3
 0B6  Var_04    C15  C11  C10  N3   -179.66  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
 0B6  chir_01  C2  C3  C7  N2  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
 0B6  plan-1  F2   0.020
 0B6  plan-1  C19  0.020
 0B6  plan-1  C7   0.020
 0B6  plan-1  C2   0.020
 0B6  plan-1  C18  0.020
 0B6  plan-1  C17  0.020
 0B6  plan-1  C9   0.020
 0B6  plan-1  C8   0.020
 0B6  plan-1  N3   0.020
 0B6  plan-1  H9   0.020
 0B6  plan-1  H10  0.020
 0B6  plan-1  H11  0.020
 0B6  plan-2  C10  0.020
 0B6  plan-2  C11  0.020
 0B6  plan-2  C15  0.020
 0B6  plan-2  C14  0.020
 0B6  plan-2  C13  0.020
 0B6  plan-2  C12  0.020
 0B6  plan-2  N4   0.020
 0B6  plan-2  C16  0.020
 0B6  plan-2  N5   0.020
 0B6  plan-2  H13  0.020
 0B6  plan-2  H14  0.020
 0B6  plan-2  H15  0.020
 0B6  plan-3  C9   0.020
 0B6  plan-3  N3   0.020
 0B6  plan-3  C10  0.020
 0B6  plan-3  O2   0.020
 0B6  plan-3  C11  0.020
 0B6  plan-3  H12  0.020
 0B6  plan-4  C2   0.020
 0B6  plan-4  N2   0.020
 0B6  plan-4  C6   0.020
 0B6  plan-4  N1   0.020
 0B6  plan-4  O1   0.020
 0B6  plan-4  H1   0.020
 0B6  plan-4  H2   0.020

