# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 04:47:24 2022
#   Inital geometry file: a 124 line input string
#   Ligand name: ~{N}-[3-[(4~{R})-2-azanyl-4-prop-1-ynyl-5,6-dihydro-1,3-oxazin-4-yl]-4-fluoranyl-phenyl]-5-cyano-pyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC#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
 GTU  GTU  ~{N}-[3-[(4~{R})-2-azanyl-4-prop-1-ynyl-5,6-dihydro-1,3-oxazin-4-yl]-4-fluoranyl-phenyl]-5-cyano-pyridine-2-carboxamide  ligand  44  28  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GTU
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
 GTU  C1   C  CSP   0  -0.152  -17.3545  -35.5212   -9.0510
 GTU  C2   C  CSP   0   0.320  -17.3953  -36.7007   -8.8206
 GTU  C3   C  CT    0  -0.149  -17.4278  -38.1480   -8.5512
 GTU  C4   C  CH2   0  -0.508  -16.9511  -38.9152   -9.8014
 GTU  C5   C  CH2   0  -0.180  -16.6477  -40.3376   -9.4068
 GTU  C6   C  C     0   0.638  -15.7716  -39.4073   -7.4343
 GTU  N1   N  N     0  -0.488  -16.5476  -38.3926   -7.4289
 GTU  N3   N  N     0  -0.395  -22.1580  -42.6846   -3.4421
 GTU  O1   O  O     0  -0.436  -22.7081  -41.1950   -5.7004
 GTU  C7   C  CR6   0  -0.043  -18.8669  -38.5476   -8.2007
 GTU  C8   C  CR16  0  -0.416  -19.1610  -39.2309   -7.0317
 GTU  C9   C  CR6   0   0.410  -20.4611  -39.6219   -6.7056
 GTU  C10  C  C     0   0.512  -21.7073  -40.9764   -5.0487
 GTU  C11  C  CR6   0   0.134  -21.5942  -41.4972   -3.6394
 GTU  C12  C  CR16  0  -0.037  -22.1513  -43.1924   -2.2271
 GTU  C13  C  CR6   0  -0.070  -21.5921  -42.5226   -1.1358
 GTU  C14  C  CR16  0  -0.111  -21.0144  -41.2753   -1.3377
 GTU  C15  C  CR16  0  -0.302  -21.0124  -40.7547   -2.6194
 GTU  C19  C  CR6   0   0.522  -19.9344  -38.2554   -9.0411
 GTU  N    N  NH2   0  -0.827  -14.9322  -39.6509   -6.3967
 GTU  O    O  O2    0  -0.457  -15.6781  -40.3673   -8.3614
 GTU  C    C  CH3   0  -0.829  -17.3208  -34.0951   -9.3376
 GTU  C18  C  CR16  0  -0.398  -21.2261  -38.6337   -8.7501
 GTU  C17  C  CR16  0  -0.305  -21.5026  -39.3228   -7.5787
 GTU  C16  C  CSP   0   0.055  -21.6300  -43.1124    0.1614
 GTU  N4   N  NS    0  -0.229  -21.6634  -43.5901    1.2083
 GTU  H1   H  HCH2  0   0.265  -16.0483  -38.4370  -10.1889
 GTU  H2   H  HCH2  0   0.273  -17.6894  -38.9028  -10.6011
 GTU  H3   H  HCH2  0   0.242  -17.5497  -40.8612   -9.0759
 GTU  H4   H  HCH2  0   0.263  -16.2190  -40.8982  -10.2355
 GTU  H5   H  HNH1  0   0.428  -19.8181  -40.2755   -4.8811
 GTU  H6   H  HCR6  0   0.284  -18.3525  -39.4581   -6.3481
 GTU  H7   H  HCR6  0   0.298  -22.6080  -44.1664   -2.0951
 GTU  H8   H  HCR6  0   0.305  -20.5825  -40.7229   -0.5144
 GTU  H9   H  HCR6  0   0.302  -20.5866  -39.7774   -2.8018
 GTU  H10  H  HNH2  0   0.394  -14.1579  -40.2760   -6.5498
 GTU  H11  H  HNH2  0   0.392  -14.7367  -38.8707   -5.7924
 GTU  H12  H  HCH3  0   0.264  -17.0157  -33.5234   -8.4608
 GTU  H13  H  HCH3  0   0.264  -16.6190  -33.8716  -10.1415
 GTU  H14  H  HCH3  0   0.264  -18.3031  -33.7348   -9.6446
 GTU  H15  H  HCR6  0   0.280  -22.0260  -38.3868   -9.4362
 GTU  H16  H  HCR6  0   0.288  -22.5205  -39.6026   -7.3654
 GTU  F    F  F     0  -0.309  -19.7143  -37.5771  -10.1794
 GTU  N2   N  NH1   0  -0.753  -20.6342  -40.2737   -5.4757

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
 GTU  F    C19  single    1.343  0.020  1.343
 GTU  C    C1   single    1.455  0.020  1.455
 GTU  C4   C5   single    1.507  0.020  1.507
 GTU  C4   C3   single    1.542  0.020  1.542
 GTU  C1   C2   triple    1.203  0.020  1.203
 GTU  C5   O    single    1.426  0.020  1.426
 GTU  C19  C18  aromatic  1.377  0.020  1.377
 GTU  C19  C7   aromatic  1.390  0.020  1.390
 GTU  C2   C3   single    1.472  0.020  1.472
 GTU  C18  C17  aromatic  1.387  0.020  1.387
 GTU  C3   C7   single    1.534  0.020  1.534
 GTU  C3   N1   single    1.447  0.020  1.447
 GTU  C7   C8   aromatic  1.386  0.020  1.386
 GTU  O    C6   single    1.338  0.020  1.338
 GTU  C17  C9   aromatic  1.392  0.020  1.392
 GTU  N1   C6   double    1.277  0.020  1.277
 GTU  C6   N    single    1.357  0.020  1.357
 GTU  C8   C9   aromatic  1.396  0.020  1.396
 GTU  C9   N2   single    1.403  0.020  1.403
 GTU  O1   C10  double    1.214  0.020  1.214
 GTU  N2   C10  single    1.352  0.020  1.352
 GTU  C10  C11  single    1.507  0.020  1.507
 GTU  C11  N3   aromatic  1.329  0.020  1.329
 GTU  C11  C15  aromatic  1.389  0.020  1.389
 GTU  N3   C12  aromatic  1.317  0.020  1.317
 GTU  C15  C14  aromatic  1.383  0.020  1.383
 GTU  C12  C13  aromatic  1.397  0.020  1.397
 GTU  C14  C13  aromatic  1.389  0.020  1.389
 GTU  C13  C16  single    1.425  0.020  1.425
 GTU  C16  N4   triple    1.151  0.020  1.151
 GTU  C4   H1   single    0.970  0.020  1.090
 GTU  C4   H2   single    0.970  0.020  1.090
 GTU  C5   H3   single    0.970  0.020  1.090
 GTU  C5   H4   single    0.970  0.020  1.090
 GTU  N2   H5   single    0.860  0.020  1.020
 GTU  C8   H6   single    0.930  0.020  1.080
 GTU  C12  H7   single    0.930  0.020  1.080
 GTU  C14  H8   single    0.930  0.020  1.080
 GTU  C15  H9   single    0.930  0.020  1.080
 GTU  N    H10  single    0.890  0.020  1.040
 GTU  N    H11  single    0.890  0.020  1.040
 GTU  C    H12  single    0.970  0.020  1.090
 GTU  C    H13  single    0.970  0.020  1.090
 GTU  C    H14  single    0.970  0.020  1.090
 GTU  C18  H15  single    0.930  0.020  1.080
 GTU  C17  H16  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
 GTU  C    C1   C2   180.00  3.000
 GTU  C3   C2   C1   180.00  3.000
 GTU  C7   C3   N1   110.45  3.000
 GTU  N1   C3   C4   110.89  3.000
 GTU  C7   C3   C4   110.21  3.000
 GTU  N1   C3   C2   107.13  3.000
 GTU  C7   C3   C2   108.57  3.000
 GTU  C4   C3   C2   109.50  3.000
 GTU  H2   C4   H1   107.15  3.000
 GTU  H2   C4   C5   109.86  3.000
 GTU  H1   C4   C5   109.85  3.000
 GTU  H2   C4   C3   112.35  3.000
 GTU  H1   C4   C3   108.98  3.000
 GTU  C5   C4   C3   108.63  3.000
 GTU  H4   C5   H3   107.96  3.000
 GTU  H4   C5   O    106.24  3.000
 GTU  H3   C5   O    109.20  3.000
 GTU  H4   C5   C4   111.47  3.000
 GTU  H3   C5   C4   111.40  3.000
 GTU  O    C5   C4   110.40  3.000
 GTU  O    C6   N    110.98  3.000
 GTU  N    C6   N1   121.01  3.000
 GTU  O    C6   N1   127.98  3.000
 GTU  C6   N1   C3   120.03  3.000
 GTU  C12  N3   C11  118.64  3.000
 GTU  C19  C7   C8   116.80  3.000
 GTU  C8   C7   C3   121.35  3.000
 GTU  C19  C7   C3   121.84  3.000
 GTU  H6   C8   C9   119.28  3.000
 GTU  H6   C8   C7   118.53  3.000
 GTU  C9   C8   C7   122.19  3.000
 GTU  C17  C9   C8   119.36  3.000
 GTU  C8   C9   N2   116.73  3.000
 GTU  C17  C9   N2   123.89  3.000
 GTU  C11  C10  O1   120.11  3.000
 GTU  C11  C10  N2   114.55  3.000
 GTU  O1   C10  N2   125.34  3.000
 GTU  C15  C11  C10  122.23  3.000
 GTU  C15  C11  N3   123.10  3.000
 GTU  C10  C11  N3   114.57  3.000
 GTU  H7   C12  C13  120.28  3.000
 GTU  H7   C12  N3   117.18  3.000
 GTU  C13  C12  N3   122.53  3.000
 GTU  C16  C13  C14  120.97  3.000
 GTU  C16  C13  C12  120.12  3.000
 GTU  C14  C13  C12  118.90  3.000
 GTU  H8   C14  C15  120.83  3.000
 GTU  H8   C14  C13  120.94  3.000
 GTU  C15  C14  C13  118.23  3.000
 GTU  H9   C15  C14  119.79  3.000
 GTU  H9   C15  C11  121.60  3.000
 GTU  C14  C15  C11  118.58  3.000
 GTU  C18  C19  F    118.13  3.000
 GTU  C18  C19  C7   122.34  3.000
 GTU  F    C19  C7   119.53  3.000
 GTU  H11  N    H10  115.05  3.000
 GTU  H11  N    C6   116.13  3.000
 GTU  H10  N    C6   118.10  3.000
 GTU  C6   O    C5   116.46  3.000
 GTU  H14  C    H13  107.73  3.000
 GTU  H14  C    H12  107.78  3.000
 GTU  H13  C    H12  107.78  3.000
 GTU  H14  C    C1   111.00  3.000
 GTU  H13  C    C1   111.16  3.000
 GTU  H12  C    C1   111.22  3.000
 GTU  H15  C18  C17  120.09  3.000
 GTU  H15  C18  C19  119.78  3.000
 GTU  C17  C18  C19  120.13  3.000
 GTU  H16  C17  C18  119.00  3.000
 GTU  H16  C17  C9   121.82  3.000
 GTU  C18  C17  C9   119.17  3.000
 GTU  N4   C16  C13  180.00  3.000
 GTU  H5   N2   C10  117.04  3.000
 GTU  H5   N2   C9   114.67  3.000
 GTU  C10  N2   C9   128.05  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
 GTU  CONST_01  C14  C15  C11  N3      0.00   0.0  0
 GTU  CONST_02  C14  C13  C12  N3      0.00   0.0  0
 GTU  CONST_03  C17  C18  C19  C7      0.00   0.0  0
 GTU  CONST_04  C17  C9   C8   C7      0.00   0.0  0
 GTU  CONST_05  C18  C19  C7   C8      0.00   0.0  0
 GTU  CONST_06  C18  C17  C9   C8      0.00   0.0  0
 GTU  CONST_07  C19  C18  C17  C9      0.00   0.0  0
 GTU  CONST_08  C19  C7   C8   C9      0.00   0.0  0
 GTU  CONST_09  C13  C12  N3   C11     0.00   0.0  0
 GTU  CONST_10  C13  C14  C15  C11     0.00   0.0  0
 GTU  CONST_11  C15  C11  N3   C12     0.00   0.0  0
 GTU  CONST_12  C15  C14  C13  C12     0.00   0.0  0
 GTU  CONST_13  C18  C19  C7   C3    180.00   0.0  0
 GTU  CONST_14  C9   C8   C7   C3    180.00   0.0  0
 GTU  CONST_15  O    C6   N1   C3      0.00   0.0  0
 GTU  CONST_16  F    C19  C7   C3      0.00   0.0  0
 GTU  CONST_17  C18  C17  C9   N2    180.00   0.0  0
 GTU  CONST_18  C7   C8   C9   N2    180.00   0.0  0
 GTU  CONST_19  C16  C13  C12  N3    180.00   0.0  0
 GTU  CONST_20  F    C19  C7   C8    180.00   0.0  0
 GTU  CONST_21  C12  N3   C11  C10   180.00   0.0  0
 GTU  CONST_22  C14  C15  C11  C10   180.00   0.0  0
 GTU  CONST_23  C16  C13  C14  C15   180.00   0.0  0
 GTU  CONST_24  C17  C18  C19  F     180.00   0.0  0
 GTU  CONST_25  N    C6   N1   C3    180.00   0.0  0
 GTU  CONST_26  H6   C8   C7   C3      0.00   0.0  0
 GTU  CONST_27  H9   C15  C11  N3    180.00   0.0  0
 GTU  CONST_28  H15  C18  C19  C7    180.00   0.0  0
 GTU  CONST_29  H16  C17  C9   C8    180.00   0.0  0
 GTU  CONST_30  H7   C12  N3   C11   180.00   0.0  0
 GTU  CONST_31  H8   C14  C15  C11   180.00   0.0  0
 GTU  CONST_32  C11  C10  N2   C9    180.00   0.0  0
 GTU  CONST_33  C10  N2   C9   C8    180.00   0.0  0
 GTU  CONST_35  H5   N2   C9   C8      0.00   0.0  0
 GTU  CONST_38  C9   N2   C10  O1      0.00   0.0  0
 GTU  Var_01    O    C5   C4   C3    -56.90  30.0  1
 GTU  Var_02    N1   C6   O    C5     -6.89  30.0  1
 GTU  Var_03    N3   C11  C10  N2   -144.70  30.0  2
 GTU  Var_04    H12  C    C1   C2    133.40  30.0  3

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
 GTU  chir_01  C3  C4  C7  N1  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
 GTU  plan-1  N3   0.020
 GTU  plan-1  C10  0.020
 GTU  plan-1  C11  0.020
 GTU  plan-1  C12  0.020
 GTU  plan-1  C13  0.020
 GTU  plan-1  C14  0.020
 GTU  plan-1  C15  0.020
 GTU  plan-1  C16  0.020
 GTU  plan-1  N4   0.020
 GTU  plan-1  H7   0.020
 GTU  plan-1  H8   0.020
 GTU  plan-1  H9   0.020
 GTU  plan-2  C3   0.020
 GTU  plan-2  C7   0.020
 GTU  plan-2  C8   0.020
 GTU  plan-2  C9   0.020
 GTU  plan-2  C19  0.020
 GTU  plan-2  C18  0.020
 GTU  plan-2  C17  0.020
 GTU  plan-2  H6   0.020
 GTU  plan-2  H15  0.020
 GTU  plan-2  H16  0.020
 GTU  plan-2  F    0.020
 GTU  plan-2  N2   0.020
 GTU  plan-3  O1   0.020
 GTU  plan-3  C9   0.020
 GTU  plan-3  C10  0.020
 GTU  plan-3  C11  0.020
 GTU  plan-3  H5   0.020
 GTU  plan-3  N2   0.020
 GTU  plan-4  C3   0.020
 GTU  plan-4  C6   0.020
 GTU  plan-4  N1   0.020
 GTU  plan-4  N    0.020
 GTU  plan-4  O    0.020
 GTU  plan-4  H10  0.020
 GTU  plan-4  H11  0.020

