# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 12:33:23 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: N-{3-[(4R)-2-amino-5,5-difluoro-4-methyl-5,6-dihydro-4H-1,3-oxazin-4-yl]-4-fluorophenyl}-5-ethoxypyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOc1ccc(nc1)C(=O)Nc2ccc(F)c(c2)[C@@]3(C)N=C(N)OCC3(F)F
#
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
 6T9  6T9  N-{3-[(4R)-2-amino-5,5-difluoro-4-methyl-5,6-dihydro-4H-1,3-oxazin-4-yl]-4-fluorophenyl}-5-ethoxypyridine-2-carboxamide  ligand  48  29  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6T9
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
 6T9  C1    C  CH2   0  -0.282  -4.8042   1.9471  -0.7912
 6T9  C2    C  CT    0   0.734  -4.1900   0.5655  -0.7341
 6T9  O3    O  O2    0  -0.460  -3.8001   2.9248  -0.6056
 6T9  C4    C  C     0   0.639  -2.8611   2.6354   0.3145
 6T9  N5    N  N     0  -0.478  -2.6711   1.5221   0.8965
 6T9  C6    C  CT    0  -0.110  -3.4485   0.3414   0.5906
 6T9  C7    C  CR6   0  -0.058  -2.4892  -0.8471   0.4482
 6T9  C8    C  CR16  0  -0.415  -1.1237  -0.6135   0.3564
 6T9  C9    C  CR6   0   0.417  -0.1860  -1.6362   0.2143
 6T9  C10   C  CR16  0  -0.314  -0.6269  -2.9564   0.1615
 6T9  C11   C  CR16  0  -0.396  -1.9855  -3.2117   0.2476
 6T9  C12   C  CR6   0   0.515  -2.8892  -2.1777   0.3815
 6T9  F13   F  F     0  -0.313  -4.1900  -2.5153   0.4462
 6T9  N14   N  NH2   0  -0.825  -2.0515   3.7034   0.5236
 6T9  C15   C  CH3   0  -0.650  -4.4302   0.1381   1.7544
 6T9  N16   N  NH1   0  -0.764   1.1521  -1.2458   0.1333
 6T9  C17   C  C     0   0.534   2.2567  -2.0077  -0.0076
 6T9  C18   C  CR6   0   0.093   3.5247  -1.2162  -0.0643
 6T9  O19   O  O     0  -0.465   2.2683  -3.2258  -0.0870
 6T9  N20   N  N     0  -0.428   3.4390   0.1008   0.0519
 6T9  C21   C  CR16  0  -0.185   4.5339   0.8402   0.0075
 6T9  C22   C  CR6   0   0.337   5.8047   0.2796  -0.1635
 6T9  C23   C  CR16  0  -0.251   5.8946  -1.1070  -0.2871
 6T9  C24   C  CR16  0  -0.269   4.7437  -1.8641  -0.2355
 6T9  O25   O  O2    0  -0.458   6.9413   0.9752  -0.2193
 6T9  F26   F  F     0  -0.328  -5.1688  -0.3494  -0.9503
 6T9  F27   F  F     0  -0.338  -3.3108   0.4388  -1.7697
 6T9  C28   C  CH2   0  -0.197   6.8980   2.3955  -0.0830
 6T9  C29   C  CH3   0  -0.682   8.3116   2.9139  -0.1816
 6T9  H11C  H  HCH2  0   0.291  -5.2545   2.1276  -1.7675
 6T9  H12C  H  HCH2  0   0.265  -5.5818   2.0464  -0.0297
 6T9  H141  H  HNH2  0   0.397  -2.4454   4.6222   0.3993
 6T9  H142  H  HNH2  0   0.396  -1.4233   3.6224   1.3058
 6T9  H151  H  HCH3  0   0.249  -5.0681  -0.7329   1.6484
 6T9  H152  H  HCH3  0   0.252  -3.8571   0.0335   2.6746
 6T9  H153  H  HCH3  0   0.240  -5.0705   1.0132   1.8704
 6T9  H8    H  HCR6  0   0.281  -0.7817   0.4119   0.4091
 6T9  H10   H  HCR6  0   0.288   0.0599  -3.7792   0.0565
 6T9  H16   H  HNH1  0   0.419   1.3321  -0.2504   0.1812
 6T9  H11   H  HCR6  0   0.278  -2.3473  -4.2310   0.2068
 6T9  H24   H  HCR6  0   0.279   4.7918  -2.9397  -0.3270
 6T9  H21   H  HCR6  0   0.288   4.3931   1.9090   0.1095
 6T9  H23   H  HCR6  0   0.286   6.8612  -1.5754  -0.4224
 6T9  H281  H  HCH2  0   0.234   6.2741   2.8276  -0.8716
 6T9  H282  H  HCH2  0   0.234   6.4542   2.6632   0.8809
 6T9  H291  H  HCH3  0   0.241   8.3047   3.9980  -0.0746
 6T9  H292  H  HCH3  0   0.238   8.9426   2.5036   0.6066
 6T9  H293  H  HCH3  0   0.238   8.7566   2.6749  -1.1474

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
 6T9  C1   C2    single    1.513  0.020  1.513
 6T9  C1   O3    single    1.414  0.020  1.414
 6T9  C2   C6    single    1.535  0.020  1.535
 6T9  C2   F26   single    1.357  0.020  1.357
 6T9  C2   F27   single    1.364  0.020  1.364
 6T9  O3   C4    single    1.346  0.020  1.346
 6T9  C4   N5    double    1.271  0.020  1.271
 6T9  C4   N14   single    1.356  0.020  1.356
 6T9  N5   C6    single    1.446  0.020  1.446
 6T9  C6   C7    single    1.534  0.020  1.534
 6T9  C6   C15   single    1.536  0.020  1.536
 6T9  C7   C8    aromatic  1.388  0.020  1.388
 6T9  C7   C12   aromatic  1.391  0.020  1.391
 6T9  C8   C9    aromatic  1.395  0.020  1.395
 6T9  C9   C10   aromatic  1.393  0.020  1.393
 6T9  C9   N16   single    1.396  0.020  1.396
 6T9  C10  C11   aromatic  1.385  0.020  1.385
 6T9  C11  C12   aromatic  1.380  0.020  1.380
 6T9  C12  F13   single    1.346  0.020  1.346
 6T9  N16  C17   single    1.349  0.020  1.349
 6T9  C17  C18   single    1.496  0.020  1.496
 6T9  C17  O19   double    1.221  0.020  1.221
 6T9  C18  N20   aromatic  1.325  0.020  1.325
 6T9  C18  C24   aromatic  1.391  0.020  1.391
 6T9  N20  C21   aromatic  1.322  0.020  1.322
 6T9  C21  C22   aromatic  1.399  0.020  1.399
 6T9  C22  C23   aromatic  1.395  0.020  1.395
 6T9  C22  O25   single    1.334  0.020  1.334
 6T9  C23  C24   aromatic  1.379  0.020  1.379
 6T9  O25  C28   single    1.428  0.020  1.428
 6T9  C28  C29   single    1.509  0.020  1.509
 6T9  C1   H11C  single    0.970  0.020  1.090
 6T9  C1   H12C  single    0.970  0.020  1.090
 6T9  N14  H141  single    0.890  0.020  1.040
 6T9  N14  H142  single    0.890  0.020  1.040
 6T9  C15  H151  single    0.970  0.020  1.090
 6T9  C15  H152  single    0.970  0.020  1.090
 6T9  C15  H153  single    0.970  0.020  1.090
 6T9  C8   H8    single    0.930  0.020  1.080
 6T9  C10  H10   single    0.930  0.020  1.080
 6T9  N16  H16   single    0.860  0.020  1.020
 6T9  C11  H11   single    0.930  0.020  1.080
 6T9  C24  H24   single    0.930  0.020  1.080
 6T9  C21  H21   single    0.930  0.020  1.080
 6T9  C23  H23   single    0.930  0.020  1.080
 6T9  C28  H281  single    0.970  0.020  1.090
 6T9  C28  H282  single    0.970  0.020  1.090
 6T9  C29  H291  single    0.970  0.020  1.090
 6T9  C29  H292  single    0.970  0.020  1.090
 6T9  C29  H293  single    0.970  0.020  1.090

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
 6T9  H12C  C1   H11C  108.36  3.000
 6T9  H12C  C1   O3    110.55  3.000
 6T9  H11C  C1   O3    107.24  3.000
 6T9  H12C  C1   C2    110.22  3.000
 6T9  H11C  C1   C2    110.65  3.000
 6T9  O3    C1   C2    109.77  3.000
 6T9  F27   C2   F26   106.33  3.000
 6T9  F27   C2   C6    109.29  3.000
 6T9  F26   C2   C6    112.80  3.000
 6T9  F27   C2   C1    108.53  3.000
 6T9  F26   C2   C1    108.47  3.000
 6T9  C6    C2   C1    111.23  3.000
 6T9  C4    O3   C1    115.88  3.000
 6T9  N14   C4   N5    122.01  3.000
 6T9  N14   C4   O3    110.64  3.000
 6T9  N5    C4   O3    127.28  3.000
 6T9  C6    N5   C4    122.56  3.000
 6T9  C15   C6   C7    111.56  3.000
 6T9  C15   C6   N5    106.94  3.000
 6T9  C7    C6   N5    108.42  3.000
 6T9  C15   C6   C2    111.38  3.000
 6T9  C7    C6   C2    109.58  3.000
 6T9  N5    C6   C2    108.85  3.000
 6T9  C12   C7   C8    116.14  3.000
 6T9  C12   C7   C6    124.46  3.000
 6T9  C8    C7   C6    119.39  3.000
 6T9  H8    C8   C9    119.16  3.000
 6T9  H8    C8   C7    117.84  3.000
 6T9  C9    C8   C7    123.00  3.000
 6T9  N16   C9   C10   124.48  3.000
 6T9  N16   C9   C8    116.43  3.000
 6T9  C10   C9   C8    119.08  3.000
 6T9  H10   C10  C11   119.40  3.000
 6T9  H10   C10  C9    121.73  3.000
 6T9  C11   C10  C9    118.87  3.000
 6T9  H11   C11  C12   119.37  3.000
 6T9  H11   C11  C10   119.94  3.000
 6T9  C12   C11  C10   120.69  3.000
 6T9  F13   C12  C11   116.73  3.000
 6T9  F13   C12  C7    121.05  3.000
 6T9  C11   C12  C7    122.22  3.000
 6T9  H142  N14  H141  114.42  3.000
 6T9  H142  N14  C4    115.41  3.000
 6T9  H141  N14  C4    117.76  3.000
 6T9  H153  C15  H152  107.23  3.000
 6T9  H153  C15  H151  108.03  3.000
 6T9  H152  C15  H151  108.35  3.000
 6T9  H153  C15  C6    110.47  3.000
 6T9  H152  C15  C6    108.45  3.000
 6T9  H151  C15  C6    114.08  3.000
 6T9  H16   N16  C17   114.49  3.000
 6T9  H16   N16  C9    116.26  3.000
 6T9  C17   N16  C9    129.25  3.000
 6T9  O19   C17  C18   121.16  3.000
 6T9  O19   C17  N16   125.31  3.000
 6T9  C18   C17  N16   113.52  3.000
 6T9  C24   C18  N20   122.04  3.000
 6T9  C24   C18  C17   120.07  3.000
 6T9  N20   C18  C17   117.89  3.000
 6T9  C21   N20  C18   119.96  3.000
 6T9  H21   C21  C22   121.67  3.000
 6T9  H21   C21  N20   116.18  3.000
 6T9  C22   C21  N20   122.15  3.000
 6T9  O25   C22  C23   117.37  3.000
 6T9  O25   C22  C21   124.75  3.000
 6T9  C23   C22  C21   117.88  3.000
 6T9  H23   C23  C24   120.83  3.000
 6T9  H23   C23  C22   119.91  3.000
 6T9  C24   C23  C22   119.26  3.000
 6T9  H24   C24  C23   120.42  3.000
 6T9  H24   C24  C18   120.87  3.000
 6T9  C23   C24  C18   118.71  3.000
 6T9  C28   O25  C22   119.28  3.000
 6T9  H282  C28  H281  107.87  3.000
 6T9  H282  C28  C29   110.70  3.000
 6T9  H281  C28  C29   110.57  3.000
 6T9  H282  C28  O25   109.85  3.000
 6T9  H281  C28  O25   109.96  3.000
 6T9  C29   C28  O25   107.89  3.000
 6T9  H293  C29  H292  108.78  3.000
 6T9  H293  C29  H291  107.93  3.000
 6T9  H292  C29  H291  107.89  3.000
 6T9  H293  C29  C28   111.42  3.000
 6T9  H292  C29  C28   111.46  3.000
 6T9  H291  C29  C28   109.24  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
 6T9  CONST_01  C10   C9   C8   C7      0.00   0.0  0
 6T9  CONST_02  C10   C11  C12  C7      0.00   0.0  0
 6T9  CONST_03  C11   C12  C7   C8      0.00   0.0  0
 6T9  CONST_04  C11   C10  C9   C8      0.00   0.0  0
 6T9  CONST_05  C12   C7   C8   C9      0.00   0.0  0
 6T9  CONST_06  C12   C11  C10  C9      0.00   0.0  0
 6T9  CONST_07  C22   C21  N20  C18     0.00   0.0  0
 6T9  CONST_08  C22   C23  C24  C18     0.00   0.0  0
 6T9  CONST_09  C23   C24  C18  N20     0.00   0.0  0
 6T9  CONST_10  C23   C22  C21  N20     0.00   0.0  0
 6T9  CONST_11  C24   C18  N20  C21     0.00   0.0  0
 6T9  CONST_12  C24   C23  C22  C21     0.00   0.0  0
 6T9  CONST_13  C9    C8   C7   C6    180.00   0.0  0
 6T9  CONST_14  C11   C12  C7   C6    180.00   0.0  0
 6T9  CONST_15  C6    N5   C4   O3      0.00   0.0  0
 6T9  CONST_16  F13   C12  C7   C6      0.00   0.0  0
 6T9  CONST_17  N16   C9   C8   C7    180.00   0.0  0
 6T9  CONST_18  F13   C12  C7   C8    180.00   0.0  0
 6T9  CONST_19  F13   C12  C11  C10   180.00   0.0  0
 6T9  CONST_20  N16   C9   C10  C11   180.00   0.0  0
 6T9  CONST_21  C21   N20  C18  C17   180.00   0.0  0
 6T9  CONST_22  C23   C24  C18  C17   180.00   0.0  0
 6T9  CONST_23  O25   C22  C21  N20   180.00   0.0  0
 6T9  CONST_24  O25   C22  C23  C24   180.00   0.0  0
 6T9  CONST_25  N14   C4   N5   C6    180.00   0.0  0
 6T9  CONST_26  H8    C8   C7   C6      0.00   0.0  0
 6T9  CONST_27  H11   C11  C12  C7    180.00   0.0  0
 6T9  CONST_28  H10   C10  C9   C8    180.00   0.0  0
 6T9  CONST_29  H21   C21  N20  C18   180.00   0.0  0
 6T9  CONST_30  H23   C23  C24  C18   180.00   0.0  0
 6T9  CONST_31  H24   C24  C18  N20   180.00   0.0  0
 6T9  CONST_32  C18   C17  N16  C9    180.00   0.0  0
 6T9  CONST_33  C17   N16  C9   C8    180.00   0.0  0
 6T9  CONST_34  C17   N16  C9   C10     0.00   0.0  0
 6T9  CONST_35  H16   N16  C9   C8      0.00   0.0  0
 6T9  CONST_37  H142  N14  C4   O3    180.00   0.0  0
 6T9  CONST_38  O19   C17  N16  C9      0.00   0.0  0
 6T9  Var_01    N5    C4   O3   C1     10.39  30.0  1
 6T9  Var_02    C6    C2   C1   O3     56.98  30.0  1
 6T9  Var_03    H11C  C1   O3   C4   -159.81  30.0  1
 6T9  Var_04    N20   C18  C17  N16     1.26  30.0  2
 6T9  Var_05    C29   C28  O25  C22   179.89  30.0  3
 6T9  Var_06    H291  C29  C28  O25  -179.68  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
 6T9  chir_01  C6  N5  C7  C2  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
 6T9  plan-1  C6    0.020
 6T9  plan-1  C7    0.020
 6T9  plan-1  C8    0.020
 6T9  plan-1  C9    0.020
 6T9  plan-1  C10   0.020
 6T9  plan-1  C11   0.020
 6T9  plan-1  C12   0.020
 6T9  plan-1  F13   0.020
 6T9  plan-1  N16   0.020
 6T9  plan-1  H8    0.020
 6T9  plan-1  H10   0.020
 6T9  plan-1  H11   0.020
 6T9  plan-2  C17   0.020
 6T9  plan-2  C18   0.020
 6T9  plan-2  N20   0.020
 6T9  plan-2  C21   0.020
 6T9  plan-2  C22   0.020
 6T9  plan-2  C23   0.020
 6T9  plan-2  C24   0.020
 6T9  plan-2  O25   0.020
 6T9  plan-2  H24   0.020
 6T9  plan-2  H21   0.020
 6T9  plan-2  H23   0.020
 6T9  plan-3  C9    0.020
 6T9  plan-3  N16   0.020
 6T9  plan-3  C17   0.020
 6T9  plan-3  C18   0.020
 6T9  plan-3  O19   0.020
 6T9  plan-3  H16   0.020
 6T9  plan-4  O3    0.020
 6T9  plan-4  C4    0.020
 6T9  plan-4  N5    0.020
 6T9  plan-4  C6    0.020
 6T9  plan-4  N14   0.020
 6T9  plan-4  H141  0.020
 6T9  plan-4  H142  0.020

