# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 12:57:17 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: N-{3-[(4S)-2-amino-5,5-difluoro-4-(fluoromethyl)-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@](CF)(c2cc(NC(=O)c3ccc(cn3)C#N)ccc2F)C(F)(F)CO1
#
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
 1HO  1HO  N-{3-[(4S)-2-amino-5,5-difluoro-4-(fluoromethyl)-5,6-dihydro-4H-1,3-oxazin-4-yl]-4-fluorophenyl}-5-cyanopyridine-2-carboxamide  ligand  42  29  .  2021-08-03  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1HO
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
 1HO  C27  C  CR16  0  -0.283  -5.3906   1.1762  -0.2778
 1HO  C28  C  CSP   0   0.060  -7.3651  -1.8536   0.5060
 1HO  C26  C  CR16  0  -0.112  -6.4890   0.3597  -0.0813
 1HO  O22  O  O     0  -0.452  -3.0246   2.6725  -0.5971
 1HO  C20  C  C     0   0.543  -2.9103   1.4973  -0.2958
 1HO  N19  N  NH1   0  -0.762  -1.7553   0.8374  -0.0999
 1HO  C15  C  CR16  0  -0.306  -0.0947   2.6270  -0.4620
 1HO  C16  C  CR16  0  -0.406   1.2451   2.9760  -0.4651
 1HO  C17  C  CR6   0   0.536   2.2183   2.0451  -0.1653
 1HO  C1   C  C     0   0.654   2.7120  -2.6453  -0.1210
 1HO  C3   C  CT    0  -0.194   2.9299  -0.3537   0.5447
 1HO  C8   C  CR6   0  -0.063   1.9116   0.7218   0.1326
 1HO  C4   C  CT    0   0.745   4.1888  -0.3845  -0.3443
 1HO  C5   C  CH2   0  -0.289   4.8302  -1.7575  -0.3473
 1HO  C9   C  CH2   0   0.031   3.2841  -0.1457   2.0253
 1HO  N2   N  N     0  -0.489   2.2701  -1.6364   0.5180
 1HO  O6   O  O2    0  -0.454   3.8946  -2.7325  -0.7517
 1HO  F10  F  F     0  -0.360   3.6520   1.1567   2.3077
 1HO  F11  F  F     0  -0.339   3.8503  -0.0567  -1.6217
 1HO  F12  F  F     0  -0.332   5.1493   0.4877   0.0536
 1HO  C13  C  CR16  0  -0.410   0.5622   0.3918   0.1312
 1HO  C14  C  CR6   0   0.424  -0.4431   1.3150  -0.1539
 1HO  C21  C  CR6   0   0.145  -4.1267   0.6320  -0.1001
 1HO  N23  N  N     0  -0.439  -3.9246  -0.6344   0.2471
 1HO  C24  C  CR16  0  -0.015  -4.9631  -1.4212   0.4382
 1HO  C25  C  CR6   0  -0.080  -6.2734  -0.9645   0.2856
 1HO  N29  N  NS    0  -0.232  -8.2440  -2.5753   0.6859
 1HO  H1   H  HCR6  0   0.295  -5.5163   2.2108  -0.5604
 1HO  H2   H  HCR6  0   0.305  -7.4924   0.7413  -0.2097
 1HO  H3   H  HNH1  0   0.426  -1.8650  -0.1399   0.1434
 1HO  H4   H  HCR6  0   0.289  -0.8358   3.3734  -0.6946
 1HO  H5   H  HCR6  0   0.280   1.5387   3.9904  -0.7015
 1HO  H6   H  HCH2  0   0.296   5.6558  -1.7845  -1.0579
 1HO  H7   H  HCH2  0   0.267   5.2235  -1.9918   0.6469
 1HO  H8   H  HCH2  0   0.232   2.3954  -0.3861   2.6093
 1HO  H9   H  HCH2  0   0.223   4.0948  -0.8096   2.3335
 1HO  H10  H  HNH2  0   0.404   1.0317  -3.7583  -0.0186
 1HO  H11  H  HNH2  0   0.405   2.3274  -4.5157  -0.8357
 1HO  H12  H  HCR6  0   0.288   0.2939  -0.6287   0.3697
 1HO  H13  H  HCR6  0   0.302  -4.7657  -2.4476   0.7222
 1HO  F18  F  F     0  -0.312   3.4889   2.4715  -0.1888
 1HO  N7   N  NH2   0  -0.822   2.0194  -3.7975  -0.2021

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
 1HO  F11  C4   single    1.362  0.020  1.362
 1HO  F12  C4   single    1.357  0.020  1.357
 1HO  F18  C17  single    1.340  0.020  1.340
 1HO  C4   C5   single    1.515  0.020  1.515
 1HO  C4   C3   single    1.541  0.020  1.541
 1HO  F10  C9   single    1.383  0.020  1.383
 1HO  C9   C3   single    1.537  0.020  1.537
 1HO  C17  C16  aromatic  1.380  0.020  1.380
 1HO  C17  C8   aromatic  1.391  0.020  1.391
 1HO  C5   O6   single    1.411  0.020  1.411
 1HO  C3   C8   single    1.537  0.020  1.537
 1HO  C3   N2   single    1.443  0.020  1.443
 1HO  C16  C15  aromatic  1.385  0.020  1.385
 1HO  C8   C13  aromatic  1.389  0.020  1.389
 1HO  O6   C1   single    1.343  0.020  1.343
 1HO  N2   C1   double    1.273  0.020  1.273
 1HO  C15  C14  aromatic  1.392  0.020  1.392
 1HO  C1   N7   single    1.347  0.020  1.347
 1HO  C13  C14  aromatic  1.394  0.020  1.394
 1HO  C14  N19  single    1.397  0.020  1.397
 1HO  O22  C20  double    1.219  0.020  1.219
 1HO  N19  C20  single    1.345  0.020  1.345
 1HO  C20  C21  single    1.506  0.020  1.506
 1HO  C21  C27  aromatic  1.387  0.020  1.387
 1HO  C21  N23  aromatic  1.329  0.020  1.329
 1HO  C27  C26  aromatic  1.383  0.020  1.383
 1HO  N23  C24  aromatic  1.317  0.020  1.317
 1HO  C26  C25  aromatic  1.391  0.020  1.391
 1HO  C24  C25  aromatic  1.396  0.020  1.396
 1HO  C25  C28  single    1.425  0.020  1.425
 1HO  C28  N29  triple    1.151  0.020  1.151
 1HO  C27  H1   single    0.930  0.020  1.080
 1HO  C26  H2   single    0.930  0.020  1.080
 1HO  N19  H3   single    0.860  0.020  1.020
 1HO  C15  H4   single    0.930  0.020  1.080
 1HO  C16  H5   single    0.930  0.020  1.080
 1HO  C5   H6   single    0.970  0.020  1.090
 1HO  C5   H7   single    0.970  0.020  1.090
 1HO  C9   H8   single    0.970  0.020  1.090
 1HO  C9   H9   single    0.970  0.020  1.090
 1HO  N7   H10  single    0.890  0.020  1.040
 1HO  N7   H11  single    0.890  0.020  1.040
 1HO  C13  H12  single    0.930  0.020  1.080
 1HO  C24  H13  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
 1HO  H1   C27  C21  121.02  3.000
 1HO  H1   C27  C26  120.69  3.000
 1HO  C21  C27  C26  118.29  3.000
 1HO  N29  C28  C25  180.00  3.000
 1HO  H2   C26  C25  120.75  3.000
 1HO  H2   C26  C27  120.80  3.000
 1HO  C25  C26  C27  118.46  3.000
 1HO  C21  C20  N19  113.14  3.000
 1HO  C21  C20  O22  120.71  3.000
 1HO  N19  C20  O22  126.15  3.000
 1HO  H3   N19  C14  116.14  3.000
 1HO  H3   N19  C20  114.55  3.000
 1HO  C14  N19  C20  129.29  3.000
 1HO  H4   C15  C14  121.91  3.000
 1HO  H4   C15  C16  119.38  3.000
 1HO  C14  C15  C16  118.70  3.000
 1HO  H5   C16  C17  119.24  3.000
 1HO  H5   C16  C15  119.95  3.000
 1HO  C17  C16  C15  120.80  3.000
 1HO  F18  C17  C8   121.03  3.000
 1HO  C8   C17  C16  122.21  3.000
 1HO  F18  C17  C16  116.76  3.000
 1HO  N7   C1   O6   111.66  3.000
 1HO  N7   C1   N2   121.97  3.000
 1HO  O6   C1   N2   126.35  3.000
 1HO  N2   C3   C9   104.10  3.000
 1HO  N2   C3   C4   110.19  3.000
 1HO  C9   C3   C4   111.73  3.000
 1HO  N2   C3   C8   108.30  3.000
 1HO  C9   C3   C8   108.44  3.000
 1HO  C4   C3   C8   113.61  3.000
 1HO  C13  C8   C3   118.53  3.000
 1HO  C13  C8   C17  116.10  3.000
 1HO  C3   C8   C17  125.24  3.000
 1HO  F12  C4   F11  107.23  3.000
 1HO  F12  C4   C5   106.46  3.000
 1HO  F11  C4   C5   108.76  3.000
 1HO  C5   C4   C3   111.40  3.000
 1HO  F12  C4   C3   113.33  3.000
 1HO  F11  C4   C3   109.46  3.000
 1HO  H7   C5   H6   108.36  3.000
 1HO  H7   C5   O6   110.54  3.000
 1HO  H6   C5   O6   107.36  3.000
 1HO  H7   C5   C4   110.13  3.000
 1HO  H6   C5   C4   110.15  3.000
 1HO  O6   C5   C4   110.25  3.000
 1HO  H9   C9   H8   108.66  3.000
 1HO  H9   C9   F10  108.51  3.000
 1HO  H8   C9   F10  108.37  3.000
 1HO  H9   C9   C3   111.14  3.000
 1HO  H8   C9   C3   107.36  3.000
 1HO  F10  C9   C3   112.68  3.000
 1HO  C3   N2   C1   123.71  3.000
 1HO  C5   O6   C1   113.86  3.000
 1HO  H12  C13  C14  119.40  3.000
 1HO  H12  C13  C8   117.69  3.000
 1HO  C14  C13  C8   122.91  3.000
 1HO  C13  C14  C15  119.27  3.000
 1HO  C13  C14  N19  116.28  3.000
 1HO  C15  C14  N19  124.45  3.000
 1HO  N23  C21  C20  117.32  3.000
 1HO  N23  C21  C27  123.08  3.000
 1HO  C20  C21  C27  119.60  3.000
 1HO  C24  N23  C21  119.18  3.000
 1HO  H13  C24  C25  120.65  3.000
 1HO  H13  C24  N23  117.42  3.000
 1HO  C25  C24  N23  121.93  3.000
 1HO  C24  C25  C26  119.07  3.000
 1HO  C24  C25  C28  119.87  3.000
 1HO  C26  C25  C28  121.06  3.000
 1HO  H11  N7   H10  116.33  3.000
 1HO  H11  N7   C1   119.42  3.000
 1HO  H10  N7   C1   117.44  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
 1HO  CONST_01  C24  N23  C21  C27    0.00   0.0  0
 1HO  CONST_02  C24  C25  C26  C27    0.00   0.0  0
 1HO  CONST_03  N23  C21  C27  C26    0.00   0.0  0
 1HO  CONST_04  N23  C24  C25  C26    0.00   0.0  0
 1HO  CONST_05  C8   C17  C16  C15    0.00   0.0  0
 1HO  CONST_06  C8   C13  C14  C15    0.00   0.0  0
 1HO  CONST_07  C13  C8   C17  C16    0.00   0.0  0
 1HO  CONST_08  C13  C14  C15  C16    0.00   0.0  0
 1HO  CONST_09  C14  C15  C16  C17    0.00   0.0  0
 1HO  CONST_10  C14  C13  C8   C17    0.00   0.0  0
 1HO  CONST_11  C25  C26  C27  C21    0.00   0.0  0
 1HO  CONST_12  C25  C24  N23  C21    0.00   0.0  0
 1HO  CONST_13  C3   C8   C17  C16  180.00   0.0  0
 1HO  CONST_14  C14  C13  C8   C3   180.00   0.0  0
 1HO  CONST_15  O6   C1   N2   C3     0.00   0.0  0
 1HO  CONST_16  C28  C25  C26  C27  180.00   0.0  0
 1HO  CONST_17  N23  C24  C25  C28  180.00   0.0  0
 1HO  CONST_18  C20  C21  C27  C26  180.00   0.0  0
 1HO  CONST_19  C24  N23  C21  C20  180.00   0.0  0
 1HO  CONST_20  C16  C15  C14  N19  180.00   0.0  0
 1HO  CONST_21  C8   C13  C14  N19  180.00   0.0  0
 1HO  CONST_22  F18  C17  C16  C15  180.00   0.0  0
 1HO  CONST_23  F18  C17  C8   C3     0.00   0.0  0
 1HO  CONST_24  F18  C17  C8   C13  180.00   0.0  0
 1HO  CONST_25  N7   C1   N2   C3   180.00   0.0  0
 1HO  CONST_26  H13  C24  C25  C26  180.00   0.0  0
 1HO  CONST_27  H12  C13  C14  C15  180.00   0.0  0
 1HO  CONST_28  H4   C15  C16  C17  180.00   0.0  0
 1HO  CONST_29  H5   C16  C17  C8   180.00   0.0  0
 1HO  CONST_30  H2   C26  C27  C21  180.00   0.0  0
 1HO  CONST_31  H1   C27  C21  N23  180.00   0.0  0
 1HO  CONST_32  C21  C20  N19  C14  180.00   0.0  0
 1HO  CONST_33  C15  C14  N19  C20    0.00   0.0  0
 1HO  CONST_34  C13  C14  N19  C20  180.00   0.0  0
 1HO  CONST_35  H3   N19  C14  C15  180.00   0.0  0
 1HO  CONST_37  H11  N7   C1   N2   180.00   0.0  0
 1HO  CONST_38  C14  N19  C20  O22    0.00   0.0  0
 1HO  Var_01    C4   C5   O6   C1   -48.15  30.0  1
 1HO  Var_02    O6   C5   C4   C3    55.97  30.0  1
 1HO  Var_03    N2   C1   O6   C5    17.87  30.0  1
 1HO  Var_04    O22  C20  C21  C27    0.64  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
 1HO  chir_01  C3  C4  C8  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
 1HO  plan-1  N19  0.020
 1HO  plan-1  C15  0.020
 1HO  plan-1  C16  0.020
 1HO  plan-1  C17  0.020
 1HO  plan-1  C3   0.020
 1HO  plan-1  C8   0.020
 1HO  plan-1  C13  0.020
 1HO  plan-1  C14  0.020
 1HO  plan-1  H4   0.020
 1HO  plan-1  H5   0.020
 1HO  plan-1  H12  0.020
 1HO  plan-1  F18  0.020
 1HO  plan-2  C27  0.020
 1HO  plan-2  C28  0.020
 1HO  plan-2  C26  0.020
 1HO  plan-2  C20  0.020
 1HO  plan-2  C21  0.020
 1HO  plan-2  N23  0.020
 1HO  plan-2  C24  0.020
 1HO  plan-2  C25  0.020
 1HO  plan-2  N29  0.020
 1HO  plan-2  H1   0.020
 1HO  plan-2  H2   0.020
 1HO  plan-2  H13  0.020
 1HO  plan-3  O22  0.020
 1HO  plan-3  C20  0.020
 1HO  plan-3  N19  0.020
 1HO  plan-3  C14  0.020
 1HO  plan-3  C21  0.020
 1HO  plan-3  H3   0.020
 1HO  plan-4  C1   0.020
 1HO  plan-4  C3   0.020
 1HO  plan-4  N2   0.020
 1HO  plan-4  O6   0.020
 1HO  plan-4  H10  0.020
 1HO  plan-4  H11  0.020
 1HO  plan-4  N7   0.020

