# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 19:05:21 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: N-{3-[(2R,3R)-5-amino-3-methyl-2-(trifluoromethyl)-3,6-dihydro-2H-1,4-oxazin-3-yl]-4-fluorophenyl}-3,5-dichloropyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@]1(N=C(N)CO[C@H]1C(F)(F)F)c2cc(NC(=O)c3ncc(Cl)cc3Cl)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
 HRV  HRV  N-{3-[(2R,3R)-5-amino-3-methyl-2-(trifluoromethyl)-3,6-dihydro-2H-1,4-oxazin-3-yl]-4-fluorophenyl}-3,5-dichloropyridine-2-carboxamide  ligand  44  30  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_HRV
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
 HRV  C1    C   CH3   0  -0.675   2.7139   2.4476   0.5401
 HRV  C10   C   CT    0   1.026   3.1880   0.5383  -2.1052
 HRV  C14   C   CR6   0  -0.033   2.2631  -0.0474   0.6974
 HRV  C15   C   CR16  0  -0.424   0.9072   0.2257   0.5633
 HRV  C16   C   CR6   0   0.423  -0.0865  -0.7370   0.7473
 HRV  C18   C   C     0   0.536  -2.5308  -1.0469   0.5039
 HRV  C2    C   CT    0  -0.033   3.3153   1.0387   0.4695
 HRV  C20   C   CR6   0   0.186  -3.7574  -0.2058   0.2576
 HRV  C22   C   CR16  0  -0.010  -4.5358   1.9515  -0.0105
 HRV  C23   C   CR6   0  -0.121  -5.8404   1.5022  -0.1800
 HRV  C25   C   CR16  0  -0.030  -6.0987   0.1489  -0.1283
 HRV  C26   C   CR6   0  -0.100  -5.0414  -0.7252   0.0948
 HRV  C28   C   CR16  0  -0.314   0.2843  -2.0339   1.0911
 HRV  C29   C   CR16  0  -0.395   1.6300  -2.3278   1.2368
 HRV  C30   C   CR6   0   0.517   2.5894  -1.3577   1.0384
 HRV  C4    C   C     0   0.385   5.4663   0.6176   1.3816
 HRV  C6    C   CH2   0  -0.267   6.0132   0.1207   0.0703
 HRV  C8    C   CH1   0  -0.158   4.0432   0.8743  -0.8906
 HRV  F11   F   F     0  -0.302   2.1497   1.3684  -2.2474
 HRV  F12   F   F     0  -0.310   3.9176   0.6345  -3.2253
 HRV  F13   F   F     0  -0.300   2.7023  -0.7040  -2.0705
 HRV  F31   F   F     0  -0.309   3.8685  -1.7359   1.1959
 HRV  N17   N   NH1   0  -0.765  -1.4050  -0.3074   0.5792
 HRV  N21   N   N     0  -0.449  -3.5517   1.1063   0.1976
 HRV  N3    N   N     0  -0.413   4.2669   0.9993   1.5690
 HRV  N5    N   NH2   0  -0.818   6.3565   0.5987   2.4065
 HRV  O19   O   O     0  -0.442  -2.5833  -2.2565   0.6159
 HRV  O7    O   O2    0  -0.484   4.9882  -0.1552  -0.8419
 HRV  CL24  CL  CL    0  -0.080  -7.1090   2.6252  -0.4516
 HRV  CL27  CL  CL    0  -0.072  -5.4232  -2.3987   0.1448
 HRV  H1    H   HCH3  0   0.249   2.2409   2.6002   1.5095
 HRV  H2    H   HCH3  0   0.254   3.5207   3.1744   0.4439
 HRV  H3    H   HCH3  0   0.235   1.9845   2.6657  -0.2357
 HRV  H4    H   HCR6  0   0.278   0.5939   1.2283   0.3049
 HRV  H5    H   HCR6  0   0.305  -4.2963   3.0071  -0.0463
 HRV  H6    H   HCR6  0   0.324  -7.1025  -0.2313  -0.2596
 HRV  H7    H   HCR6  0   0.287  -0.4442  -2.8110   1.2498
 HRV  H8    H   HCR6  0   0.279   1.9367  -3.3300   1.5066
 HRV  H9    H   HCH2  0   0.258   6.7136   0.8666  -0.3328
 HRV  H10   H   HCH2  0   0.280   6.5706  -0.8043   0.2238
 HRV  H11   H   HCH1  0   0.272   4.5307   1.8380  -1.1129
 HRV  H12   H   HNH1  0   0.427  -1.5413   0.6872   0.4476
 HRV  H13   H   HNH2  0   0.396   7.3389   0.5541   2.1923
 HRV  H14   H   HNH2  0   0.385   6.1289   1.1459   3.2210

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
 HRV  CL27  C26   single    1.717  0.020  1.717
 HRV  O19   C18   double    1.216  0.020  1.216
 HRV  C26   C25   aromatic  1.390  0.020  1.390
 HRV  C26   C20   aromatic  1.395  0.020  1.395
 HRV  C25   C23   aromatic  1.379  0.020  1.379
 HRV  C18   C20   single    1.508  0.020  1.508
 HRV  C18   N17   single    1.349  0.020  1.349
 HRV  C20   N21   aromatic  1.329  0.020  1.329
 HRV  C28   C29   aromatic  1.385  0.020  1.385
 HRV  C28   C16   aromatic  1.392  0.020  1.392
 HRV  C23   CL24  single    1.716  0.020  1.716
 HRV  C23   C22   aromatic  1.390  0.020  1.390
 HRV  C29   C30   aromatic  1.379  0.020  1.379
 HRV  N21   C22   aromatic  1.314  0.020  1.314
 HRV  N17   C16   single    1.397  0.020  1.397
 HRV  C16   C15   aromatic  1.396  0.020  1.396
 HRV  C30   F31   single    1.343  0.020  1.343
 HRV  C30   C14   aromatic  1.393  0.020  1.393
 HRV  C15   C14   aromatic  1.390  0.020  1.390
 HRV  C14   C2    single    1.529  0.020  1.529
 HRV  F12   C10   single    1.340  0.020  1.340
 HRV  F13   C10   single    1.334  0.020  1.334
 HRV  C10   C8    single    1.523  0.020  1.523
 HRV  C10   F11   single    1.337  0.020  1.337
 HRV  C2    C1    single    1.534  0.020  1.534
 HRV  C2    C8    single    1.551  0.020  1.551
 HRV  C2    N3    single    1.455  0.020  1.455
 HRV  C8    O7    single    1.398  0.020  1.398
 HRV  N3    C4    double    1.273  0.020  1.273
 HRV  O7    C6    single    1.400  0.020  1.400
 HRV  C4    C6    single    1.505  0.020  1.505
 HRV  C4    N5    single    1.358  0.020  1.358
 HRV  C1    H1    single    0.970  0.020  1.090
 HRV  C1    H2    single    0.970  0.020  1.090
 HRV  C1    H3    single    0.970  0.020  1.090
 HRV  C15   H4    single    0.930  0.020  1.080
 HRV  C22   H5    single    0.930  0.020  1.080
 HRV  C25   H6    single    0.930  0.020  1.080
 HRV  C28   H7    single    0.930  0.020  1.080
 HRV  C29   H8    single    0.930  0.020  1.080
 HRV  C6    H9    single    0.970  0.020  1.090
 HRV  C6    H10   single    0.970  0.020  1.090
 HRV  C8    H11   single    0.970  0.020  1.090
 HRV  N17   H12   single    0.860  0.020  1.020
 HRV  N5    H13   single    0.890  0.020  1.040
 HRV  N5    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
 HRV  H3    C1   H2   107.45  3.000
 HRV  H3    C1   H1   108.40  3.000
 HRV  H2    C1   H1   107.85  3.000
 HRV  H3    C1   C2   114.50  3.000
 HRV  H2    C1   C2   108.55  3.000
 HRV  H1    C1   C2   109.87  3.000
 HRV  F13   C10  F12  106.66  3.000
 HRV  F13   C10  F11  107.35  3.000
 HRV  F12   C10  F11  106.82  3.000
 HRV  F11   C10  C8   112.58  3.000
 HRV  F13   C10  C8   112.90  3.000
 HRV  F12   C10  C8   110.18  3.000
 HRV  C30   C14  C2   122.92  3.000
 HRV  C2    C14  C15  121.16  3.000
 HRV  C30   C14  C15  115.93  3.000
 HRV  H4    C15  C16  117.68  3.000
 HRV  H4    C15  C14  119.20  3.000
 HRV  C16   C15  C14  123.12  3.000
 HRV  N17   C16  C28  124.59  3.000
 HRV  N17   C16  C15  116.36  3.000
 HRV  C28   C16  C15  119.05  3.000
 HRV  O19   C18  N17  125.18  3.000
 HRV  N17   C18  C20  112.48  3.000
 HRV  O19   C18  C20  122.34  3.000
 HRV  N3    C2   C8   110.66  3.000
 HRV  N3    C2   C14  108.56  3.000
 HRV  C8    C2   C14  112.23  3.000
 HRV  N3    C2   C1   104.27  3.000
 HRV  C8    C2   C1   108.77  3.000
 HRV  C14   C2   C1   112.07  3.000
 HRV  N21   C20  C26  120.31  3.000
 HRV  N21   C20  C18  115.61  3.000
 HRV  C26   C20  C18  124.08  3.000
 HRV  H5    C22  N21  117.82  3.000
 HRV  H5    C22  C23  121.24  3.000
 HRV  N21   C22  C23  120.95  3.000
 HRV  CL24  C23  C25  120.66  3.000
 HRV  CL24  C23  C22  120.10  3.000
 HRV  C25   C23  C22  119.24  3.000
 HRV  H6    C25  C26  120.30  3.000
 HRV  H6    C25  C23  120.96  3.000
 HRV  C26   C25  C23  118.75  3.000
 HRV  CL27  C26  C25  116.65  3.000
 HRV  C25   C26  C20  119.00  3.000
 HRV  CL27  C26  C20  124.35  3.000
 HRV  H7    C28  C29  119.25  3.000
 HRV  H7    C28  C16  121.90  3.000
 HRV  C29   C28  C16  118.84  3.000
 HRV  H8    C29  C30  119.36  3.000
 HRV  H8    C29  C28  119.87  3.000
 HRV  C30   C29  C28  120.77  3.000
 HRV  F31   C30  C29  116.59  3.000
 HRV  F31   C30  C14  121.12  3.000
 HRV  C29   C30  C14  122.29  3.000
 HRV  N5    C4   N3   120.73  3.000
 HRV  N5    C4   C6   114.51  3.000
 HRV  N3    C4   C6   124.74  3.000
 HRV  H10   C6   H9   107.54  3.000
 HRV  H10   C6   O7   107.38  3.000
 HRV  H9    C6   O7   111.18  3.000
 HRV  H10   C6   C4   110.06  3.000
 HRV  H9    C6   C4   109.08  3.000
 HRV  O7    C6   C4   111.51  3.000
 HRV  H11   C8   O7   110.60  3.000
 HRV  H11   C8   C2   106.95  3.000
 HRV  O7    C8   C2   111.38  3.000
 HRV  H11   C8   C10  106.28  3.000
 HRV  O7    C8   C10  104.18  3.000
 HRV  C2    C8   C10  117.33  3.000
 HRV  H12   N17  C18  114.76  3.000
 HRV  H12   N17  C16  116.41  3.000
 HRV  C18   N17  C16  128.75  3.000
 HRV  C22   N21  C20  121.75  3.000
 HRV  C4    N3   C2   120.89  3.000
 HRV  H14   N5   H13  114.62  3.000
 HRV  H14   N5   C4   117.05  3.000
 HRV  H13   N5   C4   118.69  3.000
 HRV  C8    O7   C6   111.87  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
 HRV  CONST_01  C28   C29  C30  C14    0.00   0.0  0
 HRV  CONST_02  C28   C16  C15  C14    0.00   0.0  0
 HRV  CONST_03  C29   C28  C16  C15    0.00   0.0  0
 HRV  CONST_04  C29   C30  C14  C15    0.00   0.0  0
 HRV  CONST_05  C30   C29  C28  C16    0.00   0.0  0
 HRV  CONST_06  C30   C14  C15  C16    0.00   0.0  0
 HRV  CONST_07  C23   C25  C26  C20    0.00   0.0  0
 HRV  CONST_08  C23   C22  N21  C20    0.00   0.0  0
 HRV  CONST_09  C26   C25  C23  C22    0.00   0.0  0
 HRV  CONST_10  C26   C20  N21  C22    0.00   0.0  0
 HRV  CONST_11  N21   C20  C26  C25    0.00   0.0  0
 HRV  CONST_12  N21   C22  C23  C25    0.00   0.0  0
 HRV  CONST_13  C2    C14  C15  C16  180.00   0.0  0
 HRV  CONST_14  C29   C30  C14  C2   180.00   0.0  0
 HRV  CONST_15  C6    C4   N3   C2     0.00   0.0  0
 HRV  CONST_16  N17   C16  C15  C14  180.00   0.0  0
 HRV  CONST_17  F31   C30  C14  C15  180.00   0.0  0
 HRV  CONST_18  C25   C26  C20  C18  180.00   0.0  0
 HRV  CONST_19  C22   N21  C20  C18  180.00   0.0  0
 HRV  CONST_20  F31   C30  C14  C2     0.00   0.0  0
 HRV  CONST_21  CL27  C26  C25  C23  180.00   0.0  0
 HRV  CONST_22  CL24  C23  C25  C26  180.00   0.0  0
 HRV  CONST_23  F31   C30  C29  C28  180.00   0.0  0
 HRV  CONST_24  N17   C16  C28  C29  180.00   0.0  0
 HRV  CONST_25  CL27  C26  C20  N21  180.00   0.0  0
 HRV  CONST_26  CL24  C23  C22  N21  180.00   0.0  0
 HRV  CONST_27  N5    C4   N3   C2   180.00   0.0  0
 HRV  CONST_28  H8    C29  C30  C14  180.00   0.0  0
 HRV  CONST_29  H7    C28  C16  C15  180.00   0.0  0
 HRV  CONST_30  H4    C15  C14  C2     0.00   0.0  0
 HRV  CONST_31  H6    C25  C26  C20  180.00   0.0  0
 HRV  CONST_32  H5    C22  N21  C20  180.00   0.0  0
 HRV  CONST_33  C20   C18  N17  C16  180.00   0.0  0
 HRV  CONST_34  C18   N17  C16  C15  180.00   0.0  0
 HRV  CONST_35  C28   C16  N17  C18    0.00   0.0  0
 HRV  CONST_36  H12   N17  C16  C15    0.00   0.0  0
 HRV  CONST_39  O19   C18  N17  C16    0.00   0.0  0
 HRV  Var_01    O7    C6   C4   N3   -13.27  30.0  1
 HRV  Var_02    H9    C6   O7   C8   -75.52  30.0  1
 HRV  Var_03    O19   C18  C20  C26   -2.09  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
 HRV  chir_01  C2  C14  C8  N3   positiv
 HRV  chir_02  C8  O7   C2  C10  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
 HRV  plan-1  C18   0.020
 HRV  plan-1  C20   0.020
 HRV  plan-1  C22   0.020
 HRV  plan-1  C23   0.020
 HRV  plan-1  C25   0.020
 HRV  plan-1  C26   0.020
 HRV  plan-1  N21   0.020
 HRV  plan-1  CL24  0.020
 HRV  plan-1  CL27  0.020
 HRV  plan-1  H5    0.020
 HRV  plan-1  H6    0.020
 HRV  plan-2  C14   0.020
 HRV  plan-2  C15   0.020
 HRV  plan-2  C16   0.020
 HRV  plan-2  C2    0.020
 HRV  plan-2  C28   0.020
 HRV  plan-2  C29   0.020
 HRV  plan-2  C30   0.020
 HRV  plan-2  F31   0.020
 HRV  plan-2  N17   0.020
 HRV  plan-2  H4    0.020
 HRV  plan-2  H7    0.020
 HRV  plan-2  H8    0.020
 HRV  plan-3  C16   0.020
 HRV  plan-3  C18   0.020
 HRV  plan-3  C20   0.020
 HRV  plan-3  N17   0.020
 HRV  plan-3  O19   0.020
 HRV  plan-3  H12   0.020
 HRV  plan-4  C2    0.020
 HRV  plan-4  C4    0.020
 HRV  plan-4  C6    0.020
 HRV  plan-4  N3    0.020
 HRV  plan-4  N5    0.020
 HRV  plan-4  H13   0.020
 HRV  plan-4  H14   0.020

