# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 19:45:44 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: ~{N}-[3-[(4~{S},6~{S})-2-azanyl-4-methyl-6-(trifluoromethyl)-5,6-dihydro-1,3-thiazin-4-yl]-4-fluoranyl-phenyl]-5-(fluoranylmethoxy)pyrazine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]1(C[C@H](SC(=N1)N)C(F)(F)F)c2cc(NC(=O)c3cnc(OCF)cn3)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
 C86  C86  ~{N}-[3-[(4~{S},6~{S})-2-azanyl-4-methyl-6-(trifluoromethyl)-5,6-dihydro-1,3-thiazin-4-yl]-4-fluoranyl-phenyl]-5-(fluoranylmethoxy)pyrazine-2-carboxamide  ligand  47  31  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C86
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
 C86  C1   C  C     0   0.285  -2.2926  -1.5841  -1.6283
 C86  C2   C  CT    0  -0.010  -3.0718   0.6505  -1.4827
 C86  C3   C  CR6   0  -0.052  -2.0219   1.3949  -0.6483
 C86  C4   C  CR16  0  -0.420  -0.6883   1.0090  -0.6614
 C86  C5   C  CR6   0   0.426   0.3004   1.6734   0.0666
 C86  C6   C  C     0   0.538   2.7379   1.6076   0.5163
 C86  C7   C  CR6   0   0.056   3.9319   0.7806   0.1669
 C86  N1   N  NH2   0  -0.805  -1.6580  -2.6062  -2.2590
 C86  N2   N  N     0  -0.393  -2.4736  -0.4624  -2.1883
 C86  O1   O  O     0  -0.458   2.8421   2.5819   1.2424
 C86  C8   C  CR16  0  -0.133   4.8163  -1.0047  -0.9277
 C86  N3   N  NH1   0  -0.765   1.5953   1.1608  -0.0421
 C86  C9   C  CR6   0   0.496   6.0777  -0.6628  -0.4113
 C86  C10  C  CH2   0   0.174   8.3813  -1.1294  -0.2854
 C86  C11  C  CR16  0  -0.043   5.1813   1.1045   0.6637
 C86  C12  C  CR16  0  -0.314  -0.0502   2.7751   0.8418
 C86  C13  C  CR16  0  -0.392  -1.3747   3.1831   0.8647
 C86  C14  C  CR6   0   0.509  -2.3262   2.5053   0.1341
 C86  C15  C  CH3   0  -0.633  -3.6203   1.5868  -2.5649
 C86  N4   N  N     0  -0.384   3.7694  -0.2789  -0.6276
 C86  F1   F  F     0  -0.360   8.4851  -1.5037   1.0299
 C86  N5   N  N     0  -0.413   6.2512   0.3715   0.3726
 C86  F2   F  F     0  -0.314  -3.5938   2.9591   0.2004
 C86  C16  C  CH2   0  -0.448  -4.2407   0.1533  -0.6150
 C86  C17  C  CH1   0  -0.607  -3.7810  -0.6896   0.5600
 C86  S1   S  S2    0   0.055  -2.6481  -2.0273   0.0598
 C86  C18  C  CT    0   1.052  -4.9397  -1.3329   1.2950
 C86  F3   F  F     0  -0.305  -4.5068  -2.1018   2.3026
 C86  F4   F  F     0  -0.304  -5.7485  -0.4068   1.8225
 C86  F5   F  F     0  -0.298  -5.6877  -2.1074   0.5053
 C86  H1   H  HCR6  0   0.284  -0.3954   0.1633  -1.2689
 C86  H2   H  HNH2  0   0.396  -1.5068  -2.4795  -3.2481
 C86  H3   H  HNH2  0   0.400  -1.8750  -3.5521  -1.9891
 C86  H4   H  HCR6  0   0.296   4.6871  -1.8640  -1.5745
 C86  H5   H  HNH1  0   0.424   1.6987   0.3370  -0.6216
 C86  H6   H  HCH2  0   0.238   9.0724  -1.7246  -0.8758
 C86  H7   H  HCH2  0   0.224   8.5970  -0.0648  -0.3633
 C86  H8   H  HCR6  0   0.290   5.3309   1.9605   1.3082
 C86  H9   H  HCR6  0   0.289   0.6769   3.3153   1.4241
 C86  H10  H  HCR6  0   0.282  -1.6671   4.0388   1.4596
 C86  H11  H  HCH3  0   0.239  -2.8076   1.9417  -3.1985
 C86  H12  H  HCH3  0   0.237  -4.3273   1.0454  -3.1953
 C86  H13  H  HCH3  0   0.233  -4.1354   2.4492  -2.1470
 C86  H14  H  HCH2  0   0.284  -4.8174   0.9942  -0.2338
 C86  H15  H  HCH2  0   0.278  -4.9047  -0.4176  -1.2677
 C86  H16  H  HCH1  0   0.336  -3.2494  -0.0667   1.2842
 C86  O2   O  O2    0  -0.472   7.1074  -1.4421  -0.7568

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
 C86  F4   C18  single    1.338  0.020  1.338
 C86  F3   C18  single    1.339  0.020  1.339
 C86  C18  F5   single    1.335  0.020  1.335
 C86  C18  C17  single    1.515  0.020  1.515
 C86  F2   C14  single    1.348  0.020  1.348
 C86  C16  C17  single    1.517  0.020  1.517
 C86  C16  C2   single    1.538  0.020  1.538
 C86  C17  S1   single    1.823  0.020  1.823
 C86  C15  C2   single    1.532  0.020  1.532
 C86  C14  C13  aromatic  1.378  0.020  1.378
 C86  C14  C3   aromatic  1.392  0.020  1.392
 C86  C13  C12  aromatic  1.386  0.020  1.386
 C86  C2   C3   single    1.534  0.020  1.534
 C86  C2   N2   single    1.447  0.020  1.447
 C86  C3   C4   aromatic  1.388  0.020  1.388
 C86  S1   C1   single    1.781  0.020  1.781
 C86  C12  C5   aromatic  1.392  0.020  1.392
 C86  N2   C1   double    1.267  0.020  1.267
 C86  C1   N1   single    1.358  0.020  1.358
 C86  C4   C5   aromatic  1.396  0.020  1.396
 C86  C5   N3   single    1.397  0.020  1.397
 C86  O1   C6   double    1.220  0.020  1.220
 C86  N3   C6   single    1.348  0.020  1.348
 C86  C6   C7   single    1.494  0.020  1.494
 C86  C7   C11  aromatic  1.383  0.020  1.383
 C86  C7   N4   aromatic  1.334  0.020  1.334
 C86  C11  N5   aromatic  1.329  0.020  1.329
 C86  N4   C8   aromatic  1.309  0.020  1.309
 C86  N5   C9   aromatic  1.309  0.020  1.309
 C86  C8   C9   aromatic  1.405  0.020  1.405
 C86  C9   O2   single    1.337  0.020  1.337
 C86  O2   C10  single    1.394  0.020  1.394
 C86  C10  F1   single    1.371  0.020  1.371
 C86  C4   H1   single    0.930  0.020  1.080
 C86  N1   H2   single    0.890  0.020  1.040
 C86  N1   H3   single    0.890  0.020  1.040
 C86  C8   H4   single    0.930  0.020  1.080
 C86  N3   H5   single    0.860  0.020  1.020
 C86  C10  H6   single    0.970  0.020  1.090
 C86  C10  H7   single    0.970  0.020  1.090
 C86  C11  H8   single    0.930  0.020  1.080
 C86  C12  H9   single    0.930  0.020  1.080
 C86  C13  H10  single    0.930  0.020  1.080
 C86  C15  H11  single    0.970  0.020  1.090
 C86  C15  H12  single    0.970  0.020  1.090
 C86  C15  H13  single    0.970  0.020  1.090
 C86  C16  H14  single    0.970  0.020  1.090
 C86  C16  H15  single    0.970  0.020  1.090
 C86  C17  H16  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
 C86  S1   C1   N2   127.65  3.000
 C86  N2   C1   N1   121.86  3.000
 C86  S1   C1   N1   110.25  3.000
 C86  C16  C2   C15  108.89  3.000
 C86  C15  C2   N2   105.87  3.000
 C86  C16  C2   N2   109.91  3.000
 C86  N2   C2   C3   110.83  3.000
 C86  C15  C2   C3   109.43  3.000
 C86  C16  C2   C3   111.72  3.000
 C86  C14  C3   C4   115.91  3.000
 C86  C4   C3   C2   121.16  3.000
 C86  C14  C3   C2   122.91  3.000
 C86  H1   C4   C5   118.24  3.000
 C86  H1   C4   C3   118.86  3.000
 C86  C5   C4   C3   122.89  3.000
 C86  C12  C5   N3   124.55  3.000
 C86  N3   C5   C4   116.19  3.000
 C86  C12  C5   C4   119.26  3.000
 C86  N3   C6   O1   125.73  3.000
 C86  N3   C6   C7   113.39  3.000
 C86  O1   C6   C7   120.88  3.000
 C86  N4   C7   C11  120.66  3.000
 C86  N4   C7   C6   118.79  3.000
 C86  C11  C7   C6   120.55  3.000
 C86  H3   N1   H2   114.39  3.000
 C86  H3   N1   C1   118.79  3.000
 C86  H2   N1   C1   115.52  3.000
 C86  C2   N2   C1   121.64  3.000
 C86  H4   C8   N4   118.78  3.000
 C86  H4   C8   C9   121.30  3.000
 C86  N4   C8   C9   119.92  3.000
 C86  H5   N3   C6   114.85  3.000
 C86  H5   N3   C5   115.96  3.000
 C86  C6   N3   C5   129.19  3.000
 C86  N5   C9   O2   120.88  3.000
 C86  O2   C9   C8   117.03  3.000
 C86  N5   C9   C8   122.09  3.000
 C86  H7   C10  H6   111.75  3.000
 C86  H7   C10  F1   108.69  3.000
 C86  H6   C10  F1   108.87  3.000
 C86  H7   C10  O2   112.09  3.000
 C86  H6   C10  O2   105.95  3.000
 C86  F1   C10  O2   109.41  3.000
 C86  H8   C11  N5   117.09  3.000
 C86  H8   C11  C7   121.62  3.000
 C86  N5   C11  C7   121.29  3.000
 C86  H9   C12  C13  119.25  3.000
 C86  H9   C12  C5   121.88  3.000
 C86  C13  C12  C5   118.87  3.000
 C86  H10  C13  C14  119.59  3.000
 C86  H10  C13  C12  120.00  3.000
 C86  C14  C13  C12  120.42  3.000
 C86  F2   C14  C13  117.24  3.000
 C86  C13  C14  C3   122.65  3.000
 C86  F2   C14  C3   120.11  3.000
 C86  H13  C15  H12  107.97  3.000
 C86  H13  C15  H11  108.56  3.000
 C86  H12  C15  H11  107.99  3.000
 C86  H13  C15  C2   112.49  3.000
 C86  H12  C15  C2   109.68  3.000
 C86  H11  C15  C2   110.03  3.000
 C86  C8   N4   C7   118.65  3.000
 C86  C11  N5   C9   117.39  3.000
 C86  H15  C16  H14  106.92  3.000
 C86  H15  C16  C17  110.89  3.000
 C86  H14  C16  C17  108.57  3.000
 C86  H15  C16  C2   107.09  3.000
 C86  H14  C16  C2   110.51  3.000
 C86  C17  C16  C2   112.71  3.000
 C86  H16  C17  C18  107.00  3.000
 C86  H16  C17  S1   107.32  3.000
 C86  C18  C17  S1   107.26  3.000
 C86  H16  C17  C16  110.11  3.000
 C86  S1   C17  C16  112.55  3.000
 C86  C18  C17  C16  112.32  3.000
 C86  C17  S1   C1   101.63  3.000
 C86  F5   C18  F4   107.22  3.000
 C86  F5   C18  F3   107.04  3.000
 C86  F4   C18  F3   107.23  3.000
 C86  F5   C18  C17  112.81  3.000
 C86  F3   C18  C17  111.19  3.000
 C86  F4   C18  C17  111.08  3.000
 C86  C10  O2   C9   119.06  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
 C86  CONST_01  C12  C13  C14  C3     0.00   0.0  0
 C86  CONST_02  C12  C5   C4   C3     0.00   0.0  0
 C86  CONST_03  C13  C14  C3   C4     0.00   0.0  0
 C86  CONST_04  C13  C12  C5   C4     0.00   0.0  0
 C86  CONST_05  C14  C13  C12  C5     0.00   0.0  0
 C86  CONST_06  C14  C3   C4   C5     0.00   0.0  0
 C86  CONST_07  C9   N5   C11  C7     0.00   0.0  0
 C86  CONST_08  C9   C8   N4   C7     0.00   0.0  0
 C86  CONST_09  C11  C7   N4   C8     0.00   0.0  0
 C86  CONST_10  C11  N5   C9   C8     0.00   0.0  0
 C86  CONST_11  N5   C11  C7   N4     0.00   0.0  0
 C86  CONST_12  N5   C9   C8   N4     0.00   0.0  0
 C86  CONST_13  C13  C14  C3   C2   180.00   0.0  0
 C86  CONST_14  C5   C4   C3   C2   180.00   0.0  0
 C86  CONST_15  S1   C1   N2   C2     0.00   0.0  0
 C86  CONST_16  F2   C14  C3   C2     0.00   0.0  0
 C86  CONST_17  N3   C5   C4   C3   180.00   0.0  0
 C86  CONST_18  F2   C14  C3   C4   180.00   0.0  0
 C86  CONST_19  N5   C11  C7   C6   180.00   0.0  0
 C86  CONST_20  C8   N4   C7   C6   180.00   0.0  0
 C86  CONST_21  C11  N5   C9   O2   180.00   0.0  0
 C86  CONST_22  N4   C8   C9   O2   180.00   0.0  0
 C86  CONST_23  C13  C12  C5   N3   180.00   0.0  0
 C86  CONST_24  F2   C14  C13  C12  180.00   0.0  0
 C86  CONST_25  N1   C1   N2   C2   180.00   0.0  0
 C86  CONST_26  H1   C4   C3   C2     0.00   0.0  0
 C86  CONST_27  H10  C13  C14  C3   180.00   0.0  0
 C86  CONST_28  H9   C12  C5   C4   180.00   0.0  0
 C86  CONST_29  H4   C8   N4   C7   180.00   0.0  0
 C86  CONST_30  H8   C11  N5   C9   180.00   0.0  0
 C86  CONST_31  C7   C6   N3   C5   180.00   0.0  0
 C86  CONST_32  C6   N3   C5   C4   180.00   0.0  0
 C86  CONST_33  C12  C5   N3   C6     0.00   0.0  0
 C86  CONST_34  H5   N3   C5   C4     0.00   0.0  0
 C86  CONST_35  H2   N1   C1   N2     0.00   0.0  0
 C86  CONST_37  O1   C6   N3   C5     0.00   0.0  0
 C86  Var_01    C11  C7   C6   O1     0.10  30.0  2
 C86  Var_02    N5   C9   O2   C10   -0.89  30.0  1
 C86  Var_03    F1   C10  O2   C9    76.54  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
 C86  chir_01  C2   C16  C3   N2   negativ
 C86  chir_02  C17  S1   C16  C18  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
 C86  plan-1  C6   0.020
 C86  plan-1  C7   0.020
 C86  plan-1  C8   0.020
 C86  plan-1  C9   0.020
 C86  plan-1  C11  0.020
 C86  plan-1  N4   0.020
 C86  plan-1  N5   0.020
 C86  plan-1  H4   0.020
 C86  plan-1  H8   0.020
 C86  plan-1  O2   0.020
 C86  plan-2  C2   0.020
 C86  plan-2  C3   0.020
 C86  plan-2  C4   0.020
 C86  plan-2  C5   0.020
 C86  plan-2  N3   0.020
 C86  plan-2  C12  0.020
 C86  plan-2  C13  0.020
 C86  plan-2  C14  0.020
 C86  plan-2  F2   0.020
 C86  plan-2  H1   0.020
 C86  plan-2  H9   0.020
 C86  plan-2  H10  0.020
 C86  plan-3  C5   0.020
 C86  plan-3  C6   0.020
 C86  plan-3  C7   0.020
 C86  plan-3  O1   0.020
 C86  plan-3  N3   0.020
 C86  plan-3  H5   0.020
 C86  plan-4  C1   0.020
 C86  plan-4  C2   0.020
 C86  plan-4  N1   0.020
 C86  plan-4  N2   0.020
 C86  plan-4  S1   0.020
 C86  plan-4  H2   0.020
 C86  plan-4  H3   0.020

