# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 19:27:47 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: ~{N}-[3-[(4~{R},5~{R},6~{R})-2-azanyl-5-fluoranyl-4,6-dimethyl-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@H]1SC(=N[C@@](C)([C@H]1F)c2cc(NC(=O)c3cnc(OCF)cn3)ccc2F)N
#
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
 C83  C83  ~{N}-[3-[(4~{R},5~{R},6~{R})-2-azanyl-5-fluoranyl-4,6-dimethyl-5,6-dihydro-1,3-thiazin-4-yl]-4-fluoranyl-phenyl]-5-(fluoranylmethoxy)pyrazine-2-carboxamide  ligand  47  29  .  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_C83
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
 C83  C1   C  CT    0  -0.047   3.5941  -0.1423  -0.9141
 C83  C2   C  CR6   0  -0.061   2.4737  -1.1024  -0.4934
 C83  C3   C  CR16  0  -0.418   1.1480  -0.6897  -0.4953
 C83  C4   C  CR6   0   0.427   0.0936  -1.5302  -0.1342
 C83  C5   C  C     0   0.539  -2.3785  -1.5578   0.0547
 C83  C6   C  CR6   0   0.057  -3.5326  -0.6159  -0.0588
 C83  C7   C  CR16  0  -0.133  -4.3010   1.4876  -0.4506
 C83  N1   N  N     0  -0.384  -3.2906   0.6604  -0.3625
 C83  N2   N  N     0  -0.414  -5.8598  -0.2251   0.0790
 C83  O1   O  O     0  -0.457  -2.5536  -2.7330   0.3286
 C83  C8   C  CR6   0   0.496  -5.6074   1.0245  -0.2194
 C83  N3   N  N     0  -0.414   3.0438   1.1226  -1.3375
 C83  C9   C  CH2   0   0.172  -7.9103   1.4961  -0.1232
 C83  C10  C  CR16  0  -0.043  -4.8256  -1.0568   0.1559
 C83  C11  C  CR16  0  -0.312   0.3668  -2.8433   0.2394
 C83  C12  C  CR16  0  -0.389   1.6822  -3.2788   0.2423
 C83  C13  C  CR6   0   0.507   2.7008  -2.4235  -0.1171
 C83  C14  C  C     0   0.282   2.8686   2.1112  -0.5617
 C83  C15  C  CH1   0  -0.436   3.9531   0.5888   1.5083
 C83  F2   F  F     0  -0.366   5.6072   0.8605  -0.1563
 C83  C17  C  CH1   0   0.238   4.5795   0.0197   0.2556
 C83  C16  C  CH3   0  -0.654   4.9403   0.7398   2.6545
 C83  S    S  S2    0   0.035   3.2163   2.2206   1.1732
 C83  N4   N  NH2   0  -0.806   2.2909   3.2572  -1.0166
 C83  C    C  CH3   0  -0.642   4.3171  -0.7103  -2.1451
 C83  F1   F  F     0  -0.315   3.9562  -2.9151  -0.0868
 C83  N    N  NH1   0  -0.765  -1.1855  -0.9704  -0.1686
 C83  O    O  O2    0  -0.471  -6.5959   1.9194  -0.3133
 C83  F    F  F     0  -0.360  -8.1354   1.2870   1.2137
 C83  H1   H  HCR6  0   0.286   0.9205   0.3219  -0.8033
 C83  H2   H  HCR6  0   0.296  -4.1062   2.5236  -0.6993
 C83  H3   H  HCH2  0   0.240  -8.5396   2.3148  -0.4618
 C83  H4   H  HCH2  0   0.224  -8.1243   0.5736  -0.6607
 C83  H5   H  HCR6  0   0.291  -5.0408  -2.0886   0.3996
 C83  H6   H  HCR6  0   0.289  -0.4152  -3.5263   0.5259
 C83  H7   H  HCR6  0   0.283   1.9165  -4.2953   0.5303
 C83  H8   H  HCH1  0   0.305   3.1493  -0.0811   1.8191
 C83  H9   H  HCH1  0   0.245   5.0334  -0.9399   0.5089
 C83  H10  H  HCH3  0   0.254   4.4527   1.1579   3.5350
 C83  H11  H  HCH3  0   0.251   5.3326  -0.2396   2.9316
 C83  H12  H  HCH3  0   0.246   5.7746   1.3861   2.3877
 C83  H13  H  HNH2  0   0.391   2.2522   3.3521  -2.0197
 C83  H14  H  HNH2  0   0.397   2.4806   4.1191  -0.5308
 C83  H15  H  HCH3  0   0.239   3.5962  -0.8542  -2.9493
 C83  H16  H  HCH3  0   0.243   5.0712  -0.0084  -2.4982
 C83  H17  H  HCH3  0   0.232   4.8045  -1.6620  -1.9478
 C83  H18  H  HNH1  0   0.424  -1.2336   0.0154  -0.3935

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
 C83  C16  C15  single    1.520  0.020  1.520
 C83  F1   C13  single    1.349  0.020  1.349
 C83  F2   C17  single    1.390  0.020  1.390
 C83  C17  C15  single    1.512  0.020  1.512
 C83  C17  C1   single    1.538  0.020  1.538
 C83  C15  S    single    1.822  0.020  1.822
 C83  C13  C12  aromatic  1.378  0.020  1.378
 C83  C13  C2   aromatic  1.392  0.020  1.392
 C83  C    C1   single    1.536  0.020  1.536
 C83  C12  C11  aromatic  1.386  0.020  1.386
 C83  C1   C2   single    1.534  0.020  1.534
 C83  C1   N3   single    1.443  0.020  1.443
 C83  C2   C3   aromatic  1.388  0.020  1.388
 C83  S    C14  single    1.773  0.020  1.773
 C83  C11  C4   aromatic  1.392  0.020  1.392
 C83  N3   C14  double    1.269  0.020  1.269
 C83  C14  N4   single    1.362  0.020  1.362
 C83  C3   C4   aromatic  1.396  0.020  1.396
 C83  C4   N    single    1.397  0.020  1.397
 C83  N    C5   single    1.348  0.020  1.348
 C83  O1   C5   double    1.219  0.020  1.219
 C83  C5   C6   single    1.494  0.020  1.494
 C83  C6   C10  aromatic  1.383  0.020  1.383
 C83  C6   N1   aromatic  1.334  0.020  1.334
 C83  C10  N2   aromatic  1.329  0.020  1.329
 C83  N1   C7   aromatic  1.309  0.020  1.309
 C83  N2   C8   aromatic  1.309  0.020  1.309
 C83  C7   C8   aromatic  1.405  0.020  1.405
 C83  C8   O    single    1.337  0.020  1.337
 C83  O    C9   single    1.394  0.020  1.394
 C83  C9   F    single    1.372  0.020  1.372
 C83  C3   H1   single    0.930  0.020  1.080
 C83  C7   H2   single    0.930  0.020  1.080
 C83  C9   H3   single    0.970  0.020  1.090
 C83  C9   H4   single    0.970  0.020  1.090
 C83  C10  H5   single    0.930  0.020  1.080
 C83  C11  H6   single    0.930  0.020  1.080
 C83  C12  H7   single    0.930  0.020  1.080
 C83  C15  H8   single    0.970  0.020  1.090
 C83  C17  H9   single    0.970  0.020  1.090
 C83  C16  H10  single    0.970  0.020  1.090
 C83  C16  H11  single    0.970  0.020  1.090
 C83  C16  H12  single    0.970  0.020  1.090
 C83  N4   H13  single    0.890  0.020  1.040
 C83  N4   H14  single    0.890  0.020  1.040
 C83  C    H15  single    0.970  0.020  1.090
 C83  C    H16  single    0.970  0.020  1.090
 C83  C    H17  single    0.970  0.020  1.090
 C83  N    H18  single    0.860  0.020  1.020

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
 C83  C    C1   C17  110.29  3.000
 C83  C    C1   N3   105.57  3.000
 C83  C17  C1   N3   112.04  3.000
 C83  N3   C1   C2   110.52  3.000
 C83  C    C1   C2   109.39  3.000
 C83  C17  C1   C2   108.98  3.000
 C83  C13  C2   C3   115.99  3.000
 C83  C3   C2   C1   120.72  3.000
 C83  C13  C2   C1   123.28  3.000
 C83  H1   C3   C4   118.55  3.000
 C83  H1   C3   C2   118.64  3.000
 C83  C4   C3   C2   122.81  3.000
 C83  N    C4   C11  124.36  3.000
 C83  N    C4   C3   116.36  3.000
 C83  C11  C4   C3   119.28  3.000
 C83  N    C5   O1   125.74  3.000
 C83  O1   C5   C6   120.92  3.000
 C83  N    C5   C6   113.34  3.000
 C83  C10  C6   N1   120.66  3.000
 C83  N1   C6   C5   118.71  3.000
 C83  C10  C6   C5   120.63  3.000
 C83  H2   C7   C8   121.35  3.000
 C83  H2   C7   N1   118.76  3.000
 C83  C8   C7   N1   119.90  3.000
 C83  C7   N1   C6   118.68  3.000
 C83  C10  N2   C8   117.41  3.000
 C83  O    C8   N2   120.82  3.000
 C83  O    C8   C7   117.09  3.000
 C83  N2   C8   C7   122.09  3.000
 C83  C14  N3   C1   123.80  3.000
 C83  H4   C9   H3   111.76  3.000
 C83  H4   C9   F    108.64  3.000
 C83  H3   C9   F    108.87  3.000
 C83  H4   C9   O    112.04  3.000
 C83  H3   C9   O    105.95  3.000
 C83  F    C9   O    109.51  3.000
 C83  H5   C10  N2   117.07  3.000
 C83  H5   C10  C6   121.68  3.000
 C83  N2   C10  C6   121.26  3.000
 C83  H6   C11  C12  119.30  3.000
 C83  H6   C11  C4   121.80  3.000
 C83  C12  C11  C4   118.90  3.000
 C83  H7   C12  C13  119.51  3.000
 C83  H7   C12  C11  120.08  3.000
 C83  C13  C12  C11  120.41  3.000
 C83  F1   C13  C12  117.13  3.000
 C83  C12  C13  C2   122.61  3.000
 C83  F1   C13  C2   120.25  3.000
 C83  N4   C14  S    110.99  3.000
 C83  N4   C14  N3   120.67  3.000
 C83  S    C14  N3   128.27  3.000
 C83  H8   C15  S    107.71  3.000
 C83  H8   C15  C16  108.94  3.000
 C83  S    C15  C16  108.20  3.000
 C83  H8   C15  C17  108.06  3.000
 C83  S    C15  C17  110.63  3.000
 C83  C16  C15  C17  113.15  3.000
 C83  H9   C17  F2   107.04  3.000
 C83  H9   C17  C15  108.12  3.000
 C83  F2   C17  C15  108.91  3.000
 C83  H9   C17  C1   110.51  3.000
 C83  C15  C17  C1   113.85  3.000
 C83  F2   C17  C1   108.18  3.000
 C83  H12  C16  H11  108.65  3.000
 C83  H12  C16  H10  108.25  3.000
 C83  H11  C16  H10  107.46  3.000
 C83  H12  C16  C15  111.83  3.000
 C83  H11  C16  C15  109.62  3.000
 C83  H10  C16  C15  110.90  3.000
 C83  C15  S    C14  101.78  3.000
 C83  H14  N4   H13  113.98  3.000
 C83  H14  N4   C14  118.63  3.000
 C83  H13  N4   C14  115.33  3.000
 C83  H17  C    H16  108.21  3.000
 C83  H17  C    H15  108.36  3.000
 C83  H16  C    H15  107.70  3.000
 C83  H17  C    C1   112.90  3.000
 C83  H16  C    C1   110.32  3.000
 C83  H15  C    C1   109.20  3.000
 C83  H18  N    C5   114.77  3.000
 C83  H18  N    C4   116.06  3.000
 C83  C5   N    C4   129.16  3.000
 C83  C9   O    C8   118.98  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
 C83  CONST_01  C11  C12  C13  C2     0.00   0.0  0
 C83  CONST_02  C11  C4   C3   C2     0.00   0.0  0
 C83  CONST_03  C12  C13  C2   C3     0.00   0.0  0
 C83  CONST_04  C12  C11  C4   C3     0.00   0.0  0
 C83  CONST_05  C13  C12  C11  C4     0.00   0.0  0
 C83  CONST_06  C13  C2   C3   C4     0.00   0.0  0
 C83  CONST_07  C8   N2   C10  C6     0.00   0.0  0
 C83  CONST_08  C8   C7   N1   C6     0.00   0.0  0
 C83  CONST_09  C10  C6   N1   C7     0.00   0.0  0
 C83  CONST_10  C10  N2   C8   C7     0.00   0.0  0
 C83  CONST_11  N2   C10  C6   N1     0.00   0.0  0
 C83  CONST_12  N2   C8   C7   N1     0.00   0.0  0
 C83  CONST_13  C12  C13  C2   C1   180.00   0.0  0
 C83  CONST_14  C4   C3   C2   C1   180.00   0.0  0
 C83  CONST_15  S    C14  N3   C1     0.00   0.0  0
 C83  CONST_16  F1   C13  C2   C1     0.00   0.0  0
 C83  CONST_17  N    C4   C3   C2   180.00   0.0  0
 C83  CONST_18  F1   C13  C2   C3   180.00   0.0  0
 C83  CONST_19  N2   C10  C6   C5   180.00   0.0  0
 C83  CONST_20  C7   N1   C6   C5   180.00   0.0  0
 C83  CONST_21  O    C8   C7   N1   180.00   0.0  0
 C83  CONST_22  O    C8   N2   C10  180.00   0.0  0
 C83  CONST_23  F1   C13  C12  C11  180.00   0.0  0
 C83  CONST_24  N    C4   C11  C12  180.00   0.0  0
 C83  CONST_25  N4   C14  N3   C1   180.00   0.0  0
 C83  CONST_26  H1   C3   C2   C1     0.00   0.0  0
 C83  CONST_27  H7   C12  C13  C2   180.00   0.0  0
 C83  CONST_28  H6   C11  C4   C3   180.00   0.0  0
 C83  CONST_29  H2   C7   N1   C6   180.00   0.0  0
 C83  CONST_30  H5   C10  C6   N1   180.00   0.0  0
 C83  CONST_31  C6   C5   N    C4   180.00   0.0  0
 C83  CONST_32  C5   N    C4   C3   180.00   0.0  0
 C83  CONST_33  C11  C4   N    C5     0.00   0.0  0
 C83  CONST_34  H18  N    C4   C3     0.00   0.0  0
 C83  CONST_37  O1   C5   N    C4     0.00   0.0  0
 C83  Var_01    N4   C14  S    C15  179.56  30.0  1
 C83  Var_02    N    C5   C6   N1     0.28  30.0  2
 C83  Var_03    F    C9   O    C8    75.18  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
 C83  chir_01  C1   C17  C2   N3   negativ
 C83  chir_02  C15  S    C16  C17  positiv
 C83  chir_03  C17  F2   C15  C1   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
 C83  plan-1  C5   0.020
 C83  plan-1  C6   0.020
 C83  plan-1  C7   0.020
 C83  plan-1  N1   0.020
 C83  plan-1  N2   0.020
 C83  plan-1  C8   0.020
 C83  plan-1  C10  0.020
 C83  plan-1  O    0.020
 C83  plan-1  H2   0.020
 C83  plan-1  H5   0.020
 C83  plan-2  C1   0.020
 C83  plan-2  C2   0.020
 C83  plan-2  C3   0.020
 C83  plan-2  C4   0.020
 C83  plan-2  C11  0.020
 C83  plan-2  C12  0.020
 C83  plan-2  C13  0.020
 C83  plan-2  F1   0.020
 C83  plan-2  N    0.020
 C83  plan-2  H1   0.020
 C83  plan-2  H6   0.020
 C83  plan-2  H7   0.020
 C83  plan-3  C4   0.020
 C83  plan-3  C5   0.020
 C83  plan-3  C6   0.020
 C83  plan-3  O1   0.020
 C83  plan-3  N    0.020
 C83  plan-3  H18  0.020
 C83  plan-4  C1   0.020
 C83  plan-4  N3   0.020
 C83  plan-4  C14  0.020
 C83  plan-4  S    0.020
 C83  plan-4  N4   0.020
 C83  plan-4  H13  0.020
 C83  plan-4  H14  0.020

