# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 12:29:00 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: ~{N}-[3-[(4~{S},5~{R})-2-azanyl-4-methyl-5-phenyl-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(N=C(N)SC[C@@H]1c2ccccc2)c3cc(NC(=O)c4cnc(OCF)cn4)ccc3F
#
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
 C6R  C6R  ~{N}-[3-[(4~{S},5~{R})-2-azanyl-4-methyl-5-phenyl-5,6-dihydro-1,3-thiazin-4-yl]-4-fluoranyl-phenyl]-5-(fluoranylmethoxy)pyrazine-2-carboxamide  ligand  54  33  .  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_C6R
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
 C6R  C1   C  CR16  0  -0.318   0.0201  -1.4734  -2.2152
 C6R  C2   C  CR16  0  -0.399   1.3508  -1.7891  -2.4451
 C6R  C3   C  CR6   0   0.517   2.3069  -1.5193  -1.4902
 C6R  C4   C  CR6   0  -0.020   1.9982  -0.9271  -0.2689
 C6R  C5   C  CR16  0  -0.419   0.6632  -0.6158  -0.0625
 C6R  C6   C  CT    0   0.044   3.0811  -0.6133   0.7612
 C6R  C7   C  CH1   0  -0.350   3.9129   0.5933   0.2223
 C6R  O1   O  O2    0  -0.471  -7.1719   1.1255   1.4066
 C6R  C8   C  CH2   0  -0.579   5.1281   0.8655   1.0986
 C6R  N3   N  N     0  -0.384  -3.8110   0.3537   0.6191
 C6R  C9   C  C     0   0.273   5.1040  -1.8817   1.0673
 C6R  C10  C  C     0   0.537  -2.7817  -0.6752  -1.3320
 C6R  C11  C  CR6   0   0.057  -3.9810  -0.1778  -0.5926
 C6R  C12  C  CR16  0  -0.132  -4.8622   0.7823   1.2704
 C6R  C13  C  CR6   0   0.495  -6.1376   0.6726   0.6912
 C6R  C14  C  CR16  0  -0.043  -5.2428  -0.2727  -1.1501
 C6R  C15  C  CH3   0  -0.683   2.4732  -0.3011   2.1323
 C6R  F1   F  F     0  -0.360  -8.9338  -0.1787   0.8550
 C6R  C17  C  CH2   0   0.173  -8.4456   1.1032   0.8416
 C6R  N4   N  N     0  -0.414  -6.3198   0.1522  -0.4965
 C6R  O    O  O     0  -0.459  -2.8906  -1.1733  -2.4403
 C6R  C    C  CR6   0   0.429  -0.3299  -0.8777  -1.0074
 C6R  F    F  F     0  -0.312   3.5823  -1.8258  -1.7886
 C6R  N    N  N     0  -0.390   3.8484  -1.8306   0.9375
 C6R  S    S  S2    0   0.018   6.2676  -0.5391   1.0740
 C6R  C16  C  CR6   0   0.182   3.0785   1.8368   0.0165
 C6R  C22  C  CR16  0  -0.320   2.8545   2.7701   1.0275
 C6R  C21  C  CR16  0  -0.242   2.0737   3.8962   0.7994
 C6R  C20  C  CR16  0  -0.272   1.5030   4.1132  -0.4467
 C6R  C19  C  CR16  0  -0.239   1.7264   3.1972  -1.4657
 C6R  C18  C  CR16  0  -0.295   2.5079   2.0753  -1.2333
 C6R  H1   H  HCR6  0   0.286  -0.7127  -1.6916  -2.9738
 C6R  H2   H  HCR6  0   0.278   1.6442  -2.2491  -3.3798
 C6R  H3   H  HCR6  0   0.273   0.3643  -0.1462   0.8648
 C6R  H4   H  HCH1  0   0.279   4.3005   0.3055  -0.7584
 C6R  H5   H  HNH2  0   0.385   5.1526  -3.8768   1.2938
 C6R  H6   H  HNH2  0   0.391   6.6005  -3.1180   1.6948
 C6R  H7   H  HNH1  0   0.424  -1.7353  -0.0817   0.2599
 C6R  H8   H  HCH2  0   0.306   5.6961   1.7070   0.7026
 C6R  H9   H  HCH2  0   0.283   4.8685   1.0986   2.1293
 C6R  H10  H  HCR6  0   0.296  -4.7249   1.2174   2.2527
 C6R  H11  H  HCR6  0   0.290  -5.3994  -0.6994  -2.1317
 C6R  H12  H  HCH3  0   0.253   1.8800  -1.1465   2.4811
 C6R  H13  H  HCH3  0   0.251   3.2644  -0.1405   2.8639
 C6R  H14  H  HCH3  0   0.240   1.8408   0.5845   2.1320
 C6R  H15  H  HCH2  0   0.239  -9.0670   1.7224   1.4826
 C6R  H16  H  HCH2  0   0.224  -8.4417   1.4631  -0.1863
 C6R  H17  H  HCR6  0   0.249   3.2883   2.6355   2.0108
 C6R  H18  H  HCR6  0   0.254   1.9142   4.6059   1.6011
 C6R  H19  H  HCR6  0   0.253   0.8955   4.9913  -0.6244
 C6R  H20  H  HCR6  0   0.253   1.2959   3.3573  -2.4459
 C6R  H21  H  HCR6  0   0.247   2.6810   1.3739  -2.0409
 C6R  N1   N  NH2   0  -0.812   5.7564  -3.0823   1.1449
 C6R  N2   N  NH1   0  -0.766  -1.6312  -0.5126  -0.6505

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
 C6R  C21  C20  aromatic  1.388  0.020  1.388
 C6R  C21  C22  aromatic  1.389  0.020  1.389
 C6R  C20  C19  aromatic  1.388  0.020  1.388
 C6R  C22  C16  aromatic  1.394  0.020  1.394
 C6R  C16  C18  aromatic  1.394  0.020  1.394
 C6R  C16  C7   single    1.512  0.020  1.512
 C6R  C19  C18  aromatic  1.387  0.020  1.387
 C6R  F    C3   single    1.345  0.020  1.345
 C6R  C7   C8   single    1.523  0.020  1.523
 C6R  C7   C6   single    1.561  0.020  1.561
 C6R  C8   S    single    1.809  0.020  1.809
 C6R  C3   C2   aromatic  1.378  0.020  1.378
 C6R  C3   C4   aromatic  1.392  0.020  1.392
 C6R  C2   C1   aromatic  1.387  0.020  1.387
 C6R  C15  C6   single    1.532  0.020  1.532
 C6R  C6   C4   single    1.527  0.020  1.527
 C6R  C6   N    single    1.450  0.020  1.450
 C6R  S    C9   single    1.777  0.020  1.777
 C6R  C4   C5   aromatic  1.386  0.020  1.386
 C6R  C1   C    aromatic  1.392  0.020  1.392
 C6R  N    C9   double    1.263  0.020  1.263
 C6R  C9   N1   single    1.369  0.020  1.369
 C6R  C5   C    aromatic  1.396  0.020  1.396
 C6R  C    N2   single    1.398  0.020  1.398
 C6R  N2   C10  single    1.347  0.020  1.347
 C6R  O    C10  double    1.220  0.020  1.220
 C6R  C10  C11  single    1.494  0.020  1.494
 C6R  C11  C14  aromatic  1.383  0.020  1.383
 C6R  C11  N3   aromatic  1.334  0.020  1.334
 C6R  C14  N4   aromatic  1.330  0.020  1.330
 C6R  N3   C12  aromatic  1.309  0.020  1.309
 C6R  N4   C13  aromatic  1.309  0.020  1.309
 C6R  C12  C13  aromatic  1.405  0.020  1.405
 C6R  C13  O1   single    1.337  0.020  1.337
 C6R  O1   C17  single    1.394  0.020  1.394
 C6R  C17  F1   single    1.372  0.020  1.372
 C6R  C1   H1   single    0.930  0.020  1.080
 C6R  C2   H2   single    0.930  0.020  1.080
 C6R  C5   H3   single    0.930  0.020  1.080
 C6R  C7   H4   single    0.970  0.020  1.090
 C6R  N1   H5   single    0.890  0.020  1.040
 C6R  N1   H6   single    0.890  0.020  1.040
 C6R  N2   H7   single    0.860  0.020  1.020
 C6R  C8   H8   single    0.970  0.020  1.090
 C6R  C8   H9   single    0.970  0.020  1.090
 C6R  C12  H10  single    0.930  0.020  1.080
 C6R  C14  H11  single    0.930  0.020  1.080
 C6R  C15  H12  single    0.970  0.020  1.090
 C6R  C15  H13  single    0.970  0.020  1.090
 C6R  C15  H14  single    0.970  0.020  1.090
 C6R  C17  H15  single    0.970  0.020  1.090
 C6R  C17  H16  single    0.970  0.020  1.090
 C6R  C22  H17  single    0.930  0.020  1.080
 C6R  C21  H18  single    0.930  0.020  1.080
 C6R  C20  H19  single    0.930  0.020  1.080
 C6R  C19  H20  single    0.930  0.020  1.080
 C6R  C18  H21  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
 C6R  H1   C1   C    121.80  3.000
 C6R  H1   C1   C2   119.34  3.000
 C6R  C    C1   C2   118.86  3.000
 C6R  H2   C2   C3   119.58  3.000
 C6R  H2   C2   C1   120.00  3.000
 C6R  C3   C2   C1   120.42  3.000
 C6R  F    C3   C4   120.12  3.000
 C6R  C4   C3   C2   122.51  3.000
 C6R  F    C3   C2   117.35  3.000
 C6R  C6   C4   C5   122.43  3.000
 C6R  C5   C4   C3   116.09  3.000
 C6R  C6   C4   C3   121.47  3.000
 C6R  H3   C5   C    117.73  3.000
 C6R  H3   C5   C4   119.42  3.000
 C6R  C    C5   C4   122.85  3.000
 C6R  N    C6   C15  105.80  3.000
 C6R  N    C6   C7   114.13  3.000
 C6R  C15  C6   C7   111.27  3.000
 C6R  N    C6   C4   106.55  3.000
 C6R  C15  C6   C4   111.36  3.000
 C6R  C7   C6   C4   107.68  3.000
 C6R  H4   C7   C16  106.87  3.000
 C6R  H4   C7   C8   106.28  3.000
 C6R  C16  C7   C8   111.82  3.000
 C6R  H4   C7   C6   107.17  3.000
 C6R  C8   C7   C6   111.39  3.000
 C6R  C16  C7   C6   112.87  3.000
 C6R  C17  O1   C13  119.00  3.000
 C6R  H9   C8   H8   107.65  3.000
 C6R  H9   C8   S    109.24  3.000
 C6R  H8   C8   S    105.45  3.000
 C6R  H9   C8   C7   113.14  3.000
 C6R  H8   C8   C7   110.18  3.000
 C6R  S    C8   C7   110.86  3.000
 C6R  C12  N3   C11  118.69  3.000
 C6R  S    C9   N    128.37  3.000
 C6R  N    C9   N1   121.01  3.000
 C6R  S    C9   N1   110.52  3.000
 C6R  O    C10  C11  120.92  3.000
 C6R  C11  C10  N2   113.27  3.000
 C6R  O    C10  N2   125.81  3.000
 C6R  C14  C11  C10  120.67  3.000
 C6R  C14  C11  N3   120.65  3.000
 C6R  C10  C11  N3   118.67  3.000
 C6R  H10  C12  C13  121.35  3.000
 C6R  H10  C12  N3   118.75  3.000
 C6R  C13  C12  N3   119.89  3.000
 C6R  N4   C13  C12  122.09  3.000
 C6R  C12  C13  O1   117.09  3.000
 C6R  N4   C13  O1   120.83  3.000
 C6R  H11  C14  N4   117.06  3.000
 C6R  H11  C14  C11  121.67  3.000
 C6R  N4   C14  C11  121.27  3.000
 C6R  H14  C15  H13  107.59  3.000
 C6R  H14  C15  H12  108.36  3.000
 C6R  H13  C15  H12  107.14  3.000
 C6R  H14  C15  C6   113.34  3.000
 C6R  H13  C15  C6   110.05  3.000
 C6R  H12  C15  C6   110.14  3.000
 C6R  H16  C17  H15  111.75  3.000
 C6R  H16  C17  F1   108.62  3.000
 C6R  H15  C17  F1   108.86  3.000
 C6R  H16  C17  O1   111.97  3.000
 C6R  H15  C17  O1   105.93  3.000
 C6R  F1   C17  O1   109.65  3.000
 C6R  C14  N4   C13  117.40  3.000
 C6R  N2   C    C5   116.14  3.000
 C6R  N2   C    C1   124.58  3.000
 C6R  C5   C    C1   119.28  3.000
 C6R  C9   N    C6   124.93  3.000
 C6R  C9   S    C8   100.04  3.000
 C6R  C18  C16  C22  118.02  3.000
 C6R  C18  C16  C7   119.25  3.000
 C6R  C22  C16  C7   122.74  3.000
 C6R  H17  C22  C21  118.35  3.000
 C6R  H17  C22  C16  120.72  3.000
 C6R  C21  C22  C16  120.93  3.000
 C6R  H18  C21  C20  120.12  3.000
 C6R  H18  C21  C22  119.52  3.000
 C6R  C20  C21  C22  120.36  3.000
 C6R  H19  C20  C19  120.34  3.000
 C6R  H19  C20  C21  120.34  3.000
 C6R  C19  C20  C21  119.32  3.000
 C6R  H20  C19  C18  119.70  3.000
 C6R  H20  C19  C20  120.20  3.000
 C6R  C18  C19  C20  120.10  3.000
 C6R  H21  C18  C19  119.26  3.000
 C6R  H21  C18  C16  119.47  3.000
 C6R  C19  C18  C16  121.27  3.000
 C6R  H6   N1   H5   113.12  3.000
 C6R  H6   N1   C9   117.47  3.000
 C6R  H5   N1   C9   114.45  3.000
 C6R  H7   N2   C    115.87  3.000
 C6R  H7   N2   C10  114.73  3.000
 C6R  C    N2   C10  129.38  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
 C6R  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 C6R  CONST_02  C4   C5   C    C1      0.00   0.0  0
 C6R  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 C6R  CONST_04  C5   C    C1   C2      0.00   0.0  0
 C6R  CONST_05  C    C1   C2   C3      0.00   0.0  0
 C6R  CONST_06  C    C5   C4   C3      0.00   0.0  0
 C6R  CONST_07  N4   C14  C11  N3      0.00   0.0  0
 C6R  CONST_08  N4   C13  C12  N3      0.00   0.0  0
 C6R  CONST_09  C13  N4   C14  C11     0.00   0.0  0
 C6R  CONST_10  C13  C12  N3   C11     0.00   0.0  0
 C6R  CONST_11  C14  C11  N3   C12     0.00   0.0  0
 C6R  CONST_12  C14  N4   C13  C12     0.00   0.0  0
 C6R  CONST_13  C20  C21  C22  C16     0.00   0.0  0
 C6R  CONST_14  C20  C19  C18  C16     0.00   0.0  0
 C6R  CONST_15  C19  C20  C21  C22     0.00   0.0  0
 C6R  CONST_16  C19  C18  C16  C22     0.00   0.0  0
 C6R  CONST_17  C18  C19  C20  C21     0.00   0.0  0
 C6R  CONST_18  C18  C16  C22  C21     0.00   0.0  0
 C6R  CONST_19  C6   C4   C3   C2    180.00   0.0  0
 C6R  CONST_20  C    C5   C4   C6    180.00   0.0  0
 C6R  CONST_21  C21  C22  C16  C7    180.00   0.0  0
 C6R  CONST_22  C19  C18  C16  C7    180.00   0.0  0
 C6R  CONST_23  S    C9   N    C6      0.00   0.0  0
 C6R  CONST_24  F    C3   C2   C1    180.00   0.0  0
 C6R  CONST_25  N2   C    C1   C2    180.00   0.0  0
 C6R  CONST_26  N2   C    C5   C4    180.00   0.0  0
 C6R  CONST_27  F    C3   C4   C5    180.00   0.0  0
 C6R  CONST_28  F    C3   C4   C6      0.00   0.0  0
 C6R  CONST_29  C14  N4   C13  O1    180.00   0.0  0
 C6R  CONST_30  N3   C12  C13  O1    180.00   0.0  0
 C6R  CONST_31  N4   C14  C11  C10   180.00   0.0  0
 C6R  CONST_32  C12  N3   C11  C10   180.00   0.0  0
 C6R  CONST_33  N1   C9   N    C6    180.00   0.0  0
 C6R  CONST_34  H3   C5   C    C1    180.00   0.0  0
 C6R  CONST_35  H1   C1   C2   C3    180.00   0.0  0
 C6R  CONST_36  H2   C2   C3   C4    180.00   0.0  0
 C6R  CONST_37  H17  C22  C16  C7      0.00   0.0  0
 C6R  CONST_38  H21  C18  C16  C7      0.00   0.0  0
 C6R  CONST_39  H11  C14  C11  N3    180.00   0.0  0
 C6R  CONST_40  H10  C12  N3   C11   180.00   0.0  0
 C6R  CONST_41  H18  C21  C22  C16   180.00   0.0  0
 C6R  CONST_42  H20  C19  C18  C16   180.00   0.0  0
 C6R  CONST_43  H19  C20  C21  C22   180.00   0.0  0
 C6R  CONST_44  C    N2   C10  C11   180.00   0.0  0
 C6R  CONST_45  C10  N2   C    C1      0.00   0.0  0
 C6R  CONST_46  C10  N2   C    C5    180.00   0.0  0
 C6R  CONST_47  H7   N2   C    C1    180.00   0.0  0
 C6R  CONST_48  H5   N1   C9   N       0.00   0.0  0
 C6R  CONST_50  C    N2   C10  O       0.00   0.0  0
 C6R  Var_01    N    C9   S    C8      8.10  30.0  1
 C6R  Var_02    H8   C8   S    C9   -157.53  30.0  1
 C6R  Var_03    C14  C11  C10  N2   -179.83  30.0  2
 C6R  Var_04    N4   C13  O1   C17    -3.43  30.0  1
 C6R  Var_05    F1   C17  O1   C13    76.02  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
 C6R  chir_01  C6  C7  C4  N    negativ
 C6R  chir_02  C7  C6  C8  C16  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
 C6R  plan-1  C1   0.020
 C6R  plan-1  C2   0.020
 C6R  plan-1  C3   0.020
 C6R  plan-1  C4   0.020
 C6R  plan-1  C5   0.020
 C6R  plan-1  C6   0.020
 C6R  plan-1  C    0.020
 C6R  plan-1  F    0.020
 C6R  plan-1  H1   0.020
 C6R  plan-1  H2   0.020
 C6R  plan-1  H3   0.020
 C6R  plan-1  N2   0.020
 C6R  plan-2  O1   0.020
 C6R  plan-2  N3   0.020
 C6R  plan-2  C10  0.020
 C6R  plan-2  C11  0.020
 C6R  plan-2  C12  0.020
 C6R  plan-2  C13  0.020
 C6R  plan-2  C14  0.020
 C6R  plan-2  N4   0.020
 C6R  plan-2  H10  0.020
 C6R  plan-2  H11  0.020
 C6R  plan-3  C7   0.020
 C6R  plan-3  C16  0.020
 C6R  plan-3  C22  0.020
 C6R  plan-3  C21  0.020
 C6R  plan-3  C20  0.020
 C6R  plan-3  C19  0.020
 C6R  plan-3  C18  0.020
 C6R  plan-3  H17  0.020
 C6R  plan-3  H18  0.020
 C6R  plan-3  H19  0.020
 C6R  plan-3  H20  0.020
 C6R  plan-3  H21  0.020
 C6R  plan-4  C10  0.020
 C6R  plan-4  C11  0.020
 C6R  plan-4  O    0.020
 C6R  plan-4  C    0.020
 C6R  plan-4  H7   0.020
 C6R  plan-4  N2   0.020
 C6R  plan-5  C6   0.020
 C6R  plan-5  C9   0.020
 C6R  plan-5  N    0.020
 C6R  plan-5  S    0.020
 C6R  plan-5  H5   0.020
 C6R  plan-5  H6   0.020
 C6R  plan-5  N1   0.020

