# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 14:57:48 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: ~{N}-[3-[(4~{S})-2-azanyl-4-methyl-5,6-dihydro-1,3-thiazin-4-yl]-4-fluoranyl-phenyl]-5-chloranyl-pyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]1(CCSC(=N1)N)c2cc(NC(=O)c3ccc(Cl)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
 C6U  C6U  ~{N}-[3-[(4~{S})-2-azanyl-4-methyl-5,6-dihydro-1,3-thiazin-4-yl]-4-fluoranyl-phenyl]-5-chloranyl-pyridine-2-carboxamide  ligand  41  25  .  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_C6U
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
 C6U  C1   C   CR16  0  -0.317  -0.2765   2.9259   0.1191
 C6U  C2   C   CR16  0  -0.393  -1.5940   3.3552   0.0760
 C6U  C3   C   CR6   0   0.505  -2.6162   2.4523  -0.1224
 C6U  C4   C   CR6   0  -0.062  -2.3912   1.0893  -0.2924
 C6U  C5   C   CR16  0  -0.427  -1.0652   0.6823  -0.2455
 C6U  C6   C   CT    0   0.036  -3.5169   0.0703  -0.4935
 C6U  C7   C   CH3   0  -0.651  -4.3497   0.4283  -1.7349
 C6U  C8   C   C     0   0.272  -3.4913  -2.3100  -0.5146
 C6U  N3   N   N     0  -0.439   3.3479  -0.6361  -0.0457
 C6U  C9   C   CH2   0  -0.574  -5.5659  -0.8860   0.6875
 C6U  C10  C   CH2   0  -0.440  -4.3727   0.0412   0.7852
 C6U  C11  C   C     0   0.539   2.4626   1.6060   0.1885
 C6U  C12  C   CR6   0   0.130   3.6182   0.6465   0.1688
 C6U  C13  C   CR16  0  -0.021   4.3347  -1.5109  -0.0708
 C6U  C14  C   CR6   0  -0.109   5.6566  -1.1248   0.1235
 C6U  C15  C   CR16  0  -0.090   5.9535   0.2076   0.3492
 C6U  F    F   F     0  -0.317  -3.8730   2.9422  -0.1399
 C6U  S    S   S2    0   0.008  -5.1029  -2.5694   0.1840
 C6U  N    N   N     0  -0.407  -2.8990  -1.2140  -0.7369
 C6U  C    C   CR6   0   0.423  -0.0069   1.5693  -0.0410
 C6U  O    O   O     0  -0.458   2.6411   2.7982   0.3728
 C6U  C16  C   CR16  0  -0.298   4.9076   1.1155   0.3717
 C6U  CL   CL  CL    0  -0.095   6.9032  -2.3096   0.0807
 C6U  H1   H   HCR6  0   0.286   0.5081   3.6470   0.2753
 C6U  H2   H   HCR6  0   0.278  -1.8254   4.4053   0.1998
 C6U  H3   H   HCR6  0   0.279  -0.8626  -0.3725  -0.3795
 C6U  H4   H   HCH3  0   0.242  -3.7044   0.5015  -2.6103
 C6U  H5   H   HCH3  0   0.235  -5.0834  -0.3543  -1.9333
 C6U  H6   H   HCH3  0   0.238  -4.8891   1.3668  -1.6266
 C6U  H7   H   HNH2  0   0.393  -3.1591  -4.3158  -0.3322
 C6U  H8   H   HNH2  0   0.387  -1.9488  -3.4449  -1.1173
 C6U  H9   H   HNH1  0   0.422   1.3245   0.0063  -0.1457
 C6U  H10  H   HCH2  0   0.300  -6.0483  -0.9817   1.6594
 C6U  H11  H   HCH2  0   0.281  -6.3095  -0.5086  -0.0129
 C6U  H12  H   HCH2  0   0.256  -3.7381  -0.2556   1.6236
 C6U  H13  H   HCH2  0   0.268  -4.7588   1.0344   1.0121
 C6U  H14  H   HCR6  0   0.297   4.0805  -2.5489  -0.2489
 C6U  H15  H   HCR6  0   0.304   6.9727   0.5332   0.5048
 C6U  H16  H   HCR6  0   0.290   5.0974   2.1648   0.5446
 C6U  N1   N   NH2   0  -0.809  -2.9275  -3.5011  -0.8789
 C6U  N2   N   NH1   0  -0.762   1.2727   1.0088  -0.0113

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
 C6U  F    C3   single    1.349  0.020  1.349
 C6U  C10  C9   single    1.514  0.020  1.514
 C6U  C10  C6   single    1.539  0.020  1.539
 C6U  C9   S    single    1.817  0.020  1.817
 C6U  C7   C6   single    1.537  0.020  1.537
 C6U  C3   C2   aromatic  1.378  0.020  1.378
 C6U  C3   C4   aromatic  1.392  0.020  1.392
 C6U  C2   C1   aromatic  1.386  0.020  1.386
 C6U  C6   C4   single    1.532  0.020  1.532
 C6U  C6   N    single    1.446  0.020  1.446
 C6U  C4   C5   aromatic  1.388  0.020  1.388
 C6U  S    C8   single    1.776  0.020  1.776
 C6U  N    C8   double    1.265  0.020  1.265
 C6U  C1   C    aromatic  1.392  0.020  1.392
 C6U  C8   N1   single    1.367  0.020  1.367
 C6U  C5   C    aromatic  1.396  0.020  1.396
 C6U  C    N2   single    1.397  0.020  1.397
 C6U  N2   C11  single    1.346  0.020  1.346
 C6U  O    C11  double    1.219  0.020  1.219
 C6U  C11  C12  single    1.502  0.020  1.502
 C6U  C12  C16  aromatic  1.387  0.020  1.387
 C6U  C12  N3   aromatic  1.328  0.020  1.328
 C6U  C16  C15  aromatic  1.385  0.020  1.385
 C6U  N3   C13  aromatic  1.319  0.020  1.319
 C6U  C15  C14  aromatic  1.384  0.020  1.384
 C6U  C13  C14  aromatic  1.391  0.020  1.391
 C6U  C14  CL   single    1.720  0.020  1.720
 C6U  C1   H1   single    0.930  0.020  1.080
 C6U  C2   H2   single    0.930  0.020  1.080
 C6U  C5   H3   single    0.930  0.020  1.080
 C6U  C7   H4   single    0.970  0.020  1.090
 C6U  C7   H5   single    0.970  0.020  1.090
 C6U  C7   H6   single    0.970  0.020  1.090
 C6U  N1   H7   single    0.890  0.020  1.040
 C6U  N1   H8   single    0.890  0.020  1.040
 C6U  N2   H9   single    0.860  0.020  1.020
 C6U  C9   H10  single    0.970  0.020  1.090
 C6U  C9   H11  single    0.970  0.020  1.090
 C6U  C10  H12  single    0.970  0.020  1.090
 C6U  C10  H13  single    0.970  0.020  1.090
 C6U  C13  H14  single    0.930  0.020  1.080
 C6U  C15  H15  single    0.930  0.020  1.080
 C6U  C16  H16  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
 C6U  H1   C1   C    121.87  3.000
 C6U  H1   C1   C2   119.31  3.000
 C6U  C    C1   C2   118.82  3.000
 C6U  H2   C2   C3   119.57  3.000
 C6U  H2   C2   C1   120.00  3.000
 C6U  C3   C2   C1   120.43  3.000
 C6U  F    C3   C4   120.31  3.000
 C6U  C4   C3   C2   122.63  3.000
 C6U  F    C3   C2   117.07  3.000
 C6U  C6   C4   C5   120.77  3.000
 C6U  C5   C4   C3   115.95  3.000
 C6U  C6   C4   C3   123.28  3.000
 C6U  H3   C5   C    119.70  3.000
 C6U  H3   C5   C4   117.42  3.000
 C6U  C    C5   C4   122.89  3.000
 C6U  N    C6   C10  111.15  3.000
 C6U  N    C6   C7   107.61  3.000
 C6U  C10  C6   C7   111.97  3.000
 C6U  N    C6   C4   107.40  3.000
 C6U  C7   C6   C4   110.44  3.000
 C6U  C10  C6   C4   108.19  3.000
 C6U  H6   C7   H5   107.67  3.000
 C6U  H6   C7   H4   108.39  3.000
 C6U  H5   C7   H4   107.47  3.000
 C6U  H6   C7   C6   112.90  3.000
 C6U  H5   C7   C6   110.13  3.000
 C6U  H4   C7   C6   110.09  3.000
 C6U  N    C8   S    128.35  3.000
 C6U  N    C8   N1   120.98  3.000
 C6U  S    C8   N1   110.60  3.000
 C6U  C13  N3   C12  119.43  3.000
 C6U  H11  C9   H10  107.57  3.000
 C6U  H11  C9   S    108.47  3.000
 C6U  H10  C9   S    106.18  3.000
 C6U  H11  C9   C10  111.55  3.000
 C6U  H10  C9   C10  110.19  3.000
 C6U  S    C9   C10  112.61  3.000
 C6U  H13  C10  H12  107.08  3.000
 C6U  H13  C10  C9   107.00  3.000
 C6U  H12  C10  C9   109.93  3.000
 C6U  H13  C10  C6   110.66  3.000
 C6U  H12  C10  C6   108.65  3.000
 C6U  C9   C10  C6   113.34  3.000
 C6U  O    C11  C12  120.92  3.000
 C6U  C12  C11  N2   113.24  3.000
 C6U  O    C11  N2   125.84  3.000
 C6U  C16  C12  C11  119.82  3.000
 C6U  C16  C12  N3   122.64  3.000
 C6U  C11  C12  N3   117.54  3.000
 C6U  H14  C13  C14  120.80  3.000
 C6U  H14  C13  N3   117.58  3.000
 C6U  C14  C13  N3   121.62  3.000
 C6U  CL   C14  C15  120.79  3.000
 C6U  CL   C14  C13  119.61  3.000
 C6U  C15  C14  C13  119.61  3.000
 C6U  H15  C15  C16  120.80  3.000
 C6U  H15  C15  C14  121.05  3.000
 C6U  C16  C15  C14  118.15  3.000
 C6U  C9   S    C8   101.82  3.000
 C6U  C8   N    C6   122.67  3.000
 C6U  N2   C    C5   116.26  3.000
 C6U  N2   C    C1   124.45  3.000
 C6U  C5   C    C1   119.28  3.000
 C6U  H16  C16  C15  120.44  3.000
 C6U  H16  C16  C12  121.01  3.000
 C6U  C15  C16  C12  118.55  3.000
 C6U  H8   N1   H7   113.33  3.000
 C6U  H8   N1   C8   114.48  3.000
 C6U  H7   N1   C8   117.70  3.000
 C6U  H9   N2   C    116.18  3.000
 C6U  H9   N2   C11  114.42  3.000
 C6U  C    N2   C11  129.39  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
 C6U  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 C6U  CONST_02  C4   C5   C    C1      0.00   0.0  0
 C6U  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 C6U  CONST_04  C5   C    C1   C2      0.00   0.0  0
 C6U  CONST_05  C    C1   C2   C3      0.00   0.0  0
 C6U  CONST_06  C    C5   C4   C3      0.00   0.0  0
 C6U  CONST_07  C15  C16  C12  N3      0.00   0.0  0
 C6U  CONST_08  C15  C14  C13  N3      0.00   0.0  0
 C6U  CONST_09  C14  C15  C16  C12     0.00   0.0  0
 C6U  CONST_10  C14  C13  N3   C12     0.00   0.0  0
 C6U  CONST_11  C16  C12  N3   C13     0.00   0.0  0
 C6U  CONST_12  C16  C15  C14  C13     0.00   0.0  0
 C6U  CONST_13  C6   C4   C3   C2    180.00   0.0  0
 C6U  CONST_14  C    C5   C4   C6    180.00   0.0  0
 C6U  CONST_15  S    C8   N    C6      0.00   0.0  0
 C6U  CONST_16  F    C3   C2   C1    180.00   0.0  0
 C6U  CONST_17  N2   C    C1   C2    180.00   0.0  0
 C6U  CONST_18  N2   C    C5   C4    180.00   0.0  0
 C6U  CONST_19  F    C3   C4   C5    180.00   0.0  0
 C6U  CONST_20  F    C3   C4   C6      0.00   0.0  0
 C6U  CONST_21  CL   C14  C13  N3    180.00   0.0  0
 C6U  CONST_22  C15  C16  C12  C11   180.00   0.0  0
 C6U  CONST_23  C13  N3   C12  C11   180.00   0.0  0
 C6U  CONST_24  CL   C14  C15  C16   180.00   0.0  0
 C6U  CONST_25  N1   C8   N    C6    180.00   0.0  0
 C6U  CONST_26  H3   C5   C    C1    180.00   0.0  0
 C6U  CONST_27  H1   C1   C2   C3    180.00   0.0  0
 C6U  CONST_28  H2   C2   C3   C4    180.00   0.0  0
 C6U  CONST_29  H16  C16  C12  N3    180.00   0.0  0
 C6U  CONST_30  H15  C15  C16  C12   180.00   0.0  0
 C6U  CONST_31  H14  C13  N3   C12   180.00   0.0  0
 C6U  CONST_32  C    N2   C11  C12   180.00   0.0  0
 C6U  CONST_33  C11  N2   C    C1      0.00   0.0  0
 C6U  CONST_34  C11  N2   C    C5    180.00   0.0  0
 C6U  CONST_35  H9   N2   C    C1    180.00   0.0  0
 C6U  CONST_37  H8   N1   C8   S     180.00   0.0  0
 C6U  CONST_38  O    C11  N2   C       0.00   0.0  0
 C6U  Var_01    S    C9   C10  C6     53.29  30.0  1
 C6U  Var_02    C10  C9   S    C8    -18.26  30.0  1
 C6U  Var_03    N    C8   S    C9     -7.17  30.0  1
 C6U  Var_04    C16  C12  C11  N2   -179.48  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
 C6U  chir_01  C6  C10  C4  N  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
 C6U  plan-1  C1   0.020
 C6U  plan-1  C2   0.020
 C6U  plan-1  C3   0.020
 C6U  plan-1  C4   0.020
 C6U  plan-1  C5   0.020
 C6U  plan-1  C6   0.020
 C6U  plan-1  F    0.020
 C6U  plan-1  C    0.020
 C6U  plan-1  H1   0.020
 C6U  plan-1  H2   0.020
 C6U  plan-1  H3   0.020
 C6U  plan-1  N2   0.020
 C6U  plan-2  N3   0.020
 C6U  plan-2  C11  0.020
 C6U  plan-2  C12  0.020
 C6U  plan-2  C13  0.020
 C6U  plan-2  C14  0.020
 C6U  plan-2  C15  0.020
 C6U  plan-2  C16  0.020
 C6U  plan-2  CL   0.020
 C6U  plan-2  H14  0.020
 C6U  plan-2  H15  0.020
 C6U  plan-2  H16  0.020
 C6U  plan-3  C11  0.020
 C6U  plan-3  C12  0.020
 C6U  plan-3  C    0.020
 C6U  plan-3  O    0.020
 C6U  plan-3  H9   0.020
 C6U  plan-3  N2   0.020
 C6U  plan-4  C6   0.020
 C6U  plan-4  C8   0.020
 C6U  plan-4  S    0.020
 C6U  plan-4  N    0.020
 C6U  plan-4  H7   0.020
 C6U  plan-4  H8   0.020
 C6U  plan-4  N1   0.020

