# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 06:51:47 2022
#   Inital geometry file: a 114 line input string
#   Ligand name: ~{N}-[3-[(4~{S})-2-azanyl-4-methyl-1,3-thiazin-4-yl]-4-fluoranyl-phenyl]-5-cyano-pyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]1(C=CSC(=N1)N)c2cc(NC(=O)c3ccc(cn3)C#N)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
 H3C  H3C  ~{N}-[3-[(4~{S})-2-azanyl-4-methyl-1,3-thiazin-4-yl]-4-fluoranyl-phenyl]-5-cyano-pyridine-2-carboxamide  ligand  40  26  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H3C
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
 H3C  N5   N  NS    0  -0.229  20.6445  43.2222    0.9779
 H3C  C18  C  CSP   0   0.058  20.7943  42.9177   -0.1223
 H3C  C15  C  CR6   0  -0.079  20.9778  42.5290   -1.4813
 H3C  C14  C  CR16  0  -0.018  19.9706  41.8264   -2.1452
 H3C  N4   N  N     0  -0.435  20.1001  41.4365   -3.3964
 H3C  C16  C  CR16  0  -0.114  22.1515  42.8336   -2.1637
 H3C  C17  C  CR16  0  -0.282  22.2754  42.4194   -3.4767
 H3C  C13  C  CR6   0   0.142  21.2223  41.7197   -4.0488
 H3C  C12  C  C     0   0.540  21.3391  41.2425   -5.4718
 H3C  O    O  O     0  -0.445  22.3480  41.4615   -6.1177
 H3C  N3   N  NH1   0  -0.761  20.2500  40.5816   -5.9040
 H3C  C8   C  CR6   0   0.413  20.0068  40.0197   -7.1614
 H3C  C7   C  CR16  0  -0.420  18.6989  39.6020   -7.4135
 H3C  C9   C  CR16  0  -0.311  20.9793  39.8488   -8.1430
 H3C  C10  C  CR16  0  -0.395  20.6234  39.2605   -9.3470
 H3C  C11  C  CR6   0   0.526  19.3241  38.8565   -9.5639
 H3C  F    F  F     0  -0.312  19.0362  38.2732  -10.7414
 H3C  C6   C  CR6   0  -0.036  18.3213  39.0246   -8.6169
 H3C  C2   C  CT    0  -0.050  16.8849  38.5386   -8.8537
 H3C  C1   C  CH3   0  -0.639  16.8558  37.0147   -8.7000
 H3C  C5   C  C1    0  -0.108  16.4205  38.9256  -10.2404
 H3C  C4   C  C1    0  -0.431  16.0011  40.1505  -10.5226
 H3C  S    S  S2    0   0.052  15.9074  41.3876   -9.2842
 H3C  C3   C  C     0   0.284  15.6135  40.2935   -7.9044
 H3C  N1   N  N     0  -0.388  15.9943  39.0861   -7.8434
 H3C  N2   N  NH2   0  -0.798  14.9798  40.9174   -6.8807
 H3C  H1   H  HCR6  0   0.300  19.0446  41.5796   -1.6396
 H3C  H2   H  HCR6  0   0.303  22.9484  43.3791   -1.6769
 H3C  H3   H  HCR6  0   0.295  23.1709  42.6325   -4.0416
 H3C  H4   H  HNH1  0   0.426  19.4953  40.5188   -5.2311
 H3C  H5   H  HCR6  0   0.281  17.9522  39.7366   -6.6414
 H3C  H6   H  HCR6  0   0.286  22.0003  40.1560   -7.9896
 H3C  H7   H  HCR6  0   0.279  21.3674  39.1127  -10.1193
 H3C  H8   H  HCH3  0   0.239  17.1783  36.7299   -7.6992
 H3C  H9   H  HCH3  0   0.239  15.8411  36.6448   -8.8522
 H3C  H10  H  HCH3  0   0.232  17.5066  36.5265   -9.4241
 H3C  H11  H  H     0   0.268  16.3849  38.1640  -11.0096
 H3C  H13  H  H     0   0.296  15.6561  40.4508  -11.5031
 H3C  H15  H  HNH2  0   0.401  14.3134  41.6425   -7.0930
 H3C  H16  H  HNH2  0   0.394  14.7330  40.3348   -6.0951

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
 H3C  F    C11  single    1.345  0.020  1.345
 H3C  C5   C4   double    1.325  0.020  1.325
 H3C  C5   C2   single    1.513  0.020  1.513
 H3C  C4   S    single    1.753  0.020  1.753
 H3C  C11  C10  aromatic  1.378  0.020  1.378
 H3C  C11  C6   aromatic  1.389  0.020  1.389
 H3C  C1   C2   single    1.532  0.020  1.532
 H3C  C10  C9   aromatic  1.387  0.020  1.387
 H3C  C2   C6   single    1.535  0.020  1.535
 H3C  C2   N1   single    1.454  0.020  1.454
 H3C  C6   C7   aromatic  1.387  0.020  1.387
 H3C  S    C3   single    1.785  0.020  1.785
 H3C  C9   C8   aromatic  1.392  0.020  1.392
 H3C  N1   C3   double    1.267  0.020  1.267
 H3C  C3   N2   single    1.356  0.020  1.356
 H3C  C7   C8   aromatic  1.396  0.020  1.396
 H3C  C8   N3   single    1.399  0.020  1.399
 H3C  O    C12  double    1.218  0.020  1.218
 H3C  N3   C12  single    1.345  0.020  1.345
 H3C  C12  C13  single    1.505  0.020  1.505
 H3C  C13  C17  aromatic  1.388  0.020  1.388
 H3C  C13  N4   aromatic  1.329  0.020  1.329
 H3C  C17  C16  aromatic  1.382  0.020  1.382
 H3C  N4   C14  aromatic  1.317  0.020  1.317
 H3C  C16  C15  aromatic  1.391  0.020  1.391
 H3C  C14  C15  aromatic  1.396  0.020  1.396
 H3C  C15  C18  single    1.425  0.020  1.425
 H3C  C18  N5   triple    1.151  0.020  1.151
 H3C  C14  H1   single    0.930  0.020  1.080
 H3C  C16  H2   single    0.930  0.020  1.080
 H3C  C17  H3   single    0.930  0.020  1.080
 H3C  N3   H4   single    0.860  0.020  1.020
 H3C  C7   H5   single    0.930  0.020  1.080
 H3C  C9   H6   single    0.930  0.020  1.080
 H3C  C10  H7   single    0.930  0.020  1.080
 H3C  C1   H8   single    0.970  0.020  1.090
 H3C  C1   H9   single    0.970  0.020  1.090
 H3C  C1   H10  single    0.970  0.020  1.090
 H3C  C5   H11  single    0.930  0.020  1.080
 H3C  C4   H13  single    0.930  0.020  1.080
 H3C  N2   H15  single    0.890  0.020  1.040
 H3C  N2   H16  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
 H3C  C15  C18  N5   180.00  3.000
 H3C  C16  C15  C14  119.05  3.000
 H3C  C14  C15  C18  119.86  3.000
 H3C  C16  C15  C18  121.09  3.000
 H3C  H1   C14  N4   117.39  3.000
 H3C  H1   C14  C15  120.62  3.000
 H3C  N4   C14  C15  122.00  3.000
 H3C  C13  N4   C14  119.11  3.000
 H3C  H2   C16  C17  120.84  3.000
 H3C  H2   C16  C15  120.75  3.000
 H3C  C17  C16  C15  118.41  3.000
 H3C  H3   C17  C13  120.86  3.000
 H3C  H3   C17  C16  120.80  3.000
 H3C  C13  C17  C16  118.34  3.000
 H3C  C12  C13  C17  119.38  3.000
 H3C  C17  C13  N4   123.09  3.000
 H3C  C12  C13  N4   117.52  3.000
 H3C  N3   C12  O    126.06  3.000
 H3C  N3   C12  C13  113.37  3.000
 H3C  O    C12  C13  120.57  3.000
 H3C  H4   N3   C8   116.28  3.000
 H3C  H4   N3   C12  114.84  3.000
 H3C  C8   N3   C12  128.83  3.000
 H3C  C9   C8   C7   119.37  3.000
 H3C  C7   C8   N3   116.46  3.000
 H3C  C9   C8   N3   124.17  3.000
 H3C  H5   C7   C6   118.87  3.000
 H3C  H5   C7   C8   118.70  3.000
 H3C  C6   C7   C8   122.43  3.000
 H3C  H6   C9   C10  119.21  3.000
 H3C  H6   C9   C8   121.78  3.000
 H3C  C10  C9   C8   119.01  3.000
 H3C  H7   C10  C11  119.72  3.000
 H3C  H7   C10  C9   120.07  3.000
 H3C  C11  C10  C9   120.21  3.000
 H3C  C6   C11  F    119.64  3.000
 H3C  C6   C11  C10  122.54  3.000
 H3C  F    C11  C10  117.82  3.000
 H3C  C2   C6   C11  122.14  3.000
 H3C  C2   C6   C7   121.36  3.000
 H3C  C11  C6   C7   116.43  3.000
 H3C  N1   C2   C5   110.65  3.000
 H3C  N1   C2   C1   107.05  3.000
 H3C  C5   C2   C1   109.92  3.000
 H3C  N1   C2   C6   110.29  3.000
 H3C  C1   C2   C6   108.50  3.000
 H3C  C5   C2   C6   110.35  3.000
 H3C  H10  C1   H9   108.13  3.000
 H3C  H10  C1   H8   108.46  3.000
 H3C  H9   C1   H8   108.36  3.000
 H3C  H10  C1   C2   111.58  3.000
 H3C  H9   C1   C2   109.94  3.000
 H3C  H8   C1   C2   110.28  3.000
 H3C  H11  C5   C4   119.24  3.000
 H3C  H11  C5   C2   118.76  3.000
 H3C  C4   C5   C2   121.93  3.000
 H3C  H13  C4   S    115.30  3.000
 H3C  H13  C4   C5   123.40  3.000
 H3C  S    C4   C5   121.25  3.000
 H3C  C3   S    C4    97.03  3.000
 H3C  N2   C3   N1   122.84  3.000
 H3C  N2   C3   S    112.23  3.000
 H3C  N1   C3   S    124.86  3.000
 H3C  C3   N1   C2   120.62  3.000
 H3C  H16  N2   H15  114.71  3.000
 H3C  H16  N2   C3   115.88  3.000
 H3C  H15  N2   C3   118.77  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
 H3C  CONST_01  C13  C17  C16  C15     0.00   0.0  0
 H3C  CONST_02  C13  N4   C14  C15     0.00   0.0  0
 H3C  CONST_03  C17  C13  N4   C14     0.00   0.0  0
 H3C  CONST_04  C17  C16  C15  C14     0.00   0.0  0
 H3C  CONST_05  C16  C17  C13  N4      0.00   0.0  0
 H3C  CONST_06  C16  C15  C14  N4      0.00   0.0  0
 H3C  CONST_07  C11  C10  C9   C8      0.00   0.0  0
 H3C  CONST_08  C11  C6   C7   C8      0.00   0.0  0
 H3C  CONST_09  C10  C11  C6   C7      0.00   0.0  0
 H3C  CONST_10  C10  C9   C8   C7      0.00   0.0  0
 H3C  CONST_11  C6   C11  C10  C9      0.00   0.0  0
 H3C  CONST_12  C6   C7   C8   C9      0.00   0.0  0
 H3C  CONST_13  C2   C6   C7   C8    180.00   0.0  0
 H3C  CONST_14  C2   C6   C11  C10   180.00   0.0  0
 H3C  CONST_15  S    C3   N1   C2      0.00   0.0  0
 H3C  CONST_16  C17  C16  C15  C18   180.00   0.0  0
 H3C  CONST_17  N4   C14  C15  C18   180.00   0.0  0
 H3C  CONST_18  C12  C13  N4   C14   180.00   0.0  0
 H3C  CONST_19  C12  C13  C17  C16   180.00   0.0  0
 H3C  CONST_20  C10  C9   C8   N3    180.00   0.0  0
 H3C  CONST_21  C6   C7   C8   N3    180.00   0.0  0
 H3C  CONST_22  F    C11  C6   C7    180.00   0.0  0
 H3C  CONST_23  F    C11  C10  C9    180.00   0.0  0
 H3C  CONST_24  C2   C6   C11  F       0.00   0.0  0
 H3C  CONST_25  N2   C3   N1   C2    180.00   0.0  0
 H3C  CONST_26  H3   C17  C16  C15   180.00   0.0  0
 H3C  CONST_27  H2   C16  C15  C14   180.00   0.0  0
 H3C  CONST_28  H1   C14  C15  C16   180.00   0.0  0
 H3C  CONST_29  H7   C10  C9   C8    180.00   0.0  0
 H3C  CONST_30  H6   C9   C8   C7    180.00   0.0  0
 H3C  CONST_31  H5   C7   C8   C9    180.00   0.0  0
 H3C  CONST_32  C8   N3   C12  C13   180.00   0.0  0
 H3C  CONST_33  C9   C8   N3   C12     0.00   0.0  0
 H3C  CONST_34  C7   C8   N3   C12   180.00   0.0  0
 H3C  CONST_35  H4   N3   C8   C7      0.00   0.0  0
 H3C  CONST_37  H16  N2   C3   S     180.00   0.0  0
 H3C  CONST_38  C8   N3   C12  O       0.00   0.0  0
 H3C  Var_01    S    C4   C5   C2     -2.14  30.0  1
 H3C  Var_02    N1   C3   S    C4     27.22  30.0  1
 H3C  Var_03    O    C12  C13  N4   -179.37  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
 H3C  chir_01  C2  C5  C6  N1  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
 H3C  plan-1  N5   0.020
 H3C  plan-1  C18  0.020
 H3C  plan-1  C15  0.020
 H3C  plan-1  C14  0.020
 H3C  plan-1  N4   0.020
 H3C  plan-1  C16  0.020
 H3C  plan-1  C17  0.020
 H3C  plan-1  C13  0.020
 H3C  plan-1  C12  0.020
 H3C  plan-1  H1   0.020
 H3C  plan-1  H2   0.020
 H3C  plan-1  H3   0.020
 H3C  plan-2  N3   0.020
 H3C  plan-2  C8   0.020
 H3C  plan-2  C7   0.020
 H3C  plan-2  C9   0.020
 H3C  plan-2  C10  0.020
 H3C  plan-2  C11  0.020
 H3C  plan-2  F    0.020
 H3C  plan-2  C6   0.020
 H3C  plan-2  C2   0.020
 H3C  plan-2  H5   0.020
 H3C  plan-2  H6   0.020
 H3C  plan-2  H7   0.020
 H3C  plan-3  C13  0.020
 H3C  plan-3  C12  0.020
 H3C  plan-3  O    0.020
 H3C  plan-3  N3   0.020
 H3C  plan-3  C8   0.020
 H3C  plan-3  H4   0.020
 H3C  plan-4  C2   0.020
 H3C  plan-4  S    0.020
 H3C  plan-4  C3   0.020
 H3C  plan-4  N1   0.020
 H3C  plan-4  N2   0.020
 H3C  plan-4  H15  0.020
 H3C  plan-4  H16  0.020

