# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 14:23:57 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: (4~{S},6~{S})-4-[2,4-bis(fluoranyl)phenyl]-4-methyl-6-pyrimidin-5-yl-5,6-dihydro-1,3-thiazin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]1(C[C@H](SC(=N1)N)c2cncnc2)c3ccc(F)cc3F
#
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
 6WD  6WD  (4~{S},6~{S})-4-[2,4-bis(fluoranyl)phenyl]-4-methyl-6-pyrimidin-5-yl-5,6-dihydro-1,3-thiazin-2-amine  ligand  36  22  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_6WD
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
 6WD  C18  C  CR6   0   0.531   3.7811  -1.3142  -0.8665
 6WD  C17  C  CR16  0  -0.405   3.4907  -0.0531  -1.3394
 6WD  C16  C  CR16  0  -0.282   2.5199   0.6903  -0.6829
 6WD  C15  C  CR6   0  -0.081   1.8274   0.2179   0.4307
 6WD  C19  C  CR16  0  -0.551   3.1352  -1.8422   0.2328
 6WD  C20  C  CR6   0   0.539   2.1780  -1.0620   0.8527
 6WD  C12  C  CR16  0   0.055  -4.7417  -1.9854  -0.1619
 6WD  C1   C  CH3   0  -0.635   1.1818   1.3474   2.5832
 6WD  C2   C  CT    0   0.006   0.7622   1.0697   1.1337
 6WD  C3   C  CH2   0  -0.415  -0.5980   0.3569   1.1330
 6WD  C4   C  CH1   0  -0.504  -1.1010   0.0320  -0.2633
 6WD  S5   S  S2    0   0.047  -1.2958   1.5670  -1.2349
 6WD  C6   C  C     0   0.280  -0.1212   2.6416  -0.4388
 6WD  N7   N  N     0  -0.402   0.6881   2.3667   0.4965
 6WD  N8   N  NH2   0  -0.807  -0.2096   3.9036  -0.9428
 6WD  C9   C  CR6   0   0.057  -2.4227  -0.6742  -0.2438
 6WD  C10  C  CR16  0  -0.053  -2.5671  -1.9555  -0.7528
 6WD  N11  N  N     0  -0.386  -3.7188  -2.6147  -0.7152
 6WD  N13  N  N     0  -0.389  -4.7254  -0.7626   0.3509
 6WD  C14  C  CR16  0  -0.025  -3.5717  -0.1144   0.3041
 6WD  F21  F  F     0  -0.308   1.5687  -1.6105   1.9175
 6WD  F22  F  F     0  -0.309   4.7129  -2.0544  -1.4812
 6WD  H1   H  HCR6  0   0.283   4.0070   0.3493  -2.2002
 6WD  H2   H  HCR6  0   0.283   2.3058   1.6823  -1.0521
 6WD  H3   H  HCR6  0   0.301   3.3644  -2.8331   0.6023
 6WD  H5   H  HCH3  0   0.236   2.1599   1.8277   2.6059
 6WD  H6   H  HCH3  0   0.235   0.4624   2.0252   3.0443
 6WD  H7   H  HCH3  0   0.230   1.2244   0.4437   3.1862
 6WD  H8   H  HCH2  0   0.276  -0.5495  -0.5727   1.6998
 6WD  H9   H  HCH2  0   0.264  -1.3188   0.9974   1.6496
 6WD  H10  H  HCH1  0   0.313  -0.3779  -0.6006  -0.7827
 6WD  H11  H  HNH2  0   0.398  -0.5612   4.0316  -1.8781
 6WD  H12  H  HNH2  0   0.392   0.5524   4.5188  -0.7024
 6WD  H13  H  HCR6  0   0.280  -1.7237  -2.4663  -1.2074
 6WD  H14  H  HCR6  0   0.276  -3.5609   0.8916   0.7122
 6WD  H4   H  HCR6  0   0.269  -5.6853  -2.5184  -0.1259

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
 6WD  C12  N13  aromatic  1.326  0.020  1.326
 6WD  C12  N11  aromatic  1.322  0.020  1.322
 6WD  N13  C14  aromatic  1.324  0.020  1.324
 6WD  N11  C10  aromatic  1.328  0.020  1.328
 6WD  C14  C9   aromatic  1.391  0.020  1.391
 6WD  C10  C9   aromatic  1.386  0.020  1.386
 6WD  C9   C4   single    1.499  0.020  1.499
 6WD  F21  C20  single    1.344  0.020  1.344
 6WD  C3   C4   single    1.519  0.020  1.519
 6WD  C3   C2   single    1.536  0.020  1.536
 6WD  C4   S5   single    1.827  0.020  1.827
 6WD  C20  C19  aromatic  1.382  0.020  1.382
 6WD  C20  C15  aromatic  1.393  0.020  1.393
 6WD  C1   C2   single    1.534  0.020  1.534
 6WD  C19  C18  aromatic  1.380  0.020  1.380
 6WD  C2   C15  single    1.534  0.020  1.534
 6WD  C2   N7   single    1.447  0.020  1.447
 6WD  C15  C16  aromatic  1.394  0.020  1.394
 6WD  S5   C6   single    1.780  0.020  1.780
 6WD  N7   C6   double    1.267  0.020  1.267
 6WD  C18  F22  single    1.339  0.020  1.339
 6WD  C18  C17  aromatic  1.378  0.020  1.378
 6WD  C6   N8   single    1.362  0.020  1.362
 6WD  C16  C17  aromatic  1.388  0.020  1.388
 6WD  C17  H1   single    0.930  0.020  1.080
 6WD  C16  H2   single    0.930  0.020  1.080
 6WD  C19  H3   single    0.930  0.020  1.080
 6WD  C12  H4   single    0.930  0.020  1.080
 6WD  C1   H5   single    0.970  0.020  1.090
 6WD  C1   H6   single    0.970  0.020  1.090
 6WD  C1   H7   single    0.970  0.020  1.090
 6WD  C3   H8   single    0.970  0.020  1.090
 6WD  C3   H9   single    0.970  0.020  1.090
 6WD  C4   H10  single    0.970  0.020  1.090
 6WD  N8   H11  single    0.890  0.020  1.040
 6WD  N8   H12  single    0.890  0.020  1.040
 6WD  C10  H13  single    0.930  0.020  1.080
 6WD  C14  H14  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
 6WD  F22  C18  C19  118.67  3.000
 6WD  F22  C18  C17  119.66  3.000
 6WD  C19  C18  C17  121.66  3.000
 6WD  H1   C17  C16  120.74  3.000
 6WD  H1   C17  C18  120.88  3.000
 6WD  C16  C17  C18  118.39  3.000
 6WD  H2   C16  C15  119.08  3.000
 6WD  H2   C16  C17  117.97  3.000
 6WD  C15  C16  C17  122.95  3.000
 6WD  C2   C15  C20  123.10  3.000
 6WD  C2   C15  C16  121.52  3.000
 6WD  C20  C15  C16  115.38  3.000
 6WD  H3   C19  C20  120.70  3.000
 6WD  H3   C19  C18  121.55  3.000
 6WD  C20  C19  C18  117.75  3.000
 6WD  F21  C20  C19  116.05  3.000
 6WD  C19  C20  C15  123.87  3.000
 6WD  F21  C20  C15  120.07  3.000
 6WD  H4   C12  N13  116.81  3.000
 6WD  H4   C12  N11  116.95  3.000
 6WD  N13  C12  N11  126.24  3.000
 6WD  H7   C1   H6   107.93  3.000
 6WD  H7   C1   H5   108.63  3.000
 6WD  H6   C1   H5   108.02  3.000
 6WD  H7   C1   C2   112.60  3.000
 6WD  H6   C1   C2   109.36  3.000
 6WD  H5   C1   C2   110.17  3.000
 6WD  N7   C2   C3   111.74  3.000
 6WD  N7   C2   C1   105.53  3.000
 6WD  C3   C2   C1   109.07  3.000
 6WD  N7   C2   C15  109.35  3.000
 6WD  C1   C2   C15  110.09  3.000
 6WD  C3   C2   C15  110.91  3.000
 6WD  H9   C3   H8   106.44  3.000
 6WD  H9   C3   C4   109.94  3.000
 6WD  H8   C3   C4   108.08  3.000
 6WD  H9   C3   C2   108.16  3.000
 6WD  H8   C3   C2   110.87  3.000
 6WD  C4   C3   C2   113.14  3.000
 6WD  H10  C4   C9   108.49  3.000
 6WD  H10  C4   S5   107.72  3.000
 6WD  C9   C4   S5   107.99  3.000
 6WD  H10  C4   C3   109.98  3.000
 6WD  S5   C4   C3   110.14  3.000
 6WD  C9   C4   C3   112.39  3.000
 6WD  C6   S5   C4   101.48  3.000
 6WD  N8   C6   N7   121.04  3.000
 6WD  N8   C6   S5   110.56  3.000
 6WD  N7   C6   S5   128.37  3.000
 6WD  C6   N7   C2   123.52  3.000
 6WD  H12  N8   H11  114.06  3.000
 6WD  H12  N8   C6   115.34  3.000
 6WD  H11  N8   C6   118.95  3.000
 6WD  C14  C9   C10  115.51  3.000
 6WD  C10  C9   C4   121.51  3.000
 6WD  C14  C9   C4   122.96  3.000
 6WD  H13  C10  N11  116.88  3.000
 6WD  H13  C10  C9   120.51  3.000
 6WD  N11  C10  C9   122.61  3.000
 6WD  C10  N11  C12  116.53  3.000
 6WD  C14  N13  C12  116.64  3.000
 6WD  H14  C14  N13  116.67  3.000
 6WD  H14  C14  C9   120.86  3.000
 6WD  N13  C14  C9   122.47  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
 6WD  CONST_01  C15  C20  C19  C18    0.00   0.0  0
 6WD  CONST_02  C15  C16  C17  C18    0.00   0.0  0
 6WD  CONST_03  C20  C19  C18  C17    0.00   0.0  0
 6WD  CONST_04  C20  C15  C16  C17    0.00   0.0  0
 6WD  CONST_05  C19  C20  C15  C16    0.00   0.0  0
 6WD  CONST_06  C19  C18  C17  C16    0.00   0.0  0
 6WD  CONST_07  C9   C14  N13  C12    0.00   0.0  0
 6WD  CONST_08  C9   C10  N11  C12    0.00   0.0  0
 6WD  CONST_09  N13  C12  N11  C10    0.00   0.0  0
 6WD  CONST_10  N13  C14  C9   C10    0.00   0.0  0
 6WD  CONST_11  C14  N13  C12  N11    0.00   0.0  0
 6WD  CONST_12  C14  C9   C10  N11    0.00   0.0  0
 6WD  CONST_13  C2   C15  C16  C17  180.00   0.0  0
 6WD  CONST_14  C2   C15  C20  C19  180.00   0.0  0
 6WD  CONST_15  N13  C14  C9   C4   180.00   0.0  0
 6WD  CONST_16  N11  C10  C9   C4   180.00   0.0  0
 6WD  CONST_17  S5   C6   N7   C2     0.00   0.0  0
 6WD  CONST_18  F21  C20  C19  C18  180.00   0.0  0
 6WD  CONST_19  F21  C20  C15  C16  180.00   0.0  0
 6WD  CONST_20  F22  C18  C17  C16  180.00   0.0  0
 6WD  CONST_21  F22  C18  C19  C20  180.00   0.0  0
 6WD  CONST_22  F21  C20  C15  C2     0.00   0.0  0
 6WD  CONST_23  N8   C6   N7   C2   180.00   0.0  0
 6WD  CONST_24  H2   C16  C17  C18  180.00   0.0  0
 6WD  CONST_25  H3   C19  C18  C17  180.00   0.0  0
 6WD  CONST_26  H1   C17  C16  C15  180.00   0.0  0
 6WD  CONST_27  H14  C14  N13  C12  180.00   0.0  0
 6WD  CONST_28  H13  C10  N11  C12  180.00   0.0  0
 6WD  CONST_29  H4   C12  N11  C10  180.00   0.0  0
 6WD  CONST_31  H12  N8   C6   S5   180.00   0.0  0
 6WD  Var_01    N7   C6   S5   C4     4.04  30.0  1

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
 6WD  chir_01  C2  C3  C15  N7  negativ
 6WD  chir_02  C4  S5  C9   C3  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
 6WD  plan-1  C18  0.020
 6WD  plan-1  C17  0.020
 6WD  plan-1  C16  0.020
 6WD  plan-1  C15  0.020
 6WD  plan-1  C19  0.020
 6WD  plan-1  C20  0.020
 6WD  plan-1  C2   0.020
 6WD  plan-1  F21  0.020
 6WD  plan-1  F22  0.020
 6WD  plan-1  H1   0.020
 6WD  plan-1  H2   0.020
 6WD  plan-1  H3   0.020
 6WD  plan-2  C12  0.020
 6WD  plan-2  C4   0.020
 6WD  plan-2  C9   0.020
 6WD  plan-2  C10  0.020
 6WD  plan-2  N11  0.020
 6WD  plan-2  N13  0.020
 6WD  plan-2  C14  0.020
 6WD  plan-2  H13  0.020
 6WD  plan-2  H14  0.020
 6WD  plan-2  H4   0.020
 6WD  plan-3  C2   0.020
 6WD  plan-3  S5   0.020
 6WD  plan-3  C6   0.020
 6WD  plan-3  N7   0.020
 6WD  plan-3  N8   0.020
 6WD  plan-3  H11  0.020
 6WD  plan-3  H12  0.020

