# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 19:22:52 2021
#   Inital geometry file: a 56 line input string
#   Ligand name: (5~{R})-3,4,4-trimethyl-5-(oxidanylamino)-1,3-thiazolidine-2-thione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=S)S[C@@H](NO)C1(C)C
#
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
 S5G  S5G  (5~{R})-3,4,4-trimethyl-5-(oxidanylamino)-1,3-thiazolidine-2-thione  ligand  23  11  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_S5G
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
 S5G  C10  C  CH3   0  -0.664  -17.6778  94.4612  139.1821
 S5G  C01  C  CH3   0  -0.532  -16.0426  93.5845  136.6365
 S5G  C03  C  CR5   0   0.041  -14.5916  94.0013  138.5190
 S5G  C06  C  CR15  0  -0.218  -16.0329  92.8688  140.3211
 S5G  C09  C  CR5   0   0.093  -16.7980  93.2201  139.0314
 S5G  C11  C  CH3   0  -0.674  -17.6379  92.0148  138.6293
 S5G  N02  N  NR5   0  -0.372  -15.7345  93.5079  138.0498
 S5G  N07  N  NH1   0  -0.343  -16.8221  93.0570  141.4883
 S5G  O08  O  OH1   0  -0.570  -16.0574  92.7278  142.6142
 S5G  S04  S  S1    0  -0.344  -13.3591  94.6634  137.6271
 S5G  S05  S  S2    0   0.094  -14.4925  93.8955  140.2561
 S5G  H1   H  HCH3  0   0.253  -18.5120  94.2669  139.8558
 S5G  H2   H  HCH3  0   0.248  -17.1166  95.3184  139.5582
 S5G  H3   H  HCH3  0   0.264  -18.1025  94.7355  138.2164
 S5G  H4   H  HCH3  0   0.266  -16.8788  92.9313  136.4086
 S5G  H5   H  HCH3  0   0.256  -16.2928  94.6028  136.3353
 S5G  H6   H  HCH3  0   0.267  -15.1822  93.2581  136.0576
 S5G  H7   H  HCR5  0   0.317  -15.7106  91.8266  140.2825
 S5G  H8   H  HCH3  0   0.260  -18.2471  91.7123  139.4806
 S5G  H9   H  HCH3  0   0.253  -18.3181  92.2414  137.8086
 S5G  H10  H  HCH3  0   0.254  -17.0114  91.1698  138.3420
 S5G  H11  H  HNH1  0   0.381  -17.0710  94.0333  141.6069
 S5G  H12  H  HOH1  0   0.472  -16.5159  91.9759  143.0046

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
 S5G  C01  N02  single  1.449  0.020  1.449
 S5G  S04  C03  double  1.659  0.020  1.659
 S5G  N02  C03  single  1.330  0.020  1.330
 S5G  N02  C09  single  1.476  0.020  1.476
 S5G  C03  S05  single  1.743  0.020  1.743
 S5G  C11  C09  single  1.523  0.020  1.523
 S5G  C09  C10  single  1.529  0.020  1.529
 S5G  C09  C06  single  1.540  0.020  1.540
 S5G  S05  C06  single  1.852  0.020  1.852
 S5G  C06  N07  single  1.421  0.020  1.421
 S5G  N07  O08  single  1.400  0.020  1.400
 S5G  C10  H1   single  0.970  0.020  1.090
 S5G  C10  H2   single  0.970  0.020  1.090
 S5G  C10  H3   single  0.970  0.020  1.090
 S5G  C01  H4   single  0.970  0.020  1.090
 S5G  C01  H5   single  0.970  0.020  1.090
 S5G  C01  H6   single  0.970  0.020  1.090
 S5G  C06  H7   single  0.970  0.020  1.090
 S5G  C11  H8   single  0.970  0.020  1.090
 S5G  C11  H9   single  0.970  0.020  1.090
 S5G  C11  H10  single  0.970  0.020  1.090
 S5G  N07  H11  single  0.890  0.020  1.040
 S5G  O08  H12  single  0.850  0.020  0.980

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
 S5G  H3   C10  H2   107.94  3.000
 S5G  H3   C10  H1   107.11  3.000
 S5G  H2   C10  H1   108.69  3.000
 S5G  H3   C10  C09  109.95  3.000
 S5G  H2   C10  C09  112.07  3.000
 S5G  H1   C10  C09  110.90  3.000
 S5G  H6   C01  H5   108.35  3.000
 S5G  H6   C01  H4   108.50  3.000
 S5G  H5   C01  H4   109.10  3.000
 S5G  H6   C01  N02  109.59  3.000
 S5G  H5   C01  N02  111.56  3.000
 S5G  H4   C01  N02  109.69  3.000
 S5G  S05  C03  S04  121.18  3.000
 S5G  S05  C03  N02  112.19  3.000
 S5G  S04  C03  N02  126.63  3.000
 S5G  H7   C06  S05  106.41  3.000
 S5G  H7   C06  N07  108.62  3.000
 S5G  S05  C06  N07  114.66  3.000
 S5G  H7   C06  C09  109.56  3.000
 S5G  N07  C06  C09  112.43  3.000
 S5G  S05  C06  C09  104.91  3.000
 S5G  N02  C09  C11  112.10  3.000
 S5G  C11  C09  C06  108.34  3.000
 S5G  N02  C09  C06  104.09  3.000
 S5G  C06  C09  C10  112.86  3.000
 S5G  C11  C09  C10  110.56  3.000
 S5G  N02  C09  C10  108.78  3.000
 S5G  H10  C11  H9   108.75  3.000
 S5G  H10  C11  H8   108.17  3.000
 S5G  H9   C11  H8   107.29  3.000
 S5G  H10  C11  C09  111.47  3.000
 S5G  H9   C11  C09  112.24  3.000
 S5G  H8   C11  C09  108.76  3.000
 S5G  C09  N02  C03  117.19  3.000
 S5G  C09  N02  C01  120.41  3.000
 S5G  C03  N02  C01  120.48  3.000
 S5G  H11  N07  O08  105.44  3.000
 S5G  H11  N07  C06  111.08  3.000
 S5G  O08  N07  C06  109.02  3.000
 S5G  H12  O08  N07  104.45  3.000
 S5G  C06  S05  C03   91.22  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
 S5G  Var_01  C06  C09  N02  C03  -29.78  30.0  1
 S5G  Var_02  N02  C03  S05  C06    8.43  30.0  1
 S5G  Var_03  S05  C03  N02  C09   11.73  30.0  1
 S5G  Var_04  H4   C01  N02  C03  166.29  30.0  3
 S5G  Var_05  H8   C11  C09  C06   52.99  30.0  3
 S5G  Var_06  H1   C10  C09  C06  -68.42  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
 S5G  chir_01  C06  C09  S05  N07  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
 S5G  plan-1  C01  0.020
 S5G  plan-1  C03  0.020
 S5G  plan-1  C09  0.020
 S5G  plan-1  N02  0.020
 S5G  plan-2  C03  0.020
 S5G  plan-2  N02  0.020
 S5G  plan-2  S04  0.020
 S5G  plan-2  S05  0.020

