# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 18:45:00 2021
#   Inital geometry file: a 76 line input string
#   Ligand name: (3~{R},4~{R})-1,1-bis(oxidanylidene)-4-(pyridin-3-ylmethylamino)thiolan-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1C[S](=O)(=O)C[C@@H]1NCc2cccnc2
#
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
 S0S  S0S  (3~{R},4~{R})-1,1-bis(oxidanylidene)-4-(pyridin-3-ylmethylamino)thiolan-3-ol  ligand  30  16  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_S0S
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
 S0S  N1   N  N     0  -0.402  12.1101  22.4991  -3.2461
 S0S  C4   C  CR16  0  -0.096  11.9618  22.0032  -2.0251
 S0S  C5   C  CR16  0  -0.073  12.9307  23.5335  -3.3985
 S0S  C7   C  CR15  0  -0.087  10.9587  23.7572   1.3105
 S0S  C8   C  CH2   0  -0.646   9.4749  24.0674   1.5072
 S0S  C10  C  CR15  0   0.070  11.6528  24.2623   2.5805
 S0S  C1   C  CR16  0  -0.320  13.6307  24.1051  -2.3477
 S0S  C2   C  CR16  0  -0.180  13.4662  23.5740  -1.0769
 S0S  C3   C  CR6   0  -0.003  12.6118  22.4930  -0.8949
 S0S  C9   C  CH2   0  -0.656  11.1583  25.6998   2.7862
 S0S  N2   N  NH1   0  -0.599  11.1178  22.3328   1.1038
 S0S  O3   O  OH1   0  -0.645  13.0422  24.2091   2.4329
 S0S  S1   S  S     0   1.230   9.4037  25.6384   2.3960
 S0S  H1   H  HCR6  0   0.258  11.2897  21.1543  -1.9309
 S0S  H2   H  HCR6  0   0.263  13.0387  23.9236  -4.4045
 S0S  H3   H  HCH2  0   0.259  12.2798  20.8043   0.3683
 S0S  H4   H  HCH2  0   0.257  13.1933  22.0900   1.1217
 S0S  H5   H  HCR5  0   0.251  11.3266  24.3602   0.4650
 S0S  H7   H  HCH2  0   0.310   9.0037  23.3117   2.1379
 S0S  H8   H  HCR5  0   0.237  11.3128  23.6398   3.4182
 S0S  H9   H  HCR6  0   0.270  14.2871  24.9469  -2.5215
 S0S  H10  H  HCR6  0   0.270  13.9973  23.9958  -0.2324
 S0S  H11  H  HCH2  0   0.309  11.6379  26.3766   2.0778
 S0S  H12  H  HCH2  0   0.324  11.2876  26.0759   3.8006
 S0S  H13  H  HNH1  0   0.363  10.3322  21.9783   0.5731
 S0S  H15  H  HOH1  0   0.464  13.4510  24.3000   3.2993
 S0S  C6   C  CH2   0  -0.390  12.3509  21.8897   0.4623
 S0S  H6   H  HCH2  0   0.327   8.9214  24.1602   0.5738
 S0S  O1   O  OS    0  -0.683   8.6254  25.4690   3.6216
 S0S  O2   O  OS    0  -0.679   9.0394  26.7220   1.4867

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
 S0S  C5   N1   aromatic  1.329  0.020  1.329
 S0S  C5   C1   aromatic  1.386  0.020  1.386
 S0S  N1   C4   aromatic  1.326  0.020  1.326
 S0S  C1   C2   aromatic  1.387  0.020  1.387
 S0S  C4   C3   aromatic  1.393  0.020  1.393
 S0S  C2   C3   aromatic  1.390  0.020  1.390
 S0S  C3   C6   single    1.508  0.020  1.508
 S0S  C6   N2   single    1.459  0.020  1.459
 S0S  N2   C7   single    1.448  0.020  1.448
 S0S  C7   C8   single    1.529  0.020  1.529
 S0S  C7   C10  single    1.533  0.020  1.533
 S0S  C8   S1   single    1.806  0.020  1.806
 S0S  O2   S1   double    1.461  0.020  1.461
 S0S  S1   C9   single    1.799  0.020  1.799
 S0S  S1   O1   double    1.462  0.020  1.462
 S0S  C10  C9   single    1.534  0.020  1.534
 S0S  C10  O3   single    1.398  0.020  1.398
 S0S  C4   H1   single    0.930  0.020  1.080
 S0S  C5   H2   single    0.930  0.020  1.080
 S0S  C6   H3   single    0.970  0.020  1.090
 S0S  C6   H4   single    0.970  0.020  1.090
 S0S  C7   H5   single    0.970  0.020  1.090
 S0S  C8   H6   single    0.970  0.020  1.090
 S0S  C8   H7   single    0.970  0.020  1.090
 S0S  C10  H8   single    0.970  0.020  1.090
 S0S  C1   H9   single    0.930  0.020  1.080
 S0S  C2   H10  single    0.930  0.020  1.080
 S0S  C9   H11  single    0.970  0.020  1.090
 S0S  C9   H12  single    0.970  0.020  1.090
 S0S  N2   H13  single    0.890  0.020  1.040
 S0S  O3   H15  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
 S0S  C5   N1   C4   117.75  3.000
 S0S  H1   C4   C3   119.54  3.000
 S0S  H1   C4   N1   116.17  3.000
 S0S  C3   C4   N1   124.29  3.000
 S0S  H2   C5   C1   120.31  3.000
 S0S  H2   C5   N1   116.61  3.000
 S0S  C1   C5   N1   123.08  3.000
 S0S  H5   C7   N2   113.09  3.000
 S0S  H5   C7   C10  107.71  3.000
 S0S  N2   C7   C10  113.12  3.000
 S0S  H5   C7   C8   108.17  3.000
 S0S  C10  C7   C8   105.43  3.000
 S0S  N2   C7   C8   108.94  3.000
 S0S  H7   C8   H6   109.57  3.000
 S0S  H7   C8   S1   107.51  3.000
 S0S  H6   C8   S1   109.12  3.000
 S0S  H7   C8   C7   110.67  3.000
 S0S  H6   C8   C7   113.60  3.000
 S0S  S1   C8   C7   106.14  3.000
 S0S  H8   C10  O3   111.52  3.000
 S0S  H8   C10  C9   109.23  3.000
 S0S  O3   C10  C9   111.72  3.000
 S0S  H8   C10  C7   107.76  3.000
 S0S  O3   C10  C7   110.48  3.000
 S0S  C9   C10  C7   105.90  3.000
 S0S  H9   C1   C2   121.15  3.000
 S0S  H9   C1   C5   120.38  3.000
 S0S  C2   C1   C5   118.48  3.000
 S0S  H10  C2   C3   120.15  3.000
 S0S  H10  C2   C1   120.47  3.000
 S0S  C3   C2   C1   119.38  3.000
 S0S  C2   C3   C6   122.37  3.000
 S0S  C6   C3   C4   120.59  3.000
 S0S  C2   C3   C4   117.02  3.000
 S0S  H12  C9   H11  109.77  3.000
 S0S  H12  C9   S1   109.24  3.000
 S0S  H11  C9   S1   108.01  3.000
 S0S  H12  C9   C10  114.21  3.000
 S0S  H11  C9   C10  110.64  3.000
 S0S  S1   C9   C10  104.68  3.000
 S0S  H13  N2   C7   109.52  3.000
 S0S  H13  N2   C6   108.60  3.000
 S0S  C7   N2   C6   117.02  3.000
 S0S  H15  O3   C10  108.88  3.000
 S0S  O2   S1   O1   118.37  3.000
 S0S  O1   S1   C9   109.97  3.000
 S0S  O2   S1   C9   110.67  3.000
 S0S  O1   S1   C8   109.43  3.000
 S0S  C9   S1   C8    95.62  3.000
 S0S  O2   S1   C8   110.40  3.000
 S0S  H4   C6   H3   106.59  3.000
 S0S  H4   C6   N2   109.38  3.000
 S0S  H3   C6   N2   106.54  3.000
 S0S  H4   C6   C3   109.74  3.000
 S0S  H3   C6   C3   109.36  3.000
 S0S  N2   C6   C3   114.86  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
 S0S  CONST_01  C2   C1  C5  N1    0.00   0.0  0
 S0S  CONST_02  C2   C3  C4  N1    0.00   0.0  0
 S0S  CONST_03  C1   C5  N1  C4    0.00   0.0  0
 S0S  CONST_04  C1   C2  C3  C4    0.00   0.0  0
 S0S  CONST_05  C3   C4  N1  C5    0.00   0.0  0
 S0S  CONST_06  C3   C2  C1  C5    0.00   0.0  0
 S0S  CONST_07  C6   C3  C4  N1  180.00   0.0  0
 S0S  CONST_08  C1   C2  C3  C6  180.00   0.0  0
 S0S  CONST_09  H9   C1  C5  N1  180.00   0.0  0
 S0S  CONST_10  H2   C5  N1  C4  180.00   0.0  0
 S0S  CONST_11  H10  C2  C3  C4  180.00   0.0  0
 S0S  CONST_12  H1   C4  N1  C5  180.00   0.0  0
 S0S  Var_01    C9   S1  C8  C7  -10.67  30.0  1
 S0S  Var_02    C10  C9  S1  C8  -17.44  30.0  1
 S0S  Var_03    N2   C6  C3  C4  -79.32  30.0  2
 S0S  Var_04    C3   C6  N2  C7  -57.26  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
 S0S  chir_01  C7   N2  C8  C10  negativ
 S0S  chir_02  C10  O3  C7  C9   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
 S0S  plan-1  N1   0.020
 S0S  plan-1  C4   0.020
 S0S  plan-1  C5   0.020
 S0S  plan-1  C1   0.020
 S0S  plan-1  C2   0.020
 S0S  plan-1  C3   0.020
 S0S  plan-1  H1   0.020
 S0S  plan-1  H2   0.020
 S0S  plan-1  H9   0.020
 S0S  plan-1  H10  0.020
 S0S  plan-1  C6   0.020

