# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 17:11:17 2021
#   Inital geometry file: a 55 line input string
#   Ligand name: (2~{S},3~{R},4~{R},5~{S},6~{S})-2-(hydroxymethyl)-6-sulfanyl-oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1O[C@@H](S)[C@@H](O)[C@H](O)[C@H]1O
#
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
 RVW  RVW  (2~{S},3~{R},4~{R},5~{S},6~{S})-2-(hydroxymethyl)-6-sulfanyl-oxane-3,4,5-triol  ligand  24  12  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RVW
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
 RVW  C4   C  CH1   0   0.024  18.5285  -16.2081  -3.8529
 RVW  C5   C  CH1   0  -0.134  17.7269  -15.0025  -4.3339
 RVW  C6   C  CH2   0  -0.153  16.7793  -16.0478  -7.7087
 RVW  C1   C  CH1   0   0.029  17.6433  -17.4684  -5.8191
 RVW  C2   C  CH1   0  -0.015  17.8757  -17.5043  -4.3144
 RVW  C3   C  CH1   0  -0.016  16.8739  -16.2046  -6.2055
 RVW  O1   O  O2    0  -0.464  17.5316  -15.0522  -5.7069
 RVW  O2   O  OH1   0  -0.671  16.8934  -18.5772  -6.2500
 RVW  O3   O  OH1   0  -0.677  18.6905  -18.6247  -4.0384
 RVW  O4   O  OH1   0  -0.666  18.6451  -16.1370  -2.4548
 RVW  O5   O  OH1   0  -0.669  15.9690  -14.9356  -8.0007
 RVW  S1   S  S2    0  -0.271  16.0949  -14.8290  -3.4727
 RVW  H9   H  HCH1  0   0.241  19.5164  -16.1275  -4.3297
 RVW  H10  H  HCH1  0   0.300  18.2829  -14.0875  -4.1259
 RVW  H11  H  HCH2  0   0.214  16.3667  -16.9723  -8.1258
 RVW  H12  H  HCH2  0   0.199  17.7941  -15.9333  -8.1147
 RVW  H6   H  HCH1  0   0.211  18.6243  -17.4382  -6.3213
 RVW  H7   H  HCH1  0   0.223  16.9015  -17.6063  -3.8161
 RVW  H8   H  HCH1  0   0.231  15.8544  -16.2723  -5.7941
 RVW  H2   H  HOH1  0   0.454  17.3612  -19.3736  -5.9769
 RVW  H3   H  HOH1  0   0.459  18.5231  -18.9166  -3.1379
 RVW  H4   H  HOH1  0   0.461  19.4528  -16.5870  -2.1908
 RVW  H5   H  HOH1  0   0.457  15.9193  -14.8486  -8.9568
 RVW  H1   H  HSH1  0   0.235  16.5774  -14.2462  -2.3721

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
 RVW  O5  C6   single  1.407  0.020  1.407
 RVW  C6  C3   single  1.514  0.020  1.514
 RVW  C3  C1   single  1.529  0.020  1.529
 RVW  C3  O1   single  1.417  0.020  1.417
 RVW  O2  C1   single  1.406  0.020  1.406
 RVW  C1  C2   single  1.523  0.020  1.523
 RVW  O1  C5   single  1.388  0.020  1.388
 RVW  C5  C4   single  1.526  0.020  1.526
 RVW  C5  S1   single  1.853  0.020  1.853
 RVW  C2  O3   single  1.413  0.020  1.413
 RVW  C2  C4   single  1.523  0.020  1.523
 RVW  C4  O4   single  1.405  0.020  1.405
 RVW  C4  H9   single  0.970  0.020  1.090
 RVW  C5  H10  single  0.970  0.020  1.090
 RVW  C6  H11  single  0.970  0.020  1.090
 RVW  C6  H12  single  0.970  0.020  1.090
 RVW  C1  H6   single  0.970  0.020  1.090
 RVW  C2  H7   single  0.970  0.020  1.090
 RVW  C3  H8   single  0.970  0.020  1.090
 RVW  O2  H2   single  0.850  0.020  0.980
 RVW  O3  H3   single  0.850  0.020  0.980
 RVW  O4  H4   single  0.850  0.020  0.980
 RVW  O5  H5   single  0.850  0.020  0.980
 RVW  S1  H1   single  1.200  0.020  1.300

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
 RVW  H9   C4  O4   110.68  3.000
 RVW  H9   C4  C2   108.42  3.000
 RVW  O4   C4  C2   112.35  3.000
 RVW  H9   C4  C5   106.10  3.000
 RVW  O4   C4  C5   108.51  3.000
 RVW  C2   C4  C5   110.60  3.000
 RVW  H10  C5  S1   106.37  3.000
 RVW  H10  C5  O1   106.89  3.000
 RVW  S1   C5  O1   109.83  3.000
 RVW  H10  C5  C4   109.57  3.000
 RVW  S1   C5  C4   112.96  3.000
 RVW  O1   C5  C4   110.95  3.000
 RVW  H12  C6  H11  107.17  3.000
 RVW  H12  C6  O5   111.89  3.000
 RVW  H11  C6  O5   111.80  3.000
 RVW  H12  C6  C3   108.65  3.000
 RVW  H11  C6  C3   108.32  3.000
 RVW  O5   C6  C3   108.90  3.000
 RVW  H6   C1  O2   110.89  3.000
 RVW  H6   C1  C3   108.06  3.000
 RVW  O2   C1  C3   107.82  3.000
 RVW  H6   C1  C2   108.35  3.000
 RVW  O2   C1  C2   111.44  3.000
 RVW  C3   C1  C2   110.24  3.000
 RVW  H7   C2  O3   110.43  3.000
 RVW  H7   C2  C1   108.35  3.000
 RVW  O3   C2  C1   107.44  3.000
 RVW  H7   C2  C4   108.76  3.000
 RVW  O3   C2  C4   111.63  3.000
 RVW  C1   C2  C4   110.17  3.000
 RVW  H8   C3  O1   110.37  3.000
 RVW  H8   C3  C1   108.69  3.000
 RVW  O1   C3  C1   110.46  3.000
 RVW  H8   C3  C6   108.62  3.000
 RVW  O1   C3  C6   107.10  3.000
 RVW  C1   C3  C6   111.58  3.000
 RVW  C3   O1  C5   116.26  3.000
 RVW  H2   O2  C1   107.83  3.000
 RVW  H3   O3  C2   108.87  3.000
 RVW  H4   O4  C4   108.62  3.000
 RVW  H5   O5  C6   107.92  3.000
 RVW  H1   S1  C5    96.06  3.000

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
 RVW  chir_01  C4  C5  C2  O4  positiv
 RVW  chir_02  C5  S1  O1  C4  positiv
 RVW  chir_03  C1  O2  C3  C2  negativ
 RVW  chir_04  C2  O3  C1  C4  positiv
 RVW  chir_05  C3  O1  C1  C6  positiv

