# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 18:45:21 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: 2-deoxy-6-O-sulfo-alpha-D-arabino-hexopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1C[C@@H](O)[C@H](O)[C@@H](CO[S](O)(=O)=O)O1
#
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
 JHM  JHM  2-deoxy-6-O-sulfo-alpha-D-arabino-hexopyranose  D-saccharide  26  15  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JHM
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
 JHM  S    S  S      0   1.577  -3.1237   0.0650   0.0107
 JHM  C1   C  CH1    0   0.242   2.1572   1.7633   0.2634
 JHM  O1   O  OH1    0  -0.668   2.3491   2.1887  -1.0513
 JHM  C2   C  CH2    0  -0.513   3.3102   0.8521   0.6481
 JHM  C3   C  CH1    0   0.017   3.2311  -0.4791  -0.0883
 JHM  O3   O  OH1    0  -0.676   4.1906  -1.4036   0.3810
 JHM  C4   C  CH1    0   0.032   1.8606  -1.1048   0.1297
 JHM  O4   O  OH1    0  -0.675   1.6865  -2.2688  -0.6404
 JHM  C5   C  CH1    0  -0.018   0.7719  -0.1077  -0.2736
 JHM  O5   O  O2     0  -0.501   0.9259   1.1063   0.4354
 JHM  C6   C  CH2    0  -0.165  -0.6069  -0.6409   0.0544
 JHM  O6   O  OC2    0  -0.616  -1.5624   0.2845  -0.4440
 JHM  O7   O  OS     0  -0.747  -3.4844  -1.2812  -0.4423
 JHM  O8   O  OS    -1  -0.746  -3.1372   0.2160   1.4679
 JHM  O9   O  OS     0  -0.736  -3.7743   1.1513  -0.7181
 JHM  H1   H  HCH1   0   0.232   2.1047   2.6162   0.9488
 JHM  H2A  H  HCH2   0   0.243   3.2603   0.6714   1.7252
 JHM  H3   H  HCH1   0   0.214   3.3582  -0.3119  -1.1668
 JHM  HO3  H  HOH1   0   0.456   5.0560  -1.1386   0.0545
 JHM  H4   H  HCH1   0   0.206   1.7498  -1.3201   1.2058
 JHM  HO4  H  HOH1   0   0.453   2.3863  -2.8872  -0.4058
 JHM  H5   H  HCH1   0   0.226   0.8434   0.0619  -1.3573
 JHM  H6   H  HCH2   0   0.234  -0.7437  -1.6215  -0.4069
 JHM  H6A  H  HCH2   0   0.218  -0.7012  -0.7581   1.1398
 JHM  HO1  H  HOH1   0   0.458   1.6864   2.8557  -1.2623
 JHM  H2   H  HCH2   0   0.251   4.2622   1.3499   0.4484

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
 JHM  O9  S    deloc   1.461  0.020  1.461
 JHM  O7  S    deloc   1.466  0.020  1.466
 JHM  S   O8   deloc   1.465  0.020  1.465
 JHM  S   O6   single  1.641  0.020  1.641
 JHM  O5  C1   single  1.406  0.020  1.406
 JHM  C2  C1   single  1.519  0.020  1.519
 JHM  C1  O1   single  1.395  0.020  1.395
 JHM  C1  H1   single  0.970  0.020  1.090
 JHM  O1  HO1  single  0.850  0.020  0.980
 JHM  C2  C3   single  1.523  0.020  1.523
 JHM  C2  H2   single  0.970  0.020  1.090
 JHM  C2  H2A  single  0.970  0.020  1.090
 JHM  C4  C3   single  1.522  0.020  1.522
 JHM  O3  C3   single  1.413  0.020  1.413
 JHM  C3  H3   single  0.970  0.020  1.090
 JHM  O3  HO3  single  0.850  0.020  0.980
 JHM  C4  C5   single  1.530  0.020  1.530
 JHM  C4  O4   single  1.407  0.020  1.407
 JHM  C4  H4   single  0.970  0.020  1.090
 JHM  O4  HO4  single  0.850  0.020  0.980
 JHM  C6  C5   single  1.514  0.020  1.514
 JHM  O5  C5   single  1.414  0.020  1.414
 JHM  C5  H5   single  0.970  0.020  1.090
 JHM  O6  C6   single  1.421  0.020  1.421
 JHM  C6  H6   single  0.970  0.020  1.090
 JHM  C6  H6A  single  0.970  0.020  1.090

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
 JHM  O9   S   O8  114.55  3.000
 JHM  O8   S   O7  113.57  3.000
 JHM  O9   S   O7  114.78  3.000
 JHM  O8   S   O6  105.70  3.000
 JHM  O7   S   O6  105.75  3.000
 JHM  O9   S   O6  100.72  3.000
 JHM  H1   C1  O5  104.19  3.000
 JHM  H1   C1  C2  110.18  3.000
 JHM  O5   C1  C2  110.70  3.000
 JHM  H1   C1  O1  111.02  3.000
 JHM  C2   C1  O1  108.50  3.000
 JHM  O5   C1  O1  112.22  3.000
 JHM  HO1  O1  C1  108.83  3.000
 JHM  H2A  C2  H2  107.17  3.000
 JHM  H2A  C2  C3  109.23  3.000
 JHM  H2   C2  C3  110.79  3.000
 JHM  H2A  C2  C1  108.30  3.000
 JHM  H2   C2  C1  109.98  3.000
 JHM  C3   C2  C1  111.24  3.000
 JHM  H3   C3  C4  107.90  3.000
 JHM  H3   C3  O3  110.32  3.000
 JHM  C4   C3  O3  107.16  3.000
 JHM  H3   C3  C2  109.60  3.000
 JHM  O3   C3  C2  112.08  3.000
 JHM  C4   C3  C2  109.67  3.000
 JHM  HO3  O3  C3  108.54  3.000
 JHM  H4   C4  C5  108.23  3.000
 JHM  H4   C4  O4  111.11  3.000
 JHM  C5   C4  O4  107.87  3.000
 JHM  H4   C4  C3  108.09  3.000
 JHM  O4   C4  C3  111.91  3.000
 JHM  C5   C4  C3  109.57  3.000
 JHM  HO4  O4  C4  107.95  3.000
 JHM  H5   C5  C6  109.10  3.000
 JHM  H5   C5  O5  110.77  3.000
 JHM  C6   C5  O5  107.03  3.000
 JHM  H5   C5  C4  108.30  3.000
 JHM  O5   C5  C4  110.46  3.000
 JHM  C6   C5  C4  111.18  3.000
 JHM  C5   O5  C1  115.79  3.000
 JHM  H6A  C6  H6  108.15  3.000
 JHM  H6A  C6  O6  111.05  3.000
 JHM  H6   C6  O6  110.64  3.000
 JHM  H6A  C6  C5  109.31  3.000
 JHM  H6   C6  C5  109.80  3.000
 JHM  O6   C6  C5  107.88  3.000
 JHM  C6   O6  S   117.11  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
 JHM  Var_01  C5  C6  O6  S   -169.73  30.0  3
 JHM  Var_02  O9  S   O6  C6  -178.24  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
 JHM  chir_01  C1  O5  C2  O1  negativ
 JHM  chir_02  C3  O3  C2  C4  positiv
 JHM  chir_03  C4  O4  C3  C5  negativ
 JHM  chir_04  C5  O5  C4  C6  negativ

