# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 18:43:32 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  27  15  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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   1.667  -3.1563   0.0708  -0.1458
 JHM  C1   C  CH1   0   0.240   2.1079   1.7691   0.2778
 JHM  O1   O  OH1   0  -0.665   2.2765   2.1779  -1.0434
 JHM  C2   C  CH2   0  -0.514   3.2623   0.8561   0.6537
 JHM  C3   C  CH1   0   0.018   3.1704  -0.4821  -0.0703
 JHM  O3   O  OH1   0  -0.675   4.1319  -1.4046   0.3958
 JHM  C4   C  CH1   0   0.028   1.8017  -1.1030   0.1737
 JHM  O4   O  OH1   0  -0.673   1.6036  -2.2685  -0.5864
 JHM  C5   C  CH1   0  -0.015   0.7156  -0.1004  -0.2234
 JHM  O5   O  O2    0  -0.501   0.8753   1.1143   0.4762
 JHM  C6   C  CH2   0  -0.197  -0.6540  -0.6358   0.1264
 JHM  O6   O  OC2   0  -0.573  -1.6133   0.3247  -0.3683
 JHM  O7   O  OS    0  -0.635  -3.4953  -1.2942  -0.4605
 JHM  O8   O  OS    0  -0.711  -3.3160   0.3078   1.4158
 JHM  O9   O  OS    0  -0.621  -3.8004   1.1750  -0.7962
 JHM  H1   H  HCH1  0   0.237   2.0661   2.6279   0.9559
 JHM  H2   H  HCH2  0   0.254   4.2123   1.3492   0.4351
 JHM  H2A  H  HCH2  0   0.245   3.2274   0.6847   1.7328
 JHM  H3   H  HCH1  0   0.217   3.2829  -0.3255  -1.1519
 JHM  HO3  H  HOH1  0   0.457   4.9946  -1.1444   0.0586
 JHM  H4   H  HCH1  0   0.214   1.7061  -1.3086   1.2526
 JHM  HO4  H  HOH1  0   0.456   2.2857  -2.9035  -0.3437
 JHM  H5   H  HCH1  0   0.242   0.7695   0.0583  -1.3093
 JHM  H6   H  HCH2  0   0.275  -0.8205  -1.6023  -0.3474
 JHM  H6A  H  HCH2  0   0.255  -0.7565  -0.7414   1.2100
 JHM  HO8  H  H     0   0.514  -3.4477  -0.5172   1.9120
 JHM  HO1  H  HOH1  0   0.460   1.6235   2.8566  -1.2470

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    double  1.434  0.020  1.434
 JHM  O7  S    double  1.441  0.020  1.441
 JHM  S   O8   single  1.587  0.020  1.587
 JHM  S   O6   single  1.579  0.020  1.579
 JHM  O5  C1   single  1.410  0.020  1.410
 JHM  C2  C1   single  1.519  0.020  1.519
 JHM  C1  O1   single  1.393  0.020  1.393
 JHM  C1  H1   single  0.970  0.020  1.090
 JHM  O1  HO1  single  0.850  0.020  0.980
 JHM  C2  C3   single  1.524  0.020  1.524
 JHM  C2  H2   single  0.970  0.020  1.090
 JHM  C2  H2A  single  0.970  0.020  1.090
 JHM  C4  C3   single  1.523  0.020  1.523
 JHM  O3  C3   single  1.412  0.020  1.412
 JHM  C3  H3   single  0.970  0.020  1.090
 JHM  O3  HO3  single  0.850  0.020  0.980
 JHM  C4  C5   single  1.531  0.020  1.531
 JHM  C4  O4   single  1.405  0.020  1.405
 JHM  C4  H4   single  0.970  0.020  1.090
 JHM  O4  HO4  single  0.850  0.020  0.980
 JHM  C6  C5   single  1.512  0.020  1.512
 JHM  O5  C5   single  1.411  0.020  1.411
 JHM  C5  H5   single  0.970  0.020  1.090
 JHM  O6  C6   single  1.445  0.020  1.445
 JHM  C6  H6   single  0.970  0.020  1.090
 JHM  C6  H6A  single  0.970  0.020  1.090
 JHM  O8  HO8  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
 JHM  O9   S   O8  106.62  3.000
 JHM  O8   S   O7  109.42  3.000
 JHM  O9   S   O7  121.63  3.000
 JHM  O8   S   O6  102.29  3.000
 JHM  O7   S   O6  110.57  3.000
 JHM  O9   S   O6  104.54  3.000
 JHM  H1   C1  O5  104.11  3.000
 JHM  H1   C1  C2  110.31  3.000
 JHM  O5   C1  C2  110.51  3.000
 JHM  H1   C1  O1  111.21  3.000
 JHM  C2   C1  O1  108.61  3.000
 JHM  O5   C1  O1  112.06  3.000
 JHM  HO1  O1  C1  108.97  3.000
 JHM  H2A  C2  H2  107.22  3.000
 JHM  H2A  C2  C3  109.23  3.000
 JHM  H2   C2  C3  110.71  3.000
 JHM  H2A  C2  C1  108.32  3.000
 JHM  H2   C2  C1  109.88  3.000
 JHM  C3   C2  C1  111.37  3.000
 JHM  H3   C3  C4  107.94  3.000
 JHM  H3   C3  O3  110.39  3.000
 JHM  C4   C3  O3  107.03  3.000
 JHM  H3   C3  C2  109.65  3.000
 JHM  O3   C3  C2  112.08  3.000
 JHM  C4   C3  C2  109.64  3.000
 JHM  HO3  O3  C3  108.56  3.000
 JHM  H4   C4  C5  108.33  3.000
 JHM  H4   C4  O4  111.25  3.000
 JHM  C5   C4  O4  107.63  3.000
 JHM  H4   C4  C3  108.11  3.000
 JHM  O4   C4  C3  112.22  3.000
 JHM  C5   C4  C3  109.22  3.000
 JHM  HO4  O4  C4  108.10  3.000
 JHM  H5   C5  C6  108.93  3.000
 JHM  H5   C5  O5  111.11  3.000
 JHM  C6   C5  O5  107.03  3.000
 JHM  H5   C5  C4  108.43  3.000
 JHM  O5   C5  C4  110.80  3.000
 JHM  C6   C5  C4  110.54  3.000
 JHM  C5   O5  C1  115.41  3.000
 JHM  H6A  C6  H6  109.33  3.000
 JHM  H6A  C6  O6  109.95  3.000
 JHM  H6   C6  O6  109.84  3.000
 JHM  H6A  C6  C5  110.39  3.000
 JHM  H6   C6  C5  110.62  3.000
 JHM  O6   C6  C5  106.67  3.000
 JHM  C6   O6  S   119.57  3.000
 JHM  HO8  O8  S   112.91  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   -179.20  30.0  3
 JHM  Var_02  O9  S   O6  C6  -177.91  30.0  2

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

