# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 21:01:24 2022
#   Inital geometry file: a 65 line input string
#   Ligand name: 6-deoxy-6-sulfo-beta-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1O[C@H](C[S](O)(=O)=O)[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
 YZT  YZT  "6-deoxy-6-sulfo-beta-D-glucopyranose"  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_YZT
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
 YZT  C1    C  CH1    0   0.278  3.3256  -4.0524  -4.1080
 YZT  C2    C  CH1    0   0.007  4.3762  -3.6667  -5.1424
 YZT  C3    C  CH1    0  -0.016  5.7608  -3.8965  -4.5485
 YZT  C4    C  CH1    0   0.016  5.9103  -3.1830  -3.2107
 YZT  C5    C  CH1    0   0.017  4.7602  -3.6164  -2.2903
 YZT  C6    C  CH2    0  -0.677  4.8031  -2.9183  -0.9477
 YZT  O1    O  OH1    0  -0.652  2.0761  -3.7389  -4.5955
 YZT  O1S6  O  OS    -1  -0.762  4.0444  -2.9539   1.5431
 YZT  O2    O  OH1    0  -0.666  4.1701  -4.4431  -6.2933
 YZT  O2S6  O  OS     0  -0.763  3.7191  -5.0037   0.2132
 YZT  O3    O  OH1    0  -0.668  6.7023  -3.4540  -5.4961
 YZT  O3S6  O  OS     0  -0.757  2.2737  -3.0439  -0.1621
 YZT  O4    O  OH1    0  -0.669  7.1720  -3.5356  -2.6918
 YZT  O5    O  O2     0  -0.491  3.5383  -3.3164  -2.9281
 YZT  S6    S  S      0   1.403  3.5978  -3.5323   0.2599
 YZT  H1    H  HCH1   0   0.185  3.4186  -5.1306  -3.8839
 YZT  H1O   H  HOH1   0   0.460  1.4080  -4.1981  -4.0755
 YZT  H2    H  HCH1   0   0.211  4.2614  -2.5914  -5.3564
 YZT  H2O   H  HOH1   0   0.449  4.8914  -4.2643  -6.9058
 YZT  H3    H  HCH1   0   0.211  5.8739  -4.9784  -4.3644
 YZT  H3O   H  HOH1   0   0.452  7.5771  -3.7257  -5.2010
 YZT  H4    H  HCH1   0   0.220  5.8360  -2.0984  -3.3754
 YZT  H4O   H  HOH1   0   0.459  7.4868  -2.8289  -2.1214
 YZT  H5    H  HCH1   0   0.221  4.8483  -4.7016  -2.1253
 YZT  H61   H  HCH2   0   0.266  5.7837  -3.0762  -0.4964
 YZT  H62   H  HCH2   0   0.265  4.6544  -1.8411  -1.0586

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
 YZT  C1    O1   single  1.377  0.020  1.377
 YZT  C1    C2   single  1.524  0.020  1.524
 YZT  C1    O5   single  1.407  0.020  1.407
 YZT  C1    H1   single  0.970  0.020  1.090
 YZT  C2    O2   single  1.404  0.020  1.404
 YZT  C2    C3   single  1.524  0.020  1.524
 YZT  C2    H2   single  0.970  0.020  1.090
 YZT  C3    O3   single  1.407  0.020  1.407
 YZT  C3    C4   single  1.523  0.020  1.523
 YZT  C3    H3   single  0.970  0.020  1.090
 YZT  C4    O4   single  1.409  0.020  1.409
 YZT  C4    C5   single  1.535  0.020  1.535
 YZT  C4    H4   single  0.970  0.020  1.090
 YZT  C5    C6   single  1.514  0.020  1.514
 YZT  C5    H5   single  0.970  0.020  1.090
 YZT  C5    O5   single  1.411  0.020  1.411
 YZT  C6    S6   single  1.813  0.020  1.813
 YZT  C6    H61  single  0.970  0.020  1.090
 YZT  C6    H62  single  0.970  0.020  1.090
 YZT  O1    H1O  single  0.850  0.020  0.980
 YZT  O1S6  S6   deloc   1.477  0.020  1.477
 YZT  O2    H2O  single  0.850  0.020  0.980
 YZT  O2S6  S6   deloc   1.477  0.020  1.477
 YZT  O3    H3O  single  0.850  0.020  0.980
 YZT  O3S6  S6   deloc   1.473  0.020  1.473
 YZT  O4    H4O  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
 YZT  H1    C1  O5    109.12  3.000
 YZT  H1    C1  O1    111.73  3.000
 YZT  O5    C1  O1    108.35  3.000
 YZT  H1    C1  C2    109.06  3.000
 YZT  O5    C1  C2    109.43  3.000
 YZT  O1    C1  C2    109.12  3.000
 YZT  H2    C2  O2    111.41  3.000
 YZT  H2    C2  C3    108.51  3.000
 YZT  O2    C2  C3    111.69  3.000
 YZT  H2    C2  C1    107.87  3.000
 YZT  C3    C2  C1    108.88  3.000
 YZT  O2    C2  C1    108.38  3.000
 YZT  H3    C3  O3    110.62  3.000
 YZT  H3    C3  C4    107.62  3.000
 YZT  O3    C3  C4    112.24  3.000
 YZT  H3    C3  C2    107.82  3.000
 YZT  C4    C3  C2    111.14  3.000
 YZT  O3    C3  C2    107.33  3.000
 YZT  H4    C4  O4    111.25  3.000
 YZT  H4    C4  C5    108.52  3.000
 YZT  O4    C4  C5    112.29  3.000
 YZT  H4    C4  C3    108.89  3.000
 YZT  C5    C4  C3    108.71  3.000
 YZT  O4    C4  C3    107.10  3.000
 YZT  H5    C5  O5    110.28  3.000
 YZT  O5    C5  C6    109.11  3.000
 YZT  H5    C5  C6    108.62  3.000
 YZT  O5    C5  C4    108.53  3.000
 YZT  H5    C5  C4    107.94  3.000
 YZT  C6    C5  C4    112.35  3.000
 YZT  H62   C6  H61   107.88  3.000
 YZT  H62   C6  S6    108.11  3.000
 YZT  H61   C6  S6    105.84  3.000
 YZT  H62   C6  C5    111.13  3.000
 YZT  H61   C6  C5    109.00  3.000
 YZT  S6    C6  C5    114.56  3.000
 YZT  H1O   O1  C1    109.25  3.000
 YZT  H2O   O2  C2    107.99  3.000
 YZT  H3O   O3  C3    108.23  3.000
 YZT  H4O   O4  C4    109.13  3.000
 YZT  C5    O5  C1    113.51  3.000
 YZT  O3S6  S6  O2S6  113.27  3.000
 YZT  O3S6  S6  O1S6  113.01  3.000
 YZT  O2S6  S6  O1S6  113.13  3.000
 YZT  O3S6  S6  C6    107.12  3.000
 YZT  O2S6  S6  C6    105.17  3.000
 YZT  O1S6  S6  C6    104.18  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
 YZT  Var_01  O1S6  S6  C6  C5    166.66  30.0  3
 YZT  Var_02  O2S6  S6  C6  C5     47.43  30.0  3
 YZT  Var_03  O3S6  S6  C6  C5    -73.35  30.0  3
 YZT  Var_04  H61   C6  S6  O1S6   46.55  30.0  2
 YZT  Var_05  H62   C6  S6  O1S6  -68.83  30.0  2
 YZT  Var_06  H61   C6  S6  O2S6  -72.68  30.0  2
 YZT  Var_07  H62   C6  S6  O2S6  171.94  30.0  2
 YZT  Var_08  H61   C6  S6  O3S6  166.53  30.0  2
 YZT  Var_09  H62   C6  S6  O3S6   51.16  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
 YZT  chir_01  C1  O1  C2  O5  negativ
 YZT  chir_02  C2  O2  C1  C3  negativ
 YZT  chir_03  C3  O3  C2  C4  positiv
 YZT  chir_04  C4  O4  C5  C3  positiv
 YZT  chir_05  C5  O5  C4  C6  negativ

