# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 23:03:33 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: 6-deoxy-3-O-sulfo-alpha-L-mannopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1O[C@@H](O)[C@H](O)[C@H](O[S](O)(=O)=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
 83Y  83Y  6-deoxy-3-O-sulfo-alpha-L-mannopyranose  L-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_83Y
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
 83Y  C1   C  CH1   0   0.218  -2.0162   1.5681   0.2581
 83Y  C2   C  CH1   0  -0.006  -0.6421   1.3528  -0.3853
 83Y  C3   C  CH1   0  -0.038  -0.1148  -0.0066   0.0450
 83Y  C4   C  CH1   0   0.037  -1.0952  -1.1155  -0.2930
 83Y  C5   C  CH1   0   0.008  -2.4578  -0.7728   0.3343
 83Y  C6   C  CH3   0  -0.697  -3.5349  -1.7522  -0.0829
 83Y  O1   O  OH1   0  -0.666  -1.8161   1.7128   1.6275
 83Y  O1S  O  OS    0  -0.620   3.4839  -0.1339  -1.0334
 83Y  O2   O  OH1   0  -0.665  -0.7448   1.3486  -1.7836
 83Y  O2S  O  OS    0  -0.634   2.4762   1.1514   0.8484
 83Y  O3   O  OC2   0  -0.580   1.1179  -0.2895  -0.6651
 83Y  O3S  O  OS    0  -0.703   2.5515  -1.3220   0.9392
 83Y  O5   O  O2    0  -0.497  -2.8860   0.5218  -0.0640
 83Y  S    S  S     0   1.647   2.5092  -0.0279   0.0179
 83Y  O4   O  OH1   0  -0.662  -0.5934  -2.3157   0.2333
 83Y  H1   H  HCH1  0   0.243  -2.4810   2.4634  -0.1739
 83Y  H2   H  HCH1  0   0.252   0.0355   2.1396  -0.0326
 83Y  H3   H  HCH1  0   0.288   0.0635  -0.0069   1.1243
 83Y  H4   H  HCH1  0   0.238  -1.2143  -1.1733  -1.3824
 83Y  H5   H  HCH1  0   0.223  -2.3428  -0.8177   1.4253
 83Y  H63  H  HCH3  0   0.236  -3.2913  -2.7591   0.2535
 83Y  H62  H  HCH3  0   0.247  -4.4918  -1.4833   0.3647
 83Y  H61  H  HCH3  0   0.230  -3.6550  -1.7726  -1.1678
 83Y  H6   H  HOH1  0   0.465  -2.6387   1.9984   2.0398
 83Y  HO2  H  HOH1  0   0.462  -0.9179   2.2468  -2.0823
 83Y  H7   H  HOH1  0   0.462  -0.9105  -3.0460  -0.3048
 83Y  H8   H  H     0   0.511   3.3027  -1.2977   1.5570

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
 83Y  O2S  S    double  1.443  0.020  1.443
 83Y  O1S  S    double  1.438  0.020  1.438
 83Y  S    O3S  single  1.589  0.020  1.589
 83Y  S    O3   single  1.572  0.020  1.572
 83Y  O3   C3   single  1.451  0.020  1.451
 83Y  C3   C2   single  1.520  0.020  1.520
 83Y  C3   C4   single  1.518  0.020  1.518
 83Y  C2   O2   single  1.402  0.020  1.402
 83Y  C2   C1   single  1.532  0.020  1.532
 83Y  O1   C1   single  1.392  0.020  1.392
 83Y  C1   O5   single  1.398  0.020  1.398
 83Y  O4   C4   single  1.403  0.020  1.403
 83Y  C4   C5   single  1.539  0.020  1.539
 83Y  C5   O5   single  1.421  0.020  1.421
 83Y  C5   C6   single  1.514  0.020  1.514
 83Y  C1   H1   single  0.970  0.020  1.090
 83Y  C2   H2   single  0.970  0.020  1.090
 83Y  C3   H3   single  0.970  0.020  1.090
 83Y  C4   H4   single  0.970  0.020  1.090
 83Y  C5   H5   single  0.970  0.020  1.090
 83Y  C6   H63  single  0.970  0.020  1.090
 83Y  C6   H62  single  0.970  0.020  1.090
 83Y  C6   H61  single  0.970  0.020  1.090
 83Y  O1   H6   single  0.850  0.020  0.980
 83Y  O2   HO2  single  0.850  0.020  0.980
 83Y  O4   H7   single  0.850  0.020  0.980
 83Y  O3S  H8   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
 83Y  H1   C1   O5   104.85  3.000
 83Y  H1   C1   O1   111.32  3.000
 83Y  O5   C1   O1   113.20  3.000
 83Y  H1   C1   C2   109.22  3.000
 83Y  O5   C1   C2   110.85  3.000
 83Y  O1   C1   C2   107.39  3.000
 83Y  H2   C2   O2   111.60  3.000
 83Y  H2   C2   C3   109.64  3.000
 83Y  O2   C2   C3   107.76  3.000
 83Y  H2   C2   C1   108.55  3.000
 83Y  O2   C2   C1   110.70  3.000
 83Y  C3   C2   C1   108.53  3.000
 83Y  H3   C3   O3   110.14  3.000
 83Y  H3   C3   C4   108.95  3.000
 83Y  O3   C3   C4   107.30  3.000
 83Y  H3   C3   C2   109.64  3.000
 83Y  C4   C3   C2   111.48  3.000
 83Y  O3   C3   C2   109.31  3.000
 83Y  H4   C4   O4   111.47  3.000
 83Y  H4   C4   C5   108.68  3.000
 83Y  O4   C4   C5   110.75  3.000
 83Y  H4   C4   C3   109.24  3.000
 83Y  C5   C4   C3   108.56  3.000
 83Y  O4   C4   C3   108.08  3.000
 83Y  H5   C5   O5   110.33  3.000
 83Y  H5   C5   C6   108.77  3.000
 83Y  O5   C5   C6   107.32  3.000
 83Y  H5   C5   C4   107.66  3.000
 83Y  C6   C5   C4   111.93  3.000
 83Y  O5   C5   C4   110.83  3.000
 83Y  H61  C6   H62  108.43  3.000
 83Y  H61  C6   H63  108.32  3.000
 83Y  H62  C6   H63  107.31  3.000
 83Y  H61  C6   C5   111.35  3.000
 83Y  H62  C6   C5   110.59  3.000
 83Y  H63  C6   C5   110.71  3.000
 83Y  H6   O1   C1   109.22  3.000
 83Y  HO2  O2   C2   108.66  3.000
 83Y  S    O3   C3   120.47  3.000
 83Y  H8   O3S  S    111.61  3.000
 83Y  C5   O5   C1   115.46  3.000
 83Y  O3S  S    O3    98.05  3.000
 83Y  O3   S    O2S  111.47  3.000
 83Y  O3S  S    O2S  109.42  3.000
 83Y  O3   S    O1S  105.67  3.000
 83Y  O3S  S    O1S  110.24  3.000
 83Y  O2S  S    O1S  119.79  3.000
 83Y  H7   O4   C4   108.78  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
 83Y  Var_01  O2S  S  O3  C3  -36.33  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
 83Y  chir_01  C1  C2  O1  O5  positiv
 83Y  chir_02  C2  O2  C1  C3  negativ
 83Y  chir_03  C3  O3  C4  C2  positiv
 83Y  chir_04  C4  O4  C3  C5  positiv
 83Y  chir_05  C5  O5  C4  C6  positiv

