# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 17:55:45 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  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_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  -1.9617   1.5826   0.2293
 83Y  C2   C  CH1    0  -0.009  -0.6000   1.3558  -0.4308
 83Y  C3   C  CH1    0   0.001  -0.0645  -0.0163  -0.0384
 83Y  C4   C  CH1    0   0.030  -1.0800  -1.1010  -0.3675
 83Y  C5   C  CH1    0   0.012  -2.4265  -0.7543   0.2872
 83Y  C6   C  CH3    0  -0.698  -3.5270  -1.7146  -0.1156
 83Y  O1   O  OH1    0  -0.668  -1.7491   1.7198   1.5995
 83Y  O1S  O  OS     0  -0.737   3.5067  -0.3993  -1.0182
 83Y  O2   O  OH1    0  -0.671  -0.7275   1.3866  -1.8307
 83Y  O2S  O  OS     0  -0.741   2.5779   1.2720   0.5387
 83Y  O3   O  OC2    0  -0.621   1.1378  -0.2926  -0.7419
 83Y  O3S  O  OS    -1  -0.740   2.5460  -1.1034   1.1358
 83Y  O5   O  O2     0  -0.501  -2.8510   0.5496  -0.0862
 83Y  S    S  S      0   1.565   2.5599  -0.1132   0.0574
 83Y  O4   O  OH1    0  -0.666  -0.5922  -2.3235   0.1286
 83Y  H1   H  HCH1   0   0.233  -2.4263   2.4857  -0.1885
 83Y  H2   H  HCH1   0   0.238   0.0947   2.1269  -0.0771
 83Y  H3   H  HCH1   0   0.245   0.1032  -0.0287   1.0448
 83Y  H4   H  HCH1   0   0.220  -1.2189  -1.1440  -1.4562
 83Y  H5   H  HCH1   0   0.214  -2.2912  -0.8112   1.3758
 83Y  H63  H  HCH3   0   0.232  -3.2980  -2.7272   0.2151
 83Y  H62  H  HCH3   0   0.245  -4.4735  -1.4321   0.3461
 83Y  H61  H  HCH3   0   0.228  -3.6651  -1.7312  -1.1984
 83Y  H6   H  HOH1   0   0.462  -2.5706   1.9986   2.0183
 83Y  HO2  H  HOH1   0   0.455  -0.9449   2.2850  -2.0979
 83Y  H7   H  HOH1   0   0.455  -0.9861  -3.0385  -0.3781

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    deloc   1.466  0.020  1.466
 83Y  O1S  S    deloc   1.461  0.020  1.461
 83Y  S    O3S  deloc   1.464  0.020  1.464
 83Y  S    O3   single  1.641  0.020  1.641
 83Y  O3   C3   single  1.420  0.020  1.420
 83Y  C3   C2   single  1.524  0.020  1.524
 83Y  C3   C4   single  1.522  0.020  1.522
 83Y  C2   O2   single  1.406  0.020  1.406
 83Y  C2   C1   single  1.530  0.020  1.530
 83Y  O1   C1   single  1.393  0.020  1.393
 83Y  C1   O5   single  1.399  0.020  1.399
 83Y  O4   C4   single  1.407  0.020  1.407
 83Y  C4   C5   single  1.537  0.020  1.537
 83Y  C5   O5   single  1.421  0.020  1.421
 83Y  C5   C6   single  1.515  0.020  1.515
 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

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   104.62  3.000
 83Y  H1   C1  O1   110.96  3.000
 83Y  O5   C1  O1   113.04  3.000
 83Y  H1   C1  C2   109.53  3.000
 83Y  O5   C1  C2   111.04  3.000
 83Y  O1   C1  C2   107.64  3.000
 83Y  H2   C2  O2   111.30  3.000
 83Y  H2   C2  C3   109.11  3.000
 83Y  O2   C2  C3   107.93  3.000
 83Y  H2   C2  C1   108.70  3.000
 83Y  O2   C2  C1   110.22  3.000
 83Y  C3   C2  C1   109.57  3.000
 83Y  H3   C3  O3   110.96  3.000
 83Y  H3   C3  C4   107.92  3.000
 83Y  O3   C3  C4   108.61  3.000
 83Y  H3   C3  C2   108.56  3.000
 83Y  C4   C3  C2   110.58  3.000
 83Y  O3   C3  C2   110.19  3.000
 83Y  H4   C4  O4   111.07  3.000
 83Y  H4   C4  C5   108.68  3.000
 83Y  O4   C4  C5   110.47  3.000
 83Y  H4   C4  C3   109.07  3.000
 83Y  C5   C4  C3   109.37  3.000
 83Y  O4   C4  C3   108.17  3.000
 83Y  H5   C5  O5   110.16  3.000
 83Y  H5   C5  C6   108.66  3.000
 83Y  O5   C5  C6   107.14  3.000
 83Y  H5   C5  C4   107.62  3.000
 83Y  C6   C5  C4   112.34  3.000
 83Y  O5   C5  C4   110.90  3.000
 83Y  H61  C6  H62  108.30  3.000
 83Y  H61  C6  H63  108.27  3.000
 83Y  H62  C6  H63  107.14  3.000
 83Y  H61  C6  C5   111.42  3.000
 83Y  H62  C6  C5   110.72  3.000
 83Y  H63  C6  C5   110.84  3.000
 83Y  H6   O1  C1   109.02  3.000
 83Y  HO2  O2  C2   108.50  3.000
 83Y  S    O3  C3   118.11  3.000
 83Y  C5   O5  C1   115.36  3.000
 83Y  O3S  S   O3   106.06  3.000
 83Y  O3   S   O2S  105.89  3.000
 83Y  O3S  S   O2S  113.40  3.000
 83Y  O3   S   O1S  100.46  3.000
 83Y  O3S  S   O1S  114.58  3.000
 83Y  O2S  S   O1S  114.74  3.000
 83Y  H7   O4  C4   108.58  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  -56.77  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
 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

