# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 13:57:51 2021
#   Inital geometry file: a 55 line input string
#   Ligand name: 1-thio-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](S)[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
 Z9E  Z9E  1-thio-alpha-D-glucopyranose  D-saccharide  24  12  .  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_Z9E
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
 Z9E  C1   C  CH1   0  -0.133  61.4768  17.6989   8.3588
 Z9E  S1   S  S2    0  -0.259  60.3455  16.9229   7.1262
 Z9E  C2   C  CH1   0   0.026  62.3975  16.6247   8.9385
 Z9E  O2   O  OH1   0  -0.661  62.9478  15.8978   7.8744
 Z9E  C3   C  CH1   0  -0.003  61.6518  15.7376   9.9283
 Z9E  O3   O  OH1   0  -0.674  62.6065  14.8755  10.5010
 Z9E  C4   C  CH1   0   0.006  60.9540  16.6016  10.9690
 Z9E  O4   O  OH1   0  -0.675  60.2196  15.7483  11.8173
 Z9E  C5   C  CH1   0  -0.008  60.0372  17.5958  10.2503
 Z9E  O5   O  O2    0  -0.466  60.8074  18.3903   9.3613
 Z9E  C6   C  CH2   0  -0.191  59.2839  18.5224  11.1773
 Z9E  O6   O  OH1   0  -0.671  60.1875  19.2063  12.0115
 Z9E  H1   H  HCH1  0   0.298  62.0701  18.4420   7.8246
 Z9E  HS1  H  HSH1  0   0.228  59.7283  18.0623   6.7922
 Z9E  H2   H  HCH1  0   0.243  63.1808  17.1625   9.4963
 Z9E  HO2  H  HOH1  0   0.457  63.5234  15.2198   8.2443
 Z9E  H3   H  HCH1  0   0.217  60.8849  15.1599   9.3876
 Z9E  HO3  H  HOH1  0   0.456  62.1427  14.2206  11.0321
 Z9E  H4   H  HCH1  0   0.228  61.7177  17.1542  11.5312
 Z9E  H5   H  HCH1  0   0.232  59.2819  17.0299   9.6856
 Z9E  H61  H  HCH2  0   0.221  58.6845  19.2119  10.5684
 Z9E  H62  H  HCH2  0   0.210  58.5726  17.9157  11.7503
 Z9E  HO6  H  HOH1  0   0.460  59.6800  19.7252  12.6416
 Z9E  HO4  H  HOH1  0   0.461  60.1547  16.1555  12.6857

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
 Z9E  C1  S1   single  1.844  0.020  1.844
 Z9E  C1  C2   single  1.529  0.020  1.529
 Z9E  C1  O5   single  1.390  0.020  1.390
 Z9E  C1  H1   single  0.970  0.020  1.090
 Z9E  S1  HS1  single  1.200  0.020  1.300
 Z9E  C2  O2   single  1.401  0.020  1.401
 Z9E  C2  C3   single  1.524  0.020  1.524
 Z9E  C2  H2   single  0.970  0.020  1.090
 Z9E  O2  HO2  single  0.850  0.020  0.980
 Z9E  C3  O3   single  1.408  0.020  1.408
 Z9E  C3  C4   single  1.522  0.020  1.522
 Z9E  C3  H3   single  0.970  0.020  1.090
 Z9E  O3  HO3  single  0.850  0.020  0.980
 Z9E  C4  O4   single  1.410  0.020  1.410
 Z9E  C4  C5   single  1.531  0.020  1.531
 Z9E  C4  H4   single  0.970  0.020  1.090
 Z9E  C5  O5   single  1.419  0.020  1.419
 Z9E  C5  C6   single  1.512  0.020  1.512
 Z9E  C5  H5   single  0.970  0.020  1.090
 Z9E  C6  O6   single  1.407  0.020  1.407
 Z9E  C6  H61  single  0.970  0.020  1.090
 Z9E  C6  H62  single  0.970  0.020  1.090
 Z9E  O6  HO6  single  0.850  0.020  0.980
 Z9E  O4  HO4  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
 Z9E  H1   C1  O5   106.05  3.000
 Z9E  H1   C1  C2   109.68  3.000
 Z9E  O5   C1  C2   111.47  3.000
 Z9E  H1   C1  S1   107.04  3.000
 Z9E  O5   C1  S1   113.33  3.000
 Z9E  C2   C1  S1   109.10  3.000
 Z9E  HS1  S1  C1    95.25  3.000
 Z9E  H2   C2  C3   107.65  3.000
 Z9E  H2   C2  O2   111.00  3.000
 Z9E  C3   C2  O2   112.54  3.000
 Z9E  H2   C2  C1   106.09  3.000
 Z9E  C3   C2  C1   111.14  3.000
 Z9E  O2   C2  C1   108.24  3.000
 Z9E  HO2  O2  C2   107.95  3.000
 Z9E  H3   C3  C4   108.30  3.000
 Z9E  H3   C3  O3   110.51  3.000
 Z9E  C4   C3  O3   112.35  3.000
 Z9E  H3   C3  C2   109.09  3.000
 Z9E  C4   C3  C2   109.76  3.000
 Z9E  O3   C3  C2   106.79  3.000
 Z9E  HO3  O3  C3   108.32  3.000
 Z9E  H4   C4  C5   109.27  3.000
 Z9E  H4   C4  O4   111.04  3.000
 Z9E  C5   C4  O4   111.31  3.000
 Z9E  H4   C4  C3   108.49  3.000
 Z9E  C5   C4  C3   108.79  3.000
 Z9E  O4   C4  C3   107.86  3.000
 Z9E  HO4  O4  C4   108.80  3.000
 Z9E  H5   C5  C6   106.74  3.000
 Z9E  H5   C5  O5   109.82  3.000
 Z9E  C6   C5  O5   108.14  3.000
 Z9E  H5   C5  C4   108.55  3.000
 Z9E  C6   C5  C4   114.11  3.000
 Z9E  O5   C5  C4   109.42  3.000
 Z9E  C5   O5  C1   115.77  3.000
 Z9E  H62  C6  H61  106.45  3.000
 Z9E  H62  C6  O6   112.06  3.000
 Z9E  H61  C6  O6   111.97  3.000
 Z9E  H62  C6  C5   107.73  3.000
 Z9E  H61  C6  C5   108.48  3.000
 Z9E  O6   C6  C5   109.96  3.000
 Z9E  HO6  O6  C6   108.18  3.000

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
 Z9E  chir_01  C1  S1  C2  O5  positiv
 Z9E  chir_02  C2  O2  C1  C3  negativ
 Z9E  chir_03  C3  O3  C2  C4  positiv
 Z9E  chir_04  C4  O4  C5  C3  positiv
 Z9E  chir_05  C5  O5  C4  C6  negativ

