# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 01:06:13 2021
#   Inital geometry file: a 61 line input string
#   Ligand name: methyl 2-thio-beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1S
#
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
 U2A  U2A  'methyl 2-thio-beta-D-glucopyranoside'  D-saccharide  27  13  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U2A
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
 U2A  S2   S  S2    0  -0.222  27.2134  33.6627  34.9118
 U2A  C2   C  CH1   0  -0.476  28.4960  33.5706  33.6223
 U2A  C1   C  CH1   0   0.364  28.5322  34.9113  32.8973
 U2A  O1   O  O2    0  -0.486  27.2987  35.1716  32.3510
 U2A  C7   C  CH3   0  -0.415  27.1188  36.5101  31.9263
 U2A  O5   O  O2    0  -0.490  29.4804  34.8530  31.8661
 U2A  C3   C  CH1   0   0.035  29.8867  33.3150  34.1964
 U2A  O3   O  OH1   0  -0.669  29.9757  32.0518  34.8138
 U2A  C4   C  CH1   0   0.038  30.9302  33.3736  33.0796
 U2A  O4   O  OH1   0  -0.670  32.2309  33.2821  33.6008
 U2A  C5   C  CH1   0  -0.019  30.8069  34.6985  32.3253
 U2A  C6   C  CH2   0  -0.155  31.7242  34.7548  31.1225
 U2A  O6   O  OH1   0  -0.669  31.6047  36.0205  30.5198
 U2A  H2   H  HCH1  0   0.291  28.2328  32.7871  32.9056
 U2A  H1   H  HCH1  0   0.189  28.8180  35.7053  33.6152
 U2A  H14  H  HCH3  0   0.241  26.0767  36.6191  31.6330
 U2A  H15  H  HCH3  0   0.216  27.3296  37.2151  32.7368
 U2A  H16  H  HCH3  0   0.222  27.7514  36.7643  31.0729
 U2A  H3   H  HCH1  0   0.234  30.1109  34.1158  34.9141
 U2A  HO3  H  HOH1  0   0.464  29.9691  32.1640  35.7679
 U2A  H4   H  HCH1  0   0.212  30.7273  32.5528  32.3722
 U2A  HO4  H  HOH1  0   0.453  32.2906  32.4614  34.1019
 U2A  H5   H  HCH1  0   0.225  31.0656  35.5188  33.0154
 U2A  H61  H  HCH2  0   0.197  31.4537  33.9450  30.4304
 U2A  H62  H  HCH2  0   0.212  32.7478  34.5607  31.4596
 U2A  HO6  H  HOH1  0   0.457  32.2043  36.0490  29.7689
 U2A  HS2  H  HSH1  0   0.223  27.4909  32.4935  35.4993

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
 U2A  O6  C6   single  1.407  0.020  1.407
 U2A  C6  C5   single  1.514  0.020  1.514
 U2A  C7  O1   single  1.416  0.020  1.416
 U2A  O5  C5   single  1.412  0.020  1.412
 U2A  O5  C1   single  1.402  0.020  1.402
 U2A  C5  C4   single  1.530  0.020  1.530
 U2A  O1  C1   single  1.374  0.020  1.374
 U2A  C1  C2   single  1.525  0.020  1.525
 U2A  C4  O4   single  1.404  0.020  1.404
 U2A  C4  C3   single  1.530  0.020  1.530
 U2A  C2  C3   single  1.526  0.020  1.526
 U2A  C2  S2   single  1.821  0.020  1.821
 U2A  C3  O3   single  1.409  0.020  1.409
 U2A  C2  H2   single  0.970  0.020  1.090
 U2A  C1  H1   single  0.970  0.020  1.090
 U2A  C7  H14  single  0.970  0.020  1.090
 U2A  C7  H15  single  0.970  0.020  1.090
 U2A  C7  H16  single  0.970  0.020  1.090
 U2A  C3  H3   single  0.970  0.020  1.090
 U2A  O3  HO3  single  0.850  0.020  0.980
 U2A  C4  H4   single  0.970  0.020  1.090
 U2A  O4  HO4  single  0.850  0.020  0.980
 U2A  C5  H5   single  0.970  0.020  1.090
 U2A  C6  H61  single  0.970  0.020  1.090
 U2A  C6  H62  single  0.970  0.020  1.090
 U2A  O6  HO6  single  0.850  0.020  0.980
 U2A  S2  HS2  single  1.200  0.020  1.300

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
 U2A  HS2  S2  C2    96.93  3.000
 U2A  H2   C2  C3   110.23  3.000
 U2A  H2   C2  C1   108.90  3.000
 U2A  C3   C2  C1   107.73  3.000
 U2A  H2   C2  S2   109.31  3.000
 U2A  C3   C2  S2   112.58  3.000
 U2A  C1   C2  S2   108.00  3.000
 U2A  H1   C1  O5   109.38  3.000
 U2A  H1   C1  O1   110.70  3.000
 U2A  O5   C1  O1   108.82  3.000
 U2A  H1   C1  C2   109.16  3.000
 U2A  O1   C1  C2   109.54  3.000
 U2A  O5   C1  C2   109.23  3.000
 U2A  C7   O1  C1   114.36  3.000
 U2A  H16  C7  H15  108.49  3.000
 U2A  H16  C7  H14  108.71  3.000
 U2A  H15  C7  H14  108.63  3.000
 U2A  H16  C7  O1   112.39  3.000
 U2A  H15  C7  O1   111.24  3.000
 U2A  H14  C7  O1   107.29  3.000
 U2A  C5   O5  C1   113.62  3.000
 U2A  H3   C3  C4   108.05  3.000
 U2A  H3   C3  O3   110.76  3.000
 U2A  C4   C3  O3   108.13  3.000
 U2A  H3   C3  C2   108.04  3.000
 U2A  O3   C3  C2   111.88  3.000
 U2A  C4   C3  C2   109.92  3.000
 U2A  HO3  O3  C3   109.27  3.000
 U2A  H4   C4  C5   108.28  3.000
 U2A  H4   C4  O4   111.11  3.000
 U2A  C5   C4  O4   108.31  3.000
 U2A  H4   C4  C3   108.33  3.000
 U2A  O4   C4  C3   111.01  3.000
 U2A  C5   C4  C3   109.77  3.000
 U2A  HO4  O4  C4   107.82  3.000
 U2A  H5   C5  C6   109.11  3.000
 U2A  H5   C5  C4   108.47  3.000
 U2A  C6   C5  C4   112.03  3.000
 U2A  H5   C5  O5   110.03  3.000
 U2A  C4   C5  O5   109.32  3.000
 U2A  C6   C5  O5   107.87  3.000
 U2A  H62  C6  H61  107.06  3.000
 U2A  H62  C6  O6   111.76  3.000
 U2A  H61  C6  O6   111.85  3.000
 U2A  H62  C6  C5   108.38  3.000
 U2A  H61  C6  C5   108.89  3.000
 U2A  O6   C6  C5   108.81  3.000
 U2A  HO6  O6  C6   107.96  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
 U2A  Var_01  H14  C7  O1  C1  -173.05  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
 U2A  chir_01  C2  C1  C3  S2  negativ
 U2A  chir_02  C1  O5  O1  C2  negativ
 U2A  chir_03  C3  O3  C2  C4  positiv
 U2A  chir_04  C4  O4  C5  C3  positiv
 U2A  chir_05  C5  O5  C4  C6  negativ

