# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 01:44:52 2021
#   Inital geometry file: a 61 line input string
#   Ligand name: methyl 6-thio-beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1O[C@H](CS)[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
 U1Y  U1Y  'methyl 6-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_U1Y
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
 U1Y  S6   S  S2    0  -0.233  25.1153  28.3033  35.2083
 U1Y  C1   C  CH1   0   0.316  25.7587  32.1122  33.7495
 U1Y  O1   O  O2    0  -0.490  24.6591  32.4522  33.0002
 U1Y  C7   C  CH3   0  -0.411  24.2544  31.4655  32.0697
 U1Y  O5   O  O2    0  -0.499  25.3703  31.1499  34.7006
 U1Y  C5   C  CH1   0   0.029  26.4493  30.6625  35.4678
 U1Y  C4   C  CH1   0   0.018  27.0108  31.8078  36.3169
 U1Y  O4   O  OH1   0  -0.672  28.1523  31.4156  37.0418
 U1Y  C3   C  CH1   0  -0.020  27.4219  32.9506  35.3953
 U1Y  O3   O  OH1   0  -0.672  27.7931  34.1030  36.1140
 U1Y  C2   C  CH1   0   0.003  26.2783  33.3513  34.4681
 U1Y  O2   O  OH1   0  -0.669  26.6960  34.2784  33.5012
 U1Y  C6   C  CH2   0  -0.597  25.9324  29.5126  36.3042
 U1Y  H71  H  HCH3  0   0.239  23.4418  31.8890  31.4824
 U1Y  H72  H  HCH3  0   0.214  25.0711  31.1973  31.3915
 U1Y  H73  H  HCH3  0   0.220  23.8949  30.5563  32.5569
 U1Y  H5   H  HCH1  0   0.229  27.2452  30.2844  34.8066
 U1Y  H4   H  HCH1  0   0.225  26.2164  32.1652  36.9876
 U1Y  HO4  H  HOH1  0   0.462  27.8759  31.0140  37.8706
 U1Y  H3   H  HCH1  0   0.218  28.2604  32.5983  34.7727
 U1Y  HO3  H  HOH1  0   0.457  28.6227  33.9241  36.5676
 U1Y  H2   H  HCH1  0   0.216  25.4571  33.7545  35.0822
 U1Y  HO2  H  HOH1  0   0.453  27.1317  35.0064  33.9569
 U1Y  H61  H  HCH2  0   0.287  26.7640  29.0230  36.8075
 U1Y  H62  H  HCH2  0   0.271  25.2296  29.8675  37.0599
 U1Y  HS6  H  HSH1  0   0.220  25.3327  27.2240  35.9670
 U1Y  H1   H  HCH1  0   0.186  26.5586  31.6880  33.1127

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
 U1Y  C7  O1   single  1.415  0.020  1.415
 U1Y  O1  C1   single  1.373  0.020  1.373
 U1Y  O2  C2   single  1.403  0.020  1.403
 U1Y  C1  C2   single  1.524  0.020  1.524
 U1Y  C1  O5   single  1.408  0.020  1.408
 U1Y  C2  C3   single  1.526  0.020  1.526
 U1Y  O5  C5   single  1.411  0.020  1.411
 U1Y  C3  O3   single  1.408  0.020  1.408
 U1Y  C3  C4   single  1.525  0.020  1.525
 U1Y  C5  C4   single  1.532  0.020  1.532
 U1Y  C5  C6   single  1.513  0.020  1.513
 U1Y  C4  O4   single  1.408  0.020  1.408
 U1Y  C6  S6   single  1.825  0.020  1.825
 U1Y  C1  H1   single  0.970  0.020  1.090
 U1Y  C7  H71  single  0.970  0.020  1.090
 U1Y  C7  H72  single  0.970  0.020  1.090
 U1Y  C7  H73  single  0.970  0.020  1.090
 U1Y  C5  H5   single  0.970  0.020  1.090
 U1Y  C4  H4   single  0.970  0.020  1.090
 U1Y  O4  HO4  single  0.850  0.020  0.980
 U1Y  C3  H3   single  0.970  0.020  1.090
 U1Y  O3  HO3  single  0.850  0.020  0.980
 U1Y  C2  H2   single  0.970  0.020  1.090
 U1Y  O2  HO2  single  0.850  0.020  0.980
 U1Y  C6  H61  single  0.970  0.020  1.090
 U1Y  C6  H62  single  0.970  0.020  1.090
 U1Y  S6  HS6  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
 U1Y  HS6  S6  C6    96.97  3.000
 U1Y  H1   C1  C2   109.66  3.000
 U1Y  H1   C1  O5   109.03  3.000
 U1Y  C2   C1  O5   109.36  3.000
 U1Y  H1   C1  O1   111.07  3.000
 U1Y  O5   C1  O1   108.48  3.000
 U1Y  C2   C1  O1   109.21  3.000
 U1Y  C7   O1  C1   114.52  3.000
 U1Y  H73  C7  H72  108.53  3.000
 U1Y  H73  C7  H71  108.60  3.000
 U1Y  H72  C7  H71  108.54  3.000
 U1Y  H73  C7  O1   112.41  3.000
 U1Y  H72  C7  O1   111.38  3.000
 U1Y  H71  C7  O1   107.28  3.000
 U1Y  C5   O5  C1   113.11  3.000
 U1Y  H5   C5  C6   108.53  3.000
 U1Y  H5   C5  C4   108.93  3.000
 U1Y  C6   C5  C4   112.77  3.000
 U1Y  H5   C5  O5   110.16  3.000
 U1Y  C6   C5  O5   107.57  3.000
 U1Y  C4   C5  O5   108.87  3.000
 U1Y  H4   C4  C3   108.66  3.000
 U1Y  H4   C4  O4   111.24  3.000
 U1Y  C3   C4  O4   107.54  3.000
 U1Y  H4   C4  C5   108.44  3.000
 U1Y  O4   C4  C5   111.98  3.000
 U1Y  C3   C4  C5   108.91  3.000
 U1Y  HO4  O4  C4   109.09  3.000
 U1Y  H3   C3  C2   108.11  3.000
 U1Y  H3   C3  O3   110.45  3.000
 U1Y  C2   C3  O3   107.03  3.000
 U1Y  H3   C3  C4   107.88  3.000
 U1Y  O3   C3  C4   112.09  3.000
 U1Y  C2   C3  C4   111.23  3.000
 U1Y  HO3  O3  C3   108.41  3.000
 U1Y  H2   C2  O2   111.35  3.000
 U1Y  H2   C2  C3   108.43  3.000
 U1Y  O2   C2  C3   111.66  3.000
 U1Y  H2   C2  C1   107.83  3.000
 U1Y  C3   C2  C1   109.18  3.000
 U1Y  O2   C2  C1   108.29  3.000
 U1Y  HO2  O2  C2   107.94  3.000
 U1Y  H62  C6  H61  108.54  3.000
 U1Y  H62  C6  C5   110.84  3.000
 U1Y  H61  C6  C5   109.66  3.000
 U1Y  H62  C6  S6   110.06  3.000
 U1Y  H61  C6  S6   108.77  3.000
 U1Y  C5   C6  S6   108.94  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
 U1Y  Var_01  H71  C7  O1  C1  -174.85  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
 U1Y  chir_01  C1  O1  C2  O5  negativ
 U1Y  chir_02  C5  O5  C6  C4  positiv
 U1Y  chir_03  C4  O4  C5  C3  positiv
 U1Y  chir_04  C3  O3  C2  C4  positiv
 U1Y  chir_05  C2  O2  C3  C1  positiv

