# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 15:32:46 2021
#   Inital geometry file: a 53 line input string
#   Ligand name: methyl 4-thio-alpha-D-xylopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1OC[C@@H](S)[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
 Z4U  Z4U  'methyl 4-thio-alpha-D-xylopyranoside'  D-saccharide  23  11  .  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_Z4U
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
 Z4U  C1   C  CH1   0   0.259  21.0684  23.1871   9.4945
 Z4U  O1   O  O2    0  -0.491  21.9498  22.6119   8.5909
 Z4U  C6   C  CH3   0  -0.407  21.6012  22.7939   7.2344
 Z4U  C2   C  CH1   0   0.005  21.6956  23.1212  10.8864
 Z4U  O2   O  OH1   0  -0.667  22.9480  23.7487  10.8292
 Z4U  C3   C  CH1   0   0.048  21.7831  21.6752  11.3687
 Z4U  O3   O  OH1   0  -0.668  22.2716  21.6987  12.6853
 Z4U  C4   C  CH1   0  -0.462  20.3944  21.0470  11.2798
 Z4U  S4   S  S2    0  -0.231  20.5048  19.2755  11.7199
 Z4U  C5   C  CH2   0  -0.159  19.8231  21.2069   9.8794
 Z4U  O5   O  O2    0  -0.494  19.8097  22.5702   9.4939
 Z4U  H1   H  HCH1  0   0.238  20.8687  24.2341   9.2257
 Z4U  H21  H  HCH3  0   0.238  22.4549  22.4838   6.6344
 Z4U  H22  H  HCH3  0   0.217  20.7367  22.1936   6.9392
 Z4U  H23  H  HCH3  0   0.213  21.3824  23.8438   7.0124
 Z4U  H2   H  HCH1  0   0.226  21.0127  23.6585  11.5621
 Z4U  HO2  H  HOH1  0   0.455  23.2833  23.8308  11.7274
 Z4U  H3   H  HCH1  0   0.220  22.4660  21.1219  10.7065
 Z4U  HO3  H  HOH1  0   0.448  22.3354  20.7875  12.9952
 Z4U  H4   H  HCH1  0   0.299  19.7381  21.5288  12.0083
 Z4U  H51  H  HCH2  0   0.221  20.3924  20.5964   9.1690
 Z4U  H52  H  HCH2  0   0.254  18.7890  20.8649   9.8514
 Z4U  HS4  H  HSH1  0   0.239  19.4352  19.2162  12.5178

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
 Z4U  C1  O1   single  1.387  0.020  1.387
 Z4U  C1  C2   single  1.528  0.020  1.528
 Z4U  C1  O5   single  1.402  0.020  1.402
 Z4U  C1  H1   single  0.970  0.020  1.090
 Z4U  O1  C6   single  1.412  0.020  1.412
 Z4U  C6  H21  single  0.970  0.020  1.090
 Z4U  C6  H22  single  0.970  0.020  1.090
 Z4U  C6  H23  single  0.970  0.020  1.090
 Z4U  C2  O2   single  1.402  0.020  1.402
 Z4U  C2  C3   single  1.527  0.020  1.527
 Z4U  C2  H2   single  0.970  0.020  1.090
 Z4U  O2  HO2  single  0.850  0.020  0.980
 Z4U  C3  O3   single  1.404  0.020  1.404
 Z4U  C3  C4   single  1.527  0.020  1.527
 Z4U  C3  H3   single  0.970  0.020  1.090
 Z4U  O3  HO3  single  0.850  0.020  0.980
 Z4U  C4  S4   single  1.829  0.020  1.829
 Z4U  C4  C5   single  1.521  0.020  1.521
 Z4U  C4  H4   single  0.970  0.020  1.090
 Z4U  C5  O5   single  1.417  0.020  1.417
 Z4U  C5  H51  single  0.970  0.020  1.090
 Z4U  C5  H52  single  0.970  0.020  1.090
 Z4U  S4  HS4  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
 Z4U  H1   C1  O5   104.83  3.000
 Z4U  H1   C1  C2   109.78  3.000
 Z4U  O5   C1  C2   110.48  3.000
 Z4U  H1   C1  O1   110.56  3.000
 Z4U  O5   C1  O1   112.82  3.000
 Z4U  C2   C1  O1   108.34  3.000
 Z4U  C6   O1  C1   114.54  3.000
 Z4U  H23  C6  H22  108.29  3.000
 Z4U  H23  C6  H21  108.54  3.000
 Z4U  H22  C6  H21  108.35  3.000
 Z4U  H23  C6  O1   111.57  3.000
 Z4U  H22  C6  O1   112.57  3.000
 Z4U  H21  C6  O1   107.41  3.000
 Z4U  H2   C2  C3   107.70  3.000
 Z4U  H2   C2  O2   111.15  3.000
 Z4U  C3   C2  O2   112.68  3.000
 Z4U  H2   C2  C1   106.47  3.000
 Z4U  C3   C2  C1   110.62  3.000
 Z4U  O2   C2  C1   108.07  3.000
 Z4U  HO2  O2  C2   108.14  3.000
 Z4U  H3   C3  C4   108.82  3.000
 Z4U  H3   C3  O3   110.90  3.000
 Z4U  C4   C3  O3   112.20  3.000
 Z4U  H3   C3  C2   108.76  3.000
 Z4U  C4   C3  C2   108.61  3.000
 Z4U  O3   C3  C2   107.47  3.000
 Z4U  HO3  O3  C3   107.96  3.000
 Z4U  H4   C4  C5   110.00  3.000
 Z4U  H4   C4  S4   107.64  3.000
 Z4U  C5   C4  S4   110.25  3.000
 Z4U  H4   C4  C3   109.03  3.000
 Z4U  C5   C4  C3   110.61  3.000
 Z4U  S4   C4  C3   109.25  3.000
 Z4U  HS4  S4  C4    97.95  3.000
 Z4U  H52  C5  H51  107.55  3.000
 Z4U  H52  C5  O5   106.62  3.000
 Z4U  H51  C5  O5   111.37  3.000
 Z4U  H52  C5  C4   110.32  3.000
 Z4U  H51  C5  C4   110.07  3.000
 Z4U  O5   C5  C4   110.81  3.000
 Z4U  C5   O5  C1   114.51  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
 Z4U  Var_01  C4   C5  O5  C1   58.95  30.0  1
 Z4U  Var_02  H21  C6  O1  C1  168.72  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
 Z4U  chir_01  C1  O1  C2  O5  positiv
 Z4U  chir_02  C2  O2  C1  C3  negativ
 Z4U  chir_03  C3  O3  C2  C4  positiv
 Z4U  chir_04  C4  S4  C3  C5  negativ

