# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 17:12:31 2022
#   Inital geometry file: a 55 line input string
#   Ligand name: 6-thio-alpha-D-mannopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[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
 Z4Y  Z4Y  6-thio-alpha-D-mannopyranose  D-saccharide  24  12  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Z4Y
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
 Z4Y  O1   O  OH1   0  -0.661  30.0912  67.6142  15.6216
 Z4Y  C1   C  CH1   0   0.250  30.1314  68.2816  16.8518
 Z4Y  O5   O  O2    0  -0.489  28.8820  68.1572  17.4451
 Z4Y  C5   C  CH1   0   0.025  28.4993  66.8558  17.8548
 Z4Y  C6   C  CH2   0  -0.582  27.1105  66.9893  18.4489
 Z4Y  S1   S  S2    0  -0.253  27.0717  68.2818  19.7412
 Z4Y  C4   C  CH1   0   0.050  29.5220  66.2563  18.8184
 Z4Y  O4   O  OH1   0  -0.671  29.1135  64.9345  19.0776
 Z4Y  C3   C  CH1   0  -0.024  30.9054  66.3061  18.1850
 Z4Y  O3   O  OH1   0  -0.669  31.8298  65.8344  19.1440
 Z4Y  C2   C  CH1   0  -0.051  31.2399  67.7331  17.7523
 Z4Y  O2   O  OH1   0  -0.665  31.3436  68.6009  18.8529
 Z4Y  HO1  H  HOH1  0   0.458  30.9498  67.6872  15.1912
 Z4Y  H1   H  HCH1  0   0.230  30.2813  69.3608  16.7132
 Z4Y  H5   H  HCH1  0   0.245  28.4158  66.1838  16.9892
 Z4Y  H61  H  HCH2  0   0.282  26.3988  67.2458  17.6643
 Z4Y  H62  H  HCH2  0   0.289  26.8002  66.0420  18.8838
 Z4Y  H1S  H  HSH1  0   0.220  26.2341  67.6589  20.5756
 Z4Y  H4   H  HCH1  0   0.212  29.5314  66.8540  19.7403
 Z4Y  HO4  H  HOH1  0   0.451  29.7173  64.5567  19.7247
 Z4Y  H3   H  HCH1  0   0.224  30.9016  65.6646  17.2941
 Z4Y  HO3  H  HOH1  0   0.458  32.6349  65.5605  18.6927
 Z4Y  H2   H  HCH1  0   0.225  32.1804  67.7209  17.1774
 Z4Y  HO2  H  HOH1  0   0.448  31.9360  68.1908  19.4927

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
 Z4Y  O1   C1   single  1.400  0.020  1.400
 Z4Y  C1   O5   single  1.389  0.020  1.389
 Z4Y  C1   C2   single  1.530  0.020  1.530
 Z4Y  O5   C5   single  1.417  0.020  1.417
 Z4Y  C5   C6   single  1.516  0.020  1.516
 Z4Y  C5   C4   single  1.528  0.020  1.528
 Z4Y  C6   S1   single  1.828  0.020  1.828
 Z4Y  C4   O4   single  1.408  0.020  1.408
 Z4Y  C4   C3   single  1.522  0.020  1.522
 Z4Y  C3   O3   single  1.413  0.020  1.413
 Z4Y  C3   C2   single  1.528  0.020  1.528
 Z4Y  C2   O2   single  1.405  0.020  1.405
 Z4Y  C1   H1   single  0.970  0.020  1.090
 Z4Y  C5   H5   single  0.970  0.020  1.090
 Z4Y  C6   H61  single  0.970  0.020  1.090
 Z4Y  C6   H62  single  0.970  0.020  1.090
 Z4Y  S1   H1S  single  1.200  0.020  1.300
 Z4Y  C4   H4   single  0.970  0.020  1.090
 Z4Y  O4   HO4  single  0.850  0.020  0.980
 Z4Y  C3   H3   single  0.970  0.020  1.090
 Z4Y  O3   HO3  single  0.850  0.020  0.980
 Z4Y  C2   H2   single  0.970  0.020  1.090
 Z4Y  O2   HO2  single  0.850  0.020  0.980
 Z4Y  HO1  O1   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
 Z4Y  HO1  O1  C1   109.32  3.000
 Z4Y  H1   C1  C2   109.13  3.000
 Z4Y  H1   C1  O5   105.35  3.000
 Z4Y  C2   C1  O5   111.61  3.000
 Z4Y  H1   C1  O1   111.18  3.000
 Z4Y  C2   C1  O1   111.53  3.000
 Z4Y  O5   C1  O1   107.87  3.000
 Z4Y  C5   O5  C1   116.67  3.000
 Z4Y  H5   C5  C4   107.92  3.000
 Z4Y  H5   C5  C6   107.03  3.000
 Z4Y  C4   C5  C6   113.61  3.000
 Z4Y  H5   C5  O5   110.75  3.000
 Z4Y  C4   C5  O5   111.22  3.000
 Z4Y  C6   C5  O5   106.25  3.000
 Z4Y  H62  C6  H61  107.85  3.000
 Z4Y  H62  C6  S1   109.09  3.000
 Z4Y  H61  C6  S1   109.19  3.000
 Z4Y  H62  C6  C5   109.95  3.000
 Z4Y  H61  C6  C5   109.68  3.000
 Z4Y  S1   C6  C5   111.01  3.000
 Z4Y  H1S  S1  C6    97.19  3.000
 Z4Y  H4   C4  C3   108.87  3.000
 Z4Y  H4   C4  O4   111.03  3.000
 Z4Y  C3   C4  O4   111.78  3.000
 Z4Y  H4   C4  C5   108.75  3.000
 Z4Y  C3   C4  C5   109.45  3.000
 Z4Y  O4   C4  C5   106.88  3.000
 Z4Y  HO4  O4  C4   108.09  3.000
 Z4Y  H3   C3  C2   108.46  3.000
 Z4Y  H3   C3  O3   110.97  3.000
 Z4Y  C2   C3  O3   111.14  3.000
 Z4Y  H3   C3  C4   108.39  3.000
 Z4Y  C2   C3  C4   110.32  3.000
 Z4Y  O3   C3  C4   107.53  3.000
 Z4Y  HO3  O3  C3   108.90  3.000
 Z4Y  H2   C2  O2   110.63  3.000
 Z4Y  H2   C2  C3   108.91  3.000
 Z4Y  O2   C2  C3   111.77  3.000
 Z4Y  H2   C2  C1   108.37  3.000
 Z4Y  O2   C2  C1   107.04  3.000
 Z4Y  C3   C2  C1   110.05  3.000
 Z4Y  HO2  O2  C2   107.61  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
 Z4Y  chir_01  C1  O1  O5  C2  negativ
 Z4Y  chir_02  C5  O5  C6  C4  positiv
 Z4Y  chir_03  C4  O4  C5  C3  positiv
 Z4Y  chir_04  C3  O3  C4  C2  negativ
 Z4Y  chir_05  C2  O2  C3  C1  negativ

