# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 12:59:23 2021
#   Inital geometry file: a 61 line input string
#   Ligand name: methyl 3-thio-alpha-D-mannopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1O[C@H](CO)[C@@H](O)[C@H](S)[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
 Z4R  Z4R  'methyl 3-thio-alpha-D-mannopyranoside'  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_Z4R
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
 Z4R  O4   O  OH1   0  -0.666  28.6366  63.9085  11.2520
 Z4R  C4   C  CH1   0   0.086  28.1955  65.1590  11.7127
 Z4R  C5   C  CH1   0  -0.001  26.6839  65.0666  11.9351
 Z4R  C6   C  CH2   0  -0.162  26.3383  64.0933  13.0425
 Z4R  O6   O  OH1   0  -0.669  24.9368  63.9934  13.1345
 Z4R  O5   O  O2    0  -0.500  26.1694  66.3320  12.3124
 Z4R  C1   C  CH1   0   0.264  26.3528  67.3556  11.3786
 Z4R  O1   O  O2    0  -0.499  25.7449  67.0915  10.1581
 Z4R  C1M  C  CH3   0  -0.409  24.3376  66.9772  10.2187
 Z4R  C2   C  CH1   0   0.036  27.8369  67.5907  11.1037
 Z4R  O2   O  OH1   0  -0.668  28.3844  68.1149  12.2842
 Z4R  C3   C  CH1   0  -0.485  28.4932  66.2692  10.7030
 Z4R  S3   S  S2    0  -0.239  30.3145  66.4541  10.5854
 Z4R  HO4  H  HOH1  0   0.448  29.5777  63.9785  11.0518
 Z4R  H4   H  HCH1  0   0.217  28.6674  65.4196  12.6726
 Z4R  H5   H  HCH1  0   0.229  26.2154  64.7177  11.0039
 Z4R  H61  H  HCH2  0   0.213  26.7967  63.1270  12.8085
 Z4R  H62  H  HCH2  0   0.195  26.7865  64.4444  13.9827
 Z4R  HO6  H  HOH1  0   0.456  24.7320  63.3058  13.7743
 Z4R  H1   H  HCH1  0   0.240  25.9151  68.2479  11.8483
 Z4R  H51  H  HCH3  0   0.238  23.9751  66.9165   9.1942
 Z4R  H52  H  HCH3  0   0.220  24.0147  66.0815  10.7553
 Z4R  H53  H  HCH3  0   0.213  23.8831  67.8512  10.6974
 Z4R  H2   H  HCH1  0   0.241  27.9284  68.2993  10.2706
 Z4R  HO2  H  HOH1  0   0.452  29.3169  68.2987  12.1183
 Z4R  H3   H  HCH1  0   0.305  28.1331  65.9634   9.7186
 Z4R  HS3  H  HSH1  0   0.245  30.3759  66.7739   9.2894

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
 Z4R  O4   C4   single  1.404  0.020  1.404
 Z4R  C4   C5   single  1.531  0.020  1.531
 Z4R  C4   C3   single  1.530  0.020  1.530
 Z4R  C5   C6   single  1.514  0.020  1.514
 Z4R  C5   O5   single  1.417  0.020  1.417
 Z4R  C6   O6   single  1.408  0.020  1.408
 Z4R  O5   C1   single  1.398  0.020  1.398
 Z4R  C1   O1   single  1.389  0.020  1.389
 Z4R  C1   C2   single  1.528  0.020  1.528
 Z4R  O1   C1M  single  1.413  0.020  1.413
 Z4R  C2   O2   single  1.403  0.020  1.403
 Z4R  C2   C3   single  1.529  0.020  1.529
 Z4R  C3   S3   single  1.834  0.020  1.834
 Z4R  O4   HO4  single  0.850  0.020  0.980
 Z4R  C4   H4   single  0.970  0.020  1.090
 Z4R  C5   H5   single  0.970  0.020  1.090
 Z4R  C6   H61  single  0.970  0.020  1.090
 Z4R  C6   H62  single  0.970  0.020  1.090
 Z4R  O6   HO6  single  0.850  0.020  0.980
 Z4R  C1   H1   single  0.970  0.020  1.090
 Z4R  C1M  H51  single  0.970  0.020  1.090
 Z4R  C1M  H52  single  0.970  0.020  1.090
 Z4R  C1M  H53  single  0.970  0.020  1.090
 Z4R  C2   H2   single  0.970  0.020  1.090
 Z4R  O2   HO2  single  0.850  0.020  0.980
 Z4R  C3   H3   single  0.970  0.020  1.090
 Z4R  S3   HS3  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
 Z4R  HO4  O4   C4   108.06  3.000
 Z4R  H4   C4   C3   108.68  3.000
 Z4R  H4   C4   C5   108.12  3.000
 Z4R  C3   C4   C5   109.38  3.000
 Z4R  H4   C4   O4   111.24  3.000
 Z4R  C3   C4   O4   111.63  3.000
 Z4R  C5   C4   O4   107.72  3.000
 Z4R  H5   C5   O5   110.75  3.000
 Z4R  H5   C5   C6   108.55  3.000
 Z4R  O5   C5   C6   107.24  3.000
 Z4R  H5   C5   C4   108.47  3.000
 Z4R  O5   C5   C4   110.08  3.000
 Z4R  C6   C5   C4   111.74  3.000
 Z4R  H62  C6   H61  107.10  3.000
 Z4R  H62  C6   O6   111.87  3.000
 Z4R  H61  C6   O6   111.60  3.000
 Z4R  H62  C6   C5   109.10  3.000
 Z4R  H61  C6   C5   108.39  3.000
 Z4R  O6   C6   C5   108.70  3.000
 Z4R  HO6  O6   C6   107.84  3.000
 Z4R  C1   O5   C5   115.37  3.000
 Z4R  H1   C1   C2   109.81  3.000
 Z4R  H1   C1   O1   110.83  3.000
 Z4R  C2   C1   O1   107.24  3.000
 Z4R  H1   C1   O5   104.88  3.000
 Z4R  C2   C1   O5   111.13  3.000
 Z4R  O1   C1   O5   112.98  3.000
 Z4R  C1M  O1   C1   114.43  3.000
 Z4R  H53  C1M  H52  108.47  3.000
 Z4R  H53  C1M  H51  108.53  3.000
 Z4R  H52  C1M  H51  108.54  3.000
 Z4R  H53  C1M  O1   111.56  3.000
 Z4R  H52  C1M  O1   112.43  3.000
 Z4R  H51  C1M  O1   107.21  3.000
 Z4R  H2   C2   C3   108.87  3.000
 Z4R  H2   C2   O2   111.40  3.000
 Z4R  C3   C2   O2   112.08  3.000
 Z4R  H2   C2   C1   108.48  3.000
 Z4R  C3   C2   C1   109.34  3.000
 Z4R  O2   C2   C1   106.57  3.000
 Z4R  HO2  O2   C2   107.68  3.000
 Z4R  H3   C3   S3   107.33  3.000
 Z4R  H3   C3   C2   109.68  3.000
 Z4R  S3   C3   C2   110.85  3.000
 Z4R  H3   C3   C4   109.12  3.000
 Z4R  S3   C3   C4   107.98  3.000
 Z4R  C2   C3   C4   111.76  3.000
 Z4R  HS3  S3   C3    97.58  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
 Z4R  Var_01  H51  C1M  O1  C1  171.98  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
 Z4R  chir_01  C4  O4  C5  C3  positiv
 Z4R  chir_02  C5  O5  C4  C6  negativ
 Z4R  chir_03  C1  O5  O1  C2  positiv
 Z4R  chir_04  C2  O2  C1  C3  positiv
 Z4R  chir_05  C3  S3  C2  C4  positiv

