# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 23:54:58 2021
#   Inital geometry file: a 47 line input string
#   Ligand name: 4-thio-beta-D-xylopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[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
 TWY  TWY  4-thio-beta-D-xylopyranose  D-saccharide  20  10  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TWY
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
 TWY  S4   S  S2    0  -0.229  18.1050  62.8645  26.3382
 TWY  C4   C  CH1   0  -0.461  19.7544  62.7885  25.5566
 TWY  C5   C  CH2   0  -0.162  19.6264  62.8208  24.0402
 TWY  O5   O  O2    0  -0.480  20.8904  62.6886  23.4292
 TWY  C1   C  CH1   0   0.294  21.5072  61.4716  23.7213
 TWY  O1   O  OH1   0  -0.659  22.6906  61.4995  22.9973
 TWY  C2   C  CH1   0  -0.023  21.7571  61.3493  25.2267
 TWY  O2   O  OH1   0  -0.673  22.3509  60.0929  25.4407
 TWY  C3   C  CH1   0   0.047  20.4481  61.5002  25.9944
 TWY  O3   O  OH1   0  -0.665  20.7537  61.4881  27.3639
 TWY  H4   H  HCH1  0   0.301  20.3297  63.6490  25.9063
 TWY  H51  H  HCH2  0   0.262  19.2100  63.7729  23.7131
 TWY  H52  H  HCH2  0   0.217  18.9457  62.0244  23.7085
 TWY  H1   H  HCH1  0   0.185  20.8621  60.6322  23.3981
 TWY  HO1  H  HOH1  0   0.461  23.1058  60.6323  23.0527
 TWY  H2   H  HCH1  0   0.222  22.4314  62.1674  25.5223
 TWY  HO2  H  HOH1  0   0.460  22.6930  60.0631  26.3392
 TWY  H3   H  HCH1  0   0.214  19.7970  60.6502  25.7286
 TWY  HO3  H  HOH1  0   0.450  19.9323  61.5919  27.8585
 TWY  HS4  H  HSH1  0   0.240  18.0536  64.1874  26.5194

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
 TWY  O1  C1   single  1.388  0.020  1.388
 TWY  O5  C1   single  1.395  0.020  1.395
 TWY  O5  C5   single  1.410  0.020  1.410
 TWY  C1  C2   single  1.531  0.020  1.531
 TWY  C5  C4   single  1.522  0.020  1.522
 TWY  C2  O2   single  1.406  0.020  1.406
 TWY  C2  C3   single  1.525  0.020  1.525
 TWY  C4  C3   single  1.527  0.020  1.527
 TWY  C4  S4   single  1.827  0.020  1.827
 TWY  C3  O3   single  1.403  0.020  1.403
 TWY  C4  H4   single  0.970  0.020  1.090
 TWY  C5  H51  single  0.970  0.020  1.090
 TWY  C5  H52  single  0.970  0.020  1.090
 TWY  C1  H1   single  0.970  0.020  1.090
 TWY  O1  HO1  single  0.850  0.020  0.980
 TWY  C2  H2   single  0.970  0.020  1.090
 TWY  O2  HO2  single  0.850  0.020  0.980
 TWY  C3  H3   single  0.970  0.020  1.090
 TWY  O3  HO3  single  0.850  0.020  0.980
 TWY  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
 TWY  HS4  S4  C4    97.70  3.000
 TWY  H4   C4  C3   109.48  3.000
 TWY  H4   C4  C5   110.27  3.000
 TWY  C3   C4  C5   109.98  3.000
 TWY  H4   C4  S4   107.80  3.000
 TWY  C3   C4  S4   108.82  3.000
 TWY  C5   C4  S4   110.45  3.000
 TWY  H52  C5  H51  107.81  3.000
 TWY  H52  C5  O5   110.88  3.000
 TWY  H51  C5  O5   107.12  3.000
 TWY  H52  C5  C4   109.72  3.000
 TWY  H51  C5  C4   110.48  3.000
 TWY  O5   C5  C4   110.76  3.000
 TWY  C1   O5  C5   112.78  3.000
 TWY  H1   C1  C2   108.77  3.000
 TWY  H1   C1  O1   111.10  3.000
 TWY  C2   C1  O1   112.06  3.000
 TWY  H1   C1  O5   110.04  3.000
 TWY  C2   C1  O5   110.35  3.000
 TWY  O1   C1  O5   104.49  3.000
 TWY  HO1  O1  C1   108.63  3.000
 TWY  H2   C2  C3   108.49  3.000
 TWY  H2   C2  O2   111.38  3.000
 TWY  C3   C2  O2   111.98  3.000
 TWY  H2   C2  C1   107.74  3.000
 TWY  C3   C2  C1   110.31  3.000
 TWY  O2   C2  C1   106.86  3.000
 TWY  HO2  O2  C2   108.67  3.000
 TWY  H3   C3  O3   110.92  3.000
 TWY  H3   C3  C2   108.00  3.000
 TWY  O3   C3  C2   107.67  3.000
 TWY  H3   C3  C4   108.23  3.000
 TWY  O3   C3  C4   112.70  3.000
 TWY  C2   C3  C4   109.21  3.000
 TWY  HO3  O3  C3   108.30  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
 TWY  Var_01  H51  C5  O5  C1  -177.21  30.0  1

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
 TWY  chir_01  C4  C5  C3  S4  positiv
 TWY  chir_02  C1  O5  O1  C2  negativ
 TWY  chir_03  C2  O2  C1  C3  negativ
 TWY  chir_04  C3  O3  C2  C4  positiv

