# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 00:21:42 2022
#   Inital geometry file: a 51 line input string
#   Ligand name: 2,6-dideoxy-4-thio-beta-D-ribo-hexopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1O[C@@H](O)C[C@H](O)[C@@H]1S
#
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
 DSR  DSR  2,6-dideoxy-4-thio-beta-D-ribo-hexopyranose  D-saccharide  22  10  .  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_DSR
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
 DSR  C1   C  CH1   0   0.293  -2.3347  5.5601  -1.6007
 DSR  C2   C  CH2   0  -0.499  -1.5713  4.3414  -1.1180
 DSR  C3   C  CH1   0   0.015  -2.4650  3.1079  -1.0981
 DSR  C4   C  CH1   0  -0.405  -3.7610  3.4206  -0.3407
 DSR  C5   C  CH1   0   0.080  -4.4145  4.7089  -0.8510
 DSR  C6   C  CH3   0  -0.679  -5.6160  5.1325  -0.0312
 DSR  O1   O  OH1   0  -0.656  -1.5211  6.6717  -1.4881
 DSR  O3   O  OH1   0  -0.666  -2.7349  2.7339  -2.4341
 DSR  O5   O  O2    0  -0.498  -3.4716  5.7636  -0.7900
 DSR  S4   S  S2    0  -0.242  -4.8763  1.9842  -0.5270
 DSR  H1   H  HCH1  0   0.182  -2.6657  5.4121  -2.6422
 DSR  H2   H  HCH2  0   0.251  -0.7036  4.1526  -1.7536
 DSR  H22  H  HCH2  0   0.243  -1.2036  4.5314  -0.1055
 DSR  H3   H  HCH1  0   0.247  -1.9422  2.3018  -0.5713
 DSR  H4   H  HCH1  0   0.286  -3.5257  3.5276   0.7219
 DSR  H5   H  HCH1  0   0.208  -4.7296  4.5468  -1.8934
 DSR  H61  H  HCH3  0   0.241  -6.0217  6.0740  -0.4021
 DSR  H62  H  HCH3  0   0.231  -6.4063  4.3864  -0.0923
 DSR  H63  H  HCH3  0   0.226  -5.3491  5.2622   1.0193
 DSR  HO1  H  HOH1  0   0.456  -1.9132  7.4030  -1.9775
 DSR  HO3  H  HOH1  0   0.456  -2.9139  1.7893  -2.4658
 DSR  H4S  H  HSH1  0   0.230  -5.4814  2.0725   0.6611

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
 DSR  C1  C2   single  1.517  0.020  1.517
 DSR  C1  O1   single  1.382  0.020  1.382
 DSR  C1  O5   single  1.411  0.020  1.411
 DSR  C1  H1   single  0.970  0.020  1.090
 DSR  C2  C3   single  1.523  0.020  1.523
 DSR  C2  H2   single  0.970  0.020  1.090
 DSR  C2  H22  single  0.970  0.020  1.090
 DSR  C3  C4   single  1.533  0.020  1.533
 DSR  C3  O3   single  1.413  0.020  1.413
 DSR  C3  H3   single  0.970  0.020  1.090
 DSR  C4  C5   single  1.532  0.020  1.532
 DSR  C4  S4   single  1.828  0.020  1.828
 DSR  C4  H4   single  0.970  0.020  1.090
 DSR  C5  C6   single  1.515  0.020  1.515
 DSR  C5  O5   single  1.416  0.020  1.416
 DSR  C5  H5   single  0.970  0.020  1.090
 DSR  C6  H61  single  0.970  0.020  1.090
 DSR  C6  H62  single  0.970  0.020  1.090
 DSR  C6  H63  single  0.970  0.020  1.090
 DSR  O1  HO1  single  0.850  0.020  0.980
 DSR  O3  HO3  single  0.850  0.020  0.980
 DSR  S4  H4S  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
 DSR  H1   C1  O5   108.67  3.000
 DSR  H1   C1  O1   111.19  3.000
 DSR  O5   C1  O1   108.15  3.000
 DSR  H1   C1  C2   110.11  3.000
 DSR  O5   C1  C2   109.79  3.000
 DSR  O1   C1  C2   108.91  3.000
 DSR  H22  C2  H2   107.56  3.000
 DSR  H22  C2  C3   109.01  3.000
 DSR  H2   C2  C3   109.50  3.000
 DSR  H22  C2  C1   108.92  3.000
 DSR  H2   C2  C1   110.70  3.000
 DSR  C3   C2  C1   111.06  3.000
 DSR  H3   C3  O3   110.54  3.000
 DSR  H3   C3  C4   108.41  3.000
 DSR  O3   C3  C4   111.07  3.000
 DSR  H3   C3  C2   108.79  3.000
 DSR  O3   C3  C2   108.30  3.000
 DSR  C4   C3  C2   109.71  3.000
 DSR  H4   C4  S4   107.88  3.000
 DSR  H4   C4  C5   109.46  3.000
 DSR  S4   C4  C5   111.50  3.000
 DSR  H4   C4  C3   108.55  3.000
 DSR  S4   C4  C3   107.76  3.000
 DSR  C5   C4  C3   111.56  3.000
 DSR  H5   C5  O5   109.94  3.000
 DSR  H5   C5  C6   109.06  3.000
 DSR  O5   C5  C6   107.25  3.000
 DSR  H5   C5  C4   108.28  3.000
 DSR  O5   C5  C4   109.14  3.000
 DSR  C6   C5  C4   113.15  3.000
 DSR  H63  C6  H62  108.24  3.000
 DSR  H63  C6  H61  108.41  3.000
 DSR  H62  C6  H61  107.62  3.000
 DSR  H63  C6  C5   111.10  3.000
 DSR  H62  C6  C5   110.72  3.000
 DSR  H61  C6  C5   110.63  3.000
 DSR  HO1  O1  C1   109.24  3.000
 DSR  HO3  O3  C3   109.05  3.000
 DSR  C5   O5  C1   113.85  3.000
 DSR  H4S  S4  C4    97.69  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
 DSR  chir_01  C1  C2  O1  O5  positiv
 DSR  chir_02  C3  O3  C4  C2  positiv
 DSR  chir_03  C4  S4  C3  C5  negativ
 DSR  chir_04  C5  O5  C4  C6  negativ

