# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 19:09:23 2022
#   Inital geometry file: a 65 line input string
#   Ligand name: 6-deoxy-4-O-sulfo-alpha-L-galactopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1O[C@@H](O)[C@@H](O)[C@H](O)[C@@H]1O[S](O)(=O)=O
#
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
 X34  X34  6-deoxy-4-O-sulfo-alpha-L-galactopyranose  L-saccharide  26  15  .  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_X34
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
 X34  C5   C  CH1    0   0.021   1.3280  -22.0506  -0.5893
 X34  C4   C  CH1    0  -0.013   0.4229  -23.2561  -0.3358
 X34  C3   C  CH1    0   0.049  -0.6803  -22.8245   0.6258
 X34  C2   C  CH1    0  -0.075  -0.0673  -22.2640   1.9034
 X34  C1   C  CH1    0   0.258   0.9523  -21.1572   1.5901
 X34  O5   O  O2     0  -0.492   1.8712  -21.5720   0.6371
 X34  C6   C  CH3    0  -0.673   2.4969  -22.3246  -1.5098
 X34  O3   O  OH1    0  -0.660  -1.5367  -23.9015   0.8903
 X34  O2   O  OH1    0  -0.668  -1.1261  -21.7548   2.6901
 X34  O6   O  OS    -1  -0.732   2.2168  -26.4542   0.3548
 X34  O7   O  OS     0  -0.733   1.7915  -25.4880  -1.8741
 X34  O8   O  OS     0  -0.731  -0.0750  -26.3272  -0.5374
 X34  O4   O  OC2    0  -0.625   1.1783  -24.3135   0.2369
 X34  H5   H  HCH1   0   0.222   0.7020  -21.2766  -1.0508
 X34  H4   H  HCH1   0   0.253  -0.0291  -23.5541  -1.2893
 X34  H3   H  HCH1   0   0.208  -1.2272  -22.0110   0.1229
 X34  H2   H  HCH1   0   0.238   0.4571  -23.0709   2.4292
 X34  H1   H  HCH1   0   0.213   1.5467  -20.9524   2.4922
 X34  H63  H  HCH3   0   0.233   3.0683  -21.4101  -1.6693
 X34  H62  H  HCH3   0   0.228   3.1638  -23.0831  -1.1037
 X34  H61  H  HCH3   0   0.229   2.1408  -22.6698  -2.4790
 X34  HO3  H  HOH1   0   0.446  -2.1965  -23.6019   1.5247
 X34  HO2  H  HOH1   0   0.463  -0.8465  -21.7206   3.6110
 X34  O1   O  OH1    0  -0.667   0.3208  -19.9897   1.1461
 X34  HO1  H  HOH1   0   0.447  -0.5095  -19.9010   1.6304
 X34  S1   S  S      0   1.561   1.2776  -25.7708  -0.5308

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
 X34  O7  S1   deloc   1.466  0.020  1.466
 X34  C6  C5   single  1.513  0.020  1.513
 X34  O8  S1   deloc   1.463  0.020  1.463
 X34  S1  O6   deloc   1.461  0.020  1.461
 X34  S1  O4   single  1.650  0.020  1.650
 X34  C5  C4   single  1.529  0.020  1.529
 X34  C5  O5   single  1.424  0.020  1.424
 X34  C4  O4   single  1.420  0.020  1.420
 X34  C4  C3   single  1.526  0.020  1.526
 X34  C3  O3   single  1.401  0.020  1.401
 X34  C3  C2   single  1.524  0.020  1.524
 X34  O5  C1   single  1.387  0.020  1.387
 X34  C1  C2   single  1.537  0.020  1.537
 X34  C2  O2   single  1.414  0.020  1.414
 X34  C5  H5   single  0.970  0.020  1.090
 X34  C4  H4   single  0.970  0.020  1.090
 X34  C3  H3   single  0.970  0.020  1.090
 X34  C2  H2   single  0.970  0.020  1.090
 X34  C1  H1   single  0.970  0.020  1.090
 X34  C6  H63  single  0.970  0.020  1.090
 X34  C6  H62  single  0.970  0.020  1.090
 X34  C6  H61  single  0.970  0.020  1.090
 X34  O3  HO3  single  0.850  0.020  0.980
 X34  O2  HO2  single  0.850  0.020  0.980
 X34  C1  O1   single  1.400  0.020  1.400
 X34  O1  HO1  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
 X34  H5   C5  C6   108.22  3.000
 X34  H5   C5  O5   110.05  3.000
 X34  C6   C5  O5   106.87  3.000
 X34  H5   C5  C4   106.75  3.000
 X34  O5   C5  C4   110.37  3.000
 X34  C6   C5  C4   114.56  3.000
 X34  H4   C4  O4   111.56  3.000
 X34  H4   C4  C3   109.08  3.000
 X34  O4   C4  C3   109.94  3.000
 X34  H4   C4  C5   108.32  3.000
 X34  C3   C4  C5   108.03  3.000
 X34  O4   C4  C5   109.82  3.000
 X34  H3   C3  O3   110.50  3.000
 X34  H3   C3  C2   108.11  3.000
 X34  O3   C3  C2   111.74  3.000
 X34  H3   C3  C4   106.26  3.000
 X34  C2   C3  C4   109.97  3.000
 X34  O3   C3  C4   110.09  3.000
 X34  H2   C2  O2   110.87  3.000
 X34  H2   C2  C1   108.08  3.000
 X34  O2   C2  C1   110.54  3.000
 X34  H2   C2  C3   108.89  3.000
 X34  O2   C2  C3   107.32  3.000
 X34  C1   C2  C3   111.15  3.000
 X34  O1   C1  H1   110.41  3.000
 X34  O1   C1  O5   109.29  3.000
 X34  H1   C1  O5   105.14  3.000
 X34  O1   C1  C2   111.47  3.000
 X34  H1   C1  C2   108.99  3.000
 X34  O5   C1  C2   111.35  3.000
 X34  C1   O5  C5   116.07  3.000
 X34  H61  C6  H62  108.16  3.000
 X34  H61  C6  H63  107.89  3.000
 X34  H62  C6  H63  108.55  3.000
 X34  H61  C6  C5   110.26  3.000
 X34  H62  C6  C5   111.87  3.000
 X34  H63  C6  C5   110.00  3.000
 X34  HO3  O3  C3   107.70  3.000
 X34  HO2  O2  C2   109.11  3.000
 X34  S1   O4  C4   120.13  3.000
 X34  HO1  O1  C1   107.80  3.000
 X34  O4   S1  O8   106.40  3.000
 X34  O4   S1  O7   106.08  3.000
 X34  O8   S1  O7   113.18  3.000
 X34  O4   S1  O6    99.78  3.000
 X34  O8   S1  O6   114.80  3.000
 X34  O7   S1  O6   114.87  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
 X34  Var_01  O7  S1  O4  C4  55.91  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
 X34  chir_01  C5  C6  C4  O5  negativ
 X34  chir_02  C4  O4  C5  C3  positiv
 X34  chir_03  C3  O3  C4  C2  positiv
 X34  chir_04  C2  O2  C3  C1  negativ
 X34  chir_05  C1  O5  O1  C2  negativ

