# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 21:14:07 2022
#   Inital geometry file: a 65 line input string
#   Ligand name: 6-deoxy-2-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[S](O)(=O)=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
 X6Y  X6Y  6-deoxy-2-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 OK (reasonable std)
;

data_comp_X6Y
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
 X6Y  C5   C  CH1    0   0.025  6.7391  -10.1142   3.2020
 X6Y  C6   C  CH3    0  -0.703  7.4380   -9.8639   4.5233
 X6Y  C2   C  CH1    0  -0.008  4.3909  -10.7494   1.6850
 X6Y  C4   C  CH1    0  -0.028  6.3317  -11.5754   3.0014
 X6Y  C3   C  CH1    0   0.024  5.5747  -11.7079   1.6771
 X6Y  C1   C  CH1    0   0.239  4.8650   -9.3179   1.9639
 X6Y  O5   O  O2     0  -0.497  5.6007   -9.2649   3.1544
 X6Y  O4   O  OH1    0  -0.668  5.5019  -12.0579   4.0303
 X6Y  O1   O  OH1    0  -0.662  5.5960   -8.8773   0.8640
 X6Y  O3   O  OH1    0  -0.661  5.0975  -13.0081   1.4539
 X6Y  O6   O  OS     0  -0.736  1.7690  -12.2499   0.8749
 X6Y  O7   O  OS    -1  -0.736  1.6119   -9.8480   1.3183
 X6Y  O8   O  OS     0  -0.728  1.8269  -10.6596  -1.0033
 X6Y  O2   O  OC2    0  -0.622  3.7343  -10.7929   0.4308
 X6Y  H5   H  HCH1   0   0.213  7.4370   -9.8610   2.3930
 X6Y  H61  H  HCH3   0   0.246  7.7881   -8.8339   4.5872
 X6Y  H63  H  HCH3   0   0.227  6.7796  -10.0456   5.3740
 X6Y  H62  H  HCH3   0   0.234  8.3072  -10.5153   4.6170
 X6Y  H2   H  HCH1   0   0.247  3.7142  -11.0356   2.4975
 X6Y  H4   H  HCH1   0   0.227  7.2582  -12.1666   2.9316
 X6Y  H3   H  HCH1   0   0.220  6.2707  -11.4067   0.8806
 X6Y  H1   H  HCH1   0   0.228  3.9945   -8.6773   2.1418
 X6Y  HO4  H  HOH1   0   0.454  6.0295  -12.1765   4.8253
 X6Y  HO1  H  HOH1   0   0.458  5.7176   -7.9244   0.9333
 X6Y  HO3  H  HOH1   0   0.449  5.8551  -13.5913   1.3448
 X6Y  S1   S  S      0   1.558  2.0893  -10.8983   0.4131

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
 X6Y  O8  S1   deloc   1.460  0.020  1.460
 X6Y  O2  S1   single  1.648  0.020  1.648
 X6Y  O2  C2   single  1.416  0.020  1.416
 X6Y  S1  O6   deloc   1.464  0.020  1.464
 X6Y  S1  O7   deloc   1.466  0.020  1.466
 X6Y  O1  C1   single  1.392  0.020  1.392
 X6Y  O3  C3   single  1.403  0.020  1.403
 X6Y  C2  C3   single  1.523  0.020  1.523
 X6Y  C2  C1   single  1.534  0.020  1.534
 X6Y  C3  C4   single  1.531  0.020  1.531
 X6Y  C1  O5   single  1.400  0.020  1.400
 X6Y  C4  C5   single  1.530  0.020  1.530
 X6Y  C4  O4   single  1.407  0.020  1.407
 X6Y  O5  C5   single  1.421  0.020  1.421
 X6Y  C5  C6   single  1.516  0.020  1.516
 X6Y  C5  H5   single  0.970  0.020  1.090
 X6Y  C6  H61  single  0.970  0.020  1.090
 X6Y  C6  H63  single  0.970  0.020  1.090
 X6Y  C6  H62  single  0.970  0.020  1.090
 X6Y  C2  H2   single  0.970  0.020  1.090
 X6Y  C4  H4   single  0.970  0.020  1.090
 X6Y  C3  H3   single  0.970  0.020  1.090
 X6Y  C1  H1   single  0.970  0.020  1.090
 X6Y  O4  HO4  single  0.850  0.020  0.980
 X6Y  O1  HO1  single  0.850  0.020  0.980
 X6Y  O3  HO3  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
 X6Y  H5   C5  O5   110.28  3.000
 X6Y  H5   C5  C4   107.03  3.000
 X6Y  O5   C5  C4   110.67  3.000
 X6Y  H5   C5  C6   108.13  3.000
 X6Y  O5   C5  C6   107.45  3.000
 X6Y  C4   C5  C6   113.25  3.000
 X6Y  H62  C6  H63  108.34  3.000
 X6Y  H62  C6  H61  107.67  3.000
 X6Y  H63  C6  H61  107.79  3.000
 X6Y  H62  C6  C5   110.11  3.000
 X6Y  H63  C6  C5   111.96  3.000
 X6Y  H61  C6  C5   110.82  3.000
 X6Y  H2   C2  O2   111.25  3.000
 X6Y  H2   C2  C1   107.46  3.000
 X6Y  O2   C2  C1   109.45  3.000
 X6Y  H2   C2  C3   108.64  3.000
 X6Y  C1   C2  C3   110.37  3.000
 X6Y  O2   C2  C3   109.66  3.000
 X6Y  H4   C4  O4   111.00  3.000
 X6Y  H4   C4  C3   108.34  3.000
 X6Y  O4   C4  C3   108.13  3.000
 X6Y  H4   C4  C5   107.28  3.000
 X6Y  O4   C4  C5   112.87  3.000
 X6Y  C3   C4  C5   109.13  3.000
 X6Y  H3   C3  O3   110.72  3.000
 X6Y  H3   C3  C4   106.85  3.000
 X6Y  O3   C3  C4   112.71  3.000
 X6Y  H3   C3  C2   108.86  3.000
 X6Y  C4   C3  C2   108.98  3.000
 X6Y  O3   C3  C2   108.64  3.000
 X6Y  H1   C1  O1   111.13  3.000
 X6Y  H1   C1  O5   104.91  3.000
 X6Y  O1   C1  O5   112.57  3.000
 X6Y  H1   C1  C2   109.25  3.000
 X6Y  O5   C1  C2   110.63  3.000
 X6Y  O1   C1  C2   108.30  3.000
 X6Y  C1   O5  C5   115.26  3.000
 X6Y  HO4  O4  C4   108.87  3.000
 X6Y  HO1  O1  C1   108.82  3.000
 X6Y  HO3  O3  C3   108.17  3.000
 X6Y  S1   O2  C2   118.30  3.000
 X6Y  O2   S1  O8   100.33  3.000
 X6Y  O2   S1  O7   105.81  3.000
 X6Y  O8   S1  O7   115.04  3.000
 X6Y  O7   S1  O6   113.29  3.000
 X6Y  O2   S1  O6   105.90  3.000
 X6Y  O8   S1  O6   114.69  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
 X6Y  Var_01  O8  S1  O2  C2  169.71  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
 X6Y  chir_01  C5  C4  O5  C6  negativ
 X6Y  chir_02  C2  O2  C1  C3  positiv
 X6Y  chir_03  C4  O4  C3  C5  negativ
 X6Y  chir_04  C3  O3  C2  C4  negativ
 X6Y  chir_05  C1  O1  O5  C2  positiv

