# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 22:19:32 2022
#   Inital geometry file: a 91 line input string
#   Ligand name: methyl 3-O-methyl-2,6-di-O-sulfo-alpha-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1O[C@H](CO[S](O)(=O)=O)[C@@H](O)[C@H](OC)[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
 GU3  GU3  'methyl 3-O-methyl-2,6-di-O-sulfo-alpha-D-glucopyranoside'  D-saccharide  36  22  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GU3
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
 GU3  O4   O  OH1    0  -0.657  58.4344  -2.4896  -21.2721
 GU3  O50  O  OS     0  -0.741  53.4881  -3.1606  -24.1610
 GU3  S6   S  S      0   1.573  54.0563  -3.6714  -22.9118
 GU3  O51  O  OS    -1  -0.730  53.2365  -3.4390  -21.7261
 GU3  O52  O  OS     0  -0.742  54.6090  -5.0241  -23.0243
 GU3  O6   O  OC2    0  -0.616  55.3376  -2.6978  -22.5831
 GU3  C6   C  CH2    0  -0.185  56.4498  -2.7372  -23.4603
 GU3  C5   C  CH1    0  -0.030  57.3139  -1.5235  -23.1970
 GU3  O5   O  O2     0  -0.502  56.6034  -0.3808  -23.6429
 GU3  C1   C  CH1    0   0.268  57.3064   0.8279  -23.5531
 GU3  O1   O  O2     0  -0.491  58.4693   0.8346  -24.3084
 GU3  C8   C  CH3    0  -0.406  58.2566   0.8135  -25.7038
 GU3  C2   C  CH1    0  -0.015  57.6738   1.0965  -22.0949
 GU3  O2   O  OC2    0  -0.618  58.4631   2.2611  -21.9646
 GU3  S2   S  S      0   1.565  57.7216   3.6914  -21.6132
 GU3  O54  O  OS     0  -0.734  56.9328   3.4415  -20.4051
 GU3  O55  O  OS     0  -0.733  56.9101   4.0123  -22.7907
 GU3  O53  O  OS    -1  -0.726  58.8905   4.5438  -21.4208
 GU3  C3   C  CH1    0   0.005  58.4594  -0.0665  -21.4970
 GU3  O3   O  O2     0  -0.489  58.6176   0.1409  -20.1154
 GU3  C7   C  CH3    0  -0.405  59.9410   0.3299  -19.6820
 GU3  C4   C  CH1    0   0.015  57.7053  -1.3751  -21.7215
 GU3  HO4  H  HOH1   0   0.444  59.2514  -2.5522  -21.7806
 GU3  H61  H  HCH2   0   0.226  57.0429  -3.6409  -23.2997
 GU3  H62  H  HCH2   0   0.235  56.1371  -2.7272  -24.5101
 GU3  H5   H  HCH1   0   0.234  58.2312  -1.6599  -23.7895
 GU3  H1   H  HCH1   0   0.233  56.6048   1.5901  -23.9146
 GU3  H8   H  HCH3   0   0.212  57.5621   1.6010  -26.0162
 GU3  H8A  H  HCH3   0   0.236  59.2178   0.9904  -26.1832
 GU3  H8B  H  HCH3   0   0.216  57.8664  -0.1460  -26.0537
 GU3  H2   H  HCH1   0   0.247  56.7336   1.1894  -21.5369
 GU3  H3   H  HCH1   0   0.226  59.4367  -0.1347  -21.9984
 GU3  H7   H  HCH3   0   0.207  60.4066   1.2138  -20.1285
 GU3  H7A  H  HCH3   0   0.229  59.9133   0.4697  -18.6014
 GU3  H7B  H  HCH3   0   0.205  60.5769  -0.5361  -19.8961
 GU3  H4   H  HCH1   0   0.244  56.7946  -1.3452  -21.1160

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
 GU3  O4   C4   single  1.406  0.020  1.406
 GU3  O4   HO4  single  0.850  0.020  0.980
 GU3  O50  S6   deloc   1.464  0.020  1.464
 GU3  S6   O51  deloc   1.460  0.020  1.460
 GU3  S6   O52  deloc   1.466  0.020  1.466
 GU3  S6   O6   single  1.642  0.020  1.642
 GU3  O6   C6   single  1.417  0.020  1.417
 GU3  C6   C5   single  1.513  0.020  1.513
 GU3  C6   H61  single  0.970  0.020  1.090
 GU3  C6   H62  single  0.970  0.020  1.090
 GU3  C5   O5   single  1.417  0.020  1.417
 GU3  C5   C4   single  1.534  0.020  1.534
 GU3  C5   H5   single  0.970  0.020  1.090
 GU3  O5   C1   single  1.401  0.020  1.401
 GU3  C1   O1   single  1.387  0.020  1.387
 GU3  C1   C2   single  1.528  0.020  1.528
 GU3  C1   H1   single  0.970  0.020  1.090
 GU3  O1   C8   single  1.412  0.020  1.412
 GU3  C8   H8   single  0.970  0.020  1.090
 GU3  C8   H8A  single  0.970  0.020  1.090
 GU3  C8   H8B  single  0.970  0.020  1.090
 GU3  C2   O2   single  1.413  0.020  1.413
 GU3  C2   C3   single  1.526  0.020  1.526
 GU3  C2   H2   single  0.970  0.020  1.090
 GU3  O2   S2   single  1.649  0.020  1.649
 GU3  S2   O54  deloc   1.464  0.020  1.464
 GU3  S2   O55  deloc   1.466  0.020  1.466
 GU3  S2   O53  deloc   1.459  0.020  1.459
 GU3  C3   O3   single  1.406  0.020  1.406
 GU3  C3   C4   single  1.527  0.020  1.527
 GU3  C3   H3   single  0.970  0.020  1.090
 GU3  O3   C7   single  1.405  0.020  1.405
 GU3  C7   H7   single  0.970  0.020  1.090
 GU3  C7   H7A  single  0.970  0.020  1.090
 GU3  C7   H7B  single  0.970  0.020  1.090
 GU3  C4   H4   single  0.970  0.020  1.090

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
 GU3  HO4  O4  C4   108.80  3.000
 GU3  O6   S6  O52  105.57  3.000
 GU3  O6   S6  O51  100.44  3.000
 GU3  O52  S6  O51  114.90  3.000
 GU3  O6   S6  O50  105.46  3.000
 GU3  O52  S6  O50  113.75  3.000
 GU3  O51  S6  O50  114.79  3.000
 GU3  C6   O6  S6   118.16  3.000
 GU3  H62  C6  H61  107.65  3.000
 GU3  H62  C6  C5   108.81  3.000
 GU3  H61  C6  C5   109.13  3.000
 GU3  H62  C6  O6   111.65  3.000
 GU3  H61  C6  O6   110.98  3.000
 GU3  C5   C6  O6   108.56  3.000
 GU3  H5   C5  C4   108.50  3.000
 GU3  H5   C5  O5   110.39  3.000
 GU3  C4   C5  O5   110.64  3.000
 GU3  H5   C5  C6   106.44  3.000
 GU3  C4   C5  C6   113.00  3.000
 GU3  O5   C5  C6   107.79  3.000
 GU3  C1   O5  C5   115.07  3.000
 GU3  H1   C1  C2   110.25  3.000
 GU3  H1   C1  O1   110.70  3.000
 GU3  C2   C1  O1   108.51  3.000
 GU3  H1   C1  O5   104.91  3.000
 GU3  C2   C1  O5   109.49  3.000
 GU3  O1   C1  O5   112.96  3.000
 GU3  C8   O1  C1   114.33  3.000
 GU3  H8B  C8  H8A  108.47  3.000
 GU3  H8B  C8  H8   108.27  3.000
 GU3  H8A  C8  H8   108.50  3.000
 GU3  H8B  C8  O1   112.53  3.000
 GU3  H8A  C8  O1   107.45  3.000
 GU3  H8   C8  O1   111.51  3.000
 GU3  H2   C2  C3   107.85  3.000
 GU3  H2   C2  O2   111.22  3.000
 GU3  C3   C2  O2   107.73  3.000
 GU3  H2   C2  C1   107.11  3.000
 GU3  C3   C2  C1   111.34  3.000
 GU3  O2   C2  C1   111.55  3.000
 GU3  S2   O2  C2   118.91  3.000
 GU3  O53  S2  O55  114.93  3.000
 GU3  O53  S2  O54  114.98  3.000
 GU3  O55  S2  O54  113.70  3.000
 GU3  O53  S2  O2   100.05  3.000
 GU3  O55  S2  O2   105.53  3.000
 GU3  O54  S2  O2   105.66  3.000
 GU3  H3   C3  C4   108.57  3.000
 GU3  H3   C3  O3   110.91  3.000
 GU3  C4   C3  O3   109.05  3.000
 GU3  H3   C3  C2   109.02  3.000
 GU3  C4   C3  C2   109.96  3.000
 GU3  O3   C3  C2   109.30  3.000
 GU3  C7   O3  C3   115.39  3.000
 GU3  H7B  C7  H7A  108.05  3.000
 GU3  H7B  C7  H7   108.16  3.000
 GU3  H7A  C7  H7   108.17  3.000
 GU3  H7B  C7  O3   112.34  3.000
 GU3  H7A  C7  O3   107.40  3.000
 GU3  H7   C7  O3   112.55  3.000
 GU3  H4   C4  C3   107.84  3.000
 GU3  H4   C4  C5   108.83  3.000
 GU3  C3   C4  C5   110.51  3.000
 GU3  H4   C4  O4   106.05  3.000
 GU3  C3   C4  O4   112.11  3.000
 GU3  C5   C4  O4   111.30  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
 GU3  Var_01  C5   C6  O6  S6  164.58  30.0  3
 GU3  Var_02  O54  S2  O2  C2   53.95  30.0  3
 GU3  Var_03  H8   C8  O1  C1   51.83  30.0  3
 GU3  Var_04  H7   C7  O3  C3   61.47  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
 GU3  chir_01  C5  C6  O5  C4  negativ
 GU3  chir_02  C1  O5  O1  C2  positiv
 GU3  chir_03  C2  O2  C3  C1  positiv
 GU3  chir_04  C3  O3  C4  C2  negativ
 GU3  chir_05  C4  O4  C3  C5  negativ

