# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 10:16:17 2022
#   Inital geometry file: a 79 line input string
#   Ligand name: 2,3-di-O-methyl-6-O-sulfo-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1[C@@H](O)O[C@H](CO[S](O)(=O)=O)[C@@H](O)[C@@H]1OC
#
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
 U9G  U9G  2,3-di-O-methyl-6-O-sulfo-alpha-D-glucopyranose  D-saccharide  33  18  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U9G
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
 U9G  O4    O  OH1    0  -0.669  29.5495   1.9006  46.3098
 U9G  C4    C  CH1    0   0.030  30.2209   1.0986  47.2513
 U9G  C5    C  CH1    0  -0.007  29.2146   0.7350  48.3444
 U9G  O5    O  O2     0  -0.501  29.8540   0.0229  49.3890
 U9G  C6    C  CH2    0  -0.187  28.0657  -0.1188  47.8437
 U9G  O6    O  OC2    0  -0.616  28.5916  -1.2875  47.2388
 U9G  S37   S  S      0   1.574  27.5618  -2.2944  46.4419
 U9G  O38   O  OS    -1  -0.731  28.5009  -3.3101  45.9748
 U9G  O39   O  OS     0  -0.742  26.9571  -1.4898  45.3778
 U9G  O3A   O  OS     0  -0.743  26.6021  -2.7557  47.4479
 U9G  C3    C  CH1    0  -0.018  31.4401   1.8173  47.8335
 U9G  O3    O  O2     0  -0.495  32.4062   1.9601  46.8149
 U9G  C3D   C  CH3    0  -0.411  32.7173   3.2836  46.4544
 U9G  C2    C  CH1    0   0.009  32.0160   0.9658  48.9671
 U9G  O2    O  O2     0  -0.485  33.2333   1.4161  49.4952
 U9G  C3G   C  CH3    0  -0.399  33.3194   2.6935  50.0879
 U9G  C1    C  CH1    0   0.216  30.9245   0.6898  50.0064
 U9G  O1    O  OH1    0  -0.656  30.5306   1.8884  50.5908
 U9G  H4    H  HCH1   0   0.220  30.5814   0.1700  46.7878
 U9G  H5    H  HCH1   0   0.231  28.7637   1.6618  48.7276
 U9G  H61   H  HCH2   0   0.234  27.4159  -0.3721  48.6885
 U9G  H62   H  HCH2   0   0.228  27.4747   0.4677  47.1354
 U9G  H3    H  HCH1   0   0.229  31.1197   2.8002  48.2038
 U9G  H3D1  H  HCH3   0   0.232  33.4434   3.2382  45.6429
 U9G  H3D2  H  HCH3   0   0.207  31.8425   3.8378  46.0997
 U9G  H3D3  H  HCH3   0   0.210  33.1645   3.8488  47.2788
 U9G  H2    H  HCH1   0   0.245  32.2647  -0.0128  48.5399
 U9G  H3G1  H  HCH3   0   0.223  34.3749   2.9672  50.0838
 U9G  H3G2  H  HCH3   0   0.206  32.7758   3.4678  49.5412
 U9G  H3G3  H  HCH3   0   0.212  32.9694   2.7036  51.1221
 U9G  H1    H  HCH1   0   0.239  31.2999  -0.0147  50.7577
 U9G  HO4   H  HOH1   0   0.456  30.0527   1.8947  45.4903
 U9G  HO1   H  HOH1   0   0.462  30.0241   1.7019  51.3892

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
 U9G  O4   C4    single  1.407  0.020  1.407
 U9G  C4   C5    single  1.530  0.020  1.530
 U9G  C4   C3    single  1.530  0.020  1.530
 U9G  C4   H4    single  0.970  0.020  1.090
 U9G  C5   O5    single  1.417  0.020  1.417
 U9G  C5   C6    single  1.516  0.020  1.516
 U9G  C5   H5    single  0.970  0.020  1.090
 U9G  O5   C1    single  1.404  0.020  1.404
 U9G  C6   O6    single  1.417  0.020  1.417
 U9G  C6   H61   single  0.970  0.020  1.090
 U9G  C6   H62   single  0.970  0.020  1.090
 U9G  O6   S37   single  1.646  0.020  1.646
 U9G  S37  O38   deloc   1.460  0.020  1.460
 U9G  S37  O39   deloc   1.465  0.020  1.465
 U9G  S37  O3A   deloc   1.465  0.020  1.465
 U9G  C3   O3    single  1.411  0.020  1.411
 U9G  C3   C2    single  1.530  0.020  1.530
 U9G  C3   H3    single  0.970  0.020  1.090
 U9G  O3   C3D   single  1.407  0.020  1.407
 U9G  C3D  H3D1  single  0.970  0.020  1.090
 U9G  C3D  H3D2  single  0.970  0.020  1.090
 U9G  C3D  H3D3  single  0.970  0.020  1.090
 U9G  C2   O2    single  1.401  0.020  1.401
 U9G  C2   C1    single  1.532  0.020  1.532
 U9G  C2   H2    single  0.970  0.020  1.090
 U9G  O2   C3G   single  1.411  0.020  1.411
 U9G  C3G  H3G1  single  0.970  0.020  1.090
 U9G  C3G  H3G2  single  0.970  0.020  1.090
 U9G  C3G  H3G3  single  0.970  0.020  1.090
 U9G  C1   O1    single  1.390  0.020  1.390
 U9G  C1   H1    single  0.970  0.020  1.090
 U9G  O4   HO4   single  0.850  0.020  0.980
 U9G  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
 U9G  HO4   O4   C4    108.48  3.000
 U9G  H4    C4   C3    107.22  3.000
 U9G  H4    C4   C5    108.45  3.000
 U9G  C3    C4   C5    111.34  3.000
 U9G  H4    C4   O4    110.85  3.000
 U9G  C3    C4   O4    111.53  3.000
 U9G  C5    C4   O4    107.44  3.000
 U9G  H5    C5   C6    106.20  3.000
 U9G  H5    C5   O5    110.60  3.000
 U9G  C6    C5   O5    107.60  3.000
 U9G  H5    C5   C4    108.57  3.000
 U9G  C6    C5   C4    113.35  3.000
 U9G  O5    C5   C4    110.46  3.000
 U9G  C1    O5   C5    115.43  3.000
 U9G  H62   C6   H61   107.64  3.000
 U9G  H62   C6   O6    111.50  3.000
 U9G  H61   C6   O6    111.01  3.000
 U9G  H62   C6   C5    108.75  3.000
 U9G  H61   C6   C5    108.97  3.000
 U9G  O6    C6   C5    108.91  3.000
 U9G  S37   O6   C6    118.62  3.000
 U9G  O3A   S37  O39   113.67  3.000
 U9G  O3A   S37  O38   114.96  3.000
 U9G  O39   S37  O38   114.53  3.000
 U9G  O3A   S37  O6    105.67  3.000
 U9G  O39   S37  O6    105.90  3.000
 U9G  O38   S37  O6    100.26  3.000
 U9G  H3    C3   C2    110.98  3.000
 U9G  H3    C3   O3    110.64  3.000
 U9G  C2    C3   O3    109.48  3.000
 U9G  H3    C3   C4    108.43  3.000
 U9G  C2    C3   C4    108.68  3.000
 U9G  O3    C3   C4    108.56  3.000
 U9G  C3D   O3   C3    115.57  3.000
 U9G  H3D3  C3D  H3D2  108.00  3.000
 U9G  H3D3  C3D  H3D1  108.06  3.000
 U9G  H3D2  C3D  H3D1  108.19  3.000
 U9G  H3D3  C3D  O3    112.52  3.000
 U9G  H3D2  C3D  O3    112.50  3.000
 U9G  H3D1  C3D  O3    107.40  3.000
 U9G  H2    C2   C1    105.37  3.000
 U9G  H2    C2   O2    103.68  3.000
 U9G  C1    C2   O2    114.91  3.000
 U9G  H2    C2   C3    107.06  3.000
 U9G  C1    C2   C3    109.55  3.000
 U9G  O2    C2   C3    115.30  3.000
 U9G  C3G   O2   C2    120.15  3.000
 U9G  H3G3  C3G  H3G2  107.93  3.000
 U9G  H3G3  C3G  H3G1  108.15  3.000
 U9G  H3G2  C3G  H3G1  107.57  3.000
 U9G  H3G3  C3G  O2    112.75  3.000
 U9G  H3G2  C3G  O2    113.64  3.000
 U9G  H3G1  C3G  O2    106.55  3.000
 U9G  H1    C1   O1    111.29  3.000
 U9G  H1    C1   C2    109.68  3.000
 U9G  O1    C1   C2    109.36  3.000
 U9G  H1    C1   O5    104.90  3.000
 U9G  O1    C1   O5    112.22  3.000
 U9G  C2    C1   O5    109.30  3.000
 U9G  HO1   O1   C1    109.28  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
 U9G  Var_01  H3D1  C3D  O3  C3   -178.10  30.0  3
 U9G  Var_02  H3G1  C3G  O2  C2   -159.65  30.0  3
 U9G  Var_03  O38   S37  O6  C6    178.95  30.0  3
 U9G  Var_04  H61   C6   O6  S37    67.70  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
 U9G  chir_01  C4  O4  C5  C3  positiv
 U9G  chir_02  C5  O5  C4  C6  negativ
 U9G  chir_03  C3  O3  C4  C2  negativ
 U9G  chir_04  C2  O2  C3  C1  positiv
 U9G  chir_05  C1  O5  O1  C2  positiv

