# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 15:05:37 2021
#   Inital geometry file: a 67 line input string
#   Ligand name: 2,6-di-O-methyl-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC[C@H]1O[C@H](O)[C@H](OC)[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
 ZB3  ZB3  2,6-di-O-methyl-alpha-D-glucopyranose  D-saccharide  30  14  .  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_ZB3
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
 ZB3  C1    C  CH1   0   0.262   -8.9868  11.7317  32.6216
 ZB3  C2    C  CH1   0  -0.042   -9.0918  12.1508  34.0996
 ZB3  C2M   C  CH3   0  -0.411   -8.5329  14.4538  34.0438
 ZB3  C3    C  CH1   0   0.021   -8.8525  10.9673  35.0238
 ZB3  C4    C  CH1   0  -0.004   -9.7700   9.8210  34.6142
 ZB3  C5    C  CH1   0  -0.019   -9.5251   9.4779  33.1442
 ZB3  C6    C  CH2   0  -0.180  -10.3835   8.3459  32.6271
 ZB3  C6M   C  CH3   0  -0.394  -12.5746   7.5699  32.4302
 ZB3  O1    O  OH1   0  -0.669   -7.6638  11.4468  32.2680
 ZB3  O2    O  O2    0  -0.494   -8.1410  13.1439  34.3956
 ZB3  O3    O  OH1   0  -0.668   -9.1025  11.3878  36.3408
 ZB3  O4    O  OH1   0  -0.675   -9.4840   8.7221  35.4505
 ZB3  O5    O  O2    0  -0.498   -9.7807  10.6251  32.3462
 ZB3  O6    O  O2    0  -0.486  -11.7384   8.6065  32.8767
 ZB3  H1    H  HCH1  0   0.224   -9.3907  12.5305  31.9857
 ZB3  HO1   H  HOH1  0   0.453   -7.0801  12.0346  32.7632
 ZB3  H2    H  HCH1  0   0.239  -10.1127  12.5233  34.2724
 ZB3  H2M1  H  HCH3  0   0.242   -7.7378  15.1281  34.3580
 ZB3  H2M2  H  HCH3  0   0.214   -8.6810  14.5799  32.9668
 ZB3  H2M3  H  HCH3  0   0.218   -9.4579  14.7447  34.5518
 ZB3  H3    H  HCH1  0   0.211   -7.8096  10.6287  34.9133
 ZB3  HO3   H  HOH1  0   0.449   -8.9861  10.6257  36.9181
 ZB3  H4    H  HCH1  0   0.230  -10.8087  10.1520  34.7427
 ZB3  HO4   H  HOH1  0   0.461  -10.2850   8.2034  35.5668
 ZB3  H5    H  HCH1  0   0.235   -8.4823   9.1518  33.0298
 ZB3  H61   H  HCH2  0   0.212  -10.0617   7.4143  33.1130
 ZB3  H62   H  HCH2  0   0.226  -10.1953   8.2143  31.5515
 ZB3  H6M1  H  HCH3  0   0.235  -13.6012   7.8302  32.6843
 ZB3  H6M2  H  HCH3  0   0.205  -12.5099   7.4294  31.3445
 ZB3  H6M3  H  HCH3  0   0.205  -12.3311   6.6125  32.9068

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
 ZB3  C1   H1    single  0.970  0.020  1.090
 ZB3  C1   O1    single  1.399  0.020  1.399
 ZB3  O1   HO1   single  0.850  0.020  0.980
 ZB3  C1   O5    single  1.390  0.020  1.390
 ZB3  C1   C2    single  1.540  0.020  1.540
 ZB3  C2   H2    single  0.970  0.020  1.090
 ZB3  C2   O2    single  1.406  0.020  1.406
 ZB3  O2   C2M   single  1.412  0.020  1.412
 ZB3  C2M  H2M1  single  0.970  0.020  1.090
 ZB3  C2M  H2M2  single  0.970  0.020  1.090
 ZB3  C2M  H2M3  single  0.970  0.020  1.090
 ZB3  C2   C3    single  1.521  0.020  1.521
 ZB3  C3   H3    single  0.970  0.020  1.090
 ZB3  C3   O3    single  1.405  0.020  1.405
 ZB3  O3   HO3   single  0.850  0.020  0.980
 ZB3  C3   C4    single  1.524  0.020  1.524
 ZB3  C4   H4    single  0.970  0.020  1.090
 ZB3  C4   O4    single  1.410  0.020  1.410
 ZB3  O4   HO4   single  0.850  0.020  0.980
 ZB3  C4   C5    single  1.529  0.020  1.529
 ZB3  C5   H5    single  0.970  0.020  1.090
 ZB3  C5   O5    single  1.421  0.020  1.421
 ZB3  C5   C6    single  1.512  0.020  1.512
 ZB3  C6   H61   single  0.970  0.020  1.090
 ZB3  C6   H62   single  0.970  0.020  1.090
 ZB3  C6   O6    single  1.402  0.020  1.402
 ZB3  O6   C6M   single  1.405  0.020  1.405
 ZB3  C6M  H6M1  single  0.970  0.020  1.090
 ZB3  C6M  H6M2  single  0.970  0.020  1.090
 ZB3  C6M  H6M3  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
 ZB3  H1    C1   O5    104.74  3.000
 ZB3  O5    C1   O1    109.16  3.000
 ZB3  H1    C1   O1    110.47  3.000
 ZB3  O5    C1   C2    111.59  3.000
 ZB3  O1    C1   C2    111.26  3.000
 ZB3  H1    C1   C2    109.43  3.000
 ZB3  H2    C2   O2    110.80  3.000
 ZB3  O2    C2   C3    108.38  3.000
 ZB3  H2    C2   C3    108.30  3.000
 ZB3  C3    C2   C1    111.15  3.000
 ZB3  O2    C2   C1    110.37  3.000
 ZB3  H2    C2   C1    107.83  3.000
 ZB3  H2M3  C2M  H2M2  108.16  3.000
 ZB3  H2M3  C2M  H2M1  108.58  3.000
 ZB3  H2M2  C2M  H2M1  108.15  3.000
 ZB3  H2M3  C2M  O2    111.44  3.000
 ZB3  H2M2  C2M  O2    112.94  3.000
 ZB3  H2M1  C2M  O2    107.45  3.000
 ZB3  H3    C3   O3    110.75  3.000
 ZB3  O3    C3   C4    111.71  3.000
 ZB3  H3    C3   C4    108.16  3.000
 ZB3  C4    C3   C2    109.10  3.000
 ZB3  O3    C3   C2    107.99  3.000
 ZB3  H3    C3   C2    109.09  3.000
 ZB3  H4    C4   O4    110.95  3.000
 ZB3  O4    C4   C5    111.27  3.000
 ZB3  H4    C4   C5    109.37  3.000
 ZB3  C5    C4   C3    109.31  3.000
 ZB3  O4    C4   C3    107.73  3.000
 ZB3  H4    C4   C3    108.14  3.000
 ZB3  H5    C5   O5    110.61  3.000
 ZB3  O5    C5   C6    108.08  3.000
 ZB3  H5    C5   C6    106.33  3.000
 ZB3  C6    C5   C4    113.94  3.000
 ZB3  O5    C5   C4    109.27  3.000
 ZB3  H5    C5   C4    108.59  3.000
 ZB3  H62   C6   H61   106.31  3.000
 ZB3  H62   C6   O6    111.21  3.000
 ZB3  H61   C6   O6    111.22  3.000
 ZB3  O6    C6   C5    110.40  3.000
 ZB3  H62   C6   C5    109.08  3.000
 ZB3  H61   C6   C5    108.49  3.000
 ZB3  H6M3  C6M  H6M2  107.78  3.000
 ZB3  H6M3  C6M  H6M1  108.45  3.000
 ZB3  H6M2  C6M  H6M1  108.49  3.000
 ZB3  H6M3  C6M  O6    111.96  3.000
 ZB3  H6M2  C6M  O6    111.96  3.000
 ZB3  H6M1  C6M  O6    108.09  3.000
 ZB3  HO1   O1   C1    108.56  3.000
 ZB3  C2M   O2   C2    114.52  3.000
 ZB3  HO3   O3   C3    107.67  3.000
 ZB3  HO4   O4   C4    108.85  3.000
 ZB3  C5    O5   C1    115.40  3.000
 ZB3  C6M   O6   C6    112.42  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
 ZB3  Var_01  H2M1  C2M  O2  C2   177.71  30.0  3
 ZB3  Var_02  H6M1  C6M  O6  C6   178.35  30.0  3
 ZB3  Var_03  H61   C6   O6  C6M  -58.61  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
 ZB3  chir_01  C1  O1  O5  C2  negativ
 ZB3  chir_02  C2  O2  C3  C1  positiv
 ZB3  chir_03  C3  O3  C2  C4  positiv
 ZB3  chir_04  C4  O4  C3  C5  negativ
 ZB3  chir_05  C5  O5  C4  C6  negativ

