# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 14:11:52 2021
#   Inital geometry file: a 67 line input string
#   Ligand name: 2,3-di-O-methyl-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)[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
 ZB0  ZB0  2,3-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 PERFECT
;

data_comp_ZB0
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
 ZB0  C1    C  CH1   0   0.262  -6.7587  5.1189  38.9131
 ZB0  C2    C  CH1   0  -0.042  -5.4444  5.6516  39.5110
 ZB0  C2M   C  CH3   0  -0.408  -6.2173  7.0831  41.2373
 ZB0  C3    C  CH1   0   0.010  -4.3324  5.6301  38.4692
 ZB0  C4    C  CH1   0   0.035  -4.2328  4.2326  37.8638
 ZB0  C5    C  CH1   0  -0.003  -5.5870  3.8347  37.2832
 ZB0  C6    C  CH2   0  -0.183  -5.6160  2.4448  36.6855
 ZB0  O1    O  OH1   0  -0.670  -7.2910  6.0181  37.9824
 ZB0  O2    O  O2    0  -0.491  -5.6083  6.9714  39.9685
 ZB0  O3    O  O2    0  -0.503  -3.0778  5.9323  39.0339
 ZB0  O4    O  OH1   0  -0.673  -3.2869  4.1921  36.8263
 ZB0  O5    O  O2    0  -0.499  -6.5735  3.8844  38.3039
 ZB0  O6    O  OH1   0  -0.672  -5.2233  1.4981  37.6497
 ZB0  H1    H  HCH1  0   0.224  -7.4809  4.9281  39.7184
 ZB0  HO1   H  HOH1  0   0.453  -7.0844  6.9161  38.2692
 ZB0  H2    H  HCH1  0   0.236  -5.1572  4.9866  40.3396
 ZB0  H2M1  H  HCH3  0   0.242  -6.2027  8.1357  41.5146
 ZB0  H2M2  H  HCH3  0   0.215  -7.2577  6.7446  41.2388
 ZB0  H2M3  H  HCH3  0   0.217  -5.6706  6.5145  41.9962
 ZB0  H3    H  HCH1  0   0.219  -4.5655  6.3422  37.6626
 ZB0  H3M1  H  HCH3  0   0.230  -1.6044  7.3092  39.2021
 ZB0  H3M2  H  HCH3  0   0.207  -2.7517  7.6463  37.8985
 ZB0  H3M3  H  HCH3  0   0.216  -3.2131  7.9442  39.5836
 ZB0  H4    H  HCH1  0   0.216  -3.9700  3.5275  38.6663
 ZB0  HO4   H  HOH1  0   0.451  -2.4407  4.4758  37.1884
 ZB0  H5    H  HCH1  0   0.232  -5.8370  4.5314  36.4714
 ZB0  H61   H  HCH2  0   0.215  -6.6320  2.2522  36.3159
 ZB0  H62   H  HCH2  0   0.211  -4.9564  2.4394  35.8107
 ZB0  HO6   H  HOH1  0   0.458  -5.1847  0.6375  37.2237
 ZB0  C3M   C  CH3   0  -0.403  -2.6576  7.2741  38.9246

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
 ZB0  C1   H1    single  0.970  0.020  1.090
 ZB0  C1   O1    single  1.399  0.020  1.399
 ZB0  O1   HO1   single  0.850  0.020  0.980
 ZB0  C1   O5    single  1.389  0.020  1.389
 ZB0  C1   C2    single  1.539  0.020  1.539
 ZB0  C2   H2    single  0.970  0.020  1.090
 ZB0  C2   O2    single  1.406  0.020  1.406
 ZB0  O2   C2M   single  1.412  0.020  1.412
 ZB0  C2M  H2M1  single  0.970  0.020  1.090
 ZB0  C2M  H2M2  single  0.970  0.020  1.090
 ZB0  C2M  H2M3  single  0.970  0.020  1.090
 ZB0  C2   C3    single  1.524  0.020  1.524
 ZB0  C3   H3    single  0.970  0.020  1.090
 ZB0  C3   O3    single  1.409  0.020  1.409
 ZB0  O3   C3M   single  1.410  0.020  1.410
 ZB0  C3M  H3M1  single  0.970  0.020  1.090
 ZB0  C3M  H3M2  single  0.970  0.020  1.090
 ZB0  C3M  H3M3  single  0.970  0.020  1.090
 ZB0  C3   C4    single  1.526  0.020  1.526
 ZB0  C4   H4    single  0.970  0.020  1.090
 ZB0  C4   O4    single  1.405  0.020  1.405
 ZB0  O4   HO4   single  0.850  0.020  0.980
 ZB0  C4   C5    single  1.526  0.020  1.526
 ZB0  C5   H5    single  0.970  0.020  1.090
 ZB0  C5   O5    single  1.420  0.020  1.420
 ZB0  C5   C6    single  1.513  0.020  1.513
 ZB0  C6   H61   single  0.970  0.020  1.090
 ZB0  C6   H62   single  0.970  0.020  1.090
 ZB0  C6   O6    single  1.407  0.020  1.407
 ZB0  O6   HO6   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
 ZB0  H1    C1   O5    104.76  3.000
 ZB0  O5    C1   O1    109.28  3.000
 ZB0  H1    C1   O1    110.44  3.000
 ZB0  O5    C1   C2    111.35  3.000
 ZB0  O1    C1   C2    111.15  3.000
 ZB0  H1    C1   C2    109.68  3.000
 ZB0  H2    C2   O2    110.64  3.000
 ZB0  O2    C2   C3    108.70  3.000
 ZB0  H2    C2   C3    108.40  3.000
 ZB0  C3    C2   C1    110.65  3.000
 ZB0  O2    C2   C1    110.59  3.000
 ZB0  H2    C2   C1    107.83  3.000
 ZB0  H2M3  C2M  H2M2  108.26  3.000
 ZB0  H2M3  C2M  H2M1  108.60  3.000
 ZB0  H2M2  C2M  H2M1  108.15  3.000
 ZB0  H2M3  C2M  O2    111.50  3.000
 ZB0  H2M2  C2M  O2    112.76  3.000
 ZB0  H2M1  C2M  O2    107.44  3.000
 ZB0  H3    C3   O3    110.09  3.000
 ZB0  O3    C3   C4    107.29  3.000
 ZB0  H3    C3   C4    108.39  3.000
 ZB0  C4    C3   C2    109.37  3.000
 ZB0  O3    C3   C2    111.89  3.000
 ZB0  H3    C3   C2    109.71  3.000
 ZB0  H4    C4   O4    111.07  3.000
 ZB0  O4    C4   C5    108.00  3.000
 ZB0  H4    C4   C5    108.81  3.000
 ZB0  C5    C4   C3    109.37  3.000
 ZB0  O4    C4   C3    111.31  3.000
 ZB0  H4    C4   C3    108.25  3.000
 ZB0  H5    C5   O5    110.53  3.000
 ZB0  O5    C5   C6    107.62  3.000
 ZB0  H5    C5   C6    106.63  3.000
 ZB0  C6    C5   C4    114.00  3.000
 ZB0  O5    C5   C4    109.50  3.000
 ZB0  H5    C5   C4    108.53  3.000
 ZB0  H62   C6   H61   106.70  3.000
 ZB0  H62   C6   O6    112.08  3.000
 ZB0  H61   C6   O6    111.76  3.000
 ZB0  O6    C6   C5    109.99  3.000
 ZB0  H62   C6   C5    107.96  3.000
 ZB0  H61   C6   C5    108.16  3.000
 ZB0  HO1   O1   C1    108.59  3.000
 ZB0  C2M   O2   C2    114.63  3.000
 ZB0  C3M   O3   C3    116.00  3.000
 ZB0  HO4   O4   C4    107.78  3.000
 ZB0  C5    O5   C1    116.03  3.000
 ZB0  HO6   O6   C6    108.05  3.000
 ZB0  H3M3  C3M  H3M2  108.25  3.000
 ZB0  H3M3  C3M  H3M1  108.56  3.000
 ZB0  H3M2  C3M  H3M1  108.09  3.000
 ZB0  H3M3  C3M  O3    112.69  3.000
 ZB0  H3M2  C3M  O3    111.73  3.000
 ZB0  H3M1  C3M  O3    107.39  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
 ZB0  Var_01  H2M1  C2M  O2  C2   174.89  30.0  3
 ZB0  Var_02  H3M1  C3M  O3  C3  -167.95  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
 ZB0  chir_01  C1  O1  O5  C2  negativ
 ZB0  chir_02  C2  O2  C3  C1  positiv
 ZB0  chir_03  C3  O3  C4  C2  negativ
 ZB0  chir_04  C4  O4  C3  C5  negativ
 ZB0  chir_05  C5  O5  C4  C6  negativ

