# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 13:15:30 2021
#   Inital geometry file: a 61 line input string
#   Ligand name: 3-O-methyl-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1[C@@H](O)[C@@H](O)O[C@H](CO)[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
 ZB1  ZB1  3-O-methyl-alpha-D-glucopyranose  D-saccharide  27  13  .  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_ZB1
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
 ZB1  C1    C  CH1   0   0.248  -2.2642  3.4131  37.0671
 ZB1  C2    C  CH1   0  -0.052  -0.9584  4.1395  37.4301
 ZB1  C3    C  CH1   0   0.018  -0.5699  5.1163  36.3300
 ZB1  C4    C  CH1   0   0.033  -0.5359  4.3806  34.9932
 ZB1  C5    C  CH1   0  -0.002  -1.8881  3.7197  34.7358
 ZB1  C6    C  CH2   0  -0.183  -1.9446  2.9175  33.4535
 ZB1  O1    O  OH1   0  -0.670  -3.3582  4.2839  37.1146
 ZB1  O2    O  OH1   0  -0.661  -1.1207  4.8464  38.6397
 ZB1  O3    O  O2    0  -0.505   0.7114  5.6656  36.5370
 ZB1  O4    O  OH1   0  -0.673  -0.2762  5.2632  33.9310
 ZB1  O5    O  O2    0  -0.499  -2.1997  2.8387  35.8053
 ZB1  O6    O  OH1   0  -0.672  -0.9422  1.9298  33.4580
 ZB1  H1    H  HCH1  0   0.222  -2.4080  2.5721  37.7602
 ZB1  HO1   H  HOH1  0   0.451  -3.2430  4.8669  37.8752
 ZB1  H2    H  HCH1  0   0.236  -0.1664  3.3837  37.5182
 ZB1  HO2   H  HOH1  0   0.462  -1.0559  4.2258  39.3730
 ZB1  H3    H  HCH1  0   0.218  -1.3207  5.9194  36.2675
 ZB1  H3M1  H  HCH3  0   0.230   1.7649  7.3036  37.0859
 ZB1  H3M2  H  HCH3  0   0.207   0.0837  7.6471  36.6565
 ZB1  H3M3  H  HCH3  0   0.215   0.4631  6.8881  38.2129
 ZB1  H4    H  HCH1  0   0.215   0.2340  3.5972  35.0527
 ZB1  HO4   H  HOH1  0   0.451   0.5683  5.6908  34.1079
 ZB1  H5    H  HCH1  0   0.232  -2.6516  4.5050  34.6461
 ZB1  H61   H  HCH2  0   0.212  -1.8355  3.6130  32.6146
 ZB1  H62   H  HCH2  0   0.213  -2.9480  2.4786  33.3696
 ZB1  HO6   H  HOH1  0   0.458  -0.9194  1.5231  32.5876
 ZB1  C3M   C  CH3   0  -0.404   0.7435  6.9307  37.1584

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
 ZB1  C1   H1    single  0.970  0.020  1.090
 ZB1  C1   O1    single  1.399  0.020  1.399
 ZB1  O1   HO1   single  0.850  0.020  0.980
 ZB1  C1   O5    single  1.388  0.020  1.388
 ZB1  C1   C2    single  1.538  0.020  1.538
 ZB1  C2   H2    single  0.970  0.020  1.090
 ZB1  C2   O2    single  1.410  0.020  1.410
 ZB1  O2   HO2   single  0.850  0.020  0.980
 ZB1  C2   C3    single  1.522  0.020  1.522
 ZB1  C3   H3    single  0.970  0.020  1.090
 ZB1  C3   O3    single  1.409  0.020  1.409
 ZB1  O3   C3M   single  1.410  0.020  1.410
 ZB1  C3M  H3M1  single  0.970  0.020  1.090
 ZB1  C3M  H3M2  single  0.970  0.020  1.090
 ZB1  C3M  H3M3  single  0.970  0.020  1.090
 ZB1  C3   C4    single  1.526  0.020  1.526
 ZB1  C4   H4    single  0.970  0.020  1.090
 ZB1  C4   O4    single  1.405  0.020  1.405
 ZB1  O4   HO4   single  0.850  0.020  0.980
 ZB1  C4   C5    single  1.527  0.020  1.527
 ZB1  C5   H5    single  0.970  0.020  1.090
 ZB1  C5   O5    single  1.420  0.020  1.420
 ZB1  C5   C6    single  1.514  0.020  1.514
 ZB1  C6   H61   single  0.970  0.020  1.090
 ZB1  C6   H62   single  0.970  0.020  1.090
 ZB1  C6   O6    single  1.407  0.020  1.407
 ZB1  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
 ZB1  H1    C1   O5    105.23  3.000
 ZB1  O5    C1   O1    108.95  3.000
 ZB1  H1    C1   O1    110.64  3.000
 ZB1  O5    C1   C2    111.76  3.000
 ZB1  O1    C1   C2    111.22  3.000
 ZB1  H1    C1   C2    108.88  3.000
 ZB1  H2    C2   O2    111.04  3.000
 ZB1  O2    C2   C3    109.13  3.000
 ZB1  H2    C2   C3    108.40  3.000
 ZB1  C3    C2   C1    110.45  3.000
 ZB1  O2    C2   C1    109.97  3.000
 ZB1  H2    C2   C1    107.83  3.000
 ZB1  H3    C3   O3    110.11  3.000
 ZB1  O3    C3   C4    107.23  3.000
 ZB1  H3    C3   C4    108.48  3.000
 ZB1  C4    C3   C2    109.24  3.000
 ZB1  O3    C3   C2    112.09  3.000
 ZB1  H3    C3   C2    109.58  3.000
 ZB1  H4    C4   O4    111.03  3.000
 ZB1  O4    C4   C5    107.95  3.000
 ZB1  H4    C4   C5    108.71  3.000
 ZB1  C5    C4   C3    109.67  3.000
 ZB1  O4    C4   C3    111.31  3.000
 ZB1  H4    C4   C3    108.15  3.000
 ZB1  H5    C5   O5    110.63  3.000
 ZB1  O5    C5   C6    107.51  3.000
 ZB1  H5    C5   C6    106.47  3.000
 ZB1  C6    C5   C4    113.91  3.000
 ZB1  O5    C5   C4    109.63  3.000
 ZB1  H5    C5   C4    108.65  3.000
 ZB1  H62   C6   H61   106.63  3.000
 ZB1  H62   C6   O6    111.75  3.000
 ZB1  H61   C6   O6    112.16  3.000
 ZB1  O6    C6   C5    110.04  3.000
 ZB1  H62   C6   C5    108.10  3.000
 ZB1  H61   C6   C5    107.97  3.000
 ZB1  HO1   O1   C1    108.02  3.000
 ZB1  HO2   O2   C2    108.80  3.000
 ZB1  C3M   O3   C3    115.80  3.000
 ZB1  HO4   O4   C4    107.59  3.000
 ZB1  C5    O5   C1    115.98  3.000
 ZB1  HO6   O6   C6    108.12  3.000
 ZB1  H3M3  C3M  H3M2  108.26  3.000
 ZB1  H3M3  C3M  H3M1  108.56  3.000
 ZB1  H3M2  C3M  H3M1  108.07  3.000
 ZB1  H3M3  C3M  O3    112.63  3.000
 ZB1  H3M2  C3M  O3    111.78  3.000
 ZB1  H3M1  C3M  O3    107.40  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
 ZB1  Var_01  H3M1  C3M  O3  C3  -169.80  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
 ZB1  chir_01  C1  O1  O5  C2  negativ
 ZB1  chir_02  C2  O2  C1  C3  negativ
 ZB1  chir_03  C3  O3  C4  C2  negativ
 ZB1  chir_04  C4  O4  C3  C5  negativ
 ZB1  chir_05  C5  O5  C4  C6  negativ

