# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 18:44:08 2022
#   Inital geometry file: a 61 line input string
#   Ligand name: methyl beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1O[C@H](CO)[C@@H](O)[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
 MGL  MGL  'methyl beta-D-glucopyranoside'  D-saccharide  27  13  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MGL
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
 MGL  C1   C  CH1   0   0.318  72.6336  107.5362  40.1016
 MGL  C2   C  CH1   0   0.001  72.0733  106.6019  41.1674
 MGL  C3   C  CH1   0  -0.019  73.1703  105.6320  41.5884
 MGL  C4   C  CH1   0   0.029  73.7517  104.9055  40.3828
 MGL  C5   C  CH1   0  -0.035  74.1917  105.9336  39.3341
 MGL  C6   C  CH2   0  -0.199  74.6186  105.2944  38.0152
 MGL  O1   O  O2    0  -0.486  71.6343  108.3643  39.6524
 MGL  O2   O  OH1   0  -0.666  71.6314  107.3826  42.2467
 MGL  O3   O  OH1   0  -0.669  72.6070  104.7472  42.5285
 MGL  O4   O  OH1   0  -0.679  74.8201  104.1174  40.8460
 MGL  O5   O  O2    0  -0.502  73.1087  106.7793  39.0149
 MGL  O6   O  OH1   0  -0.659  75.6923  104.3888  38.1719
 MGL  H1   H  HCH1  0   0.183  73.4703  108.1209  40.5315
 MGL  H2   H  HCH1  0   0.213  71.2461  106.0279  40.7190
 MGL  H3   H  HCH1  0   0.212  73.9821  106.2208  42.0462
 MGL  H4   H  HCH1  0   0.201  72.9606  104.2828  39.9320
 MGL  H5   H  HCH1  0   0.222  75.0306  106.5199  39.7465
 MGL  H61  H  HCH2  0   0.234  74.8599  106.0821  37.2933
 MGL  H62  H  HCH2  0   0.231  73.7807  104.7223  37.6094
 MGL  H71  H  HCH3  0   0.218  72.4456  109.1506  37.8919
 MGL  H72  H  HCH3  0   0.212  72.8663  110.0207  39.3803
 MGL  H73  H  HCH3  0   0.238  71.2217  110.1177  38.7279
 MGL  HO2  H  HOH1  0   0.450  71.4153  106.7861  42.9720
 MGL  HO3  H  HOH1  0   0.455  73.3189  104.2728  42.9689
 MGL  HO4  H  HOH1  0   0.446  75.2759  103.7623  40.0716
 MGL  HO6  H  HOH1  0   0.459  76.4991  104.8933  38.3211
 MGL  C7   C  CH3   0  -0.409  72.0754  109.4582  38.8726

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
 MGL  C1  C2   single  1.524  0.020  1.524
 MGL  C1  O1   single  1.373  0.020  1.373
 MGL  C1  O5   single  1.407  0.020  1.407
 MGL  C1  H1   single  0.970  0.020  1.090
 MGL  C2  C3   single  1.524  0.020  1.524
 MGL  C2  O2   single  1.403  0.020  1.403
 MGL  C2  H2   single  0.970  0.020  1.090
 MGL  C3  C4   single  1.523  0.020  1.523
 MGL  C3  O3   single  1.408  0.020  1.408
 MGL  C3  H3   single  0.970  0.020  1.090
 MGL  C4  C5   single  1.533  0.020  1.533
 MGL  C4  O4   single  1.406  0.020  1.406
 MGL  C4  H4   single  0.970  0.020  1.090
 MGL  C5  C6   single  1.526  0.020  1.526
 MGL  C5  O5   single  1.411  0.020  1.411
 MGL  C5  H5   single  0.970  0.020  1.090
 MGL  C6  O6   single  1.413  0.020  1.413
 MGL  C6  H61  single  0.970  0.020  1.090
 MGL  C6  H62  single  0.970  0.020  1.090
 MGL  C7  O1   single  1.414  0.020  1.414
 MGL  C7  H71  single  0.970  0.020  1.090
 MGL  C7  H72  single  0.970  0.020  1.090
 MGL  C7  H73  single  0.970  0.020  1.090
 MGL  O2  HO2  single  0.850  0.020  0.980
 MGL  O3  HO3  single  0.850  0.020  0.980
 MGL  O4  HO4  single  0.850  0.020  0.980
 MGL  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
 MGL  H1   C1  O5   109.19  3.000
 MGL  H1   C1  O1   111.00  3.000
 MGL  O5   C1  O1   108.51  3.000
 MGL  H1   C1  C2   109.26  3.000
 MGL  O5   C1  C2   109.54  3.000
 MGL  O1   C1  C2   109.32  3.000
 MGL  H2   C2  O2   111.48  3.000
 MGL  H2   C2  C3   108.74  3.000
 MGL  O2   C2  C3   111.61  3.000
 MGL  H2   C2  C1   108.10  3.000
 MGL  O2   C2  C1   108.22  3.000
 MGL  C3   C2  C1   108.59  3.000
 MGL  H3   C3  O3   110.66  3.000
 MGL  H3   C3  C4   107.60  3.000
 MGL  O3   C3  C4   112.42  3.000
 MGL  H3   C3  C2   107.76  3.000
 MGL  O3   C3  C2   107.24  3.000
 MGL  C4   C3  C2   111.09  3.000
 MGL  H4   C4  O4   111.29  3.000
 MGL  H4   C4  C5   107.75  3.000
 MGL  O4   C4  C5   112.52  3.000
 MGL  H4   C4  C3   108.61  3.000
 MGL  O4   C4  C3   107.26  3.000
 MGL  C5   C4  C3   109.34  3.000
 MGL  H5   C5  O5   110.47  3.000
 MGL  H5   C5  C6   109.44  3.000
 MGL  O5   C5  C6   105.68  3.000
 MGL  H5   C5  C4   108.59  3.000
 MGL  O5   C5  C4   109.66  3.000
 MGL  C6   C5  C4   112.98  3.000
 MGL  H62  C6  H61  107.49  3.000
 MGL  H62  C6  O6   106.75  3.000
 MGL  H61  C6  O6   111.50  3.000
 MGL  H62  C6  C5   109.01  3.000
 MGL  H61  C6  C5   109.26  3.000
 MGL  O6   C6  C5   112.64  3.000
 MGL  C7   O1  C1   114.82  3.000
 MGL  HO2  O2  C2   107.77  3.000
 MGL  HO3  O3  C3   108.62  3.000
 MGL  HO4  O4  C4   107.48  3.000
 MGL  C5   O5  C1   114.02  3.000
 MGL  HO6  O6  C6   108.53  3.000
 MGL  H73  C7  H72  108.47  3.000
 MGL  H73  C7  H71  108.49  3.000
 MGL  H72  C7  H71  108.42  3.000
 MGL  H73  C7  O1   107.30  3.000
 MGL  H72  C7  O1   111.53  3.000
 MGL  H71  C7  O1   112.52  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
 MGL  Var_01  H71  C7  O1  C1  70.24  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
 MGL  chir_01  C1  C2  O1  O5  positiv
 MGL  chir_02  C2  O2  C1  C3  negativ
 MGL  chir_03  C3  O3  C2  C4  positiv
 MGL  chir_04  C4  O4  C5  C3  positiv
 MGL  chir_05  C5  O5  C4  C6  negativ

