# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 18:07:42 2022
#   Inital geometry file: a 61 line input string
#   Ligand name: 3-O-methyl-beta-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
 3MG  3MG  3-O-methyl-beta-D-glucopyranose  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_3MG
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
 3MG  O6   O  OH1   0  -0.657   -4.7639  21.6073  -14.1410
 3MG  C6   C  CH2   0  -0.170   -5.9931  21.7917  -14.7958
 3MG  C5   C  CH1   0  -0.034   -6.2529  20.7711  -15.8930
 3MG  O5   O  O2    0  -0.485   -6.2669  19.4961  -15.2868
 3MG  C4   C  CH1   0   0.018   -7.5817  21.0430  -16.6163
 3MG  O4   O  OH1   0  -0.664   -7.5097  22.2269  -17.3756
 3MG  C3   C  CH1   0  -0.003   -7.9185  19.8994  -17.5696
 3MG  O3   O  O2    0  -0.488   -9.2209  20.0654  -18.0729
 3MG  C7   C  CH3   0  -0.406   -9.3047  20.2113  -19.4693
 3MG  C2   C  CH1   0  -0.047   -7.8033  18.5563  -16.8571
 3MG  O2   O  OH1   0  -0.656   -8.0521  17.4577  -17.7001
 3MG  C1   C  CH1   0   0.295   -6.4252  18.4550  -16.2002
 3MG  O1   O  OH1   0  -0.656   -6.2715  17.2925  -15.4608
 3MG  HO6  H  HOH1  0   0.446   -4.0563  21.8090  -14.7615
 3MG  H61  H  HCH2  0   0.205   -6.0762  22.7977  -15.2226
 3MG  H62  H  HCH2  0   0.224   -6.7742  21.6993  -14.0360
 3MG  H5   H  HCH1  0   0.218   -5.4408  20.8285  -16.6386
 3MG  H4   H  HCH1  0   0.223   -8.3796  21.1032  -15.8612
 3MG  HO4  H  HOH1  0   0.457   -7.7963  22.9680  -16.8352
 3MG  H3   H  HCH1  0   0.221   -7.1803  19.9182  -18.3893
 3MG  H71  H  HCH3  0   0.207   -8.7630  21.0918  -19.8287
 3MG  H72  H  HCH3  0   0.206   -8.9232  19.3347  -20.0038
 3MG  H73  H  HCH3  0   0.230  -10.3576  20.3312  -19.7239
 3MG  H2   H  HCH1  0   0.244   -8.5580  18.5029  -16.0635
 3MG  HO2  H  HOH1  0   0.449   -7.4626  17.5001  -18.4626
 3MG  H1   H  HCH1  0   0.169   -5.6478  18.5296  -16.9885
 3MG  HO1  H  HOH1  0   0.453   -6.6630  16.5640  -15.9571

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
 3MG  C7  O3   single  1.406  0.020  1.406
 3MG  O3  C3   single  1.406  0.020  1.406
 3MG  O2  C2   single  1.407  0.020  1.407
 3MG  C3  C2   single  1.525  0.020  1.525
 3MG  C3  C4   single  1.526  0.020  1.526
 3MG  O4  C4   single  1.408  0.020  1.408
 3MG  C2  C1   single  1.530  0.020  1.530
 3MG  C4  C5   single  1.537  0.020  1.537
 3MG  C1  O1   single  1.386  0.020  1.386
 3MG  C1  O5   single  1.394  0.020  1.394
 3MG  C5  O5   single  1.412  0.020  1.412
 3MG  C5  C6   single  1.521  0.020  1.521
 3MG  O6  C6   single  1.405  0.020  1.405
 3MG  O6  HO6  single  0.850  0.020  0.980
 3MG  C6  H61  single  0.970  0.020  1.090
 3MG  C6  H62  single  0.970  0.020  1.090
 3MG  C5  H5   single  0.970  0.020  1.090
 3MG  C4  H4   single  0.970  0.020  1.090
 3MG  O4  HO4  single  0.850  0.020  0.980
 3MG  C3  H3   single  0.970  0.020  1.090
 3MG  C7  H71  single  0.970  0.020  1.090
 3MG  C7  H72  single  0.970  0.020  1.090
 3MG  C7  H73  single  0.970  0.020  1.090
 3MG  C2  H2   single  0.970  0.020  1.090
 3MG  O2  HO2  single  0.850  0.020  0.980
 3MG  C1  H1   single  0.970  0.020  1.090
 3MG  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
 3MG  HO6  O6  C6   108.38  3.000
 3MG  H62  C6  H61  107.10  3.000
 3MG  H62  C6  C5   108.82  3.000
 3MG  H61  C6  C5   108.79  3.000
 3MG  H62  C6  O6   106.86  3.000
 3MG  H61  C6  O6   111.61  3.000
 3MG  C5   C6  O6   113.43  3.000
 3MG  H5   C5  C4   108.00  3.000
 3MG  H5   C5  O5   110.13  3.000
 3MG  C4   C5  O5   110.68  3.000
 3MG  H5   C5  C6   109.07  3.000
 3MG  O5   C5  C6   107.34  3.000
 3MG  C4   C5  C6   111.62  3.000
 3MG  C1   O5  C5   113.22  3.000
 3MG  H4   C4  C3   108.03  3.000
 3MG  H4   C4  O4   111.17  3.000
 3MG  C3   C4  O4   107.72  3.000
 3MG  H4   C4  C5   108.28  3.000
 3MG  O4   C4  C5   110.99  3.000
 3MG  C3   C4  C5   110.62  3.000
 3MG  HO4  O4  C4   109.26  3.000
 3MG  H3   C3  C2   108.16  3.000
 3MG  H3   C3  O3   110.59  3.000
 3MG  C2   C3  O3   109.96  3.000
 3MG  H3   C3  C4   107.67  3.000
 3MG  C2   C3  C4   110.57  3.000
 3MG  O3   C3  C4   109.85  3.000
 3MG  C7   O3  C3   115.02  3.000
 3MG  H73  C7  H72  108.09  3.000
 3MG  H73  C7  H71  108.23  3.000
 3MG  H72  C7  H71  108.13  3.000
 3MG  H73  C7  O3   107.51  3.000
 3MG  H72  C7  O3   112.38  3.000
 3MG  H71  C7  O3   112.34  3.000
 3MG  H2   C2  C1   107.82  3.000
 3MG  H2   C2  O2   105.90  3.000
 3MG  C1   C2  O2   111.40  3.000
 3MG  H2   C2  C3   109.21  3.000
 3MG  C1   C2  C3   109.09  3.000
 3MG  O2   C2  C3   113.23  3.000
 3MG  HO2  O2  C2   109.34  3.000
 3MG  H1   C1  O1   110.95  3.000
 3MG  H1   C1  C2   108.76  3.000
 3MG  O1   C1  C2   112.61  3.000
 3MG  H1   C1  O5   109.61  3.000
 3MG  O1   C1  O5   105.32  3.000
 3MG  C2   C1  O5   109.52  3.000
 3MG  HO1  O1  C1   108.29  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
 3MG  Var_01  H71  C7  O3  C3  -60.98  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
 3MG  chir_01  C5  C4  O5  C6  positiv
 3MG  chir_02  C4  O4  C5  C3  positiv
 3MG  chir_03  C3  O3  C2  C4  positiv
 3MG  chir_04  C2  O2  C3  C1  positiv
 3MG  chir_05  C1  O5  O1  C2  negativ

