# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 17:51:41 2021
#   Inital geometry file: a 65 line input string
#   Ligand name: 6-deoxy-2,3-di-O-methyl-beta-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1[C@H](O)O[C@H](C)[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
 RVG  RVG  6-deoxy-2,3-di-O-methyl-beta-D-glucopyranose  D-saccharide  29  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_RVG
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
 RVG  O4   O  OH1   0  -0.666  29.7307  4.4632  41.1550
 RVG  C4   C  CH1   0   0.032  29.5095  4.1823  42.5155
 RVG  C5   C  CH1   0   0.004  30.7705  3.6058  43.1755
 RVG  O5   O  O2    0  -0.491  30.4866  3.2472  44.5168
 RVG  C6   C  CH3   0  -0.699  31.9183  4.5932  43.1977
 RVG  C3   C  CH1   0   0.014  28.3653  3.1780  42.6138
 RVG  O3   O  O2    0  -0.494  27.1641  3.7363  42.1408
 RVG  C3O  C  CH3   0  -0.407  26.7295  3.2526  40.8924
 RVG  C2   C  CH1   0  -0.009  28.1838  2.7490  44.0661
 RVG  O2   O  O2    0  -0.504  27.2634  1.6924  44.1878
 RVG  C2O  C  CH3   0  -0.402  25.9612  2.0563  44.5876
 RVG  C1   C  CH1   0   0.293  29.5192  2.2510  44.6246
 RVG  H4   H  HCH1  0   0.214  29.2222  5.0919  43.0655
 RVG  H5   H  HCH1  0   0.217  31.0746  2.7108  42.6090
 RVG  H61  H  HCH3  0   0.250  32.7861  4.1692  43.7026
 RVG  H62  H  HCH3  0   0.234  32.2292  4.8472  42.1850
 RVG  H63  H  HCH3  0   0.233  31.6356  5.5146  43.7105
 RVG  H3   H  HCH1  0   0.219  28.6391  2.2867  42.0265
 RVG  H22  H  HCH3  0   0.229  25.7971  3.7627  40.6508
 RVG  H23  H  HCH3  0   0.212  27.4478  3.4528  40.0930
 RVG  H24  H  HCH3  0   0.207  26.5319  2.1755  40.9166
 RVG  H2   H  HCH1  0   0.224  27.8682  3.6169  44.6651
 RVG  H26  H  HCH3  0   0.230  25.4202  1.1373  44.8113
 RVG  H27  H  HCH3  0   0.209  25.9705  2.6733  45.4927
 RVG  H28  H  HCH3  0   0.216  25.4198  2.5976  43.8092
 RVG  H1   H  HCH1  0   0.179  29.8292  1.3570  44.0494
 RVG  HO4  H  HOH1  0   0.457  30.2153  5.2910  41.0873
 RVG  O1   O  OH1   0  -0.658  29.4501  1.9713  45.9824
 RVG  HO1  H  HOH1  0   0.459  28.8229  1.2512  46.1106

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
 RVG  O4   C4   single  1.407  0.020  1.407
 RVG  C4   C3   single  1.526  0.020  1.526
 RVG  C4   C5   single  1.536  0.020  1.536
 RVG  C5   C6   single  1.514  0.020  1.514
 RVG  C5   O5   single  1.417  0.020  1.417
 RVG  O5   C1   single  1.393  0.020  1.393
 RVG  C3   O3   single  1.406  0.020  1.406
 RVG  C3   C2   single  1.525  0.020  1.525
 RVG  O3   C3O  single  1.408  0.020  1.408
 RVG  C2   O2   single  1.407  0.020  1.407
 RVG  C2   C1   single  1.531  0.020  1.531
 RVG  O2   C2O  single  1.410  0.020  1.410
 RVG  C4   H4   single  0.970  0.020  1.090
 RVG  C5   H5   single  0.970  0.020  1.090
 RVG  C6   H61  single  0.970  0.020  1.090
 RVG  C6   H62  single  0.970  0.020  1.090
 RVG  C6   H63  single  0.970  0.020  1.090
 RVG  C3   H3   single  0.970  0.020  1.090
 RVG  C3O  H22  single  0.970  0.020  1.090
 RVG  C3O  H23  single  0.970  0.020  1.090
 RVG  C3O  H24  single  0.970  0.020  1.090
 RVG  C2   H2   single  0.970  0.020  1.090
 RVG  C2O  H26  single  0.970  0.020  1.090
 RVG  C2O  H27  single  0.970  0.020  1.090
 RVG  C2O  H28  single  0.970  0.020  1.090
 RVG  C1   H1   single  0.970  0.020  1.090
 RVG  O4   HO4  single  0.850  0.020  0.980
 RVG  C1   O1   single  1.388  0.020  1.388
 RVG  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
 RVG  HO4  O4   C4   108.61  3.000
 RVG  H4   C4   C3   108.42  3.000
 RVG  H4   C4   C5   108.04  3.000
 RVG  C3   C4   C5   109.94  3.000
 RVG  H4   C4   O4   111.05  3.000
 RVG  C5   C4   O4   111.20  3.000
 RVG  C3   C4   O4   108.16  3.000
 RVG  H5   C5   C6   109.14  3.000
 RVG  H5   C5   O5   109.65  3.000
 RVG  C6   C5   O5   107.63  3.000
 RVG  H5   C5   C4   108.10  3.000
 RVG  O5   C5   C4   109.72  3.000
 RVG  C6   C5   C4   112.58  3.000
 RVG  C1   O5   C5   113.16  3.000
 RVG  H63  C6   H62  108.28  3.000
 RVG  H63  C6   H61  108.48  3.000
 RVG  H62  C6   H61  107.10  3.000
 RVG  H63  C6   C5   111.16  3.000
 RVG  H62  C6   C5   110.78  3.000
 RVG  H61  C6   C5   110.90  3.000
 RVG  H3   C3   C2   108.03  3.000
 RVG  H3   C3   O3   110.73  3.000
 RVG  C2   C3   O3   109.28  3.000
 RVG  H3   C3   C4   108.16  3.000
 RVG  C2   C3   C4   109.62  3.000
 RVG  O3   C3   C4   110.95  3.000
 RVG  C3O  O3   C3   115.19  3.000
 RVG  H24  C3O  H23  108.35  3.000
 RVG  H24  C3O  H22  108.11  3.000
 RVG  H23  C3O  H22  108.32  3.000
 RVG  H24  C3O  O3   111.96  3.000
 RVG  H23  C3O  O3   112.50  3.000
 RVG  H22  C3O  O3   107.45  3.000
 RVG  H2   C2   C1   107.94  3.000
 RVG  H2   C2   O2   110.95  3.000
 RVG  C1   C2   O2   107.15  3.000
 RVG  H2   C2   C3   109.30  3.000
 RVG  C1   C2   C3   109.58  3.000
 RVG  O2   C2   C3   111.82  3.000
 RVG  C2O  O2   C2   115.79  3.000
 RVG  H28  C2O  H27  108.30  3.000
 RVG  H28  C2O  H26  108.56  3.000
 RVG  H27  C2O  H26  108.04  3.000
 RVG  H28  C2O  O2   112.57  3.000
 RVG  H27  C2O  O2   111.83  3.000
 RVG  H26  C2O  O2   107.40  3.000
 RVG  O1   C1   H1   111.06  3.000
 RVG  O1   C1   C2   112.28  3.000
 RVG  H1   C1   C2   108.50  3.000
 RVG  O1   C1   O5   104.74  3.000
 RVG  H1   C1   O5   110.04  3.000
 RVG  C2   C1   O5   110.18  3.000
 RVG  HO1  O1   C1   108.25  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
 RVG  Var_01  H22  C3O  O3  C3   179.88  30.0  3
 RVG  Var_02  H26  C2O  O2  C2  -169.99  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
 RVG  chir_01  C4  O4  C3  C5  negativ
 RVG  chir_02  C5  O5  C4  C6  negativ
 RVG  chir_03  C3  O3  C2  C4  positiv
 RVG  chir_04  C2  O2  C3  C1  positiv
 RVG  chir_05  C1  O5  O1  C2  negativ

