# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 06:57:19 2022
#   Inital geometry file: a 53 line input string
#   Ligand name: 6-deoxy-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1O[C@H](O)[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
 G6D  G6D  6-deoxy-alpha-D-glucopyranose  D-saccharide  23  11  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G6D
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
 G6D  C1   C  CH1   0   0.232  24.4874   3.0139  45.0592
 G6D  O2   O  OH1   0  -0.666  23.8863   3.5477  42.8199
 G6D  C2   C  CH1   0   0.012  24.3727   2.5059  43.6246
 G6D  C3   C  CH1   0  -0.004  23.4976   1.2602  43.5715
 G6D  O3   O  OH1   0  -0.672  23.5084   0.7967  42.2415
 G6D  C4   C  CH1   0   0.009  24.0378   0.2183  44.5418
 G6D  O4   O  OH1   0  -0.671  23.1420  -0.8710  44.5295
 G6D  C5   C  CH1   0   0.016  24.1748   0.8164  45.9455
 G6D  O5   O  O2    0  -0.501  24.9709   1.9947  45.8916
 G6D  C6   C  CH3   0  -0.695  24.8455  -0.1322  46.9178
 G6D  O1   O  OH1   0  -0.661  23.2467   3.4961  45.4610
 G6D  H1   H  HCH1  0   0.233  25.2512   3.7993  45.1092
 G6D  HO2  H  HOH1  0   0.449  23.8992   3.2467  41.9060
 G6D  H2   H  HCH1  0   0.216  25.3887   2.2147  43.3162
 G6D  H3   H  HCH1  0   0.210  22.4751   1.5254  43.8811
 G6D  HO3  H  HOH1  0   0.450  22.9202   0.0370  42.1824
 G6D  H4   H  HCH1  0   0.211  25.0370  -0.0892  44.1971
 G6D  HO4  H  HOH1  0   0.457  23.6126  -1.6668  44.7931
 G6D  H5   H  HCH1  0   0.213  23.1696   1.0535  46.3192
 G6D  H61  H  HCH3  0   0.243  24.9457   0.3270  47.9015
 G6D  H62  H  HCH3  0   0.232  24.2530  -1.0381  47.0428
 G6D  H63  H  HCH3  0   0.227  25.8392  -0.4200  46.5694
 G6D  HO1  H  HOH1  0   0.459  23.3539   3.9966  46.2770

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
 G6D  C1  C2   single  1.526  0.020  1.526
 G6D  C1  O5   single  1.402  0.020  1.402
 G6D  C1  O1   single  1.390  0.020  1.390
 G6D  C1  H1   single  0.970  0.020  1.090
 G6D  O2  C2   single  1.403  0.020  1.403
 G6D  O2  HO2  single  0.850  0.020  0.980
 G6D  C2  C3   single  1.523  0.020  1.523
 G6D  C2  H2   single  0.970  0.020  1.090
 G6D  C3  O3   single  1.408  0.020  1.408
 G6D  C3  C4   single  1.523  0.020  1.523
 G6D  C3  H3   single  0.970  0.020  1.090
 G6D  O3  HO3  single  0.850  0.020  0.980
 G6D  C4  O4   single  1.410  0.020  1.410
 G6D  C4  C5   single  1.532  0.020  1.532
 G6D  C4  H4   single  0.970  0.020  1.090
 G6D  O4  HO4  single  0.850  0.020  0.980
 G6D  C5  O5   single  1.423  0.020  1.423
 G6D  C5  C6   single  1.515  0.020  1.515
 G6D  C5  H5   single  0.970  0.020  1.090
 G6D  C6  H61  single  0.970  0.020  1.090
 G6D  C6  H62  single  0.970  0.020  1.090
 G6D  C6  H63  single  0.970  0.020  1.090
 G6D  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
 G6D  H1   C1  O1   111.10  3.000
 G6D  H1   C1  O5   104.67  3.000
 G6D  O1   C1  O5   112.85  3.000
 G6D  H1   C1  C2   109.48  3.000
 G6D  O1   C1  C2   108.66  3.000
 G6D  O5   C1  C2   110.00  3.000
 G6D  HO2  O2  C2   107.92  3.000
 G6D  H2   C2  C3   107.70  3.000
 G6D  H2   C2  O2   110.83  3.000
 G6D  C3   C2  O2   112.83  3.000
 G6D  H2   C2  C1   106.38  3.000
 G6D  C3   C2  C1   110.37  3.000
 G6D  O2   C2  C1   108.54  3.000
 G6D  H3   C3  C4   108.37  3.000
 G6D  H3   C3  O3   110.61  3.000
 G6D  C4   C3  O3   111.95  3.000
 G6D  H3   C3  C2   109.07  3.000
 G6D  C4   C3  C2   109.49  3.000
 G6D  O3   C3  C2   107.31  3.000
 G6D  HO3  O3  C3   108.24  3.000
 G6D  H4   C4  C5   108.35  3.000
 G6D  H4   C4  O4   110.98  3.000
 G6D  C5   C4  O4   111.49  3.000
 G6D  H4   C4  C3   108.27  3.000
 G6D  C5   C4  C3   110.39  3.000
 G6D  O4   C4  C3   107.31  3.000
 G6D  HO4  O4  C4   109.03  3.000
 G6D  H5   C5  C6   108.78  3.000
 G6D  H5   C5  O5   110.25  3.000
 G6D  C6   C5  O5   107.17  3.000
 G6D  H5   C5  C4   108.31  3.000
 G6D  C6   C5  C4   112.53  3.000
 G6D  O5   C5  C4   109.79  3.000
 G6D  C5   O5  C1   115.56  3.000
 G6D  H63  C6  H62  108.20  3.000
 G6D  H63  C6  H61  108.38  3.000
 G6D  H62  C6  H61  107.26  3.000
 G6D  H63  C6  C5   111.30  3.000
 G6D  H62  C6  C5   110.70  3.000
 G6D  H61  C6  C5   110.86  3.000
 G6D  HO1  O1  C1   109.01  3.000

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
 G6D  chir_01  C1  C2  O5  O1  positiv
 G6D  chir_02  C2  O2  C1  C3  negativ
 G6D  chir_03  C3  O3  C2  C4  positiv
 G6D  chir_04  C4  O4  C5  C3  positiv
 G6D  chir_05  C5  O5  C4  C6  negativ

