# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:16:20 2022
#   Inital geometry file: a 53 line input string
#   Ligand name: 2-deoxy-alpha-D-lyxo-hexopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](O)C[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
 2DG  2DG  2-deoxy-alpha-D-lyxo-hexopyranose  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 PERFECT
;

data_comp_2DG
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
 2DG  C1   C  CH1   0   0.242  -12.1163  20.3505  -25.8250
 2DG  C2   C  CH2   0  -0.498  -12.0547  21.6500  -25.0367
 2DG  C3   C  CH1   0   0.050  -13.1723  22.5938  -25.4513
 2DG  C4   C  CH1   0  -0.019  -13.1411  22.8140  -26.9646
 2DG  C5   C  CH1   0  -0.002  -13.2179  21.4428  -27.6441
 2DG  C6   C  CH2   0  -0.193  -13.0812  21.5004  -29.1578
 2DG  O1   O  OH1   0  -0.664  -13.2134  19.6131  -25.3743
 2DG  O3   O  OH1   0  -0.665  -13.0311  23.7852  -24.7175
 2DG  O4   O  OH1   0  -0.672  -11.9683  23.5178  -27.2984
 2DG  O5   O  O2    0  -0.504  -12.1741  20.5901  -27.2072
 2DG  O6   O  OH1   0  -0.668  -14.0728  22.3654  -29.6585
 2DG  H1   H  HCH1  0   0.224  -11.1865  19.7867  -25.6880
 2DG  H2   H  HCH2  0   0.249  -12.1095  21.4318  -23.9681
 2DG  H22  H  HCH2  0   0.241  -11.0851  22.1183  -25.2197
 2DG  H3   H  HCH1  0   0.209  -14.1374  22.1178  -25.2272
 2DG  H4   H  HCH1  0   0.229  -14.0372  23.3824  -27.2504
 2DG  H5   H  HCH1  0   0.215  -14.1984  21.0100  -27.4005
 2DG  H61  H  HCH2  0   0.198  -12.0710  21.8423  -29.4178
 2DG  H62  H  HCH2  0   0.217  -13.1872  20.4841  -29.5576
 2DG  HO1  H  HOH1  0   0.454  -13.1854  18.7380  -25.7766
 2DG  HO3  H  HOH1  0   0.445  -13.7739  24.3612  -24.9260
 2DG  HO4  H  HOH1  0   0.453  -12.0828  23.9067  -28.1703
 2DG  HO6  H  HOH1  0   0.458  -13.9653  22.4262  -30.6117

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
 2DG  C1  C2   single  1.521  0.020  1.521
 2DG  C1  O1   single  1.397  0.020  1.397
 2DG  C1  O5   single  1.404  0.020  1.404
 2DG  C1  H1   single  0.970  0.020  1.090
 2DG  C2  C3   single  1.521  0.020  1.521
 2DG  C2  H2   single  0.970  0.020  1.090
 2DG  C2  H22  single  0.970  0.020  1.090
 2DG  C3  C4   single  1.530  0.020  1.530
 2DG  C3  O3   single  1.406  0.020  1.406
 2DG  C3  H3   single  0.970  0.020  1.090
 2DG  C4  C5   single  1.532  0.020  1.532
 2DG  C4  O4   single  1.408  0.020  1.408
 2DG  C4  H4   single  0.970  0.020  1.090
 2DG  C5  C6   single  1.521  0.020  1.521
 2DG  C5  O5   single  1.417  0.020  1.417
 2DG  C5  H5   single  0.970  0.020  1.090
 2DG  C6  O6   single  1.408  0.020  1.408
 2DG  C6  H61  single  0.970  0.020  1.090
 2DG  C6  H62  single  0.970  0.020  1.090
 2DG  O1  HO1  single  0.850  0.020  0.980
 2DG  O3  HO3  single  0.850  0.020  0.980
 2DG  O4  HO4  single  0.850  0.020  0.980
 2DG  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
 2DG  H1   C1  O5   104.23  3.000
 2DG  H1   C1  O1   110.76  3.000
 2DG  O5   C1  O1   112.05  3.000
 2DG  H1   C1  C2   109.90  3.000
 2DG  O5   C1  C2   111.47  3.000
 2DG  O1   C1  C2   108.40  3.000
 2DG  H22  C2  H2   107.11  3.000
 2DG  H22  C2  C3   109.92  3.000
 2DG  H2   C2  C3   110.73  3.000
 2DG  H22  C2  C1   108.39  3.000
 2DG  H2   C2  C1   109.54  3.000
 2DG  C3   C2  C1   111.05  3.000
 2DG  H3   C3  O3   110.40  3.000
 2DG  H3   C3  C4   106.38  3.000
 2DG  O3   C3  C4   113.09  3.000
 2DG  H3   C3  C2   108.72  3.000
 2DG  O3   C3  C2   108.05  3.000
 2DG  C4   C3  C2   110.13  3.000
 2DG  H4   C4  O4   111.04  3.000
 2DG  H4   C4  C5   107.86  3.000
 2DG  O4   C4  C5   112.58  3.000
 2DG  H4   C4  C3   108.37  3.000
 2DG  O4   C4  C3   108.88  3.000
 2DG  C5   C4  C3   107.99  3.000
 2DG  H5   C5  O5   110.60  3.000
 2DG  H5   C5  C6   108.40  3.000
 2DG  O5   C5  C6   105.28  3.000
 2DG  H5   C5  C4   107.38  3.000
 2DG  O5   C5  C4   111.40  3.000
 2DG  C6   C5  C4   113.76  3.000
 2DG  H62  C6  H61  106.92  3.000
 2DG  H62  C6  O6   111.80  3.000
 2DG  H61  C6  O6   111.87  3.000
 2DG  H62  C6  C5   108.59  3.000
 2DG  H61  C6  C5   109.29  3.000
 2DG  O6   C6  C5   108.29  3.000
 2DG  HO1  O1  C1   108.78  3.000
 2DG  HO3  O3  C3   108.44  3.000
 2DG  HO4  O4  C4   108.54  3.000
 2DG  C5   O5  C1   115.89  3.000
 2DG  HO6  O6  C6   108.23  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
 2DG  chir_01  C1  C2  O1  O5  negativ
 2DG  chir_02  C3  O3  C4  C2  negativ
 2DG  chir_03  C4  O4  C5  C3  negativ
 2DG  chir_04  C5  O5  C4  C6  negativ

