# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 20:31:26 2022
#   Inital geometry file: a 51 line input string
#   Ligand name: 2,6-dideoxy-beta-D-arabino-hexopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[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
 DDA  DDA  2,6-dideoxy-beta-D-arabino-hexopyranose  D-saccharide  22  10  .  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_DDA
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
 DDA  C1   C  CH1   0   0.289   -6.3176  -1.1174   1.3035
 DDA  C2   C  CH2   0  -0.515   -7.2410  -1.6277   0.2120
 DDA  C3   C  CH1   0   0.037   -8.2018  -0.5275  -0.2031
 DDA  C4   C  CH1   0   0.017   -8.9265   0.0144   1.0221
 DDA  C5   C  CH1   0   0.013   -7.9036   0.4501   2.0793
 DDA  C6   C  CH3   0  -0.691   -8.5520   0.9312   3.3611
 DDA  O5   O  O2    0  -0.496   -7.0659  -0.6433   2.4018
 DDA  O1   O  OH1   0  -0.654   -5.5163  -2.1542   1.7394
 DDA  O3   O  OH1   0  -0.666   -9.0932  -1.0414  -1.1624
 DDA  O4   O  OH1   0  -0.673   -9.7283   1.0930   0.5943
 DDA  H1   H  HCH1  0   0.178   -5.7140  -0.2825   0.9053
 DDA  H21  H  HCH2  0   0.252   -6.6500  -1.9542  -0.6470
 DDA  H22  H  HCH2  0   0.238   -7.8000  -2.4922   0.5846
 DDA  H3   H  HCH1  0   0.197   -7.6134   0.3032  -0.6288
 DDA  H4   H  HCH1  0   0.209   -9.5404  -0.7927   1.4504
 DDA  H5   H  HCH1  0   0.205   -7.3020   1.2696   1.6520
 DDA  H61  H  HCH3  0   0.243   -7.7978   1.2280   4.0899
 DDA  H62  H  HCH3  0   0.232   -9.1822   1.7998   3.1737
 DDA  H63  H  HCH3  0   0.228   -9.1716   0.1496   3.8052
 DDA  HO1  H  HOH1  0   0.457   -4.7914  -1.7960   2.2629
 DDA  HO3  H  HOH1  0   0.444   -9.7200  -0.3439  -1.3816
 DDA  HO4  H  HOH1  0   0.457  -10.4470   1.2191   1.2203

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
 DDA  C1  C2   single  1.518  0.020  1.518
 DDA  C1  O5   single  1.411  0.020  1.411
 DDA  C1  O1   single  1.381  0.020  1.381
 DDA  C1  H1   single  0.970  0.020  1.090
 DDA  C2  C3   single  1.518  0.020  1.518
 DDA  C2  H21  single  0.970  0.020  1.090
 DDA  C2  H22  single  0.970  0.020  1.090
 DDA  C3  C4   single  1.523  0.020  1.523
 DDA  C3  O3   single  1.407  0.020  1.407
 DDA  C3  H3   single  0.970  0.020  1.090
 DDA  C4  C5   single  1.534  0.020  1.534
 DDA  C4  O4   single  1.410  0.020  1.410
 DDA  C4  H4   single  0.970  0.020  1.090
 DDA  C5  C6   single  1.515  0.020  1.515
 DDA  C5  O5   single  1.415  0.020  1.415
 DDA  C5  H5   single  0.970  0.020  1.090
 DDA  C6  H61  single  0.970  0.020  1.090
 DDA  C6  H62  single  0.970  0.020  1.090
 DDA  C6  H63  single  0.970  0.020  1.090
 DDA  O1  HO1  single  0.850  0.020  0.980
 DDA  O3  HO3  single  0.850  0.020  0.980
 DDA  O4  HO4  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
 DDA  H1   C1  O1   111.36  3.000
 DDA  H1   C1  O5   108.45  3.000
 DDA  O1   C1  O5   108.32  3.000
 DDA  H1   C1  C2   109.10  3.000
 DDA  O1   C1  C2   109.12  3.000
 DDA  O5   C1  C2   110.49  3.000
 DDA  H22  C2  H21  107.92  3.000
 DDA  H22  C2  C3   110.01  3.000
 DDA  H21  C2  C3   110.11  3.000
 DDA  H22  C2  C1   109.35  3.000
 DDA  H21  C2  C1   109.68  3.000
 DDA  C3   C2  C1   109.75  3.000
 DDA  H3   C3  O3   110.48  3.000
 DDA  H3   C3  C4   107.23  3.000
 DDA  O3   C3  C4   112.14  3.000
 DDA  H3   C3  C2   108.27  3.000
 DDA  O3   C3  C2   108.82  3.000
 DDA  C4   C3  C2   109.81  3.000
 DDA  H4   C4  O4   111.21  3.000
 DDA  H4   C4  C5   108.17  3.000
 DDA  O4   C4  C5   111.77  3.000
 DDA  H4   C4  C3   108.51  3.000
 DDA  O4   C4  C3   107.37  3.000
 DDA  C5   C4  C3   109.76  3.000
 DDA  H5   C5  O5   109.86  3.000
 DDA  H5   C5  C6   108.99  3.000
 DDA  O5   C5  C6   107.82  3.000
 DDA  H5   C5  C4   107.93  3.000
 DDA  O5   C5  C4   109.42  3.000
 DDA  C6   C5  C4   112.82  3.000
 DDA  H63  C6  H62  108.21  3.000
 DDA  H63  C6  H61  108.40  3.000
 DDA  H62  C6  H61  107.35  3.000
 DDA  H63  C6  C5   111.09  3.000
 DDA  H62  C6  C5   110.81  3.000
 DDA  H61  C6  C5   110.86  3.000
 DDA  C5   O5  C1   113.34  3.000
 DDA  HO1  O1  C1   109.21  3.000
 DDA  HO3  O3  C3   107.64  3.000
 DDA  HO4  O4  C4   109.13  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
 DDA  chir_01  C1  C2  O5  O1  negativ
 DDA  chir_02  C3  O3  C4  C2  negativ
 DDA  chir_03  C4  O4  C5  C3  positiv
 DDA  chir_04  C5  O5  C4  C6  negativ

