# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 20:34:27 2022
#   Inital geometry file: a 51 line input string
#   Ligand name: 2,6-dideoxy-beta-D-lyxo-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
 DDL  DDL  2,6-dideoxy-beta-D-lyxo-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_DDL
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
 DDL  C1   C  CH1   0   0.289  3.9016  4.3843  20.0629
 DDL  C2   C  CH2   0  -0.533  4.2028  5.5028  19.0805
 DDL  C3   C  CH1   0   0.050  5.6956  5.5491  18.7859
 DDL  C4   C  CH1   0  -0.015  6.5006  5.6117  20.0913
 DDL  C5   C  CH1   0  -0.013  6.0783  4.4346  20.9735
 DDL  C6   C  CH3   0  -0.672  6.8057  4.3808  22.3001
 DDL  O1   O  OH1   0  -0.652  2.5704  4.4469  20.4222
 DDL  O5   O  O2    0  -0.500  4.6857  4.5228  21.2312
 DDL  O3   O  OH1   0  -0.662  5.9394  6.6414  17.9349
 DDL  O4   O  OH1   0  -0.662  6.3710  6.8473  20.7514
 DDL  H1   H  HCH1  0   0.180  4.1489  3.4148  19.5957
 DDL  H2   H  HCH2  0   0.237  3.8670  6.4572  19.5002
 DDL  H22  H  HCH2  0   0.255  3.6460  5.3376  18.1554
 DDL  H3   H  HCH1  0   0.201  5.9745  4.6031  18.2952
 DDL  H4   H  HCH1  0   0.240  7.5653  5.5002  19.8554
 DDL  H5   H  HCH1  0   0.214  6.2973  3.5067  20.4210
 DDL  H61  H  HCH3  0   0.238  6.4976  3.5066  22.8731
 DDL  H62  H  HCH3  0   0.231  7.8802  4.3060  22.1313
 DDL  H63  H  HCH3  0   0.228  6.6202  5.2695  22.9030
 DDL  HO1  H  HOH1  0   0.457  2.3211  3.6268  20.8620
 DDL  HO3  H  HOH1  0   0.446  6.8653  6.6224  17.6721
 DDL  HO4  H  HOH1  0   0.441  5.4959  6.8953  21.1516

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
 DDL  C1  C2   single  1.519  0.020  1.519
 DDL  C1  O1   single  1.380  0.020  1.380
 DDL  C1  O5   single  1.414  0.020  1.414
 DDL  C1  H1   single  0.970  0.020  1.090
 DDL  C2  C3   single  1.522  0.020  1.522
 DDL  C2  H2   single  0.970  0.020  1.090
 DDL  C2  H22  single  0.970  0.020  1.090
 DDL  C3  C4   single  1.535  0.020  1.535
 DDL  C3  O3   single  1.406  0.020  1.406
 DDL  C3  H3   single  0.970  0.020  1.090
 DDL  C4  C5   single  1.530  0.020  1.530
 DDL  C4  O4   single  1.407  0.020  1.407
 DDL  C4  H4   single  0.970  0.020  1.090
 DDL  C5  C6   single  1.514  0.020  1.514
 DDL  C5  O5   single  1.419  0.020  1.419
 DDL  C5  H5   single  0.970  0.020  1.090
 DDL  C6  H61  single  0.970  0.020  1.090
 DDL  C6  H62  single  0.970  0.020  1.090
 DDL  C6  H63  single  0.970  0.020  1.090
 DDL  O1  HO1  single  0.850  0.020  0.980
 DDL  O3  HO3  single  0.850  0.020  0.980
 DDL  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
 DDL  H1   C1  O5   108.14  3.000
 DDL  H1   C1  O1   111.47  3.000
 DDL  O5   C1  O1   108.38  3.000
 DDL  H1   C1  C2   109.18  3.000
 DDL  O5   C1  C2   110.63  3.000
 DDL  O1   C1  C2   109.04  3.000
 DDL  H22  C2  H2   107.46  3.000
 DDL  H22  C2  C3   109.91  3.000
 DDL  H2   C2  C3   110.39  3.000
 DDL  H22  C2  C1   109.59  3.000
 DDL  H2   C2  C1   109.45  3.000
 DDL  C3   C2  C1   110.00  3.000
 DDL  H3   C3  O3   110.71  3.000
 DDL  H3   C3  C4   106.33  3.000
 DDL  O3   C3  C4   113.09  3.000
 DDL  H3   C3  C2   107.96  3.000
 DDL  O3   C3  C2   108.11  3.000
 DDL  C4   C3  C2   110.54  3.000
 DDL  H4   C4  O4   106.25  3.000
 DDL  H4   C4  C5   108.29  3.000
 DDL  O4   C4  C5   112.31  3.000
 DDL  H4   C4  C3   108.80  3.000
 DDL  O4   C4  C3   112.74  3.000
 DDL  C5   C4  C3   108.31  3.000
 DDL  H5   C5  O5   109.78  3.000
 DDL  H5   C5  C6   108.30  3.000
 DDL  O5   C5  C6   108.34  3.000
 DDL  H5   C5  C4   107.68  3.000
 DDL  O5   C5  C4   109.13  3.000
 DDL  C6   C5  C4   113.57  3.000
 DDL  H63  C6  H62  108.02  3.000
 DDL  H63  C6  H61  108.37  3.000
 DDL  H62  C6  H61  107.76  3.000
 DDL  H63  C6  C5   111.96  3.000
 DDL  H62  C6  C5   109.90  3.000
 DDL  H61  C6  C5   110.70  3.000
 DDL  HO1  O1  C1   109.26  3.000
 DDL  C5   O5  C1   112.84  3.000
 DDL  HO3  O3  C3   108.46  3.000
 DDL  HO4  O4  C4   108.80  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
 DDL  chir_01  C1  C2  O1  O5  positiv
 DDL  chir_02  C3  O3  C4  C2  negativ
 DDL  chir_03  C4  O4  C3  C5  positiv
 DDL  chir_04  C5  O5  C4  C6  negativ

