# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 22:15:17 2022
#   Inital geometry file: a 51 line input string
#   Ligand name: 2,6-dideoxy-alpha-L-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
 DLF  DLF  2,6-dideoxy-alpha-L-lyxo-hexopyranose  L-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_DLF
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
 DLF  C1   C  CH1   0   0.242  -0.4104  6.4531  -5.2903
 DLF  C2   C  CH2   0  -0.489  -0.0872  5.1525  -6.0118
 DLF  C3   C  CH1   0   0.007  -1.3550  4.3953  -6.3672
 DLF  C4   C  CH1   0   0.007  -2.3127  5.3087  -7.1377
 DLF  C5   C  CH1   0   0.020  -2.5545  6.5804  -6.3321
 DLF  C6   C  CH3   0  -0.680  -3.4292  7.5874  -7.0523
 DLF  O1   O  OH1   0  -0.665  -0.8739  6.1360  -4.0099
 DLF  O3   O  OH1   0  -0.665  -0.9910  3.2693  -7.1418
 DLF  O4   O  OH1   0  -0.671  -1.7931  5.6435  -8.4007
 DLF  O5   O  O2    0  -0.498  -1.3307  7.2279  -6.0116
 DLF  H1   H  HCH1  0   0.223   0.4878  7.0786  -5.2341
 DLF  H2   H  HCH2  0   0.238   0.4651  5.3950  -6.9223
 DLF  H22  H  HCH2  0   0.249   0.5697  4.5415  -5.3896
 DLF  H3   H  HCH1  0   0.217  -1.8623  4.0809  -5.4459
 DLF  H4   H  HCH1  0   0.212  -3.2834  4.7944  -7.2341
 DLF  H5   H  HCH1  0   0.215  -3.0699  6.2732  -5.4123
 DLF  H61  H  HCH3  0   0.235  -3.6354  8.4455  -6.4123
 DLF  H62  H  HCH3  0   0.230  -2.9632  7.9472  -7.9688
 DLF  H63  H  HCH3  0   0.227  -4.3853  7.1324  -7.3129
 DLF  HO1  H  HOH1  0   0.453  -0.9663  6.9500  -3.5024
 DLF  HO3  H  HOH1  0   0.451  -1.7544  2.6856  -7.2079
 DLF  HO4  H  HOH1  0   0.442  -1.4565  4.8313  -8.7957

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
 DLF  C1  C2   single  1.522  0.020  1.522
 DLF  C1  O1   single  1.398  0.020  1.398
 DLF  C1  O5   single  1.403  0.020  1.403
 DLF  C1  H1   single  0.970  0.020  1.090
 DLF  C2  C3   single  1.519  0.020  1.519
 DLF  C2  H2   single  0.970  0.020  1.090
 DLF  C2  H22  single  0.970  0.020  1.090
 DLF  C3  C4   single  1.531  0.020  1.531
 DLF  C3  O3   single  1.414  0.020  1.414
 DLF  C3  H3   single  0.970  0.020  1.090
 DLF  C4  C5   single  1.525  0.020  1.525
 DLF  C4  O4   single  1.406  0.020  1.406
 DLF  C4  H4   single  0.970  0.020  1.090
 DLF  C5  C6   single  1.516  0.020  1.516
 DLF  C5  O5   single  1.421  0.020  1.421
 DLF  C5  H5   single  0.970  0.020  1.090
 DLF  C6  H61  single  0.970  0.020  1.090
 DLF  C6  H62  single  0.970  0.020  1.090
 DLF  C6  H63  single  0.970  0.020  1.090
 DLF  O1  HO1  single  0.850  0.020  0.980
 DLF  O3  HO3  single  0.850  0.020  0.980
 DLF  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
 DLF  H1   C1  O5   104.40  3.000
 DLF  H1   C1  O1   110.75  3.000
 DLF  O5   C1  O1   112.25  3.000
 DLF  H1   C1  C2   109.76  3.000
 DLF  O5   C1  C2   111.56  3.000
 DLF  O1   C1  C2   108.11  3.000
 DLF  H22  C2  H2   107.17  3.000
 DLF  H22  C2  C3   110.89  3.000
 DLF  H2   C2  C3   109.74  3.000
 DLF  H22  C2  C1   109.62  3.000
 DLF  H2   C2  C1   108.23  3.000
 DLF  C3   C2  C1   111.08  3.000
 DLF  H3   C3  O3   110.52  3.000
 DLF  H3   C3  C4   107.71  3.000
 DLF  O3   C3  C4   111.11  3.000
 DLF  H3   C3  C2   109.40  3.000
 DLF  O3   C3  C2   108.07  3.000
 DLF  C4   C3  C2   110.02  3.000
 DLF  H4   C4  O4   110.96  3.000
 DLF  H4   C4  C5   107.19  3.000
 DLF  O4   C4  C5   109.55  3.000
 DLF  H4   C4  C3   108.44  3.000
 DLF  O4   C4  C3   111.27  3.000
 DLF  C5   C4  C3   109.32  3.000
 DLF  H5   C5  O5   110.04  3.000
 DLF  H5   C5  C6   108.24  3.000
 DLF  O5   C5  C6   107.55  3.000
 DLF  H5   C5  C4   106.47  3.000
 DLF  O5   C5  C4   111.25  3.000
 DLF  C6   C5  C4   113.24  3.000
 DLF  H63  C6  H62  108.17  3.000
 DLF  H63  C6  H61  107.63  3.000
 DLF  H62  C6  H61  108.35  3.000
 DLF  H63  C6  C5   110.02  3.000
 DLF  H62  C6  C5   111.86  3.000
 DLF  H61  C6  C5   110.68  3.000
 DLF  HO1  O1  C1   108.81  3.000
 DLF  HO3  O3  C3   108.43  3.000
 DLF  HO4  O4  C4   107.25  3.000
 DLF  C5   O5  C1   115.42  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
 DLF  chir_01  C1  C2  O1  O5  positiv
 DLF  chir_02  C3  O3  C4  C2  positiv
 DLF  chir_03  C4  O4  C3  C5  negativ
 DLF  chir_04  C5  O5  C4  C6  positiv

