# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:38:50 2022
#   Inital geometry file: a 51 line input string
#   Ligand name: 3,6-dideoxy-alpha-D-xylo-hexopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1O[C@H](O)[C@H](O)C[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
 ABE  ABE  3,6-dideoxy-alpha-D-xylo-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_ABE
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
 ABE  C1   C  CH1   0   0.243  13.6681   -9.2938  60.7806
 ABE  C2   C  CH1   0   0.031  14.8641   -8.3641  60.9621
 ABE  C3   C  CH2   0  -0.513  14.3953   -6.9728  61.3734
 ABE  C4   C  CH1   0   0.016  13.3706   -6.4280  60.3877
 ABE  C5   C  CH1   0   0.033  12.2476   -7.4534  60.2118
 ABE  C6   C  CH3   0  -0.706  11.2417   -7.0702  59.1446
 ABE  O1   O  OH1   0  -0.664  13.0935   -9.5350  62.0248
 ABE  O2   O  OH1   0  -0.669  15.7365   -8.9427  61.9038
 ABE  O4   O  OH1   0  -0.672  14.0442   -6.1333  59.1820
 ABE  O5   O  O2    0  -0.504  12.7624   -8.7343  59.8660
 ABE  H1   H  HCH1  0   0.223  13.9933  -10.2304  60.3102
 ABE  H2   H  HCH1  0   0.213  15.3478   -8.2979  59.9788
 ABE  H31  H  HCH2  0   0.238  13.9432   -7.0151  62.3673
 ABE  H32  H  HCH2  0   0.246  15.2480   -6.2910  61.4395
 ABE  H4   H  HCH1  0   0.218  12.9159   -5.5208  60.8103
 ABE  H5   H  HCH1  0   0.207  11.7210   -7.5054  61.1740
 ABE  H61  H  HCH3  0   0.244  10.4093   -7.7735  59.1244
 ABE  H62  H  HCH3  0   0.233  10.8315   -6.0812  59.3528
 ABE  H63  H  HCH3  0   0.226  11.6865   -7.0540  58.1484
 ABE  HO1  H  HOH1  0   0.456  12.4520  -10.2481  61.9374
 ABE  HO2  H  HOH1  0   0.449  16.5499   -8.4286  61.9067
 ABE  HO4  H  HOH1  0   0.451  13.4498   -5.6460  58.6036

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
 ABE  C1  C2   single  1.526  0.020  1.526
 ABE  C1  O1   single  1.392  0.020  1.392
 ABE  C1  O5   single  1.404  0.020  1.404
 ABE  C1  H1   single  0.970  0.020  1.090
 ABE  C2  C3   single  1.525  0.020  1.525
 ABE  C2  O2   single  1.408  0.020  1.408
 ABE  C2  H2   single  0.970  0.020  1.090
 ABE  C3  C4   single  1.523  0.020  1.523
 ABE  C3  H31  single  0.970  0.020  1.090
 ABE  C3  H32  single  0.970  0.020  1.090
 ABE  C4  C5   single  1.531  0.020  1.531
 ABE  C4  O4   single  1.412  0.020  1.412
 ABE  C4  H4   single  0.970  0.020  1.090
 ABE  C5  C6   single  1.516  0.020  1.516
 ABE  C5  O5   single  1.423  0.020  1.423
 ABE  C5  H5   single  0.970  0.020  1.090
 ABE  C6  H61  single  0.970  0.020  1.090
 ABE  C6  H62  single  0.970  0.020  1.090
 ABE  C6  H63  single  0.970  0.020  1.090
 ABE  O1  HO1  single  0.850  0.020  0.980
 ABE  O2  HO2  single  0.850  0.020  0.980
 ABE  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
 ABE  H1   C1  O5   104.60  3.000
 ABE  H1   C1  O1   110.96  3.000
 ABE  O5   C1  O1   112.66  3.000
 ABE  H1   C1  C2   109.80  3.000
 ABE  O5   C1  C2   109.90  3.000
 ABE  O1   C1  C2   108.84  3.000
 ABE  H2   C2  O2   110.54  3.000
 ABE  H2   C2  C3   108.79  3.000
 ABE  O2   C2  C3   112.65  3.000
 ABE  H2   C2  C1   106.00  3.000
 ABE  O2   C2  C1   108.35  3.000
 ABE  C3   C2  C1   110.31  3.000
 ABE  H32  C3  H31  106.96  3.000
 ABE  H32  C3  C4   109.92  3.000
 ABE  H31  C3  C4   108.92  3.000
 ABE  H32  C3  C2   110.21  3.000
 ABE  H31  C3  C2   109.71  3.000
 ABE  C4   C3  C2   111.03  3.000
 ABE  H4   C4  O4   110.69  3.000
 ABE  H4   C4  C5   107.07  3.000
 ABE  O4   C4  C5   113.05  3.000
 ABE  H4   C4  C3   108.95  3.000
 ABE  O4   C4  C3   107.84  3.000
 ABE  C5   C4  C3   109.17  3.000
 ABE  H5   C5  O5   110.10  3.000
 ABE  H5   C5  C6   108.10  3.000
 ABE  O5   C5  C6   107.25  3.000
 ABE  H5   C5  C4   106.43  3.000
 ABE  O5   C5  C4   111.44  3.000
 ABE  C6   C5  C4   113.48  3.000
 ABE  H63  C6  H62  108.31  3.000
 ABE  H63  C6  H61  107.70  3.000
 ABE  H62  C6  H61  107.54  3.000
 ABE  H63  C6  C5   112.09  3.000
 ABE  H62  C6  C5   110.15  3.000
 ABE  H61  C6  C5   110.90  3.000
 ABE  HO1  O1  C1   108.80  3.000
 ABE  HO2  O2  C2   107.83  3.000
 ABE  HO4  O4  C4   108.92  3.000
 ABE  C5   O5  C1   115.71  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
 ABE  chir_01  C1  C2  O1  O5  negativ
 ABE  chir_02  C2  O2  C1  C3  negativ
 ABE  chir_03  C4  O4  C3  C5  positiv
 ABE  chir_04  C5  O5  C4  C6  negativ

