# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 14:03:04 2021
#   Inital geometry file: a 51 line input string
#   Ligand name: 2,6-dideoxy-beta-L-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
 Z5J  Z5J  2,6-dideoxy-beta-L-arabino-hexopyranose  L-saccharide  22  10  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Z5J
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
 Z5J  O4   O  OH1   0  -0.676  19.8876   8.6756  13.8177
 Z5J  C4   C  CH1   0   0.050  18.9959   9.2015  12.8659
 Z5J  C5   C  CH1   0   0.018  18.0648   8.0734  12.4134
 Z5J  C6   C  CH3   0  -0.680  18.8058   6.9234  11.7636
 Z5J  O5   O  O2    0  -0.500  17.1333   8.5703  11.4715
 Z5J  C3   C  CH1   0   0.012  18.1663  10.3434  13.4368
 Z5J  O3   O  OH1   0  -0.674  19.0531  11.3885  13.7727
 Z5J  C2   C  CH2   0  -0.548  17.1137  10.7750  12.4242
 Z5J  C1   C  CH1   0   0.280  16.2863   9.5778  11.9814
 Z5J  O1   O  OH1   0  -0.654  15.3490   9.8845  11.0132
 Z5J  HO1  H  HOH1  0   0.452  15.7620  10.4264  10.3307
 Z5J  H4   H  HCH1  0   0.199  19.5338   9.5747  11.9782
 Z5J  H5   H  HCH1  0   0.209  17.5271   7.7004  13.3005
 Z5J  H61  H  HCH3  0   0.239  18.1077   6.1466  11.4500
 Z5J  H62  H  HCH3  0   0.225  19.3622   7.2598  10.8866
 Z5J  H63  H  HCH3  0   0.238  19.5099   6.4731  12.4605
 Z5J  H3   H  HCH1  0   0.209  17.6580   9.9672  14.3382
 Z5J  HO3  H  HOH1  0   0.456  18.5806  12.0304  14.3116
 Z5J  H21  H  HCH2  0   0.252  16.4592  11.5329  12.8630
 Z5J  H22  H  HCH2  0   0.238  17.6059  11.2202  11.5519
 Z5J  H1   H  HCH1  0   0.202  15.7239   9.1768  12.8378
 Z5J  HO4  H  HOH1  0   0.451  20.4261   9.4009  14.1507

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
 Z5J  O4   C4   single  1.406  0.020  1.406
 Z5J  C4   C5   single  1.531  0.020  1.531
 Z5J  C4   C3   single  1.523  0.020  1.523
 Z5J  C4   H4   single  0.970  0.020  1.090
 Z5J  C5   C6   single  1.515  0.020  1.515
 Z5J  C5   O5   single  1.415  0.020  1.415
 Z5J  C5   H5   single  0.970  0.020  1.090
 Z5J  C6   H61  single  0.970  0.020  1.090
 Z5J  C6   H62  single  0.970  0.020  1.090
 Z5J  C6   H63  single  0.970  0.020  1.090
 Z5J  O5   C1   single  1.412  0.020  1.412
 Z5J  C3   O3   single  1.411  0.020  1.411
 Z5J  C3   C2   single  1.523  0.020  1.523
 Z5J  C3   H3   single  0.970  0.020  1.090
 Z5J  O3   HO3  single  0.850  0.020  0.980
 Z5J  C2   C1   single  1.521  0.020  1.521
 Z5J  C2   H21  single  0.970  0.020  1.090
 Z5J  C2   H22  single  0.970  0.020  1.090
 Z5J  C1   O1   single  1.382  0.020  1.382
 Z5J  C1   H1   single  0.970  0.020  1.090
 Z5J  HO1  O1   single  0.850  0.020  0.980
 Z5J  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
 Z5J  HO4  O4  C4   107.88  3.000
 Z5J  H4   C4  C3   108.28  3.000
 Z5J  H4   C4  C5   107.94  3.000
 Z5J  C3   C4  C5   109.39  3.000
 Z5J  H4   C4  O4   111.22  3.000
 Z5J  C3   C4  O4   111.85  3.000
 Z5J  C5   C4  O4   108.07  3.000
 Z5J  H5   C5  O5   109.48  3.000
 Z5J  H5   C5  C6   109.08  3.000
 Z5J  O5   C5  C6   107.65  3.000
 Z5J  H5   C5  C4   107.95  3.000
 Z5J  O5   C5  C4   109.78  3.000
 Z5J  C6   C5  C4   112.87  3.000
 Z5J  H63  C6  H62  108.19  3.000
 Z5J  H63  C6  H61  107.67  3.000
 Z5J  H62  C6  H61  108.35  3.000
 Z5J  H63  C6  C5   110.85  3.000
 Z5J  H62  C6  C5   111.10  3.000
 Z5J  H61  C6  C5   110.55  3.000
 Z5J  C1   O5  C5   113.91  3.000
 Z5J  H3   C3  C2   108.78  3.000
 Z5J  H3   C3  O3   110.38  3.000
 Z5J  C2   C3  O3   112.50  3.000
 Z5J  H3   C3  C4   107.59  3.000
 Z5J  C2   C3  C4   109.86  3.000
 Z5J  O3   C3  C4   107.60  3.000
 Z5J  HO3  O3  C3   108.59  3.000
 Z5J  H22  C2  H21  107.86  3.000
 Z5J  H22  C2  C1   109.40  3.000
 Z5J  H21  C2  C1   109.68  3.000
 Z5J  H22  C2  C3   109.51  3.000
 Z5J  H21  C2  C3   110.08  3.000
 Z5J  C1   C2  C3   110.27  3.000
 Z5J  H1   C1  O1   106.23  3.000
 Z5J  H1   C1  C2   109.77  3.000
 Z5J  O1   C1  C2   113.47  3.000
 Z5J  H1   C1  O5   109.13  3.000
 Z5J  O1   C1  O5   108.19  3.000
 Z5J  C2   C1  O5   109.91  3.000
 Z5J  HO1  O1  C1   109.27  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
 Z5J  chir_01  C4  O4  C5  C3  negativ
 Z5J  chir_02  C5  O5  C4  C6  positiv
 Z5J  chir_03  C3  O3  C4  C2  positiv
 Z5J  chir_04  C1  O1  O5  C2  negativ

