# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 12:42:15 2021
#   Inital geometry file: a 53 line input string
#   Ligand name: 2-deoxy-alpha-D-arabino-hexopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[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
 Z61  Z61  2-deoxy-alpha-D-arabino-hexopyranose  D-saccharide  23  11  .  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_Z61
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
 Z61  O4   O  OH1   0  -0.675  -0.7362  31.6694  30.7488
 Z61  C1   C  CH1   0   0.241  -3.4428  29.6188  33.1464
 Z61  C2   C  CH2   0  -0.503  -3.3267  31.1209  33.3431
 Z61  C3   C  CH1   0   0.039  -2.6351  31.7815  32.1636
 Z61  C4   C  CH1   0  -0.003  -1.3021  31.0913  31.9066
 Z61  C5   C  CH1   0  -0.011  -1.5223  29.5830  31.7305
 Z61  C6   C  CH2   0  -0.161  -0.2136  28.8361  31.5890
 Z61  O3   O  OH1   0  -0.672  -2.4654  33.1483  32.4605
 Z61  O5   O  O2    0  -0.502  -2.1917  29.0478  32.8594
 Z61  O6   O  OH1   0  -0.670  -0.4832  27.4808  31.3204
 Z61  H1   H  HCH1  0   0.231  -3.7497  29.1431  34.0843
 Z61  H21  H  HCH2  0   0.255  -4.3179  31.5501  33.5052
 Z61  H22  H  HCH2  0   0.243  -2.7457  31.3031  34.2516
 Z61  H3   H  HCH1  0   0.207  -3.2569  31.6607  31.2639
 Z61  H4   H  HCH1  0   0.217  -0.6571  31.2536  32.7829
 Z61  H5   H  HCH1  0   0.217  -2.1147  29.4260  30.8174
 Z61  H61  H  HCH2  0   0.199   0.3622  29.2957  30.7771
 Z61  H62  H  HCH2  0   0.195   0.3736  28.9611  32.5100
 Z61  HO3  H  HOH1  0   0.447  -2.0405  33.5627  31.7022
 Z61  HO6  H  HOH1  0   0.456   0.3531  27.0420  31.1419
 Z61  HO4  H  HOH1  0   0.459   0.2217  31.6400  30.8170
 Z61  O1   O  OH1   0  -0.668  -4.3768  29.3767  32.1378
 Z61  HO1  H  HOH1  0   0.458  -4.5657  28.4325  32.1083

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
 Z61  O4  C4   single  1.412  0.020  1.412
 Z61  C1  C2   single  1.519  0.020  1.519
 Z61  C1  O1   single  1.396  0.020  1.396
 Z61  C1  O5   single  1.405  0.020  1.405
 Z61  C1  H1   single  0.970  0.020  1.090
 Z61  C2  C3   single  1.519  0.020  1.519
 Z61  C2  H21  single  0.970  0.020  1.090
 Z61  C2  H22  single  0.970  0.020  1.090
 Z61  C3  C4   single  1.523  0.020  1.523
 Z61  C3  O3   single  1.409  0.020  1.409
 Z61  C3  H3   single  0.970  0.020  1.090
 Z61  C4  C5   single  1.534  0.020  1.534
 Z61  C4  H4   single  0.970  0.020  1.090
 Z61  C5  C6   single  1.513  0.020  1.513
 Z61  C5  O5   single  1.417  0.020  1.417
 Z61  C5  H5   single  0.970  0.020  1.090
 Z61  C6  O6   single  1.408  0.020  1.408
 Z61  C6  H61  single  0.970  0.020  1.090
 Z61  C6  H62  single  0.970  0.020  1.090
 Z61  O1  HO1  single  0.850  0.020  0.980
 Z61  O3  HO3  single  0.850  0.020  0.980
 Z61  O6  HO6  single  0.850  0.020  0.980
 Z61  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
 Z61  HO4  O4  C4   109.19  3.000
 Z61  H1   C1  O5   104.35  3.000
 Z61  H1   C1  O1   110.84  3.000
 Z61  O5   C1  O1   112.20  3.000
 Z61  H1   C1  C2   109.87  3.000
 Z61  O5   C1  C2   111.12  3.000
 Z61  O1   C1  C2   108.43  3.000
 Z61  H22  C2  H21  107.06  3.000
 Z61  H22  C2  C3   109.31  3.000
 Z61  H21  C2  C3   110.95  3.000
 Z61  H22  C2  C1   108.23  3.000
 Z61  H21  C2  C1   109.78  3.000
 Z61  C3   C2  C1   111.37  3.000
 Z61  H3   C3  O3   110.30  3.000
 Z61  H3   C3  C4   107.87  3.000
 Z61  O3   C3  C4   111.71  3.000
 Z61  H3   C3  C2   109.27  3.000
 Z61  O3   C3  C2   108.25  3.000
 Z61  C4   C3  C2   109.42  3.000
 Z61  H4   C4  C5   108.70  3.000
 Z61  H4   C4  C3   108.17  3.000
 Z61  C5   C4  C3   109.83  3.000
 Z61  H4   C4  O4   110.95  3.000
 Z61  C5   C4  O4   111.45  3.000
 Z61  C3   C4  O4   107.67  3.000
 Z61  H5   C5  O5   110.67  3.000
 Z61  H5   C5  C6   108.53  3.000
 Z61  O5   C5  C6   107.25  3.000
 Z61  H5   C5  C4   108.24  3.000
 Z61  O5   C5  C4   110.34  3.000
 Z61  C6   C5  C4   111.82  3.000
 Z61  H62  C6  H61  106.99  3.000
 Z61  H62  C6  O6   111.81  3.000
 Z61  H61  C6  O6   111.27  3.000
 Z61  H62  C6  C5   109.12  3.000
 Z61  H61  C6  C5   108.45  3.000
 Z61  O6   C6  C5   109.11  3.000
 Z61  HO3  O3  C3   107.74  3.000
 Z61  C5   O5  C1   115.45  3.000
 Z61  HO6  O6  C6   107.96  3.000
 Z61  HO1  O1  C1   108.86  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
 Z61  chir_01  C1  C2  O1  O5  negativ
 Z61  chir_02  C3  O3  C4  C2  negativ
 Z61  chir_03  C4  O4  C5  C3  positiv
 Z61  chir_04  C5  O5  C4  C6  negativ

