# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 21:44:17 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: beta-D-xylofuranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](O)[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
 XYZ  XYZ  'beta-D-xylofuranose      '  D-saccharide  20  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 GRAND
;

data_comp_XYZ
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
 XYZ  C4   C  CH1   0   0.011   0.8261  -0.2446   0.5827
 XYZ  O    O  O2    0  -0.512   0.1942   1.0301   0.6895
 XYZ  C1   C  CH1   0   0.243  -1.0948   1.0011   0.1372
 XYZ  C2   C  CH1   0  -0.046  -1.5050  -0.4717   0.1808
 XYZ  O2   O  OH1   0  -0.674  -1.8941  -0.8482   1.4791
 XYZ  C3   C  CH1   0  -0.030  -0.1778  -1.1771  -0.1061
 XYZ  O3   O  OH1   0  -0.664   0.0989  -1.2658  -1.4791
 XYZ  C5   C  CH2   0  -0.153   2.1643  -0.1343  -0.1145
 XYZ  O5   O  OH1   0  -0.674   3.0219   0.6256   0.7085
 XYZ  O1   O  OH1   0  -0.663  -1.1235   1.4400  -1.1828
 XYZ  H4   H  HCH1  0   0.234   1.0021  -0.6173   1.5989
 XYZ  H1   H  HCH1  0   0.221  -1.7330   1.6312   0.7706
 XYZ  H2   H  HCH1  0   0.242  -2.2762  -0.7063  -0.5633
 XYZ  HO2  H  HOH1  0   0.456  -2.6826  -0.3541   1.7242
 XYZ  H3   H  HCH1  0   0.242  -0.1619  -2.1675   0.3646
 XYZ  HO3  H  HOH1  0   0.456  -0.5141  -1.8955  -1.8702
 XYZ  H51  H  HCH2  0   0.202   2.0370   0.3274  -1.0996
 XYZ  H52  H  HCH2  0   0.198   2.5563  -1.1470  -0.2760
 XYZ  H5   H  HOH1  0   0.455   3.8636   0.7172   0.2538
 XYZ  HO1  H  HOH1  0   0.457  -1.0002   2.3947  -1.1946

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
 XYZ  C4  O    single  1.427  0.020  1.427
 XYZ  C4  C3   single  1.534  0.020  1.534
 XYZ  C4  C5   single  1.513  0.020  1.513
 XYZ  C4  H4   single  0.970  0.020  1.090
 XYZ  O   C1   single  1.403  0.020  1.403
 XYZ  C1  C2   single  1.530  0.020  1.530
 XYZ  C1  O1   single  1.391  0.020  1.391
 XYZ  C1  H1   single  0.970  0.020  1.090
 XYZ  C2  O2   single  1.407  0.020  1.407
 XYZ  C2  C3   single  1.530  0.020  1.530
 XYZ  C2  H2   single  0.970  0.020  1.090
 XYZ  O2  HO2  single  0.850  0.020  0.980
 XYZ  C3  O3   single  1.403  0.020  1.403
 XYZ  C3  H3   single  0.970  0.020  1.090
 XYZ  O3  HO3  single  0.850  0.020  0.980
 XYZ  C5  O5   single  1.411  0.020  1.411
 XYZ  C5  H51  single  0.970  0.020  1.090
 XYZ  C5  H52  single  0.970  0.020  1.090
 XYZ  O5  H5   single  0.850  0.020  0.980
 XYZ  O1  HO1  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
 XYZ  H4   C4  C5   108.05  3.000
 XYZ  H4   C4  C3   108.34  3.000
 XYZ  C5   C4  C3   114.60  3.000
 XYZ  H4   C4  O    107.78  3.000
 XYZ  C5   C4  O    111.17  3.000
 XYZ  C3   C4  O    106.67  3.000
 XYZ  C1   O   C4   111.05  3.000
 XYZ  H1   C1  O1   110.75  3.000
 XYZ  H1   C1  C2   112.35  3.000
 XYZ  O1   C1  C2   108.98  3.000
 XYZ  H1   C1  O    107.17  3.000
 XYZ  O1   C1  O    112.71  3.000
 XYZ  C2   C1  O    104.78  3.000
 XYZ  H2   C2  C3   112.58  3.000
 XYZ  H2   C2  O2   111.99  3.000
 XYZ  C3   C2  O2   106.84  3.000
 XYZ  H2   C2  C1   112.03  3.000
 XYZ  C3   C2  C1   101.88  3.000
 XYZ  O2   C2  C1   110.99  3.000
 XYZ  HO2  O2  C2   108.92  3.000
 XYZ  H3   C3  O3   111.10  3.000
 XYZ  H3   C3  C2   110.39  3.000
 XYZ  O3   C3  C2   112.56  3.000
 XYZ  H3   C3  C4   110.30  3.000
 XYZ  O3   C3  C4   110.42  3.000
 XYZ  C2   C3  C4   101.73  3.000
 XYZ  HO3  O3  C3   108.27  3.000
 XYZ  H52  C5  H51  107.34  3.000
 XYZ  H52  C5  O5   111.45  3.000
 XYZ  H51  C5  O5   111.61  3.000
 XYZ  H52  C5  C4   108.44  3.000
 XYZ  H51  C5  C4   110.02  3.000
 XYZ  O5   C5  C4   107.95  3.000
 XYZ  H5   O5  C5   107.92  3.000
 XYZ  HO1  O1  C1   108.77  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
 XYZ  chir_01  C4  O   C3  C5  negativ
 XYZ  chir_02  C1  O1  O   C2  positiv
 XYZ  chir_03  C2  O2  C1  C3  negativ
 XYZ  chir_04  C3  O3  C2  C4  positiv

