# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 00:34:16 2022
#   Inital geometry file: a 50 line input string
#   Ligand name: D-xylose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@H](O)[C@@H](O)C=O
#
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
 XLS  XLS  'D-xylose                 '  D-saccharide  20  10  .  2012-04-11  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XLS
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
 XLS  C1   C  C1    0   0.161  10.2695  34.0664  47.0756
 XLS  C2   C  CH1   0  -0.059  11.6459  34.2534  46.4925
 XLS  C3   C  CH1   0  -0.024  12.2540  32.8648  46.2622
 XLS  C4   C  CH1   0   0.009  13.7316  32.9462  45.8717
 XLS  C5   C  CH2   0  -0.193  14.3591  31.5797  45.6246
 XLS  O1   O  O     0  -0.363   9.2655  34.5622  46.6395
 XLS  O2   O  OH1   0  -0.673  11.5617  35.0559  45.3576
 XLS  O3   O  OH1   0  -0.667  11.4572  32.2093  45.3038
 XLS  O4   O  OH1   0  -0.680  13.8547  33.7370  44.7013
 XLS  O5   O  OH1   0  -0.667  14.2034  30.8002  46.7865
 XLS  H1   H  H     0   0.190  10.2570  33.4331  47.9820
 XLS  H2   H  HCH1  0   0.239  12.2424  34.7181  47.3001
 XLS  H3   H  HCH1  0   0.242  12.2221  32.3474  47.2302
 XLS  H4   H  HCH1  0   0.228  14.2513  33.4213  46.7152
 XLS  H51  H  HCH2  0   0.203  13.8882  31.1169  44.7477
 XLS  H52  H  HCH2  0   0.216  15.4186  31.7261  45.3733
 XLS  HO2  H  HOH1  0   0.454  12.3953  34.9458  44.8771
 XLS  HO3  H  HOH1  0   0.459  11.5926  31.2603  45.3831
 XLS  HO4  H  HOH1  0   0.467  14.7672  34.0320  44.6167
 XLS  HO5  H  HOH1  0   0.459  14.5348  29.9162  46.6060

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
 XLS  C1  C2   single  1.506  0.020  1.506
 XLS  C1  O1   double  1.202  0.020  1.202
 XLS  C1  H1   single  0.930  0.020  1.080
 XLS  C2  C3   single  1.533  0.020  1.533
 XLS  C2  O2   single  1.393  0.020  1.393
 XLS  C2  H2   single  0.970  0.020  1.090
 XLS  C3  C4   single  1.530  0.020  1.530
 XLS  C3  O3   single  1.408  0.020  1.408
 XLS  C3  H3   single  0.970  0.020  1.090
 XLS  C4  C5   single  1.524  0.020  1.524
 XLS  C4  O4   single  1.418  0.020  1.418
 XLS  C4  H4   single  0.970  0.020  1.090
 XLS  C5  O5   single  1.408  0.020  1.408
 XLS  C5  H51  single  0.970  0.020  1.090
 XLS  C5  H52  single  0.970  0.020  1.090
 XLS  O2  HO2  single  0.850  0.020  0.980
 XLS  O3  HO3  single  0.850  0.020  0.980
 XLS  O4  HO4  single  0.850  0.020  0.980
 XLS  O5  HO5  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
 XLS  H1   C1  O1   121.63  3.000
 XLS  H1   C1  C2   113.49  3.000
 XLS  O1   C1  C2   124.87  3.000
 XLS  H2   C2  O2   112.67  3.000
 XLS  H2   C2  C3   106.03  3.000
 XLS  O2   C2  C3   115.05  3.000
 XLS  H2   C2  C1   105.21  3.000
 XLS  O2   C2  C1   109.37  3.000
 XLS  C3   C2  C1   107.94  3.000
 XLS  H3   C3  O3   111.36  3.000
 XLS  H3   C3  C4   106.14  3.000
 XLS  O3   C3  C4   113.42  3.000
 XLS  H3   C3  C2   106.42  3.000
 XLS  O3   C3  C2   107.42  3.000
 XLS  C4   C3  C2   111.90  3.000
 XLS  H4   C4  O4   110.58  3.000
 XLS  H4   C4  C5   108.51  3.000
 XLS  O4   C4  C5   109.30  3.000
 XLS  H4   C4  C3   106.49  3.000
 XLS  O4   C4  C3   108.91  3.000
 XLS  C5   C4  C3   113.03  3.000
 XLS  H52  C5  H51  106.69  3.000
 XLS  H52  C5  O5   111.67  3.000
 XLS  H51  C5  O5   112.24  3.000
 XLS  H52  C5  C4   108.35  3.000
 XLS  H51  C5  C4   109.33  3.000
 XLS  O5   C5  C4   108.49  3.000
 XLS  HO2  O2  C2   106.67  3.000
 XLS  HO3  O3  C3   108.87  3.000
 XLS  HO4  O4  C4   109.01  3.000
 XLS  HO5  O5  C5   108.43  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
 XLS  chir_01  C2  C1  C3  O2  negativ
 XLS  chir_02  C3  O3  C2  C4  positiv
 XLS  chir_03  C4  O4  C3  C5  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 XLS  plan-1  C1  0.020
 XLS  plan-1  C2  0.020
 XLS  plan-1  O1  0.020
 XLS  plan-1  H1  0.020

