# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 04:33:25 2022
#   Inital geometry file: a 51 line input string
#   Ligand name: D-xylitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H](O)[C@@H](O)[C@H](O)CO
#
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
 XYL  XYL  'D-xylitol                '  D-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_XYL
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
 XYL  C1   C  CH2   0  -0.151  37.0778  33.6235  56.2470
 XYL  C2   C  CH1   0   0.016  35.7213  33.9505  56.8446
 XYL  C3   C  CH1   0  -0.015  34.9227  32.6691  57.1146
 XYL  C4   C  CH1   0   0.008  33.4539  32.9696  57.4264
 XYL  C5   C  CH2   0  -0.194  32.6380  31.7220  57.7431
 XYL  O1   O  OH1   0  -0.669  37.6949  34.8227  55.8382
 XYL  O2   O  OH1   0  -0.685  35.9219  34.7323  57.9967
 XYL  O3   O  OH1   0  -0.672  35.5599  31.9450  58.1438
 XYL  O4   O  OH1   0  -0.682  33.3833  33.8575  58.5315
 XYL  O5   O  OH1   0  -0.668  32.7365  30.8277  56.6594
 XYL  H11  H  HCH2  0   0.195  37.6842  33.0866  56.9870
 XYL  H12  H  HCH2  0   0.190  36.9235  32.9421  55.3999
 XYL  H2   H  HCH1  0   0.194  35.1553  34.5078  56.0784
 XYL  H3   H  HCH1  0   0.226  34.9225  32.1010  56.1754
 XYL  H4   H  HCH1  0   0.222  33.0364  33.4444  56.5278
 XYL  H51  H  HCH2  0   0.200  33.0037  31.2794  58.6787
 XYL  H52  H  HCH2  0   0.212  31.5974  32.0251  57.9240
 XYL  HO1  H  HOH1  0   0.450  38.5581  34.6033  55.4767
 XYL  HO2  H  HOH1  0   0.446  35.0653  34.7895  58.4418
 XYL  HO3  H  HOH1  0   0.454  35.3076  31.0206  58.0678
 XYL  HO4  H  HOH1  0   0.464  32.5214  34.2857  58.5371
 XYL  HO5  H  HOH1  0   0.458  32.2689  30.0201  56.8893

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
 XYL  C1  C2   single  1.518  0.020  1.518
 XYL  C1  O1   single  1.409  0.020  1.409
 XYL  C1  H11  single  0.970  0.020  1.090
 XYL  C1  H12  single  0.970  0.020  1.090
 XYL  C2  C3   single  1.534  0.020  1.534
 XYL  C2  O2   single  1.407  0.020  1.407
 XYL  C2  H2   single  0.970  0.020  1.090
 XYL  C3  C4   single  1.531  0.020  1.531
 XYL  C3  O3   single  1.411  0.020  1.411
 XYL  C3  H3   single  0.970  0.020  1.090
 XYL  C4  C5   single  1.524  0.020  1.524
 XYL  C4  O4   single  1.419  0.020  1.419
 XYL  C4  H4   single  0.970  0.020  1.090
 XYL  C5  O5   single  1.409  0.020  1.409
 XYL  C5  H51  single  0.970  0.020  1.090
 XYL  C5  H52  single  0.970  0.020  1.090
 XYL  O1  HO1  single  0.850  0.020  0.980
 XYL  O2  HO2  single  0.850  0.020  0.980
 XYL  O3  HO3  single  0.850  0.020  0.980
 XYL  O4  HO4  single  0.850  0.020  0.980
 XYL  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
 XYL  H12  C1  H11  107.12  3.000
 XYL  H12  C1  O1   111.46  3.000
 XYL  H11  C1  O1   111.72  3.000
 XYL  H12  C1  C2   108.17  3.000
 XYL  H11  C1  C2   109.50  3.000
 XYL  O1   C1  C2   108.80  3.000
 XYL  H2   C2  O2   111.16  3.000
 XYL  H2   C2  C3   106.08  3.000
 XYL  O2   C2  C3   113.23  3.000
 XYL  H2   C2  C1   107.09  3.000
 XYL  O2   C2  C1   108.34  3.000
 XYL  C3   C2  C1   110.77  3.000
 XYL  H3   C3  O3   111.03  3.000
 XYL  H3   C3  C4   106.00  3.000
 XYL  O3   C3  C4   112.67  3.000
 XYL  H3   C3  C2   106.37  3.000
 XYL  O3   C3  C2   108.79  3.000
 XYL  C4   C3  C2   111.80  3.000
 XYL  H4   C4  O4   110.34  3.000
 XYL  H4   C4  C5   108.68  3.000
 XYL  O4   C4  C5   108.89  3.000
 XYL  H4   C4  C3   106.42  3.000
 XYL  O4   C4  C3   109.21  3.000
 XYL  C5   C4  C3   113.28  3.000
 XYL  H52  C5  H51  106.65  3.000
 XYL  H52  C5  O5   111.60  3.000
 XYL  H51  C5  O5   112.12  3.000
 XYL  H52  C5  C4   108.38  3.000
 XYL  H51  C5  C4   109.19  3.000
 XYL  O5   C5  C4   108.81  3.000
 XYL  HO1  O1  C1   107.94  3.000
 XYL  HO2  O2  C2   106.47  3.000
 XYL  HO3  O3  C3   108.50  3.000
 XYL  HO4  O4  C4   109.11  3.000
 XYL  HO5  O5  C5   108.38  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
 XYL  chir_01  C2  C1  C3  O2  negativ
 XYL  chir_02  C3  O3  C2  C4  positiv
 XYL  chir_03  C4  O4  C3  C5  negativ

