# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 05:30:09 2022
#   Inital geometry file: a 47 line input string
#   Ligand name: alpha-D-xylopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CO[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
 XYS  XYS  'alpha-D-xylopyranose     '  D-saccharide  20  10  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_XYS
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
 XYS  C1   C  CH1   0   0.271  12.1553  31.2732  46.4392
 XYS  C2   C  CH1   0  -0.044  12.1301  32.7683  46.0718
 XYS  C3   C  CH1   0   0.013  13.1352  33.0326  44.9552
 XYS  C4   C  CH1   0   0.006  14.5446  32.7717  45.4917
 XYS  C5   C  CH2   0  -0.235  14.4926  31.7044  46.5886
 XYS  O1   O  OH1   0  -0.654  11.3712  30.5735  45.5426
 XYS  O2   O  OH1   0  -0.662  10.8210  33.1175  45.7253
 XYS  O3   O  OH1   0  -0.672  12.9562  34.3608  44.5188
 XYS  O4   O  OH1   0  -0.671  15.3530  32.4125  44.3928
 XYS  O5   O  O2    0  -0.497  13.4684  30.7605  46.3638
 XYS  H1   H  HCH1  0   0.205  11.7816  31.1456  47.4673
 XYS  H2   H  HCH1  0   0.220  12.4534  33.3336  46.9608
 XYS  H3   H  HCH1  0   0.222  12.9416  32.3278  44.1345
 XYS  H4   H  HCH1  0   0.216  14.9059  33.6989  45.9582
 XYS  H51  H  HCH2  0   0.252  15.4339  31.1518  46.6226
 XYS  H52  H  HCH2  0   0.217  14.3781  32.1868  47.5678
 XYS  HO1  H  HOH1  0   0.461  11.1525  29.7137  45.9162
 XYS  HO2  H  HOH1  0   0.447  10.8363  34.0380  45.4428
 XYS  HO3  H  HOH1  0   0.456  13.3552  34.4578  43.6491
 XYS  HO4  H  HOH1  0   0.450  16.2717  32.4016  44.6796

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
 XYS  C1  C2   single  1.540  0.020  1.540
 XYS  C1  O1   single  1.381  0.020  1.381
 XYS  C1  O5   single  1.412  0.020  1.412
 XYS  C1  H1   single  0.970  0.020  1.090
 XYS  C2  C3   single  1.525  0.020  1.525
 XYS  C2  O2   single  1.398  0.020  1.398
 XYS  C2  H2   single  0.970  0.020  1.090
 XYS  C3  C4   single  1.531  0.020  1.531
 XYS  C3  O3   single  1.409  0.020  1.409
 XYS  C3  H3   single  0.970  0.020  1.090
 XYS  C4  C5   single  1.531  0.020  1.531
 XYS  C4  O4   single  1.411  0.020  1.411
 XYS  C4  H4   single  0.970  0.020  1.090
 XYS  C5  O5   single  1.411  0.020  1.411
 XYS  C5  H51  single  0.970  0.020  1.090
 XYS  C5  H52  single  0.970  0.020  1.090
 XYS  O1  HO1  single  0.850  0.020  0.980
 XYS  O2  HO2  single  0.850  0.020  0.980
 XYS  O3  HO3  single  0.850  0.020  0.980
 XYS  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
 XYS  H1   C1  O5   108.87  3.000
 XYS  H1   C1  O1   110.77  3.000
 XYS  O5   C1  O1   108.02  3.000
 XYS  H1   C1  C2   109.25  3.000
 XYS  O5   C1  C2   110.80  3.000
 XYS  O1   C1  C2   109.13  3.000
 XYS  H2   C2  O2   110.27  3.000
 XYS  H2   C2  C3   107.96  3.000
 XYS  O2   C2  C3   113.09  3.000
 XYS  H2   C2  C1   107.51  3.000
 XYS  O2   C2  C1   108.47  3.000
 XYS  C3   C2  C1   109.40  3.000
 XYS  H3   C3  O3   110.53  3.000
 XYS  H3   C3  C4   108.34  3.000
 XYS  O3   C3  C4   112.72  3.000
 XYS  H3   C3  C2   108.63  3.000
 XYS  O3   C3  C2   107.83  3.000
 XYS  C4   C3  C2   108.70  3.000
 XYS  H4   C4  O4   110.92  3.000
 XYS  H4   C4  C5   107.17  3.000
 XYS  O4   C4  C5   113.58  3.000
 XYS  H4   C4  C3   107.92  3.000
 XYS  O4   C4  C3   107.34  3.000
 XYS  C5   C4  C3   109.80  3.000
 XYS  H52  C5  H51  106.54  3.000
 XYS  H52  C5  O5   111.13  3.000
 XYS  H51  C5  O5   106.99  3.000
 XYS  H52  C5  C4   109.65  3.000
 XYS  H51  C5  C4   110.22  3.000
 XYS  O5   C5  C4   112.13  3.000
 XYS  HO1  O1  C1   109.24  3.000
 XYS  HO2  O2  C2   107.24  3.000
 XYS  HO3  O3  C3   108.81  3.000
 XYS  HO4  O4  C4   108.52  3.000
 XYS  C5   O5  C1   115.07  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 XYS  Var_01  C4  C5  O5  C1  -65.87  30.0  1

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
 XYS  chir_01  C1  C2  O1  O5  negativ
 XYS  chir_02  C2  O2  C1  C3  negativ
 XYS  chir_03  C3  O3  C2  C4  positiv
 XYS  chir_04  C4  O4  C3  C5  negativ

