# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 04:22:51 2022
#   Inital geometry file: a 47 line input string
#   Ligand name: beta-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
 XYP  XYP  'beta-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 PERFECT
;

data_comp_XYP
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
 XYP  O1   O  OH1   0  -0.653  25.4903  67.6939  19.6263
 XYP  C1   C  CH1   0   0.282  26.1932  67.9909  20.7726
 XYP  C2   C  CH1   0   0.002  27.6852  67.9962  20.4533
 XYP  C3   C  CH1   0  -0.017  28.4644  68.4230  21.6942
 XYP  C4   C  CH1   0   0.004  27.9485  69.7602  22.2019
 XYP  C5   C  CH2   0  -0.226  26.4397  69.6514  22.4126
 XYP  O2   O  OH1   0  -0.666  28.0486  66.7076  20.0333
 XYP  O3   O  OH1   0  -0.669  29.8254  68.4601  21.3374
 XYP  O4   O  OH1   0  -0.665  28.6190  70.0548  23.4044
 XYP  O5   O  O2    0  -0.488  25.7974  69.2672  21.2185
 XYP  HO1  H  HOH1  0   0.461  24.5949  67.4277  19.8611
 XYP  H1   H  HCH1  0   0.185  26.0006  67.2524  21.5721
 XYP  H2   H  HCH1  0   0.210  27.8594  68.7418  19.6596
 XYP  H3   H  HCH1  0   0.212  28.2873  67.6711  22.4815
 XYP  H4   H  HCH1  0   0.214  28.1459  70.5256  21.4374
 XYP  H51  H  HCH2  0   0.210  26.2373  68.9346  23.2221
 XYP  H52  H  HCH2  0   0.247  26.0201  70.6144  22.7095
 XYP  HO2  H  HOH1  0   0.449  29.0089  66.6799  19.9639
 XYP  HO3  H  HOH1  0   0.454  30.3514  68.5356  22.1396
 XYP  HO4  H  HOH1  0   0.456  28.4619  70.9775  23.6276

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
 XYP  O1  C1   single  1.377  0.020  1.377
 XYP  O1  HO1  single  0.850  0.020  0.980
 XYP  C1  C2   single  1.526  0.020  1.526
 XYP  C1  O5   single  1.409  0.020  1.409
 XYP  C1  H1   single  0.970  0.020  1.090
 XYP  C2  C3   single  1.526  0.020  1.526
 XYP  C2  O2   single  1.403  0.020  1.403
 XYP  C2  H2   single  0.970  0.020  1.090
 XYP  C3  C4   single  1.521  0.020  1.521
 XYP  C3  O3   single  1.408  0.020  1.408
 XYP  C3  H3   single  0.970  0.020  1.090
 XYP  C4  C5   single  1.527  0.020  1.527
 XYP  C4  O4   single  1.408  0.020  1.408
 XYP  C4  H4   single  0.970  0.020  1.090
 XYP  C5  O5   single  1.409  0.020  1.409
 XYP  C5  H51  single  0.970  0.020  1.090
 XYP  C5  H52  single  0.970  0.020  1.090
 XYP  O2  HO2  single  0.850  0.020  0.980
 XYP  O3  HO3  single  0.850  0.020  0.980
 XYP  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
 XYP  HO1  O1  C1   109.34  3.000
 XYP  H1   C1  O5   109.11  3.000
 XYP  H1   C1  C2   108.91  3.000
 XYP  O5   C1  C2   109.74  3.000
 XYP  H1   C1  O1   111.66  3.000
 XYP  O5   C1  O1   108.39  3.000
 XYP  C2   C1  O1   109.01  3.000
 XYP  H2   C2  O2   111.38  3.000
 XYP  H2   C2  C3   108.39  3.000
 XYP  O2   C2  C3   111.58  3.000
 XYP  H2   C2  C1   107.91  3.000
 XYP  O2   C2  C1   108.22  3.000
 XYP  C3   C2  C1   109.27  3.000
 XYP  H3   C3  O3   110.74  3.000
 XYP  H3   C3  C4   107.86  3.000
 XYP  O3   C3  C4   112.92  3.000
 XYP  H3   C3  C2   107.93  3.000
 XYP  O3   C3  C2   107.15  3.000
 XYP  C4   C3  C2   110.13  3.000
 XYP  H4   C4  O4   111.26  3.000
 XYP  H4   C4  C5   108.83  3.000
 XYP  O4   C4  C5   111.56  3.000
 XYP  H4   C4  C3   108.61  3.000
 XYP  O4   C4  C3   107.92  3.000
 XYP  C5   C4  C3   108.57  3.000
 XYP  H52  C5  H51  107.70  3.000
 XYP  H52  C5  O5   107.20  3.000
 XYP  H51  C5  O5   111.23  3.000
 XYP  H52  C5  C4   110.76  3.000
 XYP  H51  C5  C4   109.25  3.000
 XYP  O5   C5  C4   110.66  3.000
 XYP  HO2  O2  C2   107.84  3.000
 XYP  HO3  O3  C3   108.63  3.000
 XYP  HO4  O4  C4   108.73  3.000
 XYP  C5   O5  C1   112.78  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
 XYP  Var_01  C4  C5  O5  C1  62.88  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
 XYP  chir_01  C1  O1  C2  O5  negativ
 XYP  chir_02  C2  O2  C1  C3  negativ
 XYP  chir_03  C3  O3  C2  C4  positiv
 XYP  chir_04  C4  O4  C3  C5  negativ

