# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 10:23:33 2022
#   Inital geometry file: a 47 line input string
#   Ligand name: alpha-L-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
 HSY  HSY  'alpha-L-xylopyranose     '  L-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_HSY
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
 HSY  C1   C  CH1   0   0.234  25.3318  15.1900  -2.1829
 HSY  C2   C  CH1   0   0.009  24.1261  15.4899  -3.0727
 HSY  C3   C  CH1   0  -0.007  23.7491  16.9658  -2.9938
 HSY  C4   C  CH1   0  -0.003  24.9697  17.8100  -3.3301
 HSY  C5   C  CH2   0  -0.221  26.1357  17.4057  -2.4321
 HSY  O2   O  OH1   0  -0.666  23.0762  14.6389  -2.6949
 HSY  O3   O  OH1   0  -0.671  22.6881  17.1716  -3.8981
 HSY  O4   O  OH1   0  -0.666  24.6288  19.1642  -3.1431
 HSY  O5   O  O2    0  -0.492  26.4073  16.0206  -2.5341
 HSY  O1   O  OH1   0  -0.659  24.9513  15.3372  -0.8545
 HSY  H1   H  HCH1  0   0.235  25.6892  14.1727  -2.3826
 HSY  H2   H  HCH1  0   0.216  24.4459  15.2826  -4.1058
 HSY  H3   H  HCH1  0   0.213  23.4340  17.2024  -1.9661
 HSY  H4   H  HCH1  0   0.212  25.2457  17.6130  -4.3765
 HSY  H51  H  HCH2  0   0.240  27.0470  17.9221  -2.7405
 HSY  H52  H  HCH2  0   0.212  25.9237  17.7031  -1.3981
 HSY  HO2  H  HOH1  0   0.449  22.3322  14.8091  -3.2814
 HSY  HO3  H  HOH1  0   0.452  22.3709  18.0742  -3.7941
 HSY  HO4  H  HOH1  0   0.456  25.2914  19.7116  -3.5756
 HSY  HO1  H  HOH1  0   0.460  25.6315  14.9558  -0.2888

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
 HSY  C1  C2   single  1.528  0.020  1.528
 HSY  C1  O5   single  1.404  0.020  1.404
 HSY  C1  O1   single  1.390  0.020  1.390
 HSY  C1  H1   single  0.970  0.020  1.090
 HSY  C2  C3   single  1.525  0.020  1.525
 HSY  C2  O2   single  1.403  0.020  1.403
 HSY  C2  H2   single  0.970  0.020  1.090
 HSY  C3  C4   single  1.522  0.020  1.522
 HSY  C3  O3   single  1.409  0.020  1.409
 HSY  C3  H3   single  0.970  0.020  1.090
 HSY  C4  C5   single  1.526  0.020  1.526
 HSY  C4  O4   single  1.409  0.020  1.409
 HSY  C4  H4   single  0.970  0.020  1.090
 HSY  C5  O5   single  1.415  0.020  1.415
 HSY  C5  H51  single  0.970  0.020  1.090
 HSY  C5  H52  single  0.970  0.020  1.090
 HSY  O2  HO2  single  0.850  0.020  0.980
 HSY  O3  HO3  single  0.850  0.020  0.980
 HSY  O4  HO4  single  0.850  0.020  0.980
 HSY  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
 HSY  H1   C1  O1   111.20  3.000
 HSY  H1   C1  O5   104.70  3.000
 HSY  O1   C1  O5   112.73  3.000
 HSY  H1   C1  C2   109.46  3.000
 HSY  O1   C1  C2   108.65  3.000
 HSY  O5   C1  C2   110.04  3.000
 HSY  H2   C2  O2   110.84  3.000
 HSY  H2   C2  C3   107.61  3.000
 HSY  O2   C2  C3   112.82  3.000
 HSY  H2   C2  C1   106.27  3.000
 HSY  O2   C2  C1   108.33  3.000
 HSY  C3   C2  C1   110.77  3.000
 HSY  H3   C3  O3   110.62  3.000
 HSY  H3   C3  C4   108.47  3.000
 HSY  O3   C3  C4   112.40  3.000
 HSY  H3   C3  C2   109.09  3.000
 HSY  O3   C3  C2   107.11  3.000
 HSY  C4   C3  C2   109.09  3.000
 HSY  H4   C4  O4   111.05  3.000
 HSY  H4   C4  C5   108.71  3.000
 HSY  O4   C4  C5   111.18  3.000
 HSY  H4   C4  C3   108.19  3.000
 HSY  O4   C4  C3   108.04  3.000
 HSY  C5   C4  C3   109.62  3.000
 HSY  H52  C5  H51  107.42  3.000
 HSY  H52  C5  O5   111.75  3.000
 HSY  H51  C5  O5   106.40  3.000
 HSY  H52  C5  C4   109.59  3.000
 HSY  H51  C5  C4   110.25  3.000
 HSY  O5   C5  C4   111.31  3.000
 HSY  HO2  O2  C2   107.87  3.000
 HSY  HO3  O3  C3   108.41  3.000
 HSY  HO4  O4  C4   108.69  3.000
 HSY  C5   O5  C1   114.47  3.000
 HSY  HO1  O1  C1   109.03  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
 HSY  Var_01  C4  C5  O5  C1  -59.38  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
 HSY  chir_01  C1  C2  O5  O1  negativ
 HSY  chir_02  C2  O2  C1  C3  positiv
 HSY  chir_03  C3  O3  C2  C4  negativ
 HSY  chir_04  C4  O4  C3  C5  positiv

