# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 00:29:31 2022
#   Inital geometry file: a 47 line input string
#   Ligand name: beta-D-xylulofuranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@]1(O)OC[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
 XLF  XLF  'beta-D-xylulofuranose    '  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_XLF
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
 XLF  O4   O  OH1   0  -0.659  28.5176  30.5553  2.9226
 XLF  C4   C  CR15  0  -0.034  27.2015  30.3899  3.3755
 XLF  C5   C  CH2   0  -0.179  26.3958  31.6859  3.4733
 XLF  O5   O  O     0  -0.505  25.5090  31.5296  4.5757
 XLF  C3   C  CR15  0  -0.035  27.1825  29.9285  4.8267
 XLF  O3   O  OH1   0  -0.652  27.5153  28.5959  5.0628
 XLF  C2   C  CR5   0   0.430  25.7654  30.3265  5.2604
 XLF  O2   O  OH1   0  -0.675  24.8983  29.3188  4.8421
 XLF  C1   C  CH2   0  -0.179  25.6412  30.5568  6.7581
 XLF  O1   O  OH1   0  -0.671  24.2804  30.7633  7.0619
 XLF  HO4  H  HOH1  0   0.455  28.4974  30.7180  1.9745
 XLF  H4   H  HCR5  0   0.223  26.6623  29.6582  2.7572
 XLF  H51  H  HCH2  0   0.213  27.0742  32.5257  3.6587
 XLF  H52  H  HCH2  0   0.227  25.8247  31.9038  2.5677
 XLF  H3   H  HCR5  0   0.251  27.9030  30.5379  5.3872
 XLF  HO3  H  HOH1  0   0.443  26.8066  28.0435  4.7124
 XLF  HO2  H  HOH1  0   0.452  24.0888  29.3720  5.3677
 XLF  H11  H  HCH2  0   0.220  26.0408  29.6767  7.2744
 XLF  H12  H  HCH2  0   0.210  26.2608  31.4149  7.0438
 XLF  HO1  H  HOH1  0   0.464  24.1177  30.4915  7.9690

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
 XLF  O4  C4   single  1.402  0.020  1.402
 XLF  O4  HO4  single  0.850  0.020  0.980
 XLF  C5  C4   single  1.529  0.020  1.529
 XLF  C4  C3   single  1.523  0.020  1.523
 XLF  C4  H4   single  0.970  0.020  1.090
 XLF  C5  O5   single  1.423  0.020  1.423
 XLF  C5  H51  single  0.970  0.020  1.090
 XLF  C5  H52  single  0.970  0.020  1.090
 XLF  O5  C2   single  1.408  0.020  1.408
 XLF  C3  O3   single  1.394  0.020  1.394
 XLF  C3  C2   single  1.534  0.020  1.534
 XLF  C3  H3   single  0.970  0.020  1.090
 XLF  O3  HO3  single  0.850  0.020  0.980
 XLF  O2  C2   single  1.394  0.020  1.394
 XLF  C2  C1   single  1.520  0.020  1.520
 XLF  O2  HO2  single  0.850  0.020  0.980
 XLF  C1  O1   single  1.409  0.020  1.409
 XLF  C1  H11  single  0.970  0.020  1.090
 XLF  C1  H12  single  0.970  0.020  1.090
 XLF  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
 XLF  HO4  O4  C4   108.58  3.000
 XLF  H4   C4  C3   109.15  3.000
 XLF  H4   C4  C5   109.98  3.000
 XLF  C3   C4  C5   100.91  3.000
 XLF  H4   C4  O4   110.94  3.000
 XLF  C3   C4  O4   110.82  3.000
 XLF  C5   C4  O4   114.55  3.000
 XLF  H52  C5  H51  108.13  3.000
 XLF  H52  C5  O5   109.77  3.000
 XLF  H51  C5  O5   109.81  3.000
 XLF  H52  C5  C4   113.04  3.000
 XLF  H51  C5  C4   109.53  3.000
 XLF  O5   C5  C4   106.55  3.000
 XLF  C2   O5  C5   110.92  3.000
 XLF  H3   C3  C2   108.53  3.000
 XLF  H3   C3  O3   106.72  3.000
 XLF  C2   C3  O3   114.88  3.000
 XLF  H3   C3  C4   108.07  3.000
 XLF  C2   C3  C4   101.67  3.000
 XLF  O3   C3  C4   116.62  3.000
 XLF  HO3  O3  C3   108.10  3.000
 XLF  C1   C2  O2   110.75  3.000
 XLF  C1   C2  C3   113.15  3.000
 XLF  O2   C2  C3   107.59  3.000
 XLF  C1   C2  O5   109.56  3.000
 XLF  O2   C2  O5   111.01  3.000
 XLF  C3   C2  O5   104.62  3.000
 XLF  HO2  O2  C2   108.55  3.000
 XLF  H12  C1  H11  107.44  3.000
 XLF  H12  C1  O1   112.01  3.000
 XLF  H11  C1  O1   111.60  3.000
 XLF  H12  C1  C2   109.21  3.000
 XLF  H11  C1  C2   108.22  3.000
 XLF  O1   C1  C2   108.27  3.000
 XLF  HO1  O1  C1   109.00  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
 XLF  Var_01  H51  C5  O5  C2  -112.69  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
 XLF  chir_01  C4  O4  C5  C3  positiv
 XLF  chir_02  C3  O3  C4  C2  negativ
 XLF  chir_03  C2  O5  C1  C3  positiv

