# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 22:51:40 2022
#   Inital geometry file: a 59 line input string
#   Ligand name: 3-deoxy-3-methyl-beta-D-fructofuranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1[C@H](O)[C@@H](CO)O[C@]1(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
 DFR  DFR  3-deoxy-3-methyl-beta-D-fructofuranose  D-saccharide  26  12  .  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 (reasonable std)
;

data_comp_DFR
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
 DFR  C5   C  CR15  0   0.017  32.1706  32.7484  58.9524
 DFR  C4   C  CR15  0  -0.000  32.1276  31.6359  57.8865
 DFR  C3   C  CR15  0  -0.335  33.6009  31.2300  57.7267
 DFR  C2   C  CR5   0   0.472  34.3491  32.4793  58.2124
 DFR  C1   C  CH2   0  -0.192  34.5076  33.5195  57.1003
 DFR  C6   C  CH2   0  -0.166  31.4069  32.3756  60.2030
 DFR  C7   C  CH3   0  -0.666  33.9167  29.9883  58.5521
 DFR  O5   O  O     0  -0.509  33.5304  32.9795  59.2591
 DFR  O4   O  OH1   0  -0.667  31.5334  32.1644  56.7240
 DFR  O2   O  OH1   0  -0.667  35.5876  32.1664  58.7379
 DFR  O1   O  OH1   0  -0.673  35.1983  34.6244  57.6423
 DFR  O6   O  OH1   0  -0.665  31.4484  33.4494  61.1104
 DFR  H5   H  HCR5  0   0.225  31.7185  33.6549  58.5252
 DFR  H4   H  HCR5  0   0.232  31.5442  30.7762  58.2447
 DFR  H3   H  HCR5  0   0.257  33.8253  31.0227  56.6761
 DFR  H11  H  HCH2  0   0.216  35.0672  33.0560  56.2788
 DFR  H12  H  HCH2  0   0.212  33.5302  33.8080  56.6991
 DFR  H61  H  HCH2  0   0.200  30.3786  32.1358  59.9005
 DFR  H62  H  HCH2  0   0.197  31.8345  31.4591  60.6338
 DFR  H71  H  HCH3  0   0.238  34.9546  29.6787  58.4437
 DFR  H72  H  HCH3  0   0.227  33.7218  30.1416  59.6147
 DFR  H73  H  HCH3  0   0.233  33.2900  29.1593  58.2214
 DFR  HO4  H  HOH1  0   0.449  31.4743  31.4608  56.0698
 DFR  HO2  H  HOH1  0   0.448  36.1180  32.9741  58.7587
 DFR  HO1  H  HOH1  0   0.461  35.5968  35.1205  56.9221
 DFR  HO6  H  HOH1  0   0.453  30.9467  33.2017  61.8921

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
 DFR  C5  C4   single  1.541  0.020  1.541
 DFR  C5  C6   single  1.512  0.020  1.512
 DFR  C5  O5   single  1.413  0.020  1.413
 DFR  C5  H5   single  0.970  0.020  1.090
 DFR  C4  C3   single  1.537  0.020  1.537
 DFR  C4  O4   single  1.409  0.020  1.409
 DFR  C4  H4   single  0.970  0.020  1.090
 DFR  C3  C2   single  1.535  0.020  1.535
 DFR  C3  C7   single  1.524  0.020  1.524
 DFR  C3  H3   single  0.970  0.020  1.090
 DFR  C2  C1   single  1.531  0.020  1.531
 DFR  C2  O5   single  1.420  0.020  1.420
 DFR  C2  O2   single  1.381  0.020  1.381
 DFR  C1  O1   single  1.411  0.020  1.411
 DFR  C1  H11  single  0.970  0.020  1.090
 DFR  C1  H12  single  0.970  0.020  1.090
 DFR  C6  O6   single  1.406  0.020  1.406
 DFR  C6  H61  single  0.970  0.020  1.090
 DFR  C6  H62  single  0.970  0.020  1.090
 DFR  C7  H71  single  0.970  0.020  1.090
 DFR  C7  H72  single  0.970  0.020  1.090
 DFR  C7  H73  single  0.970  0.020  1.090
 DFR  O4  HO4  single  0.850  0.020  0.980
 DFR  O2  HO2  single  0.850  0.020  0.980
 DFR  O1  HO1  single  0.850  0.020  0.980
 DFR  O6  HO6  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
 DFR  H5   C5  O5   110.19  3.000
 DFR  H5   C5  C6   108.48  3.000
 DFR  O5   C5  C6   110.30  3.000
 DFR  H5   C5  C4   108.36  3.000
 DFR  O5   C5  C4   107.16  3.000
 DFR  C6   C5  C4   112.33  3.000
 DFR  H4   C4  O4   109.79  3.000
 DFR  H4   C4  C3   109.65  3.000
 DFR  O4   C4  C3   114.70  3.000
 DFR  H4   C4  C5   110.73  3.000
 DFR  O4   C4  C5   108.16  3.000
 DFR  C3   C4  C5   103.64  3.000
 DFR  H3   C3  C7   108.85  3.000
 DFR  H3   C3  C2   110.98  3.000
 DFR  C7   C3  C2   113.00  3.000
 DFR  H3   C3  C4   110.28  3.000
 DFR  C7   C3  C4   110.95  3.000
 DFR  C2   C3  C4   102.68  3.000
 DFR  O2   C2  O5   108.44  3.000
 DFR  O2   C2  C1   109.72  3.000
 DFR  O5   C2  C1   110.84  3.000
 DFR  O2   C2  C3   111.91  3.000
 DFR  O5   C2  C3   103.82  3.000
 DFR  C1   C2  C3   111.94  3.000
 DFR  H12  C1  H11  106.99  3.000
 DFR  H12  C1  O1   111.79  3.000
 DFR  H11  C1  O1   111.64  3.000
 DFR  H12  C1  C2   110.65  3.000
 DFR  H11  C1  C2   108.05  3.000
 DFR  O1   C1  C2   107.68  3.000
 DFR  H62  C6  H61  106.86  3.000
 DFR  H62  C6  O6   111.86  3.000
 DFR  H61  C6  O6   111.84  3.000
 DFR  H62  C6  C5   109.46  3.000
 DFR  H61  C6  C5   107.39  3.000
 DFR  O6   C6  C5   109.30  3.000
 DFR  H73  C7  H72  107.42  3.000
 DFR  H73  C7  H71  107.55  3.000
 DFR  H72  C7  H71  107.89  3.000
 DFR  H73  C7  C3   109.63  3.000
 DFR  H72  C7  C3   112.08  3.000
 DFR  H71  C7  C3   112.05  3.000
 DFR  C2   O5  C5   109.71  3.000
 DFR  HO4  O4  C4   108.22  3.000
 DFR  HO2  O2  C2   108.12  3.000
 DFR  HO1  O1  C1   108.62  3.000
 DFR  HO6  O6  C6   108.20  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
 DFR  chir_01  C5  C4  C6  O5  negativ
 DFR  chir_02  C4  O4  C3  C5  negativ
 DFR  chir_03  C3  C7  C2  C4  positiv
 DFR  chir_04  C2  O5  C3  C1  negativ

