# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 10:34:24 2022
#   Inital geometry file: a 55 line input string
#   Ligand name: alpha-D-allopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](O)[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
 AFD  AFD  'alpha-D-allopyranose     '  D-saccharide  24  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 PERFECT
;

data_comp_AFD
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
 AFD  C1   C  CH1   0   0.291  -28.4529  19.2616  21.0664
 AFD  C2   C  CH1   0  -0.068  -27.4909  19.7580  22.1371
 AFD  C3   C  CH1   0  -0.045  -27.0773  21.2165  21.8215
 AFD  C4   C  CH1   0   0.016  -28.2041  21.9558  21.0643
 AFD  C5   C  CH1   0   0.018  -29.5755  21.3756  21.4166
 AFD  C6   C  CH2   0  -0.176  -30.7281  22.0840  20.7333
 AFD  O2   O  OH1   0  -0.670  -28.1128  19.6673  23.3905
 AFD  O3   O  OH1   0  -0.658  -26.7786  21.9002  23.0185
 AFD  O4   O  OH1   0  -0.662  -28.2380  23.3294  21.3295
 AFD  O5   O  O2    0  -0.504  -29.6365  20.0064  21.0465
 AFD  O6   O  OH1   0  -0.669  -30.5233  22.1147  19.3411
 AFD  O1   O  OH1   0  -0.659  -28.8661  17.9499  21.2901
 AFD  H1   H  HCH1  0   0.190  -27.9366  19.3329  20.0929
 AFD  H2   H  HCH1  0   0.224  -26.5909  19.1246  22.1028
 AFD  H3   H  HCH1  0   0.244  -26.1966  21.1913  21.1700
 AFD  H4   H  HCH1  0   0.223  -28.0339  21.7694  19.9949
 AFD  H5   H  HCH1  0   0.221  -29.7421  21.4823  22.4973
 AFD  H61  H  HCH2  0   0.204  -30.8129  23.0891  21.1609
 AFD  H62  H  HCH2  0   0.210  -31.6546  21.5547  20.9953
 AFD  HO2  H  HOH1  0   0.443  -27.7835  20.4133  23.9102
 AFD  HO3  H  HOH1  0   0.465  -25.8710  21.6959  23.2687
 AFD  HO4  H  HOH1  0   0.452  -27.3776  23.7080  21.1234
 AFD  HO6  H  HOH1  0   0.455  -31.2454  22.6081  18.9428
 AFD  HO1  H  HOH1  0   0.457  -28.2531  17.3539  20.8491

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
 AFD  O6  C6   single  1.407  0.020  1.407
 AFD  C6  C5   single  1.516  0.020  1.516
 AFD  C4  O4   single  1.399  0.020  1.399
 AFD  C4  C5   single  1.530  0.020  1.530
 AFD  C4  C3   single  1.546  0.020  1.546
 AFD  C1  O1   single  1.393  0.020  1.393
 AFD  C1  O5   single  1.399  0.020  1.399
 AFD  C1  C2   single  1.523  0.020  1.523
 AFD  O5  C5   single  1.420  0.020  1.420
 AFD  C3  C2   single  1.548  0.020  1.548
 AFD  C3  O3   single  1.411  0.020  1.411
 AFD  C2  O2   single  1.402  0.020  1.402
 AFD  C1  H1   single  0.970  0.020  1.090
 AFD  C2  H2   single  0.970  0.020  1.090
 AFD  C3  H3   single  0.970  0.020  1.090
 AFD  C4  H4   single  0.970  0.020  1.090
 AFD  C5  H5   single  0.970  0.020  1.090
 AFD  C6  H61  single  0.970  0.020  1.090
 AFD  C6  H62  single  0.970  0.020  1.090
 AFD  O2  HO2  single  0.850  0.020  0.980
 AFD  O3  HO3  single  0.850  0.020  0.980
 AFD  O4  HO4  single  0.850  0.020  0.980
 AFD  O6  HO6  single  0.850  0.020  0.980
 AFD  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
 AFD  H1   C1  O1   109.93  3.000
 AFD  H1   C1  O5   110.41  3.000
 AFD  O1   C1  O5   104.63  3.000
 AFD  H1   C1  C2   107.67  3.000
 AFD  O5   C1  C2   111.79  3.000
 AFD  O1   C1  C2   112.42  3.000
 AFD  H2   C2  O2   110.68  3.000
 AFD  H2   C2  C3   108.49  3.000
 AFD  O2   C2  C3   111.19  3.000
 AFD  H2   C2  C1   107.88  3.000
 AFD  O2   C2  C1   109.10  3.000
 AFD  C3   C2  C1   109.42  3.000
 AFD  H3   C3  O3   110.21  3.000
 AFD  H3   C3  C4   107.80  3.000
 AFD  O3   C3  C4   109.77  3.000
 AFD  H3   C3  C2   108.31  3.000
 AFD  O3   C3  C2   109.89  3.000
 AFD  C4   C3  C2   110.83  3.000
 AFD  H4   C4  O4   110.78  3.000
 AFD  H4   C4  C5   107.37  3.000
 AFD  O4   C4  C5   107.87  3.000
 AFD  H4   C4  C3   106.42  3.000
 AFD  C5   C4  C3   111.05  3.000
 AFD  O4   C4  C3   113.22  3.000
 AFD  H5   C5  O5   110.10  3.000
 AFD  H5   C5  C6   106.42  3.000
 AFD  O5   C5  C6   107.49  3.000
 AFD  H5   C5  C4   109.00  3.000
 AFD  O5   C5  C4   110.13  3.000
 AFD  C6   C5  C4   113.61  3.000
 AFD  H62  C6  H61  106.47  3.000
 AFD  H62  C6  O6   111.66  3.000
 AFD  H61  C6  O6   112.17  3.000
 AFD  H62  C6  C5   107.97  3.000
 AFD  H61  C6  C5   108.16  3.000
 AFD  O6   C6  C5   110.21  3.000
 AFD  HO2  O2  C2   106.23  3.000
 AFD  HO3  O3  C3   108.49  3.000
 AFD  HO4  O4  C4   108.90  3.000
 AFD  C5   O5  C1   118.26  3.000
 AFD  HO6  O6  C6   108.17  3.000
 AFD  HO1  O1  C1   108.70  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
 AFD  chir_01  C1  O1  O5  C2  negativ
 AFD  chir_02  C2  O2  C1  C3  negativ
 AFD  chir_03  C3  O3  C2  C4  negativ
 AFD  chir_04  C4  O4  C5  C3  positiv
 AFD  chir_05  C5  O5  C4  C6  negativ

