# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 02:24:12 2022
#   Inital geometry file: a 55 line input string
#   Ligand name: alpha-D-allofuranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@H]1O[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
 VDV  VDV  'alpha-D-allofuranose     '  ligand  24  12  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VDV
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
 VDV  C4   C  CH1   0  -0.047  22.9223   0.2437  69.2086
 VDV  C5   C  CH1   0  -0.022  23.8964  -0.6707  69.9785
 VDV  C6   C  CH1   0   0.227  23.0969  -1.0412  71.2289
 VDV  C2   C  CH1   0  -0.041  20.7230  -0.9807  68.6446
 VDV  C3   C  CH1   0   0.026  21.5480  -0.2352  69.6893
 VDV  O1   O  O2    0  -0.511  21.7832  -1.1473  70.7693
 VDV  O2   O  OH1   0  -0.666  23.2650  -0.0279  72.1702
 VDV  O3   O  OH1   0  -0.663  25.1528  -0.1178  70.2247
 VDV  O4   O  OH1   0  -0.664  23.0755   1.6027  69.5406
 VDV  O5   O  OH1   0  -0.666  21.4414  -2.0505  68.0763
 VDV  H5   H  HCH1  0   0.235  23.0462   0.0975  68.1295
 VDV  H6   H  HCH1  0   0.250  24.0471  -1.5820  69.3933
 VDV  H7   H  HCH1  0   0.234  23.3713  -2.0157  71.6458
 VDV  H3   H  HCH1  0   0.226  19.8133  -1.3452  69.1458
 VDV  H4   H  HCH1  0   0.241  20.9697   0.6210  70.0503
 VDV  H8   H  HOH1  0   0.464  23.0395  -0.3566  73.0463
 VDV  H9   H  HOH1  0   0.444  25.0654   0.4924  70.9665
 VDV  H10  H  HOH1  0   0.446  23.9317   1.8945  69.2108
 VDV  H11  H  HOH1  0   0.452  21.6244  -2.6944  68.7680
 VDV  H12  H  HOH1  0   0.458  19.2873   1.5598  67.2906
 VDV  C1   C  CH2   0  -0.172  20.2888  -0.0874  67.4919
 VDV  O6   O  OH1   0  -0.666  19.5214   0.9715  68.0136
 VDV  H2   H  HCH2  0   0.214  19.7119  -0.6965  66.7842
 VDV  H1   H  HCH2  0   0.203  21.1716   0.2766  66.9498

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
 VDV  C1  O6   single  1.408  0.020  1.408
 VDV  C1  C2   single  1.522  0.020  1.522
 VDV  O5  C2   single  1.408  0.020  1.408
 VDV  C2  C3   single  1.526  0.020  1.526
 VDV  C4  O4   single  1.407  0.020  1.407
 VDV  C4  C3   single  1.533  0.020  1.533
 VDV  C4  C5   single  1.542  0.020  1.542
 VDV  C3  O1   single  1.433  0.020  1.433
 VDV  C5  O3   single  1.395  0.020  1.395
 VDV  C5  C6   single  1.530  0.020  1.530
 VDV  O1  C6   single  1.396  0.020  1.396
 VDV  C6  O2   single  1.393  0.020  1.393
 VDV  C4  H5   single  0.970  0.020  1.090
 VDV  C5  H6   single  0.970  0.020  1.090
 VDV  C6  H7   single  0.970  0.020  1.090
 VDV  C1  H2   single  0.970  0.020  1.090
 VDV  C1  H1   single  0.970  0.020  1.090
 VDV  C2  H3   single  0.970  0.020  1.090
 VDV  C3  H4   single  0.970  0.020  1.090
 VDV  O2  H8   single  0.850  0.020  0.980
 VDV  O3  H9   single  0.850  0.020  0.980
 VDV  O4  H10  single  0.850  0.020  0.980
 VDV  O5  H11  single  0.850  0.020  0.980
 VDV  O6  H12  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
 VDV  H5   C4  O4  110.41  3.000
 VDV  H5   C4  C3  111.62  3.000
 VDV  O4   C4  C3  108.99  3.000
 VDV  H5   C4  C5  109.94  3.000
 VDV  C3   C4  C5  102.97  3.000
 VDV  O4   C4  C5  112.71  3.000
 VDV  H6   C5  O3  107.49  3.000
 VDV  H6   C5  C6  107.92  3.000
 VDV  O3   C5  C6  115.00  3.000
 VDV  H6   C5  C4  108.31  3.000
 VDV  C6   C5  C4  102.81  3.000
 VDV  O3   C5  C4  114.97  3.000
 VDV  H7   C6  O2  111.09  3.000
 VDV  H7   C6  O1  107.08  3.000
 VDV  O2   C6  O1  113.03  3.000
 VDV  H7   C6  C5  113.32  3.000
 VDV  O2   C6  C5  108.24  3.000
 VDV  O1   C6  C5  103.96  3.000
 VDV  H3   C2  O5  110.72  3.000
 VDV  H3   C2  C3  107.27  3.000
 VDV  O5   C2  C3  111.81  3.000
 VDV  H3   C2  C1  107.67  3.000
 VDV  C3   C2  C1  112.72  3.000
 VDV  O5   C2  C1  106.61  3.000
 VDV  H4   C3  O1  109.63  3.000
 VDV  H4   C3  C2  108.80  3.000
 VDV  O1   C3  C2  107.09  3.000
 VDV  H4   C3  C4  109.44  3.000
 VDV  O1   C3  C4  106.75  3.000
 VDV  C2   C3  C4  115.01  3.000
 VDV  C3   O1  C6  110.75  3.000
 VDV  H8   O2  C6  109.77  3.000
 VDV  H9   O3  C5  107.76  3.000
 VDV  H10  O4  C4  107.98  3.000
 VDV  H11  O5  C2  108.37  3.000
 VDV  H1   C1  H2  106.75  3.000
 VDV  H1   C1  O6  111.83  3.000
 VDV  H2   C1  O6  111.71  3.000
 VDV  H1   C1  C2  109.83  3.000
 VDV  H2   C1  C2  108.22  3.000
 VDV  O6   C1  C2  108.44  3.000
 VDV  H12  O6  C1  108.33  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
 VDV  chir_01  C4  O4  C3  C5  positiv
 VDV  chir_02  C5  O3  C4  C6  positiv
 VDV  chir_03  C6  O1  O2  C5  positiv
 VDV  chir_04  C2  O5  C3  C1  negativ
 VDV  chir_05  C3  O1  C4  C2  negativ

