# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 01:17:12 2022
#   Inital geometry file: a 55 line input string
#   Ligand name: beta-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
 VDS  VDS  'beta-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_VDS
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
 VDS  C4   C  CH1   0  -0.041  22.8170   0.5516  69.1514
 VDS  C5   C  CH1   0  -0.028  23.7744  -0.2471  70.0267
 VDS  C6   C  CH1   0   0.270  23.0314  -0.2979  71.3574
 VDS  C2   C  CH1   0  -0.026  20.7382  -0.9757  68.8742
 VDS  C3   C  CH1   0   0.013  21.4482   0.1104  69.6812
 VDS  O1   O  O2    0  -0.513  21.6680  -0.3880  71.0018
 VDS  O2   O  OH1   0  -0.656  23.4182  -1.4055  72.0886
 VDS  O3   O  OH1   0  -0.664  25.0346   0.3583  70.0784
 VDS  O4   O  OH1   0  -0.667  22.9373   1.9381  69.3699
 VDS  O5   O  OH1   0  -0.665  21.5339  -2.1259  68.7017
 VDS  H5   H  HCH1  0   0.240  22.9504   0.3093  68.0905
 VDS  H6   H  HCH1  0   0.221  23.8323  -1.2698  69.6311
 VDS  H7   H  HCH1  0   0.193  23.2037   0.6269  71.9281
 VDS  H3   H  HCH1  0   0.226  19.8161  -1.2245  69.4206
 VDS  H4   H  HCH1  0   0.241  20.7889   0.9824  69.7312
 VDS  H8   H  HOH1  0   0.461  23.1812  -1.2819  73.0135
 VDS  H9   H  HOH1  0   0.458  25.6363  -0.2180  70.5597
 VDS  H10  H  HOH1  0   0.448  23.8436   2.1974  69.1720
 VDS  H11  H  HOH1  0   0.453  21.6326  -2.5575  69.5563
 VDS  H12  H  HOH1  0   0.458  19.2980   0.9335  66.7200
 VDS  C1   C  CH2   0  -0.175  20.3369  -0.5149  67.4800
 VDS  O6   O  OH1   0  -0.666  19.5214   0.6264  67.6029
 VDS  H1   H  HCH2  0   0.214  19.8094  -1.3407  66.9858
 VDS  H2   H  HCH2  0   0.202  21.2351  -0.3102  66.8827

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
 VDS  C1  O6   single  1.408  0.020  1.408
 VDS  C1  C2   single  1.522  0.020  1.522
 VDS  O5  C2   single  1.409  0.020  1.409
 VDS  C2  C3   single  1.528  0.020  1.528
 VDS  C4  O4   single  1.409  0.020  1.409
 VDS  C4  C3   single  1.533  0.020  1.533
 VDS  C4  C5   single  1.523  0.020  1.523
 VDS  C3  O1   single  1.429  0.020  1.429
 VDS  C5  O3   single  1.399  0.020  1.399
 VDS  C5  C6   single  1.525  0.020  1.525
 VDS  O1  C6   single  1.412  0.020  1.412
 VDS  C6  O2   single  1.382  0.020  1.382
 VDS  C4  H5   single  0.970  0.020  1.090
 VDS  C5  H6   single  0.970  0.020  1.090
 VDS  C6  H7   single  0.970  0.020  1.090
 VDS  C1  H1   single  0.970  0.020  1.090
 VDS  C1  H2   single  0.970  0.020  1.090
 VDS  C2  H3   single  0.970  0.020  1.090
 VDS  C3  H4   single  0.970  0.020  1.090
 VDS  O2  H8   single  0.850  0.020  0.980
 VDS  O3  H9   single  0.850  0.020  0.980
 VDS  O4  H10  single  0.850  0.020  0.980
 VDS  O5  H11  single  0.850  0.020  0.980
 VDS  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
 VDS  H5   C4  O4  110.93  3.000
 VDS  H5   C4  C3  112.30  3.000
 VDS  O4   C4  C3  107.82  3.000
 VDS  H5   C4  C5  111.32  3.000
 VDS  C3   C4  C5  102.23  3.000
 VDS  O4   C4  C5  111.92  3.000
 VDS  H6   C5  O3  111.64  3.000
 VDS  H6   C5  C6  108.00  3.000
 VDS  O3   C5  C6  114.90  3.000
 VDS  H6   C5  C4  108.33  3.000
 VDS  C6   C5  C4  102.28  3.000
 VDS  O3   C5  C4  111.13  3.000
 VDS  H7   C6  O2  110.81  3.000
 VDS  H7   C6  O1  109.60  3.000
 VDS  O2   C6  O1  110.63  3.000
 VDS  H7   C6  C5  110.38  3.000
 VDS  O2   C6  C5  110.61  3.000
 VDS  O1   C6  C5  104.65  3.000
 VDS  H3   C2  O5  110.45  3.000
 VDS  H3   C2  C3  106.73  3.000
 VDS  O5   C2  C3  112.49  3.000
 VDS  H3   C2  C1  107.60  3.000
 VDS  C3   C2  C1  113.02  3.000
 VDS  O5   C2  C1  106.49  3.000
 VDS  H4   C3  O1  109.17  3.000
 VDS  H4   C3  C2  108.10  3.000
 VDS  O1   C3  C2  108.17  3.000
 VDS  H4   C3  C4  108.93  3.000
 VDS  O1   C3  C4  106.41  3.000
 VDS  C2   C3  C4  115.91  3.000
 VDS  C3   O1  C6  111.05  3.000
 VDS  H8   O2  C6  109.66  3.000
 VDS  H9   O3  C5  108.82  3.000
 VDS  H10  O4  C4  108.27  3.000
 VDS  H11  O5  C2  108.37  3.000
 VDS  H2   C1  H1  106.77  3.000
 VDS  H2   C1  O6  111.73  3.000
 VDS  H1   C1  O6  111.77  3.000
 VDS  H2   C1  C2  109.82  3.000
 VDS  H1   C1  C2  108.15  3.000
 VDS  O6   C1  C2  108.55  3.000
 VDS  H12  O6  C1  108.26  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
 VDS  chir_01  C4  O4  C3  C5  positiv
 VDS  chir_02  C5  O3  C4  C6  positiv
 VDS  chir_03  C6  O1  O2  C5  negativ
 VDS  chir_04  C2  O5  C3  C1  negativ
 VDS  chir_05  C3  O1  C4  C2  negativ

