# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:57:39 2022
#   Inital geometry file: a 55 line input string
#   Ligand name: beta-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
 ALL  ALL  'beta-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_ALL
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
 ALL  C1   C  CH1   0   0.283   4.8668  7.1270  10.4891
 ALL  C2   C  CH1   0   0.011   5.2212  8.4971  11.0615
 ALL  C3   C  CH1   0  -0.062   4.7417  8.6086  12.5089
 ALL  C4   C  CH1   0   0.013   3.2564  8.2597  12.5834
 ALL  C5   C  CH1   0   0.002   3.0208  6.8823  11.9509
 ALL  C6   C  CH2   0  -0.195   1.5728  6.4431  11.9529
 ALL  O1   O  OH1   0  -0.655   5.1846  7.1119   9.1471
 ALL  O2   O  OH1   0  -0.664   6.6066  8.6762  10.9374
 ALL  O3   O  OH1   0  -0.663   5.5223  7.7509  13.3069
 ALL  O4   O  OH1   0  -0.674   2.8853  8.2909  13.9419
 ALL  O5   O  O2    0  -0.505   3.4792  6.9152  10.6139
 ALL  O6   O  OH1   0  -0.667   0.7761  7.4162  11.3211
 ALL  H1   H  HCH1  0   0.187   5.4058  6.3385  11.0403
 ALL  H2   H  HCH1  0   0.217   4.6635  9.2473  10.4792
 ALL  H3   H  HCH1  0   0.231   4.8646  9.6544  12.8335
 ALL  H4   H  HCH1  0   0.225   2.7072  9.0117  12.0030
 ALL  H5   H  HCH1  0   0.219   3.5768  6.1282  12.5291
 ALL  H61  H  HCH2  0   0.217   1.5047  5.4688  11.4515
 ALL  H62  H  HCH2  0   0.205   1.2719  6.2764  12.9949
 ALL  HO1  H  HOH1  0   0.459   5.1966  6.2011   8.8339
 ALL  HO2  H  HOH1  0   0.451   6.8288  9.5608  11.2447
 ALL  HO3  H  HOH1  0   0.450   5.1853  7.7930  14.2079
 ALL  HO4  H  HOH1  0   0.460   1.9311  8.3881  14.0096
 ALL  HO6  H  HOH1  0   0.456  -0.1441  7.1486  11.3980

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
 ALL  C1  C2   single  1.527  0.020  1.527
 ALL  C1  O1   single  1.379  0.020  1.379
 ALL  C1  O5   single  1.409  0.020  1.409
 ALL  C1  H1   single  0.970  0.020  1.090
 ALL  C2  C3   single  1.529  0.020  1.529
 ALL  C2  O2   single  1.402  0.020  1.402
 ALL  C2  H2   single  0.970  0.020  1.090
 ALL  C3  C4   single  1.528  0.020  1.528
 ALL  C3  O3   single  1.408  0.020  1.408
 ALL  C3  H3   single  0.970  0.020  1.090
 ALL  C4  C5   single  1.534  0.020  1.534
 ALL  C4  O4   single  1.409  0.020  1.409
 ALL  C4  H4   single  0.970  0.020  1.090
 ALL  C5  C6   single  1.513  0.020  1.513
 ALL  C5  O5   single  1.414  0.020  1.414
 ALL  C5  H5   single  0.970  0.020  1.090
 ALL  C6  O6   single  1.407  0.020  1.407
 ALL  C6  H61  single  0.970  0.020  1.090
 ALL  C6  H62  single  0.970  0.020  1.090
 ALL  O1  HO1  single  0.850  0.020  0.980
 ALL  O2  HO2  single  0.850  0.020  0.980
 ALL  O3  HO3  single  0.850  0.020  0.980
 ALL  O4  HO4  single  0.850  0.020  0.980
 ALL  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
 ALL  H1   C1  O5   109.25  3.000
 ALL  H1   C1  O1   111.46  3.000
 ALL  O5   C1  O1   108.14  3.000
 ALL  H1   C1  C2   109.93  3.000
 ALL  O5   C1  C2   109.28  3.000
 ALL  O1   C1  C2   108.73  3.000
 ALL  H2   C2  O2   111.49  3.000
 ALL  H2   C2  C3   106.98  3.000
 ALL  O2   C2  C3   112.60  3.000
 ALL  H2   C2  C1   107.20  3.000
 ALL  O2   C2  C1   108.10  3.000
 ALL  C3   C2  C1   110.34  3.000
 ALL  H3   C3  O3   110.45  3.000
 ALL  H3   C3  C4   108.11  3.000
 ALL  O3   C3  C4   111.86  3.000
 ALL  H3   C3  C2   108.25  3.000
 ALL  O3   C3  C2   108.56  3.000
 ALL  C4   C3  C2   109.54  3.000
 ALL  H4   C4  O4   111.29  3.000
 ALL  H4   C4  C5   108.70  3.000
 ALL  O4   C4  C5   112.16  3.000
 ALL  H4   C4  C3   107.71  3.000
 ALL  O4   C4  C3   107.34  3.000
 ALL  C5   C4  C3   109.53  3.000
 ALL  H5   C5  O5   110.42  3.000
 ALL  H5   C5  C6   106.48  3.000
 ALL  O5   C5  C6   108.56  3.000
 ALL  H5   C5  C4   108.72  3.000
 ALL  O5   C5  C4   108.62  3.000
 ALL  C6   C5  C4   114.02  3.000
 ALL  H62  C6  H61  106.37  3.000
 ALL  H62  C6  O6   112.09  3.000
 ALL  H61  C6  O6   111.92  3.000
 ALL  H62  C6  C5   107.93  3.000
 ALL  H61  C6  C5   108.44  3.000
 ALL  O6   C6  C5   109.90  3.000
 ALL  HO1  O1  C1   109.24  3.000
 ALL  HO2  O2  C2   108.49  3.000
 ALL  HO3  O3  C3   108.05  3.000
 ALL  HO4  O4  C4   109.36  3.000
 ALL  C5   O5  C1   113.98  3.000
 ALL  HO6  O6  C6   108.27  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
 ALL  chir_01  C1  C2  O1  O5  positiv
 ALL  chir_02  C2  O2  C1  C3  negativ
 ALL  chir_03  C3  O3  C2  C4  negativ
 ALL  chir_04  C4  O4  C5  C3  positiv
 ALL  chir_05  C5  O5  C4  C6  negativ

