# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 12:45:19 2021
#   Inital geometry file: a 55 line input string
#   Ligand name: alpha-L-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
 Z2D  Z2D  'alpha-L-allopyranose     '  L-saccharide  24  12  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Z2D
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
 Z2D  C1   C  CH1   0   0.269  54.4409  34.6379  61.2040
 Z2D  C2   C  CH1   0  -0.010  54.6584  35.0469  62.6539
 Z2D  C3   C  CH1   0  -0.007  55.3627  33.8987  63.3713
 Z2D  C4   C  CH1   0  -0.006  54.6376  32.5626  63.1992
 Z2D  C5   C  CH1   0  -0.057  54.3442  32.3085  61.7147
 Z2D  C6   C  CH2   0  -0.188  55.5660  31.8365  60.9230
 Z2D  O1   O  OH1   0  -0.659  53.7061  35.6146  60.5660
 Z2D  O2   O  OH1   0  -0.670  53.4278  35.3901  63.2302
 Z2D  O3   O  OH1   0  -0.669  55.5003  34.2771  64.7186
 Z2D  O4   O  OH1   0  -0.670  53.4550  32.5821  63.9628
 Z2D  O5   O  O2    0  -0.498  53.7234  33.4266  61.1142
 Z2D  O6   O  OH1   0  -0.668  55.8852  30.5423  61.3789
 Z2D  H1   H  HCH1  0   0.193  55.4326  34.5213  60.7376
 Z2D  HO1  H  HOH1  0   0.463  53.7853  35.4966  59.6136
 Z2D  H2   H  HCH1  0   0.223  55.3454  35.9085  62.6505
 Z2D  HO2  H  HOH1  0   0.448  53.4907  35.2352  64.1785
 Z2D  H3   H  HCH1  0   0.226  56.3503  33.7891  62.8996
 Z2D  HO3  H  HOH1  0   0.457  55.8208  33.5259  65.2282
 Z2D  H4   H  HCH1  0   0.235  55.3077  31.7656  63.5529
 Z2D  HO4  H  HOH1  0   0.452  53.1242  31.6807  64.0198
 Z2D  H5   H  HCH1  0   0.256  53.6056  31.5018  61.6512
 Z2D  H62  H  HCH2  0   0.202  56.4176  32.5169  61.0436
 Z2D  H61  H  HCH2  0   0.218  55.3025  31.8404  59.8575
 Z2D  HO6  H  HOH1  0   0.460  56.7051  30.2684  60.9584

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
 Z2D  C1  O1   single  1.379  0.020  1.379
 Z2D  C1  C2   single  1.522  0.020  1.522
 Z2D  C1  O5   single  1.411  0.020  1.411
 Z2D  C1  H1   single  0.970  0.020  1.090
 Z2D  C2  O2   single  1.402  0.020  1.402
 Z2D  C2  C3   single  1.526  0.020  1.526
 Z2D  C2  H2   single  0.970  0.020  1.090
 Z2D  C3  O3   single  1.406  0.020  1.406
 Z2D  C3  C4   single  1.530  0.020  1.530
 Z2D  C3  H3   single  0.970  0.020  1.090
 Z2D  C4  H4   single  0.970  0.020  1.090
 Z2D  C4  C5   single  1.534  0.020  1.534
 Z2D  C4  O4   single  1.408  0.020  1.408
 Z2D  C5  O5   single  1.413  0.020  1.413
 Z2D  C5  C6   single  1.530  0.020  1.530
 Z2D  C5  H5   single  0.970  0.020  1.090
 Z2D  C6  H61  single  0.970  0.020  1.090
 Z2D  C6  H62  single  0.970  0.020  1.090
 Z2D  C6  O6   single  1.409  0.020  1.409
 Z2D  O1  HO1  single  0.850  0.020  0.980
 Z2D  O2  HO2  single  0.850  0.020  0.980
 Z2D  O3  HO3  single  0.850  0.020  0.980
 Z2D  O4  HO4  single  0.850  0.020  0.980
 Z2D  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
 Z2D  H1   C1  O5   109.87  3.000
 Z2D  H1   C1  O1   111.02  3.000
 Z2D  O5   C1  O1   107.92  3.000
 Z2D  H1   C1  C2   107.64  3.000
 Z2D  O5   C1  C2   111.35  3.000
 Z2D  O1   C1  C2   109.06  3.000
 Z2D  H2   C2  O2   110.93  3.000
 Z2D  H2   C2  C3   107.58  3.000
 Z2D  O2   C2  C3   113.34  3.000
 Z2D  H2   C2  C1   107.23  3.000
 Z2D  C3   C2  C1   108.15  3.000
 Z2D  O2   C2  C1   109.39  3.000
 Z2D  H3   C3  O3   110.47  3.000
 Z2D  H3   C3  C4   106.87  3.000
 Z2D  O3   C3  C4   112.90  3.000
 Z2D  H3   C3  C2   106.73  3.000
 Z2D  C4   C3  C2   112.68  3.000
 Z2D  O3   C3  C2   107.04  3.000
 Z2D  H4   C4  O4   110.34  3.000
 Z2D  O4   C4  C5   111.50  3.000
 Z2D  H4   C4  C5   107.92  3.000
 Z2D  O4   C4  C3   108.97  3.000
 Z2D  C5   C4  C3   110.12  3.000
 Z2D  H4   C4  C3   107.94  3.000
 Z2D  H5   C5  O5   105.18  3.000
 Z2D  H5   C5  C6   106.33  3.000
 Z2D  O5   C5  C6   112.02  3.000
 Z2D  H5   C5  C4   107.87  3.000
 Z2D  C6   C5  C4   113.51  3.000
 Z2D  O5   C5  C4   111.36  3.000
 Z2D  H61  C6  H62  106.91  3.000
 Z2D  H62  C6  O6   111.00  3.000
 Z2D  H61  C6  O6   111.82  3.000
 Z2D  O6   C6  C5   107.27  3.000
 Z2D  H62  C6  C5   111.82  3.000
 Z2D  H61  C6  C5   108.03  3.000
 Z2D  HO1  O1  C1   109.09  3.000
 Z2D  HO2  O2  C2   107.95  3.000
 Z2D  HO3  O3  C3   109.26  3.000
 Z2D  HO4  O4  C4   107.94  3.000
 Z2D  C5   O5  C1   115.40  3.000
 Z2D  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
 Z2D  chir_01  C1  O1  C2  O5  negativ
 Z2D  chir_02  C2  O2  C1  C3  positiv
 Z2D  chir_03  C3  O3  C2  C4  positiv
 Z2D  chir_04  C4  O4  C5  C3  negativ
 Z2D  chir_05  C5  O5  C4  C6  positiv

