# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 14:56:13 2021
#   Inital geometry file: a 55 line input string
#   Ligand name: alpha-D-idopyranose
#   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
 ZCD  ZCD  'alpha-D-idopyranose      '  D-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 GRAND
;

data_comp_ZCD
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
 ZCD  C1   C  CH1   0   0.210  -10.2917  -17.5194  -30.7424
 ZCD  C2   C  CH1   0  -0.036   -9.4357  -17.5344  -29.4660
 ZCD  C3   C  CH1   0   0.029   -9.4627  -16.1629  -28.7856
 ZCD  C4   C  CH1   0   0.025   -9.1772  -15.0155  -29.7607
 ZCD  C5   C  CH1   0   0.034   -9.9971  -15.1820  -31.0440
 ZCD  C6   C  CH2   0  -0.219   -9.5653  -14.2363  -32.1534
 ZCD  O1   O  OH1   0  -0.689  -11.6585  -17.4479  -30.4831
 ZCD  O2   O  OH1   0  -0.736   -8.1004  -17.8409  -29.7727
 ZCD  O3   O  OH1   0  -0.694  -10.7503  -15.9275  -28.2384
 ZCD  O4   O  OH1   0  -0.692   -7.7907  -14.9754  -29.9982
 ZCD  O5   O  O2    0  -0.489   -9.8764  -16.4834  -31.5905
 ZCD  O6   O  OH1   0  -0.627   -9.5635  -12.9236  -31.6396
 ZCD  H1   H  HCH1  0   0.301  -10.1039  -18.4368  -31.3119
 ZCD  HO1  H  HOH1  0   0.434  -11.8018  -17.1031  -29.5929
 ZCD  H2   H  HCH1  0   0.272   -9.8536  -18.2783  -28.7705
 ZCD  HO2  H  HOH1  0   0.458   -8.0617  -18.7553  -30.0698
 ZCD  H3   H  HCH1  0   0.264   -8.6996  -16.1429  -27.9977
 ZCD  HO3  H  HOH1  0   0.452  -10.8550  -16.4877  -27.4622
 ZCD  H4   H  HCH1  0   0.256   -9.5142  -14.0938  -29.2704
 ZCD  HO4  H  HOH1  0   0.443   -7.5739  -14.0925  -30.3124
 ZCD  H5   H  HCH1  0   0.136  -11.0453  -14.9668  -30.7947
 ZCD  H61  H  HCH2  0   0.177  -10.2585  -14.3415  -32.9971
 ZCD  H62  H  HCH2  0   0.214   -8.5729  -14.5322  -32.5161
 ZCD  HO6  H  HOH1  0   0.479   -9.2622  -12.3306  -32.3335

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
 ZCD  C1  O1   single  1.393  0.020  1.393
 ZCD  O1  HO1  single  0.850  0.020  0.980
 ZCD  C1  H1   single  0.970  0.020  1.090
 ZCD  C1  O5   single  1.402  0.020  1.402
 ZCD  C1  C2   single  1.537  0.020  1.537
 ZCD  C2  H2   single  0.970  0.020  1.090
 ZCD  C2  O2   single  1.404  0.020  1.404
 ZCD  O2  HO2  single  0.850  0.020  0.980
 ZCD  C2  C3   single  1.531  0.020  1.531
 ZCD  C3  H3   single  0.970  0.020  1.090
 ZCD  C3  O3   single  1.419  0.020  1.419
 ZCD  O3  HO3  single  0.850  0.020  0.980
 ZCD  C3  C4   single  1.533  0.020  1.533
 ZCD  C4  H4   single  0.970  0.020  1.090
 ZCD  C4  O4   single  1.407  0.020  1.407
 ZCD  O4  HO4  single  0.850  0.020  0.980
 ZCD  C4  C5   single  1.532  0.020  1.532
 ZCD  C5  H5   single  0.970  0.020  1.090
 ZCD  C5  O5   single  1.417  0.020  1.417
 ZCD  C5  C6   single  1.520  0.020  1.520
 ZCD  C6  O6   single  1.410  0.020  1.410
 ZCD  O6  HO6  single  0.850  0.020  0.980
 ZCD  C6  H61  single  0.970  0.020  1.090
 ZCD  C6  H62  single  0.970  0.020  1.090

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
 ZCD  H1   C1  O5   104.68  3.000
 ZCD  O5   C1  O1   111.43  3.000
 ZCD  H1   C1  O1   107.93  3.000
 ZCD  O5   C1  C2   110.16  3.000
 ZCD  H1   C1  C2   109.14  3.000
 ZCD  O1   C1  C2   113.10  3.000
 ZCD  H2   C2  O2   110.58  3.000
 ZCD  O2   C2  C3   108.02  3.000
 ZCD  H2   C2  C3   108.53  3.000
 ZCD  C3   C2  C1   110.52  3.000
 ZCD  O2   C2  C1   110.52  3.000
 ZCD  H2   C2  C1   108.65  3.000
 ZCD  H3   C3  O3   110.56  3.000
 ZCD  O3   C3  C4   106.87  3.000
 ZCD  H3   C3  C4   108.29  3.000
 ZCD  C4   C3  C2   112.62  3.000
 ZCD  O3   C3  C2   109.63  3.000
 ZCD  H3   C3  C2   108.86  3.000
 ZCD  H4   C4  O4   110.74  3.000
 ZCD  O4   C4  C5   112.90  3.000
 ZCD  H4   C4  C5   107.54  3.000
 ZCD  C5   C4  C3   110.60  3.000
 ZCD  O4   C4  C3   108.19  3.000
 ZCD  H4   C4  C3   106.71  3.000
 ZCD  H5   C5  O5   110.41  3.000
 ZCD  O5   C5  C6   105.41  3.000
 ZCD  H5   C5  C6   108.35  3.000
 ZCD  C6   C5  C4   113.06  3.000
 ZCD  O5   C5  C4   112.17  3.000
 ZCD  H5   C5  C4   107.41  3.000
 ZCD  H62  C6  H61  106.95  3.000
 ZCD  H62  C6  O6   111.75  3.000
 ZCD  H61  C6  O6   111.74  3.000
 ZCD  H62  C6  C5   109.29  3.000
 ZCD  H61  C6  C5   108.79  3.000
 ZCD  O6   C6  C5   108.28  3.000
 ZCD  HO1  O1  C1   109.61  3.000
 ZCD  HO2  O2  C2   108.25  3.000
 ZCD  HO3  O3  C3   108.25  3.000
 ZCD  HO4  O4  C4   107.66  3.000
 ZCD  C5   O5  C1   114.85  3.000
 ZCD  HO6  O6  C6   108.17  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
 ZCD  chir_01  C1  O1  O5  C2  negativ
 ZCD  chir_02  C2  O2  C1  C3  positiv
 ZCD  chir_03  C3  O3  C2  C4  negativ
 ZCD  chir_04  C4  O4  C5  C3  negativ
 ZCD  chir_05  C5  O5  C4  C6  negativ

