# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 12:20:09 2022
#   Inital geometry file: a 56 line input string
#   Ligand name: alpha-L-idopyranuronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1O[C@H]([C@@H](O)[C@H](O)[C@H]1O)C(O)=O
#
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
 IDR  IDR  'alpha-L-idopyranuronic acid'  L-saccharide  22  13  .  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_IDR
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
 IDR  C1   C  CH1    0   0.241  28.1314  27.8024  47.5138
 IDR  C2   C  CH1    0   0.021  27.7143  27.0389  48.7736
 IDR  C3   C  CH1    0  -0.035  27.0778  27.9496  49.8338
 IDR  C4   C  CH1    0   0.014  26.0655  28.9295  49.2282
 IDR  C5   C  CH1    0  -0.139  26.6654  29.6149  48.0022
 IDR  C6   C  C      0   0.446  25.6596  30.4977  47.2232
 IDR  O1   O  OH1    0  -0.663  29.3206  28.4787  47.7745
 IDR  O2   O  OH1    0  -0.667  26.8267  26.0407  48.3321
 IDR  O3   O  OH1    0  -0.665  28.1286  28.6282  50.4822
 IDR  O4   O  OH1    0  -0.706  24.8839  28.2380  48.9360
 IDR  O5   O  O2     0  -0.509  27.1204  28.6532  47.0550
 IDR  O6A  O  O      0  -0.565  26.1054  31.4998  46.6548
 IDR  O6B  O  OC    -1  -0.605  24.4646  30.0985  47.2091
 IDR  H1   H  HCH1   0   0.221  28.2648  27.0753  46.7022
 IDR  H2   H  HCH1   0   0.215  28.6171  26.5913  49.2142
 IDR  H3   H  HCH1   0   0.218  26.5400  27.3078  50.5519
 IDR  H4   H  HCH1   0   0.190  25.8842  29.7229  49.9776
 IDR  H5   H  HCH1   0   0.203  27.4965  30.2461  48.3354
 IDR  HO1  H  HOH1   0   0.453  29.6589  28.8307  46.9441
 IDR  HO2  H  HOH1   0   0.447  26.3957  25.6510  49.0986
 IDR  HO3  H  HOH1   0   0.448  27.7470  29.1933  51.1614
 IDR  HO4  H  HOH1   0   0.436  24.4564  28.8068  48.2495

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
 IDR  C1  C2   single  1.531  0.020  1.531
 IDR  C1  O1   single  1.393  0.020  1.393
 IDR  C1  O5   single  1.399  0.020  1.399
 IDR  C1  H1   single  0.970  0.020  1.090
 IDR  C2  C3   single  1.536  0.020  1.536
 IDR  C2  O2   single  1.407  0.020  1.407
 IDR  C2  H2   single  0.970  0.020  1.090
 IDR  C3  C4   single  1.534  0.020  1.534
 IDR  C3  O3   single  1.409  0.020  1.409
 IDR  C3  H3   single  0.970  0.020  1.090
 IDR  C4  C5   single  1.527  0.020  1.527
 IDR  C4  O4   single  1.400  0.020  1.400
 IDR  C4  H4   single  0.970  0.020  1.090
 IDR  C5  C6   single  1.548  0.020  1.548
 IDR  C5  O5   single  1.424  0.020  1.424
 IDR  C5  H5   single  0.970  0.020  1.090
 IDR  C6  O6A  deloc   1.235  0.020  1.235
 IDR  C6  O6B  deloc   1.260  0.020  1.260
 IDR  O1  HO1  single  0.850  0.020  0.980
 IDR  O2  HO2  single  0.850  0.020  0.980
 IDR  O3  HO3  single  0.850  0.020  0.980
 IDR  O4  HO4  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
 IDR  H1   C1  O5   104.38  3.000
 IDR  H1   C1  O1   110.88  3.000
 IDR  O5   C1  O1   112.53  3.000
 IDR  H1   C1  C2   108.12  3.000
 IDR  O5   C1  C2   112.10  3.000
 IDR  O1   C1  C2   108.71  3.000
 IDR  H2   C2  O2   110.78  3.000
 IDR  H2   C2  C3   107.76  3.000
 IDR  O2   C2  C3   112.08  3.000
 IDR  H2   C2  C1   108.00  3.000
 IDR  O2   C2  C1   105.52  3.000
 IDR  C3   C2  C1   112.66  3.000
 IDR  H3   C3  O3   110.13  3.000
 IDR  H3   C3  C4   107.88  3.000
 IDR  O3   C3  C4   111.49  3.000
 IDR  H3   C3  C2   107.84  3.000
 IDR  O3   C3  C2   107.11  3.000
 IDR  C4   C3  C2   112.32  3.000
 IDR  H4   C4  O4   110.93  3.000
 IDR  H4   C4  C5   106.64  3.000
 IDR  O4   C4  C5   112.69  3.000
 IDR  H4   C4  C3   107.39  3.000
 IDR  O4   C4  C3   108.90  3.000
 IDR  C5   C4  C3   110.15  3.000
 IDR  H5   C5  O5   110.42  3.000
 IDR  H5   C5  C6   108.50  3.000
 IDR  O5   C5  C6   104.94  3.000
 IDR  H5   C5  C4   108.21  3.000
 IDR  O5   C5  C4   110.87  3.000
 IDR  C6   C5  C4   113.86  3.000
 IDR  O6B  C6  O6A  126.45  3.000
 IDR  O6B  C6  C5   116.17  3.000
 IDR  O6A  C6  C5   117.36  3.000
 IDR  HO1  O1  C1   108.42  3.000
 IDR  HO2  O2  C2   108.67  3.000
 IDR  HO3  O3  C3   108.17  3.000
 IDR  HO4  O4  C4   103.04  3.000
 IDR  C5   O5  C1   115.05  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
 IDR  chir_01  C1  C2  O1  O5  positiv
 IDR  chir_02  C2  O2  C1  C3  negativ
 IDR  chir_03  C3  O3  C2  C4  positiv
 IDR  chir_04  C4  O4  C3  C5  negativ
 IDR  chir_05  C5  O5  C4  C6  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 IDR  plan-1  C5   0.020
 IDR  plan-1  C6   0.020
 IDR  plan-1  O6A  0.020
 IDR  plan-1  O6B  0.020

