# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 01:32:27 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: 2,6-anhydro-3,5-dideoxy-D-ribo-oct-2-enonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@@H]1C[C@@H](O)C=C(O1)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
 KDD  KDD  '2,6-anhydro-3,5-dideoxy-D-ribo-oct-2-enonic acid'  D-saccharide  25  14  .  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_KDD
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
 KDD  O1A  O  O      0  -0.591  -3.6273   1.0920   0.0385
 KDD  C1   C  C      0   0.369  -2.4182   1.3704  -0.0557
 KDD  O1B  O  OC    -1  -0.593  -1.8984   2.4967  -0.1040
 KDD  C2   C  C      0   0.177  -1.4593   0.1827  -0.1225
 KDD  O6   O  O2     0  -0.473  -0.1627   0.5471  -0.1942
 KDD  C6   C  CH1    0   0.011   0.7974  -0.4777   0.0239
 KDD  C7   C  CH1    0  -0.023   2.1620   0.1130  -0.3403
 KDD  C8   C  CH2    0  -0.162   2.4753   1.3374   0.5074
 KDD  O8   O  OH1    0  -0.671   3.7078   1.8743   0.0870
 KDD  O7   O  OH1    0  -0.659   3.1703  -0.8651  -0.2392
 KDD  C5   C  CH2    0  -0.485   0.4336  -1.7222  -0.7664
 KDD  C3   C  C1     0  -0.404  -1.8619  -1.0918  -0.1263
 KDD  C4   C  CH1    0   0.036  -0.9169  -2.2397  -0.2982
 KDD  H6   H  HCH1   0   0.218   0.7910  -0.7321   1.0960
 KDD  H7   H  HCH1   0   0.231   2.1387   0.4081  -1.3956
 KDD  H8   H  HCH2   0   0.213   1.6627   2.0642   0.4080
 KDD  H8A  H  HCH2   0   0.188   2.5048   1.0344   1.5659
 KDD  HO8  H  HOH1   0   0.455   3.8840   2.6578   0.6149
 KDD  HO7  H  HOH1   0   0.445   3.2574  -1.1249   0.6847
 KDD  H5   H  HCH2   0   0.239   0.3821  -1.4816  -1.8323
 KDD  H5A  H  HCH2   0   0.252   1.1972  -2.4908  -0.6439
 KDD  H3   H  H      0   0.246  -2.9216  -1.2921  -0.0403
 KDD  O61  O  OH1    0  -0.676  -0.7120  -2.9689   0.9062
 KDD  H4   H  HCH1   0   0.212  -1.3247  -2.9112  -1.0666
 KDD  H12  H  HOH1   0   0.446  -1.5629  -3.0717   1.3438

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
 KDD  O1A  C1   deloc   1.244  0.020  1.244
 KDD  C1   O1B  deloc   1.241  0.020  1.241
 KDD  C2   C1   single  1.528  0.020  1.528
 KDD  C2   O6   single  1.349  0.020  1.349
 KDD  C6   O6   single  1.421  0.020  1.421
 KDD  C6   C7   single  1.531  0.020  1.531
 KDD  C6   H6   single  0.970  0.020  1.090
 KDD  C7   C8   single  1.522  0.020  1.522
 KDD  C7   H7   single  0.970  0.020  1.090
 KDD  C8   O8   single  1.409  0.020  1.409
 KDD  C8   H8   single  0.970  0.020  1.090
 KDD  C8   H8A  single  0.970  0.020  1.090
 KDD  O8   HO8  single  0.850  0.020  0.980
 KDD  O7   C7   single  1.408  0.020  1.408
 KDD  O7   HO7  single  0.850  0.020  0.980
 KDD  C5   C6   single  1.519  0.020  1.519
 KDD  C5   H5   single  0.970  0.020  1.090
 KDD  C5   H5A  single  0.970  0.020  1.090
 KDD  C3   C2   double  1.337  0.020  1.337
 KDD  C3   H3   single  0.930  0.020  1.080
 KDD  C4   C5   single  1.520  0.020  1.520
 KDD  C4   C3   single  1.497  0.020  1.497
 KDD  C4   O61  single  1.423  0.020  1.423
 KDD  C4   H4   single  0.970  0.020  1.090
 KDD  O61  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
 KDD  C2   C1   O1B  116.15  3.000
 KDD  C2   C1   O1A  116.05  3.000
 KDD  O1B  C1   O1A  127.80  3.000
 KDD  C3   C2   O6   123.17  3.000
 KDD  C3   C2   C1   123.53  3.000
 KDD  O6   C2   C1   113.30  3.000
 KDD  C6   O6   C2   116.52  3.000
 KDD  H6   C6   C5   108.41  3.000
 KDD  C5   C6   C7   113.95  3.000
 KDD  H6   C6   C7   109.01  3.000
 KDD  C5   C6   O6   110.44  3.000
 KDD  H6   C6   O6   108.18  3.000
 KDD  C7   C6   O6   106.71  3.000
 KDD  H7   C7   O7   105.74  3.000
 KDD  O7   C7   C8   111.80  3.000
 KDD  H7   C7   C8   108.91  3.000
 KDD  O7   C7   C6   110.68  3.000
 KDD  H7   C7   C6   108.30  3.000
 KDD  C8   C7   C6   111.19  3.000
 KDD  H8A  C8   H8   106.84  3.000
 KDD  H8A  C8   O8   111.61  3.000
 KDD  H8   C8   O8   111.68  3.000
 KDD  H8A  C8   C7   108.63  3.000
 KDD  H8   C8   C7   109.31  3.000
 KDD  O8   C8   C7   108.70  3.000
 KDD  HO8  O8   C8   107.89  3.000
 KDD  HO7  O7   C7   108.71  3.000
 KDD  H5A  C5   H5   107.31  3.000
 KDD  H5A  C5   C4   110.34  3.000
 KDD  H5   C5   C4   109.46  3.000
 KDD  C4   C5   C6   109.36  3.000
 KDD  H5A  C5   C6   110.58  3.000
 KDD  H5   C5   C6   109.76  3.000
 KDD  H3   C3   C4   119.05  3.000
 KDD  C4   C3   C2   122.78  3.000
 KDD  H3   C3   C2   118.12  3.000
 KDD  H4   C4   O61  109.40  3.000
 KDD  H4   C4   C3   108.34  3.000
 KDD  O61  C4   C3   112.75  3.000
 KDD  H4   C4   C5   108.81  3.000
 KDD  O61  C4   C5   107.89  3.000
 KDD  C3   C4   C5   109.59  3.000
 KDD  H12  O61  C4   108.20  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 KDD  Var_01  C4  C3  C2  O6     -4.00  30.0  1
 KDD  Var_02  C3  C2  O6  C6    -13.63  30.0  1
 KDD  Var_03  O6  C2  C1  O1A  -178.63  30.0  2

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
 KDD  chir_01  C6  O6   C7  C5  positiv
 KDD  chir_02  C7  O7   C6  C8  negativ
 KDD  chir_03  C4  O61  C3  C5  negativ

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
 KDD  plan-1  O1A  0.020
 KDD  plan-1  C1   0.020
 KDD  plan-1  O1B  0.020
 KDD  plan-1  C2   0.020

