# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 02:11:16 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: 3,4,5-trideoxy-alpha-D-erythro-oct-3-en-2-ulopyranosonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@@H]1CC=C[C@@](O)(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
 KDB  KDB  '3,4,5-trideoxy-alpha-D-erythro-oct-3-en-2-ulopyranosonic 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_KDB
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
 KDB  O2   O  OH1    0  -0.689   1.4904   0.0888  -1.7269
 KDB  C2   C  CT     0   0.334   1.4145  -0.1313  -0.3570
 KDB  C1   C  C      0   0.389   2.4203   0.8281   0.3562
 KDB  O1B  O  O      0  -0.569   2.6754   0.6107   1.5449
 KDB  O1A  O  OC    -1  -0.604   2.8528   1.7450  -0.3764
 KDB  C3   C  C1     0  -0.242   1.7078  -1.5716  -0.0650
 KDB  C4   C  C1     0  -0.240   0.7939  -2.4016   0.4227
 KDB  C5   C  CH2    0  -0.479  -0.6208  -1.9737   0.6619
 KDB  C6   C  CH1    0   0.019  -0.8902  -0.6778  -0.0861
 KDB  O6   O  O2     0  -0.529   0.1575   0.2412   0.1617
 KDB  C7   C  CH1    0  -0.026  -2.1948   0.0023   0.3345
 KDB  O7   O  OH1    0  -0.662  -3.2670  -0.9131   0.3135
 KDB  C8   C  CH2    0  -0.161  -2.4771   1.2262  -0.5220
 KDB  O8   O  OH1    0  -0.672  -3.6263   1.8740  -0.0260
 KDB  HO2  H  HOH1   0   0.432   1.9743   0.9369  -1.7825
 KDB  H3   H  H      0   0.246   2.7161  -1.9146  -0.2710
 KDB  H4   H  H      0   0.243   1.0565  -3.4299   0.6450
 KDB  H5   H  HCH2   0   0.243  -1.3038  -2.7546   0.3228
 KDB  H5A  H  HCH2   0   0.239  -0.8061  -1.8503   1.7360
 KDB  H6   H  HCH1   0   0.206  -0.9449  -0.9033  -1.1633
 KDB  H7   H  HCH1   0   0.228  -2.0944   0.3164   1.3801
 KDB  HO7  H  HOH1   0   0.443  -3.4100  -1.1997  -0.5954
 KDB  H8   H  HCH2   0   0.208  -1.6027   1.8844  -0.5037
 KDB  H8A  H  HCH2   0   0.187  -2.6124   0.9030  -1.5659
 KDB  HO8  H  HOH1   0   0.454  -3.7782   2.6571  -0.5619

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
 KDB  O2   C2   single  1.390  0.020  1.390
 KDB  O2   HO2  single  0.850  0.020  0.980
 KDB  C2   C1   single  1.562  0.020  1.562
 KDB  C2   C3   single  1.499  0.020  1.499
 KDB  C2   O6   single  1.410  0.020  1.410
 KDB  O1B  C1   deloc   1.235  0.020  1.235
 KDB  C1   O1A  deloc   1.251  0.020  1.251
 KDB  C3   C4   double  1.327  0.020  1.327
 KDB  C3   H3   single  0.930  0.020  1.080
 KDB  C4   C5   single  1.497  0.020  1.497
 KDB  C4   H4   single  0.930  0.020  1.080
 KDB  C6   C5   single  1.520  0.020  1.520
 KDB  C5   H5   single  0.970  0.020  1.090
 KDB  C5   H5A  single  0.970  0.020  1.090
 KDB  O6   C6   single  1.416  0.020  1.416
 KDB  C6   C7   single  1.530  0.020  1.530
 KDB  C6   H6   single  0.970  0.020  1.090
 KDB  C7   C8   single  1.520  0.020  1.520
 KDB  C7   O7   single  1.410  0.020  1.410
 KDB  C7   H7   single  0.970  0.020  1.090
 KDB  O7   HO7  single  0.850  0.020  0.980
 KDB  O8   C8   single  1.409  0.020  1.409
 KDB  C8   H8   single  0.970  0.020  1.090
 KDB  C8   H8A  single  0.970  0.020  1.090
 KDB  O8   HO8  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
 KDB  HO2  O2  C2   102.73  3.000
 KDB  O6   C2  C3   110.90  3.000
 KDB  O6   C2  C1   104.11  3.000
 KDB  C3   C2  C1   112.04  3.000
 KDB  O6   C2  O2   111.69  3.000
 KDB  C3   C2  O2   109.48  3.000
 KDB  C1   C2  O2   108.52  3.000
 KDB  O1A  C1  O1B  128.41  3.000
 KDB  O1A  C1  C2   113.92  3.000
 KDB  O1B  C1  C2   117.66  3.000
 KDB  H3   C3  C4   120.80  3.000
 KDB  H3   C3  C2   116.67  3.000
 KDB  C4   C3  C2   122.53  3.000
 KDB  H4   C4  C5   117.85  3.000
 KDB  H4   C4  C3   120.10  3.000
 KDB  C5   C4  C3   122.04  3.000
 KDB  H5A  C5  H5   106.20  3.000
 KDB  H5A  C5  C6   110.85  3.000
 KDB  H5   C5  C6   110.25  3.000
 KDB  H5A  C5  C4   110.37  3.000
 KDB  H5   C5  C4   109.70  3.000
 KDB  C6   C5  C4   109.42  3.000
 KDB  H6   C6  C7   108.50  3.000
 KDB  H6   C6  O6   109.92  3.000
 KDB  C7   C6  O6   107.12  3.000
 KDB  H6   C6  C5   108.39  3.000
 KDB  C7   C6  C5   113.25  3.000
 KDB  O6   C6  C5   109.64  3.000
 KDB  C6   O6  C2   115.08  3.000
 KDB  H7   C7  C8   108.88  3.000
 KDB  H7   C7  O7   105.65  3.000
 KDB  C8   C7  O7   111.91  3.000
 KDB  H7   C7  C6   108.14  3.000
 KDB  O7   C7  C6   110.83  3.000
 KDB  C8   C7  C6   111.18  3.000
 KDB  HO7  O7  C7   108.66  3.000
 KDB  H8A  C8  H8   106.89  3.000
 KDB  H8A  C8  O8   111.62  3.000
 KDB  H8   C8  O8   111.66  3.000
 KDB  H8A  C8  C7   108.70  3.000
 KDB  H8   C8  C7   109.05  3.000
 KDB  O8   C8  C7   108.85  3.000
 KDB  HO8  O8  C8   107.89  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
 KDB  Var_01  C5  C4  C3  C2   2.76  30.0  1
 KDB  Var_02  C6  C5  C4  C3  16.10  30.0  1

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
 KDB  chir_01  C2  C1  C3  O6  negativ
 KDB  chir_02  C6  O6  C7  C5  positiv
 KDB  chir_03  C7  O7  C6  C8  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
 KDB  plan-1  C2   0.020
 KDB  plan-1  C1   0.020
 KDB  plan-1  O1B  0.020
 KDB  plan-1  O1A  0.020

