# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 03:42:08 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  26  14  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

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  -0.657   1.6006   0.4013  -1.6340
 KDB  C2    C  CT    0   0.408   1.4237  -0.0111  -0.3142
 KDB  C1    C  C     0   0.499   2.3821   0.8316   0.5444
 KDB  O1B   O  O     0  -0.418   2.0757   1.3559   1.5798
 KDB  O1A   O  OH1   0  -0.582   3.5922   0.8618   0.0163
 KDB  C3    C  C1    0  -0.324   1.7771  -1.4636  -0.1301
 KDB  C4    C  C1    0  -0.185   0.8772  -2.3478   0.2846
 KDB  C5    C  CH2   0  -0.486  -0.5508  -1.9835   0.5296
 KDB  C6    C  CH1   0  -0.003  -0.8586  -0.6603  -0.1490
 KDB  O6    O  O2    0  -0.511   0.1557   0.2826   0.1681
 KDB  C7    C  CH1   0  -0.025  -2.1882  -0.0453   0.2929
 KDB  O7    O  OH1   0  -0.658  -3.2210  -0.9994   0.2222
 KDB  C8    C  CH2   0  -0.162  -2.5112   1.2058  -0.5088
 KDB  O8    O  OH1   0  -0.670  -3.6853   1.7834   0.0107
 KDB  HO2   H  HOH1  0   0.464   1.3527  -0.3141  -2.2313
 KDB  HO1A  H  HOH1  0   0.489   4.1947   1.3549   0.5940
 KDB  H3    H  H     0   0.280   2.7963  -1.7579  -0.3498
 KDB  H4    H  H     0   0.266   1.1703  -3.3810   0.4300
 KDB  H5    H  HCH2  0   0.260  -1.1976  -2.7691   0.1370
 KDB  H5A   H  HCH2  0   0.258  -0.7474  -1.9308   1.6067
 KDB  H6    H  HCH1  0   0.220  -0.8920  -0.8260  -1.2377
 KDB  H7    H  HCH1  0   0.236  -2.1018   0.2225   1.3523
 KDB  HO7   H  HOH1  0   0.446  -3.3901  -1.2075  -0.7035
 KDB  H8    H  HCH2  0   0.210  -1.6628   1.8961  -0.4568
 KDB  H8A   H  HCH2  0   0.191  -2.6295   0.9264  -1.5675
 KDB  HO8   H  HOH1  0   0.456  -3.8800   2.5726  -0.5019

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  1.394  0.020  1.394
 KDB  O2   HO2   single  0.850  0.020  0.980
 KDB  C2   C1    single  1.538  0.020  1.538
 KDB  C2   C3    single  1.506  0.020  1.506
 KDB  C2   O6    single  1.388  0.020  1.388
 KDB  O1B  C1    double  1.200  0.020  1.200
 KDB  C1   O1A   single  1.321  0.020  1.321
 KDB  O1A  HO1A  single  0.850  0.020  0.980
 KDB  C3   C4    double  1.328  0.020  1.328
 KDB  C3   H3    single  0.930  0.020  1.080
 KDB  C4   C5    single  1.494  0.020  1.494
 KDB  C4   H4    single  0.930  0.020  1.080
 KDB  C6   C5    single  1.519  0.020  1.519
 KDB  C5   H5    single  0.970  0.020  1.090
 KDB  C5   H5A   single  0.970  0.020  1.090
 KDB  O6   C6    single  1.421  0.020  1.421
 KDB  C6   C7    single  1.530  0.020  1.530
 KDB  C6   H6    single  0.970  0.020  1.090
 KDB  C7   C8    single  1.521  0.020  1.521
 KDB  C7   O7    single  1.408  0.020  1.408
 KDB  C7   H7    single  0.970  0.020  1.090
 KDB  O7   HO7   single  0.850  0.020  0.980
 KDB  O8   C8    single  1.408  0.020  1.408
 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   109.53  3.000
 KDB  O6    C2   C3   112.08  3.000
 KDB  O6    C2   C1   105.03  3.000
 KDB  C3    C2   C1   108.30  3.000
 KDB  O6    C2   O2   112.48  3.000
 KDB  C3    C2   O2   111.79  3.000
 KDB  C1    C2   O2   106.70  3.000
 KDB  O1A   C1   O1B  124.67  3.000
 KDB  O1A   C1   C2   111.12  3.000
 KDB  O1B   C1   C2   124.18  3.000
 KDB  HO1A  O1A  C1   110.05  3.000
 KDB  H3    C3   C4   121.32  3.000
 KDB  H3    C3   C2   117.26  3.000
 KDB  C4    C3   C2   121.42  3.000
 KDB  H4    C4   C5   117.97  3.000
 KDB  H4    C4   C3   119.56  3.000
 KDB  C5    C4   C3   122.45  3.000
 KDB  H5A   C5   H5   106.38  3.000
 KDB  H5A   C5   C6   111.15  3.000
 KDB  H5    C5   C6   110.28  3.000
 KDB  H5A   C5   C4   110.14  3.000
 KDB  H5    C5   C4   109.40  3.000
 KDB  C6    C5   C4   109.45  3.000
 KDB  H6    C6   C7   108.63  3.000
 KDB  H6    C6   O6   110.00  3.000
 KDB  C7    C6   O6   106.81  3.000
 KDB  H6    C6   C5   108.46  3.000
 KDB  C7    C6   C5   113.41  3.000
 KDB  O6    C6   C5   109.50  3.000
 KDB  C6    O6   C2   115.73  3.000
 KDB  H7    C7   C8   108.98  3.000
 KDB  H7    C7   O7   105.78  3.000
 KDB  C8    C7   O7   112.04  3.000
 KDB  H7    C7   C6   107.99  3.000
 KDB  O7    C7   C6   110.53  3.000
 KDB  C8    C7   C6   111.28  3.000
 KDB  HO7   O7   C7   108.86  3.000
 KDB  H8A   C8   H8   106.79  3.000
 KDB  H8A   C8   O8   111.67  3.000
 KDB  H8    C8   O8   111.72  3.000
 KDB  H8A   C8   C7   108.71  3.000
 KDB  H8    C8   C7   109.21  3.000
 KDB  O8    C8   C7   108.67  3.000
 KDB  HO8   O8   C8   108.00  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  CONST_01  HO1A  O1A  C1  C2  180.00   0.0  0
 KDB  Var_01    C5    C4   C3  C2    3.12  30.0  1
 KDB  Var_02    C6    C5   C4  C3   16.99  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
 KDB  plan-1  HO1A  0.020

