# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 02:02:34 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: 3-deoxy-D-erythro-hex-2-ulosonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@@H](O)CC(=O)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
 KDG  KDG  '3-deoxy-D-erythro-hex-2-ulosonic acid'  ligand  21  12  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KDG
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
 KDG  O1B   O  OH1    0  -0.671  -0.3372  -0.1832   4.4632
 KDG  C1    C  CH2    0  -0.155   0.4493   0.0901   3.3263
 KDG  C2    C  CH1    0  -0.021  -0.3964  -0.1225   2.0804
 KDG  O2    O  OH1    0  -0.660  -1.5557   0.6811   2.0981
 KDG  C3    C  CH1    0   0.007   0.4233   0.1188   0.8014
 KDG  O3    O  OH1    0  -0.665   1.5959  -0.6689   0.7838
 KDG  C4    C  CH2    0  -0.576  -0.4093  -0.1141  -0.4490
 KDG  O5    O  O      0  -0.398   1.1979   1.0961  -1.7273
 KDG  C5    C  C      0   0.244   0.2630   0.3297  -1.7238
 KDG  C6    C  C      0   0.346  -0.3339  -0.1932  -3.0609
 KDG  O6A   O  OC    -1  -0.583   0.3616  -0.0101  -4.0692
 KDG  O6B   O  O      0  -0.579  -1.4520  -0.7285  -2.9702
 KDG  H1B   H  HOH1   0   0.454   0.2239  -0.0935   5.2384
 KDG  H1C1  H  HCH2   0   0.186   0.8200   1.1275   3.3313
 KDG  H1C2  H  HCH2   0   0.205   1.3293  -0.5594   3.2810
 KDG  H2    H  HCH1   0   0.223  -0.7587  -1.1585   2.0745
 KDG  HA    H  HOH1   0   0.444  -1.2858   1.6050   2.1494
 KDG  H3    H  HCH1   0   0.225   0.7718   1.1575   0.8165
 KDG  HB    H  HOH1   0   0.443   1.3369  -1.5953   0.7265
 KDG  H4C1  H  HCH2   0   0.255  -0.6918  -1.1685  -0.5300
 KDG  H4C2  H  HCH2   0   0.276  -1.3598   0.4248  -0.3840

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
 KDG  O1B  C1    single  1.409  0.020  1.409
 KDG  O1B  H1B   single  0.850  0.020  0.980
 KDG  C1   C2    single  1.521  0.020  1.521
 KDG  C1   H1C1  single  0.970  0.020  1.090
 KDG  C1   H1C2  single  0.970  0.020  1.090
 KDG  C2   O2    single  1.411  0.020  1.411
 KDG  C2   C3    single  1.538  0.020  1.538
 KDG  C2   H2    single  0.970  0.020  1.090
 KDG  O2   HA    single  0.850  0.020  0.980
 KDG  C3   O3    single  1.413  0.020  1.413
 KDG  C3   C4    single  1.520  0.020  1.520
 KDG  C3   H3    single  0.970  0.020  1.090
 KDG  O3   HB    single  0.850  0.020  0.980
 KDG  C4   C5    single  1.508  0.020  1.508
 KDG  C4   H4C1  single  0.970  0.020  1.090
 KDG  C4   H4C2  single  0.970  0.020  1.090
 KDG  O5   C5    double  1.209  0.020  1.209
 KDG  C5   C6    single  1.555  0.020  1.555
 KDG  C6   O6A   deloc   1.238  0.020  1.238
 KDG  C6   O6B   deloc   1.243  0.020  1.243

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
 KDG  H1B   O1B  C1    107.86  3.000
 KDG  H1C2  C1   H1C1  106.76  3.000
 KDG  H1C2  C1   C2    109.28  3.000
 KDG  H1C1  C1   C2    108.81  3.000
 KDG  H1C2  C1   O1B   111.54  3.000
 KDG  H1C1  C1   O1B   111.52  3.000
 KDG  C2    C1   O1B   108.87  3.000
 KDG  H2    C2   C3    108.64  3.000
 KDG  H2    C2   O2    105.46  3.000
 KDG  C3    C2   O2    111.04  3.000
 KDG  H2    C2   C1    108.66  3.000
 KDG  C3    C2   C1    111.28  3.000
 KDG  O2    C2   C1    111.54  3.000
 KDG  HA    O2   C2    108.46  3.000
 KDG  H3    C3   C4    109.31  3.000
 KDG  H3    C3   O3    105.35  3.000
 KDG  C4    C3   O3    111.03  3.000
 KDG  H3    C3   C2    107.87  3.000
 KDG  C4    C3   C2    111.59  3.000
 KDG  O3    C3   C2    111.42  3.000
 KDG  HB    O3   C3    108.28  3.000
 KDG  H4C2  C4   H4C1  104.75  3.000
 KDG  H4C2  C4   C5    107.00  3.000
 KDG  H4C1  C4   C5    109.63  3.000
 KDG  H4C2  C4   C3    110.57  3.000
 KDG  H4C1  C4   C3    110.47  3.000
 KDG  C5    C4   C3    113.96  3.000
 KDG  C6    C5   O5    120.51  3.000
 KDG  C6    C5   C4    117.18  3.000
 KDG  O5    C5   C4    122.26  3.000
 KDG  O6B   C6   O6A   128.92  3.000
 KDG  O6B   C6   C5    115.30  3.000
 KDG  O6A   C6   C5    115.77  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
 KDG  Var_01  O5   C5  C4  C3   -17.97  30.0  3
 KDG  Var_02  O6A  C6  C5  C4  -167.97  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
 KDG  chir_01  C2  C1  O2  C3  negativ
 KDG  chir_02  C3  O3  C2  C4  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
 KDG  plan-1  C4   0.020
 KDG  plan-1  O5   0.020
 KDG  plan-1  C5   0.020
 KDG  plan-1  C6   0.020
 KDG  plan-2  C5   0.020
 KDG  plan-2  C6   0.020
 KDG  plan-2  O6A  0.020
 KDG  plan-2  O6B  0.020

