# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 03:44:46 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  22  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  -0.670  -0.2999  -0.1531   4.4535
 KDG  C1    C  CH2   0  -0.158   0.4776   0.1242   3.3125
 KDG  C2    C  CH1   0  -0.022  -0.3685  -0.1190   2.0727
 KDG  O2    O  OH1   0  -0.658  -1.5375   0.6680   2.0748
 KDG  C3    C  CH1   0   0.004   0.4507   0.1094   0.7906
 KDG  O3    O  OH1   0  -0.659   1.6066  -0.6967   0.7602
 KDG  C4    C  CH2   0  -0.589  -0.4026  -0.1101  -0.4503
 KDG  O5    O  O     0  -0.344   1.2842   0.9461  -1.7922
 KDG  C5    C  C     0   0.298   0.2805   0.2898  -1.7203
 KDG  C6    C  C     0   0.483  -0.4160  -0.1656  -3.0150
 KDG  O6A   O  OH1   0  -0.570   0.1586   0.3483  -4.0794
 KDG  O6B   O  O     0  -0.404  -1.3674  -0.8998  -3.0161
 KDG  H1B   H  HOH1  0   0.455   0.2586  -0.0353   5.2266
 KDG  H1C1  H  HCH2  0   0.190   0.8269   1.1688   3.3048
 KDG  H1C2  H  HCH2  0   0.207   1.3705  -0.5078   3.2697
 KDG  H2    H  HCH1  0   0.229  -0.7158  -1.1600   2.0825
 KDG  HA    H  HOH1  0   0.446  -1.2852   1.5949   2.1522
 KDG  H3    H  HCH1  0   0.238   0.8142   1.1428   0.7989
 KDG  HB    H  HOH1  0   0.446   1.3362  -1.6218   0.7571
 KDG  H4C1  H  HCH2  0   0.283  -0.7289  -1.1528  -0.5189
 KDG  H4C2  H  HCH2  0   0.302  -1.3287   0.4723  -0.3937
 KDG  H6A   H  HOH1  0   0.493  -0.2955   0.0525  -4.8834

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  1.408  0.020  1.408
 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  1.409  0.020  1.409
 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  1.410  0.020  1.410
 KDG  C3   C4    single  1.522  0.020  1.522
 KDG  C3   H3    single  0.970  0.020  1.090
 KDG  O3   HB    single  0.850  0.020  0.980
 KDG  C4   C5    single  1.496  0.020  1.496
 KDG  C4   H4C1  single  0.970  0.020  1.090
 KDG  C4   H4C2  single  0.970  0.020  1.090
 KDG  O5   C5    double  1.201  0.020  1.201
 KDG  C5   C6    single  1.539  0.020  1.539
 KDG  C6   O6A   single  1.314  0.020  1.314
 KDG  C6   O6B   double  1.202  0.020  1.202
 KDG  O6A  H6A   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
 KDG  H1B   O1B  C1    107.87  3.000
 KDG  H1C2  C1   H1C1  106.77  3.000
 KDG  H1C2  C1   C2    109.24  3.000
 KDG  H1C1  C1   C2    108.81  3.000
 KDG  H1C2  C1   O1B   111.61  3.000
 KDG  H1C1  C1   O1B   111.56  3.000
 KDG  C2    C1   O1B   108.78  3.000
 KDG  H2    C2   C3    108.47  3.000
 KDG  H2    C2   O2    105.49  3.000
 KDG  C3    C2   O2    111.10  3.000
 KDG  H2    C2   C1    108.70  3.000
 KDG  C3    C2   C1    111.07  3.000
 KDG  O2    C2   C1    111.78  3.000
 KDG  HA    O2   C2    108.66  3.000
 KDG  H3    C3   C4    109.16  3.000
 KDG  H3    C3   O3    105.52  3.000
 KDG  C4    C3   O3    111.08  3.000
 KDG  H3    C3   C2    108.08  3.000
 KDG  C4    C3   C2    111.07  3.000
 KDG  O3    C3   C2    111.70  3.000
 KDG  HB    O3   C3    108.59  3.000
 KDG  H4C2  C4   H4C1  104.93  3.000
 KDG  H4C2  C4   C5    106.72  3.000
 KDG  H4C1  C4   C5    109.72  3.000
 KDG  H4C2  C4   C3    110.80  3.000
 KDG  H4C1  C4   C3    110.83  3.000
 KDG  C5    C4   C3    113.42  3.000
 KDG  C6    C5   O5    119.30  3.000
 KDG  C6    C5   C4    115.35  3.000
 KDG  O5    C5   C4    125.33  3.000
 KDG  O6B   C6   O6A   125.75  3.000
 KDG  O6B   C6   C5    122.67  3.000
 KDG  O6A   C6   C5    111.57  3.000
 KDG  H6A   O6A  C6    110.33  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  CONST_01  H6A  O6A  C6  C5  180.00   0.0  0
 KDG  Var_01    O5   C5   C4  C3  -13.44  30.0  3
 KDG  Var_02    O6A  C6   C5  C4  172.91  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
 KDG  plan-2  H6A  0.020

