# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 03:39:04 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: 3-deoxy-alpha-D-erythro-hex-2-ulofuranosonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@](O)(C[C@@H]1O)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
 KDF  KDF  '3-deoxy-alpha-D-erythro-hex-2-ulofuranosonic acid'  D-saccharide  22  12  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KDF
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
 KDF  O1B   O  OH1   0  -0.671   2.7601   1.9926   0.1410
 KDF  C1    C  CH2   0  -0.159   2.3361   0.8683  -0.5917
 KDF  C2    C  CH1   0   0.006   1.3982   0.0473   0.2564
 KDF  O2    O  O2    0  -0.515   0.2005   0.7719   0.4948
 KDF  C3    C  CH1   0   0.033   0.9426  -1.2442  -0.4165
 KDF  O3    O  OH1   0  -0.664   1.9093  -2.2424  -0.2334
 KDF  C4    C  CH2   0  -0.580  -0.3873  -1.4998   0.2880
 KDF  O5    O  OH1   0  -0.652  -1.4264  -0.0905   1.8997
 KDF  C6    C  C     0   0.504  -1.9481   0.4372  -0.3650
 KDF  O6A   O  OH1   0  -0.577  -1.5689   0.2769  -1.6170
 KDF  C5    C  CT    0   0.433  -0.9048  -0.0996   0.6255
 KDF  O6B   O  O     0  -0.434  -2.9744   0.9649  -0.0216
 KDF  H1B   H  HOH1  0   0.457   3.3847   2.4843  -0.3995
 KDF  H1C1  H  HCH2  0   0.198   1.8188   1.1505  -1.5188
 KDF  H1C2  H  HCH2  0   0.207   3.1797   0.2260  -0.8753
 KDF  H2    H  HCH1  0   0.228   1.8864  -0.2045   1.2097
 KDF  H3    H  HCH1  0   0.225   0.7711  -1.0582  -1.4847
 KDF  HA    H  HOH1  0   0.460   1.6951  -2.9821  -0.8093
 KDF  H4C1  H  HCH2  0   0.279  -1.0897  -2.0914  -0.2987
 KDF  H4C2  H  HCH2  0   0.273  -0.1976  -2.0324   1.2230
 KDF  H5    H  HOH1  0   0.456  -1.9876   0.6868   2.0195
 KDF  H6A   H  HOH1  0   0.492  -2.2330   0.6374  -2.2248

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
 KDF  O1B  C1    single  1.407  0.020  1.407
 KDF  C1   C2    single  1.508  0.020  1.508
 KDF  C2   O2    single  1.420  0.020  1.420
 KDF  C2   C3    single  1.526  0.020  1.526
 KDF  O2   C5    single  1.414  0.020  1.414
 KDF  C3   O3    single  1.402  0.020  1.402
 KDF  C3   C4    single  1.526  0.020  1.526
 KDF  C4   C5    single  1.530  0.020  1.530
 KDF  O5   C5    single  1.377  0.020  1.377
 KDF  C6   O6B   double  1.204  0.020  1.204
 KDF  C6   O6A   single  1.318  0.020  1.318
 KDF  C6   C5    single  1.535  0.020  1.535
 KDF  O1B  H1B   single  0.850  0.020  0.980
 KDF  C1   H1C1  single  0.970  0.020  1.090
 KDF  C1   H1C2  single  0.970  0.020  1.090
 KDF  C2   H2    single  0.970  0.020  1.090
 KDF  C3   H3    single  0.970  0.020  1.090
 KDF  O3   HA    single  0.850  0.020  0.980
 KDF  C4   H4C1  single  0.970  0.020  1.090
 KDF  C4   H4C2  single  0.970  0.020  1.090
 KDF  O5   H5    single  0.850  0.020  0.980
 KDF  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
 KDF  H1B   O1B  C1    108.16  3.000
 KDF  H1C2  C1   H1C1  107.11  3.000
 KDF  H1C2  C1   C2    107.75  3.000
 KDF  H1C1  C1   C2    108.76  3.000
 KDF  H1C2  C1   O1B   111.75  3.000
 KDF  H1C1  C1   O1B   112.09  3.000
 KDF  C2    C1   O1B   109.25  3.000
 KDF  H2    C2   C3    108.72  3.000
 KDF  H2    C2   O2    110.22  3.000
 KDF  C3    C2   O2    104.72  3.000
 KDF  H2    C2   C1    109.63  3.000
 KDF  C3    C2   C1    113.49  3.000
 KDF  O2    C2   C1    109.95  3.000
 KDF  C5    O2   C2    111.12  3.000
 KDF  H3    C3   C4    109.96  3.000
 KDF  H3    C3   O3    110.82  3.000
 KDF  C4    C3   O3    114.92  3.000
 KDF  H3    C3   C2    109.42  3.000
 KDF  C4    C3   C2    101.44  3.000
 KDF  O3    C3   C2    109.83  3.000
 KDF  HA    O3   C3    108.42  3.000
 KDF  H4C2  C4   H4C1  107.94  3.000
 KDF  H4C2  C4   C5    108.41  3.000
 KDF  H4C1  C4   C5    113.42  3.000
 KDF  H4C2  C4   C3    108.99  3.000
 KDF  H4C1  C4   C3    113.83  3.000
 KDF  C5    C4   C3    104.07  3.000
 KDF  H5    O5   C5    109.89  3.000
 KDF  O6B   C6   C5    123.26  3.000
 KDF  C5    C6   O6A   112.01  3.000
 KDF  O6B   C6   O6A   124.71  3.000
 KDF  H6A   O6A  C6    110.68  3.000
 KDF  C6    C5   O5    109.71  3.000
 KDF  C6    C5   C4    114.04  3.000
 KDF  O5    C5   C4    109.77  3.000
 KDF  C6    C5   O2    104.84  3.000
 KDF  O5    C5   O2    112.19  3.000
 KDF  C4    C5   O2    106.21  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
 KDF  CONST_01  H6A  O6A  C6  C5  180.00  0.0  0

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
 KDF  chir_01  C2  C1  O2  C3  negativ
 KDF  chir_02  C3  O3  C2  C4  positiv
 KDF  chir_03  C5  O2  C4  C6  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
 KDF  plan-1  C6   0.020
 KDF  plan-1  O6A  0.020
 KDF  plan-1  C5   0.020
 KDF  plan-1  O6B  0.020
 KDF  plan-1  H6A  0.020

