# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 03:04:21 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: 2,6-anhydro-3,5-dideoxy-D-ribo-oct-2-enonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@@H]1C[C@@H](O)C=C(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
 KDD  KDD  '2,6-anhydro-3,5-dideoxy-D-ribo-oct-2-enonic 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 PERFECT
;

data_comp_KDD
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
 KDD  O1A   O  O     0  -0.431  -3.6510   1.1339   0.0943
 KDD  C1    C  C     0   0.501  -2.4573   1.2897   0.0211
 KDD  O1B   O  OH1   0  -0.584  -1.8602   2.4678   0.0243
 KDD  C2    C  C     0   0.234  -1.4880   0.1621  -0.0856
 KDD  O6    O  O2    0  -0.477  -0.2044   0.5480  -0.1724
 KDD  C6    C  CH1   0   0.003   0.7649  -0.4755   0.0549
 KDD  C7    C  CH1   0  -0.025   2.1250   0.1194  -0.3178
 KDD  C8    C  CH2   0  -0.163   2.4500   1.3337   0.5400
 KDD  O8    O  OH1   0  -0.669   3.6760   1.8732   0.1071
 KDD  O7    O  OH1   0  -0.657   3.1299  -0.8623  -0.2370
 KDD  C5    C  CH2   0  -0.491   0.3982  -1.7210  -0.7329
 KDD  C3    C  C1    0  -0.343  -1.9050  -1.1049  -0.0914
 KDD  C4    C  CH1   0   0.019  -0.9508  -2.2479  -0.2706
 KDD  HO1B  H  HOH1  0   0.489  -2.5233   3.1716   0.0917
 KDD  H6    H  HCH1  0   0.235   0.7552  -0.7155   1.1291
 KDD  H7    H  HCH1  0   0.236   2.0893   0.4251  -1.3695
 KDD  H8    H  HCH2  0   0.213   1.6377   2.0638   0.4631
 KDD  H8A   H  HCH2  0   0.191   2.4942   1.0174   1.5940
 KDD  HO8   H  HOH1  0   0.456   3.8654   2.6466   0.6451
 KDD  HO7   H  HOH1  0   0.447   3.2500  -1.1095   0.6868
 KDD  H5    H  HCH2  0   0.251   0.3491  -1.4803  -1.7986
 KDD  H5A   H  HCH2  0   0.265   1.1606  -2.4899  -0.6098
 KDD  H3    H  H     0   0.276  -2.9617  -1.3102   0.0172
 KDD  O61   O  OH1   0  -0.665  -0.7546  -2.9661   0.9343
 KDD  H4    H  HCH1  0   0.234  -1.3583  -2.9103  -1.0454
 KDD  H12   H  HOH1  0   0.453  -1.6118  -3.2594   1.2600

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
 KDD  O1A  C1    double  1.206  0.020  1.206
 KDD  C1   O1B   single  1.321  0.020  1.321
 KDD  O1B  HO1B  single  0.850  0.020  0.980
 KDD  C2   C1    single  1.491  0.020  1.491
 KDD  C2   O6    single  1.343  0.020  1.343
 KDD  C6   O6    single  1.428  0.020  1.428
 KDD  C6   C7    single  1.531  0.020  1.531
 KDD  C6   H6    single  0.970  0.020  1.090
 KDD  C7   C8    single  1.522  0.020  1.522
 KDD  C7   H7    single  0.970  0.020  1.090
 KDD  C8   O8    single  1.408  0.020  1.408
 KDD  C8   H8    single  0.970  0.020  1.090
 KDD  C8   H8A   single  0.970  0.020  1.090
 KDD  O8   HO8   single  0.850  0.020  0.980
 KDD  O7   C7    single  1.407  0.020  1.407
 KDD  O7   HO7   single  0.850  0.020  0.980
 KDD  C5   C6    single  1.519  0.020  1.519
 KDD  C5   H5    single  0.970  0.020  1.090
 KDD  C5   H5A   single  0.970  0.020  1.090
 KDD  C3   C2    double  1.334  0.020  1.334
 KDD  C3   H3    single  0.930  0.020  1.080
 KDD  C4   C5    single  1.520  0.020  1.520
 KDD  C4   C3    single  1.500  0.020  1.500
 KDD  C4   O61   single  1.416  0.020  1.416
 KDD  C4   H4    single  0.970  0.020  1.090
 KDD  O61  H12   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
 KDD  C2    C1   O1B  112.39  3.000
 KDD  C2    C1   O1A  123.38  3.000
 KDD  O1B   C1   O1A  124.23  3.000
 KDD  HO1B  O1B  C1   109.79  3.000
 KDD  C3    C2   O6   124.85  3.000
 KDD  C3    C2   C1   121.03  3.000
 KDD  O6    C2   C1   114.13  3.000
 KDD  C6    O6   C2   115.63  3.000
 KDD  H6    C6   C5   108.99  3.000
 KDD  C5    C6   C7   114.02  3.000
 KDD  H6    C6   C7   109.28  3.000
 KDD  C5    C6   O6   109.96  3.000
 KDD  H6    C6   O6   107.79  3.000
 KDD  C7    C6   O6   106.61  3.000
 KDD  H7    C7   O7   105.84  3.000
 KDD  O7    C7   C8   111.83  3.000
 KDD  H7    C7   C8   108.98  3.000
 KDD  O7    C7   C6   110.45  3.000
 KDD  H7    C7   C6   108.25  3.000
 KDD  C8    C7   C6   111.26  3.000
 KDD  H8A   C8   H8   106.77  3.000
 KDD  H8A   C8   O8   111.68  3.000
 KDD  H8    C8   O8   111.65  3.000
 KDD  H8A   C8   C7   108.59  3.000
 KDD  H8    C8   C7   109.51  3.000
 KDD  O8    C8   C7   108.57  3.000
 KDD  HO8   O8   C8   107.93  3.000
 KDD  HO7   O7   C7   108.84  3.000
 KDD  H5A   C5   H5   107.26  3.000
 KDD  H5A   C5   C4   109.99  3.000
 KDD  H5    C5   C4   109.43  3.000
 KDD  C4    C5   C6   109.92  3.000
 KDD  H5A   C5   C6   110.56  3.000
 KDD  H5    C5   C6   109.62  3.000
 KDD  H3    C3   C4   119.26  3.000
 KDD  C4    C3   C2   121.70  3.000
 KDD  H3    C3   C2   119.02  3.000
 KDD  H4    C4   O61  110.24  3.000
 KDD  H4    C4   C3   107.94  3.000
 KDD  O61   C4   C3   111.90  3.000
 KDD  H4    C4   C5   108.89  3.000
 KDD  O61   C4   C5   108.15  3.000
 KDD  C3    C4   C5   109.68  3.000
 KDD  H12   O61  C4   108.60  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
 KDD  CONST_01  HO1B  O1B  C1  C2   180.00   0.0  0
 KDD  Var_01    C4    C3   C2  O6    -3.23  30.0  1
 KDD  Var_02    C3    C2   O6  C6   -14.89  30.0  1
 KDD  Var_03    O6    C2   C1  O1A  179.24  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
 KDD  chir_01  C6  O6   C7  C5  positiv
 KDD  chir_02  C7  O7   C6  C8  negativ
 KDD  chir_03  C4  O61  C3  C5  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
 KDD  plan-1  O1A   0.020
 KDD  plan-1  C1    0.020
 KDD  plan-1  O1B   0.020
 KDD  plan-1  C2    0.020
 KDD  plan-1  HO1B  0.020

