# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 06:13:28 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@H]1O[C@](O)(C[C@@H](O)[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
 KDO  KDO  '3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid'  D-saccharide  30  16  .  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_KDO
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
 KDO  C1   C  C     0   0.486   1.5102  -0.4860  -2.1566
 KDO  O1A  O  O     0  -0.419   1.9736  -1.5382  -1.8089
 KDO  O1B  O  OH1   0  -0.582   1.7744   0.1069  -3.3075
 KDO  C2   C  CT    0   0.412   0.4835   0.3171  -1.3405
 KDO  O2   O  OH1   0  -0.656   0.6660   1.6887  -1.4801
 KDO  C3   C  CH2   0  -0.515  -0.9193  -0.0146  -1.8550
 KDO  C4   C  CH1   0   0.028  -1.9766   0.5054  -0.8853
 KDO  O4   O  OH1   0  -0.672  -3.2703   0.0815  -1.2494
 KDO  C5   C  CH1   0   0.027  -1.7035  -0.0225   0.5202
 KDO  O5   O  OH1   0  -0.674  -1.8190  -1.4217   0.5832
 KDO  C6   C  CH1   0  -0.030  -0.2869   0.3721   0.9132
 KDO  O6   O  O2    0  -0.506   0.6585  -0.1128  -0.0285
 KDO  C7   C  CH1   0  -0.013   0.1415  -0.1703   2.2825
 KDO  O7   O  OH1   0  -0.660  -0.8303   0.1256   3.2569
 KDO  C8   C  CH2   0  -0.163   1.5121   0.3618   2.6735
 KDO  O8   O  OH1   0  -0.670   1.8892  -0.2265   3.8963
 KDO  H1B  H  HOH1  0   0.489   2.3858  -0.4359  -3.8285
 KDO  HO2  H  HOH1  0   0.459   1.5378   1.9429  -1.1525
 KDO  H31  H  HCH2  0   0.269  -1.0615   0.4148  -2.8495
 KDO  H32  H  HCH2  0   0.260  -1.0207  -1.0986  -1.9473
 KDO  H4   H  HCH1  0   0.222  -1.9254   1.6012  -0.8449
 KDO  HO4  H  HOH1  0   0.457  -3.4618   0.3945  -2.1394
 KDO  H5   H  HCH1  0   0.230  -2.3977   0.4699   1.2144
 KDO  HO5  H  HOH1  0   0.451  -2.6816  -1.6673   0.2328
 KDO  H6   H  HCH1  0   0.231  -0.2559   1.4713   0.9526
 KDO  H7   H  HCH1  0   0.239   0.1910  -1.2617   2.2280
 KDO  HO7  H  HOH1  0   0.445  -0.8329   1.0760   3.4160
 KDO  H81  H  HCH2  0   0.189   1.4589   1.4591   2.7519
 KDO  H82  H  HCH2  0   0.212   2.2298   0.1353   1.8784
 KDO  HO8  H  HOH1  0   0.455   2.7787   0.0705   4.1068

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
 KDO  C1   O1A  double  1.201  0.020  1.201
 KDO  C1   O1B  single  1.321  0.020  1.321
 KDO  C1   C2   single  1.538  0.020  1.538
 KDO  O1B  H1B  single  0.850  0.020  0.980
 KDO  C2   O2   single  1.391  0.020  1.391
 KDO  C2   C3   single  1.531  0.020  1.531
 KDO  C2   O6   single  1.392  0.020  1.392
 KDO  O2   HO2  single  0.850  0.020  0.980
 KDO  C3   C4   single  1.526  0.020  1.526
 KDO  C3   H31  single  0.970  0.020  1.090
 KDO  C3   H32  single  0.970  0.020  1.090
 KDO  C4   O4   single  1.409  0.020  1.409
 KDO  C4   C5   single  1.526  0.020  1.526
 KDO  C4   H4   single  0.970  0.020  1.090
 KDO  O4   HO4  single  0.850  0.020  0.980
 KDO  C5   O5   single  1.405  0.020  1.405
 KDO  C5   C6   single  1.522  0.020  1.522
 KDO  C5   H5   single  0.970  0.020  1.090
 KDO  O5   HO5  single  0.850  0.020  0.980
 KDO  C6   O6   single  1.420  0.020  1.420
 KDO  C6   C7   single  1.534  0.020  1.534
 KDO  C6   H6   single  0.970  0.020  1.090
 KDO  C7   O7   single  1.408  0.020  1.408
 KDO  C7   C8   single  1.521  0.020  1.521
 KDO  C7   H7   single  0.970  0.020  1.090
 KDO  O7   HO7  single  0.850  0.020  0.980
 KDO  C8   O8   single  1.408  0.020  1.408
 KDO  C8   H81  single  0.970  0.020  1.090
 KDO  C8   H82  single  0.970  0.020  1.090
 KDO  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
 KDO  C2   C1   O1B  111.18  3.000
 KDO  C2   C1   O1A  124.15  3.000
 KDO  O1B  C1   O1A  124.62  3.000
 KDO  H1B  O1B  C1   110.06  3.000
 KDO  O6   C2   C3   111.42  3.000
 KDO  O6   C2   O2   112.51  3.000
 KDO  C3   C2   O2   107.48  3.000
 KDO  O6   C2   C1   104.77  3.000
 KDO  C3   C2   C1   108.68  3.000
 KDO  O2   C2   C1   111.97  3.000
 KDO  HO2  O2   C2   110.13  3.000
 KDO  H32  C3   H31  107.52  3.000
 KDO  H32  C3   C4   109.11  3.000
 KDO  H31  C3   C4   110.75  3.000
 KDO  H32  C3   C2   109.18  3.000
 KDO  H31  C3   C2   109.88  3.000
 KDO  C4   C3   C2   110.34  3.000
 KDO  H4   C4   C5   107.64  3.000
 KDO  H4   C4   O4   110.65  3.000
 KDO  C5   C4   O4   107.35  3.000
 KDO  H4   C4   C3   109.34  3.000
 KDO  C5   C4   C3   110.08  3.000
 KDO  O4   C4   C3   111.68  3.000
 KDO  HO4  O4   C4   108.89  3.000
 KDO  H5   C5   C6   107.99  3.000
 KDO  H5   C5   O5   111.47  3.000
 KDO  C6   C5   O5   108.84  3.000
 KDO  H5   C5   C4   108.30  3.000
 KDO  C6   C5   C4   108.34  3.000
 KDO  O5   C5   C4   111.77  3.000
 KDO  HO5  O5   C5   108.14  3.000
 KDO  H6   C6   C7   108.27  3.000
 KDO  H6   C6   O6   110.26  3.000
 KDO  C7   C6   O6   106.58  3.000
 KDO  H6   C6   C5   107.12  3.000
 KDO  C7   C6   C5   113.50  3.000
 KDO  O6   C6   C5   111.09  3.000
 KDO  C6   O6   C2   115.85  3.000
 KDO  H7   C7   C8   108.72  3.000
 KDO  H7   C7   O7   105.99  3.000
 KDO  C8   C7   O7   111.75  3.000
 KDO  H7   C7   C6   108.72  3.000
 KDO  C8   C7   C6   110.94  3.000
 KDO  O7   C7   C6   110.53  3.000
 KDO  HO7  O7   C7   108.87  3.000
 KDO  H82  C8   H81  106.82  3.000
 KDO  H82  C8   O8   111.63  3.000
 KDO  H81  C8   O8   111.55  3.000
 KDO  H82  C8   C7   109.36  3.000
 KDO  H81  C8   C7   108.86  3.000
 KDO  O8   C8   C7   108.56  3.000
 KDO  HO8  O8   C8   107.99  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
 KDO  CONST_01  H1B  O1B  C1  C2  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
 KDO  chir_01  C2  O2  C3  O6  positiv
 KDO  chir_02  C4  O4  C5  C3  negativ
 KDO  chir_03  C5  O5  C4  C6  positiv
 KDO  chir_04  C6  O6  C7  C5  positiv
 KDO  chir_05  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
 KDO  plan-1  C1   0.020
 KDO  plan-1  O1A  0.020
 KDO  plan-1  O1B  0.020
 KDO  plan-1  C2   0.020
 KDO  plan-1  H1B  0.020

