# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 03:57:41 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  29  16  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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   0.349   1.5793  -0.4634  -2.1856
 KDO  O1A  O  O      0  -0.587   2.1155  -1.4670  -1.6921
 KDO  O1B  O  OC    -1  -0.607   1.7624   0.0207  -3.3175
 KDO  C2   C  CT     0   0.380   0.5122   0.2834  -1.3309
 KDO  O2   O  OH1    0  -0.681   0.6621   1.6748  -1.4201
 KDO  C3   C  CH2    0  -0.510  -0.8864  -0.0457  -1.8528
 KDO  C4   C  CH1    0   0.028  -1.9648   0.4789  -0.9142
 KDO  O4   O  OH1    0  -0.679  -3.2583   0.0515  -1.2935
 KDO  C5   C  CH1    0   0.030  -1.7222  -0.0260   0.5050
 KDO  O5   O  OH1    0  -0.679  -1.8656  -1.4233   0.5893
 KDO  C6   C  CH1    0  -0.012  -0.3037   0.3534   0.9117
 KDO  O6   O  O2     0  -0.506   0.6457  -0.1509  -0.0022
 KDO  C7   C  CH1    0  -0.016   0.0880  -0.1711   2.2989
 KDO  O7   O  OH1    0  -0.664  -0.8709   0.2043   3.2616
 KDO  C8   C  CH2    0  -0.162   1.4835   0.2962   2.6828
 KDO  O8   O  OH1    0  -0.672   1.8144  -0.2518   3.9388
 KDO  HO2  H  HOH1   0   0.444   1.5836   1.9056  -1.2602
 KDO  H31  H  HCH2   0   0.245  -1.0108   0.3710  -2.8553
 KDO  H32  H  HCH2   0   0.238  -0.9825  -1.1314  -1.9396
 KDO  H4   H  HCH1   0   0.209  -1.9199   1.5760  -0.8874
 KDO  HO4  H  HOH1   0   0.454  -3.3738   0.2158  -2.2349
 KDO  H5   H  HCH1   0   0.217  -2.4219   0.4858   1.1807
 KDO  HO5  H  HOH1   0   0.447  -2.6940  -1.6605   0.1591
 KDO  H6   H  HCH1   0   0.210  -0.2665   1.4540   0.9445
 KDO  H7   H  HCH1   0   0.232   0.0796  -1.2650   2.2804
 KDO  HO7  H  HOH1   0   0.442  -0.8427   1.1615   3.3685
 KDO  H81  H  HCH2   0   0.183   1.4989   1.3975   2.7073
 KDO  H82  H  HCH2   0   0.213   2.1913  -0.0144   1.9083
 KDO  HO8  H  HOH1   0   0.454   2.7308  -0.0304   4.1250

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  deloc   1.240  0.020  1.240
 KDO  C1  O1B  deloc   1.245  0.020  1.245
 KDO  C1  C2   single  1.558  0.020  1.558
 KDO  C2  O2   single  1.402  0.020  1.402
 KDO  C2  C3   single  1.529  0.020  1.529
 KDO  C2  O6   single  1.404  0.020  1.404
 KDO  O2  HO2  single  0.850  0.020  0.980
 KDO  C3  C4   single  1.523  0.020  1.523
 KDO  C3  H31  single  0.970  0.020  1.090
 KDO  C3  H32  single  0.970  0.020  1.090
 KDO  C4  O4   single  1.414  0.020  1.414
 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  1.407  0.020  1.407
 KDO  C5  C6   single  1.524  0.020  1.524
 KDO  C5  H5   single  0.970  0.020  1.090
 KDO  O5  HO5  single  0.850  0.020  0.980
 KDO  C6  O6   single  1.411  0.020  1.411
 KDO  C6  C7   single  1.534  0.020  1.534
 KDO  C6  H6   single  0.970  0.020  1.090
 KDO  C7  O7   single  1.410  0.020  1.410
 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  1.410  0.020  1.410
 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  114.41  3.000
 KDO  C2   C1  O1A  117.76  3.000
 KDO  O1B  C1  O1A  127.80  3.000
 KDO  O6   C2  C3   110.09  3.000
 KDO  O6   C2  O2   110.91  3.000
 KDO  C3   C2  O2   106.84  3.000
 KDO  O6   C2  C1   107.80  3.000
 KDO  C3   C2  C1   109.64  3.000
 KDO  O2   C2  C1   111.56  3.000
 KDO  HO2  O2  C2   109.23  3.000
 KDO  H32  C3  H31  107.21  3.000
 KDO  H32  C3  C4   109.19  3.000
 KDO  H31  C3  C4   110.70  3.000
 KDO  H32  C3  C2   108.74  3.000
 KDO  H31  C3  C2   109.59  3.000
 KDO  C4   C3  C2   111.30  3.000
 KDO  H4   C4  C5   107.54  3.000
 KDO  H4   C4  O4   110.23  3.000
 KDO  C5   C4  O4   107.15  3.000
 KDO  H4   C4  C3   109.28  3.000
 KDO  C5   C4  C3   110.29  3.000
 KDO  O4   C4  C3   112.23  3.000
 KDO  HO4  O4  C4   108.69  3.000
 KDO  H5   C5  C6   108.22  3.000
 KDO  H5   C5  O5   111.14  3.000
 KDO  C6   C5  O5   109.03  3.000
 KDO  H5   C5  C4   108.45  3.000
 KDO  C6   C5  C4   108.29  3.000
 KDO  O5   C5  C4   111.60  3.000
 KDO  HO5  O5  C5   107.79  3.000
 KDO  H6   C6  C7   107.82  3.000
 KDO  H6   C6  O6   110.71  3.000
 KDO  C7   C6  O6   106.96  3.000
 KDO  H6   C6  C5   106.74  3.000
 KDO  C7   C6  C5   113.20  3.000
 KDO  O6   C6  C5   111.38  3.000
 KDO  C6   O6  C2   116.00  3.000
 KDO  H7   C7  C8   108.57  3.000
 KDO  H7   C7  O7   105.82  3.000
 KDO  C8   C7  O7   111.71  3.000
 KDO  H7   C7  C6   108.94  3.000
 KDO  C8   C7  C6   110.95  3.000
 KDO  O7   C7  C6   110.67  3.000
 KDO  HO7  O7  C7   108.69  3.000
 KDO  H82  C8  H81  106.89  3.000
 KDO  H82  C8  O8   111.62  3.000
 KDO  H81  C8  O8   111.44  3.000
 KDO  H82  C8  C7   109.13  3.000
 KDO  H81  C8  C7   109.00  3.000
 KDO  O8   C8  C7   108.71  3.000
 KDO  HO8  O8  C8   107.87  3.000

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

