# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 02:16:15 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: 4,7-anhydro-3-deoxy-D-manno-oct-2-ulosonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](CC(=O)C(O)=O)[C@@H](O)[C@@H]1O
#
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
 KD5  KD5  '4,7-anhydro-3-deoxy-D-manno-oct-2-ulosonic acid'  D-saccharide  26  15  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KD5
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
 KD5  O5   O  OH1    0  -0.664   1.4161  -2.6284  -0.4486
 KD5  C4   C  CR15   0   0.059   0.2655  -0.5265  -0.3207
 KD5  C5   C  CR15   0   0.003   1.3520  -1.4228   0.2601
 KD5  C6   C  CR15   0  -0.033   2.5734  -0.5270   0.1488
 KD5  O6   O  OH1    0  -0.664   3.5971  -0.9587   1.0040
 KD5  C7   C  CR15   0   0.005   1.9768   0.8387   0.5011
 KD5  O7   O  O      0  -0.505   0.6213   0.7918   0.0738
 KD5  C8   C  CH2    0  -0.157   2.7076   1.9863  -0.1534
 KD5  H1   H  HOH1   0   0.458   2.0288  -3.2163   0.0035
 KD5  H2   H  HCR5   0   0.216   0.3027  -0.6109  -1.4162
 KD5  H4   H  HCR5   0   0.215   1.1501  -1.5973   1.3292
 KD5  H5   H  HCR5   0   0.220   2.9063  -0.5252  -0.9004
 KD5  H6   H  HOH1   0   0.458   4.4183  -0.5257   0.7538
 KD5  H7   H  HCR5   0   0.220   2.0122   0.9666   1.5931
 KD5  H8   H  HOH1   0   0.456   2.6588   3.9206  -0.1099
 KD5  H9   H  HCH2   0   0.195   3.7750   1.8957   0.0938
 KD5  H10  H  HCH2   0   0.198   2.6248   1.8860  -1.2443
 KD5  C3   C  CH2    0  -0.581  -1.1220  -0.8694   0.1709
 KD5  C2   C  C      0   0.238  -2.2299  -0.0785  -0.4757
 KD5  C1   C  C      0   0.349  -3.6596  -0.2558   0.1130
 KD5  O2   O  O      0  -0.394  -2.0361   0.6435  -1.4250
 KD5  OH   O  OC    -1  -0.582  -4.5197   0.5231  -0.3188
 KD5  O1   O  O      0  -0.577  -3.7789  -1.1676   0.9493
 KD5  H3   H  HCH2   0   0.276  -1.3184  -1.9308  -0.0158
 KD5  H11  H  HCH2   0   0.263  -1.1816  -0.7560   1.2571
 KD5  O8   O  OH1    0  -0.670   2.1714   3.2036   0.3053

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
 KD5  O8  C8   single  1.407  0.020  1.407
 KD5  C8  C7   single  1.510  0.020  1.510
 KD5  C7  C6   single  1.531  0.020  1.531
 KD5  C7  O7   single  1.422  0.020  1.422
 KD5  C6  O6   single  1.402  0.020  1.402
 KD5  C6  C5   single  1.519  0.020  1.519
 KD5  O5  C5   single  1.400  0.020  1.400
 KD5  O7  C4   single  1.421  0.020  1.421
 KD5  C5  C4   single  1.523  0.020  1.523
 KD5  O5  H1   single  0.850  0.020  0.980
 KD5  C4  H2   single  0.970  0.020  1.090
 KD5  C5  H4   single  0.970  0.020  1.090
 KD5  C6  H5   single  0.970  0.020  1.090
 KD5  O6  H6   single  0.850  0.020  0.980
 KD5  C7  H7   single  0.970  0.020  1.090
 KD5  O8  H8   single  0.850  0.020  0.980
 KD5  C8  H9   single  0.970  0.020  1.090
 KD5  C8  H10  single  0.970  0.020  1.090
 KD5  C4  C3   single  1.511  0.020  1.511
 KD5  C3  C2   single  1.507  0.020  1.507
 KD5  C2  C1   single  1.556  0.020  1.556
 KD5  C2  O2   double  1.208  0.020  1.208
 KD5  C1  OH   deloc   1.238  0.020  1.238
 KD5  C1  O1   deloc   1.243  0.020  1.243
 KD5  C3  H3   single  0.970  0.020  1.090
 KD5  C3  H11  single  0.970  0.020  1.090

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
 KD5  H1   O5  C5  108.52  3.000
 KD5  C3   C4  H2  109.74  3.000
 KD5  C3   C4  O7  110.48  3.000
 KD5  H2   C4  O7  109.84  3.000
 KD5  C3   C4  C5  113.41  3.000
 KD5  H2   C4  C5  108.10  3.000
 KD5  O7   C4  C5  105.15  3.000
 KD5  H4   C5  C6  108.17  3.000
 KD5  H4   C5  C4  109.41  3.000
 KD5  C6   C5  C4  101.45  3.000
 KD5  H4   C5  O5  111.30  3.000
 KD5  C4   C5  O5  110.26  3.000
 KD5  C6   C5  O5  115.72  3.000
 KD5  H5   C6  C7  109.61  3.000
 KD5  H5   C6  O6  111.17  3.000
 KD5  C7   C6  O6  114.75  3.000
 KD5  H5   C6  C5  108.30  3.000
 KD5  O6   C6  C5  111.16  3.000
 KD5  C7   C6  C5  101.29  3.000
 KD5  H6   O6  C6  109.04  3.000
 KD5  H7   C7  C8  109.05  3.000
 KD5  H7   C7  O7  109.43  3.000
 KD5  C8   C7  O7  110.87  3.000
 KD5  H7   C7  C6  108.64  3.000
 KD5  O7   C7  C6  105.83  3.000
 KD5  C8   C7  C6  112.93  3.000
 KD5  C7   O7  C4  110.64  3.000
 KD5  H10  C8  H9  106.79  3.000
 KD5  H10  C8  O8  111.96  3.000
 KD5  H9   C8  O8  111.59  3.000
 KD5  H10  C8  C7  108.95  3.000
 KD5  H9   C8  C7  108.05  3.000
 KD5  O8   C8  C7  109.38  3.000
 KD5  H11  C3  H3  105.07  3.000
 KD5  H11  C3  C2  109.36  3.000
 KD5  H3   C3  C2  107.67  3.000
 KD5  H11  C3  C4  110.46  3.000
 KD5  H3   C3  C4  109.21  3.000
 KD5  C2   C3  C4  114.60  3.000
 KD5  O2   C2  C1  120.84  3.000
 KD5  O2   C2  C3  122.19  3.000
 KD5  C1   C2  C3  116.95  3.000
 KD5  O1   C1  OH  129.02  3.000
 KD5  O1   C1  C2  115.23  3.000
 KD5  OH   C1  C2  115.75  3.000
 KD5  H8   O8  C8  108.13  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
 KD5  Var_01  C1  C2  C3  C4  -172.50  30.0  3
 KD5  Var_02  OH  C1  C2  C3   171.29  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
 KD5  chir_01  C4  O7  C5  C3  negativ
 KD5  chir_02  C5  O5  C4  C6  positiv
 KD5  chir_03  C6  O6  C7  C5  positiv
 KD5  chir_04  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
 KD5  plan-1  C3  0.020
 KD5  plan-1  C2  0.020
 KD5  plan-1  C1  0.020
 KD5  plan-1  O2  0.020
 KD5  plan-2  C2  0.020
 KD5  plan-2  C1  0.020
 KD5  plan-2  OH  0.020
 KD5  plan-2  O1  0.020

