# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 02:04:52 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: [(3S,4R,5S)-3,4,5,6,6-pentahydroxy-2-oxo-hexyl] dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(O)[C@@H](O)[C@@H](O)[C@H](O)C(=O)CO[P](O)(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
 KPG  KPG  '[(3S,4R,5S)-3,4,5,6,6-pentahydroxy-2-oxo-hexyl] dihydrogen phosphate'  ligand  30  17  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KPG
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
 KPG  P     P  P     0   1.451  -3.5291  -0.8330   0.0012
 KPG  C1    C  CH1   0   0.256   3.9736  -1.1826   0.2996
 KPG  C2    C  CH1   0  -0.032   3.3053   0.1153  -0.1714
 KPG  O2    O  OH1   0  -0.661   3.5560   0.3745  -1.5317
 KPG  C3    C  CH1   0  -0.070   1.7987   0.0992   0.1279
 KPG  O3    O  OH1   0  -0.657   1.5419  -0.0805   1.4990
 KPG  C4    C  CH1   0  -0.069   1.0999   1.3663  -0.3779
 KPG  O4    O  OH1   0  -0.666   1.6988   2.4931   0.1876
 KPG  C5    C  C     0   0.349  -0.3761   1.3166  -0.0250
 KPG  O5    O  O     0  -0.374  -0.9030   2.2348   0.5511
 KPG  C6    C  CH2   0  -0.275  -1.1387   0.0880  -0.4499
 KPG  O6    O  O2    0  -0.579  -2.5232   0.3564  -0.3745
 KPG  O12   O  OH1   0  -0.667   5.3481  -1.0108   0.1508
 KPG  O1P   O  O     0  -0.703  -3.3617  -2.0860  -0.7559
 KPG  O2P   O  OH1   0  -0.736  -3.3333  -1.1150   1.5601
 KPG  O3P   O  OH1   0  -0.726  -4.8708  -0.0019  -0.1919
 KPG  H2    H  HCH1  0   0.251   3.7620   0.9387   0.3865
 KPG  HO2   H  HOH1  0   0.446   3.0296  -0.2174  -2.0801
 KPG  H3    H  HCH1  0   0.264   1.3618  -0.7667  -0.3830
 KPG  HO3   H  HOH1  0   0.450   1.8622   0.6975   1.9716
 KPG  H4    H  HCH1  0   0.263   1.1515   1.3937  -1.4771
 KPG  HO4   H  HOH1  0   0.456   0.9992   3.0714   0.5207
 KPG  H6    H  HCH2  0   0.294  -0.8573  -0.1999  -1.4667
 KPG  H6A   H  HCH2  0   0.280  -0.8338  -0.7327   0.2106
 KPG  HO11  H  HOH1  0   0.442   3.7936  -2.2643  -1.3074
 KPG  HO12  H  HOH1  0   0.458   5.7992  -1.7480   0.5765
 KPG  HO2P  H  HOH1  0   0.498  -3.4887  -0.3647   2.1498
 KPG  HO3P  H  HOH1  0   0.508  -5.6765  -0.5346  -0.1442
 KPG  H1    H  HCH1  0   0.216   3.7051  -1.3592   1.3457
 KPG  O11   O  OH1   0  -0.666   3.5011  -2.3079  -0.3890

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
 KPG  O1P  P     double  1.473  0.020  1.473
 KPG  O2P  P     single  1.596  0.020  1.596
 KPG  P    O3P   single  1.590  0.020  1.590
 KPG  P    O6    single  1.602  0.020  1.602
 KPG  O12  C1    single  1.393  0.020  1.393
 KPG  C1   C2    single  1.534  0.020  1.534
 KPG  C1   O11   single  1.401  0.020  1.401
 KPG  O2   C2    single  1.407  0.020  1.407
 KPG  C2   C3    single  1.536  0.020  1.536
 KPG  C2   H2    single  0.970  0.020  1.090
 KPG  O2   HO2   single  0.850  0.020  0.980
 KPG  C4   C3    single  1.533  0.020  1.533
 KPG  C3   O3    single  1.406  0.020  1.406
 KPG  C3   H3    single  0.970  0.020  1.090
 KPG  O3   HO3   single  0.850  0.020  0.980
 KPG  C4   O4    single  1.396  0.020  1.396
 KPG  C4   C5    single  1.518  0.020  1.518
 KPG  C4   H4    single  0.970  0.020  1.090
 KPG  O4   HO4   single  0.850  0.020  0.980
 KPG  C6   C5    single  1.507  0.020  1.507
 KPG  C5   O5    double  1.205  0.020  1.205
 KPG  O6   C6    single  1.412  0.020  1.412
 KPG  C6   H6    single  0.970  0.020  1.090
 KPG  C6   H6A   single  0.970  0.020  1.090
 KPG  O11  HO11  single  0.850  0.020  0.980
 KPG  O12  HO12  single  0.850  0.020  0.980
 KPG  O2P  HO2P  single  0.850  0.020  0.980
 KPG  O3P  HO3P  single  0.850  0.020  0.980
 KPG  C1   H1    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
 KPG  O3P   P    O2P  108.33  3.000
 KPG  O3P   P    O1P  118.55  3.000
 KPG  O2P   P    O1P  109.74  3.000
 KPG  O3P   P    O6    96.50  3.000
 KPG  O2P   P    O6   106.44  3.000
 KPG  O1P   P    O6   116.07  3.000
 KPG  H1    C1   O12  111.35  3.000
 KPG  H1    C1   O11  104.91  3.000
 KPG  O12   C1   O11  112.28  3.000
 KPG  H1    C1   C2   108.85  3.000
 KPG  O11   C1   C2   112.44  3.000
 KPG  O12   C1   C2   107.02  3.000
 KPG  H2    C2   C3   108.53  3.000
 KPG  H2    C2   O2   106.25  3.000
 KPG  C3    C2   O2   111.41  3.000
 KPG  H2    C2   C1   107.35  3.000
 KPG  C3    C2   C1   111.02  3.000
 KPG  O2    C2   C1   112.02  3.000
 KPG  HO2   O2   C2   109.86  3.000
 KPG  H3    C3   C4   108.51  3.000
 KPG  H3    C3   O3   106.30  3.000
 KPG  C4    C3   O3   110.13  3.000
 KPG  H3    C3   C2   107.96  3.000
 KPG  O3    C3   C2   111.74  3.000
 KPG  C4    C3   C2   111.97  3.000
 KPG  HO3   O3   C3   108.29  3.000
 KPG  H4    C4   C5   106.17  3.000
 KPG  H4    C4   O4   111.36  3.000
 KPG  C5    C4   O4   110.45  3.000
 KPG  H4    C4   C3   109.19  3.000
 KPG  C5    C4   C3   109.84  3.000
 KPG  O4    C4   C3   109.76  3.000
 KPG  HO4   O4   C4   108.18  3.000
 KPG  C6    C5   O5   122.31  3.000
 KPG  O5    C5   C4   120.74  3.000
 KPG  C6    C5   C4   116.94  3.000
 KPG  H6A   C6   H6   106.94  3.000
 KPG  H6A   C6   O6   112.49  3.000
 KPG  H6    C6   O6   110.60  3.000
 KPG  H6A   C6   C5   107.43  3.000
 KPG  H6    C6   C5   110.28  3.000
 KPG  O6    C6   C5   109.03  3.000
 KPG  C6    O6   P    119.13  3.000
 KPG  HO12  O12  C1   108.68  3.000
 KPG  HO2P  O2P  P    116.03  3.000
 KPG  HO3P  O3P  P    114.15  3.000
 KPG  HO11  O11  C1   109.22  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
 KPG  Var_01  C5   C6  O6  P   -147.69  30.0  3
 KPG  Var_02  O6   C6  C5  C4  -164.32  30.0  1
 KPG  Var_03  O1P  P   O6  C6   -49.04  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
 KPG  chir_01  C2  C1  O2  C3  negativ
 KPG  chir_02  C3  O3  C2  C4  positiv
 KPG  chir_03  C4  O4  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
 KPG  plan-1  C4  0.020
 KPG  plan-1  C5  0.020
 KPG  plan-1  O5  0.020
 KPG  plan-1  C6  0.020

