# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:17:36 2022
#   Inital geometry file: a 54 line input string
#   Ligand name: beta-D-arabino-hexopyranos-2-ulose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](O)C(=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
 KBG  KBG  beta-D-arabino-hexopyranos-2-ulose  D-saccharide  22  12  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KBG
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
 KBG  O4   O  OH1   0  -0.649  11.3650  12.8455  18.4748
 KBG  C4   C  CH1   0  -0.008  10.3007  13.3545  19.2330
 KBG  C3   C  CH1   0  -0.077  10.5854  14.8084  19.6633
 KBG  O3   O  OH1   0  -0.648  11.7095  14.9252  20.4736
 KBG  C2   C  C     0   0.306   9.3785  15.3387  20.3881
 KBG  OAG  O  O     0  -0.363   9.3960  15.7805  21.5075
 KBG  C1   C  CH1   0   0.214   8.0787  15.1884  19.5958
 KBG  O1   O  OH1   0  -0.637   6.9869  15.6505  20.2705
 KBG  O5   O  O2    0  -0.494   7.9390  13.8064  19.3382
 KBG  C5   C  CH1   0  -0.037   8.9536  13.2854  18.5004
 KBG  C6   C  CH2   0  -0.170   8.5571  11.8877  18.0799
 KBG  O6   O  OH1   0  -0.665   8.5060  11.0500  19.2073
 KBG  HO4  H  HOH1  0   0.452  11.4225  13.3290  17.6410
 KBG  H4   H  HCH1  0   0.260  10.2499  12.7393  20.1364
 KBG  H3   H  HCH1  0   0.249  10.6740  15.4075  18.7375
 KBG  HO3  H  HOH1  0   0.456  12.4545  14.5319  20.0059
 KBG  H1   H  HCH1  0   0.235   8.1507  15.7391  18.6450
 KBG  HO1  H  HOH1  0   0.455   7.1075  15.5245  21.2212
 KBG  H5   H  HCH1  0   0.235   9.0227  13.8869  17.5768
 KBG  H61  H  HCH2  0   0.219   7.5873  11.9483  17.5690
 KBG  H62  H  HCH2  0   0.209   9.2830  11.5398  17.3360
 KBG  HO6  H  HOH1  0   0.458   8.3146  10.1561  18.9101

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
 KBG  O4  C4   single  1.402  0.020  1.402
 KBG  O4  HO4  single  0.850  0.020  0.980
 KBG  C4  C3   single  1.543  0.020  1.543
 KBG  C4  C5   single  1.535  0.020  1.535
 KBG  C4  H4   single  0.970  0.020  1.090
 KBG  C3  O3   single  1.391  0.020  1.391
 KBG  C3  C2   single  1.504  0.020  1.504
 KBG  C3  H3   single  0.970  0.020  1.090
 KBG  O3  HO3  single  0.850  0.020  0.980
 KBG  C2  OAG  double  1.203  0.020  1.203
 KBG  C2  C1   single  1.530  0.020  1.530
 KBG  C1  O1   single  1.364  0.020  1.364
 KBG  C1  O5   single  1.413  0.020  1.413
 KBG  C1  H1   single  0.970  0.020  1.090
 KBG  O1  HO1  single  0.850  0.020  0.980
 KBG  O5  C5   single  1.415  0.020  1.415
 KBG  C5  C6   single  1.512  0.020  1.512
 KBG  C5  H5   single  0.970  0.020  1.090
 KBG  C6  O6   single  1.405  0.020  1.405
 KBG  C6  H61  single  0.970  0.020  1.090
 KBG  C6  H62  single  0.970  0.020  1.090
 KBG  O6  HO6  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
 KBG  HO4  O4  C4   109.29  3.000
 KBG  H4   C4  C5   109.15  3.000
 KBG  H4   C4  C3   107.95  3.000
 KBG  C5   C4  C3   109.73  3.000
 KBG  H4   C4  O4   106.11  3.000
 KBG  C5   C4  O4   113.06  3.000
 KBG  C3   C4  O4   110.66  3.000
 KBG  H3   C3  C2   106.06  3.000
 KBG  H3   C3  O3   112.17  3.000
 KBG  C2   C3  O3   109.77  3.000
 KBG  H3   C3  C4   106.96  3.000
 KBG  C2   C3  C4   108.57  3.000
 KBG  O3   C3  C4   113.01  3.000
 KBG  HO3  O3  C3   107.93  3.000
 KBG  C1   C2  OAG  122.02  3.000
 KBG  C1   C2  C3   113.42  3.000
 KBG  OAG  C2  C3   124.46  3.000
 KBG  H1   C1  O5   109.77  3.000
 KBG  H1   C1  O1   108.06  3.000
 KBG  O5   C1  O1   110.02  3.000
 KBG  H1   C1  C2   110.04  3.000
 KBG  O5   C1  C2   105.94  3.000
 KBG  O1   C1  C2   112.99  3.000
 KBG  HO1  O1  C1   110.03  3.000
 KBG  C5   O5  C1   113.40  3.000
 KBG  H5   C5  C6   106.69  3.000
 KBG  H5   C5  O5   109.84  3.000
 KBG  C6   C5  O5   108.47  3.000
 KBG  H5   C5  C4   108.65  3.000
 KBG  C6   C5  C4   113.85  3.000
 KBG  O5   C5  C4   109.27  3.000
 KBG  H62  C6  H61  106.66  3.000
 KBG  H62  C6  O6   112.29  3.000
 KBG  H61  C6  O6   111.96  3.000
 KBG  H62  C6  C5   107.96  3.000
 KBG  H61  C6  C5   108.06  3.000
 KBG  O6   C6  C5   109.71  3.000
 KBG  HO6  O6  C6   108.27  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
 KBG  chir_01  C4  O4  C3  C5  negativ
 KBG  chir_02  C3  O3  C2  C4  positiv
 KBG  chir_03  C1  O5  O1  C2  negativ
 KBG  chir_04  C5  O5  C6  C4  positiv

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
 KBG  plan-1  C3   0.020
 KBG  plan-1  C2   0.020
 KBG  plan-1  OAG  0.020
 KBG  plan-1  C1   0.020

