# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 19:51:01 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: L-psicose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H](O)[C@H](O)[C@H](O)C(=O)CO
#
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
 LPK  LPK  'L-psicose                '  L-saccharide  24  12  .  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_LPK
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
 LPK  C1   C  CH2   0  -0.253  -2.7402  -0.7019  -0.7107
 LPK  O1   O  OH1   0  -0.656  -3.8724  -1.2030  -0.0724
 LPK  C2   C  C     0   0.363  -1.9385   0.1392   0.2362
 LPK  O2   O  O     0  -0.392  -2.3415   0.4769   1.3228
 LPK  C3   C  CH1   0  -0.106  -0.5734   0.6116  -0.2601
 LPK  O3   O  OH1   0  -0.652  -0.3895   1.9680   0.0477
 LPK  C4   C  CH1   0  -0.028   0.5088  -0.2741   0.3922
 LPK  O4   O  OH1   0  -0.658   0.0755  -1.6100   0.5223
 LPK  C5   C  CH1   0  -0.015   1.8656  -0.2134  -0.3344
 LPK  O5   O  OH1   0  -0.655   2.1580   1.0462  -0.8824
 LPK  C6   C  CH2   0  -0.158   2.9648  -0.7005   0.5974
 LPK  O6   O  OH1   0  -0.671   4.1546  -0.8551  -0.1375
 LPK  H1   H  HCH2  0   0.229  -2.0870  -1.4858  -1.1187
 LPK  H2   H  HCH2  0   0.247  -2.9792  -0.0487  -1.5660
 LPK  H3   H  HOH1  0   0.465  -4.3914  -1.6851  -0.7226
 LPK  H4   H  HCH1  0   0.267  -0.5283   0.5226  -1.3512
 LPK  H5   H  HOH1  0   0.448  -0.5897   2.0962   0.9832
 LPK  H6   H  HCH1  0   0.244   0.6309   0.0930   1.4197
 LPK  H7   H  HOH1  0   0.453   0.1715  -2.0594  -0.3247
 LPK  H8   H  HCH1  0   0.232   1.8084  -0.8921  -1.1956
 LPK  H9   H  HOH1  0   0.443   2.0783   1.7159  -0.1948
 LPK  H10  H  HCH2  0   0.197   3.0780   0.0314   1.4108
 LPK  H11  H  HCH2  0   0.202   2.6495  -1.6432   1.0611
 LPK  H12  H  HOH1  0   0.456   4.8440  -1.1417   0.4677

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
 LPK  O6  C6   single  1.407  0.020  1.407
 LPK  C6  C5   single  1.521  0.020  1.521
 LPK  O5  C5   single  1.404  0.020  1.404
 LPK  O4  C4   single  1.410  0.020  1.410
 LPK  C5  C4   single  1.540  0.020  1.540
 LPK  C4  C3   single  1.543  0.020  1.543
 LPK  O2  C2   double  1.207  0.020  1.207
 LPK  C3  C2   single  1.527  0.020  1.527
 LPK  C3  O3   single  1.403  0.020  1.403
 LPK  C2  C1   single  1.499  0.020  1.499
 LPK  O1  C1   single  1.393  0.020  1.393
 LPK  C1  H1   single  0.970  0.020  1.090
 LPK  C1  H2   single  0.970  0.020  1.090
 LPK  O1  H3   single  0.850  0.020  0.980
 LPK  C3  H4   single  0.970  0.020  1.090
 LPK  O3  H5   single  0.850  0.020  0.980
 LPK  C4  H6   single  0.970  0.020  1.090
 LPK  O4  H7   single  0.850  0.020  0.980
 LPK  C5  H8   single  0.970  0.020  1.090
 LPK  O5  H9   single  0.850  0.020  0.980
 LPK  C6  H10  single  0.970  0.020  1.090
 LPK  C6  H11  single  0.970  0.020  1.090
 LPK  O6  H12  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
 LPK  H2   C1  H1   105.28  3.000
 LPK  H2   C1  C2   105.88  3.000
 LPK  H1   C1  C2   108.48  3.000
 LPK  H2   C1  O1   113.10  3.000
 LPK  H1   C1  O1   113.37  3.000
 LPK  C2   C1  O1   110.31  3.000
 LPK  H3   O1  C1   108.02  3.000
 LPK  C3   C2  O2   120.29  3.000
 LPK  C3   C2  C1   116.50  3.000
 LPK  O2   C2  C1   123.17  3.000
 LPK  H4   C3  C4   110.21  3.000
 LPK  H4   C3  O3   106.96  3.000
 LPK  C4   C3  O3   111.73  3.000
 LPK  H4   C3  C2   109.58  3.000
 LPK  O3   C3  C2   110.17  3.000
 LPK  C4   C3  C2   108.17  3.000
 LPK  H5   O3  C3   108.29  3.000
 LPK  H6   C4  C5   109.29  3.000
 LPK  H6   C4  O4   105.34  3.000
 LPK  C5   C4  O4   110.58  3.000
 LPK  H6   C4  C3   106.36  3.000
 LPK  C5   C4  C3   113.31  3.000
 LPK  O4   C4  C3   111.54  3.000
 LPK  H7   O4  C4   109.27  3.000
 LPK  H8   C5  C6   108.67  3.000
 LPK  H8   C5  O5   105.02  3.000
 LPK  C6   C5  O5   112.07  3.000
 LPK  H8   C5  C4   107.44  3.000
 LPK  O5   C5  C4   113.76  3.000
 LPK  C6   C5  C4   109.57  3.000
 LPK  H9   O5  C5   109.13  3.000
 LPK  H11  C6  H10  106.79  3.000
 LPK  H11  C6  O6   111.68  3.000
 LPK  H10  C6  O6   111.85  3.000
 LPK  H11  C6  C5   109.06  3.000
 LPK  H10  C6  C5   108.32  3.000
 LPK  O6   C6  C5   109.05  3.000
 LPK  H12  O6  C6   108.08  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
 LPK  Var_01  O2  C2  C1  O1  -10.02  30.0  1

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
 LPK  chir_01  C3  C4  C2  O3  negativ
 LPK  chir_02  C4  O4  C3  C5  positiv
 LPK  chir_03  C5  O5  C4  C6  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
 LPK  plan-1  C1  0.020
 LPK  plan-1  C2  0.020
 LPK  plan-1  O2  0.020
 LPK  plan-1  C3  0.020

