# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 04:43:41 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (2S,3R,4S,5R)-3,4,5-trihydroxy-6-oxotetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@@H](O)[C@H](OC(=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
 15L  15L  '(2S,3R,4S,5R)-3,4,5-trihydroxy-6-oxotetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)'  D-saccharide  20  13  .  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_15L
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
 15L  C1   C  C      0   0.519   1.0356  -1.3819  -0.0971
 15L  O1   O  O      0  -0.445   1.5667  -2.4545  -0.2370
 15L  C2   C  CH1    0  -0.119   1.8123  -0.0825  -0.2797
 15L  O2   O  OH1    0  -0.662   3.1407  -0.2387   0.1313
 15L  C3   C  CH1    0   0.036   1.1944   1.0670   0.4994
 15L  O3   O  OH1    0  -0.666   1.8039   2.2914   0.1916
 15L  C4   C  CH1    0  -0.040  -0.2837   1.1448   0.1723
 15L  O4   O  OH1    0  -0.676  -0.4356   1.4141  -1.1979
 15L  C5   C  CH1    0  -0.127  -0.9520  -0.1517   0.5963
 15L  O5   O  O2     0  -0.435  -0.2609  -1.3350   0.1534
 15L  C6   C  C      0   0.416  -2.4229  -0.2639   0.1232
 15L  O6A  O  O      0  -0.573  -2.8835  -1.4000  -0.0266
 15L  O6B  O  OC    -1  -0.600  -3.0067   0.8300  -0.0261
 15L  H2   H  HCH1   0   0.269   1.7490   0.1524  -1.3522
 15L  HO2  H  HOH1   0   0.462   3.6145  -0.7611  -0.5227
 15L  H3   H  HCH1   0   0.234   1.2772   0.8439   1.5748
 15L  HO3  H  HOH1   0   0.453   2.7301   2.2388   0.4484
 15L  H4   H  HCH1   0   0.243  -0.7300   1.9384   0.7857
 15L  HO4  H  HOH1   0   0.448  -1.3873   1.4794  -1.3517
 15L  H5   H  HCH1   0   0.264  -0.9503  -0.1819   1.6933

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
 15L  C1  O1   double  1.205  0.020  1.205
 15L  C1  C2   single  1.525  0.020  1.525
 15L  C1  O5   single  1.321  0.020  1.321
 15L  C2  O2   single  1.399  0.020  1.399
 15L  C2  C3   single  1.520  0.020  1.520
 15L  C2  H2   single  0.970  0.020  1.090
 15L  O2  HO2  single  0.850  0.020  0.980
 15L  C3  O3   single  1.402  0.020  1.402
 15L  C3  C4   single  1.516  0.020  1.516
 15L  C3  H3   single  0.970  0.020  1.090
 15L  O3  HO3  single  0.850  0.020  0.980
 15L  C4  O4   single  1.405  0.020  1.405
 15L  C4  C5   single  1.519  0.020  1.519
 15L  C4  H4   single  0.970  0.020  1.090
 15L  O4  HO4  single  0.850  0.020  0.980
 15L  C5  O5   single  1.440  0.020  1.440
 15L  C5  C6   single  1.549  0.020  1.549
 15L  C5  H5   single  0.970  0.020  1.090
 15L  C6  O6A  deloc   1.235  0.020  1.235
 15L  C6  O6B  deloc   1.249  0.020  1.249

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
 15L  O5   C1  C2   119.49  3.000
 15L  O5   C1  O1   119.08  3.000
 15L  C2   C1  O1   121.34  3.000
 15L  H2   C2  C3   108.36  3.000
 15L  H2   C2  O2   111.41  3.000
 15L  C3   C2  O2   108.65  3.000
 15L  H2   C2  C1   105.63  3.000
 15L  C3   C2  C1   112.09  3.000
 15L  O2   C2  C1   110.69  3.000
 15L  HO2  O2  C2   109.18  3.000
 15L  H3   C3  C4   107.12  3.000
 15L  H3   C3  O3   111.02  3.000
 15L  C4   C3  O3   109.37  3.000
 15L  H3   C3  C2   108.46  3.000
 15L  C4   C3  C2   108.94  3.000
 15L  O3   C3  C2   111.79  3.000
 15L  HO3  O3  C3   108.18  3.000
 15L  H4   C4  C5   106.39  3.000
 15L  H4   C4  O4   111.25  3.000
 15L  C5   C4  O4   112.85  3.000
 15L  H4   C4  C3   108.24  3.000
 15L  C5   C4  C3   108.97  3.000
 15L  O4   C4  C3   109.01  3.000
 15L  HO4  O4  C4   105.94  3.000
 15L  H5   C5  C6   107.74  3.000
 15L  H5   C5  O5   106.50  3.000
 15L  C6   C5  O5   107.59  3.000
 15L  H5   C5  C4   107.57  3.000
 15L  C6   C5  C4   113.22  3.000
 15L  O5   C5  C4   113.85  3.000
 15L  C5   O5  C1   123.94  3.000
 15L  O6B  C6  O6A  128.09  3.000
 15L  O6B  C6  C5   114.64  3.000
 15L  O6A  C6  C5   117.25  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
 15L  chir_01  C2  C1  O2  C3  positiv
 15L  chir_02  C3  O3  C2  C4  positiv
 15L  chir_03  C4  O4  C3  C5  positiv
 15L  chir_04  C5  O5  C4  C6  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
 15L  plan-1  C5   0.020
 15L  plan-1  C6   0.020
 15L  plan-1  O6A  0.020
 15L  plan-1  O6B  0.020
 15L  plan-2  C1   0.020
 15L  plan-2  O1   0.020
 15L  plan-2  C2   0.020
 15L  plan-2  O5   0.020

