# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 22:48:47 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  21  13  .  2023-02-15  2023-02-16
;
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   0.531   1.0356  -1.4104  -0.0401
 15L  O1   O  O     0  -0.417   1.5938  -2.4683  -0.1286
 15L  C2   C  CH1   0  -0.111   1.7566  -0.0883  -0.2716
 15L  O2   O  OH1   0  -0.657   3.0955  -0.1732   0.1148
 15L  C3   C  CH1   0   0.016   1.1054   1.0649   0.4753
 15L  O3   O  OH1   0  -0.663   1.6339   2.3016   0.0852
 15L  C4   C  CH1   0  -0.042  -0.3836   1.0709   0.1623
 15L  O4   O  OH1   0  -0.661  -0.6503   1.1900  -1.2099
 15L  C5   C  CH1   0  -0.081  -0.9766  -0.2458   0.6362
 15L  O5   O  O2    0  -0.441  -0.2790  -1.3971   0.1836
 15L  C6   C  C     0   0.527  -2.4060  -0.3956   0.1449
 15L  O6A  O  O     0  -0.412  -2.7783  -1.2408  -0.6197
 15L  O6B  O  OH1   0  -0.588  -3.1737   0.5321   0.6885
 15L  H2   H  HCH1  0   0.276   1.6577   0.1093  -1.3492
 15L  HO2  H  HOH1  0   0.467   3.5895  -0.6574  -0.5540
 15L  H3   H  HCH1  0   0.240   1.2229   0.9019   1.5579
 15L  HO3  H  HOH1  0   0.460   2.5903   2.2810   0.1995
 15L  H4   H  HCH1  0   0.279  -0.8608   1.8712   0.7412
 15L  HO4  H  HOH1  0   0.466  -0.3265   2.0439  -1.5168
 15L  H5   H  HCH1  0   0.317  -0.9784  -0.2518   1.7314
 15L  H8   H  HOH1  0   0.494  -4.0844   0.4530   0.3654

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  1.199  0.020  1.199
 15L  C1   C2   single  1.524  0.020  1.524
 15L  C1   O5   single  1.333  0.020  1.333
 15L  C2   O2   single  1.396  0.020  1.396
 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  1.400  0.020  1.400
 15L  C3   C4   single  1.522  0.020  1.522
 15L  C3   H3   single  0.970  0.020  1.090
 15L  O3   HO3  single  0.850  0.020  0.980
 15L  C4   O4   single  1.403  0.020  1.403
 15L  C4   C5   single  1.520  0.020  1.520
 15L  C4   H4   single  0.970  0.020  1.090
 15L  O4   HO4  single  0.850  0.020  0.980
 15L  C5   O5   single  1.420  0.020  1.420
 15L  C5   C6   single  1.519  0.020  1.519
 15L  C5   H5   single  0.970  0.020  1.090
 15L  C6   O6A  double  1.199  0.020  1.199
 15L  C6   O6B  single  1.321  0.020  1.321
 15L  O6B  H8   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
 15L  O5   C1   C2   118.91  3.000
 15L  O5   C1   O1   118.68  3.000
 15L  C2   C1   O1   122.27  3.000
 15L  H2   C2   C3   107.85  3.000
 15L  H2   C2   O2   111.61  3.000
 15L  C3   C2   O2   108.72  3.000
 15L  H2   C2   C1   105.19  3.000
 15L  C3   C2   C1   112.38  3.000
 15L  O2   C2   C1   111.04  3.000
 15L  HO2  O2   C2   109.30  3.000
 15L  H3   C3   C4   107.89  3.000
 15L  H3   C3   O3   111.37  3.000
 15L  C4   C3   O3   107.97  3.000
 15L  H3   C3   C2   108.96  3.000
 15L  C4   C3   C2   108.73  3.000
 15L  O3   C3   C2   111.80  3.000
 15L  HO3  O3   C3   108.83  3.000
 15L  H4   C4   C5   107.33  3.000
 15L  H4   C4   O4   111.81  3.000
 15L  C5   C4   O4   107.72  3.000
 15L  H4   C4   C3   108.66  3.000
 15L  C5   C4   C3   108.32  3.000
 15L  O4   C4   C3   112.80  3.000
 15L  HO4  O4   C4   108.85  3.000
 15L  H5   C5   C6   108.75  3.000
 15L  H5   C5   O5   108.36  3.000
 15L  C6   C5   O5   106.21  3.000
 15L  H5   C5   C4   108.50  3.000
 15L  C6   C5   C4   110.59  3.000
 15L  O5   C5   C4   114.28  3.000
 15L  C5   O5   C1   123.08  3.000
 15L  O6B  C6   O6A  125.23  3.000
 15L  O6B  C6   C5   110.15  3.000
 15L  O6A  C6   C5   124.62  3.000
 15L  H8   O6B  C6   110.57  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
 15L  CONST_01  H8  O6B  C6  C5  180.00  0.0  0

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-1  H8   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

