# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 15:25:44 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: L-glucaric acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]([C@@H](O)[C@@H](O)C(O)=O)[C@H](O)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
 LGT  LGT  'L-glucaric acid          '  ligand  24  14  .  2021-08-13  2021-08-13  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LGT
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
 LGT  O1A   O  O     0  -0.437  -4.0585  -0.2700  -0.3035
 LGT  C1    C  C     0   0.516  -3.1176   0.3153   0.1729
 LGT  O1B   O  OH1   0  -0.579  -3.0998   1.6035   0.4490
 LGT  C2    C  CH1   0  -0.095  -1.8206  -0.3847   0.5481
 LGT  O2    O  OH1   0  -0.660  -1.9198  -1.7478   0.2554
 LGT  C3    C  CH1   0  -0.015  -0.6404   0.2331  -0.2163
 LGT  O3    O  OH1   0  -0.664  -0.7710  -0.0168  -1.5939
 LGT  C4    C  CH1   0  -0.019   0.7196  -0.2172   0.3301
 LGT  O4    O  OH1   0  -0.653   0.9820  -1.5854   0.1699
 LGT  C5    C  CH1   0  -0.093   1.8535   0.6296  -0.2892
 LGT  O5    O  OH1   0  -0.649   1.7351   1.9865   0.0285
 LGT  C6    C  C     0   0.516   3.1838   0.0809   0.2042
 LGT  O6A   O  OH1   0  -0.579   3.7551  -0.7463  -0.6526
 LGT  O6B   O  O     0  -0.443   3.6512   0.3811   1.2743
 LGT  HO1B  H  HOH1  0   0.493  -3.9384   2.0186   0.1952
 LGT  H2    H  HCH1  0   0.272  -1.6665  -0.2167   1.6241
 LGT  HO2   H  HOH1  0   0.455  -2.8376  -1.9466   0.0287
 LGT  H3    H  HCH1  0   0.270  -0.6821   1.3162  -0.0794
 LGT  HO3   H  HOH1  0   0.447  -1.0267  -0.9405  -1.7106
 LGT  H4    H  HCH1  0   0.256   0.7214  -0.0338   1.4112
 LGT  HO4   H  HOH1  0   0.447   0.9793  -1.8064  -0.7682
 LGT  H5    H  HCH1  0   0.278   1.8082   0.5531  -1.3787
 LGT  HO5   H  HOH1  0   0.451   1.8274   2.0963   0.9826
 LGT  HO6A  H  HOH1  0   0.485   4.5801  -1.0989  -0.2842

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
 LGT  O1A  C1    double  1.206  0.020  1.206
 LGT  C1   C2    single  1.521  0.020  1.521
 LGT  C1   O1B   single  1.318  0.020  1.318
 LGT  O1B  HO1B  single  0.850  0.020  0.980
 LGT  C2   C3    single  1.536  0.020  1.536
 LGT  C2   O2    single  1.398  0.020  1.398
 LGT  C2   H2    single  0.970  0.020  1.090
 LGT  O2   HO2   single  0.850  0.020  0.980
 LGT  C3   C4    single  1.533  0.020  1.533
 LGT  C3   O3    single  1.406  0.020  1.406
 LGT  C3   H3    single  0.970  0.020  1.090
 LGT  O3   HO3   single  0.850  0.020  0.980
 LGT  C4   C5    single  1.545  0.020  1.545
 LGT  C4   O4    single  1.402  0.020  1.402
 LGT  C4   H4    single  0.970  0.020  1.090
 LGT  O4   HO4   single  0.850  0.020  0.980
 LGT  C5   O5    single  1.399  0.020  1.399
 LGT  C5   C6    single  1.521  0.020  1.521
 LGT  C5   H5    single  0.970  0.020  1.090
 LGT  O5   HO5   single  0.850  0.020  0.980
 LGT  C6   O6B   double  1.206  0.020  1.206
 LGT  C6   O6A   single  1.321  0.020  1.321
 LGT  O6A  HO6A  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
 LGT  C2    C1   O1B  112.76  3.000
 LGT  O1B   C1   O1A  124.60  3.000
 LGT  C2    C1   O1A  122.64  3.000
 LGT  HO1B  O1B  C1   110.62  3.000
 LGT  H2    C2   C3   108.53  3.000
 LGT  H2    C2   O2   111.33  3.000
 LGT  C3    C2   O2   110.04  3.000
 LGT  H2    C2   C1   106.88  3.000
 LGT  O2    C2   C1   109.68  3.000
 LGT  C3    C2   C1   110.33  3.000
 LGT  HO2   O2   C2   108.50  3.000
 LGT  H3    C3   C4   106.28  3.000
 LGT  H3    C3   O3   107.19  3.000
 LGT  C4    C3   O3   112.29  3.000
 LGT  H3    C3   C2   107.88  3.000
 LGT  O3    C3   C2   110.17  3.000
 LGT  C4    C3   C2   112.71  3.000
 LGT  HO3   O3   C3   108.24  3.000
 LGT  H4    C4   C5   107.59  3.000
 LGT  H4    C4   O4   106.00  3.000
 LGT  C5    C4   O4   110.59  3.000
 LGT  H4    C4   C3   107.68  3.000
 LGT  O4    C4   C3   114.32  3.000
 LGT  C5    C4   C3   110.32  3.000
 LGT  HO4   O4   C4   109.54  3.000
 LGT  H5    C5   C6   109.53  3.000
 LGT  H5    C5   O5   106.90  3.000
 LGT  C6    C5   O5   110.51  3.000
 LGT  H5    C5   C4   109.31  3.000
 LGT  C6    C5   C4   108.31  3.000
 LGT  O5    C5   C4   112.25  3.000
 LGT  HO5   O5   C5   109.08  3.000
 LGT  O6B   C6   O6A  124.33  3.000
 LGT  O6A   C6   C5   113.18  3.000
 LGT  O6B   C6   C5   122.48  3.000
 LGT  HO6A  O6A  C6   110.44  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
 LGT  CONST_01  HO1B  O1B  C1  O1A    0.00  0.0  0
 LGT  CONST_02  HO6A  O6A  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
 LGT  chir_01  C2  C1  C3  O2  positiv
 LGT  chir_02  C3  O3  C2  C4  negativ
 LGT  chir_03  C4  O4  C3  C5  positiv
 LGT  chir_04  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
 LGT  plan-1  O1A   0.020
 LGT  plan-1  C1    0.020
 LGT  plan-1  O1B   0.020
 LGT  plan-1  C2    0.020
 LGT  plan-1  HO1B  0.020
 LGT  plan-2  C5    0.020
 LGT  plan-2  C6    0.020
 LGT  plan-2  O6A   0.020
 LGT  plan-2  O6B   0.020
 LGT  plan-2  HO6A  0.020

