# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 11:12:29 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  22  14  .  2021-08-12  2023-02-15
;
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  -0.610  -4.1148  -0.2953  -0.1656
 LGT  C1   C  C      0   0.400  -3.1750   0.3598   0.3419
 LGT  O1B  O  OC    -1  -0.594  -3.1949   1.5440   0.7092
 LGT  C2   C  CH1    0  -0.116  -1.8619  -0.4382   0.5325
 LGT  O2   O  OH1    0  -0.691  -2.0545  -1.7428   0.0509
 LGT  C3   C  CH1    0   0.012  -0.7009   0.2679  -0.1728
 LGT  O3   O  OH1    0  -0.678  -0.8722   0.2258  -1.5713
 LGT  C4   C  CH1    0   0.017   0.6754  -0.2459   0.2466
 LGT  O4   O  OH1    0  -0.704   0.8349  -1.5782  -0.1727
 LGT  C5   C  CH1    0  -0.123   1.8073   0.6301  -0.3270
 LGT  O5   O  OH1    0  -0.694   1.6537   1.9716   0.0504
 LGT  C6   C  C      0   0.426   3.1801   0.1169   0.1531
 LGT  O6A  O  OC    -1  -0.601   3.4324  -1.0969  -0.0295
 LGT  O6B  O  O      0  -0.582   3.9186   0.9597   0.6937
 LGT  H2   H  HCH1   0   0.197  -1.6425  -0.4504   1.6123
 LGT  HO2  H  HOH1   0   0.426  -2.9852  -1.7036  -0.2460
 LGT  H3   H  HCH1   0   0.233  -0.7523   1.3181   0.1225
 LGT  HO3  H  HOH1   0   0.432  -0.8820  -0.7058  -1.8179
 LGT  H4   H  HCH1   0   0.175   0.7244  -0.1615   1.3478
 LGT  HO4  H  HOH1   0   0.436   1.8050  -1.7188  -0.1924
 LGT  H5   H  HCH1   0   0.208   1.7784   0.5340  -1.4233
 LGT  HO5  H  HOH1   0   0.431   2.4937   2.1706   0.5004

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   deloc   1.253  0.020  1.253
 LGT  C1   C2   single  1.548  0.020  1.548
 LGT  C1   O1B  deloc   1.240  0.020  1.240
 LGT  C2   C3   single  1.531  0.020  1.531
 LGT  C2   O2   single  1.404  0.020  1.404
 LGT  C2   H2   single  0.970  0.020  1.090
 LGT  O2   HO2  single  0.850  0.020  0.980
 LGT  C3   C4   single  1.528  0.020  1.528
 LGT  C3   O3   single  1.410  0.020  1.410
 LGT  C3   H3   single  0.970  0.020  1.090
 LGT  O3   HO3  single  0.850  0.020  0.980
 LGT  C4   C5   single  1.542  0.020  1.542
 LGT  C4   O4   single  1.406  0.020  1.406
 LGT  C4   H4   single  0.970  0.020  1.090
 LGT  O4   HO4  single  0.850  0.020  0.980
 LGT  C5   O5   single  1.402  0.020  1.402
 LGT  C5   C6   single  1.542  0.020  1.542
 LGT  C5   H5   single  0.970  0.020  1.090
 LGT  O5   HO5  single  0.850  0.020  0.980
 LGT  C6   O6B  deloc   1.244  0.020  1.244
 LGT  C6   O6A  deloc   1.253  0.020  1.253

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  117.99  3.000
 LGT  O1B  C1  O1A  127.39  3.000
 LGT  C2   C1  O1A  114.62  3.000
 LGT  H2   C2  C3   107.79  3.000
 LGT  H2   C2  O2   110.68  3.000
 LGT  C3   C2  O2   112.00  3.000
 LGT  H2   C2  C1   107.17  3.000
 LGT  O2   C2  C1   108.68  3.000
 LGT  C3   C2  C1   110.41  3.000
 LGT  HO2  O2  C2   101.39  3.000
 LGT  H3   C3  C4   106.95  3.000
 LGT  H3   C3  O3   106.94  3.000
 LGT  C4   C3  O3   111.83  3.000
 LGT  H3   C3  C2   106.46  3.000
 LGT  O3   C3  C2   110.56  3.000
 LGT  C4   C3  C2   113.68  3.000
 LGT  HO3  O3  C3   106.50  3.000
 LGT  H4   C4  C5   107.13  3.000
 LGT  H4   C4  O4   111.37  3.000
 LGT  C5   C4  O4   110.13  3.000
 LGT  H4   C4  C3   106.72  3.000
 LGT  O4   C4  C3   109.82  3.000
 LGT  C5   C4  C3   111.60  3.000
 LGT  HO4  O4  C4   104.72  3.000
 LGT  H5   C5  C6   107.72  3.000
 LGT  H5   C5  O5   110.40  3.000
 LGT  C6   C5  O5   109.40  3.000
 LGT  H5   C5  C4   107.55  3.000
 LGT  C6   C5  C4   110.40  3.000
 LGT  O5   C5  C4   111.29  3.000
 LGT  HO5  O5  C5   103.02  3.000
 LGT  O6B  C6  O6A  126.87  3.000
 LGT  O6A  C6  C5   117.14  3.000
 LGT  O6B  C6  C5   115.99  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
 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-2  C5   0.020
 LGT  plan-2  C6   0.020
 LGT  plan-2  O6A  0.020
 LGT  plan-2  O6B  0.020

