# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 08:58:43 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: D-galactaric 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
 GAE  GAE  'D-galactaric acid        '  ligand  24  14  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GAE
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
 GAE  O6A   O  OH1   0  -0.581  -3.3018  -1.3257   0.6172
 GAE  C6    C  C     0   0.515  -3.1672  -0.0996   0.1516
 GAE  O6B   O  O     0  -0.437  -4.0076   0.4885  -0.4828
 GAE  C5    C  CH1   0  -0.086  -1.8234   0.5105   0.5030
 GAE  O5    O  OH1   0  -0.668  -1.7884   1.8540   0.1132
 GAE  C4    C  CH1   0  -0.018  -0.7030  -0.2853  -0.1869
 GAE  O4    O  OH1   0  -0.661  -0.8851  -0.2869  -1.5798
 GAE  C3    C  CH1   0  -0.021   0.6802   0.2554   0.2034
 GAE  O3    O  OH1   0  -0.661   0.8665   0.2281   1.5965
 GAE  C2    C  CH1   0  -0.086   1.8006  -0.5166  -0.5125
 GAE  C1    C  C     0   0.516   3.1435   0.0472  -0.0875
 GAE  O1A   O  O     0  -0.437   3.9554  -0.5943   0.5321
 GAE  O1B   O  OH1   0  -0.581   3.3101   1.2985  -0.4679
 GAE  O2    O  OH1   0  -0.667   1.7394  -1.8831  -0.2190
 GAE  HO6A  H  HOH1  0   0.492  -4.1632  -1.6937   0.3670
 GAE  H5    H  HCH1  0   0.277  -1.6968   0.4353   1.5894
 GAE  HO5   H  HOH1  0   0.454  -2.5611   2.0347  -0.4375
 GAE  H4    H  HCH1  0   0.266  -0.7727  -1.3282   0.1343
 GAE  HO4   H  HOH1  0   0.448  -0.8602   0.6245  -1.8943
 GAE  H3    H  HCH1  0   0.266   0.7462   1.3056  -0.0945
 GAE  HO3   H  HOH1  0   0.448   0.8174  -0.6863   1.8992
 GAE  H2    H  HCH1  0   0.277   1.6993  -0.3678  -1.5936
 GAE  HO1B  H  HOH1  0   0.492   4.1660   1.6376  -0.1635
 GAE  HO2   H  HOH1  0   0.453   2.4815  -2.1076   0.3569

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
 GAE  C6   O6A   single  1.318  0.020  1.318
 GAE  O6A  HO6A  single  0.850  0.020  0.980
 GAE  O6B  C6    double  1.206  0.020  1.206
 GAE  C6   C5    single  1.517  0.020  1.517
 GAE  C4   C5    single  1.538  0.020  1.538
 GAE  O5   C5    single  1.399  0.020  1.399
 GAE  C5   H5    single  0.970  0.020  1.090
 GAE  O5   HO5   single  0.850  0.020  0.980
 GAE  O4   C4    single  1.405  0.020  1.405
 GAE  C4   C3    single  1.536  0.020  1.536
 GAE  C4   H4    single  0.970  0.020  1.090
 GAE  O4   HO4   single  0.850  0.020  0.980
 GAE  O3   C3    single  1.406  0.020  1.406
 GAE  C2   C3    single  1.537  0.020  1.537
 GAE  C3   H3    single  0.970  0.020  1.090
 GAE  O3   HO3   single  0.850  0.020  0.980
 GAE  O2   C2    single  1.399  0.020  1.399
 GAE  C2   C1    single  1.517  0.020  1.517
 GAE  C2   H2    single  0.970  0.020  1.090
 GAE  O1A  C1    double  1.206  0.020  1.206
 GAE  C1   O1B   single  1.318  0.020  1.318
 GAE  O1B  HO1B  single  0.850  0.020  0.980
 GAE  O2   HO2   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
 GAE  HO6A  O6A  C6   110.65  3.000
 GAE  C5    C6   O6B  122.88  3.000
 GAE  C5    C6   O6A  112.50  3.000
 GAE  O6B   C6   O6A  124.62  3.000
 GAE  H5    C5   C4   108.96  3.000
 GAE  H5    C5   O5   109.82  3.000
 GAE  C4    C5   O5   110.72  3.000
 GAE  H5    C5   C6   107.71  3.000
 GAE  O5    C5   C6   110.10  3.000
 GAE  C4    C5   C6   109.47  3.000
 GAE  HO5   O5   C5   108.57  3.000
 GAE  H4    C4   C3   108.58  3.000
 GAE  H4    C4   O4   106.37  3.000
 GAE  C3    C4   O4   111.67  3.000
 GAE  H4    C4   C5   108.38  3.000
 GAE  C3    C4   C5   111.10  3.000
 GAE  O4    C4   C5   110.55  3.000
 GAE  HO4   O4   C4   108.59  3.000
 GAE  H3    C3   C2   108.14  3.000
 GAE  H3    C3   O3   106.30  3.000
 GAE  C2    C3   O3   110.80  3.000
 GAE  H3    C3   C4   108.86  3.000
 GAE  C2    C3   C4   111.18  3.000
 GAE  O3    C3   C4   111.37  3.000
 GAE  HO3   O3   C3   108.82  3.000
 GAE  H2    C2   O2   109.61  3.000
 GAE  H2    C2   C1   107.91  3.000
 GAE  O2    C2   C1   110.05  3.000
 GAE  H2    C2   C3   108.90  3.000
 GAE  C1    C2   C3   109.15  3.000
 GAE  O2    C2   C3   111.15  3.000
 GAE  O1B   C1   O1A  124.61  3.000
 GAE  O1B   C1   C2   112.56  3.000
 GAE  O1A   C1   C2   122.83  3.000
 GAE  HO1B  O1B  C1   110.66  3.000
 GAE  HO2   O2   C2   108.57  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
 GAE  CONST_01  HO6A  O6A  C6  O6B    0.00  0.0  0
 GAE  CONST_02  HO1B  O1B  C1  C2   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
 GAE  chir_01  C5  C6  C4  O5  negativ
 GAE  chir_02  C4  O4  C5  C3  positiv
 GAE  chir_03  C3  O3  C4  C2  positiv
 GAE  chir_04  C2  O2  C3  C1  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
 GAE  plan-1  O6A   0.020
 GAE  plan-1  C6    0.020
 GAE  plan-1  O6B   0.020
 GAE  plan-1  C5    0.020
 GAE  plan-1  HO6A  0.020
 GAE  plan-2  C2    0.020
 GAE  plan-2  C1    0.020
 GAE  plan-2  O1A   0.020
 GAE  plan-2  O1B   0.020
 GAE  plan-2  HO1B  0.020

