# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 05:02:32 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (2R,3S,5S)-2,3,5-trihydroxyhexanedioate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H](C[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
 DXG  DXG  '(2R,3S,5S)-2,3,5-trihydroxyhexanedioate (non-preferred name)'  ligand  21  13  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DXG
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
 DXG  O1B   O  O      0  -0.595   3.2447  -1.4034  -0.4582
 DXG  O1A   O  OC    -1  -0.611   3.9292   0.6262   0.1835
 DXG  C1    C  C      0   0.406   3.0913  -0.1877  -0.2705
 DXG  C2    C  CH1    0  -0.125   1.7264   0.4329  -0.6426
 DXG  O2    O  OH1    0  -0.700   1.7587   1.8122  -0.3644
 DXG  C3    C  CH1    0   0.035   0.5885  -0.2424   0.1213
 DXG  O3    O  OH1    0  -0.678   0.7782  -0.1014   1.5163
 DXG  C4    C  CH2    0  -0.467  -0.7759   0.2781  -0.3200
 DXG  O5    O  OH1    0  -0.703  -1.9382  -1.8094   0.0951
 DXG  C5    C  CH1    0  -0.079  -1.9504  -0.4254   0.3548
 DXG  C6    C  C      0   0.391  -3.2885   0.1707  -0.1325
 DXG  O6A   O  O      0  -0.612  -4.0324  -0.6344  -0.7410
 DXG  O6B   O  OC    -1  -0.598  -3.5107   1.3686   0.1026
 DXG  H21   H  HCH1   0   0.203   1.5602   0.2618  -1.7177
 DXG  HO21  H  HOH1   0   0.429   2.6651   1.9221  -0.0157
 DXG  H31   H  HCH1   0   0.221   0.6444  -1.3134  -0.0886
 DXG  HO31  H  HOH1   0   0.431   0.8534   0.8429   1.6951
 DXG  H41   H  HCH2   0   0.221  -0.8463   1.3512  -0.1216
 DXG  H42   H  HCH2   0   0.211  -0.8605   0.1567  -1.4063
 DXG  H51   H  HCH1   0   0.195  -1.8798  -0.2534   1.4379
 DXG  HO51  H  HOH1   0   0.424  -2.7652  -1.9236  -0.4103

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
 DXG  O1B  C1    deloc   1.240  0.020  1.240
 DXG  O1A  C1    deloc   1.253  0.020  1.253
 DXG  C1   C2    single  1.545  0.020  1.545
 DXG  C2   O2    single  1.407  0.020  1.407
 DXG  C2   C3    single  1.528  0.020  1.528
 DXG  C2   H21   single  0.970  0.020  1.090
 DXG  O2   HO21  single  0.850  0.020  0.980
 DXG  C3   O3    single  1.415  0.020  1.415
 DXG  C3   C4    single  1.526  0.020  1.526
 DXG  C3   H31   single  0.970  0.020  1.090
 DXG  O3   HO31  single  0.850  0.020  0.980
 DXG  C4   C5    single  1.526  0.020  1.526
 DXG  C4   H41   single  0.970  0.020  1.090
 DXG  C4   H42   single  0.970  0.020  1.090
 DXG  O5   C5    single  1.408  0.020  1.408
 DXG  O5   HO51  single  0.850  0.020  0.980
 DXG  C5   C6    single  1.544  0.020  1.544
 DXG  C5   H51   single  0.970  0.020  1.090
 DXG  C6   O6A   deloc   1.254  0.020  1.254
 DXG  C6   O6B   deloc   1.241  0.020  1.241

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
 DXG  C2    C1  O1A  114.65  3.000
 DXG  C2    C1  O1B  117.82  3.000
 DXG  O1A   C1  O1B  127.52  3.000
 DXG  H21   C2  C3   107.88  3.000
 DXG  H21   C2  O2   110.41  3.000
 DXG  C3    C2  O2   110.57  3.000
 DXG  H21   C2  C1   107.82  3.000
 DXG  C3    C2  C1   111.11  3.000
 DXG  O2    C2  C1   109.01  3.000
 DXG  HO21  O2  C2   101.66  3.000
 DXG  H31   C3  C4   108.95  3.000
 DXG  H31   C3  O3   106.27  3.000
 DXG  C4    C3  O3   111.78  3.000
 DXG  H31   C3  C2   107.40  3.000
 DXG  C4    C3  C2   111.76  3.000
 DXG  O3    C3  C2   110.43  3.000
 DXG  HO31  O3  C3   106.91  3.000
 DXG  H42   C4  H41  106.47  3.000
 DXG  H42   C4  C5   109.13  3.000
 DXG  H41   C4  C5   108.82  3.000
 DXG  H42   C4  C3   108.53  3.000
 DXG  H41   C4  C3   109.87  3.000
 DXG  C5    C4  C3   113.77  3.000
 DXG  HO51  O5  C5   101.72  3.000
 DXG  H51   C5  C6   107.84  3.000
 DXG  H51   C5  O5   109.57  3.000
 DXG  C6    C5  O5   109.20  3.000
 DXG  H51   C5  C4   108.30  3.000
 DXG  C6    C5  C4   110.45  3.000
 DXG  O5    C5  C4   111.40  3.000
 DXG  O6B   C6  O6A  127.28  3.000
 DXG  O6B   C6  C5   117.91  3.000
 DXG  O6A   C6  C5   114.80  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
 DXG  chir_01  C2  C1  O2  C3  positiv
 DXG  chir_02  C3  O3  C2  C4  positiv
 DXG  chir_03  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
 DXG  plan-1  O1B  0.020
 DXG  plan-1  O1A  0.020
 DXG  plan-1  C1   0.020
 DXG  plan-1  C2   0.020
 DXG  plan-2  C5   0.020
 DXG  plan-2  C6   0.020
 DXG  plan-2  O6A  0.020
 DXG  plan-2  O6B  0.020

