# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 23:10:04 2022
#   Inital geometry file: a 59 line input string
#   Ligand name: (1R,3R,4S)-1,3,4-trihydroxy-5-oxocyclohexanecarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1C[C@@](O)(CC(=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
 DQA  DQA  '(1R,3R,4S)-1,3,4-trihydroxy-5-oxocyclohexanecarboxylic acid'  ligand  22  13  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DQA
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
 DQA  C1   C  CT     0   0.057  -0.1512  -0.2105  -0.9618
 DQA  C2   C  CH2    0  -0.478   1.1828   0.0480  -0.2567
 DQA  C3   C  CH1    0   0.047   1.0949  -0.2546   1.2293
 DQA  O3   O  OH1    0  -0.671   2.3454   0.0213   1.8166
 DQA  C4   C  CH1    0  -0.049  -0.0121   0.5858   1.8827
 DQA  O4   O  OH1    0  -0.679  -0.1382   0.2644   3.2371
 DQA  C5   C  C      0   0.359  -1.3146   0.4032   1.1313
 DQA  C6   C  CH2    0  -0.560  -1.2437   0.6750  -0.3373
 DQA  C    C  C      0   0.437  -0.0285   0.1082  -2.4765
 DQA  O1   O  O      0  -0.598  -0.2441  -0.8701  -3.2265
 DQA  O2   O  OC    -1  -0.580   0.2647   1.2665  -2.8001
 DQA  O5   O  O      0  -0.402  -2.3147   0.0544   1.7200
 DQA  O6   O  OH1    0  -0.700  -0.5198  -1.5593  -0.8147
 DQA  H21  H  HCH2   0   0.237   1.4796   1.0899  -0.4047
 DQA  H22  H  HCH2   0   0.252   1.9611  -0.5748  -0.7068
 DQA  H3   H  HCH1   0   0.214   0.8327  -1.3129   1.3656
 DQA  HO3  H  HOH1   0   0.451   2.3209  -0.2745   2.7322
 DQA  H4   H  HCH1   0   0.240   0.2652   1.6473   1.7657
 DQA  HO4  H  HOH1   0   0.447  -1.0682   0.0609   3.4071
 DQA  H61  H  HCH2   0   0.276  -0.9845   1.7263  -0.4891
 DQA  H62  H  HCH2   0   0.269  -2.2132   0.4898  -0.8026
 DQA  HO6  H  HOH1   0   0.432  -0.5555  -1.8629  -1.7439

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
 DQA  C1  C2   single  1.531  0.020  1.531
 DQA  C1  C6   single  1.539  0.020  1.539
 DQA  C1  C    single  1.553  0.020  1.553
 DQA  C1  O6   single  1.406  0.020  1.406
 DQA  C2  C3   single  1.519  0.020  1.519
 DQA  C2  H21  single  0.970  0.020  1.090
 DQA  C2  H22  single  0.970  0.020  1.090
 DQA  C3  O3   single  1.409  0.020  1.409
 DQA  C3  C4   single  1.536  0.020  1.536
 DQA  C3  H3   single  0.970  0.020  1.090
 DQA  O3  HO3  single  0.850  0.020  0.980
 DQA  C4  O4   single  1.398  0.020  1.398
 DQA  C4  C5   single  1.515  0.020  1.515
 DQA  C4  H4   single  0.970  0.020  1.090
 DQA  O4  HO4  single  0.850  0.020  0.980
 DQA  C5  C6   single  1.495  0.020  1.495
 DQA  C5  O5   double  1.212  0.020  1.212
 DQA  C6  H61  single  0.970  0.020  1.090
 DQA  C6  H62  single  0.970  0.020  1.090
 DQA  C   O1   deloc   1.251  0.020  1.251
 DQA  C   O2   deloc   1.238  0.020  1.238
 DQA  O6  HO6  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
 DQA  O6   C1  C    108.65  3.000
 DQA  O6   C1  C6   108.87  3.000
 DQA  C    C1  C6   109.51  3.000
 DQA  O6   C1  C2   110.01  3.000
 DQA  C    C1  C2   110.23  3.000
 DQA  C6   C1  C2   109.55  3.000
 DQA  H22  C2  H21  107.09  3.000
 DQA  H22  C2  C3   109.29  3.000
 DQA  H21  C2  C3   109.75  3.000
 DQA  H22  C2  C1   109.54  3.000
 DQA  H21  C2  C1   109.57  3.000
 DQA  C3   C2  C1   111.50  3.000
 DQA  H3   C3  C4   107.59  3.000
 DQA  H3   C3  O3   110.41  3.000
 DQA  C4   C3  O3   110.81  3.000
 DQA  H3   C3  C2   109.08  3.000
 DQA  C4   C3  C2   110.42  3.000
 DQA  O3   C3  C2   108.51  3.000
 DQA  HO3  O3  C3   108.28  3.000
 DQA  H4   C4  C5   106.23  3.000
 DQA  H4   C4  O4   110.28  3.000
 DQA  C5   C4  O4   112.05  3.000
 DQA  H4   C4  C3   107.47  3.000
 DQA  C5   C4  C3   110.05  3.000
 DQA  O4   C4  C3   110.58  3.000
 DQA  HO4  O4  C4   107.79  3.000
 DQA  O5   C5  C6   124.66  3.000
 DQA  O5   C5  C4   120.22  3.000
 DQA  C6   C5  C4   115.13  3.000
 DQA  H62  C6  H61  108.33  3.000
 DQA  H62  C6  C5   110.23  3.000
 DQA  H61  C6  C5   108.81  3.000
 DQA  H62  C6  C1   111.10  3.000
 DQA  H61  C6  C1   109.19  3.000
 DQA  C5   C6  C1   109.13  3.000
 DQA  O2   C   O1   128.00  3.000
 DQA  O2   C   C1   117.76  3.000
 DQA  O1   C   C1   114.24  3.000
 DQA  HO6  O6  C1   102.00  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
 DQA  Var_01  C4  C5  C6  C1  55.95  30.0  1

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
 DQA  chir_01  C1  C6  C2  O6  negativ
 DQA  chir_02  C3  O3  C2  C4  positiv
 DQA  chir_03  C4  O4  C3  C5  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
 DQA  plan-1  C4  0.020
 DQA  plan-1  C5  0.020
 DQA  plan-1  C6  0.020
 DQA  plan-1  O5  0.020
 DQA  plan-2  C1  0.020
 DQA  plan-2  C   0.020
 DQA  plan-2  O1  0.020
 DQA  plan-2  O2  0.020

