# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:28:17 2022
#   Inital geometry file: a 57 line input string
#   Ligand name: (4S,5R)-4,5-dihydroxy-3-oxocyclohex-1-ene-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CC(=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
 3DS  3DS  '(4S,5R)-4,5-dihydroxy-3-oxocyclohex-1-ene-1-carboxylic acid'  ligand  19  12  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3DS
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
 3DS  OAA   O  O      0  -0.581  -2.8874   1.3227  -0.0980
 3DS  OAB   O  O      0  -0.422   2.0324   2.0240  -0.4511
 3DS  OAC   O  OC    -1  -0.584  -3.0365  -0.8558   0.3567
 3DS  OAD   O  OH1    0  -0.668   1.1705  -1.3677  -1.6055
 3DS  OAE   O  OH1    0  -0.660   1.9250  -0.2683   1.7485
 3DS  CAF   C  C1     0  -0.375  -0.1197   1.1416  -0.1219
 3DS  CAG   C  CH2    0  -0.502  -0.2976  -1.3045   0.2518
 3DS  CAH   C  C      0   0.406  -2.4124   0.1915   0.1058
 3DS  CAI   C  C      0   0.394   1.3397   1.0718  -0.1407
 3DS  CAJ   C  C      0  -0.055  -0.8875   0.0572   0.0579
 3DS  CAK   C  CH1    0  -0.021   1.1507  -1.4049  -0.1935
 3DS  CAL   C  CH1    0  -0.110   1.9637  -0.2336   0.3396
 3DS  HAF   H  H      0   0.254  -0.5758   2.1114  -0.2832
 3DS  HAG   H  HCH2   0   0.262  -0.3769  -1.5766   1.3082
 3DS  HAGA  H  HCH2   0   0.262  -0.8934  -2.0480  -0.2805
 3DS  HAK   H  HCH1   0   0.239   1.5801  -2.3425   0.1828
 3DS  HAL   H  HCH1   0   0.246   2.9951  -0.2927  -0.0333
 3DS  HOAD  H  HOH1   0   0.453   2.0683  -1.5458  -1.9034
 3DS  HOAE  H  HOH1   0   0.462   2.5834   0.3450   2.0897

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
 3DS  OAA  CAH   deloc   1.244  0.020  1.244
 3DS  OAB  CAI   double  1.218  0.020  1.218
 3DS  CAH  OAC   deloc   1.245  0.020  1.245
 3DS  CAK  OAD   single  1.413  0.020  1.413
 3DS  OAD  HOAD  single  0.850  0.020  0.980
 3DS  OAE  CAL   single  1.410  0.020  1.410
 3DS  OAE  HOAE  single  0.850  0.020  0.980
 3DS  CAI  CAF   single  1.461  0.020  1.461
 3DS  CAF  CAJ   double  1.341  0.020  1.341
 3DS  CAF  HAF   single  0.930  0.020  1.080
 3DS  CAJ  CAG   single  1.497  0.020  1.497
 3DS  CAK  CAG   single  1.519  0.020  1.519
 3DS  CAG  HAG   single  0.970  0.020  1.090
 3DS  CAG  HAGA  single  0.970  0.020  1.090
 3DS  CAJ  CAH   single  1.532  0.020  1.532
 3DS  CAI  CAL   single  1.525  0.020  1.525
 3DS  CAL  CAK   single  1.522  0.020  1.522
 3DS  CAK  HAK   single  0.970  0.020  1.090
 3DS  CAL  HAL   single  0.970  0.020  1.090

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
 3DS  HOAD  OAD  CAK  108.52  3.000
 3DS  HOAE  OAE  CAL  108.66  3.000
 3DS  HAF   CAF  CAJ  120.18  3.000
 3DS  HAF   CAF  CAI  117.46  3.000
 3DS  CAJ   CAF  CAI  122.34  3.000
 3DS  HAGA  CAG  HAG  105.19  3.000
 3DS  HAGA  CAG  CAK  109.43  3.000
 3DS  HAG   CAG  CAK  109.63  3.000
 3DS  HAGA  CAG  CAJ  109.97  3.000
 3DS  HAG   CAG  CAJ  108.84  3.000
 3DS  CAK   CAG  CAJ  113.45  3.000
 3DS  CAJ   CAH  OAC  115.58  3.000
 3DS  CAJ   CAH  OAA  117.06  3.000
 3DS  OAC   CAH  OAA  127.36  3.000
 3DS  CAL   CAI  CAF  116.46  3.000
 3DS  CAL   CAI  OAB  121.13  3.000
 3DS  CAF   CAI  OAB  122.28  3.000
 3DS  CAH   CAJ  CAG  117.92  3.000
 3DS  CAH   CAJ  CAF  120.22  3.000
 3DS  CAG   CAJ  CAF  121.84  3.000
 3DS  HAK   CAK  CAL  109.16  3.000
 3DS  HAK   CAK  CAG  109.21  3.000
 3DS  CAL   CAK  CAG  110.85  3.000
 3DS  HAK   CAK  OAD  111.07  3.000
 3DS  CAL   CAK  OAD  108.80  3.000
 3DS  CAG   CAK  OAD  107.75  3.000
 3DS  HAL   CAL  CAK  109.95  3.000
 3DS  HAL   CAL  CAI  108.87  3.000
 3DS  CAK   CAL  CAI  109.26  3.000
 3DS  HAL   CAL  OAE  111.33  3.000
 3DS  CAK   CAL  OAE  108.45  3.000
 3DS  CAI   CAL  OAE  108.95  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
 3DS  Var_01  CAK  CAG  CAJ  CAF  -17.80  30.0  1
 3DS  Var_02  CAI  CAF  CAJ  CAG   -0.03  30.0  1
 3DS  Var_03  CAL  CAI  CAF  CAJ  -12.34  30.0  1
 3DS  Var_04  CAF  CAJ  CAH  OAA    3.67  30.0  2

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
 3DS  chir_01  CAK  OAD  CAG  CAL  positiv
 3DS  chir_02  CAL  OAE  CAK  CAI  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
 3DS  plan-1  OAB  0.020
 3DS  plan-1  CAF  0.020
 3DS  plan-1  CAI  0.020
 3DS  plan-1  CAL  0.020
 3DS  plan-2  OAA  0.020
 3DS  plan-2  OAC  0.020
 3DS  plan-2  CAH  0.020
 3DS  plan-2  CAJ  0.020

