# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 23:37:23 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (5S)-2,5-dihydroxy-3-methylcyclohex-2-ene-1,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C(O)C(=O)C[C@H](O)C1=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
 TR9  TR9  (5S)-2,5-dihydroxy-3-methylcyclohex-2-ene-1,4-dione  ligand  19  11  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TR9
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
 TR9  C1  C  CH2   0  -0.619  -0.3965   1.6662   0.3731
 TR9  C2  C  CH1   0  -0.031  -1.3725   0.7627  -0.3642
 TR9  C3  C  C     0   0.320  -1.1177  -0.6957  -0.0228
 TR9  C4  C  C     0  -0.135   0.2727  -1.1572   0.0297
 TR9  C5  C  C     0   0.286   1.2694  -0.2461   0.0804
 TR9  C6  C  C     0   0.354   1.0156   1.2187   0.1913
 TR9  C7  C  CH3   0  -0.703   0.5111  -2.6318   0.0260
 TR9  O1  O  OH1   0  -0.592   2.5468  -0.5978   0.0668
 TR9  O2  O  OH1   0  -0.658  -2.6711   1.1608  -0.0523
 TR9  O3  O  O     0  -0.402  -2.0505  -1.4614   0.1182
 TR9  O4  O  O     0  -0.392   1.9690   1.9668   0.1874
 TR9  H1  H  HCH2  0   0.301  -0.4971   2.7044   0.0561
 TR9  H2  H  HCH1  0   0.261  -1.1723   0.8473  -1.4453
 TR9  H3  H  HCH3  0   0.258   0.1820  -3.0790  -0.9138
 TR9  H4  H  HCH3  0   0.256   1.5595  -2.8805   0.1672
 TR9  H5  H  HOH1  0   0.479   3.0935   0.2021   0.1325
 TR9  H6  H  HOH1  0   0.455  -3.2774   0.4614  -0.3236
 TR9  H7  H  HCH3  0   0.257  -0.0588  -3.1119   0.8219
 TR9  H8  H  HCH2  0   0.306  -0.6106   1.6255   1.4475

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
 TR9  C1  C2  single  1.521  0.020  1.521
 TR9  C1  C6  single  1.492  0.020  1.492
 TR9  C1  H1  single  0.970  0.020  1.090
 TR9  C2  C3  single  1.519  0.020  1.519
 TR9  C2  O2  single  1.394  0.020  1.394
 TR9  C2  H2  single  0.970  0.020  1.090
 TR9  C3  C4  single  1.466  0.020  1.466
 TR9  C3  O3  double  1.215  0.020  1.215
 TR9  C4  C5  double  1.351  0.020  1.351
 TR9  C4  C7  single  1.494  0.020  1.494
 TR9  C5  C6  single  1.491  0.020  1.491
 TR9  C5  O1  single  1.325  0.020  1.325
 TR9  C6  O4  double  1.212  0.020  1.212
 TR9  C7  H3  single  0.970  0.020  1.090
 TR9  C7  H4  single  0.970  0.020  1.090
 TR9  C7  H7  single  0.970  0.020  1.090
 TR9  O1  H5  single  0.850  0.020  0.980
 TR9  O2  H6  single  0.850  0.020  0.980
 TR9  C1  H8  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
 TR9  H8  C1  H1  107.59  3.000
 TR9  H8  C1  C6  107.04  3.000
 TR9  H1  C1  C6  109.72  3.000
 TR9  H8  C1  C2  109.14  3.000
 TR9  H1  C1  C2  111.45  3.000
 TR9  C6  C1  C2  111.72  3.000
 TR9  H2  C2  O2  111.51  3.000
 TR9  H2  C2  C3  105.28  3.000
 TR9  O2  C2  C3  112.34  3.000
 TR9  H2  C2  C1  108.25  3.000
 TR9  O2  C2  C1  108.66  3.000
 TR9  C3  C2  C1  110.72  3.000
 TR9  O3  C3  C4  121.71  3.000
 TR9  O3  C3  C2  120.15  3.000
 TR9  C4  C3  C2  117.99  3.000
 TR9  C7  C4  C5  123.23  3.000
 TR9  C7  C4  C3  117.52  3.000
 TR9  C5  C4  C3  119.25  3.000
 TR9  O1  C5  C6  115.20  3.000
 TR9  O1  C5  C4  122.12  3.000
 TR9  C6  C5  C4  122.66  3.000
 TR9  O4  C6  C5  118.19  3.000
 TR9  O4  C6  C1  124.03  3.000
 TR9  C5  C6  C1  117.69  3.000
 TR9  H7  C7  H4  107.98  3.000
 TR9  H7  C7  H3  106.89  3.000
 TR9  H4  C7  H3  108.00  3.000
 TR9  H7  C7  C4  110.46  3.000
 TR9  H4  C7  C4  112.31  3.000
 TR9  H3  C7  C4  111.00  3.000
 TR9  H5  O1  C5  108.86  3.000
 TR9  H6  O2  C2  108.40  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
 TR9  Var_01  C4  C5  C6  C1    5.49  30.0  1
 TR9  Var_02  C5  C6  C1  C2  -33.92  30.0  1
 TR9  Var_03  C5  C4  C3  C2   14.94  30.0  1
 TR9  Var_04  C6  C5  C4  C3    4.84  30.0  1
 TR9  Var_05  H3  C7  C4  C3   64.73  30.0  3

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
 TR9  chir_01  C2  C1  C3  O2  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
 TR9  plan-1  C2  0.020
 TR9  plan-1  C3  0.020
 TR9  plan-1  C4  0.020
 TR9  plan-1  O3  0.020
 TR9  plan-2  C1  0.020
 TR9  plan-2  C5  0.020
 TR9  plan-2  C6  0.020
 TR9  plan-2  O4  0.020

