# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 08:05:58 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: (1S,4S,5R)-3,4,5-trihydroxycyclohex-2-ene-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1C[C@@H](C=C(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
 DHK  DHK  '(1S,4S,5R)-3,4,5-trihydroxycyclohex-2-ene-1-carboxylic acid'  ligand  22  12  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DHK
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
 DHK  C2    C  C1    0  -0.369  -1.1604  -0.2638  -0.4599
 DHK  C3    C  C     0   0.334  -1.2820   0.0960   0.8180
 DHK  O3    O  OH1   0  -0.632  -2.4572   0.3378   1.4351
 DHK  C4    C  CH1   0  -0.051  -0.1110   0.3004   1.7496
 DHK  O4    O  OH1   0  -0.669  -0.3512  -0.2564   3.0224
 DHK  C5    C  CH1   0   0.053   1.1352  -0.3697   1.1872
 DHK  C1    C  CH1   0  -0.427   0.1791  -0.5094  -1.1077
 DHK  C6    C  CH2   0  -0.478   1.3235   0.0335  -0.2618
 DHK  C     C  C     0   0.574   0.2068   0.0693  -2.5074
 DHK  O1    O  O     0  -0.435   0.9731   0.9138  -2.8968
 DHK  O2    O  OH1   0  -0.594  -0.7220  -0.4790  -3.2823
 DHK  O5    O  OH1   0  -0.672   2.2862  -0.0008   1.9074
 DHK  H2    H  H     0   0.265  -2.0525  -0.4122  -1.0603
 DHK  H3    H  HOH1  0   0.471  -3.1901   0.2088   0.8215
 DHK  H4    H  HCH1  0   0.236   0.0847   1.3806   1.8313
 DHK  HA    H  HOH1  0   0.459  -0.9578   0.3121   3.5061
 DHK  H5    H  HCH1  0   0.209   0.9792  -1.4595   1.2358
 DHK  H1    H  HCH1  0   0.291   0.3151  -1.5930  -1.2338
 DHK  H6C1  H  HCH2  0   0.242   1.3645   1.1237  -0.3338
 DHK  H6C2  H  HCH2  0   0.260   2.2749  -0.3541  -0.6306
 DHK  HC    H  HOH1  0   0.482  -0.6927  -0.0855  -4.1673
 DHK  HB    H  HOH1  0   0.449   2.1528  -0.2416   2.8302

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
 DHK  C2  C3    double  1.333  0.020  1.333
 DHK  C2  C1    single  1.508  0.020  1.508
 DHK  C2  H2    single  0.930  0.020  1.080
 DHK  C3  O3    single  1.349  0.020  1.349
 DHK  C3  C4    single  1.510  0.020  1.510
 DHK  O3  H3    single  0.850  0.020  0.980
 DHK  C4  O4    single  1.410  0.020  1.410
 DHK  C4  C5    single  1.523  0.020  1.523
 DHK  C4  H4    single  0.970  0.020  1.090
 DHK  O4  HA    single  0.850  0.020  0.980
 DHK  C5  C6    single  1.516  0.020  1.516
 DHK  C5  O5    single  1.407  0.020  1.407
 DHK  C5  H5    single  0.970  0.020  1.090
 DHK  C1  C6    single  1.523  0.020  1.523
 DHK  C1  C     single  1.515  0.020  1.515
 DHK  C1  H1    single  0.970  0.020  1.090
 DHK  C6  H6C1  single  0.970  0.020  1.090
 DHK  C6  H6C2  single  0.970  0.020  1.090
 DHK  C   O1    double  1.205  0.020  1.205
 DHK  C   O2    single  1.328  0.020  1.328
 DHK  O2  HC    single  0.850  0.020  0.980
 DHK  O5  HB    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
 DHK  H2    C2  C1    118.04  3.000
 DHK  H2    C2  C3    119.48  3.000
 DHK  C1    C2  C3    122.46  3.000
 DHK  C4    C3  O3    111.65  3.000
 DHK  C4    C3  C2    123.85  3.000
 DHK  O3    C3  C2    124.49  3.000
 DHK  H3    O3  C3    110.30  3.000
 DHK  H4    C4  C5    108.29  3.000
 DHK  H4    C4  O4    110.53  3.000
 DHK  C5    C4  O4    107.41  3.000
 DHK  H4    C4  C3    108.45  3.000
 DHK  C5    C4  C3    110.32  3.000
 DHK  O4    C4  C3    111.79  3.000
 DHK  HA    O4  C4    109.15  3.000
 DHK  H5    C5  O5    110.64  3.000
 DHK  H5    C5  C6    108.84  3.000
 DHK  O5    C5  C6    108.54  3.000
 DHK  H5    C5  C4    107.65  3.000
 DHK  O5    C5  C4    111.41  3.000
 DHK  C6    C5  C4    109.74  3.000
 DHK  H1    C1  C     105.56  3.000
 DHK  H1    C1  C6    108.79  3.000
 DHK  C     C1  C6    111.30  3.000
 DHK  H1    C1  C2    108.64  3.000
 DHK  C     C1  C2    110.54  3.000
 DHK  C6    C1  C2    111.76  3.000
 DHK  H6C2  C6  H6C1  107.40  3.000
 DHK  H6C2  C6  C1    109.92  3.000
 DHK  H6C1  C6  C1    110.30  3.000
 DHK  H6C2  C6  C5    109.68  3.000
 DHK  H6C1  C6  C5    109.44  3.000
 DHK  C1    C6  C5    110.05  3.000
 DHK  O2    C   O1    123.06  3.000
 DHK  O2    C   C1    111.63  3.000
 DHK  O1    C   C1    125.30  3.000
 DHK  HC    O2  C     110.13  3.000
 DHK  HB    O5  C5    108.16  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
 DHK  CONST_01  HC  O2  C   C1  180.00   0.0  0
 DHK  Var_01    C1  C2  C3  C4    0.19  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
 DHK  chir_01  C4  C3  O4  C5  negativ
 DHK  chir_02  C5  O5  C4  C6  negativ
 DHK  chir_03  C1  C2  C6  C   positiv

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
 DHK  plan-1  C1  0.020
 DHK  plan-1  C   0.020
 DHK  plan-1  O1  0.020
 DHK  plan-1  O2  0.020
 DHK  plan-1  HC  0.020

