# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 08:55:26 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  21  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 GRAND
;

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  -0.365  -1.1380  -0.2614  -0.4606
 DHK  C3    C  C      0   0.314  -1.2698   0.0984   0.8152
 DHK  O3    O  OH1    0  -0.646  -2.4530   0.3616   1.4278
 DHK  C4    C  CH1    0  -0.051  -0.1053   0.3008   1.7511
 DHK  O4    O  OH1    0  -0.674  -0.3409  -0.2724   3.0219
 DHK  C5    C  CH1    0   0.058   1.1477  -0.3520   1.1851
 DHK  C1    C  CH1    0  -0.430   0.1906  -0.5035  -1.1178
 DHK  C6    C  CH2    0  -0.466   1.3307   0.0424  -0.2669
 DHK  C     C  C      0   0.438   0.2081   0.0111  -2.5804
 DHK  O1    O  O      0  -0.600   1.2496   0.5670  -2.9772
 DHK  O2    O  OC    -1  -0.612  -0.8174  -0.2093  -3.2552
 DHK  O5    O  OH1    0  -0.677   2.2939   0.0266   1.9151
 DHK  H2    H  H      0   0.238  -2.0230  -0.3865  -1.0773
 DHK  H3    H  HOH1   0   0.465  -3.1778   0.2268   0.8067
 DHK  H4    H  HCH1   0   0.224   0.0830   1.3814   1.8515
 DHK  HA    H  HOH1   0   0.456  -0.9711   0.2749   3.4996
 DHK  H5    H  HCH1   0   0.196   1.0028  -1.4440   1.2360
 DHK  H1    H  HCH1   0   0.236   0.3292  -1.5933  -1.2052
 DHK  H6C1  H  HCH2   0   0.217   1.3712   1.1332  -0.3471
 DHK  H6C2  H  HCH2   0   0.234   2.2863  -0.3391  -0.6307
 DHK  HB    H  HOH1   0   0.445   2.1406  -0.1866   2.8417

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  1.332  0.020  1.332
 DHK  C2  C1    single  1.502  0.020  1.502
 DHK  C2  H2    single  0.930  0.020  1.080
 DHK  C3  O3    single  1.358  0.020  1.358
 DHK  C3  C4    single  1.508  0.020  1.508
 DHK  O3  H3    single  0.850  0.020  0.980
 DHK  C4  O4    single  1.414  0.020  1.414
 DHK  C4  C5    single  1.522  0.020  1.522
 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  1.411  0.020  1.411
 DHK  C5  H5    single  0.970  0.020  1.090
 DHK  C1  C6    single  1.524  0.020  1.524
 DHK  C1  C     single  1.551  0.020  1.551
 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    deloc   1.245  0.020  1.245
 DHK  C   O2    deloc   1.247  0.020  1.247
 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    116.99  3.000
 DHK  H2    C2  C3    119.63  3.000
 DHK  C1    C2  C3    123.38  3.000
 DHK  C4    C3  O3    111.52  3.000
 DHK  C4    C3  C2    123.67  3.000
 DHK  O3    C3  C2    124.79  3.000
 DHK  H3    O3  C3    109.71  3.000
 DHK  H4    C4  C5    108.30  3.000
 DHK  H4    C4  O4    110.14  3.000
 DHK  C5    C4  O4    107.31  3.000
 DHK  H4    C4  C3    108.68  3.000
 DHK  C5    C4  C3    110.33  3.000
 DHK  O4    C4  C3    112.01  3.000
 DHK  HA    O4  C4    108.96  3.000
 DHK  H5    C5  O5    110.40  3.000
 DHK  H5    C5  C6    108.53  3.000
 DHK  O5    C5  C6    109.14  3.000
 DHK  H5    C5  C4    107.42  3.000
 DHK  O5    C5  C4    111.18  3.000
 DHK  C6    C5  C4    110.13  3.000
 DHK  H1    C1  C     104.60  3.000
 DHK  H1    C1  C6    107.73  3.000
 DHK  C     C1  C6    113.54  3.000
 DHK  H1    C1  C2    107.78  3.000
 DHK  C     C1  C2    111.67  3.000
 DHK  C6    C1  C2    111.08  3.000
 DHK  H6C2  C6  H6C1  106.95  3.000
 DHK  H6C2  C6  C1    110.10  3.000
 DHK  H6C1  C6  C1    110.11  3.000
 DHK  H6C2  C6  C5    109.52  3.000
 DHK  H6C1  C6  C5    109.51  3.000
 DHK  C1    C6  C5    110.57  3.000
 DHK  O2    C   O1    126.45  3.000
 DHK  O2    C   C1    116.26  3.000
 DHK  O1    C   C1    117.26  3.000
 DHK  HB    O5  C5    108.01  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  Var_01  C1  C2  C3  C4  -0.21  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

