# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 11:59:51 2022
#   Inital geometry file: a 58 line input string
#   Ligand name: (3R,4S,5R)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CC(=C[C@@H](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
 SKM  SKM  '(3R,4S,5R)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid'  ligand  21  12  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SKM
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
 SKM  O12  O  OH1    0  -0.672   3.0978  -0.0819   0.4135
 SKM  C8   C  CH1    0   0.049   1.7036  -0.0211   0.5740
 SKM  C6   C  CH1    0   0.051   1.1371   1.0470  -0.3448
 SKM  O7   O  OH1    0  -0.675   1.8638   2.2410  -0.1463
 SKM  C5   C  CH2    0  -0.544  -0.3438   1.2377  -0.0338
 SKM  C4   C  C      0  -0.090  -1.0999  -0.0522   0.0809
 SKM  C1   C  C      0   0.395  -2.6241   0.0053   0.0572
 SKM  O2   O  OC    -1  -0.595  -3.1257   1.1431  -0.0389
 SKM  O3   O  O      0  -0.596  -3.2424  -1.0733   0.1435
 SKM  C10  C  C1     0  -0.292  -0.4654  -1.2142   0.2362
 SKM  C9   C  CH1    0  -0.050   1.0269  -1.3608   0.2854
 SKM  O11  O  OH1    0  -0.666   1.5382  -1.8681  -0.9364
 SKM  H12  H  HOH1   0   0.447   3.4367  -0.7827   0.9795
 SKM  H8   H  HCH1   0   0.204   1.4384   0.2499   1.6093
 SKM  H6   H  HCH1   0   0.201   1.2413   0.7051  -1.3851
 SKM  HO7  H  HOH1   0   0.447   1.4742   2.9175  -0.7090
 SKM  H51  H  HCH2   0   0.235  -0.4309   1.7966   0.9058
 SKM  H52  H  HCH2   0   0.244  -0.8033   1.8711  -0.7966
 SKM  H10  H  H      0   0.243  -1.0501  -2.1249   0.3158
 SKM  H9   H  HCH1   0   0.215   1.2797  -2.0514   1.1054
 SKM  H11  H  HOH1   0   0.450   1.0601  -2.6770  -1.1447

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
 SKM  O12  C8   single  1.405  0.020  1.405
 SKM  O12  H12  single  0.850  0.020  0.980
 SKM  C8   C6   single  1.519  0.020  1.519
 SKM  C8   C9   single  1.528  0.020  1.528
 SKM  C8   H8   single  0.970  0.020  1.090
 SKM  C6   O7   single  1.412  0.020  1.412
 SKM  C6   C5   single  1.525  0.020  1.525
 SKM  C6   H6   single  0.970  0.020  1.090
 SKM  O7   HO7  single  0.850  0.020  0.980
 SKM  C5   C4   single  1.500  0.020  1.500
 SKM  C5   H51  single  0.970  0.020  1.090
 SKM  C5   H52  single  0.970  0.020  1.090
 SKM  C4   C1   single  1.525  0.020  1.525
 SKM  C4   C10  double  1.333  0.020  1.333
 SKM  C1   O2   deloc   1.247  0.020  1.247
 SKM  C1   O3   deloc   1.246  0.020  1.246
 SKM  C10  C9   single  1.500  0.020  1.500
 SKM  C10  H10  single  0.930  0.020  1.080
 SKM  C9   O11  single  1.418  0.020  1.418
 SKM  C9   H9   single  0.970  0.020  1.090
 SKM  O11  H11  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
 SKM  H12  O12  C8   108.29  3.000
 SKM  H8   C8   C9   106.63  3.000
 SKM  H8   C8   C6   107.79  3.000
 SKM  C9   C8   C6   109.70  3.000
 SKM  H8   C8   O12  110.89  3.000
 SKM  C9   C8   O12  112.33  3.000
 SKM  C6   C8   O12  109.37  3.000
 SKM  H6   C6   C5   108.88  3.000
 SKM  H6   C6   O7   110.30  3.000
 SKM  C5   C6   O7   111.43  3.000
 SKM  H6   C6   C8   108.56  3.000
 SKM  C5   C6   C8   109.08  3.000
 SKM  O7   C6   C8   108.53  3.000
 SKM  HO7  O7   C6   107.69  3.000
 SKM  H52  C5   H51  105.62  3.000
 SKM  H52  C5   C4   109.88  3.000
 SKM  H51  C5   C4   109.44  3.000
 SKM  H52  C5   C6   109.78  3.000
 SKM  H51  C5   C6   108.39  3.000
 SKM  C4   C5   C6   113.43  3.000
 SKM  C10  C4   C1   120.68  3.000
 SKM  C10  C4   C5   121.25  3.000
 SKM  C1   C4   C5   118.05  3.000
 SKM  O3   C1   O2   126.54  3.000
 SKM  O3   C1   C4   117.52  3.000
 SKM  O2   C1   C4   115.94  3.000
 SKM  H10  C10  C9   116.84  3.000
 SKM  H10  C10  C4   118.93  3.000
 SKM  C9   C10  C4   124.22  3.000
 SKM  H9   C9   O11  109.53  3.000
 SKM  H9   C9   C10  108.30  3.000
 SKM  O11  C9   C10  111.42  3.000
 SKM  H9   C9   C8   107.90  3.000
 SKM  O11  C9   C8   108.45  3.000
 SKM  C10  C9   C8   111.16  3.000
 SKM  H11  O11  C9   107.94  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
 SKM  Var_01  C10  C4   C5  C6  16.10  30.0  1
 SKM  Var_02  C9   C10  C4  C5  -1.20  30.0  1
 SKM  Var_03  O2   C1   C4  C5  -0.97  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
 SKM  chir_01  C8  O12  C6   C9  negativ
 SKM  chir_02  C6  O7   C8   C5  negativ
 SKM  chir_03  C9  O11  C10  C8  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
 SKM  plan-1  C4  0.020
 SKM  plan-1  C1  0.020
 SKM  plan-1  O2  0.020
 SKM  plan-1  O3  0.020

