# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 03:45:27 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: (3~{R},4~{R},5~{R})-5-[(~{E})-3-(4-hydroxyphenyl)prop-2-enoyl]oxy-3,4-bis(oxidanyl)cyclohexene-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1C=C(C[C@@H](OC(=O)\C=C\c2ccc(O)cc2)[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
 SKT  SKT  '(3~{R},4~{R},5~{R})-5-[(~{E})-3-(4-hydroxyphenyl)prop-2-enoyl]oxy-3,4-bis(oxidanyl)cyclohexene-1-carboxylic acid'  ligand  38  23  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SKT
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
 SKT  C01  C  C      0  -0.085   4.1759  -0.7026   0.2759
 SKT  C02  C  C1     0  -0.258   4.8241   0.4617   0.2404
 SKT  C03  C  CH1    0  -0.048   4.1504   1.8005   0.1766
 SKT  C04  C  CH1    0   0.018   2.6912   1.7006   0.6211
 SKT  C05  C  CH1    0   0.025   2.0293   0.5504  -0.1154
 SKT  C06  C  CH2    0  -0.558   2.6761  -0.7703   0.2751
 SKT  C07  C  C      0   0.334   4.9421  -2.0229   0.3264
 SKT  O08  O  O      0  -0.440   6.1858  -1.9689   0.2813
 SKT  O09  O  OC    -1  -0.648   4.2423  -3.0510   0.4147
 SKT  O10  O  OH1    0  -0.687   4.1793   2.3313  -1.1375
 SKT  O11  O  OH1    0  -0.661   1.9670   2.8754   0.3677
 SKT  O12  O  O2     0  -0.463   0.6467   0.5475   0.2567
 SKT  C13  C  C      0   0.615  -0.2520   0.0631  -0.5956
 SKT  C14  C  C1     0  -0.455  -1.6080   0.1635  -0.0389
 SKT  C15  C  C1     0  -0.164  -2.6605  -0.2848  -0.7363
 SKT  C16  C  CR6    0   0.126  -4.0558  -0.2696  -0.3315
 SKT  O17  O  O      0  -0.419   0.0252  -0.3901  -1.6828
 SKT  C18  C  CR16   0  -0.252  -5.0155  -0.8064  -1.1958
 SKT  C19  C  CR16   0  -0.333  -6.3583  -0.8236  -0.8716
 SKT  C20  C  CR6    0   0.433  -6.7807  -0.2959   0.3469
 SKT  C21  C  CR16   0  -0.368  -5.8389   0.2482   1.2236
 SKT  C22  C  CR16   0  -0.281  -4.5011   0.2611   0.8836
 SKT  O23  O  OH1    0  -0.597  -8.0912  -0.3410   0.6309
 SKT  H6   H  H      0   0.225   5.9089   0.4584   0.2278
 SKT  H5   H  HCH1   0   0.232   4.6662   2.4862   0.8666
 SKT  H4   H  HCH1   0   0.252   2.7012   1.4649   1.6971
 SKT  H3   H  HCH1   0   0.283   2.1206   0.7107  -1.1933
 SKT  H1   H  HCH2   0   0.250   2.3384  -1.5619  -0.3953
 SKT  H2   H  HCH2   0   0.257   2.3302  -1.0565   1.2747
 SKT  H8   H  HOH1   0   0.428   5.0926   2.3220  -1.4402
 SKT  H9   H  HOH1   0   0.415   2.3894   3.6006   0.8385
 SKT  H10  H  H      0   0.222  -1.7118   0.6074   0.9435
 SKT  H11  H  H      0   0.244  -2.4683  -0.7165  -1.7143
 SKT  H12  H  HCR6   0   0.242  -4.7007  -1.2209  -2.1460
 SKT  H13  H  HCR6   0   0.203  -7.0827  -1.2460  -1.5561
 SKT  H14  H  HCR6   0   0.234  -6.1542   0.6574   2.1765
 SKT  H15  H  HCR6   0   0.220  -3.7977   0.6887   1.5864
 SKT  H16  H  HOH1   0   0.460  -8.2663   0.0454   1.4961

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
 SKT  O08  C07  deloc     1.246  0.020  1.246
 SKT  C02  C03  single    1.500  0.020  1.500
 SKT  C02  C01  double    1.333  0.020  1.333
 SKT  C07  C01  single    1.527  0.020  1.527
 SKT  C07  O09  deloc     1.247  0.020  1.247
 SKT  O10  C03  single    1.418  0.020  1.418
 SKT  C03  C04  single    1.529  0.020  1.529
 SKT  C01  C06  single    1.501  0.020  1.501
 SKT  C04  O11  single    1.403  0.020  1.403
 SKT  C04  C05  single    1.518  0.020  1.518
 SKT  C06  C05  single    1.522  0.020  1.522
 SKT  C05  O12  single    1.432  0.020  1.432
 SKT  O12  C13  single    1.330  0.020  1.330
 SKT  O17  C13  double    1.210  0.020  1.210
 SKT  C13  C14  single    1.469  0.020  1.469
 SKT  C14  C15  double    1.340  0.020  1.340
 SKT  C15  C16  single    1.453  0.020  1.453
 SKT  C16  C18  aromatic  1.399  0.020  1.399
 SKT  C16  C22  aromatic  1.399  0.020  1.399
 SKT  C18  C19  aromatic  1.382  0.020  1.382
 SKT  C22  C21  aromatic  1.380  0.020  1.380
 SKT  C19  C20  aromatic  1.393  0.020  1.393
 SKT  C21  C20  aromatic  1.397  0.020  1.397
 SKT  C20  O23  single    1.342  0.020  1.342
 SKT  C02  H6   single    0.930  0.020  1.080
 SKT  C03  H5   single    0.970  0.020  1.090
 SKT  C04  H4   single    0.970  0.020  1.090
 SKT  C05  H3   single    0.970  0.020  1.090
 SKT  C06  H1   single    0.970  0.020  1.090
 SKT  C06  H2   single    0.970  0.020  1.090
 SKT  O10  H8   single    0.850  0.020  0.980
 SKT  O11  H9   single    0.850  0.020  0.980
 SKT  C14  H10  single    0.930  0.020  1.080
 SKT  C15  H11  single    0.930  0.020  1.080
 SKT  C18  H12  single    0.930  0.020  1.080
 SKT  C19  H13  single    0.930  0.020  1.080
 SKT  C21  H14  single    0.930  0.020  1.080
 SKT  C22  H15  single    0.930  0.020  1.080
 SKT  O23  H16  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
 SKT  C07  C01  C06  117.53  3.000
 SKT  C06  C01  C02  121.68  3.000
 SKT  C07  C01  C02  120.79  3.000
 SKT  H6   C02  C03  116.82  3.000
 SKT  H6   C02  C01  118.95  3.000
 SKT  C03  C02  C01  124.21  3.000
 SKT  H5   C03  O10  109.76  3.000
 SKT  H5   C03  C04  107.80  3.000
 SKT  O10  C03  C04  108.27  3.000
 SKT  H5   C03  C02  108.59  3.000
 SKT  C04  C03  C02  110.98  3.000
 SKT  O10  C03  C02  111.37  3.000
 SKT  H4   C04  O11  111.12  3.000
 SKT  H4   C04  C05  108.41  3.000
 SKT  O11  C04  C05  108.77  3.000
 SKT  H4   C04  C03  106.82  3.000
 SKT  C05  C04  C03  108.95  3.000
 SKT  O11  C04  C03  112.67  3.000
 SKT  H3   C05  O12  109.70  3.000
 SKT  H3   C05  C06  110.17  3.000
 SKT  O12  C05  C06  110.00  3.000
 SKT  H3   C05  C04  109.32  3.000
 SKT  O12  C05  C04  107.25  3.000
 SKT  C06  C05  C04  110.36  3.000
 SKT  H2   C06  H1   105.86  3.000
 SKT  H2   C06  C05  109.07  3.000
 SKT  H1   C06  C05  109.91  3.000
 SKT  H2   C06  C01  109.07  3.000
 SKT  H1   C06  C01  110.02  3.000
 SKT  C05  C06  C01  112.68  3.000
 SKT  O09  C07  O08  126.78  3.000
 SKT  O09  C07  C01  115.69  3.000
 SKT  O08  C07  C01  117.52  3.000
 SKT  H8   O10  C03  107.90  3.000
 SKT  H9   O11  C04  108.42  3.000
 SKT  C13  O12  C05  119.13  3.000
 SKT  O17  C13  C14  125.27  3.000
 SKT  C14  C13  O12  110.85  3.000
 SKT  O17  C13  O12  123.88  3.000
 SKT  H10  C14  C15  122.28  3.000
 SKT  H10  C14  C13  117.40  3.000
 SKT  C15  C14  C13  120.32  3.000
 SKT  H11  C15  C16  115.15  3.000
 SKT  H11  C15  C14  117.56  3.000
 SKT  C16  C15  C14  127.29  3.000
 SKT  C22  C16  C18  117.65  3.000
 SKT  C22  C16  C15  123.49  3.000
 SKT  C18  C16  C15  118.86  3.000
 SKT  H12  C18  C19  118.91  3.000
 SKT  H12  C18  C16  119.31  3.000
 SKT  C19  C18  C16  121.78  3.000
 SKT  H13  C19  C20  119.86  3.000
 SKT  H13  C19  C18  120.46  3.000
 SKT  C20  C19  C18  119.67  3.000
 SKT  O23  C20  C21  122.60  3.000
 SKT  O23  C20  C19  117.93  3.000
 SKT  C21  C20  C19  119.47  3.000
 SKT  H14  C21  C22  119.66  3.000
 SKT  H14  C21  C20  120.17  3.000
 SKT  C22  C21  C20  120.16  3.000
 SKT  H15  C22  C21  118.27  3.000
 SKT  H15  C22  C16  120.47  3.000
 SKT  C21  C22  C16  121.26  3.000
 SKT  H16  O23  C20  110.73  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
 SKT  CONST_01  C20  C19  C18  C16     0.00   0.0  0
 SKT  CONST_02  C20  C21  C22  C16     0.00   0.0  0
 SKT  CONST_03  C21  C22  C16  C18     0.00   0.0  0
 SKT  CONST_04  C21  C20  C19  C18     0.00   0.0  0
 SKT  CONST_05  C22  C16  C18  C19     0.00   0.0  0
 SKT  CONST_06  C22  C21  C20  C19     0.00   0.0  0
 SKT  CONST_07  C19  C18  C16  C15   180.00   0.0  0
 SKT  CONST_08  C21  C22  C16  C15   180.00   0.0  0
 SKT  CONST_09  O23  C20  C19  C18   180.00   0.0  0
 SKT  CONST_10  O23  C20  C21  C22   180.00   0.0  0
 SKT  CONST_11  H13  C19  C18  C16   180.00   0.0  0
 SKT  CONST_12  H14  C21  C22  C16   180.00   0.0  0
 SKT  CONST_13  H15  C22  C16  C18   180.00   0.0  0
 SKT  CONST_14  H12  C18  C19  C20   180.00   0.0  0
 SKT  Var_01    C05  C06  C01  C02    14.33  30.0  1
 SKT  Var_02    C06  C01  C02  C03    -0.93  30.0  1
 SKT  Var_03    O08  C07  C01  C02    -2.68  30.0  3
 SKT  Var_04    C18  C16  C15  C14  -179.01  30.0  2
 SKT  Var_05    C16  C15  C14  C13   179.56   0.0  2
 SKT  Var_06    O17  C13  O12  C05     0.37  30.0  3
 SKT  Var_07    C15  C14  C13  O12  -179.25  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
 SKT  chir_01  C03  C02  O10  C04  negativ
 SKT  chir_02  C04  O11  C05  C03  negativ
 SKT  chir_03  C05  O12  C06  C04  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
 SKT  plan-1  C15  0.020
 SKT  plan-1  C16  0.020
 SKT  plan-1  C18  0.020
 SKT  plan-1  C19  0.020
 SKT  plan-1  C20  0.020
 SKT  plan-1  C21  0.020
 SKT  plan-1  C22  0.020
 SKT  plan-1  O23  0.020
 SKT  plan-1  H12  0.020
 SKT  plan-1  H13  0.020
 SKT  plan-1  H14  0.020
 SKT  plan-1  H15  0.020
 SKT  plan-2  C01  0.020
 SKT  plan-2  C07  0.020
 SKT  plan-2  O08  0.020
 SKT  plan-2  O09  0.020
 SKT  plan-3  O12  0.020
 SKT  plan-3  C13  0.020
 SKT  plan-3  C14  0.020
 SKT  plan-3  O17  0.020
 SKT  plan-4  C13  0.020
 SKT  plan-4  C14  0.020
 SKT  plan-4  C15  0.020
 SKT  plan-4  C16  0.020
 SKT  plan-4  H10  0.020
 SKT  plan-4  H11  0.020

