# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 26 06:56:38 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: (1R,4R,5R)-1,4,5-trihydroxy-3-[3-(phenylsulfanyl)phenyl]cyclohex-2-ene-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1C[C@@](O)(C=C([C@H]1O)c2cccc(Sc3ccccc3)c2)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
 RP4  RP4  '(1R,4R,5R)-1,4,5-trihydroxy-3-[3-(phenylsulfanyl)phenyl]cyclohex-2-ene-1-carboxylic acid'  ligand  43  25  .  2022-07-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_RP4
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
 RP4  O3    O  O     0  -0.424  -1.9600  -2.8300   0.7037
 RP4  C2    C  C     0   0.535  -2.3213  -2.3489  -0.3391
 RP4  O1    O  OH1   0  -0.587  -2.3067  -2.9977  -1.4921
 RP4  C4    C  CT    0   0.069  -2.7848  -0.8939  -0.5071
 RP4  O5    O  OH1   0  -0.656  -3.6697  -0.7643  -1.5949
 RP4  C12   C  CH2   0  -0.490  -3.5226  -0.4333   0.7451
 RP4  C10   C  CH1   0   0.055  -3.5767   1.0809   0.8119
 RP4  O11   O  OH1   0  -0.674  -4.3921   1.4388   1.9009
 RP4  C8    C  CH1   0  -0.033  -2.1633   1.6244   0.9699
 RP4  O9    O  OH1   0  -0.663  -2.2435   3.0296   0.9197
 RP4  C7    C  C     0   0.019  -1.2476   1.0505  -0.0936
 RP4  C6    C  C1    0  -0.262  -1.5296  -0.0839  -0.7318
 RP4  C13   C  CR6   0   0.055   0.0398   1.7348  -0.3605
 RP4  C25   C  CR16  0  -0.309   0.1061   3.0005  -0.9417
 RP4  C24   C  CR16  0  -0.230   1.3429   3.5751  -1.1990
 RP4  C23   C  CR16  0  -0.276   2.5172   2.9088  -0.8831
 RP4  C15   C  CR6   0  -0.102   2.4560   1.6466  -0.2978
 RP4  C14   C  CR16  0  -0.265   1.2197   1.0695  -0.0332
 RP4  S16   S  S2    0   0.077   3.9938   0.8636   0.1038
 RP4  C17   C  CR6   0  -0.185   3.5072  -0.8163   0.3849
 RP4  C22   C  CR16  0  -0.207   3.2287  -1.6521  -0.6935
 RP4  C21   C  CR16  0  -0.243   2.8434  -2.9642  -0.4649
 RP4  C20   C  CR16  0  -0.244   2.7528  -3.4483   0.8348
 RP4  C19   C  CR16  0  -0.248   3.0483  -2.6188   1.9075
 RP4  C18   C  CR16  0  -0.221   3.4225  -1.2996   1.6858
 RP4  H1    H  HOH1  0   0.486  -1.9622  -3.8949  -1.3654
 RP4  H5    H  HOH1  0   0.457  -3.1773  -0.7779  -2.4230
 RP4  H121  H  HCH2  0   0.260  -3.0169  -0.8108   1.6353
 RP4  H122  H  HCH2  0   0.270  -4.5322  -0.8508   0.7407
 RP4  H10   H  HCH1  0   0.215  -3.9877   1.4751  -0.1299
 RP4  H11   H  HOH1  0   0.449  -4.3990   2.3998   1.9642
 RP4  H8    H  HCH1  0   0.242  -1.7766   1.2988   1.9482
 RP4  H9    H  HOH1  0   0.464  -1.4747   3.4082   1.3571
 RP4  H6    H  H     0   0.279  -0.8406  -0.4530  -1.4873
 RP4  H25   H  HCR6  0   0.257  -0.7981   3.5218  -1.2220
 RP4  H24   H  HCR6  0   0.263   1.3956   4.5497  -1.6668
 RP4  H23   H  HCR6  0   0.267   3.4737   3.3673  -1.1021
 RP4  H14   H  HCR6  0   0.261   1.1586   0.0925   0.4287
 RP4  H22   H  HCR6  0   0.273   3.3061  -1.2753  -1.7052
 RP4  H21   H  HCR6  0   0.264   2.6210  -3.6115  -1.3030
 RP4  H20   H  HCR6  0   0.264   2.4542  -4.4734   1.0108
 RP4  H19   H  HCR6  0   0.265   2.9808  -2.9937   2.9204
 RP4  H18   H  HCR6  0   0.272   3.6398  -0.6463   2.5209

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
 RP4  O3   C2    double    1.204  0.020  1.204
 RP4  C2   O1    single    1.323  0.020  1.323
 RP4  C2   C4    single    1.536  0.020  1.536
 RP4  O1   H1    single    0.850  0.020  0.980
 RP4  C4   O5    single    1.408  0.020  1.408
 RP4  C4   C12   single    1.525  0.020  1.525
 RP4  C4   C6    single    1.511  0.020  1.511
 RP4  O5   H5    single    0.850  0.020  0.980
 RP4  C12  C10   single    1.517  0.020  1.517
 RP4  C12  H121  single    0.970  0.020  1.090
 RP4  C12  H122  single    0.970  0.020  1.090
 RP4  C10  O11   single    1.407  0.020  1.407
 RP4  C10  C8    single    1.522  0.020  1.522
 RP4  C10  H10   single    0.970  0.020  1.090
 RP4  O11  H11   single    0.850  0.020  0.980
 RP4  C8   O9    single    1.408  0.020  1.408
 RP4  C8   C7    single    1.516  0.020  1.516
 RP4  C8   H8    single    0.970  0.020  1.090
 RP4  O9   H9    single    0.850  0.020  0.980
 RP4  C7   C6    double    1.332  0.020  1.332
 RP4  C7   C13   single    1.482  0.020  1.482
 RP4  C6   H6    single    0.930  0.020  1.080
 RP4  C13  C25   aromatic  1.394  0.020  1.394
 RP4  C13  C14   aromatic  1.394  0.020  1.394
 RP4  C25  C24   aromatic  1.388  0.020  1.388
 RP4  C25  H25   single    0.930  0.020  1.080
 RP4  C24  C23   aromatic  1.387  0.020  1.387
 RP4  C24  H24   single    0.930  0.020  1.080
 RP4  C23  C15   aromatic  1.393  0.020  1.393
 RP4  C23  H23   single    0.930  0.020  1.080
 RP4  C15  C14   aromatic  1.390  0.020  1.390
 RP4  C15  S16   single    1.772  0.020  1.772
 RP4  C14  H14   single    0.930  0.020  1.080
 RP4  S16  C17   single    1.771  0.020  1.771
 RP4  C17  C22   aromatic  1.393  0.020  1.393
 RP4  C17  C18   aromatic  1.390  0.020  1.390
 RP4  C22  C21   aromatic  1.386  0.020  1.386
 RP4  C22  H22   single    0.930  0.020  1.080
 RP4  C21  C20   aromatic  1.390  0.020  1.390
 RP4  C21  H21   single    0.930  0.020  1.080
 RP4  C20  C19   aromatic  1.388  0.020  1.388
 RP4  C20  H20   single    0.930  0.020  1.080
 RP4  C19  C18   aromatic  1.389  0.020  1.389
 RP4  C19  H19   single    0.930  0.020  1.080
 RP4  C18  H18   single    0.930  0.020  1.080

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
 RP4  C4    C2   O1    111.87  3.000
 RP4  C4    C2   O3    124.31  3.000
 RP4  O1    C2   O3    123.75  3.000
 RP4  H1    O1   C2    110.11  3.000
 RP4  C6    C4   C12   111.24  3.000
 RP4  C6    C4   O5    110.97  3.000
 RP4  C12   C4   O5    107.61  3.000
 RP4  C6    C4   C2    105.87  3.000
 RP4  C12   C4   C2    110.02  3.000
 RP4  O5    C4   C2    111.17  3.000
 RP4  H5    O5   C4    109.97  3.000
 RP4  H122  C12  H121  107.42  3.000
 RP4  H122  C12  C10   110.41  3.000
 RP4  H121  C12  C10   109.03  3.000
 RP4  H122  C12  C4    109.18  3.000
 RP4  H121  C12  C4    109.95  3.000
 RP4  C10   C12  C4    110.80  3.000
 RP4  H10   C10  C8    107.92  3.000
 RP4  H10   C10  O11   110.78  3.000
 RP4  C8    C10  O11   111.52  3.000
 RP4  H10   C10  C12   109.46  3.000
 RP4  C8    C10  C12   109.14  3.000
 RP4  O11   C10  C12   107.98  3.000
 RP4  H11   O11  C10   107.99  3.000
 RP4  H8    C8   C7    107.40  3.000
 RP4  H8    C8   O9    110.29  3.000
 RP4  C7    C8   O9    112.77  3.000
 RP4  H8    C8   C10   108.22  3.000
 RP4  C7    C8   C10   110.65  3.000
 RP4  O9    C8   C10   107.44  3.000
 RP4  H9    O9   C8    109.33  3.000
 RP4  C13   C7   C6    119.40  3.000
 RP4  C13   C7   C8    118.43  3.000
 RP4  C6    C7   C8    122.05  3.000
 RP4  H6    C6   C7    119.21  3.000
 RP4  H6    C6   C4    116.62  3.000
 RP4  C7    C6   C4    124.15  3.000
 RP4  C14   C13  C25   119.41  3.000
 RP4  C14   C13  C7    118.21  3.000
 RP4  C25   C13  C7    122.38  3.000
 RP4  H25   C25  C24   119.86  3.000
 RP4  H25   C25  C13   120.41  3.000
 RP4  C24   C25  C13   119.70  3.000
 RP4  H24   C24  C23   119.33  3.000
 RP4  H24   C24  C25   119.76  3.000
 RP4  C23   C24  C25   120.90  3.000
 RP4  H23   C23  C15   120.49  3.000
 RP4  H23   C23  C24   119.90  3.000
 RP4  C15   C23  C24   119.61  3.000
 RP4  S16   C15  C14   123.05  3.000
 RP4  S16   C15  C23   117.24  3.000
 RP4  C14   C15  C23   119.70  3.000
 RP4  H14   C14  C15   120.42  3.000
 RP4  H14   C14  C13   118.91  3.000
 RP4  C15   C14  C13   120.68  3.000
 RP4  C17   S16  C15   102.51  3.000
 RP4  C18   C17  C22   120.25  3.000
 RP4  C18   C17  S16   119.66  3.000
 RP4  C22   C17  S16   120.08  3.000
 RP4  H22   C22  C21   120.23  3.000
 RP4  H22   C22  C17   120.04  3.000
 RP4  C21   C22  C17   119.73  3.000
 RP4  H21   C21  C20   120.17  3.000
 RP4  H21   C21  C22   119.70  3.000
 RP4  C20   C21  C22   120.13  3.000
 RP4  H20   C20  C19   119.95  3.000
 RP4  H20   C20  C21   120.00  3.000
 RP4  C19   C20  C21   120.05  3.000
 RP4  H19   C19  C18   119.68  3.000
 RP4  H19   C19  C20   120.21  3.000
 RP4  C18   C19  C20   120.11  3.000
 RP4  H18   C18  C19   120.28  3.000
 RP4  H18   C18  C17   119.99  3.000
 RP4  C19   C18  C17   119.73  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
 RP4  CONST_01  C23  C24  C25  C13    0.00   0.0  0
 RP4  CONST_02  C23  C15  C14  C13    0.00   0.0  0
 RP4  CONST_03  C15  C14  C13  C25    0.00   0.0  0
 RP4  CONST_04  C15  C23  C24  C25    0.00   0.0  0
 RP4  CONST_05  C14  C13  C25  C24    0.00   0.0  0
 RP4  CONST_06  C14  C15  C23  C24    0.00   0.0  0
 RP4  CONST_07  C20  C21  C22  C17    0.00   0.0  0
 RP4  CONST_08  C20  C19  C18  C17    0.00   0.0  0
 RP4  CONST_09  C19  C18  C17  C22    0.00   0.0  0
 RP4  CONST_10  C19  C20  C21  C22    0.00   0.0  0
 RP4  CONST_11  C18  C17  C22  C21    0.00   0.0  0
 RP4  CONST_12  C18  C19  C20  C21    0.00   0.0  0
 RP4  CONST_13  C24  C25  C13  C7   180.00   0.0  0
 RP4  CONST_14  C15  C14  C13  C7   180.00   0.0  0
 RP4  CONST_15  S16  C15  C14  C13  180.00   0.0  0
 RP4  CONST_16  S16  C15  C23  C24  180.00   0.0  0
 RP4  CONST_17  C21  C22  C17  S16  180.00   0.0  0
 RP4  CONST_18  C19  C18  C17  S16  180.00   0.0  0
 RP4  CONST_19  H25  C25  C13  C7     0.00   0.0  0
 RP4  CONST_20  H14  C14  C13  C7     0.00   0.0  0
 RP4  CONST_21  H24  C24  C25  C13  180.00   0.0  0
 RP4  CONST_22  H23  C23  C24  C25  180.00   0.0  0
 RP4  CONST_23  H21  C21  C22  C17  180.00   0.0  0
 RP4  CONST_24  H19  C19  C18  C17  180.00   0.0  0
 RP4  CONST_25  H18  C18  C17  C22  180.00   0.0  0
 RP4  CONST_26  H20  C20  C21  C22  180.00   0.0  0
 RP4  CONST_27  H22  C22  C21  C20  180.00   0.0  0
 RP4  CONST_28  H1   O1   C2   C4   180.00   0.0  0
 RP4  Var_01    C8   C7   C6   C4     1.83  30.0  1
 RP4  Var_02    C25  C13  C7   C8   -68.07  30.0  2
 RP4  Var_03    C22  C17  S16  C15   76.83  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
 RP4  chir_01  C4   O5   C12  C6  positiv
 RP4  chir_02  C10  O11  C12  C8  positiv
 RP4  chir_03  C8   O9   C10  C7  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
 RP4  plan-1  C7   0.020
 RP4  plan-1  C13  0.020
 RP4  plan-1  C25  0.020
 RP4  plan-1  C24  0.020
 RP4  plan-1  C23  0.020
 RP4  plan-1  C15  0.020
 RP4  plan-1  C14  0.020
 RP4  plan-1  S16  0.020
 RP4  plan-1  H25  0.020
 RP4  plan-1  H24  0.020
 RP4  plan-1  H23  0.020
 RP4  plan-1  H14  0.020
 RP4  plan-2  S16  0.020
 RP4  plan-2  C17  0.020
 RP4  plan-2  C22  0.020
 RP4  plan-2  C21  0.020
 RP4  plan-2  C20  0.020
 RP4  plan-2  C19  0.020
 RP4  plan-2  C18  0.020
 RP4  plan-2  H22  0.020
 RP4  plan-2  H21  0.020
 RP4  plan-2  H20  0.020
 RP4  plan-2  H19  0.020
 RP4  plan-2  H18  0.020
 RP4  plan-3  O3   0.020
 RP4  plan-3  C2   0.020
 RP4  plan-3  O1   0.020
 RP4  plan-3  C4   0.020
 RP4  plan-3  H1   0.020

