# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 11:10:42 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: dimethyl {(1S)-3-[bis(4-hydroxyphenyl)methylidene]cyclohexyl}propanedioate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)C([C@H]1CCCC(C1)=C(c2ccc(O)cc2)c3ccc(O)cc3)C(=O)OC
#
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
 5K8  5K8  'dimethyl {(1S)-3-[bis(4-hydroxyphenyl)methylidene]cyclohexyl}propanedioate'  ligand  56  30  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5K8
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
 5K8  O01  O  OH1   0  -0.633  -6.7336   2.1155   0.9139
 5K8  C02  C  CR6   0   0.340  -5.5370   1.5926   0.5772
 5K8  C03  C  CR16  0  -0.370  -5.3969   0.5869  -0.3767
 5K8  C04  C  CR16  0  -0.280  -4.1402   0.0850  -0.6751
 5K8  C05  C  CR6   0   0.011  -2.9921   0.5762  -0.0554
 5K8  C06  C  C     0  -0.024  -1.6555   0.0162  -0.3774
 5K8  C07  C  CR6   0   0.025  -1.5523  -1.4551  -0.2160
 5K8  C08  C  CR16  0  -0.279  -1.9477  -2.0710   0.9729
 5K8  C09  C  CR16  0  -0.324  -1.8747  -3.4426   1.1401
 5K8  C10  C  CR6   0   0.339  -1.4141  -4.2471   0.0993
 5K8  O11  O  OH1   0  -0.633  -1.3628  -5.5793   0.3046
 5K8  C12  C  CR16  0  -0.372  -1.0383  -3.6554  -1.1026
 5K8  C13  C  CR16  0  -0.288  -1.1118  -2.2781  -1.2501
 5K8  C14  C  C     0   0.112  -0.6299   0.7835  -0.7891
 5K8  C15  C  CH2   0  -0.505  -0.7463   2.2473  -1.1098
 5K8  C16  C  CH2   0  -0.430   0.2058   3.0758  -0.2496
 5K8  C17  C  CH2   0  -0.439   1.6413   2.5824  -0.3799
 5K8  C18  C  CH1   0  -0.215   1.7458   1.0907  -0.0615
 5K8  C19  C  CH1   0  -0.484   3.1761   0.5603  -0.2528
 5K8  C20  C  C     0   0.598   4.1788   1.4290   0.4847
 5K8  O21  O  O2    0  -0.439   4.8943   2.1764  -0.3334
 5K8  C22  C  CH3   0  -0.430   5.8394   3.0780   0.2512
 5K8  O23  O  O     0  -0.436   4.2882   1.4361   1.6849
 5K8  C24  C  C     0   0.610   3.3562  -0.8440   0.2987
 5K8  O25  O  O2    0  -0.450   4.4209  -1.4189  -0.2385
 5K8  C26  C  CH3   0  -0.428   4.7655  -2.7297   0.2169
 5K8  O27  O  O     0  -0.424   2.6608  -1.3591   1.1325
 5K8  C28  C  CH2   0  -0.506   0.7789   0.2816  -0.9448
 5K8  C29  C  CR16  0  -0.282  -3.1551   1.5732   0.9063
 5K8  C30  C  CR16  0  -0.327  -4.4046   2.0814   1.2233
 5K8  H1   H  HOH1  0   0.473  -7.4357   1.7050   0.3970
 5K8  H2   H  HCR6  0   0.269  -6.2686   0.1928  -0.8873
 5K8  H3   H  HCR6  0   0.250  -4.0542  -0.7025  -1.4140
 5K8  H4   H  HCR6  0   0.245  -2.3176  -1.4666   1.7927
 5K8  H5   H  HCR6  0   0.260  -2.1785  -3.8951   2.0761
 5K8  H6   H  HOH1  0   0.473  -1.0284  -6.0252  -0.4814
 5K8  H7   H  HCR6  0   0.267  -0.6959  -4.2659  -1.9309
 5K8  H8   H  HCR6  0   0.256  -0.8273  -1.8400  -2.1989
 5K8  H9   H  HCH2  0   0.237  -0.4626   2.3807  -2.1617
 5K8  H10  H  HCH2  0   0.250  -1.7675   2.6125  -1.0132
 5K8  H11  H  HCH2  0   0.238   0.1492   4.1277  -0.5373
 5K8  H12  H  HCH2  0   0.222  -0.1061   3.0192   0.7982
 5K8  H13  H  HCH2  0   0.224   1.9988   2.7648  -1.3994
 5K8  H14  H  HCH2  0   0.242   2.2780   3.1690   0.2873
 5K8  H15  H  HCH1  0   0.247   1.4584   0.9419   0.9845
 5K8  H16  H  HCH1  0   0.304   3.4196   0.5570  -1.3188
 5K8  H17  H  HCH3  0   0.246   6.5899   2.5424   0.8309
 5K8  H18  H  HCH3  0   0.257   6.3171   3.5869  -0.5801
 5K8  H19  H  HCH3  0   0.244   5.3435   3.8091   0.8887
 5K8  H20  H  HCH3  0   0.243   4.9954  -2.7314   1.2818
 5K8  H21  H  HCH3  0   0.243   3.9635  -3.4401   0.0190
 5K8  H22  H  HCH3  0   0.256   5.6488  -3.0173  -0.3448
 5K8  H23  H  HCH2  0   0.270   0.8534  -0.7749  -0.6954
 5K8  H24  H  HCH2  0   0.234   1.0933   0.3883  -1.9910
 5K8  H25  H  HCR6  0   0.252  -2.2867   1.9557   1.4289
 5K8  H26  H  HCR6  0   0.261  -4.5040   2.8529   1.9767

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
 5K8  O11  C10  single    1.349  0.020  1.349
 5K8  C10  C09  aromatic  1.394  0.020  1.394
 5K8  C10  C12  aromatic  1.391  0.020  1.391
 5K8  C09  C08  aromatic  1.384  0.020  1.384
 5K8  C12  C13  aromatic  1.387  0.020  1.387
 5K8  C08  C07  aromatic  1.396  0.020  1.396
 5K8  C13  C07  aromatic  1.393  0.020  1.393
 5K8  C07  C06  single    1.484  0.020  1.484
 5K8  C06  C05  single    1.484  0.020  1.484
 5K8  C06  C14  double    1.345  0.020  1.345
 5K8  C05  C04  aromatic  1.394  0.020  1.394
 5K8  C05  C29  aromatic  1.395  0.020  1.395
 5K8  C04  C03  aromatic  1.386  0.020  1.386
 5K8  C29  C30  aromatic  1.386  0.020  1.386
 5K8  C30  C02  aromatic  1.392  0.020  1.392
 5K8  C03  C02  aromatic  1.393  0.020  1.393
 5K8  C02  O01  single    1.349  0.020  1.349
 5K8  C15  C14  single    1.503  0.020  1.503
 5K8  C15  C16  single    1.527  0.020  1.527
 5K8  C14  C28  single    1.504  0.020  1.504
 5K8  C16  C17  single    1.523  0.020  1.523
 5K8  C28  C18  single    1.539  0.020  1.539
 5K8  C17  C18  single    1.529  0.020  1.529
 5K8  C18  C19  single    1.537  0.020  1.537
 5K8  O27  C24  double    1.202  0.020  1.202
 5K8  O21  C20  single    1.319  0.020  1.319
 5K8  O21  C22  single    1.431  0.020  1.431
 5K8  C19  C20  single    1.518  0.020  1.518
 5K8  C19  C24  single    1.519  0.020  1.519
 5K8  C20  O23  double    1.205  0.020  1.205
 5K8  C24  O25  single    1.324  0.020  1.324
 5K8  O25  C26  single    1.430  0.020  1.430
 5K8  O01  H1   single    0.850  0.020  0.980
 5K8  C03  H2   single    0.930  0.020  1.080
 5K8  C04  H3   single    0.930  0.020  1.080
 5K8  C08  H4   single    0.930  0.020  1.080
 5K8  C09  H5   single    0.930  0.020  1.080
 5K8  O11  H6   single    0.850  0.020  0.980
 5K8  C12  H7   single    0.930  0.020  1.080
 5K8  C13  H8   single    0.930  0.020  1.080
 5K8  C15  H9   single    0.970  0.020  1.090
 5K8  C15  H10  single    0.970  0.020  1.090
 5K8  C16  H11  single    0.970  0.020  1.090
 5K8  C16  H12  single    0.970  0.020  1.090
 5K8  C17  H13  single    0.970  0.020  1.090
 5K8  C17  H14  single    0.970  0.020  1.090
 5K8  C18  H15  single    0.970  0.020  1.090
 5K8  C19  H16  single    0.970  0.020  1.090
 5K8  C22  H17  single    0.970  0.020  1.090
 5K8  C22  H18  single    0.970  0.020  1.090
 5K8  C22  H19  single    0.970  0.020  1.090
 5K8  C26  H20  single    0.970  0.020  1.090
 5K8  C26  H21  single    0.970  0.020  1.090
 5K8  C26  H22  single    0.970  0.020  1.090
 5K8  C28  H23  single    0.970  0.020  1.090
 5K8  C28  H24  single    0.970  0.020  1.090
 5K8  C29  H25  single    0.930  0.020  1.080
 5K8  C30  H26  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
 5K8  H1   O01  C02  110.33  3.000
 5K8  C30  C02  C03  119.30  3.000
 5K8  C03  C02  O01  122.69  3.000
 5K8  C30  C02  O01  118.01  3.000
 5K8  H2   C03  C04  119.73  3.000
 5K8  H2   C03  C02  120.26  3.000
 5K8  C04  C03  C02  120.01  3.000
 5K8  H3   C04  C05  119.61  3.000
 5K8  H3   C04  C03  118.83  3.000
 5K8  C05  C04  C03  121.56  3.000
 5K8  C29  C05  C06  121.63  3.000
 5K8  C29  C05  C04  117.52  3.000
 5K8  C06  C05  C04  120.81  3.000
 5K8  C14  C06  C07  123.08  3.000
 5K8  C14  C06  C05  122.52  3.000
 5K8  C07  C06  C05  114.40  3.000
 5K8  C13  C07  C08  117.45  3.000
 5K8  C13  C07  C06  121.81  3.000
 5K8  C08  C07  C06  120.69  3.000
 5K8  H4   C08  C09  118.65  3.000
 5K8  H4   C08  C07  119.66  3.000
 5K8  C09  C08  C07  121.68  3.000
 5K8  H5   C09  C10  119.79  3.000
 5K8  H5   C09  C08  120.25  3.000
 5K8  C10  C09  C08  119.96  3.000
 5K8  C12  C10  O11  122.77  3.000
 5K8  C12  C10  C09  119.27  3.000
 5K8  O11  C10  C09  117.96  3.000
 5K8  H6   O11  C10  110.25  3.000
 5K8  H7   C12  C13  119.63  3.000
 5K8  H7   C12  C10  120.38  3.000
 5K8  C13  C12  C10  119.99  3.000
 5K8  H8   C13  C12  118.74  3.000
 5K8  H8   C13  C07  119.62  3.000
 5K8  C12  C13  C07  121.63  3.000
 5K8  C28  C14  C15  112.05  3.000
 5K8  C28  C14  C06  123.75  3.000
 5K8  C15  C14  C06  124.17  3.000
 5K8  H10  C15  H9   106.66  3.000
 5K8  H10  C15  C16  110.65  3.000
 5K8  H9   C15  C16  108.22  3.000
 5K8  H10  C15  C14  112.35  3.000
 5K8  H9   C15  C14  107.63  3.000
 5K8  C16  C15  C14  111.09  3.000
 5K8  H12  C16  H11  106.70  3.000
 5K8  H12  C16  C17  109.49  3.000
 5K8  H11  C16  C17  109.77  3.000
 5K8  H12  C16  C15  109.47  3.000
 5K8  H11  C16  C15  109.99  3.000
 5K8  C17  C16  C15  111.31  3.000
 5K8  H14  C17  H13  106.77  3.000
 5K8  H14  C17  C18  110.90  3.000
 5K8  H13  C17  C18  109.51  3.000
 5K8  H14  C17  C16  108.83  3.000
 5K8  H13  C17  C16  109.46  3.000
 5K8  C18  C17  C16  111.26  3.000
 5K8  H15  C18  C28  108.17  3.000
 5K8  H15  C18  C19  108.44  3.000
 5K8  C28  C18  C19  109.36  3.000
 5K8  H15  C18  C17  108.27  3.000
 5K8  C19  C18  C17  111.98  3.000
 5K8  C28  C18  C17  110.51  3.000
 5K8  H16  C19  C24  108.95  3.000
 5K8  H16  C19  C20  109.16  3.000
 5K8  C24  C19  C20  105.92  3.000
 5K8  H16  C19  C18  109.24  3.000
 5K8  C24  C19  C18  112.58  3.000
 5K8  C20  C19  C18  110.89  3.000
 5K8  O23  C20  O21  124.40  3.000
 5K8  O23  C20  C19  123.18  3.000
 5K8  O21  C20  C19  112.41  3.000
 5K8  C22  O21  C20  117.51  3.000
 5K8  H19  C22  H18  109.50  3.000
 5K8  H19  C22  H17  109.40  3.000
 5K8  H18  C22  H17  109.57  3.000
 5K8  H19  C22  O21  111.17  3.000
 5K8  H18  C22  O21  105.85  3.000
 5K8  H17  C22  O21  111.27  3.000
 5K8  O27  C24  O25  124.12  3.000
 5K8  O25  C24  C19  110.44  3.000
 5K8  O27  C24  C19  125.41  3.000
 5K8  C26  O25  C24  117.56  3.000
 5K8  H22  C26  H21  109.40  3.000
 5K8  H22  C26  H20  109.50  3.000
 5K8  H21  C26  H20  109.39  3.000
 5K8  H22  C26  O25  105.91  3.000
 5K8  H21  C26  O25  111.25  3.000
 5K8  H20  C26  O25  111.32  3.000
 5K8  H24  C28  H23  107.06  3.000
 5K8  H24  C28  C18  108.41  3.000
 5K8  H23  C28  C18  109.62  3.000
 5K8  H24  C28  C14  109.55  3.000
 5K8  H23  C28  C14  111.37  3.000
 5K8  C18  C28  C14  110.71  3.000
 5K8  H25  C29  C30  118.88  3.000
 5K8  H25  C29  C05  119.42  3.000
 5K8  C30  C29  C05  121.69  3.000
 5K8  H26  C30  C29  120.22  3.000
 5K8  H26  C30  C02  119.88  3.000
 5K8  C29  C30  C02  119.90  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
 5K8  CONST_01  C05  C29  C30  C02     0.00   0.0  0
 5K8  CONST_02  C05  C04  C03  C02     0.00   0.0  0
 5K8  CONST_03  C29  C05  C04  C03     0.00   0.0  0
 5K8  CONST_04  C29  C30  C02  C03     0.00   0.0  0
 5K8  CONST_05  C30  C29  C05  C04     0.00   0.0  0
 5K8  CONST_06  C30  C02  C03  C04     0.00   0.0  0
 5K8  CONST_07  C10  C09  C08  C07     0.00   0.0  0
 5K8  CONST_08  C10  C12  C13  C07     0.00   0.0  0
 5K8  CONST_09  C12  C10  C09  C08     0.00   0.0  0
 5K8  CONST_10  C12  C13  C07  C08     0.00   0.0  0
 5K8  CONST_11  C13  C12  C10  C09     0.00   0.0  0
 5K8  CONST_12  C13  C07  C08  C09     0.00   0.0  0
 5K8  CONST_13  C29  C30  C02  O01   180.00   0.0  0
 5K8  CONST_14  C04  C03  C02  O01   180.00   0.0  0
 5K8  CONST_15  C06  C05  C04  C03   180.00   0.0  0
 5K8  CONST_16  C09  C08  C07  C06   180.00   0.0  0
 5K8  CONST_17  C12  C13  C07  C06   180.00   0.0  0
 5K8  CONST_18  C30  C29  C05  C06   180.00   0.0  0
 5K8  CONST_19  O11  C10  C09  C08   180.00   0.0  0
 5K8  CONST_20  C13  C12  C10  O11   180.00   0.0  0
 5K8  CONST_21  H25  C29  C30  C02   180.00   0.0  0
 5K8  CONST_22  H3   C04  C03  C02   180.00   0.0  0
 5K8  CONST_23  H26  C30  C02  C03   180.00   0.0  0
 5K8  CONST_24  H2   C03  C04  C05   180.00   0.0  0
 5K8  CONST_25  H5   C09  C08  C07   180.00   0.0  0
 5K8  CONST_26  H7   C12  C13  C07   180.00   0.0  0
 5K8  CONST_27  H8   C13  C07  C08   180.00   0.0  0
 5K8  CONST_28  H4   C08  C09  C10   180.00   0.0  0
 5K8  Var_01    C17  C16  C15  C14    54.81  30.0  1
 5K8  Var_02    C18  C28  C14  C15    56.89  30.0  1
 5K8  Var_03    C18  C17  C16  C15   -54.75  30.0  1
 5K8  Var_04    C28  C14  C15  C16   -56.30  30.0  1
 5K8  Var_05    C07  C06  C05  C04   -54.40  30.0  2
 5K8  Var_06    C08  C07  C06  C05   -51.81  30.0  2
 5K8  Var_07    C15  C14  C06  C05    -6.77  30.0  2
 5K8  Var_08    O21  C20  C19  C18  -106.85  30.0  3
 5K8  Var_09    O27  C24  C19  C18   -21.69  30.0  3
 5K8  Var_10    H17  C22  O21  C20    60.85  30.0  3
 5K8  Var_11    H20  C26  O25  C24   -61.46  30.0  3

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
 5K8  chir_01  C18  C28  C17  C19  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
 5K8  plan-1  O01  0.020
 5K8  plan-1  C02  0.020
 5K8  plan-1  C03  0.020
 5K8  plan-1  C04  0.020
 5K8  plan-1  C05  0.020
 5K8  plan-1  C06  0.020
 5K8  plan-1  C29  0.020
 5K8  plan-1  C30  0.020
 5K8  plan-1  H2   0.020
 5K8  plan-1  H3   0.020
 5K8  plan-1  H25  0.020
 5K8  plan-1  H26  0.020
 5K8  plan-2  C06  0.020
 5K8  plan-2  C07  0.020
 5K8  plan-2  C08  0.020
 5K8  plan-2  C09  0.020
 5K8  plan-2  C10  0.020
 5K8  plan-2  O11  0.020
 5K8  plan-2  C12  0.020
 5K8  plan-2  C13  0.020
 5K8  plan-2  H4   0.020
 5K8  plan-2  H5   0.020
 5K8  plan-2  H7   0.020
 5K8  plan-2  H8   0.020
 5K8  plan-3  C19  0.020
 5K8  plan-3  C24  0.020
 5K8  plan-3  O25  0.020
 5K8  plan-3  O27  0.020
 5K8  plan-4  C19  0.020
 5K8  plan-4  C20  0.020
 5K8  plan-4  O21  0.020
 5K8  plan-4  O23  0.020

