# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 16:09:39 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: (2Z)-4-[4-(4-chlorobenzyl)-1-(cyclohexylmethyl)piperidin-4-yl]-2-hydroxy-4-oxobut-2-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C(/O)=C/C(=O)C1(CCN(CC1)CC2CCCCC2)Cc3ccc(Cl)cc3
#
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
 SL6  SL6  '(2Z)-4-[4-(4-chlorobenzyl)-1-(cyclohexylmethyl)piperidin-4-yl]-2-hydroxy-4-oxobut-2-enoic acid'  ligand  59  29  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SL6
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
 SL6  CL2   CL  CL    0  -0.135   5.6890   3.6677  -0.1935
 SL6  C19   C   CR6   0  -0.059   4.2574   2.7678   0.1956
 SL6  C18   C   CR16  0  -0.196   3.0175   3.3769   0.0892
 SL6  C17   C   CR16  0  -0.326   1.8796   2.6487   0.4034
 SL6  C20   C   CR16  0  -0.194   4.3698   1.4545   0.6210
 SL6  C21   C   CR16  0  -0.310   3.2185   0.7444   0.9288
 SL6  C16   C   CR6   0   0.165   1.9543   1.3190   0.8142
 SL6  C15   C   CH2   0  -0.528   0.7140   0.5283   1.1273
 SL6  C11   C   CT    0  -0.244   0.0462  -0.1551  -0.0970
 SL6  C10   C   CH2   0  -0.420  -0.5427   0.8656  -1.0742
 SL6  C9    C   CH2   0  -0.288  -1.7582   1.5799  -0.5055
 SL6  C14   C   C     0   0.453   1.0962  -1.0137  -0.8025
 SL6  O27   O   O     0  -0.395   1.4457  -0.7816  -1.9423
 SL6  C22   C   C1    0  -0.446   1.6544  -2.1294  -0.0266
 SL6  C23   C   C     0   0.239   2.5944  -2.9861  -0.4631
 SL6  O28   O   OH1   0  -0.573   3.1388  -2.9315  -1.6690
 SL6  C24   C   C     0   0.516   3.0647  -4.0680   0.4757
 SL6  O26   O   OH1   0  -0.605   4.0120  -4.7954  -0.0880
 SL6  O25   O   O     0  -0.404   2.6332  -4.2333   1.5841
 SL6  C12   C   CH2   0  -0.427  -1.1030  -1.0646   0.3815
 SL6  C13   C   CH2   0  -0.285  -2.3084  -0.2793   0.8810
 SL6  N8    N   NT    0  -0.415  -2.7934   0.6386  -0.1277
 SL6  C7    C   CH2   0  -0.232  -4.0133   1.3171   0.2636
 SL6  C2    C   CH1   0  -0.272  -5.2376   0.4110   0.3646
 SL6  C3    C   CH2   0  -0.410  -6.4738   1.2473   0.6991
 SL6  C4    C   CH2   0  -0.430  -7.7328   0.3904   0.7915
 SL6  C5    C   CH2   0  -0.427  -7.9527  -0.4091  -0.4887
 SL6  C6    C   CH2   0  -0.432  -6.7245  -1.2479  -0.8270
 SL6  C1    C   CH2   0  -0.406  -5.4695  -0.3849  -0.9179
 SL6  H18   H   HCR6  0   0.278   2.9342   4.4074  -0.2284
 SL6  H20   H   HCR6  0   0.277   5.3403   0.9876   0.7210
 SL6  H17   H   HCR6  0   0.262   0.9170   3.1392   0.3296
 SL6  H21   H   HCR6  0   0.257   3.3174  -0.2775   1.2734
 SL6  H151  H   HCH2  0   0.260   0.9474  -0.2347   1.8738
 SL6  H152  H   HCH2  0   0.275  -0.0201   1.1822   1.6014
 SL6  H101  H   HCH2  0   0.242   0.2043   1.6035  -1.3704
 SL6  H102  H   HCH2  0   0.237  -0.8504   0.3496  -1.9864
 SL6  H121  H   HCH2  0   0.244  -1.4265  -1.6978  -0.4499
 SL6  H122  H   HCH2  0   0.240  -0.7700  -1.7311   1.1800
 SL6  H91C  H   HCH2  0   0.187  -1.4705   2.2272   0.3429
 SL6  H92C  H   HCH2  0   0.239  -2.1608   2.2476  -1.2708
 SL6  H22   H   H     0   0.288   1.2981  -2.2876   0.9800
 SL6  H28   H   HOH1  0   0.489   3.7899  -3.6350  -1.7939
 SL6  H26   H   HOH1  0   0.505   4.3275  -5.4933   0.5072
 SL6  H131  H   HCH2  0   0.246  -3.0931  -0.9961   1.1263
 SL6  H132  H   HCH2  0   0.197  -2.0623   0.2425   1.8234
 SL6  H71C  H   HCH2  0   0.191  -3.8875   1.8625   1.2173
 SL6  H72C  H   HCH2  0   0.216  -4.2207   2.0774  -0.4974
 SL6  H2    H   HCH1  0   0.213  -5.0973  -0.3036   1.1865
 SL6  H31C  H   HCH2  0   0.223  -6.3175   1.7908   1.6357
 SL6  H32C  H   HCH2  0   0.204  -6.6105   2.0057  -0.0817
 SL6  H11C  H   HCH2  0   0.198  -5.5717   0.3180  -1.7546
 SL6  H12C  H   HCH2  0   0.229  -4.5970  -1.0027  -1.1400
 SL6  H41C  H   HCH2  0   0.207  -7.6389  -0.2994   1.6374
 SL6  H42C  H   HCH2  0   0.224  -8.6011   1.0210   0.9988
 SL6  H51C  H   HCH2  0   0.223  -8.8355  -1.0464  -0.3925
 SL6  H52C  H   HCH2  0   0.205  -8.1547   0.2822  -1.3147
 SL6  H61C  H   HCH2  0   0.206  -6.5829  -2.0085  -0.0510
 SL6  H62C  H   HCH2  0   0.222  -6.8787  -1.7871  -1.7652

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
 SL6  CL2  C19   single    1.735  0.020  1.735
 SL6  C19  C18   aromatic  1.386  0.020  1.386
 SL6  C19  C20   aromatic  1.385  0.020  1.385
 SL6  C18  C17   aromatic  1.387  0.020  1.387
 SL6  C17  C16   aromatic  1.394  0.020  1.394
 SL6  C20  C21   aromatic  1.387  0.020  1.387
 SL6  C21  C16   aromatic  1.393  0.020  1.393
 SL6  C16  C15   single    1.504  0.020  1.504
 SL6  C15  C11   single    1.553  0.020  1.553
 SL6  C11  C10   single    1.531  0.020  1.531
 SL6  C11  C14   single    1.529  0.020  1.529
 SL6  C11  C12   single    1.542  0.020  1.542
 SL6  C10  C9    single    1.520  0.020  1.520
 SL6  C9   N8    single    1.449  0.020  1.449
 SL6  C14  O27   double    1.215  0.020  1.215
 SL6  C14  C22   single    1.469  0.020  1.469
 SL6  C22  C23   double    1.345  0.020  1.345
 SL6  C23  O28   single    1.324  0.020  1.324
 SL6  C23  C24   single    1.508  0.020  1.508
 SL6  C24  O26   single    1.321  0.020  1.321
 SL6  C24  O25   double    1.201  0.020  1.201
 SL6  C12  C13   single    1.523  0.020  1.523
 SL6  C13  N8    single    1.448  0.020  1.448
 SL6  N8   C7    single    1.450  0.020  1.450
 SL6  C7   C2    single    1.526  0.020  1.526
 SL6  C2   C3    single    1.530  0.020  1.530
 SL6  C2   C1    single    1.527  0.020  1.527
 SL6  C3   C4    single    1.526  0.020  1.526
 SL6  C4   C5    single    1.525  0.020  1.525
 SL6  C5   C6    single    1.525  0.020  1.525
 SL6  C6   C1    single    1.526  0.020  1.526
 SL6  C18  H18   single    0.930  0.020  1.080
 SL6  C20  H20   single    0.930  0.020  1.080
 SL6  C17  H17   single    0.930  0.020  1.080
 SL6  C21  H21   single    0.930  0.020  1.080
 SL6  C15  H151  single    0.970  0.020  1.090
 SL6  C15  H152  single    0.970  0.020  1.090
 SL6  C10  H101  single    0.970  0.020  1.090
 SL6  C10  H102  single    0.970  0.020  1.090
 SL6  C12  H121  single    0.970  0.020  1.090
 SL6  C12  H122  single    0.970  0.020  1.090
 SL6  C9   H91C  single    0.970  0.020  1.090
 SL6  C9   H92C  single    0.970  0.020  1.090
 SL6  C22  H22   single    0.930  0.020  1.080
 SL6  O28  H28   single    0.850  0.020  0.980
 SL6  O26  H26   single    0.850  0.020  0.980
 SL6  C13  H131  single    0.970  0.020  1.090
 SL6  C13  H132  single    0.970  0.020  1.090
 SL6  C7   H71C  single    0.970  0.020  1.090
 SL6  C7   H72C  single    0.970  0.020  1.090
 SL6  C2   H2    single    0.970  0.020  1.090
 SL6  C3   H31C  single    0.970  0.020  1.090
 SL6  C3   H32C  single    0.970  0.020  1.090
 SL6  C1   H11C  single    0.970  0.020  1.090
 SL6  C1   H12C  single    0.970  0.020  1.090
 SL6  C4   H41C  single    0.970  0.020  1.090
 SL6  C4   H42C  single    0.970  0.020  1.090
 SL6  C5   H51C  single    0.970  0.020  1.090
 SL6  C5   H52C  single    0.970  0.020  1.090
 SL6  C6   H61C  single    0.970  0.020  1.090
 SL6  C6   H62C  single    0.970  0.020  1.090

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
 SL6  C20   C19  C18   120.87  3.000
 SL6  C20   C19  CL2   119.58  3.000
 SL6  C18   C19  CL2   119.55  3.000
 SL6  H18   C18  C17   120.24  3.000
 SL6  H18   C18  C19   120.68  3.000
 SL6  C17   C18  C19   119.08  3.000
 SL6  H17   C17  C16   119.99  3.000
 SL6  H17   C17  C18   118.43  3.000
 SL6  C16   C17  C18   121.58  3.000
 SL6  H20   C20  C21   120.21  3.000
 SL6  H20   C20  C19   120.70  3.000
 SL6  C21   C20  C19   119.09  3.000
 SL6  H21   C21  C16   119.88  3.000
 SL6  H21   C21  C20   118.54  3.000
 SL6  C16   C21  C20   121.58  3.000
 SL6  C15   C16  C21   120.96  3.000
 SL6  C15   C16  C17   121.25  3.000
 SL6  C21   C16  C17   117.79  3.000
 SL6  H152  C15  H151  105.38  3.000
 SL6  H152  C15  C11   108.47  3.000
 SL6  H151  C15  C11   108.85  3.000
 SL6  H152  C15  C16   109.28  3.000
 SL6  H151  C15  C16   109.46  3.000
 SL6  C11   C15  C16   114.96  3.000
 SL6  C12   C11  C14   108.90  3.000
 SL6  C12   C11  C10   107.74  3.000
 SL6  C14   C11  C10   110.13  3.000
 SL6  C12   C11  C15   109.60  3.000
 SL6  C14   C11  C15   108.39  3.000
 SL6  C10   C11  C15   112.03  3.000
 SL6  H102  C10  H101  106.60  3.000
 SL6  H102  C10  C9    108.01  3.000
 SL6  H101  C10  C9    109.35  3.000
 SL6  H102  C10  C11   109.05  3.000
 SL6  H101  C10  C11   111.16  3.000
 SL6  C9    C10  C11   112.46  3.000
 SL6  H92C  C9   H91C  106.01  3.000
 SL6  H92C  C9   N8    108.44  3.000
 SL6  H91C  C9   N8    111.49  3.000
 SL6  H92C  C9   C10   108.64  3.000
 SL6  H91C  C9   C10   110.74  3.000
 SL6  N8    C9   C10   111.31  3.000
 SL6  C22   C14  O27   122.10  3.000
 SL6  C22   C14  C11   116.34  3.000
 SL6  O27   C14  C11   121.56  3.000
 SL6  H22   C22  C23   116.11  3.000
 SL6  H22   C22  C14   118.58  3.000
 SL6  C23   C22  C14   125.31  3.000
 SL6  C24   C23  O28   117.93  3.000
 SL6  C24   C23  C22   118.23  3.000
 SL6  O28   C23  C22   123.83  3.000
 SL6  H28   O28  C23   111.38  3.000
 SL6  O25   C24  O26   125.16  3.000
 SL6  O25   C24  C23   124.16  3.000
 SL6  O26   C24  C23   110.68  3.000
 SL6  H26   O26  C24   111.57  3.000
 SL6  H122  C12  H121  107.02  3.000
 SL6  H122  C12  C13   108.43  3.000
 SL6  H121  C12  C13   108.29  3.000
 SL6  H122  C12  C11   111.08  3.000
 SL6  H121  C12  C11   109.02  3.000
 SL6  C13   C12  C11   112.81  3.000
 SL6  H132  C13  H131  106.19  3.000
 SL6  H132  C13  N8    111.69  3.000
 SL6  H131  C13  N8    109.41  3.000
 SL6  H132  C13  C12   110.30  3.000
 SL6  H131  C13  C12   107.72  3.000
 SL6  N8    C13  C12   111.32  3.000
 SL6  C7    N8   C13   112.99  3.000
 SL6  C7    N8   C9    111.56  3.000
 SL6  C13   N8   C9    110.74  3.000
 SL6  H72C  C7   H71C  106.16  3.000
 SL6  H72C  C7   C2    107.83  3.000
 SL6  H71C  C7   C2    109.09  3.000
 SL6  H72C  C7   N8    107.25  3.000
 SL6  H71C  C7   N8    111.58  3.000
 SL6  C2    C7   N8    114.51  3.000
 SL6  H2    C2   C1    107.99  3.000
 SL6  H2    C2   C3    107.18  3.000
 SL6  C1    C2   C3    110.24  3.000
 SL6  H2    C2   C7    109.47  3.000
 SL6  C1    C2   C7    112.06  3.000
 SL6  C3    C2   C7    109.76  3.000
 SL6  H32C  C3   H31C  106.48  3.000
 SL6  H32C  C3   C4    109.19  3.000
 SL6  H31C  C3   C4    110.18  3.000
 SL6  H32C  C3   C2    108.85  3.000
 SL6  H31C  C3   C2    110.08  3.000
 SL6  C4    C3   C2    111.90  3.000
 SL6  H42C  C4   H41C  106.55  3.000
 SL6  H42C  C4   C5    110.31  3.000
 SL6  H41C  C4   C5    109.29  3.000
 SL6  H42C  C4   C3    110.06  3.000
 SL6  H41C  C4   C3    109.25  3.000
 SL6  C5    C4   C3    111.25  3.000
 SL6  H52C  C5   H51C  106.57  3.000
 SL6  H52C  C5   C6    109.16  3.000
 SL6  H51C  C5   C6    110.44  3.000
 SL6  H52C  C5   C4    109.18  3.000
 SL6  H51C  C5   C4    110.37  3.000
 SL6  C6    C5   C4    110.99  3.000
 SL6  H62C  C6   H61C  106.47  3.000
 SL6  H62C  C6   C1    110.11  3.000
 SL6  H61C  C6   C1    109.18  3.000
 SL6  H62C  C6   C5    110.37  3.000
 SL6  H61C  C6   C5    109.19  3.000
 SL6  C1    C6   C5    111.38  3.000
 SL6  H12C  C1   H11C  106.36  3.000
 SL6  H12C  C1   C6    110.45  3.000
 SL6  H11C  C1   C6    109.33  3.000
 SL6  H12C  C1   C2    110.14  3.000
 SL6  H11C  C1   C2    108.70  3.000
 SL6  C6    C1   C2    111.69  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
 SL6  CONST_01  C16  C17  C18  C19     0.00   0.0  0
 SL6  CONST_02  C16  C21  C20  C19     0.00   0.0  0
 SL6  CONST_03  C21  C20  C19  C18     0.00   0.0  0
 SL6  CONST_04  C21  C16  C17  C18     0.00   0.0  0
 SL6  CONST_05  C20  C19  C18  C17     0.00   0.0  0
 SL6  CONST_06  C20  C21  C16  C17     0.00   0.0  0
 SL6  CONST_07  C17  C18  C19  CL2   180.00   0.0  0
 SL6  CONST_08  C21  C20  C19  CL2   180.00   0.0  0
 SL6  CONST_09  C15  C16  C17  C18   180.00   0.0  0
 SL6  CONST_10  C15  C16  C21  C20   180.00   0.0  0
 SL6  CONST_11  H17  C17  C18  C19   180.00   0.0  0
 SL6  CONST_12  H21  C21  C20  C19   180.00   0.0  0
 SL6  CONST_13  H20  C20  C19  C18   180.00   0.0  0
 SL6  CONST_14  H18  C18  C19  C20   180.00   0.0  0
 SL6  CONST_15  H26  O26  C24  C23   180.00   0.0  0
 SL6  Var_01    N8   C9   C10  C11   -57.42  30.0  1
 SL6  Var_02    N8   C13  C12  C11    55.89  30.0  1
 SL6  Var_03    C13  N8   C9   C10    60.13  30.0  1
 SL6  Var_04    C12  C13  N8   C9    -59.30  30.0  1
 SL6  Var_05    C5   C4   C3   C2    -55.57  30.0  1
 SL6  Var_06    C5   C6   C1   C2     55.88  30.0  1
 SL6  Var_07    C6   C5   C4   C3     55.01  30.0  1
 SL6  Var_08    C1   C6   C5   C4    -55.25  30.0  1
 SL6  Var_09    C11  C15  C16  C17    85.97  30.0  2
 SL6  Var_10    C2   C7   N8   C9    166.61  30.0  3
 SL6  Var_11    C23  C22  C14  C11  -179.26  30.0  2
 SL6  Var_12    O28  C23  C22  C14    -0.26   0.0  2
 SL6  Var_13    O26  C24  C23  C22  -178.14  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
 SL6  chir_01  C11  C10  C14  C12  positiv
 SL6  chir_02  C2   C7   C3   C1   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
 SL6  plan-1  CL2  0.020
 SL6  plan-1  C19  0.020
 SL6  plan-1  C18  0.020
 SL6  plan-1  C17  0.020
 SL6  plan-1  C20  0.020
 SL6  plan-1  C21  0.020
 SL6  plan-1  C16  0.020
 SL6  plan-1  C15  0.020
 SL6  plan-1  H18  0.020
 SL6  plan-1  H20  0.020
 SL6  plan-1  H17  0.020
 SL6  plan-1  H21  0.020
 SL6  plan-2  C11  0.020
 SL6  plan-2  C14  0.020
 SL6  plan-2  O27  0.020
 SL6  plan-2  C22  0.020
 SL6  plan-3  C23  0.020
 SL6  plan-3  C24  0.020
 SL6  plan-3  O26  0.020
 SL6  plan-3  O25  0.020
 SL6  plan-3  H26  0.020
 SL6  plan-4  C14  0.020
 SL6  plan-4  C22  0.020
 SL6  plan-4  C23  0.020
 SL6  plan-4  O28  0.020
 SL6  plan-4  C24  0.020
 SL6  plan-4  H22  0.020

