# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 03:36:03 2021
#   Inital geometry file: a 147 line input string
#   Ligand name: {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S,3S)-2-hydroxypentan-3-yl]-3-methyl-2-oxopiperidin-3-yl}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H]([C@H](C)O)N1[C@@H]([C@H](C[C@](C)(CC(O)=O)C1=O)c2cccc(Cl)c2)c3ccc(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
 0R3  0R3  '{(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S,3S)-2-hydroxypentan-3-yl]-3-methyl-2-oxopiperidin-3-yl}acetic acid'  ligand  61  32  .  2022-11-17  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_0R3
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
 0R3  C17  C   CR16  0  -0.262  -16.2892   2.5718  -15.2782
 0R3  C16  C   CR6   0  -0.021  -17.2541   3.5655  -15.3115
 0R3  CL2  CL  CL    0  -0.132  -16.9349   5.0784  -14.5244
 0R3  C15  C   CR16  0  -0.232  -18.4639   3.3786  -15.9593
 0R3  C14  C   CR16  0  -0.244  -18.6978   2.1619  -16.5848
 0R3  C13  C   CR16  0  -0.311  -17.7402   1.1589  -16.5615
 0R3  C6   C   CR6   0   0.195  -16.5276   1.3538  -15.9054
 0R3  C2   C   CH1   0  -0.396  -15.4542   0.2956  -15.9046
 0R3  C3   C   CH2   0  -0.408  -15.9574  -1.0984  -15.5891
 0R3  C4   C   CT    0  -0.246  -14.7970  -2.0835  -15.4741
 0R3  C23  C   CH2   0  -0.536  -13.8638  -1.8061  -14.2657
 0R3  C25  C   C     0   0.530  -14.5813  -1.8154  -12.9426
 0R3  O3   O   O     0  -0.437  -15.1706  -0.8676  -12.4830
 0R3  O2   O   OH1   0  -0.583  -14.5012  -2.9876  -12.3251
 0R3  C24  C   CH3   0  -0.641  -15.3635  -3.5034  -15.3910
 0R3  C5   C   C     0   0.601  -13.8898  -2.0016  -16.7069
 0R3  O1   O   O     0  -0.490  -13.1367  -2.9323  -16.9575
 0R3  N1   N   NT    0  -0.508  -13.9454  -0.9104  -17.5031
 0R3  C18  C   CH1   0  -0.059  -13.2262  -0.9280  -18.7921
 0R3  C19  C   CH2   0  -0.453  -11.6962  -1.0069  -18.6439
 0R3  C22  C   CH3   0  -0.679  -10.9657   0.0560  -19.4560
 0R3  C20  C   CH1   0   0.030  -13.8128  -1.9854  -19.7452
 0R3  O4   O   OH1   0  -0.670  -15.2215  -1.8584  -19.8238
 0R3  C21  C   CH3   0  -0.686  -13.2720  -1.8175  -21.1529
 0R3  C1   C   CH1   0  -0.103  -14.7502   0.2917  -17.2700
 0R3  C7   C   CR6   0   0.125  -13.9141   1.5451  -17.4015
 0R3  C8   C   CR16  0  -0.293  -12.7489   1.7078  -16.6587
 0R3  C9   C   CR16  0  -0.198  -12.0052   2.8731  -16.7441
 0R3  C10  C   CR6   0  -0.053  -12.4406   3.8902  -17.5809
 0R3  CL1  CL  CL    0  -0.130  -11.5137   5.3507  -17.6994
 0R3  C11  C   CR16  0  -0.195  -13.6004   3.7568  -18.3250
 0R3  C12  C   CR16  0  -0.294  -14.3286   2.5796  -18.2289
 0R3  H1   H   HCR6  0   0.271  -15.3476   2.7432  -14.7719
 0R3  H2   H   HCR6  0   0.280  -19.2088   4.1622  -15.9771
 0R3  H3   H   HCR6  0   0.268  -19.6378   1.9993  -17.0955
 0R3  H4   H   HCR6  0   0.254  -17.9487   0.2199  -17.0592
 0R3  H5   H   HCH1  0   0.278  -14.7269   0.5749  -15.1374
 0R3  H6   H   HCH2  0   0.268  -16.5509  -1.0934  -14.6743
 0R3  H7   H   HCH2  0   0.245  -16.6296  -1.4489  -16.3788
 0R3  H8   H   HCH2  0   0.289  -13.0696  -2.5535  -14.2664
 0R3  H9   H   HCH2  0   0.282  -13.3843  -0.8310  -14.3679
 0R3  H10  H   HOH1  0   0.481  -14.9952  -2.9560  -11.4915
 0R3  H11  H   HCH3  0   0.239  -16.0874  -3.5788  -14.5787
 0R3  H12  H   HCH3  0   0.238  -15.8877  -3.7657  -16.3111
 0R3  H13  H   HCH3  0   0.246  -14.5864  -4.2461  -15.2221
 0R3  H14  H   HCH1  0   0.255  -13.4633   0.0368  -19.2465
 0R3  H15  H   HCH2  0   0.236  -11.3405  -2.0012  -18.9248
 0R3  H16  H   HCH2  0   0.240  -11.4253  -0.8839  -17.5947
 0R3  H17  H   HCH3  0   0.231   -9.8869  -0.0259  -19.3188
 0R3  H18  H   HCH3  0   0.227  -11.1674  -0.0278  -20.5243
 0R3  H19  H   HCH3  0   0.228  -11.2639   1.0577  -19.1428
 0R3  H20  H   HCH1  0   0.221  -13.5386  -2.9839  -19.3896
 0R3  H21  H   HOH1  0   0.444  -15.6124  -2.2039  -19.0170
 0R3  H22  H   HCH3  0   0.237  -12.1940  -1.9688  -21.1839
 0R3  H23  H   HCH3  0   0.244  -13.7221  -2.5552  -21.8180
 0R3  H24  H   HCH3  0   0.225  -13.4881  -0.8238  -21.5506
 0R3  H25  H   HCH1  0   0.269  -15.5227   0.3188  -18.0488
 0R3  H26  H   HCR6  0   0.260  -12.3991   0.9174  -16.0051
 0R3  H27  H   HCR6  0   0.281  -11.0976   2.9834  -16.1665
 0R3  H28  H   HCR6  0   0.280  -13.9338   4.5535  -18.9758
 0R3  H29  H   HCR6  0   0.262  -15.2318   2.4707  -18.8171

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
 0R3  C21  C20  single    1.517  0.020  1.517
 0R3  C20  O4   single    1.417  0.020  1.417
 0R3  C20  C18  single    1.540  0.020  1.540
 0R3  C22  C19  single    1.524  0.020  1.524
 0R3  C11  C12  aromatic  1.388  0.020  1.388
 0R3  C11  C10  aromatic  1.384  0.020  1.384
 0R3  C18  C19  single    1.539  0.020  1.539
 0R3  C18  N1   single    1.476  0.020  1.476
 0R3  C12  C7   aromatic  1.388  0.020  1.388
 0R3  CL1  C10  single    1.734  0.020  1.734
 0R3  C10  C9   aromatic  1.387  0.020  1.387
 0R3  C7   C1   single    1.512  0.020  1.512
 0R3  C7   C8   aromatic  1.391  0.020  1.391
 0R3  N1   C1   single    1.465  0.020  1.465
 0R3  N1   C5   single    1.352  0.020  1.352
 0R3  C1   C2   single    1.536  0.020  1.536
 0R3  C9   C8   aromatic  1.385  0.020  1.385
 0R3  O1   C5   double    1.223  0.020  1.223
 0R3  C5   C4   single    1.533  0.020  1.533
 0R3  C13  C14  aromatic  1.387  0.020  1.387
 0R3  C13  C6   aromatic  1.392  0.020  1.392
 0R3  C14  C15  aromatic  1.388  0.020  1.388
 0R3  C2   C6   single    1.507  0.020  1.507
 0R3  C2   C3   single    1.515  0.020  1.515
 0R3  C6   C17  aromatic  1.391  0.020  1.391
 0R3  C15  C16  aromatic  1.385  0.020  1.385
 0R3  C3   C4   single    1.526  0.020  1.526
 0R3  C24  C4   single    1.531  0.020  1.531
 0R3  C4   C23  single    1.552  0.020  1.552
 0R3  C17  C16  aromatic  1.385  0.020  1.385
 0R3  C16  CL2  single    1.735  0.020  1.735
 0R3  C23  C25  single    1.505  0.020  1.505
 0R3  C25  O3   double    1.207  0.020  1.207
 0R3  C25  O2   single    1.327  0.020  1.327
 0R3  C17  H1   single    0.930  0.020  1.080
 0R3  C15  H2   single    0.930  0.020  1.080
 0R3  C14  H3   single    0.930  0.020  1.080
 0R3  C13  H4   single    0.930  0.020  1.080
 0R3  C2   H5   single    0.970  0.020  1.090
 0R3  C3   H6   single    0.970  0.020  1.090
 0R3  C3   H7   single    0.970  0.020  1.090
 0R3  C23  H8   single    0.970  0.020  1.090
 0R3  C23  H9   single    0.970  0.020  1.090
 0R3  O2   H10  single    0.850  0.020  0.980
 0R3  C24  H11  single    0.970  0.020  1.090
 0R3  C24  H12  single    0.970  0.020  1.090
 0R3  C24  H13  single    0.970  0.020  1.090
 0R3  C18  H14  single    0.970  0.020  1.090
 0R3  C19  H15  single    0.970  0.020  1.090
 0R3  C19  H16  single    0.970  0.020  1.090
 0R3  C22  H17  single    0.970  0.020  1.090
 0R3  C22  H18  single    0.970  0.020  1.090
 0R3  C22  H19  single    0.970  0.020  1.090
 0R3  C20  H20  single    0.970  0.020  1.090
 0R3  O4   H21  single    0.850  0.020  0.980
 0R3  C21  H22  single    0.970  0.020  1.090
 0R3  C21  H23  single    0.970  0.020  1.090
 0R3  C21  H24  single    0.970  0.020  1.090
 0R3  C1   H25  single    0.970  0.020  1.090
 0R3  C8   H26  single    0.930  0.020  1.080
 0R3  C9   H27  single    0.930  0.020  1.080
 0R3  C11  H28  single    0.930  0.020  1.080
 0R3  C12  H29  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
 0R3  H1   C17  C6   119.92  3.000
 0R3  H1   C17  C16  120.22  3.000
 0R3  C6   C17  C16  119.86  3.000
 0R3  C15  C16  CL2  119.38  3.000
 0R3  CL2  C16  C17  119.10  3.000
 0R3  C15  C16  C17  121.52  3.000
 0R3  H2   C15  C14  120.79  3.000
 0R3  H2   C15  C16  120.77  3.000
 0R3  C14  C15  C16  118.44  3.000
 0R3  H3   C14  C13  119.94  3.000
 0R3  H3   C14  C15  119.40  3.000
 0R3  C13  C14  C15  120.67  3.000
 0R3  H4   C13  C6   120.37  3.000
 0R3  H4   C13  C14  119.10  3.000
 0R3  C6   C13  C14  120.53  3.000
 0R3  C2   C6   C13  121.47  3.000
 0R3  C2   C6   C17  119.51  3.000
 0R3  C13  C6   C17  118.98  3.000
 0R3  H5   C2   C1   108.63  3.000
 0R3  H5   C2   C3   108.05  3.000
 0R3  C1   C2   C3   109.57  3.000
 0R3  H5   C2   C6   107.13  3.000
 0R3  C3   C2   C6   114.17  3.000
 0R3  C1   C2   C6   109.13  3.000
 0R3  H7   C3   H6   105.80  3.000
 0R3  H7   C3   C4   108.33  3.000
 0R3  H6   C3   C4   110.70  3.000
 0R3  H7   C3   C2   110.38  3.000
 0R3  H6   C3   C2   110.56  3.000
 0R3  C4   C3   C2   110.91  3.000
 0R3  C5   C4   C24  108.19  3.000
 0R3  C24  C4   C23  110.24  3.000
 0R3  C5   C4   C23  105.12  3.000
 0R3  C23  C4   C3   113.61  3.000
 0R3  C24  C4   C3   108.74  3.000
 0R3  C5   C4   C3   110.79  3.000
 0R3  H9   C23  H8   107.00  3.000
 0R3  H9   C23  C25  107.29  3.000
 0R3  H8   C23  C25  110.09  3.000
 0R3  H9   C23  C4   110.55  3.000
 0R3  H8   C23  C4   108.36  3.000
 0R3  C25  C23  C4   113.38  3.000
 0R3  O2   C25  O3   123.08  3.000
 0R3  O2   C25  C23  112.68  3.000
 0R3  O3   C25  C23  124.23  3.000
 0R3  H10  O2   C25  109.90  3.000
 0R3  H13  C24  H12  108.05  3.000
 0R3  H13  C24  H11  108.13  3.000
 0R3  H12  C24  H11  107.01  3.000
 0R3  H13  C24  C4   112.16  3.000
 0R3  H12  C24  C4   110.79  3.000
 0R3  H11  C24  C4   110.50  3.000
 0R3  N1   C5   O1   121.25  3.000
 0R3  O1   C5   C4   119.25  3.000
 0R3  N1   C5   C4   119.50  3.000
 0R3  C1   N1   C18  114.60  3.000
 0R3  C1   N1   C5   126.23  3.000
 0R3  C18  N1   C5   118.99  3.000
 0R3  H14  C18  C20  105.45  3.000
 0R3  H14  C18  C19  107.52  3.000
 0R3  C20  C18  C19  113.77  3.000
 0R3  H14  C18  N1   104.30  3.000
 0R3  C19  C18  N1   113.63  3.000
 0R3  C20  C18  N1   111.29  3.000
 0R3  H16  C19  H15  105.60  3.000
 0R3  H16  C19  C22  108.36  3.000
 0R3  H15  C19  C22  109.97  3.000
 0R3  H16  C19  C18  109.50  3.000
 0R3  H15  C19  C18  110.21  3.000
 0R3  C22  C19  C18  112.92  3.000
 0R3  H19  C22  H18  107.53  3.000
 0R3  H19  C22  H17  107.65  3.000
 0R3  H18  C22  H17  107.48  3.000
 0R3  H19  C22  C19  110.87  3.000
 0R3  H18  C22  C19  112.32  3.000
 0R3  H17  C22  C19  110.78  3.000
 0R3  H20  C20  C21  108.24  3.000
 0R3  H20  C20  O4   110.42  3.000
 0R3  C21  C20  O4   107.04  3.000
 0R3  H20  C20  C18  109.26  3.000
 0R3  O4   C20  C18  110.59  3.000
 0R3  C21  C20  C18  111.26  3.000
 0R3  H21  O4   C20  109.01  3.000
 0R3  H24  C21  H23  108.17  3.000
 0R3  H24  C21  H22  108.17  3.000
 0R3  H23  C21  H22  107.29  3.000
 0R3  H24  C21  C20  111.60  3.000
 0R3  H23  C21  C20  110.12  3.000
 0R3  H22  C21  C20  111.34  3.000
 0R3  H25  C1   C7   107.88  3.000
 0R3  H25  C1   N1   107.10  3.000
 0R3  C7   C1   N1   111.25  3.000
 0R3  H25  C1   C2   107.95  3.000
 0R3  N1   C1   C2   113.28  3.000
 0R3  C7   C1   C2   109.18  3.000
 0R3  C12  C7   C8   118.77  3.000
 0R3  C8   C7   C1   120.89  3.000
 0R3  C12  C7   C1   120.29  3.000
 0R3  H26  C8   C9   118.53  3.000
 0R3  H26  C8   C7   120.47  3.000
 0R3  C9   C8   C7   121.01  3.000
 0R3  H27  C9   C10  120.72  3.000
 0R3  H27  C9   C8   120.24  3.000
 0R3  C10  C9   C8   119.05  3.000
 0R3  C11  C10  CL1  119.49  3.000
 0R3  CL1  C10  C9   119.41  3.000
 0R3  C11  C10  C9   121.10  3.000
 0R3  H28  C11  C12  120.32  3.000
 0R3  H28  C11  C10  120.72  3.000
 0R3  C12  C11  C10  118.96  3.000
 0R3  H29  C12  C11  119.03  3.000
 0R3  H29  C12  C7   119.85  3.000
 0R3  C11  C12  C7   121.12  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
 0R3  CONST_01  C14  C13  C6   C17    0.00   0.0  0
 0R3  CONST_02  C14  C15  C16  C17    0.00   0.0  0
 0R3  CONST_03  C13  C14  C15  C16    0.00   0.0  0
 0R3  CONST_04  C13  C6   C17  C16    0.00   0.0  0
 0R3  CONST_05  C6   C13  C14  C15    0.00   0.0  0
 0R3  CONST_06  C6   C17  C16  C15    0.00   0.0  0
 0R3  CONST_07  C10  C11  C12  C7     0.00   0.0  0
 0R3  CONST_08  C10  C9   C8   C7     0.00   0.0  0
 0R3  CONST_09  C11  C12  C7   C8     0.00   0.0  0
 0R3  CONST_10  C11  C10  C9   C8     0.00   0.0  0
 0R3  CONST_11  C12  C11  C10  C9     0.00   0.0  0
 0R3  CONST_12  C12  C7   C8   C9     0.00   0.0  0
 0R3  CONST_13  C2   C6   C17  C16  180.00   0.0  0
 0R3  CONST_14  C2   C6   C13  C14  180.00   0.0  0
 0R3  CONST_15  C11  C12  C7   C1   180.00   0.0  0
 0R3  CONST_16  C9   C8   C7   C1   180.00   0.0  0
 0R3  CONST_17  C1   N1   C5   C4     0.00   0.0  0
 0R3  CONST_18  C14  C15  C16  CL2  180.00   0.0  0
 0R3  CONST_19  C6   C17  C16  CL2  180.00   0.0  0
 0R3  CONST_20  CL1  C10  C9   C8   180.00   0.0  0
 0R3  CONST_21  C12  C11  C10  CL1  180.00   0.0  0
 0R3  CONST_22  C18  N1   C5   C4   180.00   0.0  0
 0R3  CONST_23  C1   N1   C5   O1   180.00   0.0  0
 0R3  CONST_24  H4   C13  C6   C17  180.00   0.0  0
 0R3  CONST_25  H2   C15  C16  C17  180.00   0.0  0
 0R3  CONST_26  H3   C14  C15  C16  180.00   0.0  0
 0R3  CONST_27  H1   C17  C16  C15  180.00   0.0  0
 0R3  CONST_28  H29  C12  C7   C1     0.00   0.0  0
 0R3  CONST_29  H26  C8   C7   C1     0.00   0.0  0
 0R3  CONST_30  H28  C11  C12  C7   180.00   0.0  0
 0R3  CONST_31  H27  C9   C8   C7   180.00   0.0  0
 0R3  CONST_32  C18  N1   C5   O1     0.00   0.0  0
 0R3  CONST_33  H10  O2   C25  C23  180.00   0.0  0
 0R3  Var_01    O3   C25  C23  C4   -83.95  30.0  3
 0R3  Var_02    H17  C22  C19  C18  179.49  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
 0R3  chir_01  C2   C1  C6   C3   negativ
 0R3  chir_02  C4   C3  C5   C23  negativ
 0R3  chir_03  C18  N1  C20  C19  positiv
 0R3  chir_04  C20  O4  C18  C21  positiv
 0R3  chir_05  C1   N1  C7   C2   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
 0R3  plan-1  C17  0.020
 0R3  plan-1  C16  0.020
 0R3  plan-1  CL2  0.020
 0R3  plan-1  C15  0.020
 0R3  plan-1  C14  0.020
 0R3  plan-1  C13  0.020
 0R3  plan-1  C6   0.020
 0R3  plan-1  C2   0.020
 0R3  plan-1  H1   0.020
 0R3  plan-1  H2   0.020
 0R3  plan-1  H3   0.020
 0R3  plan-1  H4   0.020
 0R3  plan-2  C1   0.020
 0R3  plan-2  C7   0.020
 0R3  plan-2  C8   0.020
 0R3  plan-2  C9   0.020
 0R3  plan-2  C10  0.020
 0R3  plan-2  CL1  0.020
 0R3  plan-2  C11  0.020
 0R3  plan-2  C12  0.020
 0R3  plan-2  H26  0.020
 0R3  plan-2  H27  0.020
 0R3  plan-2  H28  0.020
 0R3  plan-2  H29  0.020
 0R3  plan-3  C23  0.020
 0R3  plan-3  C25  0.020
 0R3  plan-3  O3   0.020
 0R3  plan-3  O2   0.020
 0R3  plan-3  H10  0.020
 0R3  plan-4  C4   0.020
 0R3  plan-4  C5   0.020
 0R3  plan-4  O1   0.020
 0R3  plan-4  N1   0.020
 0R3  plan-4  C18  0.020
 0R3  plan-4  C1   0.020

