# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 08:11:04 2022
#   Inital geometry file: a 119 line input string
#   Ligand name: (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(5-chloranylfuran-2-yl)methyl]pyrrolidine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCc3oc(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
 QKE  QKE  (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(5-chloranylfuran-2-yl)methyl]pyrrolidine-2-carboxamide  ligand  48  26  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QKE
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
 QKE  C4   C   CR16  0  -0.242  21.0627  -11.7690  24.3297
 QKE  C7   C   CR16  0  -0.305  20.6243  -14.5034  24.3161
 QKE  C6   C   CR16  0  -0.241  21.8965  -14.0041  24.0706
 QKE  C9   C   CH2   0  -0.281  18.9978  -13.5089  21.0818
 QKE  C8   C   C     0   0.579  17.2287  -12.9860  22.7974
 QKE  C18  C   CR5   0   0.250  12.7929  -10.3731  23.5039
 QKE  C16  C   CR15  0  -0.364  12.6469  -10.6922  21.3282
 QKE  C2   C   CR6   0   0.105  19.5541  -13.6467  24.5678
 QKE  C3   C   CR16  0  -0.290  19.7924  -12.2733  24.5737
 QKE  C5   C   CR16  0  -0.267  22.1197  -12.6332  24.0752
 QKE  C10  C   CH2   0  -0.473  19.8737  -12.4795  20.3834
 QKE  C11  C   CH2   0  -0.476  18.8759  -11.4031  19.9744
 QKE  C12  C   CH1   0  -0.170  17.9149  -11.3445  21.1680
 QKE  C14  C   CH2   0  -0.413  14.7622   -9.2861  20.7434
 QKE  C15  C   CR5   0   0.376  13.7204   -9.9148  21.5985
 QKE  C17  C   CR15  0  -0.286  12.0277  -10.9938  22.5808
 QKE  N    N   NH2   0  -0.780  16.0460  -14.9044  23.6280
 QKE  C    C   CH1   0  -0.208  17.3766  -14.3535  23.4516
 QKE  N1   N   NT    0  -0.475  17.9848  -12.6829  21.7335
 QKE  O2   O   O     0  -0.403  13.8130   -9.7149  22.9389
 QKE  H1   H   HCR6  0   0.252  21.2272  -10.6990  24.3424
 QKE  H2   H   HCR6  0   0.248  20.4589  -15.5750  24.3118
 QKE  H3   H   HCR6  0   0.252  22.7148  -14.6865  23.8786
 QKE  H4   H   HCH2  0   0.247  18.5342  -14.1891  20.3616
 QKE  H5   H   HCH2  0   0.265  19.5619  -14.1005  21.7993
 QKE  H6   H   HCR5  0   0.269  12.3289  -11.0194  20.3515
 QKE  H9   H   HCR6  0   0.247  18.9758  -11.5891  24.7745
 QKE  H10  H   HCR6  0   0.252  23.1111  -12.2416  23.8873
 QKE  H11  H   HCH2  0   0.257  20.4164  -12.9023  19.5392
 QKE  H12  H   HCH2  0   0.242  20.6048  -12.0752  21.0865
 QKE  H13  H   HCH2  0   0.264  19.3347  -10.4351  19.7803
 QKE  H14  H   HCH2  0   0.250  18.3433  -11.7109  19.0725
 QKE  H15  H   HCH1  0   0.272  18.2735  -10.6175  21.9053
 QKE  H16  H   HCH2  0   0.286  14.7633   -8.2022  20.8696
 QKE  H17  H   HCH2  0   0.276  14.5114   -9.4834  19.7011
 QKE  H18  H   HCR5  0   0.279  11.1499  -11.5908  22.7628
 QKE  H19  H   HNH2  0   0.353  16.1202  -15.8141  24.0664
 QKE  H20  H   HNH2  0   0.343  15.5200  -14.3219  24.2685
 QKE  H22  H   HCH1  0   0.263  17.9258  -15.0383  22.8031
 QKE  C1   C   CH2   0  -0.523  18.1684  -14.1917  24.7684
 QKE  O    O   O     0  -0.502  16.4411  -12.1708  23.2683
 QKE  C13  C   C     0   0.568  16.4975  -11.0013  20.7298
 QKE  N2   N   NH1   0  -0.632  16.0970   -9.7569  21.0373
 QKE  O1   O   O     0  -0.476  15.8180  -11.7828  20.0870
 QKE  CL   CL  CL    0  -0.095  12.6798  -10.2893  25.1934
 QKE  H7   H   HCH2  0   0.248  17.5977  -13.5421  25.4372
 QKE  H8   H   HCH2  0   0.256  18.2188  -15.1750  25.2425
 QKE  H23  H   HNH1  0   0.406  16.6645   -9.2016  21.6568

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
 QKE  C11  C10  single    1.524  0.020  1.524
 QKE  C11  C12  single    1.533  0.020  1.533
 QKE  C10  C9   single    1.521  0.020  1.521
 QKE  O1   C13  double    1.219  0.020  1.219
 QKE  C14  N2   single    1.446  0.020  1.446
 QKE  C14  C15  single    1.487  0.020  1.487
 QKE  C13  N2   single    1.343  0.020  1.343
 QKE  C13  C12  single    1.523  0.020  1.523
 QKE  C9   N1   single    1.461  0.020  1.461
 QKE  C12  N1   single    1.455  0.020  1.455
 QKE  N1   C8   single    1.340  0.020  1.340
 QKE  C15  C16  aromatic  1.353  0.020  1.353
 QKE  C15  O2   aromatic  1.358  0.020  1.358
 QKE  C16  C17  aromatic  1.429  0.020  1.429
 QKE  O2   C18  aromatic  1.339  0.020  1.339
 QKE  C8   O    double    1.227  0.020  1.227
 QKE  C8   C    single    1.523  0.020  1.523
 QKE  N    C    single    1.451  0.020  1.451
 QKE  C    C1   single    1.545  0.020  1.545
 QKE  C17  C18  aromatic  1.350  0.020  1.350
 QKE  C18  CL   single    1.695  0.020  1.695
 QKE  C7   C6   aromatic  1.389  0.020  1.389
 QKE  C7   C2   aromatic  1.394  0.020  1.394
 QKE  C6   C5   aromatic  1.389  0.020  1.389
 QKE  C1   C2   single    1.502  0.020  1.502
 QKE  C2   C3   aromatic  1.394  0.020  1.394
 QKE  C5   C4   aromatic  1.389  0.020  1.389
 QKE  C3   C4   aromatic  1.388  0.020  1.388
 QKE  C4   H1   single    0.930  0.020  1.080
 QKE  C7   H2   single    0.930  0.020  1.080
 QKE  C6   H3   single    0.930  0.020  1.080
 QKE  C9   H4   single    0.970  0.020  1.090
 QKE  C9   H5   single    0.970  0.020  1.090
 QKE  C16  H6   single    0.930  0.020  1.080
 QKE  C1   H7   single    0.970  0.020  1.090
 QKE  C1   H8   single    0.970  0.020  1.090
 QKE  C3   H9   single    0.930  0.020  1.080
 QKE  C5   H10  single    0.930  0.020  1.080
 QKE  C10  H11  single    0.970  0.020  1.090
 QKE  C10  H12  single    0.970  0.020  1.090
 QKE  C11  H13  single    0.970  0.020  1.090
 QKE  C11  H14  single    0.970  0.020  1.090
 QKE  C12  H15  single    0.970  0.020  1.090
 QKE  C14  H16  single    0.970  0.020  1.090
 QKE  C14  H17  single    0.970  0.020  1.090
 QKE  C17  H18  single    0.930  0.020  1.080
 QKE  N    H19  single    0.890  0.020  1.040
 QKE  N    H20  single    0.890  0.020  1.040
 QKE  C    H22  single    0.970  0.020  1.090
 QKE  N2   H23  single    0.860  0.020  1.020

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
 QKE  H1   C4   C5   120.10  3.000
 QKE  H1   C4   C3   119.74  3.000
 QKE  C5   C4   C3   120.17  3.000
 QKE  H2   C7   C2   119.41  3.000
 QKE  H2   C7   C6   119.64  3.000
 QKE  C2   C7   C6   120.96  3.000
 QKE  H3   C6   C5   120.08  3.000
 QKE  H3   C6   C7   119.82  3.000
 QKE  C5   C6   C7   120.10  3.000
 QKE  H5   C9   H4   108.41  3.000
 QKE  H5   C9   N1   111.90  3.000
 QKE  H4   C9   N1   110.58  3.000
 QKE  H5   C9   C10  111.86  3.000
 QKE  H4   C9   C10  111.26  3.000
 QKE  N1   C9   C10  102.80  3.000
 QKE  N1   C8   O    121.10  3.000
 QKE  O    C8   C    119.59  3.000
 QKE  N1   C8   C    119.30  3.000
 QKE  CL   C18  O2   116.56  3.000
 QKE  CL   C18  C17  131.78  3.000
 QKE  O2   C18  C17  111.66  3.000
 QKE  H6   C16  C17  127.02  3.000
 QKE  H6   C16  C15  126.13  3.000
 QKE  C17  C16  C15  106.85  3.000
 QKE  C3   C2   C1   120.96  3.000
 QKE  C3   C2   C7   118.37  3.000
 QKE  C1   C2   C7   120.62  3.000
 QKE  H9   C3   C2   119.60  3.000
 QKE  H9   C3   C4   119.51  3.000
 QKE  C2   C3   C4   120.90  3.000
 QKE  H10  C5   C6   120.25  3.000
 QKE  H10  C5   C4   120.25  3.000
 QKE  C6   C5   C4   119.50  3.000
 QKE  H12  C10  H11  108.01  3.000
 QKE  H12  C10  C11  110.47  3.000
 QKE  H11  C10  C11  113.11  3.000
 QKE  H12  C10  C9   109.90  3.000
 QKE  H11  C10  C9   112.34  3.000
 QKE  C11  C10  C9   102.96  3.000
 QKE  H14  C11  H13  108.00  3.000
 QKE  H14  C11  C12  110.37  3.000
 QKE  H13  C11  C12  111.65  3.000
 QKE  H14  C11  C10  110.00  3.000
 QKE  H13  C11  C10  113.58  3.000
 QKE  C12  C11  C10  103.21  3.000
 QKE  H15  C12  N1   109.46  3.000
 QKE  H15  C12  C11  110.12  3.000
 QKE  N1   C12  C11  103.73  3.000
 QKE  H15  C12  C13  110.41  3.000
 QKE  N1   C12  C13  111.34  3.000
 QKE  C11  C12  C13  111.59  3.000
 QKE  H17  C14  H16  106.90  3.000
 QKE  H17  C14  N2   110.36  3.000
 QKE  H16  C14  N2   107.40  3.000
 QKE  H17  C14  C15  108.18  3.000
 QKE  H16  C14  C15  110.73  3.000
 QKE  N2   C14  C15  113.09  3.000
 QKE  O2   C15  C14  117.22  3.000
 QKE  O2   C15  C16  109.63  3.000
 QKE  C14  C15  C16  133.16  3.000
 QKE  H18  C17  C16  128.17  3.000
 QKE  H18  C17  C18  126.95  3.000
 QKE  C16  C17  C18  104.87  3.000
 QKE  H20  N    H19  106.31  3.000
 QKE  H20  N    C    109.56  3.000
 QKE  H19  N    C    109.06  3.000
 QKE  H22  C    N    107.18  3.000
 QKE  H22  C    C1   108.31  3.000
 QKE  N    C    C1   113.97  3.000
 QKE  H22  C    C8   110.91  3.000
 QKE  C1   C    C8   108.77  3.000
 QKE  N    C    C8   107.71  3.000
 QKE  C12  N1   C8   119.32  3.000
 QKE  C8   N1   C9   128.15  3.000
 QKE  C12  N1   C9   112.34  3.000
 QKE  C15  O2   C18  106.98  3.000
 QKE  H8   C1   H7   107.06  3.000
 QKE  H8   C1   C    107.41  3.000
 QKE  H7   C1   C    108.42  3.000
 QKE  H8   C1   C2   109.99  3.000
 QKE  H7   C1   C2   110.35  3.000
 QKE  C    C1   C2   113.38  3.000
 QKE  O1   C13  N2   123.27  3.000
 QKE  N2   C13  C12  114.87  3.000
 QKE  O1   C13  C12  121.75  3.000
 QKE  H23  N2   C14  117.77  3.000
 QKE  H23  N2   C13  118.93  3.000
 QKE  C14  N2   C13  122.04  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
 QKE  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 QKE  CONST_02  C7   C2   C3   C4      0.00   0.0  0
 QKE  CONST_03  C3   C2   C7   C6      0.00   0.0  0
 QKE  CONST_04  C3   C4   C5   C6      0.00   0.0  0
 QKE  CONST_05  C16  C15  O2   C18     0.00   0.0  0
 QKE  CONST_06  C15  C16  C17  C18     0.00   0.0  0
 QKE  CONST_07  O2   C18  C17  C16     0.00   0.0  0
 QKE  CONST_08  C5   C6   C7   C2      0.00   0.0  0
 QKE  CONST_09  C5   C4   C3   C2      0.00   0.0  0
 QKE  CONST_10  C17  C18  O2   C15     0.00   0.0  0
 QKE  CONST_11  O2   C15  C16  C17     0.00   0.0  0
 QKE  CONST_12  C1   C2   C3   C4    180.00   0.0  0
 QKE  CONST_13  C1   C2   C7   C6    180.00   0.0  0
 QKE  CONST_14  C14  C15  O2   C18   180.00   0.0  0
 QKE  CONST_15  CL   C18  C17  C16   180.00   0.0  0
 QKE  CONST_16  C17  C16  C15  C14   180.00   0.0  0
 QKE  CONST_17  CL   C18  O2   C15   180.00   0.0  0
 QKE  CONST_18  H3   C6   C5   C4    180.00   0.0  0
 QKE  CONST_19  H10  C5   C6   C7    180.00   0.0  0
 QKE  CONST_20  H9   C3   C2   C7    180.00   0.0  0
 QKE  CONST_21  H1   C4   C5   C6    180.00   0.0  0
 QKE  CONST_22  H6   C16  C17  C18   180.00   0.0  0
 QKE  CONST_23  H2   C7   C2   C3    180.00   0.0  0
 QKE  CONST_24  H18  C17  C16  C15   180.00   0.0  0
 QKE  CONST_25  O    C8   N1   C9    180.00   0.0  0
 QKE  CONST_26  C    C8   N1   C9      0.00   0.0  0
 QKE  CONST_27  O    C8   N1   C12     0.00   0.0  0
 QKE  CONST_28  C    C8   N1   C12   180.00   0.0  0
 QKE  CONST_29  C14  N2   C13  C12   180.00   0.0  0
 QKE  CONST_30  H23  N2   C13  C12     0.00   0.0  0
 QKE  CONST_31  O1   C13  N2   C14     0.00   0.0  0
 QKE  Var_01    C12  C11  C10  C9     38.41  30.0  1
 QKE  Var_02    C12  N1   C9   C10    18.05  30.0  1
 QKE  Var_03    N1   C9   C10  C11   -34.45  30.0  1
 QKE  Var_04    C    C1   C2   C7    -88.05  30.0  3
 QKE  Var_05    N2   C14  C15  C16  -118.29  30.0  1
 QKE  Var_06    C15  C14  N2   C13    70.58  30.0  1

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
 QKE  chir_01  C12  C11  C13  N1  negativ
 QKE  chir_02  C    N    C1   C8  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
 QKE  plan-1  C18  0.020
 QKE  plan-1  C16  0.020
 QKE  plan-1  C14  0.020
 QKE  plan-1  C15  0.020
 QKE  plan-1  C17  0.020
 QKE  plan-1  O2   0.020
 QKE  plan-1  H6   0.020
 QKE  plan-1  H18  0.020
 QKE  plan-1  CL   0.020
 QKE  plan-2  C4   0.020
 QKE  plan-2  C7   0.020
 QKE  plan-2  C6   0.020
 QKE  plan-2  C2   0.020
 QKE  plan-2  C3   0.020
 QKE  plan-2  C5   0.020
 QKE  plan-2  H1   0.020
 QKE  plan-2  H2   0.020
 QKE  plan-2  H3   0.020
 QKE  plan-2  H9   0.020
 QKE  plan-2  H10  0.020
 QKE  plan-2  C1   0.020
 QKE  plan-3  C12  0.020
 QKE  plan-3  C14  0.020
 QKE  plan-3  C13  0.020
 QKE  plan-3  N2   0.020
 QKE  plan-3  O1   0.020
 QKE  plan-3  H23  0.020
 QKE  plan-4  C9   0.020
 QKE  plan-4  C8   0.020
 QKE  plan-4  C12  0.020
 QKE  plan-4  C    0.020
 QKE  plan-4  N1   0.020
 QKE  plan-4  O    0.020

