# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 21:21:34 2021
#   Inital geometry file: a 142 line input string
#   Ligand name: N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)OCc1ccccc1)C(=O)N[C@H](CO)C[C@@H]2CCNC2=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
 UED  UED  N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide  ligand  60  29  .  2022-03-23  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_UED
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
 UED  C7   C  CH2   0  -0.223  -13.7216  -10.4668  -0.6661
 UED  O8   O  O2    0  -0.489  -14.4181  -11.6454  -1.0359
 UED  C9   C  C     0   0.768  -14.5696  -12.5930  -0.1004
 UED  O10  O  O     0  -0.492  -14.2169  -12.4763   1.0526
 UED  C1   C  CR6   0   0.044  -12.2260  -10.6391  -0.6145
 UED  C2   C  CR16  0  -0.283  -11.5751  -11.7530  -1.1320
 UED  C3   C  CR16  0  -0.240  -10.1875  -11.8294  -1.1061
 UED  C4   C  CR16  0  -0.262   -9.4341  -10.7935  -0.5748
 UED  C5   C  CR16  0  -0.244  -10.0796   -9.6790  -0.0537
 UED  C6   C  CR16  0  -0.289  -11.4642   -9.6073  -0.0700
 UED  N11  N  NH1   0  -0.656  -15.1924  -13.6738  -0.6117
 UED  C12  C  CH1   0  -0.215  -15.2664  -14.8945   0.1475
 UED  C17  C  C     0   0.573  -13.8626  -15.4725   0.3524
 UED  O18  O  O     0  -0.486  -13.0264  -15.4176  -0.5352
 UED  C13  C  CH2   0  -0.442  -16.1281  -15.9221  -0.5862
 UED  C14  C  CH1   0  -0.230  -17.5675  -15.4819  -0.8639
 UED  C15  C  CH3   0  -0.667  -18.2995  -15.0812   0.4121
 UED  C16  C  CH3   0  -0.654  -18.3070  -16.6044  -1.5856
 UED  N19  N  NH1   0  -0.634  -13.6692  -16.0584   1.5436
 UED  C20  C  CH1   0  -0.135  -12.4175  -16.6341   1.9909
 UED  C21  C  CH2   0  -0.127  -12.6269  -18.1239   2.2406
 UED  O22  O  OH1   0  -0.668  -11.4014  -18.6959   2.6284
 UED  C24  C  CH2   0  -0.426  -11.9043  -15.8941   3.2262
 UED  C25  C  CH1   0  -0.423  -11.7230  -14.4061   2.9789
 UED  C26  C  CH2   0  -0.469  -10.7045  -14.0258   1.9049
 UED  C27  C  CH2   0  -0.257  -10.2265  -12.6406   2.3382
 UED  N28  N  NH1   0  -0.630  -10.3889  -12.6980   3.7772
 UED  C29  C  C     0   0.566  -11.2339  -13.6499   4.2035
 UED  O30  O  O     0  -0.501  -11.5632  -13.8557   5.3619
 UED  H1   H  HCH2  0   0.273  -13.9793   -9.7395  -1.4373
 UED  H2   H  HCH2  0   0.251  -14.0916  -10.0738   0.2834
 UED  H3   H  HCR6  0   0.248  -12.1338  -12.5774  -1.5560
 UED  H4   H  HCR6  0   0.253   -9.6965  -12.7072  -1.5060
 UED  H5   H  HCR6  0   0.253   -8.3537  -10.8559  -0.5593
 UED  H6   H  HCR6  0   0.254   -9.5060   -8.8658   0.3725
 UED  H7   H  HCR6  0   0.251  -11.9590   -8.7361   0.3444
 UED  H8   H  HNH1  0   0.401  -15.2937  -13.7330  -1.6134
 UED  H9   H  HCH1  0   0.270  -15.7181  -14.6774   1.1192
 UED  H10  H  HCH2  0   0.245  -16.1478  -16.8341   0.0183
 UED  H11  H  HCH2  0   0.247  -15.6382  -16.1865  -1.5291
 UED  H12  H  HCH1  0   0.224  -17.5467  -14.6143  -1.5320
 UED  H13  H  HCH3  0   0.230  -17.8721  -14.1883   0.8710
 UED  H14  H  HCH3  0   0.233  -19.3486  -14.8643   0.2060
 UED  H15  H  HCH3  0   0.217  -18.2655  -15.8846   1.1519
 UED  H16  H  HCH3  0   0.230  -19.3180  -16.2975  -1.8568
 UED  H17  H  HCH3  0   0.227  -17.7915  -16.8955  -2.5025
 UED  H18  H  HCH3  0   0.216  -18.3867  -17.4924  -0.9540
 UED  H19  H  HNH1  0   0.397  -14.4094  -15.9943   2.2262
 UED  H20  H  HCH1  0   0.263  -11.7017  -16.5165   1.1755
 UED  H21  H  HCH2  0   0.232  -12.6046  -16.0467   4.0540
 UED  H22  H  HCH2  0   0.246  -10.9530  -16.3361   3.5303
 UED  H23  H  HCH1  0   0.288  -12.6904  -13.9594   2.7167
 UED  H24  H  HCH2  0   0.266  -11.1215  -14.0168   0.9007
 UED  H25  H  HCH2  0   0.236   -9.8681  -14.7309   1.9184
 UED  H26  H  HCH2  0   0.242   -9.1895  -12.4464   2.0673
 UED  H27  H  HCH2  0   0.243  -10.8400  -11.8500   1.8963
 UED  H28  H  HNH1  0   0.393  -10.0279  -11.9877   4.3948
 UED  H29  H  HCH2  0   0.192  -13.3984  -18.2514   3.0132
 UED  H30  H  HCH2  0   0.209  -13.0142  -18.5792   1.3205
 UED  H31  H  HOH1  0   0.459  -11.5502  -19.6263   2.8185

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
 UED  C16  C14  single    1.526  0.020  1.526
 UED  C3   C2   aromatic  1.390  0.020  1.390
 UED  C3   C4   aromatic  1.387  0.020  1.387
 UED  C2   C1   aromatic  1.390  0.020  1.390
 UED  C14  C13  single    1.531  0.020  1.531
 UED  C14  C15  single    1.525  0.020  1.525
 UED  C13  C12  single    1.529  0.020  1.529
 UED  C4   C5   aromatic  1.389  0.020  1.389
 UED  O8   C7   single    1.418  0.020  1.418
 UED  O8   C9   single    1.340  0.020  1.340
 UED  N11  C12  single    1.439  0.020  1.439
 UED  N11  C9   single    1.348  0.020  1.348
 UED  C1   C7   single    1.506  0.020  1.506
 UED  C1   C6   aromatic  1.393  0.020  1.393
 UED  O18  C17  double    1.221  0.020  1.221
 UED  C5   C6   aromatic  1.387  0.020  1.387
 UED  C12  C17  single    1.532  0.020  1.532
 UED  C9   O10  double    1.211  0.020  1.211
 UED  C17  N19  single    1.342  0.020  1.342
 UED  C26  C27  single    1.528  0.020  1.528
 UED  C26  C25  single    1.528  0.020  1.528
 UED  N19  C20  single    1.448  0.020  1.448
 UED  C20  C21  single    1.525  0.020  1.525
 UED  C20  C24  single    1.529  0.020  1.529
 UED  C27  N28  single    1.449  0.020  1.449
 UED  O22  C21  single    1.407  0.020  1.407
 UED  C25  C24  single    1.519  0.020  1.519
 UED  C25  C29  single    1.520  0.020  1.520
 UED  N28  C29  single    1.342  0.020  1.342
 UED  C29  O30  double    1.222  0.020  1.222
 UED  C7   H1   single    0.970  0.020  1.090
 UED  C7   H2   single    0.970  0.020  1.090
 UED  C2   H3   single    0.930  0.020  1.080
 UED  C3   H4   single    0.930  0.020  1.080
 UED  C4   H5   single    0.930  0.020  1.080
 UED  C5   H6   single    0.930  0.020  1.080
 UED  C6   H7   single    0.930  0.020  1.080
 UED  N11  H8   single    0.890  0.020  1.040
 UED  C12  H9   single    0.970  0.020  1.090
 UED  C13  H10  single    0.970  0.020  1.090
 UED  C13  H11  single    0.970  0.020  1.090
 UED  C14  H12  single    0.970  0.020  1.090
 UED  C15  H13  single    0.970  0.020  1.090
 UED  C15  H14  single    0.970  0.020  1.090
 UED  C15  H15  single    0.970  0.020  1.090
 UED  C16  H16  single    0.970  0.020  1.090
 UED  C16  H17  single    0.970  0.020  1.090
 UED  C16  H18  single    0.970  0.020  1.090
 UED  N19  H19  single    0.860  0.020  1.020
 UED  C20  H20  single    0.970  0.020  1.090
 UED  C24  H21  single    0.970  0.020  1.090
 UED  C24  H22  single    0.970  0.020  1.090
 UED  C25  H23  single    0.970  0.020  1.090
 UED  C26  H24  single    0.970  0.020  1.090
 UED  C26  H25  single    0.970  0.020  1.090
 UED  C27  H26  single    0.970  0.020  1.090
 UED  C27  H27  single    0.970  0.020  1.090
 UED  N28  H28  single    0.860  0.020  1.020
 UED  C21  H29  single    0.970  0.020  1.090
 UED  C21  H30  single    0.970  0.020  1.090
 UED  O22  H31  single    0.850  0.020  0.980

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
 UED  H2   C7   H1   107.14  3.000
 UED  H2   C7   C1   110.35  3.000
 UED  H1   C7   C1   109.57  3.000
 UED  H2   C7   O8   111.06  3.000
 UED  H1   C7   O8   104.70  3.000
 UED  C1   C7   O8   113.67  3.000
 UED  C9   O8   C7   117.46  3.000
 UED  N11  C9   O10  124.94  3.000
 UED  O10  C9   O8   124.29  3.000
 UED  N11  C9   O8   110.75  3.000
 UED  C6   C1   C2   118.87  3.000
 UED  C6   C1   C7   118.14  3.000
 UED  C2   C1   C7   122.94  3.000
 UED  H3   C2   C3   118.73  3.000
 UED  H3   C2   C1   120.96  3.000
 UED  C3   C2   C1   120.30  3.000
 UED  H4   C3   C4   120.06  3.000
 UED  H4   C3   C2   119.38  3.000
 UED  C4   C3   C2   120.56  3.000
 UED  H5   C4   C5   120.31  3.000
 UED  H5   C4   C3   120.31  3.000
 UED  C5   C4   C3   119.38  3.000
 UED  H6   C5   C6   119.66  3.000
 UED  H6   C5   C4   120.27  3.000
 UED  C6   C5   C4   120.07  3.000
 UED  H7   C6   C5   119.52  3.000
 UED  H7   C6   C1   119.66  3.000
 UED  C5   C6   C1   120.82  3.000
 UED  H8   N11  C12  117.97  3.000
 UED  H8   N11  C9   118.05  3.000
 UED  C12  N11  C9   120.23  3.000
 UED  H9   C12  C13  109.09  3.000
 UED  H9   C12  C17  109.56  3.000
 UED  C13  C12  C17  109.10  3.000
 UED  H9   C12  N11  108.76  3.000
 UED  C17  C12  N11  110.08  3.000
 UED  C13  C12  N11  110.23  3.000
 UED  N19  C17  O18  124.51  3.000
 UED  N19  C17  C12  114.56  3.000
 UED  O18  C17  C12  120.90  3.000
 UED  H11  C13  H10  106.41  3.000
 UED  H11  C13  C14  109.51  3.000
 UED  H10  C13  C14  108.84  3.000
 UED  H11  C13  C12  108.87  3.000
 UED  H10  C13  C12  107.77  3.000
 UED  C14  C13  C12  115.08  3.000
 UED  H12  C14  C16  107.66  3.000
 UED  H12  C14  C15  108.15  3.000
 UED  C16  C14  C15  110.89  3.000
 UED  H12  C14  C13  108.70  3.000
 UED  C15  C14  C13  112.04  3.000
 UED  C16  C14  C13  109.27  3.000
 UED  H15  C15  H14  107.70  3.000
 UED  H15  C15  H13  107.74  3.000
 UED  H14  C15  H13  107.07  3.000
 UED  H15  C15  C14  111.00  3.000
 UED  H14  C15  C14  110.85  3.000
 UED  H13  C15  C14  112.27  3.000
 UED  H18  C16  H17  107.66  3.000
 UED  H18  C16  H16  107.74  3.000
 UED  H17  C16  H16  107.69  3.000
 UED  H18  C16  C14  111.09  3.000
 UED  H17  C16  C14  111.39  3.000
 UED  H16  C16  C14  111.09  3.000
 UED  H19  N19  C20  116.76  3.000
 UED  H19  N19  C17  117.85  3.000
 UED  C20  N19  C17  124.91  3.000
 UED  H20  C20  C24  109.35  3.000
 UED  H20  C20  C21  108.52  3.000
 UED  C24  C20  C21  112.75  3.000
 UED  H20  C20  N19  107.05  3.000
 UED  C24  C20  N19  110.32  3.000
 UED  C21  C20  N19  108.68  3.000
 UED  H30  C21  H29  107.07  3.000
 UED  H30  C21  O22  111.71  3.000
 UED  H29  C21  O22  111.74  3.000
 UED  H30  C21  C20  108.46  3.000
 UED  H29  C21  C20  108.95  3.000
 UED  O22  C21  C20  108.83  3.000
 UED  H31  O22  C21  108.25  3.000
 UED  H22  C24  H21  106.88  3.000
 UED  H22  C24  C25  109.74  3.000
 UED  H21  C24  C25  109.63  3.000
 UED  H22  C24  C20  108.75  3.000
 UED  H21  C24  C20  109.19  3.000
 UED  C25  C24  C20  112.49  3.000
 UED  H23  C25  C29  105.88  3.000
 UED  H23  C25  C26  108.56  3.000
 UED  C29  C25  C26  103.18  3.000
 UED  H23  C25  C24  109.42  3.000
 UED  C29  C25  C24  113.23  3.000
 UED  C26  C25  C24  115.95  3.000
 UED  H25  C26  H24  108.06  3.000
 UED  H25  C26  C27  109.97  3.000
 UED  H24  C26  C27  111.98  3.000
 UED  H25  C26  C25  109.91  3.000
 UED  H24  C26  C25  113.29  3.000
 UED  C27  C26  C25  103.58  3.000
 UED  H27  C27  H26  107.74  3.000
 UED  H27  C27  N28  111.52  3.000
 UED  H26  C27  N28  111.14  3.000
 UED  H27  C27  C26  111.42  3.000
 UED  H26  C27  C26  112.88  3.000
 UED  N28  C27  C26  102.15  3.000
 UED  H28  N28  C29  122.03  3.000
 UED  H28  N28  C27  122.71  3.000
 UED  C29  N28  C27  114.45  3.000
 UED  O30  C29  N28  126.17  3.000
 UED  O30  C29  C25  126.39  3.000
 UED  N28  C29  C25  107.43  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
 UED  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 UED  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 UED  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 UED  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 UED  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 UED  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 UED  CONST_07  C27  N28  C29  C25     0.00   0.0  0
 UED  CONST_08  C3   C2   C1   C7    180.00   0.0  0
 UED  CONST_09  C5   C6   C1   C7    180.00   0.0  0
 UED  CONST_10  O30  C29  N28  C27   180.00   0.0  0
 UED  CONST_11  H4   C3   C2   C1    180.00   0.0  0
 UED  CONST_12  H6   C5   C6   C1    180.00   0.0  0
 UED  CONST_13  H5   C4   C3   C2    180.00   0.0  0
 UED  CONST_14  H7   C6   C1   C2    180.00   0.0  0
 UED  CONST_15  H3   C2   C3   C4    180.00   0.0  0
 UED  CONST_16  H28  N28  C29  C25   180.00   0.0  0
 UED  CONST_17  C20  N19  C17  C12   180.00   0.0  0
 UED  CONST_18  C20  N19  C17  O18     0.00   0.0  0
 UED  CONST_19  H19  N19  C17  C12     0.00   0.0  0
 UED  Var_01    N28  C27  C26  C25    28.92  30.0  1
 UED  Var_02    C29  N28  C27  C26   -19.88  30.0  1
 UED  Var_03    C2   C1   C7   O8     12.12  30.0  2
 UED  Var_04    C1   C7   O8   C9     77.37  30.0  3
 UED  Var_05    N11  C9   O8   C7   -177.14  30.0  3
 UED  Var_06    C12  N11  C9   O8    169.82  30.0  1
 UED  Var_07    C16  C14  C13  C12  -179.52  30.0  1
 UED  Var_08    H16  C16  C14  C13  -176.27  30.0  3
 UED  Var_09    H13  C15  C14  C13    65.80  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
 UED  chir_01  C12  C13  N11  C17  positiv
 UED  chir_02  C20  N19  C21  C24  positiv
 UED  chir_03  C25  C29  C24  C26  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
 UED  plan-1  C7   0.020
 UED  plan-1  C1   0.020
 UED  plan-1  C2   0.020
 UED  plan-1  C3   0.020
 UED  plan-1  C4   0.020
 UED  plan-1  C5   0.020
 UED  plan-1  C6   0.020
 UED  plan-1  H3   0.020
 UED  plan-1  H4   0.020
 UED  plan-1  H5   0.020
 UED  plan-1  H6   0.020
 UED  plan-1  H7   0.020
 UED  plan-2  C12  0.020
 UED  plan-2  C17  0.020
 UED  plan-2  O18  0.020
 UED  plan-2  N19  0.020
 UED  plan-2  C20  0.020
 UED  plan-2  H19  0.020
 UED  plan-3  C25  0.020
 UED  plan-3  C27  0.020
 UED  plan-3  N28  0.020
 UED  plan-3  C29  0.020
 UED  plan-3  O30  0.020
 UED  plan-3  H28  0.020
 UED  plan-4  O8   0.020
 UED  plan-4  C9   0.020
 UED  plan-4  O10  0.020
 UED  plan-4  N11  0.020

