# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 03:42:13 2020
#   Inital geometry file: a 165 line input string
#   Ligand name: ethyl (2Z,4S)-4-{[N-(3-methylbutanoyl)-L-phenylalanyl]amino}-5-[(3S)-2-oxopyrrolidin-3-yl]pent-2-enoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)\C=C/[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](Cc2ccccc2)NC(=O)CC(C)C
#
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
 5EC  5EC  'ethyl (2Z,4S)-4-{[N-(3-methylbutanoyl)-L-phenylalanyl]amino}-5-[(3S)-2-oxopyrrolidin-3-yl]pent-2-enoate'  ligand  68  33  .  2021-08-04  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5EC
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
 5EC  C2   C  CH1   0  -0.202  -1.2235   0.1146   0.1528
 5EC  C3   C  CH2   0  -0.554  -1.2893  -1.4121  -0.0304
 5EC  C4   C  CR6   0   0.158  -2.6726  -1.9426   0.2259
 5EC  C5   C  CR16  0  -0.299  -3.1819  -2.0017   1.5217
 5EC  C6   C  CR16  0  -0.238  -4.4738  -2.4492   1.7557
 5EC  C7   C  CR16  0  -0.266  -5.2789  -2.8468   0.6948
 5EC  N1   N  NR15  0  -0.616   4.7587   3.7764  -0.9455
 5EC  C8   C  CR16  0  -0.234  -4.7795  -2.7969  -0.5987
 5EC  C20  C  CH2   0  -0.548  -3.7568   2.4571  -1.3780
 5EC  C22  C  CH1   0  -0.238  -5.1362   2.4732  -0.7047
 5EC  C23  C  CH3   0  -0.653  -6.1668   3.0673  -1.6585
 5EC  C24  C  CH3   0  -0.654  -5.5606   1.0807  -0.2474
 5EC  O    O  O     0  -0.501  -2.2851   2.6638   0.5058
 5EC  N5   N  NH1   0  -0.615  -2.2086   0.7483  -0.6723
 5EC  C9   C  CR16  0  -0.323  -3.4854  -2.3475  -0.8281
 5EC  C17  C  C     0   0.572   0.1826   0.6153  -0.1914
 5EC  O4   O  O     0  -0.481   0.4410   1.1214  -1.2686
 5EC  N    N  NH1   0  -0.638   1.0884   0.4087   0.7768
 5EC  C10  C  CH1   0  -0.112   2.5132   0.6046   0.5823
 5EC  C11  C  CH2   0  -0.447   2.9489   1.9828   1.0820
 5EC  C12  C  CR15  0  -0.413   4.4232   2.3162   0.8183
 5EC  C13  C  CR5   0   0.547   4.6812   2.4633  -0.6759
 5EC  O1   O  O     0  -0.493   4.7731   1.5575  -1.4902
 5EC  C25  C  CH2   0  -0.262   4.5633   4.6436   0.1961
 5EC  C26  C  CH2   0  -0.465   4.8125   3.6912   1.3685
 5EC  C14  C  C1    0  -0.160   3.2597  -0.4941   1.2963
 5EC  C15  C  C1    0  -0.366   3.3182  -1.7881   0.9791
 5EC  C16  C  C     0   0.586   2.6688  -2.4003  -0.1966
 5EC  O3   O  O     0  -0.442   2.0617  -1.8104  -1.0582
 5EC  O2   O  O2    0  -0.465   2.8395  -3.7173  -0.1923
 5EC  C18  C  CH2   0  -0.181   2.2626  -4.4718  -1.2684
 5EC  C19  C  CH3   0  -0.688   2.5888  -5.9273  -1.0367
 5EC  H1   H  HCH1  0   0.279  -1.4405   0.3494   1.1993
 5EC  H2   H  HCH2  0   0.269  -0.9661  -1.6695  -1.0425
 5EC  H3   H  HCH2  0   0.273  -0.5719  -1.8741   0.6496
 5EC  H4   H  HCR6  0   0.246  -2.5630  -1.6969   2.3585
 5EC  H5   H  HCR6  0   0.254  -4.8520  -2.4927   2.7692
 5EC  H6   H  HCR6  0   0.253  -6.2865  -3.1966   0.8787
 5EC  H7   H  HNR5  0   0.396   4.8147   4.1241  -1.8905
 5EC  H8   H  HCR6  0   0.253  -5.3960  -3.1076  -1.4326
 5EC  H9   H  HCH2  0   0.241  -3.7991   1.8272  -2.2718
 5EC  H10  H  HCH2  0   0.263  -3.5004   3.4669  -1.7077
 5EC  H11  H  HCH1  0   0.228  -5.0743   3.1238   0.1737
 5EC  H12  H  HCH3  0   0.216  -6.2838   2.4442  -2.5482
 5EC  H13  H  HCH3  0   0.230  -7.1435   3.1436  -1.1783
 5EC  H14  H  HCH3  0   0.227  -5.8775   4.0668  -1.9877
 5EC  H15  H  HCH3  0   0.226  -6.5698   1.1038   0.1673
 5EC  H16  H  HCH3  0   0.216  -5.5612   0.3747  -1.0813
 5EC  H17  H  HCH3  0   0.235  -4.9034   0.6697   0.5202
 5EC  H18  H  HNH1  0   0.401  -2.5347   0.2608  -1.4905
 5EC  H19  H  HCR6  0   0.249  -3.1031  -2.3145  -1.8421
 5EC  H20  H  HNH1  0   0.399   0.7804   0.0284   1.6581
 5EC  H21  H  HCH1  0   0.284   2.7010   0.5309  -0.4878
 5EC  H22  H  HCH2  0   0.256   2.3081   2.7385   0.6191
 5EC  H23  H  HCH2  0   0.249   2.7719   2.0436   2.1605
 5EC  H24  H  HCR5  0   0.279   5.0594   1.5247   1.2223
 5EC  H25  H  HCH2  0   0.254   5.2634   5.4783   0.1802
 5EC  H26  H  HCH2  0   0.238   3.5503   5.0556   0.2109
 5EC  H27  H  HCH2  0   0.254   4.2482   3.9738   2.2566
 5EC  H28  H  HCH2  0   0.258   5.8713   3.7018   1.6306
 5EC  H29  H  H     0   0.274   3.7849  -0.1984   2.1999
 5EC  H31  H  H     0   0.275   3.8762  -2.4554   1.6241
 5EC  H33  H  HCH2  0   0.234   1.1822  -4.3124  -1.2911
 5EC  H34  H  HCH2  0   0.236   2.6714  -4.1267  -2.2202
 5EC  H35  H  HCH3  0   0.236   3.6650  -6.0999  -1.0266
 5EC  H36  H  HCH3  0   0.236   2.1678  -6.2885  -0.0985
 5EC  H37  H  HCH3  0   0.240   2.1636  -6.5220  -1.8446
 5EC  C    C  C     0   0.535  -2.6762   1.9851  -0.4351

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
 5EC  O3   C16  double    1.208  0.020  1.208
 5EC  C16  O2   single    1.328  0.020  1.328
 5EC  C16  C15  single    1.476  0.020  1.476
 5EC  O2   C18  single    1.435  0.020  1.435
 5EC  C19  C18  single    1.509  0.020  1.509
 5EC  C15  C14  double    1.334  0.020  1.334
 5EC  C14  C10  single    1.508  0.020  1.508
 5EC  C11  C10  single    1.529  0.020  1.529
 5EC  C11  C12  single    1.534  0.020  1.534
 5EC  C10  N    single    1.451  0.020  1.451
 5EC  O1   C13  double    1.221  0.020  1.221
 5EC  C13  C12  single    1.523  0.020  1.523
 5EC  C13  N1   single    1.343  0.020  1.343
 5EC  C12  C26  single    1.531  0.020  1.531
 5EC  C26  C25  single    1.531  0.020  1.531
 5EC  N    C17  single    1.342  0.020  1.342
 5EC  N1   C25  single    1.447  0.020  1.447
 5EC  O4   C17  double    1.218  0.020  1.218
 5EC  C17  C2   single    1.532  0.020  1.532
 5EC  C3   C2   single    1.539  0.020  1.539
 5EC  C3   C4   single    1.504  0.020  1.504
 5EC  C2   N5   single    1.433  0.020  1.433
 5EC  C5   C4   aromatic  1.394  0.020  1.394
 5EC  C5   C6   aromatic  1.387  0.020  1.387
 5EC  C4   C9   aromatic  1.391  0.020  1.391
 5EC  O    C    double    1.224  0.020  1.224
 5EC  N5   C    single    1.343  0.020  1.343
 5EC  C6   C7   aromatic  1.390  0.020  1.390
 5EC  C9   C8   aromatic  1.389  0.020  1.389
 5EC  C    C20  single    1.510  0.020  1.510
 5EC  C8   C7   aromatic  1.387  0.020  1.387
 5EC  C20  C22  single    1.535  0.020  1.535
 5EC  C24  C22  single    1.526  0.020  1.526
 5EC  C22  C23  single    1.525  0.020  1.525
 5EC  C2   H1   single    0.970  0.020  1.090
 5EC  C3   H2   single    0.970  0.020  1.090
 5EC  C3   H3   single    0.970  0.020  1.090
 5EC  C5   H4   single    0.930  0.020  1.080
 5EC  C6   H5   single    0.930  0.020  1.080
 5EC  C7   H6   single    0.930  0.020  1.080
 5EC  N1   H7   single    0.860  0.020  1.020
 5EC  C8   H8   single    0.930  0.020  1.080
 5EC  C20  H9   single    0.970  0.020  1.090
 5EC  C20  H10  single    0.970  0.020  1.090
 5EC  C22  H11  single    0.970  0.020  1.090
 5EC  C23  H12  single    0.970  0.020  1.090
 5EC  C23  H13  single    0.970  0.020  1.090
 5EC  C23  H14  single    0.970  0.020  1.090
 5EC  C24  H15  single    0.970  0.020  1.090
 5EC  C24  H16  single    0.970  0.020  1.090
 5EC  C24  H17  single    0.970  0.020  1.090
 5EC  N5   H18  single    0.860  0.020  1.020
 5EC  C9   H19  single    0.930  0.020  1.080
 5EC  N    H20  single    0.860  0.020  1.020
 5EC  C10  H21  single    0.970  0.020  1.090
 5EC  C11  H22  single    0.970  0.020  1.090
 5EC  C11  H23  single    0.970  0.020  1.090
 5EC  C12  H24  single    0.970  0.020  1.090
 5EC  C25  H25  single    0.970  0.020  1.090
 5EC  C25  H26  single    0.970  0.020  1.090
 5EC  C26  H27  single    0.970  0.020  1.090
 5EC  C26  H28  single    0.970  0.020  1.090
 5EC  C14  H29  single    0.930  0.020  1.080
 5EC  C15  H31  single    0.930  0.020  1.080
 5EC  C18  H33  single    0.970  0.020  1.090
 5EC  C18  H34  single    0.970  0.020  1.090
 5EC  C19  H35  single    0.970  0.020  1.090
 5EC  C19  H36  single    0.970  0.020  1.090
 5EC  C19  H37  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
 5EC  H1   C2   C17  109.07  3.000
 5EC  H1   C2   N5   108.63  3.000
 5EC  C17  C2   N5   110.93  3.000
 5EC  H1   C2   C3   108.56  3.000
 5EC  N5   C2   C3   109.92  3.000
 5EC  C17  C2   C3   109.68  3.000
 5EC  H3   C3   H2   106.43  3.000
 5EC  H3   C3   C4   110.44  3.000
 5EC  H2   C3   C4   110.29  3.000
 5EC  H3   C3   C2   108.52  3.000
 5EC  H2   C3   C2   109.34  3.000
 5EC  C4   C3   C2   111.66  3.000
 5EC  C9   C4   C5   118.59  3.000
 5EC  C9   C4   C3   120.73  3.000
 5EC  C5   C4   C3   120.65  3.000
 5EC  H4   C5   C6   119.47  3.000
 5EC  H4   C5   C4   119.80  3.000
 5EC  C6   C5   C4   120.73  3.000
 5EC  H5   C6   C7   120.05  3.000
 5EC  H5   C6   C5   119.75  3.000
 5EC  C7   C6   C5   120.20  3.000
 5EC  H6   C7   C8   120.34  3.000
 5EC  H6   C7   C6   120.13  3.000
 5EC  C8   C7   C6   119.53  3.000
 5EC  H7   N1   C25  122.69  3.000
 5EC  H7   N1   C13  121.91  3.000
 5EC  C25  N1   C13  114.83  3.000
 5EC  H8   C8   C9   119.75  3.000
 5EC  H8   C8   C7   120.19  3.000
 5EC  C9   C8   C7   120.06  3.000
 5EC  H10  C20  H9   107.13  3.000
 5EC  H10  C20  C    108.02  3.000
 5EC  H9   C20  C    110.96  3.000
 5EC  H10  C20  C22  109.48  3.000
 5EC  H9   C20  C22  109.25  3.000
 5EC  C    C20  C22  111.87  3.000
 5EC  H11  C22  C24  108.52  3.000
 5EC  H11  C22  C23  107.97  3.000
 5EC  C24  C22  C23  110.79  3.000
 5EC  H11  C22  C20  107.90  3.000
 5EC  C23  C22  C20  109.70  3.000
 5EC  C24  C22  C20  111.83  3.000
 5EC  H14  C23  H13  107.81  3.000
 5EC  H14  C23  H12  107.76  3.000
 5EC  H13  C23  H12  107.61  3.000
 5EC  H14  C23  C22  111.49  3.000
 5EC  H13  C23  C22  110.92  3.000
 5EC  H12  C23  C22  111.08  3.000
 5EC  H17  C24  H16  107.09  3.000
 5EC  H17  C24  H15  107.32  3.000
 5EC  H16  C24  H15  107.65  3.000
 5EC  H17  C24  C22  112.78  3.000
 5EC  H16  C24  C22  111.17  3.000
 5EC  H15  C24  C22  110.60  3.000
 5EC  H18  N5   C    118.46  3.000
 5EC  H18  N5   C2   118.46  3.000
 5EC  C    N5   C2   123.02  3.000
 5EC  H19  C9   C8   119.53  3.000
 5EC  H19  C9   C4   119.59  3.000
 5EC  C8   C9   C4   120.89  3.000
 5EC  N    C17  O4   123.99  3.000
 5EC  O4   C17  C2   121.96  3.000
 5EC  N    C17  C2   114.02  3.000
 5EC  H20  N    C10  117.91  3.000
 5EC  H20  N    C17  118.86  3.000
 5EC  C10  N    C17  123.03  3.000
 5EC  H21  C10  C14  109.31  3.000
 5EC  H21  C10  C11  109.45  3.000
 5EC  C14  C10  C11  111.15  3.000
 5EC  H21  C10  N    106.97  3.000
 5EC  C11  C10  N    110.94  3.000
 5EC  C14  C10  N    108.92  3.000
 5EC  H23  C11  H22  106.49  3.000
 5EC  H23  C11  C12  108.22  3.000
 5EC  H22  C11  C12  109.89  3.000
 5EC  H23  C11  C10  109.02  3.000
 5EC  H22  C11  C10  108.51  3.000
 5EC  C12  C11  C10  114.42  3.000
 5EC  H24  C12  C26  111.69  3.000
 5EC  H24  C12  C13  109.51  3.000
 5EC  C26  C12  C13  102.86  3.000
 5EC  H24  C12  C11  109.78  3.000
 5EC  C26  C12  C11  112.18  3.000
 5EC  C13  C12  C11  110.62  3.000
 5EC  O1   C13  C12  126.51  3.000
 5EC  C12  C13  N1   107.53  3.000
 5EC  O1   C13  N1   125.95  3.000
 5EC  H26  C25  H25  107.87  3.000
 5EC  H26  C25  C26  112.01  3.000
 5EC  H25  C25  C26  112.53  3.000
 5EC  H26  C25  N1   111.19  3.000
 5EC  H25  C25  N1   111.15  3.000
 5EC  C26  C25  N1   102.09  3.000
 5EC  H28  C26  H27  107.72  3.000
 5EC  H28  C26  C25  109.63  3.000
 5EC  H27  C26  C25  112.25  3.000
 5EC  H28  C26  C12  109.98  3.000
 5EC  H27  C26  C12  113.21  3.000
 5EC  C25  C26  C12  104.01  3.000
 5EC  H29  C14  C15  116.16  3.000
 5EC  H29  C14  C10  115.78  3.000
 5EC  C15  C14  C10  128.02  3.000
 5EC  H31  C15  C16  116.46  3.000
 5EC  H31  C15  C14  118.61  3.000
 5EC  C16  C15  C14  124.94  3.000
 5EC  O2   C16  O3   123.45  3.000
 5EC  O2   C16  C15  110.62  3.000
 5EC  O3   C16  C15  125.92  3.000
 5EC  C18  O2   C16  117.86  3.000
 5EC  H34  C18  H33  107.82  3.000
 5EC  H34  C18  C19  110.96  3.000
 5EC  H33  C18  C19  110.96  3.000
 5EC  H34  C18  O2   109.69  3.000
 5EC  H33  C18  O2   109.66  3.000
 5EC  C19  C18  O2   107.75  3.000
 5EC  H37  C19  H36  107.85  3.000
 5EC  H37  C19  H35  107.80  3.000
 5EC  H36  C19  H35  108.72  3.000
 5EC  H37  C19  C18  109.16  3.000
 5EC  H36  C19  C18  111.60  3.000
 5EC  H35  C19  C18  111.57  3.000
 5EC  N5   C    O    122.34  3.000
 5EC  N5   C    C20  115.26  3.000
 5EC  O    C    C20  122.36  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
 5EC  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 5EC  CONST_02  C7   C8   C9   C4      0.00   0.0  0
 5EC  CONST_03  C8   C9   C4   C5      0.00   0.0  0
 5EC  CONST_04  C8   C7   C6   C5      0.00   0.0  0
 5EC  CONST_05  C9   C4   C5   C6      0.00   0.0  0
 5EC  CONST_06  C9   C8   C7   C6      0.00   0.0  0
 5EC  CONST_07  C25  N1   C13  C12     0.00   0.0  0
 5EC  CONST_08  C6   C5   C4   C3    180.00   0.0  0
 5EC  CONST_09  C8   C9   C4   C3    180.00   0.0  0
 5EC  CONST_10  C25  N1   C13  O1    180.00   0.0  0
 5EC  CONST_11  H5   C6   C5   C4    180.00   0.0  0
 5EC  CONST_12  H8   C8   C9   C4    180.00   0.0  0
 5EC  CONST_13  H19  C9   C4   C5    180.00   0.0  0
 5EC  CONST_14  H6   C7   C6   C5    180.00   0.0  0
 5EC  CONST_15  H4   C5   C6   C7    180.00   0.0  0
 5EC  CONST_16  H7   N1   C13  C12   180.00   0.0  0
 5EC  CONST_17  C10  N    C17  C2    180.00   0.0  0
 5EC  CONST_18  O    C    N5   C2      0.00   0.0  0
 5EC  CONST_19  C20  C    N5   C2    180.00   0.0  0
 5EC  CONST_20  C10  N    C17  O4      0.00   0.0  0
 5EC  CONST_21  H20  N    C17  C2      0.00   0.0  0
 5EC  CONST_22  H18  N5   C    C20     0.00   0.0  0
 5EC  Var_01    C12  C26  C25  N1    -27.95  30.0  1
 5EC  Var_02    C26  C25  N1   C13    18.68  30.0  1
 5EC  Var_03    C5   C4   C3   C2    -72.45  30.0  2
 5EC  Var_04    C16  C15  C14  C10     1.89   0.0  2
 5EC  Var_05    O    C    C20  C22   -71.00  30.0  2
 5EC  Var_06    C    C20  C22  C23   175.22  30.0  2
 5EC  Var_07    O3   C16  C15  C14     4.05  30.0  2
 5EC  Var_08    C19  C18  O2   C16  -179.85  30.0  3
 5EC  Var_09    H15  C24  C22  C20  -176.22  30.0  3
 5EC  Var_10    H12  C23  C22  C20    63.77  30.0  3
 5EC  Var_11    H35  C19  C18  O2    -60.76  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
 5EC  chir_01  C2   C17  C3   N5   positiv
 5EC  chir_02  C10  N    C14  C11  positiv
 5EC  chir_03  C12  C26  C13  C11  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
 5EC  plan-1  C3   0.020
 5EC  plan-1  C4   0.020
 5EC  plan-1  C5   0.020
 5EC  plan-1  C6   0.020
 5EC  plan-1  C7   0.020
 5EC  plan-1  C8   0.020
 5EC  plan-1  C9   0.020
 5EC  plan-1  H4   0.020
 5EC  plan-1  H5   0.020
 5EC  plan-1  H6   0.020
 5EC  plan-1  H8   0.020
 5EC  plan-1  H19  0.020
 5EC  plan-2  C2   0.020
 5EC  plan-2  C20  0.020
 5EC  plan-2  O    0.020
 5EC  plan-2  N5   0.020
 5EC  plan-2  H18  0.020
 5EC  plan-2  C    0.020
 5EC  plan-3  C2   0.020
 5EC  plan-3  C17  0.020
 5EC  plan-3  O4   0.020
 5EC  plan-3  N    0.020
 5EC  plan-3  C10  0.020
 5EC  plan-3  H20  0.020
 5EC  plan-4  N1   0.020
 5EC  plan-4  C12  0.020
 5EC  plan-4  C13  0.020
 5EC  plan-4  O1   0.020
 5EC  plan-4  C25  0.020
 5EC  plan-4  H7   0.020
 5EC  plan-5  C15  0.020
 5EC  plan-5  C16  0.020
 5EC  plan-5  O3   0.020
 5EC  plan-5  O2   0.020
 5EC  plan-6  C10  0.020
 5EC  plan-6  C14  0.020
 5EC  plan-6  C15  0.020
 5EC  plan-6  C16  0.020
 5EC  plan-6  H29  0.020
 5EC  plan-6  H31  0.020

