# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 22:36:02 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: ethyl (2Z,4S)-4-{[(2S)-2-methyl-3-phenylpropanoyl]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](C)Cc2ccccc2
#
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
 5E8  5E8  'ethyl (2Z,4S)-4-{[(2S)-2-methyl-3-phenylpropanoyl]amino}-5-[(3S)-2-oxopyrrolidin-3-yl]pent-2-enoate'  ligand  55  27  .  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_5E8
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
 5E8  O1   O  O     0  -0.482  -3.2957   0.1261   1.4202
 5E8  O2   O  O2    0  -0.457  -3.4586  -3.0630   0.1052
 5E8  C3   C  CH2   0  -0.498   3.8135  -0.1537   0.4268
 5E8  C5   C  CR16  0  -0.306   5.6519  -0.3145  -1.2829
 5E8  C7   C  CR16  0  -0.273   7.8691   0.5171  -0.8516
 5E8  C8   C  CR16  0  -0.242   7.4691   0.8927   0.4235
 5E8  C12  C  CH1   0  -0.418  -3.1576   1.3773  -0.6885
 5E8  C9   C  CR16  0  -0.310   6.1630   0.6662   0.8398
 5E8  C13  C  C     0   0.578  -3.7379   0.9712   0.6579
 5E8  C14  C  C1    0  -0.153  -1.3491  -0.8638  -1.5609
 5E8  C15  C  C1    0  -0.352  -1.9714  -2.0126  -1.3137
 5E8  C16  C  C     0   0.565  -2.2372  -2.5535   0.0403
 5E8  C17  C  C     0   0.575   1.4278   0.5471   0.2372
 5E8  C18  C  CH2   0  -0.180  -3.9072  -3.5780   1.3676
 5E8  O3   O  O     0  -0.452  -1.4489  -2.5679   0.9531
 5E8  C19  C  CH3   0  -0.690  -5.3350  -4.0360   1.1951
 5E8  C10  C  CH1   0  -0.163  -0.8734   0.1535  -0.5656
 5E8  C11  C  CH2   0  -0.420  -1.6389   1.4734  -0.7511
 5E8  C26  C  CH2   0  -0.454  -3.8647   2.7007  -0.9848
 5E8  C25  C  CH2   0  -0.260  -5.1961   2.5800  -0.2437
 5E8  N1   N  NH1   0  -0.630  -4.8520   1.6973   0.8507
 5E8  N    N  NH1   0  -0.638   0.5473   0.3752  -0.7644
 5E8  O4   O  O     0  -0.499   1.1248   0.4659   1.4195
 5E8  C2   C  CH1   0  -0.378   2.8483   0.8673  -0.1977
 5E8  C1   C  CH3   0  -0.651   3.1824   2.3007   0.2096
 5E8  C4   C  CR6   0   0.129   5.2363   0.0626  -0.0064
 5E8  C6   C  CR16  0  -0.240   6.9548  -0.0899  -1.7044
 5E8  H2   H  HCH2  0   0.257   3.4961  -1.1610   0.1434
 5E8  H3   H  HCR6  0   0.246   4.9479  -0.7951  -1.9533
 5E8  H4   H  HCR6  0   0.253   8.8867   0.6913  -1.1768
 5E8  H5   H  HCR6  0   0.253   8.1745   1.3621   1.0976
 5E8  H6   H  HCH1  0   0.284  -3.5032   0.6187  -1.4026
 5E8  H7   H  HCR6  0   0.247   5.8599   0.9640   1.8368
 5E8  H8   H  H     0   0.274  -1.2297  -0.5791  -2.6038
 5E8  H10  H  H     0   0.284  -2.3500  -2.5959  -2.1459
 5E8  H12  H  HCH2  0   0.234  -3.2671  -4.4063   1.6791
 5E8  H13  H  HCH2  0   0.235  -3.8360  -2.7929   2.1224
 5E8  H14  H  HCH3  0   0.239  -5.7058  -4.4183   2.1456
 5E8  H15  H  HCH3  0   0.235  -5.9845  -3.2155   0.8895
 5E8  H16  H  HCH3  0   0.236  -5.4158  -4.8365   0.4596
 5E8  H17  H  HCH1  0   0.288  -1.0083  -0.2066   0.4488
 5E8  H18  H  HCH2  0   0.240  -1.3720   1.8914  -1.7273
 5E8  H19  H  HCH2  0   0.249  -1.2828   2.1863  -0.0018
 5E8  H20  H  HCH2  0   0.244  -3.2851   3.5280  -0.5673
 5E8  H21  H  HCH2  0   0.256  -3.9946   2.8868  -2.0493
 5E8  H22  H  HCH2  0   0.251  -5.5631   3.5379   0.1232
 5E8  H23  H  HCH2  0   0.235  -5.9737   2.1413  -0.8762
 5E8  H24  H  HNH1  0   0.395  -5.4798   1.5156   1.6185
 5E8  H25  H  HNH1  0   0.398   0.8678   0.5338  -1.7072
 5E8  H26  H  HCH1  0   0.257   2.9223   0.7881  -1.2874
 5E8  H27  H  HCH3  0   0.242   4.1731   2.5805  -0.1465
 5E8  H28  H  HCH3  0   0.239   2.4681   3.0082  -0.2134
 5E8  H29  H  HCH3  0   0.228   3.1701   2.4115   1.2945
 5E8  H30  H  HCR6  0   0.253   7.2578  -0.3932  -2.6984
 5E8  H1   H  HCH2  0   0.249   3.7409  -0.0908   1.5144

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
 5E8  O1   C13  double    1.221  0.020  1.221
 5E8  C13  N1   single    1.344  0.020  1.344
 5E8  C13  C12  single    1.521  0.020  1.521
 5E8  C11  C12  single    1.523  0.020  1.523
 5E8  C11  C10  single    1.537  0.020  1.537
 5E8  N1   C25  single    1.448  0.020  1.448
 5E8  C12  C26  single    1.529  0.020  1.529
 5E8  C14  C10  single    1.501  0.020  1.501
 5E8  C14  C15  double    1.330  0.020  1.330
 5E8  N    C10  single    1.452  0.020  1.452
 5E8  N    C17  single    1.345  0.020  1.345
 5E8  C25  C26  single    1.529  0.020  1.529
 5E8  C2   C17  single    1.520  0.020  1.520
 5E8  C2   C1   single    1.527  0.020  1.527
 5E8  C2   C3   single    1.538  0.020  1.538
 5E8  C9   C8   aromatic  1.389  0.020  1.389
 5E8  C9   C4   aromatic  1.393  0.020  1.393
 5E8  C15  C16  single    1.482  0.020  1.482
 5E8  C17  O4   double    1.223  0.020  1.223
 5E8  C8   C7   aromatic  1.388  0.020  1.388
 5E8  C3   C4   single    1.503  0.020  1.503
 5E8  C4   C5   aromatic  1.394  0.020  1.394
 5E8  O3   C16  double    1.206  0.020  1.206
 5E8  C16  O2   single    1.325  0.020  1.325
 5E8  C7   C6   aromatic  1.390  0.020  1.390
 5E8  C5   C6   aromatic  1.388  0.020  1.388
 5E8  O2   C18  single    1.435  0.020  1.435
 5E8  C18  C19  single    1.509  0.020  1.509
 5E8  C3   H1   single    0.970  0.020  1.090
 5E8  C3   H2   single    0.970  0.020  1.090
 5E8  C5   H3   single    0.930  0.020  1.080
 5E8  C7   H4   single    0.930  0.020  1.080
 5E8  C8   H5   single    0.930  0.020  1.080
 5E8  C12  H6   single    0.970  0.020  1.090
 5E8  C9   H7   single    0.930  0.020  1.080
 5E8  C14  H8   single    0.930  0.020  1.080
 5E8  C15  H10  single    0.930  0.020  1.080
 5E8  C18  H12  single    0.970  0.020  1.090
 5E8  C18  H13  single    0.970  0.020  1.090
 5E8  C19  H14  single    0.970  0.020  1.090
 5E8  C19  H15  single    0.970  0.020  1.090
 5E8  C19  H16  single    0.970  0.020  1.090
 5E8  C10  H17  single    0.970  0.020  1.090
 5E8  C11  H18  single    0.970  0.020  1.090
 5E8  C11  H19  single    0.970  0.020  1.090
 5E8  C26  H20  single    0.970  0.020  1.090
 5E8  C26  H21  single    0.970  0.020  1.090
 5E8  C25  H22  single    0.970  0.020  1.090
 5E8  C25  H23  single    0.970  0.020  1.090
 5E8  N1   H24  single    0.860  0.020  1.020
 5E8  N    H25  single    0.860  0.020  1.020
 5E8  C2   H26  single    0.970  0.020  1.090
 5E8  C1   H27  single    0.970  0.020  1.090
 5E8  C1   H28  single    0.970  0.020  1.090
 5E8  C1   H29  single    0.970  0.020  1.090
 5E8  C6   H30  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
 5E8  C18  O2   C16  117.98  3.000
 5E8  H2   C3   H1   106.97  3.000
 5E8  H2   C3   C4   109.43  3.000
 5E8  H1   C3   C4   109.99  3.000
 5E8  H2   C3   C2   108.92  3.000
 5E8  H1   C3   C2   108.94  3.000
 5E8  C4   C3   C2   112.44  3.000
 5E8  H3   C5   C6   119.57  3.000
 5E8  H3   C5   C4   119.49  3.000
 5E8  C6   C5   C4   120.94  3.000
 5E8  H4   C7   C6   120.29  3.000
 5E8  H4   C7   C8   120.22  3.000
 5E8  C6   C7   C8   119.49  3.000
 5E8  H5   C8   C9   119.77  3.000
 5E8  H5   C8   C7   120.10  3.000
 5E8  C9   C8   C7   120.13  3.000
 5E8  H6   C12  C26  109.05  3.000
 5E8  H6   C12  C11  109.32  3.000
 5E8  C26  C12  C11  113.48  3.000
 5E8  H6   C12  C13  105.73  3.000
 5E8  C26  C12  C13  103.06  3.000
 5E8  C11  C12  C13  115.69  3.000
 5E8  H7   C9   C4   119.47  3.000
 5E8  H7   C9   C8   119.58  3.000
 5E8  C4   C9   C8   120.94  3.000
 5E8  N1   C13  C12  107.40  3.000
 5E8  C12  C13  O1   126.81  3.000
 5E8  N1   C13  O1   125.78  3.000
 5E8  H8   C14  C10  115.07  3.000
 5E8  H8   C14  C15  117.11  3.000
 5E8  C10  C14  C15  127.64  3.000
 5E8  H10  C15  C16  116.24  3.000
 5E8  H10  C15  C14  119.04  3.000
 5E8  C16  C15  C14  124.69  3.000
 5E8  O3   C16  C15  125.34  3.000
 5E8  O3   C16  O2   124.12  3.000
 5E8  C15  C16  O2   110.51  3.000
 5E8  C2   C17  O4   121.48  3.000
 5E8  O4   C17  N    123.32  3.000
 5E8  C2   C17  N    115.21  3.000
 5E8  H13  C18  H12  108.06  3.000
 5E8  H13  C18  C19  111.04  3.000
 5E8  H12  C18  C19  110.91  3.000
 5E8  H13  C18  O2   109.26  3.000
 5E8  H12  C18  O2   109.86  3.000
 5E8  C19  C18  O2   107.70  3.000
 5E8  H16  C19  H15  108.63  3.000
 5E8  H16  C19  H14  107.80  3.000
 5E8  H15  C19  H14  107.82  3.000
 5E8  H16  C19  C18  111.72  3.000
 5E8  H15  C19  C18  111.54  3.000
 5E8  H14  C19  C18  109.19  3.000
 5E8  H17  C10  N    107.49  3.000
 5E8  H17  C10  C11  109.63  3.000
 5E8  N    C10  C11  109.86  3.000
 5E8  H17  C10  C14  110.84  3.000
 5E8  N    C10  C14  108.85  3.000
 5E8  C11  C10  C14  110.13  3.000
 5E8  H19  C11  H18  106.41  3.000
 5E8  H19  C11  C10  108.35  3.000
 5E8  H18  C11  C10  108.30  3.000
 5E8  H19  C11  C12  109.73  3.000
 5E8  H18  C11  C12  107.68  3.000
 5E8  C10  C11  C12  115.95  3.000
 5E8  H21  C26  H20  107.90  3.000
 5E8  H21  C26  C25  112.56  3.000
 5E8  H20  C26  C25  109.67  3.000
 5E8  H21  C26  C12  113.11  3.000
 5E8  H20  C26  C12  109.62  3.000
 5E8  C25  C26  C12  103.91  3.000
 5E8  H23  C25  H22  107.93  3.000
 5E8  H23  C25  N1   111.20  3.000
 5E8  H22  C25  N1   111.20  3.000
 5E8  H23  C25  C26  111.74  3.000
 5E8  H22  C25  C26  112.78  3.000
 5E8  N1   C25  C26  101.99  3.000
 5E8  H24  N1   C25  122.52  3.000
 5E8  H24  N1   C13  121.88  3.000
 5E8  C25  N1   C13  114.71  3.000
 5E8  H25  N    C10  117.59  3.000
 5E8  H25  N    C17  117.92  3.000
 5E8  C10  N    C17  123.95  3.000
 5E8  H26  C2   C1   108.57  3.000
 5E8  H26  C2   C17  109.43  3.000
 5E8  C1   C2   C17  109.02  3.000
 5E8  H26  C2   C3   108.29  3.000
 5E8  C1   C2   C3   112.19  3.000
 5E8  C17  C2   C3   109.30  3.000
 5E8  H29  C1   H28  108.21  3.000
 5E8  H29  C1   H27  108.02  3.000
 5E8  H28  C1   H27  107.59  3.000
 5E8  H29  C1   C2   110.99  3.000
 5E8  H28  C1   C2   111.23  3.000
 5E8  H27  C1   C2   110.66  3.000
 5E8  C9   C4   C5   118.37  3.000
 5E8  C5   C4   C3   120.47  3.000
 5E8  C9   C4   C3   121.15  3.000
 5E8  H30  C6   C7   120.11  3.000
 5E8  H30  C6   C5   119.76  3.000
 5E8  C7   C6   C5   120.13  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
 5E8  CONST_01  C8   C9   C4   C5      0.00   0.0  0
 5E8  CONST_02  C8   C7   C6   C5      0.00   0.0  0
 5E8  CONST_03  C4   C9   C8   C7      0.00   0.0  0
 5E8  CONST_04  C4   C5   C6   C7      0.00   0.0  0
 5E8  CONST_05  C6   C7   C8   C9      0.00   0.0  0
 5E8  CONST_06  C6   C5   C4   C9      0.00   0.0  0
 5E8  CONST_07  C25  N1   C13  C12     0.00   0.0  0
 5E8  CONST_08  C8   C9   C4   C3    180.00   0.0  0
 5E8  CONST_09  C6   C5   C4   C3    180.00   0.0  0
 5E8  CONST_10  C25  N1   C13  O1    180.00   0.0  0
 5E8  CONST_11  H7   C9   C4   C5    180.00   0.0  0
 5E8  CONST_12  H4   C7   C6   C5    180.00   0.0  0
 5E8  CONST_13  H3   C5   C6   C7    180.00   0.0  0
 5E8  CONST_14  H30  C6   C7   C8    180.00   0.0  0
 5E8  CONST_15  H5   C8   C9   C4    180.00   0.0  0
 5E8  CONST_16  H24  N1   C13  C12   180.00   0.0  0
 5E8  CONST_17  C2   C17  N    C10   180.00   0.0  0
 5E8  CONST_18  O4   C17  N    C10     0.00   0.0  0
 5E8  CONST_19  C10  C14  C15  C16     0.00   0.0  0
 5E8  CONST_20  H25  N    C17  O4    180.00   0.0  0
 5E8  CONST_21  H8   C14  C15  C16   180.00   0.0  0
 5E8  CONST_22  H10  C15  C14  C10   180.00   0.0  0
 5E8  Var_01    N1   C25  C26  C12    28.57  30.0  1
 5E8  Var_02    C26  C25  N1   C13   -19.83  30.0  1
 5E8  Var_03    C2   C3   C4   C5    -75.55  30.0  2
 5E8  Var_04    C14  C15  C16  O2    138.11  30.0  1
 5E8  Var_05    C19  C18  O2   C16   177.42  30.0  3
 5E8  Var_06    H14  C19  C18  O2   -179.13  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
 5E8  chir_01  C12  C13  C11  C26  positiv
 5E8  chir_02  C10  N    C14  C11  positiv
 5E8  chir_03  C2   C17  C1   C3   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
 5E8  plan-1  C3   0.020
 5E8  plan-1  C5   0.020
 5E8  plan-1  C7   0.020
 5E8  plan-1  C8   0.020
 5E8  plan-1  C9   0.020
 5E8  plan-1  C4   0.020
 5E8  plan-1  C6   0.020
 5E8  plan-1  H3   0.020
 5E8  plan-1  H4   0.020
 5E8  plan-1  H5   0.020
 5E8  plan-1  H7   0.020
 5E8  plan-1  H30  0.020
 5E8  plan-2  C17  0.020
 5E8  plan-2  C10  0.020
 5E8  plan-2  N    0.020
 5E8  plan-2  O4   0.020
 5E8  plan-2  C2   0.020
 5E8  plan-2  H25  0.020
 5E8  plan-3  O1   0.020
 5E8  plan-3  C12  0.020
 5E8  plan-3  C13  0.020
 5E8  plan-3  C25  0.020
 5E8  plan-3  N1   0.020
 5E8  plan-3  H24  0.020
 5E8  plan-4  C14  0.020
 5E8  plan-4  C15  0.020
 5E8  plan-4  C16  0.020
 5E8  plan-4  C10  0.020
 5E8  plan-4  H8   0.020
 5E8  plan-4  H10  0.020
 5E8  plan-5  O2   0.020
 5E8  plan-5  C15  0.020
 5E8  plan-5  C16  0.020
 5E8  plan-5  O3   0.020

