# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 13:59:52 2022
#   Inital geometry file: a 174 line input string
#   Ligand name: (2~{S},3~{R})-2-[(2~{S},3~{R})-1-[(2~{R})-2-azanyl-3-oxidanylidene-propoxy]-3-oxidanyl-1-oxidanylidene-butan-2-yl]-4-[(3~{S},5~{S})-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl]sulfanyl-3-methyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@H]([C@@H]1N=C([C@@H](S[C@@H]2CN[C@@H](C2)C(=O)Nc3cccc(c3)C(O)=O)[C@@H]1C)C(O)=O)C(=O)OC[C@@H](N)C=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
 O2E  O2E  '(2~{S},3~{R})-2-[(2~{S},3~{R})-1-[(2~{R})-2-azanyl-3-oxidanylidene-propoxy]-3-oxidanyl-1-oxidanylidene-butan-2-yl]-4-[(3~{S},5~{S})-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl]sulfanyl-3-methyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid'  L-peptide  69  39  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_O2E
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
 O2E  C11  C  CR15   0  -0.447  18.2953  -30.6930  49.9724
 O2E  C18  C  CR6    0  -0.085  24.2932  -32.7178  54.3325
 O2E  C17  C  CR16   0  -0.371  23.5887  -33.2493  53.2549
 O2E  C6   C  CH1    0   0.041  13.5997  -29.5356  49.9220
 O2E  O6   O  OC    -1  -0.573  18.0679  -32.2480  53.2022
 O2E  C5   C  CH1    0  -0.405  15.1247  -29.3519  49.7698
 O2E  O5   O  O      0  -0.581  19.0844  -30.2880  52.8071
 O2E  C16  C  CR6    0   0.380  22.1937  -33.2537  53.2479
 O2E  O4   O  OH1    0  -0.664  13.2410  -30.4176  50.9601
 O2E  C2   C  CH2    0  -0.174  15.3268  -27.2742  52.8558
 O2E  C1   C  C      0   0.615  15.7367  -28.3851  50.7631
 O2E  C12  C  CH1    0  -0.417  19.2471  -33.2466  48.9804
 O2E  C21  C  CR16   0  -0.233  22.2076  -32.1971  55.4134
 O2E  C22  C  CR16   0  -0.357  21.5060  -32.7220  54.3420
 O2E  C20  C  CR16   0  -0.316  23.5956  -32.1888  55.4134
 O2E  C7   C  CH3    0  -0.679  12.9900  -30.0748  48.6385
 O2E  C8   C  CR15   0  -0.125  15.8949  -30.6937  49.7835
 O2E  C9   C  CR5    0   0.170  17.5589  -31.0330  51.2401
 O2E  C13  C  CH2    0  -0.248  18.3872  -34.0865  49.9122
 O2E  C14  C  CH1    0  -0.167  20.6326  -34.8246  50.1842
 O2E  O7   O  O      0  -0.588  26.3856  -32.1631  55.2802
 O2E  O1   O  O      0  -0.440  16.7523  -27.7686  50.5607
 O2E  O2   O  O2     0  -0.465  15.0238  -28.2785  51.8794
 O2E  CA   C  CH1    0  -0.228  16.2218  -27.7811  53.9763
 O2E  C    C  C1     0   0.173  15.9728  -27.0025  55.2530
 O2E  O    O  O      0  -0.363  14.9899  -26.3552  55.4982
 O2E  N    N  NH2    0  -0.819  17.6375  -27.6689  53.6699
 O2E  N2   N  N      0  -0.380  16.2932  -31.0389  51.1467
 O2E  S1   S  S2     0   0.015  19.8080  -31.6549  49.6637
 O2E  N3   N  NH1    0  -0.629  19.3396  -34.6833  50.8383
 O2E  O8   O  OC    -1  -0.586  26.3723  -33.2841  53.3523
 O2E  C23  C  CH2    0  -0.482  20.4822  -34.1336  48.8179
 O2E  C24  C  CR15   0  -0.235  17.1866  -30.7788  48.9235
 O2E  C25  C  CH3    0  -0.681  17.3500  -29.8179  47.7618
 O2E  H1   H  HCR5   0   0.304  18.6771  -29.6705  50.0598
 O2E  H3   H  HCH1   0   0.217  13.1634  -28.5409  50.0924
 O2E  H5   H  HCH1   0   0.294  15.2754  -28.8847  48.7930
 O2E  H6   H  HOH1   0   0.444  13.6329  -30.0986  51.7792
 O2E  H7   H  HCH2   0   0.248  15.7737  -26.3974  52.3852
 O2E  H8   H  HCH2   0   0.258  14.3545  -26.9946  53.2566
 O2E  H9   H  HCH1   0   0.294  18.7563  -33.0756  48.0229
 O2E  H10  H  HCR6   0   0.245  21.6613  -31.7872  56.2538
 O2E  H11  H  HCR6   0   0.261  20.4223  -32.7133  54.3430
 O2E  H12  H  HCR6   0   0.236  24.1370  -31.7738  56.2523
 O2E  H13  H  HCH3   0   0.231  13.1874  -29.3951  47.8098
 O2E  H14  H  HCH3   0   0.229  13.3883  -31.0555  48.3739
 O2E  H15  H  HCH3   0   0.241  11.9086  -30.1697  48.7412
 O2E  H16  H  HCR5   0   0.258  15.1944  -31.4547  49.4330
 O2E  H17  H  HCH2   0   0.249  17.6250  -33.5156  50.4423
 O2E  H18  H  HCH2   0   0.229  17.8655  -34.8361  49.3035
 O2E  H19  H  HCH1   0   0.277  20.8972  -35.8763  50.0296
 O2E  H20  H  HCH1   0   0.265  15.9060  -28.8120  54.2233
 O2E  H21  H  H      0   0.210  16.7877  -27.0986  55.9957
 O2E  H22  H  HNH2   0   0.346  18.1768  -27.8916  54.4994
 O2E  H23  H  HNH2   0   0.367  17.9124  -28.3786  53.0010
 O2E  H25  H  HNH1   0   0.370  19.0033  -35.5587  51.2120
 O2E  H29  H  HCH2   0   0.270  21.3768  -33.5981  48.5003
 O2E  H30  H  HCH2   0   0.273  20.2686  -34.8791  48.0505
 O2E  H31  H  HCR5   0   0.264  17.1791  -31.7898  48.5090
 O2E  H32  H  HCH3   0   0.240  18.2591  -30.0557  47.2077
 O2E  H33  H  HCH3   0   0.235  16.5138  -29.8903  47.0649
 O2E  H34  H  HCH3   0   0.228  17.4278  -28.7836  48.0970
 O2E  C10  C  C      0   0.403  18.3030  -31.2228  52.5450
 O2E  C15  C  C      0   0.508  21.7877  -34.2495  51.0066
 O2E  O9   O  O      0  -0.478  22.9265  -34.2767  50.5658
 O2E  N4   N  NH1    0  -0.737  21.4179  -33.7831  52.2132
 O2E  C19  C  C      0   0.396  25.8227  -32.7224  54.3194
 O2E  H27  H  HNH1   0   0.409  20.4082  -33.7932  52.3397
 O2E  H2   H  HCR6   0   0.261  24.1426  -33.6574  52.4262

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
 O2E  C7   C6   single    1.520  0.020  1.520
 O2E  C6   O4   single    1.409  0.020  1.409
 O2E  C6   C5   single    1.543  0.020  1.543
 O2E  C25  C24  single    1.516  0.020  1.516
 O2E  C24  C8   single    1.554  0.020  1.554
 O2E  C24  C11  single    1.529  0.020  1.529
 O2E  O9   C15  double    1.222  0.020  1.222
 O2E  C5   C8   single    1.547  0.020  1.547
 O2E  C5   C1   single    1.515  0.020  1.515
 O2E  C8   N2   single    1.462  0.020  1.462
 O2E  S1   C11  single    1.819  0.020  1.819
 O2E  S1   C12  single    1.821  0.020  1.821
 O2E  C11  C9   single    1.505  0.020  1.505
 O2E  C15  N4   single    1.345  0.020  1.345
 O2E  C15  C14  single    1.530  0.020  1.530
 O2E  C1   O1   double    1.205  0.020  1.205
 O2E  C1   O2   single    1.329  0.020  1.329
 O2E  C23  C14  single    1.538  0.020  1.538
 O2E  C23  C12  single    1.529  0.020  1.529
 O2E  O2   C2   single    1.433  0.020  1.433
 O2E  N2   C9   double    1.269  0.020  1.269
 O2E  O7   C19  deloc     1.246  0.020  1.246
 O2E  N4   C16  single    1.397  0.020  1.397
 O2E  C14  N3   single    1.456  0.020  1.456
 O2E  C17  C16  aromatic  1.395  0.020  1.395
 O2E  C17  C18  aromatic  1.393  0.020  1.393
 O2E  C12  C13  single    1.521  0.020  1.521
 O2E  C9   C10  single    1.514  0.020  1.514
 O2E  C16  C22  aromatic  1.397  0.020  1.397
 O2E  C19  C18  single    1.530  0.020  1.530
 O2E  C19  O8   deloc     1.246  0.020  1.246
 O2E  C2   CA   single    1.521  0.020  1.521
 O2E  C18  C20  aromatic  1.391  0.020  1.391
 O2E  N    CA   single    1.458  0.019  1.458
 O2E  C22  C21  aromatic  1.384  0.020  1.384
 O2E  C20  C21  aromatic  1.388  0.020  1.388
 O2E  CA   C    single    1.525  0.021  1.525
 O2E  C13  N3   single    1.456  0.020  1.456
 O2E  C10  O5   deloc     1.246  0.020  1.246
 O2E  C10  O6   deloc     1.240  0.020  1.240
 O2E  C    O    double    1.231  0.020  1.231
 O2E  C11  H1   single    0.970  0.020  1.090
 O2E  C17  H2   single    0.930  0.020  1.080
 O2E  C6   H3   single    0.970  0.020  1.090
 O2E  C5   H5   single    0.970  0.020  1.090
 O2E  O4   H6   single    0.850  0.020  0.980
 O2E  C2   H7   single    0.970  0.020  1.090
 O2E  C2   H8   single    0.970  0.020  1.090
 O2E  C12  H9   single    0.970  0.020  1.090
 O2E  C21  H10  single    0.930  0.020  1.080
 O2E  C22  H11  single    0.930  0.020  1.080
 O2E  C20  H12  single    0.930  0.020  1.080
 O2E  C7   H13  single    0.970  0.020  1.090
 O2E  C7   H14  single    0.970  0.020  1.090
 O2E  C7   H15  single    0.970  0.020  1.090
 O2E  C8   H16  single    0.970  0.020  1.090
 O2E  C13  H17  single    0.970  0.020  1.090
 O2E  C13  H18  single    0.970  0.020  1.090
 O2E  C14  H19  single    0.970  0.020  1.090
 O2E  CA   H20  single    0.970  0.020  1.090
 O2E  C    H21  single    0.930  0.020  1.080
 O2E  N    H22  single    0.890  0.020  1.040
 O2E  N    H23  single    0.890  0.020  1.040
 O2E  N3   H25  single    0.890  0.020  1.040
 O2E  N4   H27  single    0.860  0.020  1.020
 O2E  C23  H29  single    0.970  0.020  1.090
 O2E  C23  H30  single    0.970  0.020  1.090
 O2E  C24  H31  single    0.970  0.020  1.090
 O2E  C25  H32  single    0.970  0.020  1.090
 O2E  C25  H33  single    0.970  0.020  1.090
 O2E  C25  H34  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
 O2E  H1   C11  C24  111.10  3.000
 O2E  H1   C11  S1   102.56  3.000
 O2E  C24  C11  S1   117.20  3.000
 O2E  H1   C11  C9   108.32  3.000
 O2E  S1   C11  C9   115.50  3.000
 O2E  C24  C11  C9   102.15  3.000
 O2E  C20  C18  C19  120.61  3.000
 O2E  C20  C18  C17  119.51  3.000
 O2E  C19  C18  C17  119.87  3.000
 O2E  H2   C17  C16  120.61  3.000
 O2E  H2   C17  C18  118.66  3.000
 O2E  C16  C17  C18  120.72  3.000
 O2E  H3   C6   C7   107.02  3.000
 O2E  H3   C6   O4   110.56  3.000
 O2E  C7   C6   O4   107.34  3.000
 O2E  H3   C6   C5   107.44  3.000
 O2E  O4   C6   C5   113.50  3.000
 O2E  C7   C6   C5   110.81  3.000
 O2E  H5   C5   C8   108.06  3.000
 O2E  H5   C5   C1   104.91  3.000
 O2E  C8   C5   C1   110.27  3.000
 O2E  H5   C5   C6   105.97  3.000
 O2E  C1   C5   C6   114.23  3.000
 O2E  C8   C5   C6   112.82  3.000
 O2E  N4   C16  C22  116.78  3.000
 O2E  C22  C16  C17  119.15  3.000
 O2E  N4   C16  C17  124.06  3.000
 O2E  H6   O4   C6   108.42  3.000
 O2E  H8   C2   H7   108.57  3.000
 O2E  H8   C2   CA   109.88  3.000
 O2E  H7   C2   CA   110.16  3.000
 O2E  H8   C2   O2   104.01  3.000
 O2E  H7   C2   O2   110.85  3.000
 O2E  CA   C2   O2   113.13  3.000
 O2E  O2   C1   O1   123.51  3.000
 O2E  O2   C1   C5   112.66  3.000
 O2E  O1   C1   C5   123.83  3.000
 O2E  H9   C12  C23  111.20  3.000
 O2E  H9   C12  S1   109.35  3.000
 O2E  C23  C12  S1   107.34  3.000
 O2E  H9   C12  C13  111.74  3.000
 O2E  C23  C12  C13  101.62  3.000
 O2E  S1   C12  C13  115.28  3.000
 O2E  H10  C21  C20  120.14  3.000
 O2E  H10  C21  C22  119.25  3.000
 O2E  C20  C21  C22  120.61  3.000
 O2E  H11  C22  C21  120.20  3.000
 O2E  H11  C22  C16  119.73  3.000
 O2E  C21  C22  C16  120.06  3.000
 O2E  H12  C20  C21  120.21  3.000
 O2E  H12  C20  C18  119.85  3.000
 O2E  C21  C20  C18  119.95  3.000
 O2E  H15  C7   H14  107.85  3.000
 O2E  H15  C7   H13  107.79  3.000
 O2E  H14  C7   H13  108.06  3.000
 O2E  H15  C7   C6   110.44  3.000
 O2E  H14  C7   C6   112.16  3.000
 O2E  H13  C7   C6   110.38  3.000
 O2E  H16  C8   C24  108.50  3.000
 O2E  H16  C8   N2   108.04  3.000
 O2E  C24  C8   N2   106.06  3.000
 O2E  H16  C8   C5   106.39  3.000
 O2E  N2   C8   C5   110.41  3.000
 O2E  C24  C8   C5   117.15  3.000
 O2E  N2   C9   C10  123.57  3.000
 O2E  C10  C9   C11  120.92  3.000
 O2E  N2   C9   C11  115.28  3.000
 O2E  H18  C13  H17  107.16  3.000
 O2E  H18  C13  N3   112.57  3.000
 O2E  H17  C13  N3   111.26  3.000
 O2E  H18  C13  C12  107.83  3.000
 O2E  H17  C13  C12  113.83  3.000
 O2E  N3   C13  C12  104.25  3.000
 O2E  H19  C14  C23  109.24  3.000
 O2E  H19  C14  N3   111.78  3.000
 O2E  C23  C14  N3   105.58  3.000
 O2E  H19  C14  C15  104.74  3.000
 O2E  N3   C14  C15  113.11  3.000
 O2E  C23  C14  C15  112.48  3.000
 O2E  C1   O2   C2   121.01  3.000
 O2E  H20  CA   N    113.41  3.000
 O2E  H20  CA   C    104.11  3.000
 O2E  N    CA   C    111.00  2.800
 O2E  H20  CA   C2   107.89  3.000
 O2E  C    CA   C2   110.64  3.000
 O2E  N    CA   C2   113.09  3.000
 O2E  H21  C    O    120.79  3.000
 O2E  H21  C    CA   113.55  3.000
 O2E  O    C    CA   120.80  1.700
 O2E  H23  N    H22  103.99  3.000
 O2E  H23  N    CA   110.46  3.000
 O2E  H22  N    CA   109.19  3.000
 O2E  C9   N2   C8   109.83  3.000
 O2E  C12  S1   C11  105.65  3.000
 O2E  H25  N3   C14  112.21  3.000
 O2E  H25  N3   C13  111.89  3.000
 O2E  C14  N3   C13  109.56  3.000
 O2E  H30  C23  H29  106.94  3.000
 O2E  H30  C23  C14  109.69  3.000
 O2E  H29  C23  C14  113.53  3.000
 O2E  H30  C23  C12  108.23  3.000
 O2E  H29  C23  C12  114.14  3.000
 O2E  C14  C23  C12  104.19  3.000
 O2E  H31  C24  C25  107.24  3.000
 O2E  H31  C24  C8   104.77  3.000
 O2E  C25  C24  C8   118.61  3.000
 O2E  H31  C24  C11  108.49  3.000
 O2E  C8   C24  C11  102.71  3.000
 O2E  C25  C24  C11  114.33  3.000
 O2E  H34  C25  H33  108.31  3.000
 O2E  H34  C25  H32  107.67  3.000
 O2E  H33  C25  H32  107.45  3.000
 O2E  H34  C25  C24  111.93  3.000
 O2E  H33  C25  C24  111.39  3.000
 O2E  H32  C25  C24  109.92  3.000
 O2E  C9   C10  O5   113.28  3.000
 O2E  O5   C10  O6   128.87  3.000
 O2E  C9   C10  O6   117.85  3.000
 O2E  N4   C15  O9   125.99  3.000
 O2E  N4   C15  C14  113.88  3.000
 O2E  O9   C15  C14  120.10  3.000
 O2E  H27  N4   C15  112.38  3.000
 O2E  H27  N4   C16  117.55  3.000
 O2E  C15  N4   C16  130.00  3.000
 O2E  O8   C19  O7   126.97  3.000
 O2E  O8   C19  C18  116.68  3.000
 O2E  O7   C19  C18  116.35  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
 O2E  CONST_01  C22  C16  C17  C18    0.00   0.0  0
 O2E  CONST_02  C22  C21  C20  C18    0.00   0.0  0
 O2E  CONST_03  C21  C22  C16  C17    0.00   0.0  0
 O2E  CONST_04  C21  C20  C18  C17    0.00   0.0  0
 O2E  CONST_05  C20  C18  C17  C16    0.00   0.0  0
 O2E  CONST_06  C20  C21  C22  C16    0.00   0.0  0
 O2E  CONST_07  N4   C16  C17  C18  180.00   0.0  0
 O2E  CONST_08  C19  C18  C17  C16  180.00   0.0  0
 O2E  CONST_09  C21  C20  C18  C19  180.00   0.0  0
 O2E  CONST_10  N4   C16  C22  C21  180.00   0.0  0
 O2E  CONST_11  H10  C21  C20  C18  180.00   0.0  0
 O2E  CONST_12  H11  C22  C16  C17  180.00   0.0  0
 O2E  CONST_13  H12  C20  C18  C17  180.00   0.0  0
 O2E  CONST_14  H2   C17  C16  C22  180.00   0.0  0
 O2E  CONST_15  C14  C15  N4   C16  180.00   0.0  0
 O2E  CONST_16  C15  N4   C16  C17    0.00   0.0  0
 O2E  CONST_17  C22  C16  N4   C15  180.00   0.0  0
 O2E  CONST_18  H27  N4   C16  C17  180.00   0.0  0
 O2E  CONST_19  O9   C15  N4   C16    0.00   0.0  0
 O2E  Var_01    C14  N3   C13  C12  -28.02  30.0  1
 O2E  Var_02    O5   C10  C9   C11   50.41  30.0  2
 O2E  Var_03    O7   C19  C18  C17  176.06  30.0  2
 O2E  Var_04    O1   C1   O2   C2     8.54  30.0  1
 O2E  Var_05    CA   C2   O2   C1   -95.39  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
 O2E  chir_01  C11  C24  S1   C9   positiv
 O2E  chir_02  C6   O4   C7   C5   positiv
 O2E  chir_03  C5   C6   C8   C1   positiv
 O2E  chir_04  C12  S1   C13  C23  positiv
 O2E  chir_05  C8   N2   C24  C5   positiv
 O2E  chir_06  C14  N3   C15  C23  positiv
 O2E  chir_07  CA   C2   N    C    negativ
 O2E  chir_08  C24  C25  C8   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
 O2E  plan-1  CA   0.020
 O2E  plan-1  C    0.020
 O2E  plan-1  O    0.020
 O2E  plan-1  H21  0.020
 O2E  plan-2  C16  0.020
 O2E  plan-2  C14  0.020
 O2E  plan-2  C15  0.020
 O2E  plan-2  O9   0.020
 O2E  plan-2  N4   0.020
 O2E  plan-2  H27  0.020
 O2E  plan-3  C18  0.020
 O2E  plan-3  C17  0.020
 O2E  plan-3  C16  0.020
 O2E  plan-3  C21  0.020
 O2E  plan-3  C22  0.020
 O2E  plan-3  C20  0.020
 O2E  plan-3  H10  0.020
 O2E  plan-3  H11  0.020
 O2E  plan-3  H12  0.020
 O2E  plan-3  N4   0.020
 O2E  plan-3  C19  0.020
 O2E  plan-3  H2   0.020
 O2E  plan-4  O6   0.020
 O2E  plan-4  O5   0.020
 O2E  plan-4  C9   0.020
 O2E  plan-4  C10  0.020
 O2E  plan-5  C18  0.020
 O2E  plan-5  O7   0.020
 O2E  plan-5  O8   0.020
 O2E  plan-5  C19  0.020
 O2E  plan-6  C5   0.020
 O2E  plan-6  C1   0.020
 O2E  plan-6  O1   0.020
 O2E  plan-6  O2   0.020

