# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 12:54:41 2020
#   Inital geometry file: a 173 line input string
#   Ligand name: N-{(2S)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-isoleucyl-L-aspartamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](C)[C@H](NC(=O)[C@H](CC(=O)NC)Cc1ccc(O[P](O)(O)=O)cc1)C(=O)N[C@@H](CC(N)=O)C(N)=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
 FYI  FYI  N-{(2S)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-isoleucyl-L-aspartamide  peptide  69  37  .  2022-03-18  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FYI
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
 FYI  C1   C  C1     0  -0.306  -4.1978  -1.2424   0.5094
 FYI  C2   C  C1     0  -0.339  -5.4241  -1.1058  -0.1248
 FYI  C3   C  C      0   0.382  -5.8917   0.1535  -0.5076
 FYI  C4   C  C1     0  -0.337  -5.1168   1.2691  -0.1867
 FYI  C5   C  C1     0  -0.301  -3.8912   1.1197   0.4465
 FYI  C6   C  C      0   0.082  -3.4041  -0.1355   0.8040
 FYI  O1   O  O2     0  -0.673  -7.0312   0.2824  -1.1994
 FYI  P1   P  P      0   1.203  -8.5247   0.5679  -0.3346
 FYI  O2   O  OP    -1  -0.884  -9.4767   0.6884  -1.5118
 FYI  O3   O  O      0  -0.878  -8.6888  -0.6760   0.5224
 FYI  O4   O  OP    -1  -0.876  -8.2631   1.8504   0.4367
 FYI  C7   C  CH2    0  -0.484  -2.0492  -0.2910   1.4367
 FYI  C8   C  CH1    0  -0.381  -0.9788  -0.7271   0.4268
 FYI  C9   C  C      0   0.574   0.3710  -0.9364   1.1099
 FYI  O5   O  O      0  -0.485   0.5296  -0.8324   2.3157
 FYI  C10  C  CH2    0  -0.599  -0.8434   0.2065  -0.7909
 FYI  C11  C  C      0   0.552  -0.0246   1.4489  -0.5103
 FYI  N1   N  NH1    0  -0.616   0.9052   1.7413  -1.4293
 FYI  C12  C  CH3    0  -0.525   1.8139   2.8542  -1.2976
 FYI  O7   O  O      0  -0.496  -0.2094   2.1420   0.4832
 FYI  N2   N  NH1    0  -0.643   1.3788  -1.2445   0.2684
 FYI  C13  C  CH1    0  -0.206   2.7664  -1.3145   0.6560
 FYI  C14  C  C      0   0.601   3.5598  -0.4927  -0.3543
 FYI  O8   O  O      0  -0.485   3.2830  -0.4884  -1.5444
 FYI  C15  C  CH1    0  -0.226   3.2732  -2.7709   0.7604
 FYI  C16  C  CH2    0  -0.445   4.6948  -2.8674   1.3196
 FYI  C17  C  CH3    0  -0.668   3.1635  -3.5314  -0.5566
 FYI  C18  C  CH3    0  -0.675   4.8638  -2.3455   2.7412
 FYI  N3   N  NH1    0  -0.644   4.5772   0.2290   0.1379
 FYI  C19  C  CH1    0  -0.179   5.4166   1.0158  -0.7268
 FYI  C20  C  C      0   0.528   6.1505   0.1230  -1.7317
 FYI  O10  O  O      0  -0.471   6.5374  -0.9935  -1.4331
 FYI  C21  C  CH2    0  -0.612   6.4465   1.7718   0.1072
 FYI  C22  C  C      0   0.518   5.7803   2.7680   1.0409
 FYI  O11  O  O      0  -0.476   4.9382   3.5561   0.6379
 FYI  N4   N  NH2    0  -0.796   6.1851   2.7039   2.3152
 FYI  N5   N  NH2    0  -0.799   6.3729   0.7031  -2.9160
 FYI  H1   H  H      0   0.236  -3.8533  -2.2340   0.7839
 FYI  H2   H  H      0   0.236  -6.0218  -1.9816  -0.3446
 FYI  H3   H  H      0   0.237  -5.4718   2.2552  -0.4566
 FYI  H4   H  H      0   0.238  -3.2929   1.9987   0.6607
 FYI  H7   H  HCH2   0   0.249  -1.7516   0.6461   1.9049
 FYI  H8   H  HCH2   0   0.243  -2.0995  -1.0403   2.2293
 FYI  H9   H  HCH1   0   0.290  -1.2832  -1.7021   0.0284
 FYI  H11  H  HCH2   0   0.264  -0.4374  -0.3403  -1.6445
 FYI  H12  H  HCH2   0   0.299  -1.8408   0.5237  -1.1048
 FYI  H13  H  HNH1   0   0.399   1.0789   1.0808  -2.1672
 FYI  H14  H  HCH3   0   0.242   1.2760   3.7965  -1.1982
 FYI  H15  H  HCH3   0   0.239   2.4789   2.7454  -0.4395
 FYI  H16  H  HCH3   0   0.245   2.4232   2.9048  -2.1959
 FYI  H17  H  HNH1   0   0.399   1.1856  -1.3388  -0.7159
 FYI  H19  H  HCH1   0   0.281   2.8463  -0.8561   1.6428
 FYI  H20  H  HCH1   0   0.240   2.6003  -3.2483   1.4823
 FYI  H21  H  HCH2   0   0.234   4.9755  -3.9241   1.3101
 FYI  H22  H  HCH2   0   0.233   5.3987  -2.3710   0.6452
 FYI  H23  H  HCH3   0   0.227   3.8461  -3.1396  -1.3115
 FYI  H24  H  HCH3   0   0.234   3.4166  -4.5804  -0.3979
 FYI  H25  H  HCH3   0   0.228   2.1530  -3.5035  -0.9668
 FYI  H26  H  HCH3   0   0.239   5.8804  -2.5168   3.0958
 FYI  H27  H  HCH3   0   0.208   4.6738  -1.2745   2.8397
 FYI  H28  H  HCH3   0   0.229   4.1852  -2.8518   3.4296
 FYI  H30  H  HNH1   0   0.395   4.7818   0.1949   1.1235
 FYI  H32  H  HCH1   0   0.285   4.7994   1.7436  -1.2623
 FYI  H33  H  HCH2   0   0.279   7.0794   1.0663   0.6501
 FYI  H34  H  HCH2   0   0.308   7.1009   2.3346  -0.5626
 FYI  H35  H  HNH2   0   0.413   6.9157   2.0792   2.6104
 FYI  H36  H  HNH2   0   0.406   5.8400   3.3639   2.9942
 FYI  H38  H  HNH2   0   0.409   6.0182   1.6176  -3.1371
 FYI  H39  H  HNH2   0   0.406   6.9174   0.2363  -3.6230

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
 FYI  C1   C2   aromatic  1.387  0.020  1.387
 FYI  C1   C6   aromatic  1.394  0.020  1.394
 FYI  C1   H1   single    0.930  0.020  1.080
 FYI  C2   C3   aromatic  1.397  0.020  1.397
 FYI  C2   H2   single    0.930  0.020  1.080
 FYI  C3   C4   aromatic  1.396  0.020  1.396
 FYI  C3   O1   single    1.339  0.020  1.339
 FYI  C4   C5   aromatic  1.388  0.020  1.388
 FYI  C4   H3   single    0.930  0.020  1.080
 FYI  C5   C6   aromatic  1.393  0.020  1.393
 FYI  C5   H4   single    0.930  0.020  1.080
 FYI  C6   C7   single    1.503  0.020  1.503
 FYI  O1   P1   single    1.749  0.020  1.749
 FYI  P1   O2   deloc     1.519  0.020  1.519
 FYI  P1   O3   deloc     1.519  0.020  1.519
 FYI  P1   O4   deloc     1.519  0.020  1.519
 FYI  C7   C8   single    1.535  0.020  1.535
 FYI  C7   H7   single    0.970  0.020  1.090
 FYI  C7   H8   single    0.970  0.020  1.090
 FYI  C8   C9   single    1.527  0.020  1.527
 FYI  C8   C10  single    1.540  0.020  1.540
 FYI  C8   H9   single    0.970  0.020  1.090
 FYI  C9   O5   double    1.221  0.020  1.221
 FYI  C9   N2   single    1.349  0.020  1.349
 FYI  C10  C11  single    1.514  0.020  1.514
 FYI  C10  H11  single    0.970  0.020  1.090
 FYI  C10  H12  single    0.970  0.020  1.090
 FYI  C11  N1   single    1.340  0.020  1.340
 FYI  C11  O7   double    1.225  0.020  1.225
 FYI  N1   C12  single    1.443  0.020  1.443
 FYI  N1   H13  single    0.860  0.020  1.020
 FYI  C12  H14  single    0.970  0.020  1.090
 FYI  C12  H15  single    0.970  0.020  1.090
 FYI  C12  H16  single    0.970  0.020  1.090
 FYI  N2   C13  single    1.442  0.020  1.442
 FYI  N2   H17  single    0.860  0.020  1.020
 FYI  C13  C14  single    1.525  0.020  1.525
 FYI  C13  C15  single    1.546  0.020  1.546
 FYI  C13  H19  single    0.970  0.020  1.090
 FYI  C14  O8   double    1.222  0.020  1.222
 FYI  C14  N3   single    1.341  0.020  1.341
 FYI  C15  C16  single    1.531  0.020  1.531
 FYI  C15  C17  single    1.525  0.020  1.525
 FYI  C15  H20  single    0.970  0.020  1.090
 FYI  C16  C18  single    1.524  0.020  1.524
 FYI  C16  H21  single    0.970  0.020  1.090
 FYI  C16  H22  single    0.970  0.020  1.090
 FYI  C17  H23  single    0.970  0.020  1.090
 FYI  C17  H24  single    0.970  0.020  1.090
 FYI  C17  H25  single    0.970  0.020  1.090
 FYI  C18  H26  single    0.970  0.020  1.090
 FYI  C18  H27  single    0.970  0.020  1.090
 FYI  C18  H28  single    0.970  0.020  1.090
 FYI  N3   C19  single    1.439  0.020  1.439
 FYI  N3   H30  single    0.860  0.020  1.020
 FYI  C19  C20  single    1.532  0.020  1.532
 FYI  C19  C21  single    1.526  0.020  1.526
 FYI  C19  H32  single    0.970  0.020  1.090
 FYI  C20  O10  double    1.219  0.020  1.219
 FYI  C20  N5   single    1.337  0.020  1.337
 FYI  C21  C22  single    1.519  0.020  1.519
 FYI  C21  H33  single    0.970  0.020  1.090
 FYI  C21  H34  single    0.970  0.020  1.090
 FYI  C22  O11  double    1.222  0.020  1.222
 FYI  C22  N4   single    1.339  0.020  1.339
 FYI  N4   H35  single    0.860  0.020  1.020
 FYI  N4   H36  single    0.860  0.020  1.020
 FYI  N5   H38  single    0.860  0.020  1.020
 FYI  N5   H39  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
 FYI  H1   C1   C6   119.45  3.000
 FYI  H1   C1   C2   119.09  3.000
 FYI  C6   C1   C2   121.46  3.000
 FYI  H2   C2   C3   119.26  3.000
 FYI  H2   C2   C1   120.07  3.000
 FYI  C3   C2   C1   120.66  3.000
 FYI  O1   C3   C4   120.95  3.000
 FYI  O1   C3   C2   120.87  3.000
 FYI  C4   C3   C2   118.15  3.000
 FYI  H3   C4   C5   120.11  3.000
 FYI  H3   C4   C3   119.26  3.000
 FYI  C5   C4   C3   120.61  3.000
 FYI  H4   C5   C6   119.12  3.000
 FYI  H4   C5   C4   119.34  3.000
 FYI  C6   C5   C4   121.53  3.000
 FYI  C7   C6   C5   121.09  3.000
 FYI  C7   C6   C1   121.34  3.000
 FYI  C5   C6   C1   117.54  3.000
 FYI  P1   O1   C3   119.13  3.000
 FYI  O4   P1   O3   115.05  3.000
 FYI  O4   P1   O2   115.75  3.000
 FYI  O3   P1   O2   115.75  3.000
 FYI  O4   P1   O1   103.99  3.000
 FYI  O3   P1   O1   103.74  3.000
 FYI  O2   P1   O1    99.49  3.000
 FYI  H8   C7   H7   106.92  3.000
 FYI  H8   C7   C8   108.34  3.000
 FYI  H7   C7   C8   109.68  3.000
 FYI  H8   C7   C6   109.57  3.000
 FYI  H7   C7   C6   109.77  3.000
 FYI  C8   C7   C6   112.39  3.000
 FYI  H9   C8   C10  106.03  3.000
 FYI  H9   C8   C9   106.62  3.000
 FYI  C10  C8   C9   111.03  3.000
 FYI  H9   C8   C7   107.35  3.000
 FYI  C10  C8   C7   114.16  3.000
 FYI  C9   C8   C7   111.16  3.000
 FYI  N2   C9   O5   122.60  3.000
 FYI  N2   C9   C8   114.37  3.000
 FYI  O5   C9   C8   123.03  3.000
 FYI  H12  C10  H11  105.08  3.000
 FYI  H12  C10  C11  107.97  3.000
 FYI  H11  C10  C11  110.77  3.000
 FYI  H12  C10  C8   108.83  3.000
 FYI  H11  C10  C8   110.31  3.000
 FYI  C11  C10  C8   113.48  3.000
 FYI  O7   C11  N1   122.51  3.000
 FYI  O7   C11  C10  122.19  3.000
 FYI  N1   C11  C10  115.30  3.000
 FYI  H13  N1   C12  117.70  3.000
 FYI  H13  N1   C11  118.68  3.000
 FYI  C12  N1   C11  122.88  3.000
 FYI  H16  C12  H15  108.24  3.000
 FYI  H16  C12  H14  108.17  3.000
 FYI  H15  C12  H14  108.39  3.000
 FYI  H16  C12  N1   108.28  3.000
 FYI  H15  C12  N1   112.26  3.000
 FYI  H14  C12  N1   111.38  3.000
 FYI  H17  N2   C13  116.26  3.000
 FYI  H17  N2   C9   119.20  3.000
 FYI  C13  N2   C9   124.21  3.000
 FYI  H19  C13  C15  108.10  3.000
 FYI  H19  C13  C14  109.55  3.000
 FYI  C15  C13  C14  112.46  3.000
 FYI  H19  C13  N2   107.04  3.000
 FYI  C15  C13  N2   112.29  3.000
 FYI  C14  C13  N2   107.24  3.000
 FYI  N3   C14  O8   121.84  3.000
 FYI  N3   C14  C13  116.20  3.000
 FYI  O8   C14  C13  121.95  3.000
 FYI  H20  C15  C17  107.90  3.000
 FYI  H20  C15  C16  107.58  3.000
 FYI  C17  C15  C16  110.55  3.000
 FYI  H20  C15  C13  104.69  3.000
 FYI  C17  C15  C13  112.83  3.000
 FYI  C16  C15  C13  112.87  3.000
 FYI  H22  C16  H21  105.54  3.000
 FYI  H22  C16  C18  110.39  3.000
 FYI  H21  C16  C18  108.10  3.000
 FYI  H22  C16  C15  110.11  3.000
 FYI  H21  C16  C15  107.23  3.000
 FYI  C18  C16  C15  114.98  3.000
 FYI  H25  C17  H24  107.11  3.000
 FYI  H25  C17  H23  108.08  3.000
 FYI  H24  C17  H23  107.52  3.000
 FYI  H25  C17  C15  112.25  3.000
 FYI  H24  C17  C15  109.71  3.000
 FYI  H23  C17  C15  111.94  3.000
 FYI  H28  C18  H27  106.85  3.000
 FYI  H28  C18  H26  107.56  3.000
 FYI  H27  C18  H26  106.68  3.000
 FYI  H28  C18  C16  111.14  3.000
 FYI  H27  C18  C16  113.63  3.000
 FYI  H26  C18  C16  110.67  3.000
 FYI  H30  N3   C19  119.21  3.000
 FYI  H30  N3   C14  119.68  3.000
 FYI  C19  N3   C14  121.07  3.000
 FYI  H32  C19  C21  108.58  3.000
 FYI  H32  C19  C20  109.69  3.000
 FYI  C21  C19  C20  108.91  3.000
 FYI  H32  C19  N3   109.19  3.000
 FYI  C21  C19  N3   109.64  3.000
 FYI  C20  C19  N3   110.79  3.000
 FYI  N5   C20  O10  124.16  3.000
 FYI  N5   C20  C19  114.07  3.000
 FYI  O10  C20  C19  121.69  3.000
 FYI  H34  C21  H33  106.87  3.000
 FYI  H34  C21  C22  107.56  3.000
 FYI  H33  C21  C22  111.85  3.000
 FYI  H34  C21  C19  108.94  3.000
 FYI  H33  C21  C19  110.05  3.000
 FYI  C22  C21  C19  111.40  3.000
 FYI  N4   C22  O11  123.59  3.000
 FYI  N4   C22  C21  114.90  3.000
 FYI  O11  C22  C21  121.50  3.000
 FYI  H36  N4   H35  117.25  3.000
 FYI  H36  N4   C22  120.43  3.000
 FYI  H35  N4   C22  121.93  3.000
 FYI  H39  N5   H38  117.26  3.000
 FYI  H39  N5   C20  120.70  3.000
 FYI  H38  N5   C20  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
 FYI  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 FYI  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 FYI  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 FYI  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 FYI  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 FYI  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 FYI  CONST_07  O1   C3   C2   C1   180.00   0.0  0
 FYI  CONST_08  C7   C6   C1   C2   180.00   0.0  0
 FYI  CONST_09  C7   C6   C5   C4   180.00   0.0  0
 FYI  CONST_10  O1   C3   C4   C5   180.00   0.0  0
 FYI  CONST_11  H4   C5   C6   C1   180.00   0.0  0
 FYI  CONST_12  H3   C4   C3   C2   180.00   0.0  0
 FYI  CONST_13  H1   C1   C2   C3   180.00   0.0  0
 FYI  CONST_14  H2   C2   C3   C4   180.00   0.0  0
 FYI  CONST_15  C13  N2   C9   C8   180.00   0.0  0
 FYI  CONST_16  C13  N2   C9   O5     0.00   0.0  0
 FYI  CONST_17  C12  N1   C11  C10  180.00   0.0  0
 FYI  CONST_18  O7   C11  N1   C12    0.00   0.0  0
 FYI  CONST_19  C19  N3   C14  C13  180.00   0.0  0
 FYI  CONST_20  C19  N3   C14  O8     0.00   0.0  0
 FYI  CONST_21  H17  N2   C9   C8     0.00   0.0  0
 FYI  CONST_22  H13  N1   C11  C10    0.00   0.0  0
 FYI  CONST_23  H30  N3   C14  C13    0.00   0.0  0
 FYI  CONST_24  H38  N5   C20  C19    0.00   0.0  0
 FYI  CONST_25  H39  N5   C20  C19  180.00   0.0  0
 FYI  CONST_26  H35  N4   C22  C21    0.00   0.0  0
 FYI  CONST_27  H36  N4   C22  C21  180.00   0.0  0
 FYI  Var_01    C8   C7   C6   C1    77.89  30.0  2
 FYI  Var_02    O2   P1   O1   C3   178.03  30.0  3
 FYI  Var_03    N1   C11  C10  C8   132.99  30.0  3
 FYI  Var_04    O11  C22  C21  C19  -49.41  30.0  3
 FYI  Var_05    H14  C12  N1   C11  -58.01  30.0  3
 FYI  Var_06    H26  C18  C16  C15  175.67  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
 FYI  chir_01  C8   C7   C9   C10  positiv
 FYI  chir_02  C13  N2   C14  C15  positiv
 FYI  chir_03  C15  C13  C16  C17  positiv
 FYI  chir_04  C19  N3   C20  C21  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
 FYI  plan-1  C1   0.020
 FYI  plan-1  C2   0.020
 FYI  plan-1  C3   0.020
 FYI  plan-1  C4   0.020
 FYI  plan-1  C5   0.020
 FYI  plan-1  C6   0.020
 FYI  plan-1  O1   0.020
 FYI  plan-1  C7   0.020
 FYI  plan-1  H1   0.020
 FYI  plan-1  H2   0.020
 FYI  plan-1  H3   0.020
 FYI  plan-1  H4   0.020
 FYI  plan-2  C8   0.020
 FYI  plan-2  C9   0.020
 FYI  plan-2  O5   0.020
 FYI  plan-2  N2   0.020
 FYI  plan-2  C13  0.020
 FYI  plan-2  H17  0.020
 FYI  plan-3  C10  0.020
 FYI  plan-3  C11  0.020
 FYI  plan-3  N1   0.020
 FYI  plan-3  C12  0.020
 FYI  plan-3  O7   0.020
 FYI  plan-3  H13  0.020
 FYI  plan-4  C13  0.020
 FYI  plan-4  C14  0.020
 FYI  plan-4  O8   0.020
 FYI  plan-4  N3   0.020
 FYI  plan-4  C19  0.020
 FYI  plan-4  H30  0.020
 FYI  plan-5  C19  0.020
 FYI  plan-5  C20  0.020
 FYI  plan-5  O10  0.020
 FYI  plan-5  N5   0.020
 FYI  plan-5  H38  0.020
 FYI  plan-5  H39  0.020
 FYI  plan-6  C21  0.020
 FYI  plan-6  C22  0.020
 FYI  plan-6  O11  0.020
 FYI  plan-6  N4   0.020
 FYI  plan-6  H35  0.020
 FYI  plan-6  H36  0.020

