
FMODB ID: 3MMML
Calculation Name: 2PK5-A-Xray547
Preferred Name: Gag-Pol polyprotein
Target Type: SINGLE PROTEIN
Ligand Name: (4r)-n-[(1s,2r)-2-hydroxy-2,3-dihydro-1h-inden-1-yl]-3-[(2s,3s)-2-hydroxy-3-({n-[(isoquinolin-5-yloxy)acetyl]-3-(methyl sulfonyl)-l-alanyl}amino)-4-phenylbutanoyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide
Ligand 3-letter code: 075
Ligand of Interest (LOI):
PDB ID: 2PK5
Chain ID: A
ChEMBL ID: CHEMBL3638326
UniProt ID: P03367
Base Structure: X-ray
Registration Date: 2025-10-05
Reference: Sci Data 11, 1164 (2024).
DOI: https://doi.org/10.1038/s41597-024-03999-2
Apendix: None
Modeling method
Optimization | MOE:Amber10:EHT |
---|---|
Restraint | OptAll |
Protonation | MOE:Protonate 3D |
Complement | MOE:Homology Modeling |
Water | No |
Procedure | Manual calculation |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 99 |
LigandResidueName | |
LigandFragmentNumber | 0 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
FMO2-HF: Electronic energy | -685678.790266 |
---|---|
FMO2-HF: Nuclear repulsion | 647949.939573 |
FMO2-HF: Total energy | -37728.850693 |
FMO2-MP2: Total energy | -37838.436028 |
3D Structure
Ligand structure

Ligand Interaction

Ligand binding energy
IFIE [kcal/mol] | PIEDA [kcal/mol] | Charge transfer value [e] | |||
---|---|---|---|---|---|
IFIE SUMIFIE SUM at MP2 level. | ESElectro static interaction energy. | EXExchange-repulsion energy. | CT+mixCharge transfer and mixing terms energy. | DI(MP2)Dispersion energy. | q(I=>J)Charge transfer value from I to J fragments. |
N/A | N/A | N/A | N/A | N/A | N/A |
Interactive mode: IFIE and PIEDA for fragment #1(A:1:PRO)
Summations of interaction energy for
fragment #1(A:1:PRO)
IFIE [kcal/mol] | PIEDA [kcal/mol] | Charge transfer value [e] | |||
---|---|---|---|---|---|
IFIE SUMIFIE SUM at MP2 level. | ESElectro static interaction energy. | EXExchange-repulsion energy. | CT+mixCharge transfer and mixing terms energy. | DI(MP2)Dispersion energy. | q(I=>J)Charge transfer value from I to J fragments. |
-6.738 | -3.921 | 0.067 | -1.137 | -1.747 | -0.004 |
Interaction energy analysis for fragmet #1(A:1:PRO)
frag_NumFragment number. | ChainChain species. | Res #Residue number. | RES3-letter code of amino acid residue, ligand and solvent molecule. | FCHARGEFormal charge [e]. | q_MullikenFragment charge evaluated by Mulliken charge [e]. | q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. | DISTDistance from Ligand [Å]. | TotalIFIE at MP2 level [kcal/mol]. | ESElectro static interaction energy by PIEDA [kcal/mol]. | EXExchange-repulsion energy by PIEDA [kcal/mol]. | CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. | DI(MP2)Dispersion energy by PIEDA [kcal/mol]. | q(I=>J)Charge transfer value from I to J fragmens [e]. |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3 | A | 3 | ILE | 0 | 0.001 | -0.003 | 3.278 | -0.492 | 1.788 | 0.053 | -0.935 | -1.398 | -0.003 |
4 | A | 4 | THR | 0 | 0.003 | 0.002 | 5.162 | 3.567 | 3.581 | -0.001 | -0.003 | -0.009 | 0.000 |
67 | A | 67 | CYS | 0 | -0.006 | -0.005 | 4.042 | -2.092 | -1.926 | 0.000 | -0.020 | -0.146 | 0.000 |
69 | A | 69 | HIS | 0 | -0.043 | -0.014 | 3.322 | -1.698 | -1.341 | 0.015 | -0.179 | -0.194 | -0.001 |
5 | A | 5 | LEU | 0 | 0.037 | 0.005 | 8.795 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | TRP | 0 | 0.007 | 0.013 | 11.797 | 1.803 | 1.803 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 7 | LYS | 1 | 0.952 | 0.982 | 10.693 | 24.487 | 24.487 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | ARG | 1 | 1.002 | 0.997 | 12.500 | 14.862 | 14.862 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | PRO | 0 | 0.034 | 0.028 | 8.937 | -0.493 | -0.493 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | LEU | 0 | -0.037 | -0.016 | 9.984 | -0.205 | -0.205 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | VAL | 0 | -0.010 | -0.012 | 5.995 | -2.735 | -2.735 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | THR | 0 | 0.003 | 0.002 | 8.973 | 2.056 | 2.056 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | ILE | 0 | -0.006 | -0.006 | 9.567 | -2.282 | -2.282 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | LYS | 1 | 0.941 | 0.971 | 12.200 | 18.232 | 18.232 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | ILE | 0 | 0.070 | 0.027 | 15.005 | -0.339 | -0.339 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | GLY | 0 | 0.035 | 0.019 | 18.071 | 0.527 | 0.527 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | GLY | 0 | -0.047 | -0.020 | 20.350 | 0.557 | 0.557 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | GLN | 0 | -0.004 | -0.004 | 20.047 | -0.305 | -0.305 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | LEU | 0 | -0.001 | -0.006 | 14.120 | -0.774 | -0.774 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | LYS | 1 | 0.829 | 0.904 | 15.349 | 15.292 | 15.292 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | GLU | -1 | -0.898 | -0.942 | 13.107 | -20.328 | -20.328 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | ALA | 0 | -0.006 | -0.015 | 12.533 | 1.334 | 1.334 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | LEU | 0 | -0.003 | -0.001 | 11.579 | -1.711 | -1.711 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | LEU | 0 | -0.026 | -0.014 | 5.991 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | ASP | -1 | -0.844 | -0.930 | 10.664 | -17.759 | -17.759 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | THR | 0 | 0.001 | -0.019 | 12.235 | 0.375 | 0.375 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | GLY | 0 | -0.008 | 0.003 | 14.865 | 0.729 | 0.729 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | ALA | 0 | -0.018 | 0.006 | 17.313 | 0.953 | 0.953 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | ASP | -1 | -0.825 | -0.895 | 17.663 | -15.382 | -15.382 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | ASP | -1 | -0.847 | -0.931 | 18.896 | -13.990 | -13.990 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | THR | 0 | -0.010 | -0.011 | 16.126 | -0.778 | -0.778 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | VAL | 0 | -0.034 | -0.016 | 18.004 | 0.929 | 0.929 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | ILE | 0 | -0.030 | -0.011 | 16.579 | -0.753 | -0.753 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | GLU | -1 | -0.733 | -0.851 | 20.364 | -13.523 | -13.523 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | GLU | -1 | -0.825 | -0.903 | 22.976 | -10.847 | -10.847 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | MET | 0 | -0.019 | 0.002 | 21.395 | -0.277 | -0.277 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | SER | 0 | -0.012 | -0.008 | 25.835 | 0.353 | 0.353 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | LEU | 0 | 0.002 | -0.002 | 22.008 | -0.475 | -0.475 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | PRO | 0 | 0.003 | 0.003 | 24.628 | 0.491 | 0.491 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | GLY | 0 | 0.036 | 0.018 | 27.281 | -0.216 | -0.216 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | ARG | 1 | 0.932 | 0.957 | 29.700 | 9.578 | 9.578 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | TRP | 0 | 0.020 | 0.014 | 29.229 | -0.346 | -0.346 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | LYS | 1 | 0.889 | 0.956 | 29.069 | 11.101 | 11.101 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | PRO | 0 | -0.019 | -0.009 | 30.504 | -0.329 | -0.329 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | LYS | 1 | 0.863 | 0.936 | 25.265 | 12.189 | 12.189 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | MET | 0 | -0.014 | 0.003 | 30.292 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | ILE | 0 | 0.012 | 0.000 | 23.794 | -0.174 | -0.174 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | GLY | 0 | 0.041 | 0.005 | 26.800 | 0.345 | 0.345 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | GLY | 0 | 0.015 | 0.016 | 25.761 | -0.473 | -0.473 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | ILE | 0 | 0.003 | 0.002 | 24.519 | 0.497 | 0.497 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 51 | GLY | 0 | 0.003 | 0.007 | 27.552 | -0.151 | -0.151 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 52 | GLY | 0 | -0.015 | 0.010 | 29.995 | 0.345 | 0.345 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 53 | PHE | 0 | 0.005 | -0.016 | 29.447 | -0.383 | -0.383 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | ILE | 0 | 0.002 | 0.013 | 25.535 | 0.265 | 0.265 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | LYS | 1 | 0.975 | 0.975 | 29.577 | 8.790 | 8.790 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | VAL | 0 | -0.018 | -0.008 | 25.578 | -0.106 | -0.106 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | ARG | 1 | 0.801 | 0.868 | 27.964 | 11.045 | 11.045 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | GLN | 0 | -0.011 | -0.035 | 25.707 | -0.216 | -0.216 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | TYR | 0 | 0.042 | 0.026 | 24.462 | 0.546 | 0.546 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 60 | ASP | -1 | -0.798 | -0.885 | 24.155 | -12.345 | -12.345 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | GLN | 0 | -0.032 | -0.023 | 22.156 | 0.331 | 0.331 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | ILE | 0 | 0.032 | 0.030 | 19.517 | 0.089 | 0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 63 | ILE | 0 | -0.008 | -0.006 | 16.301 | -0.584 | -0.584 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 64 | ILE | 0 | -0.024 | -0.012 | 13.180 | 0.617 | 0.617 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 65 | GLU | -1 | -0.960 | -0.975 | 10.910 | -23.023 | -23.023 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 66 | ILE | 0 | 0.054 | 0.014 | 7.257 | 0.996 | 0.996 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 68 | GLY | 0 | 0.014 | 0.019 | 5.588 | -4.417 | -4.417 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 70 | LYS | 1 | 0.922 | 0.961 | 7.928 | 20.670 | 20.670 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 71 | ALA | 0 | 0.052 | 0.034 | 11.695 | -0.247 | -0.247 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 72 | ILE | 0 | -0.017 | -0.020 | 13.422 | 0.899 | 0.899 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 73 | GLY | 0 | 0.029 | 0.010 | 17.207 | -0.218 | -0.218 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 74 | THR | 0 | -0.071 | -0.043 | 19.452 | 0.333 | 0.333 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 75 | VAL | 0 | -0.014 | -0.001 | 18.537 | -0.826 | -0.826 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 76 | LEU | 0 | -0.035 | -0.008 | 21.126 | 0.885 | 0.885 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 77 | VAL | 0 | -0.020 | -0.003 | 22.245 | -0.488 | -0.488 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 78 | GLY | 0 | 0.029 | 0.017 | 24.677 | 0.545 | 0.545 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 79 | PRO | 0 | -0.014 | 0.005 | 25.555 | -0.363 | -0.363 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 80 | THR | 0 | -0.005 | -0.017 | 21.069 | 0.282 | 0.282 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 81 | PRO | 0 | -0.022 | -0.009 | 22.974 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 82 | VAL | 0 | -0.004 | -0.011 | 17.164 | -0.236 | -0.236 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 83 | ASN | 0 | -0.040 | 0.002 | 16.594 | 0.682 | 0.682 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 84 | ILE | 0 | 0.013 | -0.001 | 15.286 | -1.092 | -1.092 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 85 | ILE | 0 | -0.001 | -0.004 | 10.890 | 0.613 | 0.613 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 86 | GLY | 0 | 0.099 | 0.049 | 13.322 | -0.828 | -0.828 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 87 | ARG | 1 | 0.879 | 0.903 | 14.482 | 15.169 | 15.169 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 88 | ASN | 0 | -0.028 | -0.013 | 15.093 | -1.345 | -1.345 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 89 | LEU | 0 | -0.009 | -0.003 | 13.322 | 0.158 | 0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 90 | LEU | 0 | -0.011 | -0.006 | 9.355 | -2.027 | -2.027 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 91 | THR | 0 | -0.010 | -0.007 | 10.004 | -2.201 | -2.201 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 92 | GLN | 0 | -0.059 | -0.018 | 11.804 | -0.448 | -0.448 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 93 | ILE | 0 | -0.042 | -0.017 | 6.541 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 94 | GLY | 0 | -0.001 | 0.009 | 6.681 | -5.110 | -5.110 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 95 | CYS | 0 | -0.087 | -0.035 | 6.254 | -4.491 | -4.491 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 96 | THR | 0 | -0.009 | -0.016 | 7.047 | 3.746 | 3.746 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 97 | LEU | 0 | -0.041 | -0.017 | 8.402 | -1.989 | -1.989 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 98 | ASN | 0 | -0.035 | -0.025 | 8.988 | -1.633 | -1.633 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 99 | PHE | -1 | -0.898 | -0.927 | 11.544 | -20.523 | -20.523 | 0.000 | 0.000 | 0.000 | 0.000 |