![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 6Y28Z
Calculation Name: 3TYS-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3TYS
Chain ID: A
UniProt ID: Q6WRY9
Base Structure: X-ray
Registration Date: 2023-09-23
Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.
Modeling method
Optimization | MOE:Amber10:EHT |
---|---|
Restraint | OptAll |
Protonation | MOE:Protonate 3D |
Complement | MOE:Structure Preparation |
Water | No |
Procedure | Auto-FMO protocol ver. 2.20220422 |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 75 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -463559.400744 |
---|---|
FMO2-HF: Nuclear repulsion | 433069.881723 |
FMO2-HF: Total energy | -30489.519022 |
FMO2-MP2: Total energy | -30576.92744 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F037612/ligand_interaction/ligand_F037612.png)
Ligand Interaction
![ligand interaction](./Kdata/F037612/ligand_interaction/ligand_interaction_F037612.png)
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:-7:ARG)
Summations of interaction energy for
fragment #1(A:-7:ARG)
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. |
28.332 | 29.651 | 0.017 | -0.356 | -0.98 | 0.002 |
Interaction energy analysis for fragmet #1(A:-7:ARG)
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 | -5 | ASN | 0 | -0.048 | -0.021 | 3.474 | 10.305 | 11.624 | 0.017 | -0.356 | -0.980 | 0.002 |
4 | A | -4 | LEU | 0 | 0.005 | 0.002 | 6.321 | 2.110 | 2.110 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | -3 | TYR | 0 | 0.017 | 0.007 | 8.690 | 1.916 | 1.916 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | -2 | PHE | 0 | -0.015 | -0.006 | 11.618 | 1.772 | 1.772 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | -1 | GLN | 0 | -0.025 | -0.032 | 9.537 | -0.405 | -0.405 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 0 | GLY | 0 | 0.057 | 0.056 | 12.376 | 0.239 | 0.239 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 1 | MET | 0 | -0.074 | -0.040 | 14.841 | 0.876 | 0.876 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 2 | ARG | 1 | 0.852 | 0.928 | 14.605 | 13.410 | 13.410 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 3 | VAL | 0 | 0.013 | 0.018 | 16.125 | 0.482 | 0.482 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 4 | SER | 0 | -0.008 | -0.017 | 17.893 | 0.552 | 0.552 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 5 | TYR | 0 | 0.040 | -0.007 | 17.487 | -0.188 | -0.188 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 6 | ASN | 0 | -0.023 | -0.024 | 23.593 | 0.385 | 0.385 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 7 | LYS | 1 | 0.795 | 0.921 | 24.904 | 12.371 | 12.371 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 8 | LEU | 0 | 0.066 | 0.046 | 23.806 | 0.335 | 0.335 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 9 | TRP | 0 | -0.062 | -0.051 | 24.659 | 0.337 | 0.337 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 10 | LYS | 1 | 0.900 | 0.964 | 29.636 | 9.970 | 9.970 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 11 | LEU | 0 | 0.080 | 0.040 | 28.478 | 0.233 | 0.233 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 12 | LEU | 0 | -0.045 | -0.024 | 29.028 | 0.108 | 0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 13 | ILE | 0 | 0.010 | 0.007 | 32.530 | 0.243 | 0.243 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 14 | ASP | -1 | -0.913 | -0.953 | 34.159 | -8.598 | -8.598 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 15 | ARG | 1 | 0.804 | 0.887 | 31.886 | 9.378 | 9.378 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 16 | ASP | -1 | -0.891 | -0.929 | 36.885 | -7.472 | -7.472 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 17 | MET | 0 | -0.064 | -0.025 | 32.364 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 18 | LYS | 1 | 0.816 | 0.881 | 34.087 | 8.061 | 8.061 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 19 | LYS | 1 | 0.969 | 0.967 | 27.896 | 9.926 | 9.926 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 20 | GLY | 0 | -0.029 | -0.012 | 29.295 | -0.300 | -0.300 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 21 | GLU | -1 | -0.748 | -0.854 | 30.993 | -8.556 | -8.556 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 22 | LEU | 0 | 0.026 | 0.022 | 25.813 | -0.112 | -0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 23 | ARG | 1 | 0.748 | 0.840 | 25.854 | 9.769 | 9.769 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 24 | GLU | -1 | -0.796 | -0.877 | 27.221 | -9.980 | -9.980 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 25 | ALA | 0 | -0.032 | -0.001 | 29.551 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 26 | VAL | 0 | -0.006 | 0.003 | 23.651 | -0.108 | -0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 27 | GLY | 0 | 0.015 | 0.023 | 24.717 | -0.429 | -0.429 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 28 | VAL | 0 | -0.050 | -0.016 | 21.125 | -0.499 | -0.499 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 29 | SER | 0 | 0.042 | 0.021 | 20.036 | 0.348 | 0.348 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 30 | LYS | 1 | 1.005 | 0.977 | 22.338 | 10.041 | 10.041 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 31 | SER | 0 | 0.015 | 0.012 | 19.171 | 0.171 | 0.171 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 32 | THR | 0 | 0.017 | 0.001 | 17.507 | -0.592 | -0.592 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 33 | PHE | 0 | 0.055 | 0.010 | 19.343 | -0.135 | -0.135 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 34 | ALA | 0 | -0.019 | -0.014 | 21.536 | 0.193 | 0.193 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 35 | LYS | 1 | 0.865 | 0.951 | 12.670 | 18.415 | 18.415 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 36 | LEU | 0 | 0.044 | 0.033 | 19.196 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 37 | GLY | 0 | -0.059 | -0.031 | 21.510 | 0.260 | 0.260 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 38 | LYS | 1 | 0.790 | 0.881 | 19.034 | 13.661 | 13.661 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 39 | ASN | 0 | 0.025 | 0.032 | 20.025 | -0.359 | -0.359 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 40 | GLU | -1 | -0.771 | -0.863 | 15.577 | -14.814 | -14.814 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 41 | ASN | 0 | 0.056 | 0.029 | 10.907 | 1.459 | 1.459 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 42 | VAL | 0 | 0.006 | 0.014 | 13.755 | -0.383 | -0.383 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 43 | SER | 0 | 0.008 | 0.000 | 12.427 | -0.555 | -0.555 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 44 | LEU | 0 | 0.098 | 0.026 | 12.002 | 1.064 | 1.064 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 45 | THR | 0 | 0.030 | 0.014 | 14.384 | 0.503 | 0.503 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 46 | VAL | 0 | -0.017 | 0.000 | 16.354 | 0.942 | 0.942 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 47 | LEU | 0 | -0.012 | -0.004 | 16.431 | 0.725 | 0.725 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 48 | LEU | 0 | 0.039 | 0.020 | 16.925 | 0.556 | 0.556 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 49 | ALA | 0 | 0.048 | 0.033 | 20.251 | 0.626 | 0.626 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 50 | ILE | 0 | -0.034 | -0.022 | 21.642 | 0.647 | 0.647 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 51 | CYS | 0 | -0.038 | -0.019 | 22.835 | 0.331 | 0.331 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 52 | GLU | -1 | -0.943 | -0.963 | 24.294 | -11.584 | -11.584 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 53 | TYR | 0 | 0.005 | -0.008 | 26.126 | 0.503 | 0.503 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 54 | LEU | 0 | -0.028 | -0.027 | 27.284 | 0.427 | 0.427 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 55 | ASN | 0 | -0.058 | -0.013 | 28.892 | 0.442 | 0.442 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 56 | CYS | 0 | -0.083 | -0.020 | 26.186 | 0.260 | 0.260 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 57 | ASP | -1 | -0.750 | -0.879 | 23.570 | -13.477 | -13.477 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 58 | PHE | 0 | 0.002 | -0.030 | 17.332 | -0.145 | -0.145 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 59 | GLY | 0 | -0.024 | -0.012 | 22.325 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 60 | ASP | -1 | -0.838 | -0.912 | 24.832 | -10.502 | -10.502 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 61 | ILE | 0 | -0.054 | -0.044 | 21.613 | 0.243 | 0.243 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 62 | ILE | 0 | -0.055 | -0.037 | 18.481 | -0.129 | -0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 63 | GLU | -1 | -0.856 | -0.909 | 22.012 | -11.491 | -11.491 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 64 | ALA | 0 | -0.006 | -0.010 | 18.647 | -0.608 | -0.608 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 65 | LEU | 0 | -0.006 | -0.005 | 19.706 | 0.557 | 0.557 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 66 | PRO | 0 | 0.038 | 0.006 | 19.247 | -0.705 | -0.705 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 67 | GLU | -1 | -0.982 | -0.977 | 16.909 | -14.635 | -14.635 | 0.000 | 0.000 | 0.000 | 0.000 |