![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 7675K
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 | OptH |
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 | -462206.258962 |
---|---|
FMO2-HF: Nuclear repulsion | 431717.632353 |
FMO2-HF: Total energy | -30488.626609 |
FMO2-MP2: Total energy | -30576.068119 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F037614/ligand_interaction/ligand_F037614.png)
Ligand Interaction
![ligand interaction](./Kdata/F037614/ligand_interaction/ligand_interaction_F037614.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. |
21.907 | 23.262 | 0.016 | -0.513 | -0.859 | 0.001 |
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 | -0.001 | -0.003 | 3.585 | 5.710 | 7.065 | 0.016 | -0.513 | -0.859 | 0.001 |
4 | A | -4 | LEU | 0 | 0.004 | 0.004 | 6.191 | 1.584 | 1.584 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | -3 | TYR | 0 | 0.012 | 0.000 | 8.731 | 1.385 | 1.385 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | -2 | PHE | 0 | 0.000 | 0.000 | 11.618 | 1.651 | 1.651 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | -1 | GLN | 0 | -0.059 | -0.046 | 9.483 | -0.370 | -0.370 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 0 | GLY | 0 | 0.071 | 0.056 | 12.456 | 0.414 | 0.414 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 1 | MET | 0 | -0.056 | -0.019 | 15.118 | 0.814 | 0.814 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 2 | ARG | 1 | 0.850 | 0.932 | 14.911 | 12.989 | 12.989 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 3 | VAL | 0 | 0.008 | 0.012 | 16.303 | 0.441 | 0.441 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 4 | SER | 0 | 0.008 | 0.001 | 18.052 | 0.556 | 0.556 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 5 | TYR | 0 | 0.036 | -0.011 | 17.321 | -0.304 | -0.304 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 6 | ASN | 0 | -0.012 | -0.013 | 23.388 | 0.363 | 0.363 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 7 | LYS | 1 | 0.924 | 0.970 | 25.703 | 11.699 | 11.699 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 8 | LEU | 0 | 0.076 | 0.053 | 24.088 | 0.256 | 0.256 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 9 | TRP | 0 | -0.051 | -0.028 | 24.992 | 0.341 | 0.341 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 10 | LYS | 1 | 0.938 | 0.964 | 29.735 | 9.875 | 9.875 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 11 | LEU | 0 | 0.067 | 0.049 | 28.438 | 0.240 | 0.240 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 12 | LEU | 0 | -0.037 | -0.034 | 28.946 | 0.150 | 0.150 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 13 | ILE | 0 | -0.005 | 0.007 | 32.474 | 0.225 | 0.225 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 14 | ASP | -1 | -0.911 | -0.947 | 34.746 | -8.388 | -8.388 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 15 | ARG | 1 | 0.780 | 0.888 | 31.823 | 9.472 | 9.472 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 16 | ASP | -1 | -0.932 | -0.957 | 36.268 | -7.542 | -7.542 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 17 | MET | 0 | -0.029 | -0.005 | 32.465 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 18 | LYS | 1 | 0.910 | 0.946 | 34.171 | 7.787 | 7.787 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 19 | LYS | 1 | 1.007 | 0.981 | 28.096 | 9.863 | 9.863 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 20 | GLY | 0 | -0.093 | -0.056 | 29.420 | -0.305 | -0.305 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 21 | GLU | -1 | -0.766 | -0.882 | 30.845 | -8.646 | -8.646 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 22 | LEU | 0 | 0.037 | 0.035 | 25.817 | -0.128 | -0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 23 | ARG | 1 | 0.834 | 0.918 | 25.594 | 10.006 | 10.006 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 24 | GLU | -1 | -0.965 | -1.000 | 26.728 | -9.667 | -9.667 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 25 | ALA | 0 | 0.000 | 0.023 | 29.328 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 26 | VAL | 0 | -0.006 | 0.000 | 23.324 | -0.155 | -0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 27 | GLY | 0 | 0.035 | 0.036 | 24.615 | -0.346 | -0.346 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 28 | VAL | 0 | -0.080 | -0.033 | 20.567 | -0.519 | -0.519 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 29 | SER | 0 | 0.054 | 0.024 | 19.732 | 0.489 | 0.489 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 30 | LYS | 1 | 1.014 | 0.981 | 22.667 | 10.417 | 10.417 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 31 | SER | 0 | 0.009 | 0.002 | 19.139 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 32 | THR | 0 | 0.011 | -0.001 | 17.498 | -0.569 | -0.569 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 33 | PHE | 0 | 0.076 | 0.035 | 19.322 | -0.076 | -0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 34 | ALA | 0 | -0.021 | -0.020 | 21.667 | 0.187 | 0.187 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 35 | LYS | 1 | 0.916 | 0.974 | 13.694 | 17.779 | 17.779 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 36 | LEU | 0 | 0.055 | 0.041 | 19.445 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 37 | GLY | 0 | -0.053 | -0.016 | 21.704 | 0.263 | 0.263 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 38 | LYS | 1 | 0.882 | 0.949 | 19.960 | 12.971 | 12.971 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 39 | ASN | 0 | 0.029 | 0.017 | 20.031 | -0.284 | -0.284 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 40 | GLU | -1 | -0.891 | -0.947 | 15.617 | -15.067 | -15.067 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 41 | ASN | 0 | 0.056 | 0.030 | 10.902 | 1.255 | 1.255 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 42 | VAL | 0 | -0.014 | -0.009 | 14.353 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 43 | SER | 0 | -0.006 | -0.004 | 12.275 | -0.505 | -0.505 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 44 | LEU | 0 | 0.126 | 0.044 | 11.904 | 1.051 | 1.051 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 45 | THR | 0 | 0.003 | 0.002 | 13.980 | 0.546 | 0.546 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 46 | VAL | 0 | -0.012 | -0.002 | 15.956 | 0.975 | 0.975 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 47 | LEU | 0 | -0.004 | -0.006 | 16.169 | 0.778 | 0.778 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 48 | LEU | 0 | 0.037 | 0.019 | 16.478 | 0.548 | 0.548 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 49 | ALA | 0 | 0.035 | 0.032 | 19.848 | 0.635 | 0.635 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 50 | ILE | 0 | -0.037 | -0.021 | 21.702 | 0.647 | 0.647 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 51 | CYS | 0 | -0.045 | -0.024 | 21.888 | 0.469 | 0.469 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 52 | GLU | -1 | -0.933 | -0.963 | 23.989 | -11.541 | -11.541 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 53 | TYR | 0 | -0.026 | -0.011 | 25.826 | 0.468 | 0.468 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 54 | LEU | 0 | -0.047 | -0.035 | 27.081 | 0.436 | 0.436 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 55 | ASN | 0 | 0.003 | 0.020 | 28.583 | 0.202 | 0.202 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 56 | CYS | 0 | -0.085 | -0.029 | 25.547 | 0.243 | 0.243 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 57 | ASP | -1 | -0.802 | -0.893 | 23.162 | -13.210 | -13.210 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 58 | PHE | 0 | 0.007 | -0.025 | 17.453 | -0.086 | -0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 59 | GLY | 0 | -0.024 | -0.016 | 21.951 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 60 | ASP | -1 | -0.841 | -0.919 | 24.210 | -10.490 | -10.490 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 61 | ILE | 0 | -0.062 | -0.052 | 21.430 | 0.257 | 0.257 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 62 | ILE | 0 | -0.069 | -0.034 | 17.929 | -0.201 | -0.201 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 63 | GLU | -1 | -0.960 | -0.982 | 21.511 | -11.259 | -11.259 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 64 | ALA | 0 | -0.022 | -0.007 | 18.476 | -0.406 | -0.406 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 65 | LEU | 0 | -0.005 | -0.013 | 19.823 | 0.582 | 0.582 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 66 | PRO | 0 | 0.031 | 0.017 | 19.581 | -0.678 | -0.678 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 67 | GLU | -1 | -0.992 | -0.992 | 17.253 | -14.205 | -14.205 | 0.000 | 0.000 | 0.000 | 0.000 |