![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: PLLJ9
Calculation Name: 3TYS-A-Xray13
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: 2018-02-14
Reference:
Modeling method
Optimization | MOE:Amber10:EHT |
---|---|
Restraint | OptH |
Protonation | MOE:Protonate 3D |
Complement | Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE. |
Water | No |
Procedure | Auto-FMO protocol ver. 1.20181228 |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 76 |
LigandCharge | |
Software | MIZUHO/ABINIT-MP 3.0 |
Total energy (hartree)
FMO2-HF: Electronic energy | -464937.033174 |
---|---|
FMO2-HF: Nuclear repulsion | 434297.224473 |
FMO2-HF: Total energy | -30639.808701 |
FMO2-MP2: Total energy | -30727.691292 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F000451/ligand_interaction/ligand_F000451.png)
Ligand Interaction
![ligand interaction](./Kdata/F000451/ligand_interaction/ligand_interaction_F000451.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:-8:ACE)
Summations of interaction energy for
fragment #1(A:-8:ACE)
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. |
-0.607 | 0.756 | -0.013 | -0.614 | -0.736 | -0.001 |
Interaction energy analysis for fragmet #1(A:-8:ACE)
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 | -6 | GLU | -1 | -0.898 | -0.932 | 3.829 | -0.582 | 0.716 | -0.012 | -0.611 | -0.675 | -0.001 |
4 | A | -5 | ASN | 0 | 0.002 | -0.002 | 5.108 | 0.241 | 0.306 | -0.001 | -0.003 | -0.061 | 0.000 |
5 | A | -4 | LEU | 0 | 0.006 | 0.005 | 7.763 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | -3 | TYR | 0 | 0.007 | -0.003 | 9.931 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | -2 | PHE | 0 | -0.002 | -0.003 | 12.392 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | -1 | GLN | 0 | -0.073 | -0.056 | 9.778 | 0.066 | 0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 0 | GLY | 0 | 0.073 | 0.056 | 12.348 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 1 | MET | 0 | -0.047 | -0.008 | 14.668 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 2 | ARG | 1 | 0.864 | 0.943 | 14.015 | -0.276 | -0.276 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 3 | VAL | 0 | -0.007 | 0.002 | 14.776 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 4 | SER | 0 | 0.019 | 0.007 | 16.434 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 5 | TYR | 0 | 0.028 | -0.015 | 15.275 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 6 | ASN | 0 | -0.011 | -0.012 | 21.659 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 7 | LYS | 1 | 0.923 | 0.970 | 24.720 | -0.104 | -0.104 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 8 | LEU | 0 | 0.074 | 0.052 | 22.622 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 9 | TRP | 0 | -0.050 | -0.027 | 22.628 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 10 | LYS | 1 | 0.938 | 0.964 | 27.948 | -0.100 | -0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 11 | LEU | 0 | 0.066 | 0.048 | 27.825 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 12 | LEU | 0 | -0.037 | -0.034 | 27.222 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 13 | ILE | 0 | -0.005 | 0.007 | 31.033 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 14 | ASP | -1 | -0.911 | -0.947 | 33.646 | 0.058 | 0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 15 | ARG | 1 | 0.778 | 0.888 | 31.921 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 16 | ASP | -1 | -0.934 | -0.958 | 35.316 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 17 | MET | 0 | -0.030 | -0.006 | 31.488 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 18 | LYS | 1 | 0.910 | 0.946 | 32.111 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 19 | LYS | 1 | 1.010 | 0.983 | 25.699 | -0.125 | -0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 20 | GLY | 0 | -0.093 | -0.056 | 27.550 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 21 | GLU | -1 | -0.768 | -0.883 | 29.241 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 22 | LEU | 0 | 0.038 | 0.035 | 24.523 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 23 | ARG | 1 | 0.836 | 0.919 | 23.957 | -0.102 | -0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 24 | GLU | -1 | -0.967 | -1.001 | 25.730 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 25 | ALA | 0 | -0.001 | 0.022 | 28.385 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 26 | VAL | 0 | -0.006 | 0.001 | 23.074 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 27 | GLY | 0 | 0.033 | 0.035 | 24.628 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 28 | VAL | 0 | -0.080 | -0.034 | 19.377 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 29 | SER | 0 | 0.050 | 0.022 | 18.192 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 30 | LYS | 1 | 1.012 | 0.980 | 20.838 | -0.089 | -0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 31 | SER | 0 | 0.005 | 0.000 | 16.851 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 32 | THR | 0 | 0.021 | 0.002 | 15.619 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 33 | PHE | 0 | 0.077 | 0.038 | 17.168 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 34 | ALA | 0 | -0.023 | -0.021 | 19.392 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 35 | LYS | 1 | 0.917 | 0.975 | 11.446 | -0.500 | -0.500 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 36 | LEU | 0 | 0.053 | 0.040 | 17.054 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 37 | GLY | 0 | -0.056 | -0.018 | 19.303 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 38 | LYS | 1 | 0.878 | 0.946 | 17.582 | -0.273 | -0.273 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 39 | ASN | 0 | 0.037 | 0.021 | 17.868 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 40 | GLU | -1 | -0.886 | -0.943 | 13.181 | 0.447 | 0.447 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 41 | ASN | 0 | 0.058 | 0.031 | 8.861 | -0.141 | -0.141 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 42 | VAL | 0 | -0.017 | -0.011 | 11.993 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 43 | SER | 0 | -0.009 | -0.006 | 11.886 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 44 | LEU | 0 | 0.128 | 0.045 | 12.828 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 45 | THR | 0 | 0.001 | 0.000 | 14.980 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 46 | VAL | 0 | -0.015 | -0.004 | 16.221 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 47 | LEU | 0 | 0.000 | -0.004 | 15.975 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 48 | LEU | 0 | 0.036 | 0.018 | 18.450 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 49 | ALA | 0 | 0.033 | 0.030 | 20.755 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 50 | ILE | 0 | -0.035 | -0.021 | 20.764 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 51 | CYS | 0 | -0.043 | -0.022 | 22.403 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 52 | GLU | -1 | -0.936 | -0.964 | 24.958 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 53 | TYR | 0 | -0.028 | -0.011 | 26.658 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 54 | LEU | 0 | -0.047 | -0.034 | 26.591 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 55 | ASN | 0 | 0.001 | 0.019 | 29.329 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 56 | CYS | 0 | -0.085 | -0.029 | 25.856 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 57 | ASP | -1 | -0.805 | -0.895 | 24.741 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 58 | PHE | 0 | 0.007 | -0.025 | 18.549 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 59 | GLY | 0 | -0.021 | -0.014 | 22.543 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 60 | ASP | -1 | -0.844 | -0.921 | 24.434 | 0.067 | 0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 61 | ILE | 0 | -0.066 | -0.054 | 21.294 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 62 | ILE | 0 | -0.069 | -0.034 | 17.571 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 63 | GLU | -1 | -0.965 | -0.984 | 20.472 | 0.099 | 0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 64 | ALA | 0 | -0.027 | -0.011 | 18.118 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 65 | LEU | 0 | -0.017 | -0.021 | 18.769 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 66 | PRO | 0 | -0.008 | -0.006 | 18.619 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 67 | GLU | -2 | -1.896 | -1.941 | 16.340 | 0.506 | 0.506 | 0.000 | 0.000 | 0.000 | 0.000 |