![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 536YZ
Calculation Name: 2NN4-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2NN4
Chain ID: A
UniProt ID: P54494
Base Structure: X-ray
Registration Date: 2023-06-20
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 | 62 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -393758.965692 |
---|---|
FMO2-HF: Nuclear repulsion | 367178.366646 |
FMO2-HF: Total energy | -26580.599046 |
FMO2-MP2: Total energy | -26657.526717 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F021731/ligand_interaction/ligand_F021731.png)
Ligand Interaction
![ligand interaction](./Kdata/F021731/ligand_interaction/ligand_interaction_F021731.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:1:LEU)
Summations of interaction energy for
fragment #1(A:1:LEU)
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. |
-4.148 | 3.769 | 1.483 | -3.76 | -5.639 | -0.002 |
Interaction energy analysis for fragmet #1(A:1:LEU)
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 | THR | 0 | -0.027 | -0.013 | 3.675 | -4.697 | -0.855 | -0.037 | -2.005 | -1.800 | -0.005 |
4 | A | 4 | PHE | 0 | 0.106 | 0.039 | 4.905 | 1.313 | 1.410 | -0.001 | -0.005 | -0.091 | 0.000 |
5 | A | 5 | TYR | 0 | 0.007 | 0.005 | 7.358 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | ASP | -1 | -0.798 | -0.899 | 2.707 | 3.193 | 4.271 | 1.170 | -0.764 | -1.483 | 0.002 |
7 | A | 7 | VAL | 0 | 0.004 | -0.002 | 3.467 | -1.626 | -1.227 | 0.009 | -0.080 | -0.328 | 0.000 |
8 | A | 8 | GLN | 0 | 0.025 | 0.008 | 5.041 | -0.687 | -0.657 | -0.001 | -0.003 | -0.027 | 0.000 |
9 | A | 9 | GLN | 0 | -0.044 | -0.018 | 6.562 | -0.512 | -0.512 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | LEU | 0 | -0.029 | -0.005 | 4.558 | -0.398 | -0.306 | -0.001 | -0.002 | -0.088 | 0.000 |
11 | A | 11 | LEU | 0 | 0.072 | 0.013 | 6.816 | -0.120 | -0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | LYS | 1 | 0.932 | 0.996 | 9.922 | -0.287 | -0.287 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | THR | 0 | -0.105 | -0.043 | 9.842 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | PHE | 0 | -0.047 | -0.038 | 9.941 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | GLY | 0 | 0.001 | 0.011 | 13.863 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | HIS | 0 | -0.023 | -0.007 | 13.517 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | ILE | 0 | -0.070 | -0.031 | 13.496 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | VAL | 0 | -0.015 | -0.008 | 14.621 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | TYR | 0 | -0.029 | -0.024 | 15.996 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | PHE | 0 | -0.039 | -0.029 | 18.133 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | GLY | 0 | -0.028 | 0.001 | 20.019 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | ASP | -1 | -0.866 | -0.929 | 19.896 | 0.118 | 0.118 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | ARG | 1 | 0.890 | 0.944 | 12.921 | -0.395 | -0.395 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | GLU | -1 | -0.913 | -0.958 | 15.452 | 0.104 | 0.104 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | LEU | 0 | 0.049 | 0.019 | 16.804 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | GLU | -1 | -0.871 | -0.941 | 14.515 | 0.258 | 0.258 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | ILE | 0 | -0.043 | -0.031 | 11.430 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | GLU | -1 | -0.932 | -0.965 | 12.925 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | PHE | 0 | 0.042 | 0.033 | 15.097 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | MET | 0 | -0.056 | -0.037 | 8.911 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | LEU | 0 | -0.030 | -0.020 | 10.343 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | ASP | -1 | -0.914 | -0.942 | 12.310 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | GLU | -1 | -0.878 | -0.946 | 12.934 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | LEU | 0 | -0.048 | -0.027 | 7.470 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | LYS | 1 | 0.929 | 0.966 | 11.336 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | GLU | -1 | -0.852 | -0.925 | 14.133 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | LEU | 0 | 0.000 | 0.005 | 11.191 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | TYR | 0 | -0.040 | -0.027 | 12.503 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | MET | 0 | -0.077 | -0.034 | 14.273 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | ASN | 0 | -0.094 | -0.053 | 17.378 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | HIS | 0 | -0.036 | -0.018 | 16.681 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | MET | 0 | -0.041 | -0.014 | 14.573 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | ILE | 0 | -0.041 | -0.005 | 9.378 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | GLU | -1 | -0.901 | -0.947 | 10.175 | -0.344 | -0.344 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | LYS | 1 | 0.949 | 0.968 | 10.585 | 0.199 | 0.199 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | GLU | -1 | -0.913 | -0.969 | 7.703 | -0.355 | -0.355 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | GLN | 0 | 0.032 | 0.012 | 5.909 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | TRP | 0 | 0.041 | 0.029 | 5.988 | -0.240 | -0.240 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | ALA | 0 | -0.010 | -0.004 | 8.026 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | ARG | 1 | 0.820 | 0.896 | 2.888 | 0.154 | 1.966 | 0.298 | -0.732 | -1.378 | 0.002 |
51 | A | 51 | ALA | 0 | 0.016 | 0.009 | 3.710 | -0.457 | -0.356 | 0.000 | -0.031 | -0.070 | 0.000 |
52 | A | 52 | ALA | 0 | 0.065 | 0.025 | 4.671 | 0.365 | 0.384 | -0.001 | -0.002 | -0.016 | 0.000 |
53 | A | 53 | ALA | 0 | -0.027 | -0.012 | 7.085 | 0.132 | 0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | VAL | 0 | -0.049 | -0.020 | 2.883 | -0.365 | 0.082 | 0.047 | -0.136 | -0.358 | -0.001 |
55 | A | 55 | LEU | 0 | 0.025 | 0.008 | 6.075 | 0.279 | 0.279 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | ARG | 1 | 0.935 | 0.970 | 8.537 | 0.084 | 0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | LYS | 1 | 0.923 | 0.974 | 9.181 | -0.155 | -0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | GLU | -1 | -0.906 | -0.971 | 9.210 | 0.649 | 0.649 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | LEU | 0 | 0.037 | 0.012 | 11.167 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 60 | GLU | -1 | -0.979 | -0.972 | 13.929 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | GLN | 0 | -0.091 | -0.054 | 11.842 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | THR | 0 | -0.047 | -0.002 | 14.623 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |