![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: YQ252
Calculation Name: 2NN4-A-Xray316
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: 2021-09-06
Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.
Modeling method
Optimization | MOE:Amber10:EHT |
---|---|
Restraint | OptH |
Protonation | MOE:Protonate 3D |
Complement | MOE:Structure Preparation |
Water | No |
Procedure | Auto-FMO protocol ver. 1.20200129 |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 64 |
LigandCharge | |
Software | ABINIT-MP - Open Ver.1 Rev. 15 / 20190524 |
Total energy (hartree)
FMO2-HF: Electronic energy | -399291.123997 |
---|---|
FMO2-HF: Nuclear repulsion | 372539.569734 |
FMO2-HF: Total energy | -26751.554263 |
FMO2-MP2: Total energy | -26829.033797 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F015919/ligand_interaction/ligand_F015919.png)
Ligand Interaction
![ligand interaction](./Kdata/F015919/ligand_interaction/ligand_interaction_F015919.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:0:ACE )
Summations of interaction energy for
fragment #1(A:0: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. |
1.614 | 2.239 | 7.395 | -3.83 | -4.19 | -0.031 |
Interaction energy analysis for fragmet #1(A:0: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 | 2 | ASN | 0 | -0.034 | -0.001 | 3.836 | 1.087 | 1.805 | -0.005 | -0.360 | -0.353 | 0.000 |
4 | A | 3 | THR | 0 | -0.023 | -0.010 | 5.175 | 0.399 | 0.399 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 4 | PHE | 0 | 0.109 | 0.038 | 4.357 | 0.255 | 0.354 | 0.000 | -0.014 | -0.085 | 0.000 |
6 | A | 5 | TYR | 0 | 0.013 | 0.009 | 5.815 | 0.397 | 0.397 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 6 | ASP | -1 | -0.796 | -0.898 | 2.949 | -0.951 | -0.720 | 0.428 | -0.254 | -0.404 | -0.001 |
8 | A | 7 | VAL | 0 | 0.018 | -0.009 | 2.328 | 0.089 | 1.067 | 4.771 | -3.568 | -2.181 | -0.022 |
9 | A | 8 | GLN | 0 | 0.010 | 0.009 | 2.907 | 0.670 | -1.159 | 0.185 | 1.651 | -0.007 | -0.002 |
10 | A | 9 | GLN | 0 | -0.038 | -0.016 | 4.791 | -0.315 | -0.338 | 0.000 | -0.007 | 0.030 | 0.000 |
11 | A | 10 | LEU | 0 | -0.020 | -0.002 | 2.368 | -0.491 | -0.431 | 1.962 | -1.109 | -0.913 | -0.005 |
12 | A | 11 | LEU | 0 | 0.070 | 0.013 | 4.422 | -0.517 | -0.549 | 0.000 | -0.026 | 0.058 | 0.000 |
13 | A | 12 | LYS | 1 | 0.934 | 0.997 | 7.520 | -0.589 | -0.589 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 13 | THR | 0 | -0.101 | -0.041 | 7.693 | -0.223 | -0.223 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 14 | PHE | 0 | -0.049 | -0.038 | 7.996 | -0.110 | -0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 15 | GLY | 0 | 0.001 | 0.011 | 11.528 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 16 | HIS | 0 | -0.022 | -0.008 | 11.210 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 17 | ILE | 0 | -0.070 | -0.031 | 11.173 | 0.103 | 0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 18 | VAL | 0 | -0.018 | -0.009 | 12.550 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 19 | TYR | 0 | -0.027 | -0.024 | 13.966 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 20 | PHE | 0 | -0.039 | -0.030 | 16.453 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 21 | GLY | 0 | -0.028 | 0.001 | 18.319 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 22 | ASP | -1 | -0.865 | -0.929 | 18.358 | 0.177 | 0.177 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 23 | ARG | 1 | 0.890 | 0.944 | 12.076 | -0.296 | -0.296 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 24 | GLU | -1 | -0.916 | -0.959 | 14.320 | 0.230 | 0.230 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 25 | LEU | 0 | 0.051 | 0.020 | 15.800 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 26 | GLU | -1 | -0.874 | -0.942 | 12.880 | 0.370 | 0.370 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 27 | ILE | 0 | -0.040 | -0.030 | 10.468 | 0.109 | 0.109 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 28 | GLU | -1 | -0.933 | -0.965 | 11.815 | 0.299 | 0.299 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 29 | PHE | 0 | 0.044 | 0.034 | 13.234 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 30 | MET | 0 | -0.055 | -0.038 | 7.205 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 31 | LEU | 0 | -0.030 | -0.020 | 9.464 | 0.095 | 0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 32 | ASP | -1 | -0.914 | -0.941 | 10.983 | 0.269 | 0.269 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 33 | GLU | -1 | -0.875 | -0.945 | 10.768 | 0.383 | 0.383 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 34 | LEU | 0 | -0.051 | -0.030 | 5.274 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 35 | LYS | 1 | 0.931 | 0.967 | 9.181 | -0.313 | -0.313 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 36 | GLU | -1 | -0.852 | -0.925 | 12.253 | 0.156 | 0.156 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 37 | LEU | 0 | -0.001 | 0.004 | 8.651 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 38 | TYR | 0 | -0.040 | -0.027 | 10.577 | -0.088 | -0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 39 | MET | 0 | -0.074 | -0.032 | 12.149 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 40 | ASN | 0 | -0.094 | -0.052 | 15.037 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 41 | HIS | 0 | -0.038 | -0.019 | 14.760 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 42 | MET | 0 | -0.042 | -0.014 | 12.477 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 43 | ILE | 0 | -0.041 | -0.006 | 7.234 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 44 | GLU | -1 | -0.902 | -0.947 | 9.582 | -0.259 | -0.259 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 45 | LYS | 1 | 0.948 | 0.967 | 9.175 | 0.117 | 0.117 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 46 | GLU | -1 | -0.913 | -0.968 | 9.692 | -0.197 | -0.197 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 47 | GLN | 0 | 0.040 | 0.016 | 5.056 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 48 | TRP | 0 | 0.036 | 0.026 | 4.895 | 0.021 | 0.047 | 0.000 | -0.003 | -0.023 | 0.000 |
50 | A | 49 | ALA | 0 | -0.009 | -0.003 | 7.138 | 0.110 | 0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 50 | ARG | 1 | 0.827 | 0.900 | 4.928 | 1.151 | 1.151 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 51 | ALA | 0 | 0.015 | 0.008 | 3.046 | -0.150 | 0.129 | 0.053 | -0.114 | -0.218 | -0.001 |
53 | A | 52 | ALA | 0 | 0.065 | 0.025 | 4.232 | 0.068 | 0.131 | 0.001 | -0.012 | -0.052 | 0.000 |
54 | A | 53 | ALA | 0 | -0.025 | -0.011 | 7.919 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 54 | VAL | 0 | -0.055 | -0.022 | 4.355 | -0.114 | -0.059 | 0.000 | -0.014 | -0.042 | 0.000 |
56 | A | 55 | LEU | 0 | 0.024 | 0.007 | 6.362 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 56 | ARG | 1 | 0.934 | 0.970 | 8.379 | -0.263 | -0.263 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 57 | LYS | 1 | 0.923 | 0.974 | 10.038 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 58 | GLU | -1 | -0.906 | -0.971 | 9.107 | 0.224 | 0.224 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 59 | LEU | 0 | 0.045 | 0.017 | 11.210 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 60 | GLU | -1 | -0.976 | -0.976 | 13.876 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 61 | GLN | 0 | -0.097 | -0.061 | 12.295 | -0.067 | -0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 62 | THR | 0 | -0.048 | -0.012 | 14.107 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 63 | NME | 0 | -0.007 | 0.015 | 16.875 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |