![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: YY892
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 | OptHSide |
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 | -394068.336929 |
---|---|
FMO2-HF: Nuclear repulsion | 367487.15631 |
FMO2-HF: Total energy | -26581.180618 |
FMO2-MP2: Total energy | -26658.099291 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F021730/ligand_interaction/ligand_F021730.png)
Ligand Interaction
![ligand interaction](./Kdata/F021730/ligand_interaction/ligand_interaction_F021730.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. |
-9.869 | -1.158 | 3.296 | -5.482 | -6.527 | -0.02 |
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 | -0.007 | -0.002 | 3.589 | -2.494 | 1.476 | -0.041 | -2.034 | -1.896 | -0.006 |
4 | A | 4 | PHE | 0 | 0.116 | 0.042 | 4.209 | 0.051 | 0.187 | -0.001 | -0.031 | -0.105 | 0.000 |
5 | A | 5 | TYR | 0 | 0.025 | 0.013 | 6.707 | 0.105 | 0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | ASP | -1 | -0.799 | -0.902 | 2.044 | -5.529 | -3.805 | 3.124 | -2.425 | -2.423 | -0.016 |
7 | A | 7 | VAL | 0 | 0.017 | 0.007 | 3.788 | -0.184 | 0.322 | 0.013 | -0.101 | -0.417 | 0.000 |
8 | A | 8 | GLN | 0 | 0.023 | 0.009 | 4.824 | -0.266 | -0.240 | -0.001 | -0.004 | -0.021 | 0.000 |
9 | A | 9 | GLN | 0 | -0.017 | -0.001 | 6.579 | 0.108 | 0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | LEU | 0 | -0.011 | 0.006 | 4.574 | -0.032 | 0.067 | -0.001 | -0.003 | -0.094 | 0.000 |
11 | A | 11 | LEU | 0 | 0.061 | 0.011 | 6.832 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | LYS | 1 | 0.894 | 0.971 | 9.932 | 0.282 | 0.282 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | THR | 0 | -0.115 | -0.053 | 9.585 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | PHE | 0 | -0.037 | -0.029 | 9.720 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | GLY | 0 | 0.004 | 0.012 | 13.869 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | HIS | 0 | -0.032 | -0.017 | 13.471 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | ILE | 0 | -0.059 | -0.030 | 13.448 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | VAL | 0 | -0.028 | -0.012 | 14.610 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | TYR | 0 | -0.031 | -0.026 | 15.571 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | PHE | 0 | -0.040 | -0.028 | 18.082 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | GLY | 0 | -0.027 | 0.003 | 19.694 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | ASP | -1 | -0.868 | -0.938 | 19.708 | 0.136 | 0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | ARG | 1 | 0.876 | 0.927 | 12.071 | -0.147 | -0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | GLU | -1 | -0.898 | -0.945 | 15.572 | 0.248 | 0.248 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | LEU | 0 | 0.047 | 0.024 | 17.230 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | GLU | -1 | -0.862 | -0.939 | 14.573 | 0.140 | 0.140 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | ILE | 0 | -0.046 | -0.032 | 11.633 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | GLU | -1 | -0.918 | -0.955 | 13.570 | 0.330 | 0.330 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | PHE | 0 | 0.008 | 0.007 | 15.234 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | MET | 0 | -0.039 | -0.028 | 8.916 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | LEU | 0 | -0.016 | -0.010 | 11.298 | 0.108 | 0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | ASP | -1 | -0.857 | -0.913 | 13.181 | 0.307 | 0.307 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | GLU | -1 | -0.861 | -0.931 | 13.397 | 0.209 | 0.209 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | LEU | 0 | -0.040 | -0.022 | 7.829 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | LYS | 1 | 0.847 | 0.915 | 11.729 | -0.331 | -0.331 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | GLU | -1 | -0.840 | -0.926 | 14.666 | 0.165 | 0.165 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | LEU | 0 | -0.003 | 0.007 | 11.385 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | TYR | 0 | -0.041 | -0.026 | 12.657 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | MET | 0 | -0.068 | -0.024 | 14.340 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | ASN | 0 | -0.102 | -0.056 | 17.368 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | HIS | 0 | -0.042 | -0.022 | 16.591 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | MET | 0 | -0.038 | -0.011 | 14.449 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | ILE | 0 | -0.032 | -0.006 | 9.146 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | GLU | -1 | -0.871 | -0.919 | 9.967 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | LYS | 1 | 0.910 | 0.931 | 10.550 | -0.163 | -0.163 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | GLU | -1 | -0.845 | -0.915 | 8.432 | 0.441 | 0.441 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | GLN | 0 | -0.043 | -0.036 | 5.987 | 0.302 | 0.302 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | TRP | 0 | 0.029 | 0.025 | 6.328 | 0.835 | 0.835 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | ALA | 0 | -0.006 | -0.003 | 8.858 | 0.220 | 0.220 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | ARG | 1 | 0.833 | 0.906 | 3.083 | -2.235 | -0.557 | 0.191 | -0.682 | -1.187 | 0.001 |
51 | A | 51 | ALA | 0 | 0.026 | 0.013 | 4.694 | 0.872 | 0.953 | -0.001 | -0.017 | -0.063 | 0.000 |
52 | A | 52 | ALA | 0 | 0.057 | 0.021 | 5.635 | -0.433 | -0.424 | -0.001 | 0.000 | -0.009 | 0.000 |
53 | A | 53 | ALA | 0 | -0.021 | -0.007 | 7.529 | -0.243 | -0.243 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | VAL | 0 | -0.057 | -0.024 | 3.664 | -1.163 | -0.681 | 0.014 | -0.185 | -0.312 | 0.001 |
55 | A | 55 | LEU | 0 | 0.019 | 0.006 | 6.916 | -0.521 | -0.521 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | ARG | 1 | 0.885 | 0.935 | 9.276 | -0.702 | -0.702 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | LYS | 1 | 0.876 | 0.932 | 9.137 | -0.335 | -0.335 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | GLU | -1 | -0.888 | -0.945 | 9.349 | 0.071 | 0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | LEU | 0 | 0.020 | 0.004 | 11.364 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 60 | GLU | -1 | -0.901 | -0.935 | 14.446 | 0.239 | 0.239 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | GLN | 0 | -0.066 | -0.015 | 11.056 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | THR | 0 | -0.064 | -0.011 | 14.497 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |