![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: VRLV1
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 | OptAll |
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 | -396093.297941 |
---|---|
FMO2-HF: Nuclear repulsion | 369511.971603 |
FMO2-HF: Total energy | -26581.326338 |
FMO2-MP2: Total energy | -26658.27571 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F021729/ligand_interaction/ligand_F021729.png)
Ligand Interaction
![ligand interaction](./Kdata/F021729/ligand_interaction/ligand_interaction_F021729.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. |
-10.715 | -2.383 | 7.751 | -7.84 | -8.241 | -0.037 |
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 | -0.034 | -0.028 | 3.124 | -1.220 | 1.847 | -0.011 | -1.596 | -1.461 | -0.002 |
4 | A | 4 | PHE | 0 | 0.122 | 0.049 | 3.803 | 0.081 | 0.420 | 0.002 | -0.128 | -0.213 | -0.001 |
5 | A | 5 | TYR | 0 | 0.043 | 0.028 | 6.400 | 0.083 | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | ASP | -1 | -0.753 | -0.882 | 1.779 | -7.348 | -6.095 | 7.334 | -4.829 | -3.757 | -0.036 |
7 | A | 7 | VAL | 0 | 0.014 | 0.008 | 3.449 | -0.416 | 0.329 | 0.064 | -0.209 | -0.600 | 0.001 |
8 | A | 8 | GLN | 0 | 0.022 | 0.012 | 4.875 | -0.293 | -0.285 | -0.001 | -0.006 | -0.001 | 0.000 |
9 | A | 9 | GLN | 0 | -0.025 | 0.000 | 6.426 | 0.101 | 0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | LEU | 0 | -0.010 | 0.004 | 4.552 | -0.009 | 0.095 | -0.001 | -0.005 | -0.097 | 0.000 |
11 | A | 11 | LEU | 0 | 0.049 | 0.016 | 6.692 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | LYS | 1 | 0.913 | 0.964 | 9.720 | 0.272 | 0.272 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | THR | 0 | -0.127 | -0.064 | 9.533 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | PHE | 0 | -0.019 | -0.015 | 9.750 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | GLY | 0 | -0.005 | 0.008 | 13.984 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | HIS | 0 | -0.043 | -0.031 | 12.821 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | ILE | 0 | -0.066 | -0.039 | 13.185 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | VAL | 0 | -0.020 | 0.004 | 14.759 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | TYR | 0 | -0.042 | -0.030 | 15.202 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | PHE | 0 | -0.059 | -0.037 | 17.535 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | GLY | 0 | -0.025 | 0.002 | 19.260 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | ASP | -1 | -0.865 | -0.931 | 19.313 | 0.159 | 0.159 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | ARG | 1 | 0.890 | 0.945 | 11.377 | -0.198 | -0.198 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | GLU | -1 | -0.888 | -0.936 | 15.143 | 0.287 | 0.287 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | LEU | 0 | 0.045 | 0.017 | 16.763 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | GLU | -1 | -0.849 | -0.940 | 14.029 | 0.173 | 0.173 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | ILE | 0 | -0.033 | -0.021 | 11.296 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | GLU | -1 | -0.932 | -0.964 | 13.317 | 0.350 | 0.350 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | PHE | 0 | 0.001 | 0.000 | 14.907 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | MET | 0 | -0.043 | -0.023 | 8.653 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | LEU | 0 | -0.011 | -0.009 | 10.946 | 0.129 | 0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | ASP | -1 | -0.843 | -0.907 | 12.646 | 0.302 | 0.302 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | GLU | -1 | -0.819 | -0.910 | 13.379 | 0.201 | 0.201 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | LEU | 0 | -0.041 | -0.020 | 7.442 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | LYS | 1 | 0.747 | 0.872 | 11.553 | -0.322 | -0.322 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | GLU | -1 | -0.806 | -0.918 | 14.665 | 0.181 | 0.181 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | LEU | 0 | -0.005 | -0.001 | 11.494 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | TYR | 0 | -0.037 | -0.020 | 12.733 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | MET | 0 | -0.057 | -0.021 | 14.450 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | ASN | 0 | -0.091 | -0.047 | 17.487 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | HIS | 0 | -0.048 | -0.029 | 16.654 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | MET | 0 | -0.034 | -0.003 | 14.541 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | ILE | 0 | -0.036 | -0.004 | 9.171 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | GLU | -1 | -0.860 | -0.912 | 9.893 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | LYS | 1 | 0.876 | 0.913 | 10.680 | -0.130 | -0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | GLU | -1 | -0.825 | -0.902 | 8.573 | 0.380 | 0.380 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | GLN | 0 | -0.047 | -0.045 | 6.118 | 0.238 | 0.238 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | TRP | 0 | 0.021 | 0.018 | 6.415 | 0.723 | 0.723 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | ALA | 0 | 0.014 | 0.008 | 8.700 | 0.270 | 0.270 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | ARG | 1 | 0.832 | 0.909 | 2.953 | -1.842 | 0.073 | 0.323 | -0.761 | -1.477 | 0.000 |
51 | A | 51 | ALA | 0 | 0.031 | 0.009 | 4.452 | 0.925 | 1.057 | -0.001 | -0.035 | -0.096 | 0.000 |
52 | A | 52 | ALA | 0 | 0.055 | 0.024 | 5.389 | -0.410 | -0.394 | -0.001 | -0.001 | -0.013 | 0.000 |
53 | A | 53 | ALA | 0 | -0.019 | -0.009 | 7.555 | -0.228 | -0.228 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | VAL | 0 | -0.065 | -0.024 | 3.473 | -1.568 | -0.815 | 0.043 | -0.270 | -0.526 | 0.001 |
55 | A | 55 | LEU | 0 | 0.017 | 0.007 | 6.583 | -0.571 | -0.571 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | ARG | 1 | 0.856 | 0.909 | 8.854 | -0.740 | -0.740 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | LYS | 1 | 0.872 | 0.938 | 7.758 | -0.353 | -0.353 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | GLU | -1 | -0.878 | -0.948 | 8.879 | 0.109 | 0.109 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | LEU | 0 | 0.040 | 0.036 | 10.880 | -0.093 | -0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 60 | GLU | -1 | -0.840 | -0.891 | 14.134 | 0.285 | 0.285 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | GLN | 0 | -0.099 | -0.035 | 10.281 | -0.063 | -0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | THR | 0 | -0.098 | -0.062 | 14.256 | -0.070 | -0.070 | 0.000 | 0.000 | 0.000 | 0.000 |