![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: JM889
Calculation Name: 2Z3X-A-Xray317
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2Z3X
Chain ID: A
UniProt ID: P02958
Base Structure: X-ray
Registration Date: 2021-09-07
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 | 57 |
LigandCharge | |
Software | ABINIT-MP - Open Ver.1 Rev. 15 / 20190524 |
Total energy (hartree)
FMO2-HF: Electronic energy | -243713.608178 |
---|---|
FMO2-HF: Nuclear repulsion | 222919.277463 |
FMO2-HF: Total energy | -20794.330715 |
FMO2-MP2: Total energy | -20854.476557 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F015993/ligand_interaction/ligand_F015993.png)
Ligand Interaction
![ligand interaction](./Kdata/F015993/ligand_interaction/ligand_interaction_F015993.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:2:ALA )
Summations of interaction energy for
fragment #1(A:2:ALA )
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. |
-0.017 | 1.221 | -0.006 | -0.548 | -0.684 | 0.002 |
Interaction energy analysis for fragmet #1(A:2:ALA )
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 | 4 | LEU | 0 | 0.041 | 0.028 | 3.811 | -0.686 | 0.552 | -0.006 | -0.548 | -0.684 | 0.002 |
4 | A | 5 | LEU | 0 | 0.032 | -0.001 | 6.304 | 0.432 | 0.432 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 6 | ILE | 0 | 0.043 | 0.022 | 9.548 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 7 | PRO | 0 | -0.028 | -0.017 | 8.328 | -0.121 | -0.121 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 8 | GLN | 0 | 0.040 | 0.016 | 9.621 | -0.069 | -0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 9 | ALA | 0 | 0.025 | 0.010 | 11.457 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 10 | ALA | 0 | -0.002 | 0.001 | 8.044 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 11 | SER | 0 | 0.083 | 0.033 | 9.170 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 12 | ALA | 0 | 0.014 | 0.011 | 11.971 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 13 | ILE | 0 | -0.031 | -0.022 | 6.461 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 14 | GLU | -1 | -0.956 | -0.970 | 9.155 | -0.723 | -0.723 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 15 | GLN | 0 | 0.029 | 0.003 | 10.121 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 16 | MET | 0 | -0.018 | 0.008 | 12.417 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 17 | LYS | 1 | 0.931 | 0.962 | 7.351 | 0.900 | 0.900 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 18 | LEU | 0 | -0.023 | -0.021 | 11.707 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 19 | GLU | -1 | -0.884 | -0.934 | 14.105 | -0.184 | -0.184 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 20 | ILE | 0 | -0.018 | -0.014 | 13.830 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 21 | ALA | 0 | -0.044 | -0.022 | 14.174 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 22 | SER | 0 | 0.004 | -0.002 | 16.096 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 23 | GLU | -1 | -0.893 | -0.932 | 19.470 | -0.167 | -0.167 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 24 | PHE | 0 | -0.097 | -0.056 | 17.543 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 25 | GLY | 0 | 0.001 | 0.021 | 20.188 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 26 | VAL | 0 | -0.088 | -0.033 | 15.598 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 27 | GLN | 0 | 0.028 | 0.008 | 17.171 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 28 | LEU | 0 | -0.023 | -0.007 | 10.866 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 29 | GLY | 0 | 0.040 | 0.016 | 12.945 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 30 | ALA | 0 | -0.018 | -0.014 | 13.217 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 31 | GLU | -1 | -0.914 | -0.956 | 14.006 | -0.120 | -0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 32 | THR | 0 | -0.067 | -0.023 | 15.325 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 33 | THR | 0 | 0.020 | 0.007 | 16.132 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 34 | SER | 0 | 0.055 | 0.007 | 14.277 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 35 | ARG | 1 | 0.985 | 0.998 | 14.631 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 36 | ALA | 0 | 0.024 | 0.019 | 16.475 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 37 | ASN | 0 | 0.048 | 0.028 | 11.583 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 38 | GLY | 0 | -0.007 | -0.007 | 11.952 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 39 | SER | 0 | -0.072 | -0.059 | 12.998 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 40 | VAL | 0 | 0.075 | 0.041 | 11.358 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 41 | GLY | 0 | 0.005 | 0.003 | 10.097 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 42 | GLY | 0 | -0.011 | -0.013 | 10.714 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 43 | GLU | -1 | -0.831 | -0.916 | 13.897 | -0.142 | -0.142 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 44 | ILE | 0 | -0.002 | 0.014 | 9.263 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 45 | THR | 0 | 0.006 | 0.003 | 11.424 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 46 | LYS | 1 | 0.937 | 0.985 | 13.425 | 0.135 | 0.135 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 47 | ARG | 1 | 0.806 | 0.873 | 16.236 | 0.223 | 0.223 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 48 | LEU | 0 | 0.013 | 0.007 | 11.654 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 49 | VAL | 0 | -0.001 | 0.007 | 15.979 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 50 | ARG | 1 | 0.942 | 0.967 | 18.132 | 0.113 | 0.113 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 51 | LEU | 0 | 0.001 | -0.005 | 17.794 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 52 | ALA | 0 | -0.008 | 0.010 | 18.825 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 53 | GLN | 0 | -0.023 | -0.027 | 20.814 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 54 | GLN | 0 | 0.015 | 0.010 | 23.757 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 55 | ASN | 0 | -0.046 | -0.007 | 23.330 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 56 | MET | 0 | -0.048 | -0.041 | 23.715 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 57 | GLY | 0 | -0.031 | -0.006 | 26.444 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 1 | NME | 0 | -0.021 | 0.006 | 28.824 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |