![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: YVMJ2
Calculation Name: 2A6Q-B-Xray372
Preferred Name: Antitoxin YefM
Target Type: SINGLE PROTEIN
Ligand Name:
ligand 3-letter code:
PDB ID: 2A6Q
Chain ID: B
ChEMBL ID: CHEMBL3309007
UniProt ID: P69346
Base Structure: X-ray
Registration Date: 2023-09-23
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 | 58 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -286503.025528 |
---|---|
FMO2-HF: Nuclear repulsion | 262571.035899 |
FMO2-HF: Total energy | -23931.989629 |
FMO2-MP2: Total energy | -23998.113504 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F036025/ligand_interaction/ligand_F036025.png)
Ligand Interaction
![ligand interaction](./Kdata/F036025/ligand_interaction/ligand_interaction_F036025.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(B:7:GLY)
Summations of interaction energy for
fragment #1(B:7:GLY)
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. |
-0.241 | 1.061 | -0.006 | -0.68 | -0.617 | 0.003 |
Interaction energy analysis for fragmet #1(B:7:GLY)
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 | B | 9 | HIS | 0 | -0.022 | -0.032 | 3.874 | -0.254 | 1.048 | -0.006 | -0.680 | -0.617 | 0.003 |
4 | B | 10 | MET | 0 | -0.034 | -0.009 | 6.673 | 0.638 | 0.638 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | B | 11 | ARG | 1 | 0.887 | 0.920 | 8.284 | 1.405 | 1.405 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | B | 12 | THR | 0 | -0.027 | -0.007 | 11.197 | 0.139 | 0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | B | 13 | ILE | 0 | 0.033 | 0.034 | 11.868 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | B | 14 | SER | 0 | -0.005 | 0.002 | 14.441 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | B | 15 | TYR | 0 | 0.054 | 0.008 | 17.416 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | B | 16 | SER | 0 | -0.035 | -0.028 | 20.857 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | B | 17 | GLU | -1 | -0.798 | -0.890 | 13.490 | -0.195 | -0.195 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | B | 18 | ALA | 0 | 0.058 | 0.028 | 18.450 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | B | 19 | ARG | 1 | 0.805 | 0.902 | 19.216 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | B | 20 | GLN | 0 | -0.010 | -0.005 | 20.643 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | B | 21 | ASN | 0 | -0.002 | -0.001 | 16.285 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | B | 22 | LEU | 0 | 0.014 | 0.035 | 17.857 | -0.055 | -0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | B | 23 | SER | 0 | 0.035 | 0.012 | 19.627 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | B | 24 | ALA | 0 | 0.054 | 0.021 | 15.132 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | B | 25 | THR | 0 | -0.039 | -0.033 | 15.147 | -0.083 | -0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | B | 26 | MET | 0 | -0.033 | -0.021 | 16.361 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | B | 27 | MET | 0 | -0.003 | 0.012 | 17.213 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | B | 28 | LYS | 1 | 0.870 | 0.937 | 9.157 | 1.507 | 1.507 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | B | 29 | ALA | 0 | -0.016 | -0.009 | 14.492 | -0.085 | -0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | B | 30 | VAL | 0 | -0.001 | 0.000 | 16.642 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | B | 31 | GLU | -1 | -0.938 | -0.980 | 13.961 | -0.581 | -0.581 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | B | 32 | ASP | -1 | -0.845 | -0.895 | 11.217 | -1.651 | -1.651 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | B | 33 | HIS | 0 | -0.062 | -0.019 | 14.216 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | B | 34 | ALA | 0 | 0.027 | 0.024 | 14.405 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | B | 35 | PRO | 0 | 0.024 | 0.026 | 15.784 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | B | 36 | ILE | 0 | -0.055 | -0.032 | 13.173 | -0.114 | -0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | B | 37 | LEU | 0 | -0.022 | -0.008 | 15.378 | 0.081 | 0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | B | 38 | ILE | 0 | 0.010 | -0.003 | 16.320 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | B | 39 | THR | 0 | 0.008 | -0.011 | 17.124 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | B | 40 | ARG | 1 | 0.927 | 0.949 | 19.480 | 0.130 | 0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | B | 41 | GLN | 0 | -0.026 | -0.006 | 22.638 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | B | 42 | ASN | 0 | -0.012 | -0.020 | 23.835 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | B | 43 | GLY | 0 | 0.013 | 0.010 | 26.272 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | B | 44 | GLU | -1 | -0.876 | -0.928 | 25.613 | -0.124 | -0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | B | 45 | ALA | 0 | -0.050 | -0.020 | 20.932 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | B | 46 | CYS | 0 | -0.035 | -0.023 | 21.850 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | B | 47 | VAL | 0 | 0.000 | -0.006 | 19.372 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | B | 48 | LEU | 0 | -0.030 | -0.004 | 18.727 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | B | 49 | MET | 0 | -0.017 | -0.004 | 18.739 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | B | 50 | SER | 0 | 0.009 | 0.005 | 20.566 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | B | 51 | LEU | 0 | 0.009 | 0.005 | 22.196 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | B | 52 | GLU | -1 | -0.875 | -0.952 | 24.281 | -0.305 | -0.305 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | B | 53 | GLU | -1 | -0.789 | -0.894 | 19.795 | -0.500 | -0.500 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | B | 54 | TYR | 0 | -0.096 | -0.072 | 23.825 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | B | 55 | ASN | 0 | 0.003 | -0.005 | 26.177 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | B | 56 | SER | 0 | 0.044 | 0.038 | 26.036 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | B | 57 | LEU | 0 | -0.007 | 0.004 | 24.615 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | B | 58 | GLU | -1 | -0.805 | -0.883 | 27.531 | -0.163 | -0.163 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | B | 59 | GLU | -1 | -0.939 | -0.978 | 31.010 | -0.205 | -0.205 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | B | 60 | THR | 0 | -0.073 | -0.049 | 28.848 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | B | 61 | ALA | 0 | -0.047 | -0.023 | 31.130 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | B | 62 | TYR | 0 | -0.112 | -0.067 | 32.708 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | B | 63 | LEU | 0 | -0.067 | -0.022 | 34.819 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | B | 64 | LEU | 0 | -0.080 | -0.030 | 35.062 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |