![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 5JQ4Z
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 | 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 | 58 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -286839.320606 |
---|---|
FMO2-HF: Nuclear repulsion | 262907.546604 |
FMO2-HF: Total energy | -23931.774002 |
FMO2-MP2: Total energy | -23997.920118 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F036026/ligand_interaction/ligand_F036026.png)
Ligand Interaction
![ligand interaction](./Kdata/F036026/ligand_interaction/ligand_interaction_F036026.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. |
-1.03 | 0.471 | -0.01 | -0.829 | -0.662 | 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 | -0.046 | -0.041 | 3.833 | -0.547 | 0.954 | -0.010 | -0.829 | -0.662 | 0.003 |
4 | B | 10 | MET | 0 | 0.010 | 0.017 | 6.761 | 0.384 | 0.384 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | B | 11 | ARG | 1 | 0.871 | 0.917 | 8.559 | 1.216 | 1.216 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | B | 12 | THR | 0 | -0.034 | -0.021 | 11.305 | 0.142 | 0.142 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | B | 13 | ILE | 0 | 0.041 | 0.033 | 12.211 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | B | 14 | SER | 0 | 0.038 | 0.044 | 14.771 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | B | 15 | TYR | 0 | 0.098 | 0.020 | 17.872 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | B | 16 | SER | 0 | -0.041 | -0.031 | 20.652 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | B | 17 | GLU | -1 | -0.880 | -0.942 | 13.752 | -0.208 | -0.208 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | B | 18 | ALA | 0 | 0.043 | 0.019 | 18.549 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | B | 19 | ARG | 1 | 0.801 | 0.904 | 19.380 | 0.086 | 0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | B | 20 | GLN | 0 | -0.017 | -0.018 | 20.889 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | B | 21 | ASN | 0 | 0.002 | 0.014 | 16.827 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | B | 22 | LEU | 0 | 0.027 | 0.042 | 18.242 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | B | 23 | SER | 0 | 0.044 | 0.012 | 20.068 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | B | 24 | ALA | 0 | 0.048 | 0.021 | 15.644 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | B | 25 | THR | 0 | -0.022 | -0.035 | 15.537 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | B | 26 | MET | 0 | -0.041 | -0.025 | 16.683 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | B | 27 | MET | 0 | 0.003 | 0.007 | 17.339 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | B | 28 | LYS | 1 | 0.872 | 0.946 | 9.485 | 1.448 | 1.448 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | B | 29 | ALA | 0 | -0.026 | -0.010 | 14.743 | -0.078 | -0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | B | 30 | VAL | 0 | -0.006 | -0.014 | 16.807 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | B | 31 | GLU | -1 | -0.952 | -0.975 | 14.180 | -0.613 | -0.613 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | B | 32 | ASP | -1 | -0.854 | -0.905 | 11.542 | -1.609 | -1.609 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | B | 33 | HIS | 0 | -0.035 | -0.002 | 14.631 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | B | 34 | ALA | 0 | 0.018 | 0.014 | 14.358 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | B | 35 | PRO | 0 | 0.043 | 0.034 | 16.364 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | B | 36 | ILE | 0 | -0.076 | -0.040 | 13.736 | -0.095 | -0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | B | 37 | LEU | 0 | -0.022 | -0.004 | 15.497 | 0.077 | 0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | B | 38 | ILE | 0 | 0.008 | -0.011 | 16.410 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | B | 39 | THR | 0 | 0.032 | 0.002 | 17.413 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | B | 40 | ARG | 1 | 0.945 | 0.953 | 19.761 | 0.123 | 0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | B | 41 | GLN | 0 | -0.049 | -0.011 | 22.888 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | B | 42 | ASN | 0 | 0.000 | -0.007 | 23.858 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | B | 43 | GLY | 0 | -0.019 | -0.008 | 27.370 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | B | 44 | GLU | -1 | -0.834 | -0.908 | 26.077 | -0.111 | -0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | B | 45 | ALA | 0 | -0.082 | -0.042 | 21.078 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | B | 46 | CYS | 0 | -0.021 | -0.009 | 22.085 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | B | 47 | VAL | 0 | 0.017 | 0.006 | 19.606 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | B | 48 | LEU | 0 | -0.033 | -0.003 | 18.999 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | B | 49 | MET | 0 | -0.008 | -0.001 | 19.327 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | B | 50 | SER | 0 | 0.026 | 0.030 | 21.080 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | B | 51 | LEU | 0 | 0.037 | 0.019 | 22.761 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | B | 52 | GLU | -1 | -0.885 | -0.957 | 24.413 | -0.309 | -0.309 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | B | 53 | GLU | -1 | -0.852 | -0.944 | 19.969 | -0.492 | -0.492 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | B | 54 | TYR | 0 | -0.102 | -0.077 | 23.960 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | B | 55 | ASN | 0 | 0.033 | -0.002 | 26.388 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | B | 56 | SER | 0 | 0.013 | 0.033 | 26.052 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | B | 57 | LEU | 0 | -0.005 | -0.008 | 24.507 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | B | 58 | GLU | -1 | -0.846 | -0.918 | 27.601 | -0.165 | -0.165 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | B | 59 | GLU | -1 | -0.931 | -0.972 | 31.116 | -0.203 | -0.203 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | B | 60 | THR | 0 | -0.078 | -0.040 | 28.957 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | B | 61 | ALA | 0 | -0.065 | -0.024 | 30.997 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | B | 62 | TYR | 0 | -0.031 | -0.009 | 32.656 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | B | 63 | LEU | 0 | -0.101 | -0.036 | 34.893 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | B | 64 | LEU | 0 | -0.063 | -0.027 | 35.164 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |