![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: R8K68
Calculation Name: 2A6Q-E-Xray372
Preferred Name: Antitoxin YefM
Target Type: SINGLE PROTEIN
Ligand Name:
ligand 3-letter code:
PDB ID: 2A6Q
Chain ID: E
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 | OptH |
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 | 84 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -644658.94741 |
---|---|
FMO2-HF: Nuclear repulsion | 609210.232796 |
FMO2-HF: Total energy | -35448.714614 |
FMO2-MP2: Total energy | -35553.639016 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F036030/ligand_interaction/ligand_F036030.png)
Ligand Interaction
![ligand interaction](./Kdata/F036030/ligand_interaction/ligand_interaction_F036030.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(E:1:MET)
Summations of interaction energy for
fragment #1(E:1:MET)
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. |
-18.475 | -14.275 | 18.602 | -5.779 | -17.021 | -0.032 |
Interaction energy analysis for fragmet #1(E:1:MET)
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 | E | 3 | LEU | 0 | -0.008 | -0.009 | 2.786 | -4.073 | -0.661 | 0.379 | -1.830 | -1.962 | -0.005 |
4 | E | 4 | ILE | 0 | 0.027 | 0.025 | 5.305 | -0.023 | 0.064 | -0.001 | -0.004 | -0.082 | 0.000 |
5 | E | 5 | TRP | 0 | -0.018 | -0.021 | 7.804 | 0.195 | 0.195 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | E | 6 | SER | 0 | 0.019 | 0.024 | 10.896 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | E | 7 | GLU | -1 | -0.873 | -0.953 | 14.191 | 0.098 | 0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | E | 8 | GLU | -1 | -0.857 | -0.928 | 17.271 | 0.097 | 0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | E | 9 | SER | 0 | -0.038 | -0.022 | 12.247 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | E | 10 | TRP | 0 | -0.014 | -0.009 | 12.884 | 0.071 | 0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | E | 11 | ASP | -1 | -0.826 | -0.913 | 15.526 | 0.163 | 0.163 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | E | 12 | ASP | -1 | -0.870 | -0.942 | 16.748 | 0.228 | 0.228 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | E | 13 | TYR | 0 | -0.081 | -0.087 | 13.565 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | E | 14 | LEU | 0 | 0.029 | 0.000 | 16.597 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | E | 15 | TYR | 0 | 0.045 | 0.032 | 19.316 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | E | 16 | TRP | 0 | -0.024 | -0.048 | 17.975 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | E | 17 | GLN | 0 | 0.001 | -0.011 | 17.266 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | E | 18 | GLU | -1 | -0.982 | -0.975 | 20.828 | 0.178 | 0.178 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | E | 19 | THR | 0 | -0.046 | -0.005 | 23.793 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | E | 20 | ASP | -1 | -0.860 | -0.956 | 23.634 | 0.207 | 0.207 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | E | 21 | LYS | 1 | 0.952 | 0.969 | 18.841 | -0.315 | -0.315 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | E | 22 | ARG | 1 | 0.940 | 0.968 | 20.942 | -0.183 | -0.183 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | E | 23 | ILE | 0 | -0.010 | -0.004 | 19.218 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | E | 24 | VAL | 0 | -0.016 | 0.028 | 16.862 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | E | 25 | LYS | 1 | 0.901 | 0.947 | 16.070 | -0.325 | -0.325 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | E | 26 | LYS | 1 | 0.912 | 0.969 | 15.904 | -0.270 | -0.270 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | E | 27 | ILE | 0 | 0.080 | 0.048 | 12.649 | 0.062 | 0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | E | 28 | ASN | 0 | 0.023 | 0.021 | 11.568 | 0.150 | 0.150 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | E | 29 | GLU | -1 | -0.915 | -0.942 | 10.853 | 0.666 | 0.666 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | E | 30 | LEU | 0 | -0.009 | 0.002 | 11.466 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | E | 31 | ILE | 0 | 0.030 | 0.041 | 6.693 | 0.215 | 0.215 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | E | 32 | LYS | 1 | 0.800 | 0.874 | 6.620 | -0.133 | -0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | E | 33 | ASP | -1 | -0.857 | -0.918 | 7.590 | 0.740 | 0.740 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | E | 34 | THR | 0 | -0.018 | -0.005 | 5.243 | -0.354 | -0.261 | -0.001 | -0.008 | -0.084 | 0.000 |
35 | E | 35 | ARG | 1 | 0.855 | 0.910 | 2.300 | -3.679 | -1.300 | 1.607 | -1.353 | -2.632 | 0.002 |
36 | E | 36 | ARG | 1 | 0.904 | 0.970 | 4.332 | -1.009 | -0.711 | 0.004 | 0.001 | -0.302 | 0.000 |
37 | E | 37 | THR | 0 | -0.011 | -0.022 | 7.060 | -0.414 | -0.414 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | E | 38 | PRO | 0 | 0.045 | 0.015 | 3.171 | -0.579 | 0.003 | 0.068 | -0.121 | -0.529 | 0.000 |
39 | E | 39 | PHE | 0 | 0.000 | -0.015 | 5.763 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | E | 40 | GLU | -1 | -0.912 | -0.937 | 8.927 | -0.124 | -0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | E | 41 | GLY | 0 | 0.044 | 0.043 | 10.958 | 0.158 | 0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | E | 42 | LYS | 1 | 0.917 | 0.939 | 13.532 | -0.523 | -0.523 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | E | 43 | GLY | 0 | 0.026 | 0.002 | 13.712 | 0.066 | 0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | E | 44 | LYS | 1 | 0.917 | 0.970 | 16.071 | -0.152 | -0.152 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | E | 45 | PRO | 0 | -0.004 | -0.004 | 11.729 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | E | 46 | GLU | -1 | -0.885 | -0.937 | 13.861 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | E | 47 | PRO | 0 | -0.018 | 0.015 | 13.514 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | E | 48 | LEU | 0 | -0.009 | -0.010 | 14.454 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | E | 49 | LYS | 1 | 0.969 | 0.969 | 16.619 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | E | 50 | HIS | 0 | 0.040 | 0.020 | 19.323 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | E | 51 | ASN | 0 | 0.041 | 0.018 | 19.564 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | E | 52 | LEU | 0 | 0.018 | 0.022 | 16.986 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | E | 53 | SER | 0 | -0.036 | -0.032 | 15.576 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | E | 54 | GLY | 0 | -0.008 | 0.001 | 12.138 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | E | 55 | PHE | 0 | -0.030 | -0.016 | 10.584 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | E | 56 | TRP | 0 | 0.001 | -0.003 | 9.876 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | E | 57 | SER | 0 | -0.008 | -0.003 | 12.061 | 0.092 | 0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | E | 58 | ARG | 1 | 0.812 | 0.918 | 9.044 | -0.845 | -0.845 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | E | 59 | ARG | 1 | 0.906 | 0.939 | 14.427 | -0.192 | -0.192 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | E | 60 | ILE | 0 | -0.028 | 0.014 | 15.503 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | E | 61 | THR | 0 | -0.013 | -0.024 | 18.100 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | E | 62 | GLU | -1 | -0.946 | -0.980 | 21.407 | 0.172 | 0.172 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | E | 63 | GLU | -1 | -0.843 | -0.877 | 23.690 | 0.123 | 0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | E | 64 | HIS | 0 | 0.064 | 0.042 | 19.664 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | E | 65 | ARG | 1 | 0.894 | 0.932 | 16.650 | -0.186 | -0.186 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | E | 66 | LEU | 0 | 0.006 | 0.011 | 9.747 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | E | 67 | VAL | 0 | -0.012 | -0.009 | 12.826 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | E | 68 | TYR | 0 | -0.001 | -0.016 | 7.078 | 0.124 | 0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | E | 69 | ALA | 0 | 0.071 | 0.049 | 8.318 | -0.153 | -0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | E | 70 | VAL | 0 | -0.028 | -0.024 | 2.462 | 0.533 | 0.274 | 2.379 | -0.446 | -1.674 | -0.003 |
71 | E | 71 | THR | 0 | 0.002 | 0.016 | 3.699 | -0.485 | -0.273 | 0.000 | -0.037 | -0.175 | 0.000 |
72 | E | 72 | ASP | -1 | -0.955 | -0.989 | 3.181 | -5.472 | -4.764 | 0.061 | -0.313 | -0.456 | -0.003 |
73 | E | 73 | ASP | -1 | -0.769 | -0.883 | 4.450 | -2.521 | -2.174 | -0.001 | -0.064 | -0.282 | 0.000 |
74 | E | 74 | SER | 0 | -0.119 | -0.079 | 1.843 | -2.439 | -2.989 | 8.815 | -4.765 | -3.499 | -0.013 |
75 | E | 75 | LEU | 0 | -0.001 | -0.011 | 2.503 | 2.357 | -0.409 | 5.218 | 2.669 | -5.121 | -0.011 |
76 | E | 76 | LEU | 0 | -0.020 | -0.002 | 3.620 | -0.729 | -1.072 | 0.074 | 0.492 | -0.223 | 0.001 |
77 | E | 77 | ILE | 0 | 0.007 | -0.004 | 7.260 | 0.175 | 0.175 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | E | 78 | ALA | 0 | 0.027 | 0.012 | 9.440 | -0.123 | -0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | E | 79 | ALA | 0 | 0.023 | 0.005 | 12.954 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | E | 80 | CYS | 0 | -0.083 | -0.023 | 13.785 | 0.092 | 0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | E | 81 | ARG | 1 | 0.934 | 0.986 | 15.650 | -0.171 | -0.171 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | E | 82 | TYR | 0 | -0.034 | -0.008 | 19.438 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | E | 83 | HIS | 0 | -0.044 | -0.039 | 20.736 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | E | 84 | TYR | 0 | -0.061 | -0.059 | 24.759 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |