![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: VQ6J1
Calculation Name: 2A6Q-A-Xray372
Preferred Name: Antitoxin YefM
Target Type: SINGLE PROTEIN
Ligand Name:
ligand 3-letter code:
PDB ID: 2A6Q
Chain ID: A
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 | 86 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -464964.523368 |
---|---|
FMO2-HF: Nuclear repulsion | 430131.823562 |
FMO2-HF: Total energy | -34832.699806 |
FMO2-MP2: Total energy | -34930.107601 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F036024/ligand_interaction/ligand_F036024.png)
Ligand Interaction
![ligand interaction](./Kdata/F036024/ligand_interaction/ligand_interaction_F036024.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:7:GLY)
Summations of interaction energy for
fragment #1(A: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. |
-0.312 | 1.081 | 0.003 | -0.806 | -0.59 | 0.003 |
Interaction energy analysis for fragmet #1(A: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 | A | 9 | HIS | 0 | 0.031 | 0.021 | 3.565 | -0.980 | 0.413 | 0.003 | -0.806 | -0.590 | 0.003 |
4 | A | 10 | MET | 0 | -0.001 | 0.017 | 6.476 | 0.901 | 0.901 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 11 | ARG | 1 | 0.981 | 0.998 | 8.826 | 0.561 | 0.561 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 12 | THR | 0 | 0.013 | 0.008 | 8.386 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 13 | ILE | 0 | 0.023 | 0.016 | 11.413 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 14 | SER | 0 | 0.049 | 0.028 | 14.393 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 15 | TYR | 0 | 0.048 | 0.003 | 16.248 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 16 | SER | 0 | 0.000 | -0.018 | 18.378 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 17 | GLU | -1 | -0.913 | -0.937 | 19.172 | -0.240 | -0.240 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 18 | ALA | 0 | 0.055 | 0.020 | 18.302 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 19 | ARG | 1 | 0.907 | 0.952 | 20.391 | 0.110 | 0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 20 | GLN | 0 | -0.065 | -0.035 | 23.321 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 21 | ASN | 0 | -0.025 | -0.010 | 23.073 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 22 | LEU | 0 | 0.035 | 0.038 | 22.534 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 23 | SER | 0 | 0.012 | -0.005 | 24.060 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 24 | ALA | 0 | 0.078 | 0.030 | 24.723 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 25 | THR | 0 | -0.025 | -0.019 | 18.997 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 26 | MET | 0 | -0.040 | -0.028 | 21.071 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 27 | MET | 0 | 0.001 | -0.001 | 23.014 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 28 | LYS | 1 | 0.901 | 0.947 | 20.477 | 0.377 | 0.377 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 29 | ALA | 0 | -0.018 | 0.003 | 19.406 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 30 | VAL | 0 | -0.057 | -0.048 | 20.363 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 31 | GLU | -1 | -0.988 | -0.991 | 23.532 | -0.275 | -0.275 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 32 | ASP | -1 | -0.827 | -0.907 | 19.764 | -0.426 | -0.426 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 33 | HIS | 1 | 0.783 | 0.917 | 20.340 | 0.352 | 0.352 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 34 | ALA | 0 | 0.029 | 0.026 | 15.671 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 35 | PRO | 0 | -0.043 | -0.017 | 12.434 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 36 | ILE | 0 | -0.007 | -0.010 | 13.011 | -0.077 | -0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 37 | LEU | 0 | 0.002 | -0.012 | 7.597 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 38 | ILE | 0 | -0.008 | 0.001 | 11.676 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 39 | THR | 0 | 0.009 | -0.006 | 10.154 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 40 | ARG | 1 | 0.916 | 0.966 | 13.313 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 41 | GLN | 0 | -0.029 | -0.014 | 14.858 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 42 | ASN | 0 | -0.030 | -0.045 | 16.715 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 43 | GLY | 0 | 0.012 | 0.012 | 13.055 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 44 | GLU | -1 | -0.877 | -0.926 | 12.549 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 45 | ALA | 0 | 0.007 | -0.005 | 10.599 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 46 | CYS | 0 | -0.040 | -0.008 | 12.447 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 47 | VAL | 0 | 0.024 | 0.013 | 10.889 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 48 | LEU | 0 | -0.030 | -0.001 | 13.526 | 0.091 | 0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 49 | MET | 0 | 0.028 | 0.002 | 14.983 | -0.078 | -0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 50 | SER | 0 | 0.054 | 0.043 | 18.205 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 51 | LEU | 0 | 0.037 | 0.009 | 21.308 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 52 | GLU | -1 | -0.910 | -0.957 | 23.575 | -0.309 | -0.309 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 53 | GLU | -1 | -0.874 | -0.946 | 18.803 | -0.520 | -0.520 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 54 | TYR | 0 | -0.038 | -0.023 | 18.514 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 55 | ASN | 0 | 0.017 | -0.011 | 20.280 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 56 | SER | 0 | -0.011 | 0.020 | 21.482 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 57 | LEU | 0 | 0.016 | 0.006 | 14.870 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 58 | GLU | -1 | -0.862 | -0.939 | 19.199 | -0.289 | -0.289 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 59 | GLU | -1 | -0.854 | -0.929 | 20.888 | -0.203 | -0.203 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 60 | THR | 0 | -0.065 | -0.037 | 19.497 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 61 | ALA | 0 | -0.030 | -0.025 | 18.328 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 62 | TYR | 0 | -0.036 | -0.015 | 20.079 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 63 | LEU | 0 | -0.013 | -0.002 | 23.628 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 64 | LEU | 0 | -0.034 | -0.020 | 19.531 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 65 | ARG | 1 | 0.864 | 0.943 | 19.157 | 0.277 | 0.277 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 66 | SER | 0 | -0.006 | 0.006 | 22.482 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 67 | PRO | 0 | 0.058 | 0.017 | 23.733 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 68 | ALA | 0 | -0.011 | -0.008 | 25.460 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 69 | ASN | 0 | -0.038 | -0.027 | 27.140 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 70 | ALA | 0 | 0.055 | 0.032 | 23.257 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 71 | ARG | 1 | 0.944 | 0.978 | 25.306 | 0.081 | 0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 72 | ARG | 1 | 0.976 | 0.984 | 27.236 | 0.101 | 0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 73 | LEU | 0 | 0.016 | 0.017 | 25.760 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 74 | MET | 0 | 0.021 | -0.004 | 23.552 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 75 | ASP | -1 | -0.873 | -0.922 | 26.624 | -0.118 | -0.118 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 76 | SER | 0 | -0.066 | -0.039 | 29.942 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 77 | ILE | 0 | -0.008 | -0.012 | 26.495 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 78 | ASP | -1 | -0.904 | -0.941 | 26.953 | -0.178 | -0.178 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 79 | SER | 0 | -0.059 | -0.039 | 29.497 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 80 | LEU | 0 | -0.005 | -0.011 | 32.027 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 81 | LYS | 1 | 0.932 | 0.975 | 24.699 | 0.252 | 0.252 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 82 | SER | 0 | -0.084 | -0.038 | 31.550 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 83 | GLY | 0 | 0.001 | 0.008 | 33.753 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 84 | LYS | 1 | 0.898 | 0.949 | 35.770 | 0.103 | 0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 85 | GLY | 0 | -0.002 | 0.011 | 38.052 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 86 | THR | 0 | -0.040 | -0.026 | 38.626 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 87 | GLU | -1 | -0.934 | -0.957 | 41.834 | -0.089 | -0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 88 | LYS | 1 | 0.879 | 0.919 | 43.924 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 89 | ASP | -1 | -0.828 | -0.895 | 44.799 | -0.083 | -0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 90 | ILE | 0 | -0.057 | -0.034 | 44.400 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 91 | ILE | 0 | -0.072 | -0.034 | 46.830 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 92 | GLU | -1 | -0.955 | -0.971 | 49.167 | -0.071 | -0.071 | 0.000 | 0.000 | 0.000 | 0.000 |