![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 1N38Z
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 | 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 | 86 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -465273.884717 |
---|---|
FMO2-HF: Nuclear repulsion | 430440.681694 |
FMO2-HF: Total energy | -34833.203022 |
FMO2-MP2: Total energy | -34930.588408 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F036023/ligand_interaction/ligand_F036023.png)
Ligand Interaction
![ligand interaction](./Kdata/F036023/ligand_interaction/ligand_interaction_F036023.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. |
-0.102 | 1.403 | 0.011 | -0.87 | -0.646 | 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 | 0.021 | 0.016 | 3.329 | -0.694 | 0.811 | 0.011 | -0.870 | -0.646 | 0.003 |
4 | A | 10 | MET | 0 | -0.008 | 0.011 | 6.480 | 0.887 | 0.887 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 11 | ARG | 1 | 0.994 | 1.007 | 8.828 | 0.524 | 0.524 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 12 | THR | 0 | 0.031 | 0.016 | 8.422 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 13 | ILE | 0 | -0.027 | -0.008 | 11.415 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 14 | SER | 0 | 0.053 | 0.030 | 14.394 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 15 | TYR | 0 | 0.060 | 0.008 | 16.249 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 16 | SER | 0 | 0.002 | -0.014 | 18.379 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 17 | GLU | -1 | -0.909 | -0.938 | 18.662 | -0.248 | -0.248 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 18 | ALA | 0 | 0.056 | 0.026 | 18.286 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 19 | ARG | 1 | 0.916 | 0.948 | 20.393 | 0.111 | 0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 20 | GLN | 0 | -0.063 | -0.028 | 23.322 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 21 | ASN | 0 | -0.034 | -0.018 | 23.158 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 22 | LEU | 0 | 0.035 | 0.047 | 22.525 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 23 | SER | 0 | 0.045 | 0.007 | 24.062 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 24 | ALA | 0 | 0.032 | 0.013 | 24.783 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 25 | THR | 0 | -0.019 | -0.027 | 19.002 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 26 | MET | 0 | -0.037 | -0.024 | 21.073 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 27 | MET | 0 | 0.000 | -0.001 | 23.016 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 28 | LYS | 1 | 0.839 | 0.931 | 20.788 | 0.349 | 0.349 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 29 | ALA | 0 | 0.005 | 0.012 | 19.340 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 30 | VAL | 0 | -0.052 | -0.046 | 20.363 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 31 | GLU | -1 | -0.917 | -0.947 | 23.532 | -0.281 | -0.281 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 32 | ASP | -1 | -0.871 | -0.952 | 19.838 | -0.411 | -0.411 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 33 | HIS | 1 | 0.763 | 0.893 | 20.340 | 0.346 | 0.346 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 34 | ALA | 0 | 0.022 | 0.022 | 15.718 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 35 | PRO | 0 | -0.039 | -0.015 | 12.342 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 36 | ILE | 0 | -0.016 | -0.015 | 13.012 | -0.074 | -0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 37 | LEU | 0 | 0.004 | -0.010 | 7.598 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 38 | ILE | 0 | -0.009 | -0.001 | 11.678 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 39 | THR | 0 | 0.021 | 0.007 | 10.088 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 40 | ARG | 1 | 0.860 | 0.920 | 13.314 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 41 | GLN | 0 | -0.023 | -0.013 | 14.857 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 42 | ASN | 0 | -0.043 | -0.037 | 16.653 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 43 | GLY | 0 | 0.012 | 0.016 | 13.053 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 44 | GLU | -1 | -0.830 | -0.910 | 12.548 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 45 | ALA | 0 | 0.008 | -0.001 | 10.608 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 46 | CYS | 0 | -0.038 | -0.007 | 12.445 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 47 | VAL | 0 | 0.027 | 0.015 | 10.870 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 48 | LEU | 0 | -0.036 | -0.003 | 13.524 | 0.089 | 0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 49 | MET | 0 | 0.031 | 0.000 | 14.751 | -0.073 | -0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 50 | SER | 0 | 0.055 | 0.043 | 18.205 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 51 | LEU | 0 | 0.038 | 0.008 | 21.308 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 52 | GLU | -1 | -0.897 | -0.950 | 23.573 | -0.302 | -0.302 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 53 | GLU | -1 | -0.842 | -0.913 | 18.805 | -0.488 | -0.488 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 54 | TYR | 0 | -0.047 | -0.025 | 18.355 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 55 | ASN | 0 | 0.003 | -0.019 | 20.278 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 56 | SER | 0 | 0.004 | 0.026 | 21.371 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 57 | LEU | 0 | 0.010 | 0.006 | 14.733 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 58 | GLU | -1 | -0.821 | -0.895 | 19.196 | -0.287 | -0.287 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 59 | GLU | -1 | -0.863 | -0.937 | 20.886 | -0.198 | -0.198 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 60 | THR | 0 | -0.053 | -0.036 | 19.548 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 61 | ALA | 0 | -0.026 | -0.020 | 18.304 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 62 | TYR | 0 | -0.049 | -0.019 | 20.083 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 63 | LEU | 0 | -0.009 | 0.003 | 23.626 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 64 | LEU | 0 | -0.035 | -0.019 | 19.672 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 65 | ARG | 1 | 0.837 | 0.909 | 19.461 | 0.271 | 0.271 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 66 | SER | 0 | 0.000 | 0.008 | 22.483 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 67 | PRO | 0 | 0.062 | 0.018 | 23.837 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 68 | ALA | 0 | -0.015 | -0.009 | 25.460 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 69 | ASN | 0 | -0.044 | -0.035 | 26.992 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 70 | ALA | 0 | 0.057 | 0.033 | 23.242 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 71 | ARG | 1 | 0.926 | 0.970 | 25.308 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 72 | ARG | 1 | 0.972 | 0.983 | 27.238 | 0.101 | 0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 73 | LEU | 0 | 0.030 | 0.026 | 25.553 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 74 | MET | 0 | 0.013 | 0.000 | 23.353 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 75 | ASP | -1 | -0.886 | -0.942 | 26.626 | -0.116 | -0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 76 | SER | 0 | -0.024 | -0.020 | 29.944 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 77 | ILE | 0 | -0.028 | -0.020 | 26.244 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 78 | ASP | -1 | -0.831 | -0.900 | 26.791 | -0.191 | -0.191 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 79 | SER | 0 | -0.044 | -0.023 | 29.500 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 80 | LEU | 0 | -0.003 | -0.012 | 32.040 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 81 | LYS | 1 | 0.863 | 0.940 | 24.758 | 0.228 | 0.228 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 82 | SER | 0 | -0.103 | -0.060 | 31.555 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 83 | GLY | 0 | 0.011 | 0.012 | 33.758 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 84 | LYS | 1 | 0.892 | 0.948 | 35.080 | 0.106 | 0.106 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 85 | GLY | 0 | -0.001 | 0.012 | 38.022 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 86 | THR | 0 | -0.048 | -0.033 | 38.630 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 87 | GLU | -1 | -0.924 | -0.950 | 41.839 | -0.089 | -0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 88 | LYS | 1 | 0.881 | 0.921 | 43.929 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 89 | ASP | -1 | -0.836 | -0.898 | 44.804 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 90 | ILE | 0 | -0.057 | -0.037 | 44.314 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 91 | ILE | 0 | -0.075 | -0.039 | 46.835 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 92 | GLU | -1 | -0.945 | -0.961 | 49.172 | -0.067 | -0.067 | 0.000 | 0.000 | 0.000 | 0.000 |