![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: QV4ZY
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 | 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 | 84 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -643904.607458 |
---|---|
FMO2-HF: Nuclear repulsion | 608455.366849 |
FMO2-HF: Total energy | -35449.240609 |
FMO2-MP2: Total energy | -35554.12205 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F036029/ligand_interaction/ligand_F036029.png)
Ligand Interaction
![ligand interaction](./Kdata/F036029/ligand_interaction/ligand_interaction_F036029.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. |
-27.117 | -19.989 | 13.804 | -5.504 | -15.428 | -0.022 |
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 | -0.010 | -0.008 | 2.972 | -2.276 | 0.649 | 0.170 | -1.453 | -1.642 | -0.005 |
4 | E | 4 | ILE | 0 | 0.018 | 0.018 | 5.527 | -0.157 | -0.157 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | E | 5 | TRP | 0 | -0.010 | -0.018 | 7.978 | 0.355 | 0.355 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | E | 6 | SER | 0 | -0.013 | -0.020 | 11.087 | -0.083 | -0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | E | 7 | GLU | -1 | -0.875 | -0.952 | 14.360 | 0.114 | 0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | E | 8 | GLU | -1 | -0.816 | -0.883 | 17.487 | 0.181 | 0.181 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | E | 9 | SER | 0 | -0.046 | -0.036 | 12.544 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | E | 10 | TRP | 0 | -0.013 | -0.007 | 13.311 | 0.107 | 0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | E | 11 | ASP | -1 | -0.831 | -0.916 | 15.745 | 0.237 | 0.237 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | E | 12 | ASP | -1 | -0.832 | -0.923 | 16.921 | 0.412 | 0.412 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | E | 13 | TYR | 0 | -0.069 | -0.085 | 14.018 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | E | 14 | LEU | 0 | 0.015 | -0.001 | 16.825 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | E | 15 | TYR | 0 | 0.040 | 0.027 | 19.551 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | E | 16 | TRP | 0 | -0.012 | -0.039 | 18.235 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | E | 17 | GLN | 0 | -0.029 | -0.008 | 17.121 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | E | 18 | GLU | -1 | -0.986 | -0.977 | 21.062 | 0.246 | 0.246 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | E | 19 | THR | 0 | -0.038 | -0.008 | 24.025 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | E | 20 | ASP | -1 | -0.803 | -0.914 | 23.856 | 0.365 | 0.365 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | E | 21 | LYS | 1 | 0.944 | 0.963 | 19.972 | -0.452 | -0.452 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | E | 22 | ARG | 1 | 0.856 | 0.915 | 20.982 | -0.313 | -0.313 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | E | 23 | ILE | 0 | -0.019 | -0.012 | 19.507 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | E | 24 | VAL | 0 | 0.015 | 0.036 | 16.871 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | E | 25 | LYS | 1 | 0.923 | 0.958 | 16.111 | -0.533 | -0.533 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | E | 26 | LYS | 1 | 0.883 | 0.950 | 15.935 | -0.490 | -0.490 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | E | 27 | ILE | 0 | 0.074 | 0.046 | 13.053 | 0.123 | 0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | E | 28 | ASN | 0 | 0.032 | 0.027 | 11.609 | 0.238 | 0.238 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | E | 29 | GLU | -1 | -0.865 | -0.919 | 10.881 | 1.458 | 1.458 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | E | 30 | LEU | 0 | 0.008 | 0.006 | 11.482 | 0.167 | 0.167 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | E | 31 | ILE | 0 | 0.036 | 0.045 | 6.771 | 0.338 | 0.338 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | E | 32 | LYS | 1 | 0.824 | 0.888 | 6.644 | -0.430 | -0.430 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | E | 33 | ASP | -1 | -0.860 | -0.932 | 7.587 | 1.616 | 1.616 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | E | 34 | THR | 0 | -0.016 | -0.013 | 5.180 | -0.429 | -0.331 | -0.001 | -0.009 | -0.087 | 0.000 |
35 | E | 35 | ARG | 1 | 0.867 | 0.924 | 2.180 | -10.403 | -8.013 | 2.078 | -1.605 | -2.863 | 0.008 |
36 | E | 36 | ARG | 1 | 0.906 | 0.969 | 4.328 | -1.750 | -1.450 | 0.010 | 0.036 | -0.346 | 0.000 |
37 | E | 37 | THR | 0 | 0.003 | -0.008 | 6.881 | -0.696 | -0.696 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | E | 38 | PRO | 0 | 0.049 | 0.017 | 2.759 | -0.807 | -0.086 | 0.358 | -0.194 | -0.886 | -0.001 |
39 | E | 39 | PHE | 0 | -0.003 | -0.010 | 5.318 | -0.020 | 0.035 | -0.001 | -0.002 | -0.052 | 0.000 |
40 | E | 40 | GLU | -1 | -0.910 | -0.938 | 8.551 | 0.106 | 0.106 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | E | 41 | GLY | 0 | 0.031 | 0.026 | 10.459 | 0.246 | 0.246 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | E | 42 | LYS | 1 | 0.823 | 0.909 | 12.990 | -1.329 | -1.329 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | E | 43 | GLY | 0 | 0.021 | 0.003 | 13.564 | 0.095 | 0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | E | 44 | LYS | 1 | 0.928 | 0.974 | 15.937 | -0.347 | -0.347 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | E | 45 | PRO | 0 | 0.004 | 0.006 | 11.346 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | E | 46 | GLU | -1 | -0.911 | -0.949 | 13.524 | 0.153 | 0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | E | 47 | PRO | 0 | -0.010 | 0.018 | 13.334 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | E | 48 | LEU | 0 | -0.022 | -0.015 | 14.328 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | E | 49 | LYS | 1 | 0.971 | 0.970 | 16.599 | -0.075 | -0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | E | 50 | HIS | 0 | 0.051 | 0.025 | 19.353 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | E | 51 | ASN | 0 | 0.046 | 0.028 | 19.716 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | E | 52 | LEU | 0 | 0.014 | 0.017 | 17.167 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | E | 53 | SER | 0 | -0.035 | -0.035 | 15.687 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | E | 54 | GLY | 0 | -0.009 | 0.000 | 12.283 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | E | 55 | PHE | 0 | -0.038 | -0.018 | 10.714 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | E | 56 | TRP | 0 | -0.005 | -0.010 | 9.845 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | E | 57 | SER | 0 | -0.001 | -0.001 | 11.973 | 0.112 | 0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | E | 58 | ARG | 1 | 0.828 | 0.927 | 8.575 | -1.441 | -1.441 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | E | 59 | ARG | 1 | 0.912 | 0.944 | 14.342 | -0.390 | -0.390 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | E | 60 | ILE | 0 | -0.022 | 0.018 | 15.591 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | E | 61 | THR | 0 | 0.006 | -0.013 | 18.011 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | E | 62 | GLU | -1 | -0.905 | -0.961 | 21.327 | 0.343 | 0.343 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | E | 63 | GLU | -1 | -0.861 | -0.885 | 23.613 | 0.251 | 0.251 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | E | 64 | HIS | 0 | 0.035 | 0.023 | 19.747 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | E | 65 | ARG | 1 | 0.869 | 0.919 | 16.590 | -0.369 | -0.369 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | E | 66 | LEU | 0 | 0.010 | 0.011 | 9.709 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | E | 67 | VAL | 0 | -0.011 | -0.010 | 12.792 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | E | 68 | TYR | 0 | -0.009 | -0.019 | 6.875 | 0.159 | 0.159 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | E | 69 | ALA | 0 | 0.067 | 0.044 | 8.408 | -0.191 | -0.191 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | E | 70 | VAL | 0 | -0.038 | -0.029 | 2.584 | 0.117 | 0.420 | 1.578 | -0.341 | -1.540 | -0.002 |
71 | E | 71 | THR | 0 | 0.021 | 0.023 | 4.177 | -0.689 | -0.542 | -0.001 | -0.020 | -0.126 | 0.000 |
72 | E | 72 | ASP | -1 | -0.935 | -0.972 | 3.435 | -4.856 | -4.355 | 0.016 | -0.200 | -0.316 | -0.002 |
73 | E | 73 | ASP | -1 | -0.755 | -0.850 | 4.689 | -3.346 | -3.104 | -0.001 | -0.047 | -0.194 | 0.000 |
74 | E | 74 | SER | 0 | -0.136 | -0.098 | 2.029 | -3.273 | -2.683 | 5.784 | -3.427 | -2.947 | -0.011 |
75 | E | 75 | LEU | 0 | -0.001 | -0.006 | 2.604 | 1.476 | 0.451 | 3.763 | 1.519 | -4.258 | -0.009 |
76 | E | 76 | LEU | 0 | -0.015 | 0.000 | 3.703 | -0.912 | -1.031 | 0.051 | 0.239 | -0.171 | 0.000 |
77 | E | 77 | ILE | 0 | 0.007 | -0.005 | 7.372 | 0.213 | 0.213 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | E | 78 | ALA | 0 | 0.027 | 0.023 | 9.600 | -0.179 | -0.179 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | E | 79 | ALA | 0 | 0.012 | 0.008 | 13.102 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | E | 80 | CYS | 0 | -0.102 | -0.046 | 13.882 | 0.149 | 0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | E | 81 | ARG | 1 | 0.945 | 0.999 | 15.834 | -0.292 | -0.292 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | E | 82 | TYR | 0 | -0.048 | -0.015 | 19.620 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | E | 83 | HIS | 0 | -0.035 | -0.039 | 20.786 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | E | 84 | TYR | 0 | -0.044 | -0.042 | 24.925 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |