![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: KGZJ3
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 | OptAll |
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 | -644066.361121 |
---|---|
FMO2-HF: Nuclear repulsion | 608616.770004 |
FMO2-HF: Total energy | -35449.591116 |
FMO2-MP2: Total energy | -35554.43696 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F036028/ligand_interaction/ligand_F036028.png)
Ligand Interaction
![ligand interaction](./Kdata/F036028/ligand_interaction/ligand_interaction_F036028.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. |
-29.558 | -19.509 | 11.738 | -5.708 | -16.078 | -0.055 |
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 | -0.023 | -0.018 | 2.588 | -2.274 | 0.172 | 0.925 | -1.443 | -1.928 | -0.010 |
4 | E | 4 | ILE | 0 | -0.006 | -0.001 | 5.211 | -0.304 | -0.231 | -0.001 | -0.005 | -0.067 | 0.000 |
5 | E | 5 | TRP | 0 | -0.005 | -0.012 | 7.882 | 0.395 | 0.395 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | E | 6 | SER | 0 | -0.011 | -0.022 | 11.122 | -0.097 | -0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | E | 7 | GLU | -1 | -0.891 | -0.957 | 14.566 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | E | 8 | GLU | -1 | -0.804 | -0.879 | 17.837 | 0.133 | 0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | E | 9 | SER | 0 | -0.056 | -0.038 | 12.584 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | E | 10 | TRP | 0 | -0.012 | -0.007 | 13.542 | 0.106 | 0.106 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | E | 11 | ASP | -1 | -0.824 | -0.917 | 15.671 | 0.198 | 0.198 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | E | 12 | ASP | -1 | -0.822 | -0.919 | 16.853 | 0.369 | 0.369 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | E | 13 | TYR | 0 | -0.066 | -0.075 | 14.399 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | E | 14 | LEU | 0 | -0.002 | -0.006 | 16.848 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | E | 15 | TYR | 0 | 0.046 | 0.026 | 19.669 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | E | 16 | TRP | 0 | -0.016 | -0.044 | 18.044 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | E | 17 | GLN | 0 | -0.046 | -0.021 | 17.154 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | E | 18 | GLU | -1 | -0.966 | -0.967 | 21.038 | 0.208 | 0.208 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | E | 19 | THR | 0 | -0.035 | 0.001 | 24.066 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | E | 20 | ASP | -1 | -0.795 | -0.903 | 23.760 | 0.351 | 0.351 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | E | 21 | LYS | 1 | 0.947 | 0.965 | 20.522 | -0.381 | -0.381 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | E | 22 | ARG | 1 | 0.850 | 0.907 | 21.343 | -0.295 | -0.295 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | E | 23 | ILE | 0 | -0.018 | -0.003 | 19.393 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | E | 24 | VAL | 0 | 0.030 | 0.034 | 16.971 | 0.081 | 0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | E | 25 | LYS | 1 | 0.915 | 0.961 | 16.478 | -0.496 | -0.496 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | E | 26 | LYS | 1 | 0.882 | 0.938 | 16.302 | -0.464 | -0.464 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | E | 27 | ILE | 0 | 0.060 | 0.040 | 13.086 | 0.112 | 0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | E | 28 | ASN | 0 | 0.041 | 0.036 | 12.183 | 0.202 | 0.202 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | E | 29 | GLU | -1 | -0.824 | -0.899 | 11.477 | 1.374 | 1.374 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | E | 30 | LEU | 0 | 0.013 | 0.021 | 12.002 | 0.155 | 0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | E | 31 | ILE | 0 | 0.032 | 0.040 | 7.052 | 0.342 | 0.342 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | E | 32 | LYS | 1 | 0.810 | 0.881 | 7.066 | -0.497 | -0.497 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | E | 33 | ASP | -1 | -0.850 | -0.920 | 7.620 | 1.777 | 1.777 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | E | 34 | THR | 0 | -0.005 | -0.011 | 5.240 | -0.291 | -0.197 | -0.001 | -0.009 | -0.084 | 0.000 |
35 | E | 35 | ARG | 1 | 0.859 | 0.917 | 2.450 | -6.913 | -4.787 | 0.878 | -0.919 | -2.084 | 0.004 |
36 | E | 36 | ARG | 1 | 0.908 | 0.974 | 4.184 | -1.353 | -1.096 | 0.000 | -0.010 | -0.247 | 0.000 |
37 | E | 37 | THR | 0 | 0.017 | -0.001 | 7.036 | -0.583 | -0.583 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | E | 38 | PRO | 0 | 0.044 | 0.026 | 3.362 | -0.712 | -0.182 | 0.051 | -0.114 | -0.466 | 0.000 |
39 | E | 39 | PHE | 0 | 0.005 | -0.002 | 5.857 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | E | 40 | GLU | -1 | -0.917 | -0.949 | 9.146 | 0.240 | 0.240 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | E | 41 | GLY | 0 | 0.033 | 0.021 | 11.157 | 0.249 | 0.249 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | E | 42 | LYS | 1 | 0.754 | 0.862 | 12.833 | -1.423 | -1.423 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | E | 43 | GLY | 0 | 0.041 | 0.007 | 13.926 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | E | 44 | LYS | 1 | 0.839 | 0.924 | 16.347 | -0.375 | -0.375 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | E | 45 | PRO | 0 | 0.014 | 0.021 | 11.846 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | E | 46 | GLU | -1 | -0.865 | -0.921 | 13.955 | 0.194 | 0.194 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | E | 47 | PRO | 0 | -0.003 | 0.017 | 13.575 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | E | 48 | LEU | 0 | -0.019 | -0.010 | 14.452 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | E | 49 | LYS | 1 | 0.921 | 0.944 | 16.349 | -0.138 | -0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | E | 50 | HIS | 0 | 0.053 | 0.027 | 18.953 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | E | 51 | ASN | 0 | 0.036 | 0.018 | 19.766 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | E | 52 | LEU | 0 | 0.013 | 0.015 | 16.869 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | E | 53 | SER | 0 | -0.026 | -0.032 | 15.530 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | E | 54 | GLY | 0 | -0.007 | 0.006 | 12.083 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | E | 55 | PHE | 0 | -0.024 | -0.007 | 10.465 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | E | 56 | TRP | 0 | -0.004 | -0.008 | 9.852 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | E | 57 | SER | 0 | 0.011 | 0.002 | 12.082 | 0.084 | 0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | E | 58 | ARG | 1 | 0.834 | 0.914 | 8.940 | -1.538 | -1.538 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | E | 59 | ARG | 1 | 0.920 | 0.959 | 14.711 | -0.392 | -0.392 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | E | 60 | ILE | 0 | 0.003 | 0.019 | 15.734 | 0.067 | 0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | E | 61 | THR | 0 | -0.080 | -0.072 | 18.212 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | E | 62 | GLU | -1 | -0.790 | -0.887 | 21.551 | 0.348 | 0.348 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | E | 63 | GLU | -1 | -0.856 | -0.874 | 23.986 | 0.243 | 0.243 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | E | 64 | HIS | 0 | 0.028 | 0.006 | 20.051 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | E | 65 | ARG | 1 | 0.832 | 0.895 | 16.823 | -0.369 | -0.369 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | E | 66 | LEU | 0 | 0.015 | 0.022 | 9.789 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | E | 67 | VAL | 0 | -0.023 | -0.016 | 13.038 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | E | 68 | TYR | 0 | -0.002 | -0.008 | 7.115 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | E | 69 | ALA | 0 | 0.061 | 0.041 | 8.650 | -0.168 | -0.168 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | E | 70 | VAL | 0 | -0.023 | -0.023 | 2.570 | 0.161 | 0.520 | 1.479 | -0.334 | -1.504 | 0.000 |
71 | E | 71 | THR | 0 | 0.015 | 0.011 | 3.430 | -0.976 | -0.669 | 0.003 | -0.061 | -0.249 | 0.000 |
72 | E | 72 | ASP | -1 | -0.898 | -0.955 | 2.658 | -7.369 | -6.249 | 0.578 | -0.682 | -1.016 | -0.010 |
73 | E | 73 | ASP | -1 | -0.771 | -0.847 | 3.961 | -4.186 | -3.515 | 0.005 | -0.233 | -0.443 | -0.001 |
74 | E | 74 | SER | 0 | -0.086 | -0.078 | 2.255 | -6.225 | -3.203 | 4.581 | -3.660 | -3.943 | -0.031 |
75 | E | 75 | LEU | 0 | -0.003 | 0.005 | 2.482 | 2.134 | 1.489 | 3.178 | 1.339 | -3.872 | -0.008 |
76 | E | 76 | LEU | 0 | -0.025 | -0.014 | 3.850 | -1.174 | -1.485 | 0.062 | 0.423 | -0.175 | 0.001 |
77 | E | 77 | ILE | 0 | 0.005 | -0.005 | 7.511 | 0.133 | 0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | E | 78 | ALA | 0 | 0.034 | 0.024 | 9.724 | -0.183 | -0.183 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | E | 79 | ALA | 0 | 0.026 | 0.014 | 13.326 | -0.077 | -0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | E | 80 | CYS | 0 | -0.117 | -0.050 | 13.688 | 0.151 | 0.151 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | E | 81 | ARG | 1 | 0.927 | 0.990 | 15.624 | -0.267 | -0.267 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | E | 82 | TYR | 0 | -0.032 | -0.009 | 19.468 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | E | 83 | HIS | 0 | -0.016 | -0.029 | 20.745 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | E | 84 | TYR | 0 | -0.048 | -0.041 | 25.134 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |