![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: G54Z1
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 | 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 | 86 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -466032.975115 |
---|---|
FMO2-HF: Nuclear repulsion | 431199.527052 |
FMO2-HF: Total energy | -34833.448063 |
FMO2-MP2: Total energy | -34930.831146 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F036022/ligand_interaction/ligand_F036022.png)
Ligand Interaction
![ligand interaction](./Kdata/F036022/ligand_interaction/ligand_interaction_F036022.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. |
0.199 | 1.673 | 0.014 | -0.815 | -0.673 | 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 | 0.008 | 0.012 | 3.225 | -0.212 | 1.262 | 0.014 | -0.815 | -0.673 | 0.003 |
4 | A | 10 | MET | 0 | 0.004 | 0.019 | 6.608 | 0.773 | 0.773 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 11 | ARG | 1 | 0.942 | 0.986 | 8.570 | 0.386 | 0.386 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 12 | THR | 0 | 0.039 | 0.023 | 7.992 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 13 | ILE | 0 | -0.055 | -0.018 | 10.712 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 14 | SER | 0 | 0.032 | 0.017 | 14.189 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 15 | TYR | 0 | 0.037 | -0.002 | 15.894 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 16 | SER | 0 | 0.008 | -0.006 | 18.093 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 17 | GLU | -1 | -0.805 | -0.893 | 17.293 | -0.217 | -0.217 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 18 | ALA | 0 | 0.051 | 0.019 | 17.871 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 19 | ARG | 1 | 0.913 | 0.949 | 19.992 | 0.090 | 0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 20 | GLN | 0 | -0.056 | -0.019 | 22.975 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 21 | ASN | 0 | -0.030 | -0.019 | 22.804 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 22 | LEU | 0 | 0.030 | 0.039 | 22.140 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 23 | SER | 0 | 0.048 | 0.009 | 23.731 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 24 | ALA | 0 | 0.039 | 0.016 | 24.729 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 25 | THR | 0 | -0.037 | -0.027 | 18.752 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 26 | MET | 0 | -0.033 | -0.024 | 20.703 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 27 | MET | 0 | -0.018 | 0.003 | 22.606 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 28 | LYS | 1 | 0.799 | 0.896 | 20.423 | 0.319 | 0.319 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 29 | ALA | 0 | 0.029 | 0.014 | 18.747 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 30 | VAL | 0 | -0.054 | -0.037 | 19.998 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 31 | GLU | -1 | -0.905 | -0.941 | 23.283 | -0.259 | -0.259 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 32 | ASP | -1 | -0.864 | -0.938 | 19.438 | -0.387 | -0.387 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 33 | HIS | 1 | 0.774 | 0.888 | 20.094 | 0.342 | 0.342 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 34 | ALA | 0 | 0.023 | 0.027 | 15.758 | -0.059 | -0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 35 | PRO | 0 | -0.030 | -0.016 | 12.250 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 36 | ILE | 0 | -0.015 | -0.017 | 12.709 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 37 | LEU | 0 | -0.002 | -0.010 | 7.431 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 38 | ILE | 0 | 0.009 | 0.006 | 11.388 | 0.093 | 0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 39 | THR | 0 | 0.014 | -0.001 | 9.939 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 40 | ARG | 1 | 0.814 | 0.887 | 13.178 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 41 | GLN | 0 | -0.010 | -0.012 | 14.843 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 42 | ASN | 0 | -0.074 | -0.046 | 16.300 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 43 | GLY | 0 | 0.032 | 0.026 | 13.255 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 44 | GLU | -1 | -0.789 | -0.863 | 12.422 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 45 | ALA | 0 | 0.016 | 0.001 | 10.339 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 46 | CYS | 0 | -0.056 | -0.032 | 12.433 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 47 | VAL | 0 | 0.006 | 0.005 | 10.573 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 48 | LEU | 0 | -0.020 | 0.003 | 13.149 | 0.088 | 0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 49 | MET | 0 | 0.033 | 0.005 | 14.842 | -0.081 | -0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 50 | SER | 0 | 0.073 | 0.045 | 18.010 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 51 | LEU | 0 | 0.025 | 0.002 | 21.106 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 52 | GLU | -1 | -0.898 | -0.952 | 23.570 | -0.300 | -0.300 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 53 | GLU | -1 | -0.831 | -0.907 | 18.774 | -0.481 | -0.481 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 54 | TYR | 0 | -0.027 | -0.017 | 18.436 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 55 | ASN | 0 | 0.004 | -0.011 | 20.361 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 56 | SER | 0 | 0.007 | 0.023 | 21.272 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 57 | LEU | 0 | -0.007 | 0.001 | 15.059 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 58 | GLU | -1 | -0.795 | -0.876 | 19.295 | -0.333 | -0.333 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 59 | GLU | -1 | -0.856 | -0.935 | 21.100 | -0.221 | -0.221 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 60 | THR | 0 | -0.047 | -0.033 | 19.680 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 61 | ALA | 0 | -0.021 | -0.019 | 18.213 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 62 | TYR | 0 | -0.054 | -0.009 | 19.985 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 63 | LEU | 0 | -0.006 | 0.004 | 23.606 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 64 | LEU | 0 | -0.028 | -0.021 | 19.633 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 65 | ARG | 1 | 0.785 | 0.873 | 20.222 | 0.310 | 0.310 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 66 | SER | 0 | 0.008 | 0.011 | 22.760 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 67 | PRO | 0 | 0.045 | 0.006 | 23.628 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 68 | ALA | 0 | -0.002 | 0.004 | 25.545 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 69 | ASN | 0 | -0.046 | -0.033 | 27.184 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 70 | ALA | 0 | 0.039 | 0.024 | 23.356 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 71 | ARG | 1 | 0.857 | 0.915 | 25.452 | 0.114 | 0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 72 | ARG | 1 | 0.946 | 0.974 | 27.217 | 0.124 | 0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 73 | LEU | 0 | 0.029 | 0.025 | 25.392 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 74 | MET | 0 | 0.008 | 0.003 | 23.670 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 75 | ASP | -1 | -0.809 | -0.894 | 26.991 | -0.132 | -0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 76 | SER | 0 | -0.008 | 0.004 | 30.330 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 77 | ILE | 0 | -0.011 | -0.004 | 26.564 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 78 | ASP | -1 | -0.779 | -0.887 | 26.747 | -0.218 | -0.218 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 79 | SER | 0 | -0.033 | -0.012 | 29.700 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 80 | LEU | 0 | -0.002 | -0.009 | 32.207 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 81 | LYS | 1 | 0.814 | 0.895 | 24.653 | 0.246 | 0.246 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 82 | SER | 0 | -0.084 | -0.051 | 31.567 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 83 | GLY | 0 | 0.031 | 0.021 | 34.078 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 84 | LYS | 1 | 0.843 | 0.926 | 34.385 | 0.125 | 0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 85 | GLY | 0 | 0.010 | 0.018 | 38.183 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 86 | THR | 0 | -0.049 | -0.033 | 38.889 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 87 | GLU | -1 | -0.916 | -0.948 | 42.489 | -0.092 | -0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 88 | LYS | 1 | 0.839 | 0.896 | 44.378 | 0.086 | 0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 89 | ASP | -1 | -0.818 | -0.884 | 45.140 | -0.086 | -0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 90 | ILE | 0 | -0.046 | -0.032 | 44.635 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 91 | ILE | 0 | -0.066 | -0.034 | 47.065 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 92 | GLU | -1 | -0.966 | -0.973 | 49.207 | -0.072 | -0.072 | 0.000 | 0.000 | 0.000 | 0.000 |