![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: VQVY1
Calculation Name: 2VXQ-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2VXQ
Chain ID: A
UniProt ID: P01857
Base Structure: X-ray
Registration Date: 2023-09-22
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 | 92 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -663640.262026 |
---|---|
FMO2-HF: Nuclear repulsion | 627183.994853 |
FMO2-HF: Total energy | -36456.267172 |
FMO2-MP2: Total energy | -36562.489566 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F034364/ligand_interaction/ligand_F034364.png)
Ligand Interaction
![ligand interaction](./Kdata/F034364/ligand_interaction/ligand_interaction_F034364.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:3:LYS)
Summations of interaction energy for
fragment #1(A:3:LYS)
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. |
-144.124 | -135.305 | 2.876 | -4.946 | -6.751 | -0.045 |
Interaction energy analysis for fragmet #1(A:3:LYS)
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 | 5 | THR | 0 | -0.045 | -0.014 | 3.828 | 4.310 | 6.312 | -0.023 | -0.978 | -1.002 | -0.002 |
4 | A | 6 | PHE | 0 | 0.069 | 0.015 | 6.412 | -0.878 | -0.878 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 7 | THR | 0 | 0.019 | 0.027 | 10.217 | 1.019 | 1.019 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 8 | VAL | 0 | 0.002 | 0.020 | 12.562 | 0.196 | 0.196 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 9 | GLU | -1 | -0.837 | -0.922 | 16.155 | -15.795 | -15.795 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 10 | LYS | 1 | 0.954 | 0.961 | 18.540 | 11.550 | 11.550 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 11 | GLY | 0 | -0.028 | -0.015 | 22.193 | -0.102 | -0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 12 | SER | 0 | 0.007 | 0.008 | 20.369 | 0.131 | 0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 13 | ASN | 0 | -0.104 | -0.069 | 22.956 | 0.511 | 0.511 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 14 | GLU | -1 | -0.851 | -0.939 | 25.132 | -9.955 | -9.955 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 15 | LYS | 1 | 0.879 | 0.950 | 26.849 | 9.319 | 9.319 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 16 | HIS | 0 | -0.056 | -0.034 | 23.498 | -0.454 | -0.454 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 17 | LEU | 0 | 0.007 | 0.025 | 17.580 | -0.075 | -0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 18 | ALA | 0 | 0.046 | 0.024 | 19.350 | -0.254 | -0.254 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 19 | VAL | 0 | -0.016 | -0.017 | 13.803 | -0.159 | -0.159 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 20 | LEU | 0 | -0.003 | 0.017 | 11.741 | -0.487 | -0.487 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 21 | VAL | 0 | -0.020 | -0.002 | 8.797 | -1.283 | -1.283 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 22 | LYS | 1 | 0.835 | 0.906 | 6.460 | 37.748 | 37.748 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 23 | TYR | 0 | 0.043 | -0.001 | 2.484 | -24.928 | -21.916 | 2.280 | -1.966 | -3.327 | -0.025 |
22 | A | 24 | GLU | -1 | -0.883 | -0.928 | 2.682 | -41.081 | -39.423 | 0.518 | -0.736 | -1.441 | -0.004 |
23 | A | 25 | GLY | 0 | -0.007 | -0.007 | 2.911 | -16.846 | -14.699 | 0.101 | -1.266 | -0.981 | -0.014 |
24 | A | 26 | ASP | -1 | -0.832 | -0.906 | 5.233 | -37.125 | -37.125 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 27 | THR | 0 | 0.013 | 0.015 | 6.986 | 0.516 | 0.516 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 28 | MET | 0 | -0.025 | -0.001 | 7.020 | -1.004 | -1.004 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 29 | ALA | 0 | 0.005 | 0.005 | 11.157 | 1.768 | 1.768 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 30 | GLU | -1 | -0.927 | -0.976 | 13.424 | -16.526 | -16.526 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 31 | VAL | 0 | -0.022 | -0.018 | 11.701 | -2.380 | -2.380 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 32 | GLU | -1 | -0.794 | -0.876 | 14.166 | -15.043 | -15.043 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 33 | LEU | 0 | 0.013 | -0.004 | 14.876 | -1.327 | -1.327 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 34 | ARG | 1 | 0.908 | 0.957 | 17.056 | 15.293 | 15.293 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 35 | GLU | -1 | -0.800 | -0.895 | 18.475 | -12.587 | -12.587 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 36 | HIS | 0 | -0.086 | -0.046 | 19.565 | 0.677 | 0.677 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 37 | GLY | 0 | -0.015 | -0.016 | 21.382 | 0.143 | 0.143 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 38 | SER | 0 | -0.028 | 0.005 | 23.005 | 0.468 | 0.468 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 39 | ASP | -1 | -0.913 | -0.967 | 23.205 | -11.425 | -11.425 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 40 | GLU | -1 | -0.962 | -0.973 | 23.791 | -11.523 | -11.523 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 41 | TRP | 0 | -0.092 | -0.059 | 15.229 | -0.607 | -0.607 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 42 | VAL | 0 | 0.037 | 0.025 | 20.106 | 0.459 | 0.459 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 43 | ALA | 0 | 0.020 | 0.011 | 19.292 | -0.893 | -0.893 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 44 | MET | 0 | -0.068 | -0.017 | 16.679 | 0.109 | 0.109 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 45 | THR | 0 | -0.012 | -0.012 | 19.196 | -0.129 | -0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 46 | LYS | 1 | 0.806 | 0.923 | 15.258 | 19.431 | 19.431 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 47 | GLY | 0 | 0.044 | 0.019 | 18.619 | 0.945 | 0.945 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 48 | GLU | -1 | -0.936 | -0.981 | 19.094 | -15.224 | -15.224 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 49 | GLY | 0 | -0.031 | -0.020 | 16.841 | -0.320 | -0.320 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 50 | GLY | 0 | 0.004 | -0.006 | 13.621 | -0.643 | -0.643 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 51 | VAL | 0 | -0.014 | -0.002 | 13.998 | -1.022 | -1.022 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 52 | TRP | 0 | -0.011 | -0.006 | 13.336 | 0.460 | 0.460 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 53 | THR | 0 | 0.016 | -0.006 | 17.166 | -0.093 | -0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 54 | PHE | 0 | 0.005 | -0.001 | 20.323 | -0.213 | -0.213 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 55 | ASP | -1 | -0.856 | -0.905 | 22.264 | -11.808 | -11.808 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 56 | SER | 0 | -0.034 | -0.034 | 25.610 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 57 | GLU | -1 | -0.910 | -0.949 | 27.378 | -9.394 | -9.394 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 58 | GLU | -1 | -0.897 | -0.960 | 29.966 | -8.673 | -8.673 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 59 | PRO | 0 | -0.076 | -0.026 | 28.673 | -0.363 | -0.363 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 60 | LEU | 0 | -0.017 | 0.012 | 22.498 | -0.172 | -0.172 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 61 | GLN | 0 | -0.120 | -0.075 | 24.645 | 0.312 | 0.312 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 62 | GLY | 0 | -0.013 | 0.007 | 20.623 | -0.279 | -0.279 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 63 | PRO | 0 | -0.047 | -0.059 | 17.748 | 0.585 | 0.585 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 64 | PHE | 0 | 0.014 | 0.010 | 16.270 | 0.318 | 0.318 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 65 | ASN | 0 | 0.002 | 0.023 | 14.167 | -1.360 | -1.360 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 66 | PHE | 0 | 0.025 | 0.002 | 11.172 | 0.451 | 0.451 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 67 | ARG | 1 | 0.798 | 0.895 | 11.613 | 15.865 | 15.865 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 68 | PHE | 0 | 0.029 | 0.007 | 5.517 | -0.605 | -0.605 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 69 | LEU | 0 | 0.010 | 0.013 | 11.271 | -1.255 | -1.255 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 70 | THR | 0 | -0.060 | -0.048 | 6.321 | 1.719 | 1.719 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 71 | GLU | -1 | -0.831 | -0.940 | 9.722 | -19.456 | -19.456 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 72 | LYS | 1 | 0.816 | 0.910 | 7.396 | 37.675 | 37.675 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 73 | GLY | 0 | 0.012 | 0.019 | 10.338 | 0.828 | 0.828 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 74 | MET | 0 | -0.081 | -0.035 | 5.359 | 2.568 | 2.568 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 75 | LYS | 1 | 0.946 | 0.970 | 8.554 | 23.959 | 23.959 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 76 | ASN | 0 | -0.076 | -0.041 | 6.438 | -6.057 | -6.057 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 77 | VAL | 0 | 0.042 | 0.014 | 9.746 | 1.135 | 1.135 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 78 | PHE | 0 | -0.077 | -0.042 | 4.986 | -2.267 | -2.267 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 79 | ASP | -1 | -0.821 | -0.930 | 10.138 | -17.107 | -17.107 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 80 | ASP | -1 | -0.890 | -0.950 | 12.694 | -15.815 | -15.815 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 81 | VAL | 0 | -0.046 | -0.008 | 9.543 | -0.399 | -0.399 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 82 | VAL | 0 | -0.027 | -0.008 | 12.222 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 83 | PRO | 0 | 0.013 | 0.011 | 15.069 | 0.560 | 0.560 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 84 | GLU | -1 | -0.776 | -0.874 | 18.221 | -10.944 | -10.944 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 85 | LYS | 1 | 0.816 | 0.896 | 21.736 | 10.952 | 10.952 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 86 | TYR | 0 | -0.007 | 0.019 | 18.042 | -0.190 | -0.190 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 87 | THR | 0 | -0.028 | -0.026 | 18.440 | 0.795 | 0.795 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 88 | ILE | 0 | -0.011 | -0.011 | 18.095 | -0.637 | -0.637 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 89 | GLY | 0 | -0.017 | -0.011 | 17.301 | 0.492 | 0.492 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 90 | ALA | 0 | -0.044 | -0.008 | 15.163 | -0.474 | -0.474 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 91 | THR | 0 | -0.018 | -0.030 | 8.652 | -0.110 | -0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 92 | TYR | 0 | 0.014 | 0.006 | 10.596 | 0.812 | 0.812 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 93 | ALA | 0 | 0.015 | 0.001 | 5.560 | -1.979 | -1.979 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 94 | PRO | 0 | -0.004 | 0.019 | 5.092 | 1.515 | 1.515 | 0.000 | 0.000 | 0.000 | 0.000 |