![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: YV9R2
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 | OptH |
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 | -663485.994827 |
---|---|
FMO2-HF: Nuclear repulsion | 627030.859715 |
FMO2-HF: Total energy | -36455.135112 |
FMO2-MP2: Total energy | -36561.343246 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F034365/ligand_interaction/ligand_F034365.png)
Ligand Interaction
![ligand interaction](./Kdata/F034365/ligand_interaction/ligand_interaction_F034365.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. |
-118.983 | -114.538 | 0.457 | -1.907 | -2.997 | -0.007 |
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 | -0.043 | -0.016 | 3.673 | 1.112 | 3.545 | -0.024 | -1.205 | -1.205 | -0.003 |
4 | A | 6 | PHE | 0 | 0.063 | 0.012 | 6.581 | -0.308 | -0.308 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 7 | THR | 0 | 0.022 | 0.034 | 10.267 | 0.597 | 0.597 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 8 | VAL | 0 | 0.006 | 0.027 | 12.968 | 0.291 | 0.291 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 9 | GLU | -1 | -0.860 | -0.932 | 16.395 | -15.034 | -15.034 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 10 | LYS | 1 | 0.967 | 0.955 | 19.001 | 11.006 | 11.006 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 11 | GLY | 0 | -0.027 | -0.018 | 22.691 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 12 | SER | 0 | -0.015 | 0.007 | 20.532 | 0.080 | 0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 13 | ASN | 0 | -0.071 | -0.057 | 23.071 | 0.304 | 0.304 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 14 | GLU | -1 | -0.874 | -0.951 | 24.955 | -9.828 | -9.828 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 15 | LYS | 1 | 0.944 | 0.998 | 26.662 | 9.134 | 9.134 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 16 | HIS | 0 | -0.034 | -0.021 | 23.575 | -0.340 | -0.340 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 17 | LEU | 0 | 0.003 | 0.025 | 17.311 | -0.111 | -0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 18 | ALA | 0 | 0.033 | 0.018 | 19.148 | -0.196 | -0.196 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 19 | VAL | 0 | -0.015 | -0.015 | 13.685 | -0.210 | -0.210 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 20 | LEU | 0 | 0.005 | 0.019 | 11.888 | -0.319 | -0.319 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 21 | VAL | 0 | -0.025 | -0.003 | 8.778 | -1.256 | -1.256 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 22 | LYS | 1 | 0.911 | 0.966 | 6.094 | 31.946 | 31.946 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 23 | TYR | 0 | 0.026 | -0.003 | 4.368 | -8.833 | -8.237 | 0.004 | -0.139 | -0.462 | -0.001 |
22 | A | 24 | GLU | -1 | -0.965 | -0.998 | 2.556 | -32.486 | -31.436 | 0.480 | -0.547 | -0.982 | -0.003 |
23 | A | 25 | GLY | 0 | -0.011 | -0.003 | 4.355 | -5.628 | -5.526 | -0.001 | -0.008 | -0.094 | 0.000 |
24 | A | 26 | ASP | -1 | -0.833 | -0.926 | 7.070 | -30.576 | -30.576 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 27 | THR | 0 | 0.000 | 0.002 | 8.696 | 0.507 | 0.507 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 28 | MET | 0 | -0.049 | -0.016 | 7.684 | -0.821 | -0.821 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 29 | ALA | 0 | 0.023 | 0.018 | 11.807 | 1.336 | 1.336 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 30 | GLU | -1 | -0.953 | -0.987 | 13.931 | -15.645 | -15.645 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 31 | VAL | 0 | -0.017 | -0.017 | 11.656 | -2.115 | -2.115 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 32 | GLU | -1 | -0.819 | -0.901 | 13.986 | -14.656 | -14.656 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 33 | LEU | 0 | 0.018 | 0.005 | 14.512 | -1.390 | -1.390 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 34 | ARG | 1 | 0.905 | 0.950 | 16.758 | 15.692 | 15.692 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 35 | GLU | -1 | -0.807 | -0.902 | 18.371 | -12.532 | -12.532 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 36 | HIS | 0 | -0.041 | -0.012 | 20.331 | 0.620 | 0.620 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 37 | GLY | 0 | -0.006 | -0.011 | 21.413 | 0.124 | 0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 38 | SER | 0 | -0.028 | 0.002 | 22.930 | 0.465 | 0.465 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 39 | ASP | -1 | -0.913 | -0.968 | 23.107 | -11.628 | -11.628 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 40 | GLU | -1 | -0.949 | -0.969 | 23.528 | -11.483 | -11.483 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 41 | TRP | 0 | -0.113 | -0.064 | 14.787 | -0.654 | -0.654 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 42 | VAL | 0 | 0.044 | 0.026 | 19.768 | 0.474 | 0.474 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 43 | ALA | 0 | 0.014 | 0.008 | 19.013 | -0.840 | -0.840 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 44 | MET | 0 | -0.063 | -0.018 | 16.196 | 0.066 | 0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 45 | THR | 0 | 0.004 | -0.007 | 18.919 | -0.076 | -0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 46 | LYS | 1 | 0.859 | 0.939 | 16.934 | 16.522 | 16.522 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 47 | GLY | 0 | 0.036 | 0.018 | 18.621 | 0.825 | 0.825 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 48 | GLU | -1 | -0.947 | -0.985 | 19.143 | -13.763 | -13.763 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 49 | GLY | 0 | -0.018 | -0.016 | 16.822 | -0.301 | -0.301 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 50 | GLY | 0 | 0.007 | -0.004 | 13.602 | -0.538 | -0.538 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 51 | VAL | 0 | -0.001 | 0.006 | 13.998 | -0.978 | -0.978 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 52 | TRP | 0 | -0.014 | -0.008 | 13.343 | 0.555 | 0.555 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 53 | THR | 0 | -0.009 | -0.013 | 16.952 | 0.164 | 0.164 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 54 | PHE | 0 | 0.037 | 0.008 | 19.980 | -0.222 | -0.222 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 55 | ASP | -1 | -0.849 | -0.893 | 21.852 | -11.281 | -11.281 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 56 | SER | 0 | -0.054 | -0.055 | 25.342 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 57 | GLU | -1 | -0.933 | -0.970 | 27.051 | -9.290 | -9.290 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 58 | GLU | -1 | -0.934 | -0.981 | 29.674 | -8.620 | -8.620 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 59 | PRO | 0 | -0.079 | -0.018 | 28.443 | -0.364 | -0.364 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 60 | LEU | 0 | -0.011 | 0.010 | 22.308 | -0.201 | -0.201 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 61 | GLN | 0 | -0.115 | -0.065 | 24.595 | 0.279 | 0.279 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 62 | GLY | 0 | -0.029 | -0.003 | 20.479 | -0.304 | -0.304 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 63 | PRO | 0 | -0.012 | -0.043 | 17.688 | 0.548 | 0.548 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 64 | PHE | 0 | 0.001 | 0.004 | 16.153 | 0.335 | 0.335 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 65 | ASN | 0 | 0.037 | 0.054 | 14.145 | -1.644 | -1.644 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 66 | PHE | 0 | 0.015 | -0.004 | 10.925 | 0.652 | 0.652 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 67 | ARG | 1 | 0.808 | 0.910 | 11.293 | 15.336 | 15.336 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 68 | PHE | 0 | 0.019 | 0.002 | 5.436 | -0.303 | -0.303 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 69 | LEU | 0 | 0.012 | 0.011 | 11.357 | -1.357 | -1.357 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 70 | THR | 0 | -0.033 | -0.014 | 7.686 | 1.235 | 1.235 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 71 | GLU | -1 | -0.855 | -0.944 | 11.085 | -17.676 | -17.676 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 72 | LYS | 1 | 0.796 | 0.909 | 8.783 | 32.196 | 32.196 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 73 | GLY | 0 | 0.004 | 0.013 | 12.239 | 0.398 | 0.398 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 74 | MET | 0 | -0.094 | -0.038 | 6.007 | 0.722 | 0.722 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 75 | LYS | 1 | 0.968 | 0.977 | 9.760 | 22.633 | 22.633 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 76 | ASN | 0 | -0.073 | -0.036 | 6.670 | -5.118 | -5.118 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 77 | VAL | 0 | 0.032 | 0.006 | 9.505 | 1.593 | 1.593 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 78 | PHE | 0 | -0.087 | -0.047 | 4.708 | -3.299 | -3.189 | -0.001 | -0.003 | -0.106 | 0.000 |
77 | A | 79 | ASP | -1 | -0.840 | -0.935 | 10.163 | -17.455 | -17.455 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 80 | ASP | -1 | -0.925 | -0.979 | 12.901 | -17.034 | -17.034 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 81 | VAL | 0 | -0.061 | -0.017 | 9.367 | -0.586 | -0.586 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 82 | VAL | 0 | -0.028 | -0.008 | 12.051 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 83 | PRO | 0 | 0.004 | 0.009 | 14.636 | 0.545 | 0.545 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 84 | GLU | -1 | -0.845 | -0.925 | 17.634 | -11.280 | -11.280 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 85 | LYS | 1 | 0.883 | 0.940 | 21.271 | 11.126 | 11.126 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 86 | TYR | 0 | 0.011 | 0.022 | 17.798 | -0.187 | -0.187 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 87 | THR | 0 | -0.025 | -0.025 | 18.396 | 0.838 | 0.838 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 88 | ILE | 0 | -0.017 | -0.015 | 18.286 | -0.598 | -0.598 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 89 | GLY | 0 | -0.030 | -0.017 | 17.933 | 0.454 | 0.454 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 90 | ALA | 0 | -0.043 | -0.007 | 15.479 | -0.410 | -0.410 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 91 | THR | 0 | -0.016 | -0.035 | 9.097 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 92 | TYR | 0 | 0.017 | 0.011 | 10.428 | 0.661 | 0.661 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 93 | ALA | 0 | 0.016 | -0.002 | 5.081 | -1.587 | -1.587 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 94 | PRO | 0 | -0.011 | 0.019 | 4.742 | 1.057 | 1.211 | -0.001 | -0.005 | -0.148 | 0.000 |