![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 2NQ8R
Calculation Name: 3TYS-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3TYS
Chain ID: A
UniProt ID: Q6WRY9
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 | 75 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -462503.212475 |
---|---|
FMO2-HF: Nuclear repulsion | 432013.956596 |
FMO2-HF: Total energy | -30489.25588 |
FMO2-MP2: Total energy | -30576.699245 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F037613/ligand_interaction/ligand_F037613.png)
Ligand Interaction
![ligand interaction](./Kdata/F037613/ligand_interaction/ligand_interaction_F037613.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:ARG)
Summations of interaction energy for
fragment #1(A:-7:ARG)
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. |
24.967 | 26.352 | 0.01 | -0.516 | -0.879 | 0.001 |
Interaction energy analysis for fragmet #1(A:-7:ARG)
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 | ASN | 0 | -0.016 | -0.013 | 3.520 | 7.425 | 8.810 | 0.010 | -0.516 | -0.879 | 0.001 |
4 | A | -4 | LEU | 0 | 0.006 | 0.007 | 6.229 | 1.351 | 1.351 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | -3 | TYR | 0 | 0.017 | 0.001 | 8.781 | 1.858 | 1.858 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | -2 | PHE | 0 | -0.003 | -0.002 | 11.673 | 1.692 | 1.692 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | -1 | GLN | 0 | -0.055 | -0.045 | 9.711 | -0.566 | -0.566 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 0 | GLY | 0 | 0.067 | 0.057 | 12.496 | 0.434 | 0.434 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 1 | MET | 0 | -0.059 | -0.023 | 15.146 | 0.849 | 0.849 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 2 | ARG | 1 | 0.861 | 0.927 | 14.951 | 13.255 | 13.255 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 3 | VAL | 0 | 0.005 | 0.015 | 16.186 | 0.439 | 0.439 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 4 | SER | 0 | 0.002 | -0.004 | 17.961 | 0.568 | 0.568 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 5 | TYR | 0 | 0.037 | -0.019 | 17.131 | -0.297 | -0.297 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 6 | ASN | 0 | -0.025 | -0.017 | 23.216 | 0.421 | 0.421 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 7 | LYS | 1 | 0.859 | 0.938 | 25.211 | 12.046 | 12.046 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 8 | LEU | 0 | 0.070 | 0.049 | 23.749 | 0.267 | 0.267 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 9 | TRP | 0 | -0.058 | -0.033 | 24.663 | 0.337 | 0.337 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 10 | LYS | 1 | 0.951 | 0.970 | 29.521 | 9.850 | 9.850 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 11 | LEU | 0 | 0.066 | 0.052 | 28.375 | 0.242 | 0.242 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 12 | LEU | 0 | -0.046 | -0.034 | 28.706 | 0.158 | 0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 13 | ILE | 0 | -0.010 | 0.000 | 32.242 | 0.233 | 0.233 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 14 | ASP | -1 | -0.894 | -0.939 | 34.465 | -8.514 | -8.514 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 15 | ARG | 1 | 0.787 | 0.894 | 31.439 | 9.550 | 9.550 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 16 | ASP | -1 | -0.914 | -0.947 | 36.168 | -7.530 | -7.530 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 17 | MET | 0 | -0.072 | -0.030 | 32.283 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 18 | LYS | 1 | 0.848 | 0.906 | 33.848 | 7.989 | 7.989 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 19 | LYS | 1 | 1.006 | 0.983 | 28.136 | 9.885 | 9.885 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 20 | GLY | 0 | -0.058 | -0.034 | 29.252 | -0.306 | -0.306 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 21 | GLU | -1 | -0.742 | -0.867 | 30.892 | -8.595 | -8.595 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 22 | LEU | 0 | 0.044 | 0.040 | 25.630 | -0.119 | -0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 23 | ARG | 1 | 0.769 | 0.866 | 25.696 | 9.882 | 9.882 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 24 | GLU | -1 | -0.881 | -0.943 | 26.775 | -9.718 | -9.718 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 25 | ALA | 0 | -0.009 | 0.018 | 29.351 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 26 | VAL | 0 | -0.004 | -0.001 | 23.327 | -0.145 | -0.145 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 27 | GLY | 0 | 0.032 | 0.035 | 24.628 | -0.339 | -0.339 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 28 | VAL | 0 | -0.076 | -0.031 | 20.592 | -0.510 | -0.510 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 29 | SER | 0 | 0.057 | 0.029 | 20.054 | 0.372 | 0.372 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 30 | LYS | 1 | 1.022 | 0.986 | 22.698 | 10.290 | 10.290 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 31 | SER | 0 | 0.017 | 0.008 | 19.315 | 0.062 | 0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 32 | THR | 0 | -0.002 | -0.013 | 17.107 | -0.548 | -0.548 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 33 | PHE | 0 | 0.058 | 0.026 | 19.282 | -0.108 | -0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 34 | ALA | 0 | -0.010 | -0.012 | 21.693 | 0.168 | 0.168 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 35 | LYS | 1 | 0.908 | 0.965 | 13.293 | 18.134 | 18.134 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 36 | LEU | 0 | 0.038 | 0.033 | 19.418 | -0.087 | -0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 37 | GLY | 0 | -0.053 | -0.016 | 21.480 | 0.260 | 0.260 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 38 | LYS | 1 | 0.788 | 0.886 | 19.244 | 13.607 | 13.607 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 39 | ASN | 0 | 0.027 | 0.025 | 20.052 | -0.331 | -0.331 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 40 | GLU | -1 | -0.776 | -0.870 | 15.734 | -14.868 | -14.868 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 41 | ASN | 0 | 0.049 | 0.027 | 10.877 | 1.302 | 1.302 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 42 | VAL | 0 | -0.006 | -0.003 | 14.158 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 43 | SER | 0 | -0.001 | -0.002 | 12.223 | -0.448 | -0.448 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 44 | LEU | 0 | 0.117 | 0.040 | 11.557 | 1.079 | 1.079 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 45 | THR | 0 | 0.015 | 0.007 | 13.871 | 0.513 | 0.513 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 46 | VAL | 0 | -0.016 | -0.005 | 15.836 | 1.005 | 1.005 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 47 | LEU | 0 | -0.011 | -0.010 | 16.274 | 0.773 | 0.773 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 48 | LEU | 0 | 0.036 | 0.019 | 16.424 | 0.538 | 0.538 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 49 | ALA | 0 | 0.036 | 0.029 | 19.751 | 0.652 | 0.652 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 50 | ILE | 0 | -0.030 | -0.017 | 21.475 | 0.657 | 0.657 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 51 | CYS | 0 | -0.036 | -0.014 | 22.479 | 0.351 | 0.351 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 52 | GLU | -1 | -0.939 | -0.963 | 23.892 | -11.645 | -11.645 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 53 | TYR | 0 | -0.017 | -0.011 | 25.729 | 0.488 | 0.488 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 54 | LEU | 0 | -0.029 | -0.028 | 26.985 | 0.459 | 0.459 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 55 | ASN | 0 | -0.050 | -0.012 | 28.462 | 0.418 | 0.418 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 56 | CYS | 0 | -0.070 | -0.014 | 25.569 | 0.209 | 0.209 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 57 | ASP | -1 | -0.788 | -0.899 | 23.125 | -13.401 | -13.401 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 58 | PHE | 0 | 0.005 | -0.025 | 17.197 | -0.137 | -0.137 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 59 | GLY | 0 | -0.030 | -0.017 | 21.895 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 60 | ASP | -1 | -0.839 | -0.909 | 24.169 | -10.544 | -10.544 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 61 | ILE | 0 | -0.067 | -0.057 | 21.403 | 0.262 | 0.262 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 62 | ILE | 0 | -0.064 | -0.030 | 17.911 | -0.222 | -0.222 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 63 | GLU | -1 | -0.890 | -0.943 | 21.439 | -11.313 | -11.313 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 64 | ALA | 0 | -0.006 | 0.001 | 18.506 | -0.395 | -0.395 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 65 | LEU | 0 | -0.011 | -0.017 | 19.864 | 0.622 | 0.622 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 66 | PRO | 0 | 0.036 | 0.015 | 19.622 | -0.674 | -0.674 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 67 | GLU | -1 | -0.987 | -0.987 | 17.006 | -14.543 | -14.543 | 0.000 | 0.000 | 0.000 | 0.000 |