![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 6YGRZ
Calculation Name: 4FI5-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 4FI5
Chain ID: A
UniProt ID: P05133
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 | 71 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -405182.599734 |
---|---|
FMO2-HF: Nuclear repulsion | 376227.680409 |
FMO2-HF: Total energy | -28954.919326 |
FMO2-MP2: Total energy | -29039.234765 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F033992/ligand_interaction/ligand_F033992.png)
Ligand Interaction
![ligand interaction](./Kdata/F033992/ligand_interaction/ligand_interaction_F033992.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:0:SER)
Summations of interaction energy for
fragment #1(A:0:SER)
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. |
-1.543 | -0.093 | -0.017 | -0.649 | -0.782 | 0.002 |
Interaction energy analysis for fragmet #1(A:0:SER)
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 | 2 | THR | 0 | 0.020 | -0.007 | 3.842 | -0.635 | 0.700 | -0.016 | -0.632 | -0.686 | 0.002 |
4 | A | 3 | MET | 0 | 0.044 | 0.014 | 6.521 | 0.447 | 0.447 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 4 | GLU | -1 | -0.900 | -0.954 | 9.015 | -0.336 | -0.336 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 5 | GLU | -1 | -0.913 | -0.951 | 6.095 | -1.205 | -1.205 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 6 | LEU | 0 | 0.033 | 0.026 | 7.097 | 0.227 | 0.227 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 7 | GLN | 0 | -0.013 | -0.015 | 9.302 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 8 | ARG | 1 | 0.912 | 0.952 | 11.255 | 0.132 | 0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 9 | GLU | -1 | -0.840 | -0.913 | 8.909 | 0.890 | 0.890 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 10 | ILE | 0 | -0.021 | 0.000 | 11.755 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 11 | ASN | 0 | 0.033 | 0.014 | 14.016 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 12 | ALA | 0 | -0.020 | -0.003 | 14.581 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 13 | HIS | 0 | -0.078 | -0.060 | 12.069 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 14 | GLU | -1 | -0.817 | -0.924 | 16.648 | 0.188 | 0.188 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 15 | GLY | 0 | 0.002 | 0.004 | 19.500 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 16 | GLN | 0 | -0.024 | -0.022 | 15.892 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 17 | LEU | 0 | 0.011 | 0.024 | 20.689 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 18 | VAL | 0 | -0.006 | -0.002 | 22.300 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 19 | ILE | 0 | -0.043 | -0.024 | 23.397 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 20 | ALA | 0 | 0.007 | -0.002 | 23.606 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 21 | ARG | 1 | 0.973 | 0.980 | 24.789 | -0.194 | -0.194 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 22 | GLN | 0 | -0.014 | -0.006 | 28.091 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 23 | LYS | 1 | 0.920 | 0.950 | 25.959 | -0.204 | -0.204 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 24 | VAL | 0 | 0.019 | 0.022 | 28.604 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 25 | ARG | 1 | 0.908 | 0.978 | 30.283 | -0.131 | -0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 26 | ASP | -1 | -0.894 | -0.953 | 33.772 | 0.105 | 0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 27 | ALA | 0 | -0.047 | -0.026 | 33.346 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 28 | GLU | -1 | -0.873 | -0.944 | 34.805 | 0.110 | 0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 29 | LYS | 1 | 0.990 | 1.002 | 37.156 | -0.092 | -0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 30 | GLN | 0 | -0.115 | -0.042 | 38.103 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 31 | TYR | 0 | -0.001 | -0.014 | 38.362 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 32 | GLU | -1 | -0.942 | -0.980 | 40.255 | 0.083 | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 33 | LYS | 1 | 0.832 | 0.938 | 42.344 | -0.089 | -0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 34 | ASP | -1 | -0.963 | -0.998 | 43.427 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 35 | PRO | 0 | 0.017 | 0.046 | 42.389 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 36 | ASP | -1 | -0.844 | -0.924 | 41.781 | 0.094 | 0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 37 | GLU | -1 | -0.854 | -0.964 | 40.456 | 0.105 | 0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 38 | LEU | 0 | -0.031 | -0.020 | 37.274 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 39 | ASN | 0 | 0.008 | -0.008 | 36.840 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 40 | LYS | 1 | 0.913 | 0.970 | 36.740 | -0.094 | -0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 41 | ARG | 1 | 0.949 | 0.981 | 33.125 | -0.139 | -0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 42 | THR | 0 | -0.038 | -0.020 | 32.375 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 43 | LEU | 0 | 0.012 | 0.013 | 31.738 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 44 | THR | 0 | 0.021 | 0.012 | 30.868 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 45 | ASP | -1 | -0.898 | -0.945 | 28.364 | 0.199 | 0.199 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 46 | ARG | 1 | 0.835 | 0.910 | 27.094 | -0.162 | -0.162 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 47 | GLU | -1 | -0.875 | -0.945 | 27.004 | 0.159 | 0.159 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 48 | GLY | 0 | 0.014 | 0.012 | 25.749 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 49 | VAL | 0 | -0.028 | -0.013 | 22.118 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 50 | ALA | 0 | 0.019 | 0.010 | 21.929 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 51 | VAL | 0 | -0.017 | -0.002 | 22.386 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 52 | SER | 0 | -0.044 | -0.031 | 19.034 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 53 | ILE | 0 | 0.015 | -0.003 | 17.729 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 54 | GLN | 0 | -0.036 | -0.027 | 17.547 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 55 | ALA | 0 | 0.037 | 0.025 | 17.750 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 56 | LYS | 1 | 0.925 | 0.978 | 9.226 | -1.204 | -1.204 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 57 | ILE | 0 | -0.031 | -0.025 | 13.456 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 58 | ASP | -1 | -0.886 | -0.939 | 15.029 | 0.281 | 0.281 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 59 | GLU | -1 | -0.884 | -0.934 | 10.769 | 0.541 | 0.541 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 60 | LEU | 0 | -0.043 | -0.017 | 8.897 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 61 | LYS | 1 | 0.919 | 0.945 | 11.346 | -0.253 | -0.253 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 62 | ARG | 1 | 0.895 | 0.959 | 13.216 | -0.393 | -0.393 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 63 | GLN | 0 | -0.009 | -0.008 | 6.851 | 0.321 | 0.321 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 64 | LEU | 0 | -0.023 | -0.015 | 9.860 | -0.102 | -0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 65 | ALA | 0 | 0.001 | -0.004 | 11.173 | -0.098 | -0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 66 | ASP | -1 | -0.886 | -0.946 | 11.204 | 0.068 | 0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 67 | ARG | 1 | 0.801 | 0.889 | 4.110 | -0.302 | -0.187 | -0.001 | -0.017 | -0.096 | 0.000 |
69 | A | 68 | ILE | 0 | -0.039 | -0.009 | 10.529 | -0.076 | -0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 69 | ALA | 0 | -0.026 | -0.004 | 13.829 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 70 | THR | 0 | -0.074 | -0.024 | 10.032 | -0.076 | -0.076 | 0.000 | 0.000 | 0.000 | 0.000 |