![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: R8YK8
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 | 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 | 71 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -407268.219901 |
---|---|
FMO2-HF: Nuclear repulsion | 378312.629654 |
FMO2-HF: Total energy | -28955.590248 |
FMO2-MP2: Total energy | -29039.945054 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F033990/ligand_interaction/ligand_F033990.png)
Ligand Interaction
![ligand interaction](./Kdata/F033990/ligand_interaction/ligand_interaction_F033990.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. |
-0.623 | 0.943 | -0.018 | -0.752 | -0.796 | 0.001 |
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 | 0.030 | -0.018 | 3.873 | 2.111 | 3.568 | -0.017 | -0.735 | -0.705 | 0.001 |
4 | A | 3 | MET | 0 | -0.001 | 0.014 | 7.107 | 0.406 | 0.406 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 4 | GLU | -1 | -0.854 | -0.940 | 9.604 | 0.727 | 0.727 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 5 | GLU | -1 | -0.883 | -0.915 | 6.820 | -0.779 | -0.779 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 6 | LEU | 0 | 0.022 | 0.031 | 7.246 | -0.179 | -0.179 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 7 | GLN | 0 | 0.007 | -0.007 | 9.083 | -0.129 | -0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 8 | ARG | 1 | 0.902 | 0.947 | 10.972 | -0.243 | -0.243 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 9 | GLU | -1 | -0.776 | -0.884 | 9.099 | -0.239 | -0.239 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 10 | ILE | 0 | -0.001 | 0.005 | 12.070 | -0.081 | -0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 11 | ASN | 0 | 0.007 | 0.008 | 14.103 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 12 | ALA | 0 | -0.001 | 0.004 | 14.781 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 13 | HIS | 0 | -0.036 | -0.024 | 12.398 | -0.084 | -0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 14 | GLU | -1 | -0.779 | -0.890 | 16.856 | 0.241 | 0.241 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 15 | GLY | 0 | 0.003 | 0.004 | 19.896 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 16 | GLN | 0 | -0.038 | -0.030 | 15.631 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 17 | LEU | 0 | -0.008 | 0.014 | 20.829 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 18 | VAL | 0 | -0.003 | 0.001 | 22.397 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 19 | ILE | 0 | -0.018 | -0.015 | 23.370 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 20 | ALA | 0 | -0.022 | -0.012 | 23.438 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 21 | ARG | 1 | 0.939 | 0.945 | 24.387 | -0.087 | -0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 22 | GLN | 0 | -0.027 | -0.005 | 28.043 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 23 | LYS | 1 | 0.927 | 0.951 | 25.917 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 24 | VAL | 0 | -0.001 | 0.016 | 28.300 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 25 | ARG | 1 | 0.935 | 0.974 | 30.936 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 26 | ASP | -1 | -0.865 | -0.912 | 33.564 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 27 | ALA | 0 | -0.013 | -0.001 | 32.966 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 28 | GLU | -1 | -0.870 | -0.945 | 34.399 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 29 | LYS | 1 | 0.886 | 0.927 | 36.830 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 30 | GLN | 0 | -0.017 | -0.007 | 37.579 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 31 | TYR | 0 | -0.010 | -0.001 | 38.007 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 32 | GLU | -1 | -0.949 | -0.982 | 39.962 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 33 | LYS | 1 | 0.725 | 0.863 | 42.395 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 34 | ASP | -1 | -0.864 | -0.944 | 43.103 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 35 | PRO | 0 | 0.028 | 0.033 | 42.092 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 36 | ASP | -1 | -0.776 | -0.888 | 40.740 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 37 | GLU | -1 | -0.811 | -0.892 | 39.529 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 38 | LEU | 0 | -0.050 | -0.025 | 37.103 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 39 | ASN | 0 | -0.017 | 0.008 | 36.027 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 40 | LYS | 1 | 0.833 | 0.905 | 36.016 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 41 | ARG | 1 | 0.823 | 0.903 | 31.286 | 0.074 | 0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 42 | THR | 0 | -0.051 | -0.049 | 31.957 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 43 | LEU | 0 | -0.017 | -0.005 | 31.361 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 44 | THR | 0 | 0.031 | 0.005 | 30.234 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 45 | ASP | -1 | -0.857 | -0.910 | 27.755 | -0.078 | -0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 46 | ARG | 1 | 0.856 | 0.933 | 26.401 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 47 | GLU | -1 | -0.839 | -0.918 | 26.585 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 48 | GLY | 0 | 0.027 | 0.014 | 25.415 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 49 | VAL | 0 | -0.025 | -0.012 | 21.816 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 50 | ALA | 0 | 0.018 | 0.008 | 21.712 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 51 | VAL | 0 | -0.013 | -0.006 | 22.623 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 52 | SER | 0 | -0.062 | -0.037 | 18.757 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 53 | ILE | 0 | 0.006 | -0.010 | 17.637 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 54 | GLN | 0 | -0.013 | -0.004 | 17.816 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 55 | ALA | 0 | 0.046 | 0.029 | 17.885 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 56 | LYS | 1 | 0.838 | 0.926 | 9.874 | 0.128 | 0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 57 | ILE | 0 | -0.022 | -0.017 | 13.595 | 0.088 | 0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 58 | ASP | -1 | -0.853 | -0.924 | 14.847 | 0.335 | 0.335 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 59 | GLU | -1 | -0.843 | -0.900 | 10.595 | 0.803 | 0.803 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 60 | LEU | 0 | -0.041 | -0.014 | 9.002 | 0.178 | 0.178 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 61 | LYS | 1 | 0.842 | 0.892 | 11.088 | -0.149 | -0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 62 | ARG | 1 | 0.878 | 0.954 | 12.850 | -0.477 | -0.477 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 63 | GLN | 0 | -0.003 | -0.019 | 6.403 | 0.641 | 0.641 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 64 | LEU | 0 | -0.023 | -0.018 | 9.886 | 0.245 | 0.245 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 65 | ALA | 0 | 0.004 | 0.001 | 11.361 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 66 | ASP | -1 | -0.868 | -0.938 | 11.105 | 0.914 | 0.914 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 67 | ARG | 1 | 0.779 | 0.876 | 4.571 | -4.857 | -4.748 | -0.001 | -0.017 | -0.091 | 0.000 |
69 | A | 68 | ILE | 0 | -0.052 | -0.018 | 10.850 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 69 | ALA | 0 | -0.033 | -0.007 | 14.402 | -0.091 | -0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 70 | THR | 0 | -0.090 | -0.048 | 10.692 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |