![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 6N65Z
Calculation Name: 3FBN-C-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3FBN
Chain ID: C
UniProt ID: P38633
Base Structure: X-ray
Registration Date: 2023-06-21
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 | 48 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -205814.167564 |
---|---|
FMO2-HF: Nuclear repulsion | 186346.134038 |
FMO2-HF: Total energy | -19468.033526 |
FMO2-MP2: Total energy | -19524.451962 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F024977/ligand_interaction/ligand_F024977.png)
Ligand Interaction
![ligand interaction](./Kdata/F024977/ligand_interaction/ligand_interaction_F024977.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(C:16:THR)
Summations of interaction energy for
fragment #1(C:16:THR)
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. |
0.776 | 2.304 | -0.025 | -0.67 | -0.832 | 0.003 |
Interaction energy analysis for fragmet #1(C:16:THR)
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 | C | 18 | PRO | 0 | 0.006 | -0.003 | 3.576 | 1.912 | 3.440 | -0.025 | -0.670 | -0.832 | 0.003 |
4 | C | 19 | SER | 0 | 0.082 | 0.037 | 6.073 | 0.432 | 0.432 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | C | 20 | TYR | 0 | 0.000 | -0.013 | 7.868 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | C | 21 | VAL | 0 | 0.043 | 0.019 | 6.866 | -0.123 | -0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | C | 22 | LYS | 1 | 0.967 | 0.994 | 9.688 | -1.061 | -1.061 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | C | 23 | PHE | 0 | -0.023 | -0.015 | 11.443 | -0.048 | -0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | C | 24 | PHE | 0 | -0.021 | -0.001 | 12.656 | -0.089 | -0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | C | 25 | THR | 0 | 0.015 | 0.012 | 14.869 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | C | 26 | GLN | 0 | 0.101 | 0.025 | 17.119 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | C | 27 | SER | 0 | 0.031 | 0.023 | 20.266 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | C | 28 | ASN | 0 | -0.025 | -0.031 | 18.270 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | C | 29 | LEU | 0 | 0.004 | 0.008 | 17.913 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | C | 30 | GLU | -1 | -0.898 | -0.945 | 21.630 | 0.089 | 0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | C | 31 | LYS | 1 | 0.875 | 0.940 | 23.774 | -0.214 | -0.214 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | C | 32 | LEU | 0 | -0.045 | -0.007 | 21.299 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | C | 33 | PRO | 0 | 0.007 | 0.001 | 24.839 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | C | 34 | LYS | 1 | 1.030 | 1.007 | 28.013 | -0.076 | -0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | C | 35 | TYR | 0 | -0.072 | -0.067 | 24.716 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | C | 36 | LYS | 1 | 0.942 | 0.960 | 23.617 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | C | 37 | GLU | -1 | -0.889 | -0.931 | 28.287 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | C | 38 | LYS | 1 | 0.929 | 0.968 | 30.983 | -0.090 | -0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | C | 39 | LYS | 1 | 0.862 | 0.928 | 25.211 | -0.055 | -0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | C | 40 | ALA | 0 | -0.044 | 0.011 | 31.017 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | C | 41 | ALA | 0 | -0.018 | -0.019 | 33.769 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | C | 60 | THR | 0 | -0.001 | -0.003 | 22.181 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | C | 61 | CYS | 0 | -0.022 | -0.014 | 21.675 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | C | 62 | ALA | 0 | 0.028 | 0.016 | 18.587 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | C | 63 | LEU | 0 | 0.044 | 0.008 | 18.599 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | C | 64 | ASP | -1 | -0.781 | -0.861 | 20.443 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | C | 65 | TYR | 0 | -0.015 | -0.010 | 14.661 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | C | 66 | LEU | 0 | -0.091 | -0.033 | 16.224 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | C | 67 | ILE | 0 | -0.047 | -0.032 | 18.223 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | C | 68 | PRO | 0 | -0.024 | -0.004 | 18.723 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | C | 69 | PRO | 0 | 0.028 | 0.025 | 16.980 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | C | 70 | PRO | 0 | 0.024 | 0.011 | 20.172 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | C | 71 | MET | 0 | -0.017 | -0.022 | 21.730 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | C | 72 | PRO | 0 | -0.011 | -0.003 | 20.609 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | C | 73 | LYS | 1 | 0.995 | 0.995 | 23.311 | 0.063 | 0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | C | 74 | ASN | 0 | -0.006 | 0.011 | 23.538 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | C | 75 | GLN | 0 | -0.001 | -0.009 | 24.810 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | C | 76 | GLN | 0 | 0.017 | 0.000 | 21.368 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | C | 77 | TYR | 0 | 0.011 | -0.001 | 18.077 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | C | 78 | ARG | 1 | 0.930 | 0.974 | 21.768 | 0.179 | 0.179 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | C | 79 | ALA | 0 | 0.064 | 0.039 | 22.943 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | C | 80 | PHE | 0 | 0.006 | -0.001 | 23.055 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | C | 81 | GLY | 0 | -0.003 | 0.010 | 26.876 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |