![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: V5RY1
Calculation Name: 3FBN-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3FBN
Chain ID: A
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 | 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 | 54 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -248542.993496 |
---|---|
FMO2-HF: Nuclear repulsion | 226477.521732 |
FMO2-HF: Total energy | -22065.471764 |
FMO2-MP2: Total energy | -22129.655269 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F024969/ligand_interaction/ligand_F024969.png)
Ligand Interaction
![ligand interaction](./Kdata/F024969/ligand_interaction/ligand_interaction_F024969.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:16:THR)
Summations of interaction energy for
fragment #1(A: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. |
-0.944 | 1.93 | 0.052 | -1.541 | -1.384 | 0.004 |
Interaction energy analysis for fragmet #1(A: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 | A | 18 | PRO | 0 | 0.037 | 0.012 | 3.243 | -1.177 | 1.697 | 0.052 | -1.541 | -1.384 | 0.004 |
4 | A | 19 | SER | 0 | 0.036 | 0.013 | 5.938 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 20 | TYR | 0 | 0.026 | 0.005 | 6.825 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 21 | VAL | 0 | 0.030 | 0.014 | 7.486 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 22 | LYS | 1 | 0.936 | 0.981 | 9.246 | -0.186 | -0.186 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 23 | PHE | 0 | 0.019 | 0.004 | 10.871 | 0.071 | 0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 24 | PHE | 0 | -0.005 | 0.015 | 12.563 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 25 | THR | 0 | -0.009 | -0.010 | 14.949 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 26 | GLN | 0 | 0.076 | 0.029 | 17.077 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 27 | SER | 0 | 0.055 | 0.038 | 20.410 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 28 | ASN | 0 | -0.071 | -0.043 | 17.470 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 29 | LEU | 0 | 0.031 | 0.016 | 18.209 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 30 | GLU | -1 | -0.904 | -0.965 | 21.669 | -0.088 | -0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 31 | LYS | 1 | 0.853 | 0.921 | 22.236 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 32 | LEU | 0 | -0.036 | -0.002 | 21.035 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 33 | PRO | 0 | -0.004 | -0.002 | 24.611 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 34 | LYS | 1 | 1.046 | 1.019 | 28.020 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 35 | TYR | 0 | -0.089 | -0.064 | 23.501 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 36 | LYS | 1 | 0.894 | 0.946 | 22.102 | 0.196 | 0.196 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 37 | GLU | -1 | -0.912 | -0.954 | 27.885 | -0.074 | -0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 38 | LYS | 1 | 0.927 | 0.961 | 30.008 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 39 | LYS | 1 | 0.785 | 0.872 | 24.244 | 0.080 | 0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 40 | ALA | 0 | -0.021 | 0.007 | 29.864 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 41 | ALA | 0 | -0.045 | -0.009 | 32.578 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 57 | GLU | -1 | -1.001 | -1.014 | 17.885 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 58 | GLU | -1 | -0.846 | -0.927 | 21.828 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 59 | ILE | 0 | -0.037 | -0.006 | 17.629 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 60 | THR | 0 | -0.044 | -0.020 | 20.937 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 61 | CYS | 0 | -0.058 | -0.020 | 21.178 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 62 | ALA | 0 | 0.019 | -0.011 | 17.481 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 63 | LEU | 0 | 0.025 | -0.005 | 17.615 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 64 | ASP | -1 | -0.687 | -0.797 | 19.806 | -0.089 | -0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 65 | TYR | 0 | 0.003 | 0.001 | 14.488 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 66 | LEU | 0 | -0.049 | -0.008 | 15.873 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 67 | ILE | 0 | -0.004 | -0.023 | 18.294 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 68 | PRO | 0 | -0.009 | 0.003 | 18.728 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 69 | PRO | 0 | 0.036 | 0.030 | 17.098 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 70 | PRO | 0 | 0.006 | 0.006 | 19.997 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 71 | MET | 0 | 0.018 | -0.002 | 22.522 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 72 | PRO | 0 | -0.003 | 0.006 | 21.272 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 73 | LYS | 1 | 0.957 | 0.972 | 24.344 | 0.101 | 0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 74 | ASN | 0 | 0.012 | 0.007 | 23.789 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 75 | GLN | 0 | 0.063 | 0.012 | 25.624 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 76 | GLN | 0 | 0.036 | 0.027 | 23.878 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 77 | TYR | 0 | 0.009 | 0.007 | 18.612 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 78 | ARG | 1 | 0.863 | 0.942 | 21.954 | 0.147 | 0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 79 | ALA | 0 | 0.015 | 0.006 | 22.278 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 80 | PHE | 0 | 0.002 | -0.001 | 21.766 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 81 | GLY | 0 | 0.037 | 0.014 | 25.113 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 82 | SER | 0 | -0.083 | -0.038 | 22.889 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 83 | ILE | 0 | 0.014 | 0.008 | 19.815 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 84 | TRP | 0 | 0.036 | 0.029 | 20.687 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |