![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: R9548
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 | 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 | 48 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -206615.125736 |
---|---|
FMO2-HF: Nuclear repulsion | 187146.620205 |
FMO2-HF: Total energy | -19468.505531 |
FMO2-MP2: Total energy | -19524.917056 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F024975/ligand_interaction/ligand_F024975.png)
Ligand Interaction
![ligand interaction](./Kdata/F024975/ligand_interaction/ligand_interaction_F024975.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. |
-0.066 | 2.409 | -0.015 | -1.412 | -1.048 | 0.006 |
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 | 0.005 | -0.004 | 3.891 | 0.588 | 3.063 | -0.015 | -1.412 | -1.048 | 0.006 |
4 | C | 19 | SER | 0 | 0.039 | 0.016 | 6.949 | 0.295 | 0.295 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | C | 20 | TYR | 0 | 0.013 | -0.010 | 7.824 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | C | 21 | VAL | 0 | 0.054 | 0.031 | 7.669 | -0.087 | -0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | C | 22 | LYS | 1 | 0.951 | 0.990 | 10.402 | -0.638 | -0.638 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | C | 23 | PHE | 0 | -0.001 | -0.006 | 12.135 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | C | 24 | PHE | 0 | 0.002 | 0.012 | 13.349 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | C | 25 | THR | 0 | 0.002 | 0.004 | 15.543 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | C | 26 | GLN | 0 | 0.075 | 0.027 | 17.620 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | C | 27 | SER | 0 | 0.123 | 0.074 | 20.674 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | C | 28 | ASN | 0 | -0.093 | -0.046 | 18.452 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | C | 29 | LEU | 0 | 0.027 | 0.009 | 18.246 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | C | 30 | GLU | -1 | -0.900 | -0.960 | 22.086 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | C | 31 | LYS | 1 | 0.811 | 0.887 | 23.144 | -0.119 | -0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | C | 32 | LEU | 0 | -0.040 | -0.002 | 21.481 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | C | 33 | PRO | 0 | 0.005 | -0.001 | 25.203 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | C | 34 | LYS | 1 | 1.025 | 1.013 | 28.382 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | C | 35 | TYR | 0 | -0.090 | -0.071 | 24.397 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | C | 36 | LYS | 1 | 0.884 | 0.937 | 22.550 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | C | 37 | GLU | -1 | -0.882 | -0.935 | 28.656 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | C | 38 | LYS | 1 | 0.935 | 0.969 | 31.455 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | C | 39 | LYS | 1 | 0.838 | 0.913 | 25.400 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | C | 40 | ALA | 0 | -0.026 | 0.009 | 31.335 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | C | 41 | ALA | 0 | -0.023 | -0.008 | 34.167 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | C | 60 | THR | 0 | -0.031 | -0.027 | 22.271 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | C | 61 | CYS | 0 | -0.067 | -0.021 | 21.905 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | C | 62 | ALA | 0 | 0.045 | 0.005 | 18.530 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | C | 63 | LEU | 0 | 0.028 | 0.004 | 18.730 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | C | 64 | ASP | -1 | -0.695 | -0.822 | 20.765 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | C | 65 | TYR | 0 | -0.031 | -0.012 | 14.714 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | C | 66 | LEU | 0 | -0.024 | 0.006 | 16.600 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | C | 67 | ILE | 0 | -0.018 | -0.025 | 18.943 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | C | 68 | PRO | 0 | 0.007 | 0.011 | 19.310 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | C | 69 | PRO | 0 | 0.019 | 0.021 | 17.115 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | C | 70 | PRO | 0 | 0.003 | 0.002 | 20.268 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | C | 71 | MET | 0 | 0.016 | -0.003 | 22.062 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | C | 72 | PRO | 0 | -0.007 | -0.004 | 20.611 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | C | 73 | LYS | 1 | 0.975 | 0.983 | 23.439 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | C | 74 | ASN | 0 | -0.001 | 0.010 | 23.578 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | C | 75 | GLN | 0 | 0.057 | 0.030 | 24.125 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | C | 76 | GLN | 0 | 0.007 | 0.001 | 20.816 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | C | 77 | TYR | 0 | 0.038 | 0.009 | 18.097 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | C | 78 | ARG | 1 | 0.867 | 0.935 | 22.040 | 0.122 | 0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | C | 79 | ALA | 0 | 0.023 | 0.016 | 22.496 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | C | 80 | PHE | 0 | 0.016 | 0.008 | 22.675 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | C | 81 | GLY | 0 | -0.004 | 0.010 | 26.804 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |