![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: K9KM3
Calculation Name: 5UA4-B-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 5UA4
Chain ID: B
UniProt ID: P42485
Base Structure: X-ray
Registration Date: 2023-06-22
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 | OptHSide |
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 | 32 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -101950.659232 |
---|---|
FMO2-HF: Nuclear repulsion | 89290.881575 |
FMO2-HF: Total energy | -12659.777657 |
FMO2-MP2: Total energy | -12696.567352 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F026613/ligand_interaction/ligand_F026613.png)
Ligand Interaction
![ligand interaction](./Kdata/F026613/ligand_interaction/ligand_interaction_F026613.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(B:26:SER)
Summations of interaction energy for
fragment #1(B:26: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. |
-6.197 | -3.449 | 3.166 | -2.77 | -3.144 | -0.001 |
Interaction energy analysis for fragmet #1(B:26: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 | B | 28 | GLU | -1 | -0.745 | -0.864 | 3.434 | -1.848 | 0.334 | 0.036 | -0.980 | -1.237 | 0.004 |
4 | B | 29 | ALA | 0 | -0.029 | -0.021 | 2.223 | -2.011 | -2.292 | 3.120 | -1.371 | -1.468 | -0.006 |
5 | B | 30 | VAL | 0 | 0.003 | -0.004 | 3.631 | -0.745 | 0.102 | 0.010 | -0.419 | -0.439 | 0.001 |
6 | B | 31 | ILE | 0 | 0.017 | 0.013 | 5.726 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | B | 32 | ARG | 1 | 0.861 | 0.904 | 6.861 | -1.573 | -1.573 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | B | 33 | ASP | -1 | -0.874 | -0.930 | 7.646 | -0.623 | -0.623 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | B | 34 | ILE | 0 | 0.008 | 0.003 | 9.389 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | B | 35 | ALA | 0 | 0.017 | 0.005 | 11.272 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | B | 36 | ARG | 1 | 0.843 | 0.929 | 11.842 | 0.273 | 0.273 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | B | 37 | HIS | 0 | -0.019 | -0.020 | 11.865 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | B | 38 | LEU | 0 | 0.010 | 0.002 | 15.526 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | B | 39 | ALA | 0 | 0.010 | 0.021 | 16.736 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | B | 40 | ARG | 1 | 0.962 | 0.980 | 16.198 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | B | 41 | ILE | 0 | -0.032 | -0.017 | 19.069 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | B | 42 | GLY | 0 | 0.044 | 0.023 | 21.216 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | B | 43 | ASP | -1 | -0.864 | -0.936 | 21.558 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | B | 44 | ARG | 1 | 0.852 | 0.907 | 22.213 | 0.081 | 0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | B | 45 | MET | 0 | -0.073 | -0.023 | 25.737 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | B | 46 | GLU | -1 | -0.915 | -0.952 | 26.714 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | B | 47 | TYR | 0 | -0.043 | -0.006 | 25.383 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | B | 48 | GLY | 0 | 0.014 | 0.010 | 29.861 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | B | 49 | ILE | 0 | -0.096 | -0.050 | 25.490 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | B | 50 | ARG | 1 | 0.961 | 0.990 | 28.987 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | B | 51 | PRO | 0 | -0.005 | -0.012 | 28.470 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | B | 52 | GLY | 0 | 0.014 | 0.002 | 28.481 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | B | 53 | LEU | 0 | -0.030 | -0.015 | 28.839 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | B | 54 | VAL | 0 | 0.008 | 0.004 | 31.970 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | B | 55 | ASP | -1 | -0.909 | -0.943 | 35.086 | -0.100 | -0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | B | 56 | SER | 0 | -0.061 | -0.035 | 37.651 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | B | 57 | LEU | 0 | -0.005 | 0.005 | 41.316 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |