FMODB ID: ZV8VN
Calculation Name: 3HJ2-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3HJ2
Chain ID: A
UniProt ID: P59665
Base Structure: X-ray
Registration Date: 2023-09-23
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 | 30 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -122016.330792 |
---|---|
FMO2-HF: Nuclear repulsion | 107522.481408 |
FMO2-HF: Total energy | -14493.849384 |
FMO2-MP2: Total energy | -14530.005925 |
3D Structure
Ligand structure
Ligand Interaction
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:1:CYS)
Summations of interaction energy for
fragment #1(A:1:CYS)
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. |
-0.904 | 1.48 | -0.014 | -1.387 | -0.983 | 0.006 |
Interaction energy analysis for fragmet #1(A:1:CYS)
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 | 3 | GLY | 0 | -0.025 | -0.014 | 3.874 | -1.372 | 1.012 | -0.014 | -1.387 | -0.983 | 0.006 |
4 | A | 4 | ALA | 0 | 0.018 | 0.020 | 5.820 | 0.421 | 0.421 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 33 | CYS | 0 | 0.017 | 0.021 | 7.587 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | TYR | 0 | 0.015 | 0.006 | 6.528 | 0.400 | 0.400 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 7 | CYS | 0 | -0.028 | 0.015 | 12.182 | -0.114 | -0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | ARG | 1 | 0.805 | 0.877 | 10.935 | -0.303 | -0.303 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | ILE | 0 | 0.021 | 0.029 | 17.887 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | PRO | 0 | 0.019 | 0.006 | 21.516 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | ALA | 0 | -0.023 | -0.033 | 20.956 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | CYS | 0 | -0.072 | -0.031 | 14.242 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | ILE | 0 | 0.034 | 0.013 | 13.588 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | ALA | 0 | 0.012 | 0.001 | 15.634 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | GLY | 0 | 0.041 | 0.022 | 13.646 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | GLU | -1 | -0.798 | -0.849 | 11.664 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | ARG | 1 | 0.942 | 0.962 | 13.877 | 0.271 | 0.271 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | ARG | 1 | 0.913 | 0.938 | 15.960 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | TYR | 0 | 0.000 | -0.007 | 14.899 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | GLY | 0 | 0.040 | 0.022 | 18.724 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | THR | 0 | -0.034 | -0.015 | 20.631 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 23 | ILE | 0 | 0.059 | 0.018 | 20.245 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 24 | TYR | 0 | 0.033 | 0.016 | 18.926 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 25 | GLN | 0 | 0.043 | 0.023 | 21.375 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 26 | GLY | 0 | 0.026 | 0.024 | 24.424 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 27 | ARG | 1 | 0.892 | 0.945 | 24.352 | -0.154 | -0.154 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 28 | LEU | 0 | 0.018 | 0.008 | 24.003 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 29 | TRP | 0 | -0.032 | -0.022 | 19.292 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 30 | ALA | 0 | -0.016 | -0.007 | 19.294 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 31 | PHE | 0 | 0.048 | 0.010 | 13.969 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |