FMODB ID: ZY4ZN
Calculation Name: 3SWY-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3SWY
Chain ID: A
UniProt ID: Q16281
Base Structure: X-ray
Registration Date: 2023-06-20
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 | 46 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -174133.570956 |
---|---|
FMO2-HF: Nuclear repulsion | 155518.902321 |
FMO2-HF: Total energy | -18614.668635 |
FMO2-MP2: Total energy | -18667.980607 |
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:GLY)
Summations of interaction energy for
fragment #1(A:1:GLY)
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. |
-10.431 | -11.271 | 13.197 | -6.49 | -5.868 | -0.045 |
Interaction energy analysis for fragmet #1(A:1:GLY)
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 | LEU | 0 | -0.041 | -0.006 | 3.800 | 0.129 | 2.276 | -0.006 | -1.178 | -0.963 | 0.004 |
4 | A | 4 | GLU | -1 | -0.828 | -0.922 | 1.866 | -14.497 | -18.269 | 13.201 | -5.129 | -4.301 | -0.049 |
5 | A | 5 | GLU | -1 | -0.889 | -0.945 | 3.573 | -0.550 | 0.156 | 0.003 | -0.177 | -0.532 | 0.000 |
6 | A | 6 | LYS | 1 | 0.936 | 0.977 | 5.387 | 2.690 | 2.769 | -0.001 | -0.006 | -0.072 | 0.000 |
7 | A | 7 | VAL | 0 | -0.021 | -0.016 | 7.466 | 0.700 | 0.700 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | GLU | -1 | -0.872 | -0.926 | 7.515 | -0.706 | -0.706 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | GLN | 0 | -0.026 | -0.007 | 8.837 | 0.486 | 0.486 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | LEU | 0 | -0.046 | -0.014 | 11.441 | 0.276 | 0.276 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | GLY | 0 | 0.023 | 0.018 | 12.479 | 0.166 | 0.166 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | SER | 0 | 0.056 | 0.016 | 12.959 | 0.144 | 0.144 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | SER | 0 | -0.048 | -0.031 | 15.253 | 0.135 | 0.135 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | LEU | 0 | -0.030 | -0.010 | 17.000 | 0.090 | 0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | ASP | -1 | -0.851 | -0.923 | 17.458 | -0.414 | -0.414 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | THR | 0 | -0.061 | -0.032 | 19.079 | 0.077 | 0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | LEU | 0 | -0.042 | -0.026 | 21.271 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | GLN | 0 | 0.023 | 0.009 | 22.458 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | THR | 0 | -0.038 | -0.027 | 23.419 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | ARG | 1 | 0.896 | 0.937 | 24.728 | 0.302 | 0.302 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | PHE | 0 | 0.012 | 0.009 | 27.203 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | ALA | 0 | 0.025 | 0.009 | 28.617 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | ARG | 1 | 0.910 | 0.971 | 27.541 | 0.212 | 0.212 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | LEU | 0 | 0.079 | 0.042 | 31.813 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | LEU | 0 | 0.006 | 0.009 | 33.112 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | ALA | 0 | 0.005 | 0.006 | 34.930 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | GLU | -1 | -0.908 | -0.968 | 34.384 | -0.144 | -0.144 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | TYR | 0 | 0.014 | 0.026 | 37.481 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | ASN | 0 | -0.027 | -0.023 | 38.252 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | ALA | 0 | 0.022 | 0.015 | 40.903 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | THR | 0 | -0.049 | -0.046 | 41.368 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | GLN | 0 | -0.005 | -0.002 | 43.273 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | MET | 0 | -0.031 | -0.019 | 45.026 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | LYS | 1 | 0.950 | 0.981 | 47.043 | 0.076 | 0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | MET | 0 | 0.003 | -0.009 | 46.534 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | LYS | 1 | 0.979 | 0.991 | 47.233 | 0.095 | 0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | GLN | 0 | -0.014 | -0.001 | 51.362 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | ARG | 1 | 0.905 | 0.945 | 50.222 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | LEU | 0 | 0.010 | 0.011 | 51.186 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | SER | 0 | 0.059 | 0.009 | 55.088 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | GLN | 0 | -0.047 | -0.009 | 57.154 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | LEU | 0 | 0.006 | 0.020 | 56.852 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | GLU | -1 | -0.874 | -0.937 | 57.143 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | SER | 0 | -0.115 | -0.059 | 60.853 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | GLN | 0 | -0.050 | -0.024 | 62.195 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | VAL | 0 | -0.030 | -0.001 | 62.751 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |