FMODB ID: 82Q4Y
Calculation Name: 3LE4-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3LE4
Chain ID: A
UniProt ID: Q8WYQ5
Base Structure: X-ray
Registration Date: 2023-03-14
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 | OptH |
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 | 55 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -267183.461293 |
---|---|
FMO2-HF: Nuclear repulsion | 245388.327288 |
FMO2-HF: Total energy | -21795.134005 |
FMO2-MP2: Total energy | -21858.756443 |
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:298:PRO)
Summations of interaction energy for
fragment #1(A:298:PRO)
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. |
-6.183 | -1.322 | 3.032 | -2.587 | -5.307 | -0.009 |
Interaction energy analysis for fragmet #1(A:298:PRO)
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 | 300 | THR | 0 | -0.044 | -0.034 | 2.930 | -3.219 | -0.752 | 0.217 | -1.330 | -1.354 | -0.003 |
4 | A | 301 | GLU | -1 | -0.872 | -0.916 | 5.234 | -0.330 | -0.207 | -0.001 | -0.005 | -0.117 | 0.000 |
5 | A | 302 | PRO | 0 | -0.011 | -0.010 | 7.821 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 303 | LEU | 0 | -0.033 | -0.012 | 11.213 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 304 | PRO | 0 | 0.009 | 0.010 | 12.972 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 305 | ASP | -1 | -0.841 | -0.922 | 15.900 | -0.076 | -0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 306 | GLY | 0 | -0.050 | -0.028 | 19.363 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 307 | TRP | 0 | -0.045 | -0.027 | 15.833 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 308 | ILE | 0 | -0.025 | -0.009 | 16.025 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 309 | MET | 0 | -0.007 | 0.009 | 9.993 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 310 | THR | 0 | -0.031 | -0.025 | 13.793 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 311 | PHE | 0 | 0.051 | 0.029 | 15.180 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 312 | HIS | 0 | 0.070 | 0.056 | 16.332 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 313 | ASN | 0 | 0.031 | -0.005 | 17.838 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 314 | SER | 0 | -0.067 | -0.044 | 17.383 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 315 | GLY | 0 | 0.000 | 0.002 | 16.372 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 316 | VAL | 0 | -0.032 | 0.004 | 11.771 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 317 | PRO | 0 | -0.014 | -0.008 | 9.314 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 318 | VAL | 0 | -0.006 | 0.000 | 12.358 | -0.048 | -0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 319 | TYR | 0 | -0.015 | -0.021 | 8.390 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 320 | LEU | 0 | -0.003 | -0.003 | 14.742 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 321 | HIS | 0 | 0.084 | 0.071 | 18.389 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 322 | ARG | 1 | 0.942 | 0.946 | 20.439 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 323 | GLU | -1 | -0.959 | -0.983 | 23.147 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 324 | SER | 0 | -0.004 | -0.022 | 23.347 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 325 | ARG | 1 | 0.899 | 0.952 | 24.074 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 326 | VAL | 0 | 0.044 | 0.042 | 19.977 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 327 | VAL | 0 | -0.008 | -0.012 | 17.646 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 328 | THR | 0 | 0.000 | 0.002 | 13.934 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 329 | TRP | 0 | 0.040 | 0.003 | 13.725 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 330 | SER | 0 | -0.021 | 0.004 | 9.932 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 331 | ARG | 1 | 0.892 | 0.943 | 6.962 | 0.439 | 0.439 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 332 | PRO | 0 | 0.006 | 0.024 | 9.599 | -0.077 | -0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 333 | TYR | 0 | 0.001 | -0.056 | 10.235 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 334 | PHE | 0 | 0.023 | 0.012 | 12.390 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 335 | LEU | 0 | 0.008 | 0.018 | 14.364 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 336 | GLY | 0 | 0.028 | 0.012 | 16.197 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 337 | THR | 0 | -0.036 | -0.029 | 19.184 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 338 | GLY | 0 | 0.035 | 0.034 | 17.710 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 339 | SER | 0 | -0.026 | -0.015 | 18.788 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 340 | ILE | 0 | 0.096 | 0.025 | 17.422 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 341 | ARG | 1 | 0.913 | 0.938 | 17.810 | 0.111 | 0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 342 | LYS | 1 | 0.942 | 0.961 | 18.462 | 0.123 | 0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 343 | HIS | 0 | -0.041 | 0.051 | 12.987 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 344 | ASP | -1 | -0.832 | -0.907 | 10.701 | -0.284 | -0.284 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 345 | PRO | 0 | -0.046 | -0.024 | 8.516 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 346 | PRO | 0 | 0.066 | 0.034 | 6.597 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 347 | LEU | 0 | 0.050 | 0.010 | 2.584 | -1.149 | -0.294 | 1.188 | -0.557 | -1.486 | 0.000 |
51 | A | 348 | SER | 0 | -0.040 | -0.012 | 2.326 | -2.706 | -0.873 | 1.595 | -1.301 | -2.128 | -0.006 |
52 | A | 349 | SER | 0 | -0.071 | -0.069 | 3.155 | 0.976 | 0.559 | 0.033 | 0.606 | -0.222 | 0.000 |
53 | A | 350 | ILE | 0 | -0.053 | -0.002 | 5.053 | 0.279 | 0.279 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 351 | PRO | 0 | 0.001 | 0.008 | 6.074 | -0.157 | -0.157 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 352 | CYS | 0 | -0.010 | -0.002 | 8.826 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |