FMODB ID: 828QY
Calculation Name: 4GEH-B-Xray318
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 4GEH
Chain ID: B
UniProt ID: Q9BUL8
Base Structure: X-ray
Registration Date: 2021-09-07
Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.
Modeling method
Optimization | MOE:Amber10:EHT |
---|---|
Restraint | OptH |
Protonation | MOE:Protonate 3D |
Complement | MOE:Structure Preparation |
Water | No |
Procedure | Auto-FMO protocol ver. 1.20200129 |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 68 |
LigandCharge | |
Software | ABINIT-MP - Open Ver.1 Rev. 15 / 20190524 |
Total energy (hartree)
FMO2-HF: Electronic energy | -338615.188497 |
---|---|
FMO2-HF: Nuclear repulsion | 311974.40438 |
FMO2-HF: Total energy | -26640.784116 |
FMO2-MP2: Total energy | -26715.169512 |
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(B:344:ACE )
Summations of interaction energy for
fragment #1(B:344:ACE )
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. |
1.634 | 2.404 | 0.048 | -0.336 | -0.481 | 0 |
Interaction energy analysis for fragmet #1(B:344:ACE )
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 | 346 | LEU | 0 | -0.062 | -0.022 | 3.248 | 1.671 | 2.441 | 0.048 | -0.336 | -0.481 | 0.000 |
4 | B | 347 | VAL | 0 | -0.036 | -0.020 | 5.987 | 0.319 | 0.319 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | B | 348 | GLN | 0 | -0.015 | -0.022 | 9.039 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | B | 349 | THR | 0 | -0.038 | -0.011 | 9.998 | -0.128 | -0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | B | 350 | LEU | 0 | 0.089 | 0.051 | 12.155 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | B | 351 | SER | 0 | 0.004 | -0.038 | 14.819 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | B | 352 | CYS | 0 | 0.030 | 0.039 | 17.368 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | B | 353 | LEU | 0 | 0.058 | 0.034 | 19.072 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | B | 354 | SER | 0 | 0.037 | 0.036 | 15.945 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | B | 355 | MET | 0 | -0.048 | -0.014 | 11.806 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | B | 356 | ILE | 0 | -0.012 | -0.014 | 16.025 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | B | 357 | ILE | 0 | -0.024 | -0.012 | 18.661 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | B | 358 | THR | 0 | 0.044 | 0.024 | 19.934 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | B | 359 | PRO | 0 | -0.013 | 0.005 | 16.979 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | B | 360 | ALA | 0 | 0.060 | 0.042 | 19.842 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | B | 361 | PHE | 0 | 0.001 | -0.025 | 22.339 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | B | 362 | ALA | 0 | -0.029 | -0.013 | 21.970 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | B | 363 | GLU | -1 | -0.899 | -0.954 | 20.348 | -0.198 | -0.198 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | B | 364 | LEU | 0 | -0.084 | -0.038 | 23.985 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | B | 365 | LYS | 1 | 0.906 | 0.952 | 27.006 | 0.151 | 0.151 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | B | 366 | GLN | 0 | 0.009 | 0.004 | 22.876 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | B | 367 | GLN | 0 | -0.085 | -0.030 | 27.315 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | B | 368 | ASP | -1 | -0.925 | -0.966 | 29.845 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | B | 369 | GLU | -1 | -0.842 | -0.923 | 28.083 | -0.108 | -0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | B | 370 | ASN | 0 | -0.095 | -0.052 | 32.150 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | B | 371 | ASN | 0 | -0.003 | 0.015 | 34.962 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | B | 372 | ALA | 0 | 0.016 | 0.001 | 35.648 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | B | 373 | SER | 0 | 0.005 | 0.003 | 37.053 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | B | 374 | ARG | 1 | 0.898 | 0.951 | 30.516 | 0.094 | 0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | B | 375 | ASN | 0 | 0.030 | -0.001 | 32.126 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | B | 376 | GLN | 0 | 0.027 | 0.030 | 32.788 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | B | 377 | ALA | 0 | -0.006 | 0.000 | 34.851 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | B | 378 | ILE | 0 | -0.030 | -0.011 | 28.866 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | B | 379 | GLU | -1 | -0.912 | -0.968 | 30.247 | -0.119 | -0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | B | 380 | GLU | -1 | -0.971 | -0.989 | 31.259 | -0.084 | -0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | B | 381 | LEU | 0 | -0.023 | -0.006 | 30.334 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | B | 382 | GLU | -1 | -0.874 | -0.957 | 24.584 | -0.188 | -0.188 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | B | 383 | LYS | 1 | 0.951 | 0.982 | 28.376 | 0.089 | 0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | B | 384 | SER | 0 | -0.017 | -0.020 | 30.525 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | B | 385 | ILE | 0 | -0.024 | -0.004 | 26.257 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | B | 386 | ALA | 0 | 0.023 | 0.004 | 26.985 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | B | 387 | VAL | 0 | -0.041 | -0.010 | 27.908 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | B | 388 | ALA | 0 | -0.015 | -0.012 | 30.097 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | B | 389 | GLU | -1 | -0.798 | -0.888 | 23.899 | -0.169 | -0.169 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | B | 390 | ALA | 0 | -0.037 | -0.020 | 27.552 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | B | 391 | ALA | 0 | -0.029 | -0.002 | 29.052 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | B | 392 | CYS | 0 | -0.090 | -0.043 | 29.983 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | B | 393 | PRO | 0 | 0.074 | 0.044 | 25.160 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | B | 394 | GLY | 0 | -0.021 | -0.022 | 23.379 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | B | 395 | ILE | 0 | -0.056 | -0.029 | 24.443 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | B | 396 | THR | 0 | 0.016 | -0.016 | 23.430 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | B | 397 | ASP | -1 | -0.923 | -0.967 | 20.098 | -0.192 | -0.192 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | B | 398 | LYS | 1 | 0.940 | 0.961 | 22.659 | 0.126 | 0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | B | 399 | MET | 0 | -0.033 | -0.009 | 25.837 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | B | 400 | VAL | 0 | 0.044 | 0.016 | 21.273 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | B | 401 | LYS | 1 | 0.881 | 0.928 | 23.354 | 0.104 | 0.104 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | B | 402 | LYS | 1 | 0.939 | 0.961 | 24.488 | 0.091 | 0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | B | 403 | LEU | 0 | -0.012 | 0.009 | 26.300 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | B | 404 | ILE | 0 | 0.028 | 0.007 | 22.498 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | B | 405 | GLU | -1 | -0.860 | -0.920 | 25.861 | -0.076 | -0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | B | 406 | LYS | 1 | 0.935 | 0.965 | 27.885 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | B | 407 | PHE | 0 | 0.015 | 0.009 | 28.081 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | B | 408 | GLN | 0 | -0.029 | -0.018 | 22.858 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | B | 409 | LYS | 1 | 0.868 | 0.937 | 26.967 | 0.071 | 0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | B | 410 | CYS | 0 | -0.027 | -0.001 | 31.524 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | B | 411 | NME | 0 | 0.006 | 0.021 | 33.205 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |