FMODB ID: 72QLK
Calculation Name: 3RCZ-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3RCZ
Chain ID: A
UniProt ID: Q9USX3
Base Structure: X-ray
Registration Date: 2023-09-19
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 | 74 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -500222.709115 |
---|---|
FMO2-HF: Nuclear repulsion | 469956.753732 |
FMO2-HF: Total energy | -30265.955383 |
FMO2-MP2: Total energy | -30355.561323 |
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:330:HIS)
Summations of interaction energy for
fragment #1(A:330:HIS)
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. |
-6.926 | -3.839 | -0.015 | -1.389 | -1.684 | 0.002 |
Interaction energy analysis for fragmet #1(A:330:HIS)
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 | 333 | LEU | 0 | -0.051 | -0.014 | 3.219 | -2.938 | -0.033 | -0.014 | -1.361 | -1.531 | 0.002 |
4 | A | 334 | ILE | 0 | 0.070 | 0.061 | 4.300 | -0.899 | -0.717 | -0.001 | -0.028 | -0.153 | 0.000 |
5 | A | 335 | THR | 0 | -0.028 | -0.025 | 7.078 | 0.506 | 0.506 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 336 | LEU | 0 | 0.034 | 0.039 | 9.977 | -0.138 | -0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 337 | LEU | 0 | -0.050 | -0.028 | 13.405 | 0.113 | 0.113 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 338 | LEU | 0 | -0.007 | 0.002 | 16.060 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 339 | ARG | 1 | 0.855 | 0.915 | 19.392 | 0.149 | 0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 340 | SER | 0 | 0.019 | 0.010 | 22.854 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 341 | SER | 0 | -0.043 | -0.027 | 26.091 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 342 | LYS | 1 | 0.911 | 0.925 | 29.477 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 343 | SER | 0 | -0.012 | 0.015 | 26.054 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 344 | GLU | -1 | -0.906 | -0.945 | 25.582 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 345 | ASP | -1 | -0.823 | -0.892 | 21.320 | -0.059 | -0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 346 | LEU | 0 | -0.018 | -0.003 | 18.134 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 347 | ARG | 1 | 0.911 | 0.963 | 14.820 | 0.112 | 0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 348 | LEU | 0 | -0.021 | -0.008 | 13.825 | 0.089 | 0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 349 | SER | 0 | 0.041 | 0.027 | 8.515 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 350 | ILE | 0 | -0.060 | -0.030 | 9.717 | 0.291 | 0.291 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 351 | PRO | 0 | 0.008 | -0.014 | 7.542 | -0.130 | -0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 352 | VAL | 0 | 0.054 | 0.027 | 6.337 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 353 | ASP | -1 | -0.945 | -0.970 | 8.887 | 0.908 | 0.908 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 354 | PHE | 0 | -0.040 | -0.018 | 10.881 | 0.129 | 0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 355 | THR | 0 | -0.004 | 0.005 | 13.492 | -0.120 | -0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 356 | VAL | 0 | 0.076 | 0.049 | 16.525 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 357 | LYS | 1 | 0.942 | 0.966 | 18.144 | -0.131 | -0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 358 | ASP | -1 | -0.895 | -0.940 | 16.453 | 0.348 | 0.348 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 359 | LEU | 0 | 0.003 | 0.009 | 14.466 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 360 | ILE | 0 | 0.014 | 0.005 | 16.919 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 361 | LYS | 1 | 0.874 | 0.936 | 20.356 | -0.229 | -0.229 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 362 | ARG | 1 | 0.966 | 0.980 | 13.877 | -0.622 | -0.622 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 363 | TYR | 0 | 0.100 | 0.045 | 18.891 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 364 | CYS | 0 | -0.061 | -0.027 | 20.107 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 365 | THR | 0 | -0.022 | -0.018 | 20.977 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 366 | GLU | -1 | -0.987 | -0.982 | 18.674 | 0.417 | 0.417 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 367 | VAL | 0 | -0.004 | -0.001 | 21.554 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 368 | LYS | 1 | 0.838 | 0.934 | 24.432 | -0.260 | -0.260 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 369 | ILE | 0 | 0.021 | 0.020 | 25.988 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 370 | SER | 0 | -0.045 | -0.029 | 27.217 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 371 | PHE | 0 | 0.056 | 0.012 | 24.225 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 372 | HIS | 0 | -0.020 | -0.025 | 27.443 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 373 | GLU | -1 | -0.892 | -0.964 | 27.836 | 0.098 | 0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 374 | ARG | 1 | 0.914 | 0.974 | 28.798 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 375 | ILE | 0 | -0.066 | -0.019 | 24.976 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 376 | ARG | 1 | 0.946 | 0.979 | 25.019 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 377 | LEU | 0 | 0.017 | 0.009 | 18.907 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 378 | GLU | -1 | -0.917 | -0.962 | 22.758 | -0.186 | -0.186 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 379 | PHE | 0 | 0.058 | 0.017 | 17.610 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 380 | GLU | -1 | -0.888 | -0.935 | 20.834 | -0.438 | -0.438 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 381 | GLY | 0 | -0.063 | -0.026 | 23.586 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 382 | GLU | -1 | -0.956 | -0.969 | 23.831 | -0.226 | -0.226 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 383 | TRP | 0 | -0.107 | -0.077 | 24.109 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 384 | LEU | 0 | 0.059 | 0.029 | 18.057 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 385 | ASP | -1 | -0.833 | -0.914 | 21.547 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 386 | PRO | 0 | -0.061 | -0.045 | 20.847 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 387 | ASN | 0 | -0.054 | -0.056 | 20.854 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 388 | ASP | -1 | -0.845 | -0.890 | 17.782 | -0.128 | -0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 389 | GLN | 0 | -0.038 | -0.028 | 13.132 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 390 | VAL | 0 | 0.068 | 0.028 | 10.832 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 391 | GLN | 0 | -0.067 | -0.041 | 8.956 | -0.286 | -0.286 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 392 | SER | 0 | -0.092 | -0.044 | 11.045 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 393 | THR | 0 | -0.069 | -0.034 | 13.863 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 394 | GLU | -1 | -0.895 | -0.949 | 14.088 | -0.690 | -0.690 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 395 | LEU | 0 | -0.101 | -0.039 | 13.264 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 396 | GLU | -1 | -0.941 | -0.968 | 10.905 | -1.296 | -1.296 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 397 | ASP | -1 | -0.924 | -0.987 | 8.104 | -0.633 | -0.633 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 398 | GLU | -1 | -0.957 | -0.999 | 10.196 | -0.239 | -0.239 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 399 | ASP | -1 | -0.811 | -0.871 | 13.138 | -0.577 | -0.577 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 400 | GLN | 0 | -0.081 | -0.053 | 15.411 | 0.083 | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 401 | VAL | 0 | 0.013 | 0.012 | 16.710 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 402 | SER | 0 | -0.024 | -0.016 | 19.456 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 403 | VAL | 0 | -0.022 | -0.013 | 21.658 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 404 | VAL | 0 | -0.068 | -0.039 | 24.108 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |