![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: R8N28
Calculation Name: 2PJW-H-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2PJW
Chain ID: H
UniProt ID: P38753
Base Structure: X-ray
Registration Date: 2023-09-20
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 | 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 | 88 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -469816.170338 |
---|---|
FMO2-HF: Nuclear repulsion | 434726.46046 |
FMO2-HF: Total energy | -35089.709878 |
FMO2-MP2: Total energy | -35190.547993 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F032070/ligand_interaction/ligand_F032070.png)
Ligand Interaction
![ligand interaction](./Kdata/F032070/ligand_interaction/ligand_interaction_F032070.png)
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(H:288:LYS)
Summations of interaction energy for
fragment #1(H:288:LYS)
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. |
104.017 | 101.078 | 19.492 | -6.59 | -9.962 | -0.017 |
Interaction energy analysis for fragmet #1(H:288:LYS)
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 | H | 290 | ALA | 0 | 0.020 | 0.011 | 2.762 | 1.048 | 3.161 | 0.098 | -0.839 | -1.372 | 0.002 |
4 | H | 291 | ILE | 0 | -0.010 | 0.011 | 1.885 | 4.530 | 0.332 | 11.890 | -3.578 | -4.115 | -0.004 |
5 | H | 292 | VAL | 0 | 0.008 | 0.005 | 4.560 | 3.402 | 3.585 | -0.001 | -0.031 | -0.151 | 0.000 |
6 | H | 293 | PHE | 0 | -0.035 | -0.026 | 6.776 | 3.534 | 3.534 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | H | 294 | SER | 0 | 0.011 | 0.020 | 7.320 | 2.924 | 2.924 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | H | 295 | GLN | 0 | -0.024 | -0.022 | 9.407 | 2.683 | 2.683 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | H | 296 | LYS | 1 | 0.943 | 0.975 | 11.765 | 20.214 | 20.214 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | H | 297 | THR | 0 | 0.058 | 0.020 | 13.821 | 0.499 | 0.499 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | H | 298 | THR | 0 | 0.039 | 0.034 | 14.711 | 0.928 | 0.928 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | H | 299 | ILE | 0 | -0.010 | 0.005 | 12.522 | 0.590 | 0.590 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | H | 300 | ASP | -1 | -0.923 | -0.947 | 16.719 | -14.114 | -14.114 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | H | 301 | GLN | 0 | 0.011 | -0.010 | 19.611 | 0.250 | 0.250 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | H | 302 | LEU | 0 | 0.043 | 0.016 | 18.446 | 0.556 | 0.556 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | H | 303 | HIS | 0 | -0.038 | -0.008 | 20.593 | 0.363 | 0.363 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | H | 304 | ASN | 0 | -0.027 | -0.021 | 22.168 | 0.325 | 0.325 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | H | 305 | SER | 0 | 0.002 | 0.008 | 23.915 | 0.457 | 0.457 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | H | 306 | LEU | 0 | 0.066 | 0.022 | 22.699 | 0.445 | 0.445 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | H | 307 | ASN | 0 | -0.089 | -0.050 | 26.070 | 0.687 | 0.687 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | H | 308 | ALA | 0 | -0.010 | -0.005 | 27.827 | 0.380 | 0.380 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | H | 309 | ALA | 0 | 0.056 | 0.035 | 29.614 | 0.367 | 0.367 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | H | 310 | SER | 0 | -0.069 | -0.045 | 29.648 | 0.305 | 0.305 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | H | 311 | LYS | 1 | 0.895 | 0.945 | 31.549 | 9.181 | 9.181 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | H | 312 | THR | 0 | -0.022 | -0.007 | 34.455 | 0.294 | 0.294 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | H | 313 | GLY | 0 | -0.023 | -0.002 | 34.946 | 0.206 | 0.206 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | H | 314 | ASN | 0 | -0.018 | -0.039 | 32.586 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | H | 315 | SER | 0 | -0.032 | -0.032 | 32.488 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | H | 316 | ASN | 0 | 0.031 | 0.024 | 31.913 | -0.387 | -0.387 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | H | 317 | GLU | -1 | -0.846 | -0.893 | 31.856 | -8.852 | -8.852 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | H | 318 | VAL | 0 | 0.021 | -0.001 | 27.337 | -0.194 | -0.194 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | H | 319 | LEU | 0 | -0.071 | -0.031 | 27.753 | -0.308 | -0.308 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | H | 320 | GLN | 0 | -0.106 | -0.035 | 27.619 | -0.390 | -0.390 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | H | 321 | ASP | -1 | -0.828 | -0.914 | 27.173 | -11.095 | -11.095 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | H | 322 | PRO | 0 | 0.016 | -0.010 | 25.510 | -0.328 | -0.328 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | H | 323 | HIS | 0 | 0.078 | 0.062 | 21.306 | -0.669 | -0.669 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | H | 324 | ILE | 0 | 0.017 | 0.010 | 21.973 | -0.763 | -0.763 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | H | 325 | GLY | 0 | 0.000 | 0.005 | 21.548 | -0.620 | -0.620 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | H | 326 | ASP | -1 | -0.862 | -0.942 | 19.719 | -14.329 | -14.329 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | H | 327 | MET | 0 | -0.085 | -0.041 | 17.595 | -1.001 | -1.001 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | H | 328 | TYR | 0 | 0.025 | 0.008 | 16.616 | -1.232 | -1.232 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | H | 329 | GLY | 0 | -0.018 | 0.002 | 16.487 | -1.033 | -1.033 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | H | 330 | SER | 0 | -0.047 | -0.011 | 13.025 | -1.094 | -1.094 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | H | 331 | VAL | 0 | 0.011 | -0.004 | 11.905 | -1.974 | -1.974 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | H | 332 | THR | 0 | -0.059 | -0.045 | 12.677 | -1.333 | -1.333 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | H | 333 | PRO | 0 | 0.002 | -0.005 | 10.918 | -0.690 | -0.690 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | H | 334 | LEU | 0 | -0.022 | -0.019 | 8.114 | -3.435 | -3.435 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | H | 335 | ARG | 1 | 0.977 | 1.013 | 9.511 | 17.451 | 17.451 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | H | 336 | PRO | 0 | 0.065 | 0.062 | 8.579 | -0.738 | -0.738 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | H | 337 | GLN | 0 | 0.038 | 0.012 | 3.137 | -10.954 | -9.617 | 0.084 | -0.577 | -0.843 | -0.005 |
51 | H | 338 | VAL | 0 | 0.048 | 0.017 | 6.433 | -2.241 | -2.241 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | H | 339 | THR | 0 | -0.040 | -0.064 | 8.816 | 2.002 | 2.002 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | H | 340 | ARG | 1 | 0.848 | 0.933 | 2.132 | 64.124 | 61.280 | 7.409 | -1.428 | -3.136 | -0.009 |
54 | H | 341 | MET | 0 | -0.076 | -0.039 | 3.420 | 1.536 | 2.006 | 0.012 | -0.137 | -0.345 | -0.001 |
55 | H | 342 | LEU | 0 | 0.026 | 0.026 | 7.366 | 2.248 | 2.248 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | H | 343 | GLY | 0 | 0.065 | 0.032 | 10.770 | 1.733 | 1.733 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | H | 344 | LYS | 1 | 0.835 | 0.904 | 6.020 | 35.154 | 35.154 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | H | 345 | TYR | 0 | -0.047 | -0.063 | 7.193 | 2.930 | 2.930 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | H | 346 | ALA | 0 | -0.039 | 0.001 | 11.920 | 1.933 | 1.933 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | H | 347 | LYS | 1 | 0.853 | 0.926 | 12.737 | 18.801 | 18.801 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | H | 348 | GLU | -1 | -0.770 | -0.864 | 10.339 | -25.758 | -25.758 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | H | 349 | LYS | 1 | 0.912 | 0.962 | 14.535 | 16.670 | 16.670 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | H | 350 | GLU | -1 | -0.893 | -0.961 | 17.198 | -13.258 | -13.258 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | H | 351 | ASP | -1 | -0.820 | -0.905 | 15.780 | -17.342 | -17.342 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | H | 352 | MET | 0 | -0.034 | -0.018 | 17.011 | 1.051 | 1.051 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | H | 353 | LEU | 0 | -0.060 | -0.026 | 20.239 | 0.884 | 0.884 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | H | 354 | SER | 0 | 0.011 | 0.003 | 22.231 | 0.844 | 0.844 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | H | 355 | LEU | 0 | -0.003 | -0.012 | 21.560 | 0.577 | 0.577 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | H | 356 | ARG | 1 | 0.968 | 0.985 | 24.072 | 12.392 | 12.392 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | H | 357 | GLN | 0 | -0.019 | -0.001 | 26.016 | 0.643 | 0.643 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | H | 358 | VAL | 0 | 0.048 | 0.023 | 26.841 | 0.420 | 0.420 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | H | 359 | LEU | 0 | -0.027 | -0.016 | 26.938 | 0.373 | 0.373 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | H | 360 | ALA | 0 | 0.045 | 0.023 | 29.782 | 0.390 | 0.390 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | H | 361 | ASN | 0 | -0.081 | -0.043 | 31.792 | 0.150 | 0.150 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | H | 362 | ALA | 0 | 0.038 | 0.023 | 32.793 | 0.328 | 0.328 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | H | 363 | GLU | -1 | -0.919 | -0.949 | 32.916 | -9.193 | -9.193 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | H | 364 | ARG | 1 | 0.936 | 0.969 | 34.117 | 9.090 | 9.090 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | H | 365 | SER | 0 | -0.019 | -0.007 | 37.355 | 0.292 | 0.292 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | H | 366 | TYR | 0 | -0.025 | -0.010 | 37.713 | 0.234 | 0.234 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | H | 367 | ASN | 0 | 0.039 | -0.011 | 38.016 | 0.224 | 0.224 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | H | 368 | GLN | 0 | -0.017 | 0.014 | 41.405 | 0.297 | 0.297 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | H | 369 | LEU | 0 | -0.069 | -0.043 | 42.324 | 0.204 | 0.204 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | H | 370 | MET | 0 | -0.041 | -0.042 | 42.138 | 0.164 | 0.164 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | H | 371 | ASP | -1 | -0.801 | -0.886 | 45.029 | -6.898 | -6.898 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | H | 372 | ARG | 1 | 0.827 | 0.933 | 47.407 | 6.653 | 6.653 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | H | 373 | ALA | 0 | -0.034 | -0.025 | 47.828 | 0.105 | 0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | H | 374 | ALA | 0 | -0.068 | -0.018 | 49.750 | 0.066 | 0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | H | 375 | ASN | 0 | -0.024 | -0.013 | 51.075 | 0.151 | 0.151 | 0.000 | 0.000 | 0.000 | 0.000 |