FMODB ID: Q12MY
Calculation Name: 3RNV-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3RNV
Chain ID: A
UniProt ID: P89509
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 | 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 | 123 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -1075764.466172 |
---|---|
FMO2-HF: Nuclear repulsion | 1026233.35731 |
FMO2-HF: Total energy | -49531.108863 |
FMO2-MP2: Total energy | -49674.412892 |
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:336:MET)
Summations of interaction energy for
fragment #1(A:336:MET)
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. |
0.796 | 2.475 | -0.02 | -0.791 | -0.869 | 0.003 |
Interaction energy analysis for fragmet #1(A:336:MET)
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 | 338 | ILE | 0 | -0.021 | -0.018 | 3.826 | -0.041 | 1.638 | -0.020 | -0.791 | -0.869 | 0.003 |
4 | A | 339 | ALA | 0 | 0.030 | 0.010 | 6.566 | 0.074 | 0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 340 | LYS | 1 | 0.966 | 0.978 | 9.489 | -0.140 | -0.140 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 341 | GLU | -1 | -0.884 | -0.948 | 12.439 | 0.219 | 0.219 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 342 | GLY | 0 | 0.030 | 0.008 | 16.113 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 343 | TYR | 0 | -0.005 | -0.026 | 12.740 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 344 | CYS | 0 | 0.000 | 0.010 | 11.225 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 345 | TYR | 0 | -0.004 | -0.017 | 11.574 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 346 | ILE | 0 | 0.013 | 0.010 | 8.552 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 347 | ASN | 0 | 0.010 | -0.006 | 7.382 | -0.578 | -0.578 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 348 | ILE | 0 | 0.012 | 0.018 | 8.562 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 349 | PHE | 0 | 0.039 | -0.007 | 10.874 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 350 | LEU | 0 | -0.039 | -0.021 | 4.890 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 351 | ALA | 0 | 0.024 | 0.022 | 6.512 | -0.264 | -0.264 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 352 | MET | 0 | -0.043 | -0.015 | 7.851 | 0.089 | 0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 353 | LEU | 0 | -0.028 | -0.015 | 6.051 | 0.074 | 0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 354 | VAL | 0 | -0.018 | 0.006 | 7.119 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 355 | ASN | 0 | -0.027 | -0.012 | 9.602 | 0.090 | 0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 356 | VAL | 0 | -0.040 | -0.003 | 11.406 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 357 | LYS | 1 | 0.987 | 0.992 | 13.006 | 0.256 | 0.256 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 358 | GLU | -1 | -0.820 | -0.924 | 12.499 | -0.717 | -0.717 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 359 | SER | 0 | -0.094 | -0.042 | 14.207 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 360 | GLN | 0 | 0.003 | -0.014 | 15.409 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 361 | ALA | 0 | 0.068 | 0.051 | 10.056 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 362 | LYS | 1 | 0.949 | 0.955 | 11.297 | 0.674 | 0.674 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 363 | GLU | -1 | -0.931 | -0.963 | 12.648 | -0.358 | -0.358 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 364 | PHE | 0 | 0.100 | 0.054 | 10.760 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 365 | THR | 0 | -0.002 | -0.014 | 8.512 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 366 | LYS | 1 | 0.900 | 0.947 | 10.996 | 0.505 | 0.505 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 367 | VAL | 0 | 0.040 | 0.045 | 14.177 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 368 | VAL | 0 | 0.019 | 0.005 | 10.905 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 369 | ARG | 1 | 0.827 | 0.904 | 10.637 | 0.596 | 0.596 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 370 | ASP | -1 | -0.868 | -0.936 | 13.256 | -0.287 | -0.287 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 371 | LYS | 1 | 0.811 | 0.914 | 16.853 | 0.212 | 0.212 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 372 | LEU | 0 | 0.003 | -0.005 | 15.785 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 373 | VAL | 0 | 0.001 | 0.001 | 12.866 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 374 | GLY | 0 | -0.028 | -0.011 | 16.239 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 375 | GLU | -1 | -0.868 | -0.918 | 19.418 | -0.128 | -0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 376 | LEU | 0 | -0.043 | -0.016 | 17.196 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 377 | GLY | 0 | 0.042 | 0.037 | 19.231 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 378 | LYS | 1 | 0.874 | 0.940 | 18.181 | -0.128 | -0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 379 | TRP | 0 | -0.029 | -0.016 | 18.784 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 380 | PRO | 0 | 0.060 | 0.060 | 18.285 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 381 | THR | 0 | 0.040 | 0.003 | 21.233 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 382 | LEU | 0 | 0.007 | -0.007 | 19.787 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 383 | LEU | 0 | 0.002 | 0.001 | 21.600 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 384 | ASP | -1 | -0.844 | -0.915 | 22.873 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 385 | VAL | 0 | -0.009 | -0.004 | 16.614 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 386 | ALA | 0 | -0.010 | -0.019 | 18.753 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 387 | THR | 0 | -0.014 | -0.016 | 20.431 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 388 | ALA | 0 | 0.012 | 0.009 | 18.352 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 389 | CYS | 0 | -0.057 | -0.026 | 16.551 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 390 | TYR | 0 | -0.030 | -0.014 | 18.147 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 391 | PHE | 0 | 0.015 | 0.006 | 19.766 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 392 | LEU | 0 | 0.018 | 0.005 | 14.581 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 393 | LYS | 1 | 0.871 | 0.926 | 18.591 | 0.097 | 0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 394 | VAL | 0 | -0.031 | -0.009 | 19.942 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 395 | PHE | 0 | -0.028 | -0.008 | 20.247 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 396 | TYR | 0 | -0.085 | -0.048 | 16.712 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 397 | PRO | 0 | 0.040 | 0.020 | 18.053 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 398 | ASP | -1 | -0.882 | -0.942 | 17.448 | -0.210 | -0.210 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 399 | VAL | 0 | -0.001 | -0.010 | 13.709 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 400 | ALA | 0 | -0.038 | -0.024 | 15.652 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 401 | ASN | 0 | -0.040 | -0.034 | 17.516 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 402 | ALA | 0 | 0.026 | 0.041 | 11.920 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 403 | GLU | -1 | -0.923 | -0.958 | 12.276 | 0.220 | 0.220 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 404 | LEU | 0 | -0.058 | -0.031 | 11.288 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 405 | PRO | 0 | 0.038 | 0.022 | 8.982 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 406 | ARG | 1 | 0.888 | 0.958 | 11.486 | -0.631 | -0.631 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 407 | MET | 0 | 0.002 | -0.002 | 14.557 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 408 | LEU | 0 | -0.002 | -0.004 | 17.089 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 409 | VAL | 0 | -0.019 | -0.015 | 19.375 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 410 | ASP | -1 | -0.815 | -0.910 | 22.620 | 0.177 | 0.177 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 411 | HIS | 0 | 0.025 | 0.004 | 24.710 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 412 | LYS | 1 | 0.930 | 0.982 | 27.956 | -0.136 | -0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 413 | THR | 0 | -0.034 | -0.026 | 24.954 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 414 | LYS | 1 | 0.877 | 0.952 | 26.763 | -0.091 | -0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 415 | ILE | 0 | 0.011 | 0.019 | 20.580 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 416 | ILE | 0 | -0.021 | -0.012 | 18.308 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 417 | HIS | 0 | 0.029 | -0.002 | 16.291 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 418 | VAL | 0 | -0.007 | 0.003 | 11.404 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 419 | VAL | 0 | -0.049 | -0.032 | 11.367 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 420 | ASP | -1 | -0.869 | -0.936 | 7.726 | 1.279 | 1.279 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 421 | SER | 0 | 0.000 | -0.009 | 8.988 | 0.336 | 0.336 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 422 | TYR | 0 | 0.035 | 0.022 | 11.607 | -0.130 | -0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 423 | GLY | 0 | 0.005 | 0.000 | 14.744 | -0.088 | -0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 424 | SER | 0 | -0.034 | -0.027 | 17.747 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 425 | LEU | 0 | 0.038 | 0.025 | 19.603 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 426 | SER | 0 | 0.018 | 0.018 | 19.985 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 427 | THR | 0 | -0.003 | -0.018 | 21.371 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 428 | GLY | 0 | 0.036 | 0.016 | 24.320 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 429 | TYR | 0 | 0.021 | 0.000 | 26.025 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 430 | HIS | 0 | 0.014 | 0.010 | 23.722 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 431 | VAL | 0 | -0.015 | 0.015 | 19.664 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 432 | LEU | 0 | 0.015 | 0.015 | 20.272 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 433 | LYS | 1 | 0.922 | 0.961 | 20.020 | -0.133 | -0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 434 | THR | 0 | -0.035 | -0.014 | 18.506 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 435 | ASN | 0 | 0.057 | 0.017 | 17.064 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 436 | THR | 0 | 0.014 | 0.007 | 15.701 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 437 | VAL | 0 | 0.068 | 0.038 | 14.627 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 438 | GLU | -1 | -0.814 | -0.896 | 17.125 | -0.059 | -0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 439 | GLN | 0 | -0.090 | -0.049 | 20.049 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 440 | LEU | 0 | 0.058 | 0.036 | 17.437 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 441 | ILE | 0 | 0.030 | 0.013 | 20.062 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 442 | LYS | 1 | 0.852 | 0.920 | 22.671 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 443 | PHE | 0 | -0.034 | -0.009 | 23.923 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 444 | THR | 0 | 0.013 | -0.006 | 23.424 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 445 | ARG | 1 | 0.958 | 0.987 | 25.788 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 446 | CYS | 0 | -0.066 | -0.009 | 28.169 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 447 | ASN | 0 | 0.072 | 0.009 | 30.898 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 448 | LEU | 0 | -0.017 | 0.003 | 33.484 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 449 | GLU | -1 | -0.858 | -0.941 | 32.432 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 450 | SER | 0 | -0.023 | -0.008 | 29.479 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 451 | SER | 0 | 0.064 | 0.016 | 30.438 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | A | 452 | LEU | 0 | -0.007 | -0.018 | 25.290 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | A | 453 | LYS | 1 | 0.879 | 0.973 | 25.530 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
119 | A | 454 | HIS | 0 | 0.039 | 0.021 | 25.810 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
120 | A | 455 | TYR | 0 | -0.093 | -0.057 | 24.099 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
121 | A | 456 | ARG | 1 | 0.895 | 0.951 | 22.303 | -0.079 | -0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
122 | A | 457 | VAL | 0 | 0.024 | 0.020 | 16.567 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
123 | A | 458 | GLY | 0 | -0.005 | 0.004 | 15.583 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |