FMODB ID: 52VGZ
Calculation Name: 2PEH-B-Xray372
Preferred Name: Splicing factor 3B subunit 1
Target Type: SINGLE PROTEIN
Ligand Name:
ligand 3-letter code:
PDB ID: 2PEH
Chain ID: B
ChEMBL ID: CHEMBL1229013
UniProt ID: O75533
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 | 104 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -807333.736437 |
---|---|
FMO2-HF: Nuclear repulsion | 765899.061073 |
FMO2-HF: Total energy | -41434.675364 |
FMO2-MP2: Total energy | -41552.826441 |
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:298:ALA)
Summations of interaction energy for
fragment #1(B:298:ALA)
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. |
-1.366 | 2.39 | 0.649 | -1.605 | -2.799 | -0.001 |
Interaction energy analysis for fragmet #1(B:298:ALA)
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 | 300 | GLY | 0 | 0.052 | 0.027 | 3.604 | -0.796 | 0.683 | -0.011 | -0.628 | -0.840 | 0.002 |
4 | B | 301 | LYS | 1 | 0.913 | 0.959 | 2.559 | 0.785 | 1.862 | 0.531 | -0.362 | -1.245 | 0.002 |
5 | B | 302 | CYS | 0 | -0.030 | -0.007 | 4.753 | 0.463 | 0.609 | -0.001 | -0.015 | -0.130 | 0.000 |
6 | B | 303 | PRO | 0 | 0.001 | -0.003 | 6.870 | 0.194 | 0.194 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | B | 304 | THR | 0 | -0.046 | -0.046 | 10.040 | 0.103 | 0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | B | 305 | LYS | 1 | 0.932 | 0.950 | 12.831 | 0.117 | 0.117 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | B | 306 | VAL | 0 | -0.018 | 0.013 | 13.387 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | B | 307 | VAL | 0 | -0.016 | -0.008 | 12.564 | -0.095 | -0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | B | 308 | LEU | 0 | -0.035 | -0.022 | 9.370 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | B | 309 | LEU | 0 | 0.002 | -0.005 | 11.868 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | B | 310 | ARG | 1 | 0.901 | 0.938 | 7.814 | 0.351 | 0.351 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | B | 311 | ASN | 0 | -0.015 | -0.040 | 14.365 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | B | 312 | MET | 0 | -0.030 | 0.002 | 17.077 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | B | 313 | VAL | 0 | 0.037 | 0.021 | 19.578 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | B | 314 | GLY | 0 | -0.035 | -0.013 | 20.435 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | B | 315 | ALA | 0 | -0.022 | -0.029 | 22.282 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | B | 316 | GLY | 0 | -0.047 | -0.029 | 23.231 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | B | 317 | GLU | -1 | -0.955 | -0.967 | 24.877 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | B | 318 | VAL | 0 | -0.017 | -0.010 | 23.317 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | B | 319 | ASP | -1 | -0.879 | -0.942 | 25.808 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | B | 320 | GLU | -1 | -0.978 | -0.998 | 27.900 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | B | 321 | ASP | -1 | -0.932 | -0.967 | 29.908 | -0.048 | -0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | B | 322 | LEU | 0 | 0.037 | 0.035 | 22.514 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | B | 323 | GLU | -1 | -0.965 | -0.978 | 24.352 | -0.074 | -0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | B | 324 | VAL | 0 | 0.017 | 0.009 | 25.408 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | B | 325 | GLU | -1 | -0.928 | -0.943 | 26.503 | -0.084 | -0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | B | 326 | THR | 0 | -0.064 | -0.059 | 20.448 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | B | 327 | LYS | 1 | 0.928 | 0.956 | 23.332 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | B | 328 | GLU | -1 | -0.919 | -0.986 | 24.477 | -0.073 | -0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | B | 329 | GLU | -1 | -0.848 | -0.910 | 23.722 | -0.119 | -0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | B | 330 | CYS | 0 | -0.091 | -0.073 | 20.746 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | B | 331 | GLU | -1 | -0.780 | -0.907 | 22.859 | -0.108 | -0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | B | 332 | LYS | 1 | 0.826 | 0.941 | 24.205 | 0.133 | 0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | B | 333 | TYR | 0 | -0.142 | -0.093 | 20.663 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | B | 334 | GLY | 0 | -0.090 | -0.063 | 22.741 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | B | 335 | LYS | 1 | 0.857 | 0.939 | 24.371 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | B | 336 | VAL | 0 | 0.020 | 0.026 | 22.151 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | B | 337 | GLY | 0 | -0.048 | -0.018 | 22.724 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | B | 338 | LYS | 1 | 0.876 | 0.924 | 21.276 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | B | 339 | CYS | 0 | -0.003 | 0.011 | 20.747 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | B | 340 | VAL | 0 | 0.008 | 0.010 | 19.605 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | B | 341 | ILE | 0 | 0.072 | 0.034 | 19.480 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | B | 342 | PHE | 0 | -0.030 | -0.016 | 17.019 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | B | 343 | GLU | -1 | -0.799 | -0.889 | 18.635 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | B | 344 | ILE | 0 | -0.059 | -0.044 | 14.390 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | B | 345 | PRO | 0 | -0.007 | -0.018 | 18.852 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | B | 346 | GLY | 0 | -0.023 | -0.013 | 20.709 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | B | 347 | ALA | 0 | -0.027 | 0.009 | 16.838 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | B | 348 | PRO | 0 | 0.004 | -0.009 | 16.001 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | B | 349 | ASP | -1 | -0.795 | -0.900 | 18.297 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | B | 350 | ASP | -1 | -0.937 | -0.969 | 16.026 | -0.077 | -0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | B | 351 | GLU | -1 | -0.963 | -0.996 | 11.913 | -0.154 | -0.154 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | B | 352 | ALA | 0 | -0.027 | 0.001 | 15.250 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | B | 353 | VAL | 0 | 0.049 | 0.050 | 18.171 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | B | 354 | ARG | 1 | 0.795 | 0.906 | 9.979 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | B | 355 | ILE | 0 | 0.067 | 0.035 | 16.089 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | B | 356 | PHE | 0 | -0.032 | -0.026 | 12.529 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | B | 357 | LEU | 0 | 0.050 | 0.015 | 16.381 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | B | 358 | GLU | -1 | -0.904 | -0.946 | 17.024 | -0.121 | -0.121 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | B | 359 | PHE | 0 | 0.057 | 0.018 | 17.377 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | B | 360 | GLU | -1 | -0.811 | -0.917 | 20.454 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | B | 361 | ARG | 1 | 0.889 | 0.934 | 21.239 | 0.119 | 0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | B | 362 | VAL | 0 | 0.071 | 0.026 | 14.876 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | B | 363 | GLU | -1 | -0.889 | -0.956 | 16.728 | -0.217 | -0.217 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | B | 364 | SER | 0 | -0.063 | -0.047 | 18.832 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | B | 365 | ALA | 0 | 0.035 | 0.040 | 14.783 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | B | 366 | ILE | 0 | -0.018 | -0.015 | 13.701 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | B | 367 | LYS | 1 | 0.884 | 0.950 | 15.224 | 0.165 | 0.165 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | B | 368 | ALA | 0 | 0.081 | 0.042 | 16.756 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | B | 369 | VAL | 0 | -0.005 | 0.010 | 10.621 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | B | 370 | VAL | 0 | -0.073 | -0.048 | 13.942 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | B | 371 | ASP | -1 | -0.883 | -0.901 | 15.376 | -0.162 | -0.162 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | B | 372 | LEU | 0 | -0.002 | -0.011 | 16.038 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | B | 373 | ASN | 0 | -0.008 | 0.007 | 11.603 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | B | 374 | GLY | 0 | -0.034 | -0.019 | 14.478 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | B | 375 | ARG | 1 | 0.853 | 0.947 | 16.869 | 0.170 | 0.170 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | B | 376 | TYR | 0 | -0.032 | -0.026 | 19.425 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | B | 377 | PHE | 0 | 0.022 | 0.008 | 21.348 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | B | 378 | GLY | 0 | 0.082 | 0.047 | 23.016 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | B | 379 | GLY | 0 | -0.043 | -0.021 | 25.487 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | B | 380 | ARG | 1 | 0.861 | 0.939 | 20.111 | 0.076 | 0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | B | 381 | VAL | 0 | -0.020 | -0.002 | 16.611 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | B | 382 | VAL | 0 | 0.052 | 0.045 | 15.274 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | B | 383 | LYS | 1 | 0.931 | 0.974 | 10.590 | 0.170 | 0.170 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | B | 384 | ALA | 0 | 0.016 | 0.008 | 11.936 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | B | 385 | CYS | 0 | -0.098 | -0.043 | 6.868 | -0.084 | -0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | B | 386 | PHE | 0 | 0.023 | 0.033 | 7.820 | 0.194 | 0.194 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | B | 387 | TYR | 0 | 0.032 | -0.020 | 8.031 | -0.182 | -0.182 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | B | 388 | ASN | 0 | 0.003 | 0.005 | 8.733 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | B | 389 | LEU | 0 | 0.029 | 0.006 | 10.383 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | B | 390 | ASP | -1 | -0.878 | -0.952 | 13.828 | 0.079 | 0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | B | 391 | LYS | 1 | 0.893 | 0.967 | 10.335 | -0.462 | -0.462 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | B | 392 | PHE | 0 | 0.001 | 0.005 | 13.616 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | B | 393 | ARG | 1 | 0.865 | 0.927 | 15.309 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | B | 394 | VAL | 0 | -0.033 | -0.002 | 16.334 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | B | 395 | LEU | 0 | -0.026 | -0.007 | 17.879 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | B | 396 | ASP | -1 | -0.857 | -0.906 | 13.765 | 0.188 | 0.188 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | B | 397 | LEU | 0 | -0.021 | 0.001 | 13.313 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | B | 398 | ALA | 0 | 0.032 | 0.013 | 13.157 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | B | 399 | GLU | -1 | -0.894 | -0.943 | 8.500 | 0.460 | 0.460 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | B | 400 | GLN | 0 | 0.010 | -0.004 | 6.271 | -0.150 | -0.150 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | B | 401 | VAL | 0 | 0.005 | 0.000 | 3.101 | -2.166 | -1.112 | 0.130 | -0.600 | -0.584 | -0.005 |