FMODB ID: JQNG9
Calculation Name: 1MTP-B-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1MTP
Chain ID: B
UniProt ID: Q47NK3
Base Structure: X-ray
Registration Date: 2023-09-23
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 | OptAll |
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 | 35 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -110842.75909 |
---|---|
FMO2-HF: Nuclear repulsion | 97666.852786 |
FMO2-HF: Total energy | -13175.906305 |
FMO2-MP2: Total energy | -13215.575395 |
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:333:THR)
Summations of interaction energy for
fragment #1(B:333:THR)
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. |
1.8 | 3.002 | -0.005 | -0.476 | -0.721 | 0.001 |
Interaction energy analysis for fragmet #1(B:333:THR)
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 | 335 | ARG | 1 | 0.973 | 0.984 | 3.846 | 1.492 | 2.694 | -0.005 | -0.476 | -0.721 | 0.001 |
4 | B | 336 | PHE | 0 | -0.011 | -0.007 | 6.299 | 0.473 | 0.473 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | B | 337 | SER | 0 | -0.052 | -0.048 | 8.487 | 0.103 | 0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | B | 338 | VAL | 0 | -0.029 | -0.018 | 11.395 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | B | 339 | ASP | -1 | -0.788 | -0.851 | 14.583 | -0.475 | -0.475 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | B | 340 | ARG | 1 | 0.868 | 0.929 | 14.608 | 0.433 | 0.433 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | B | 341 | PRO | 0 | 0.006 | -0.001 | 19.558 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | B | 342 | PHE | 0 | -0.021 | 0.005 | 18.143 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | B | 343 | HIS | 0 | 0.036 | 0.027 | 19.443 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | B | 344 | ILE | 0 | 0.000 | 0.005 | 19.256 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | B | 345 | VAL | 0 | 0.022 | -0.004 | 20.544 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | B | 346 | VAL | 0 | 0.001 | 0.022 | 21.385 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | B | 347 | ARG | 1 | 0.994 | 0.990 | 18.141 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | B | 348 | ARG | 1 | 0.961 | 0.970 | 23.714 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | B | 349 | ARG | 1 | 0.929 | 0.951 | 26.235 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | B | 350 | GLY | 0 | 0.047 | 0.038 | 26.842 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | B | 351 | ALA | 0 | 0.022 | 0.030 | 28.169 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | B | 352 | ILE | 0 | 0.000 | -0.016 | 25.759 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | B | 353 | LEU | 0 | -0.062 | -0.029 | 26.899 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | B | 354 | PHE | 0 | 0.042 | 0.012 | 26.036 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | B | 355 | LEU | 0 | -0.009 | -0.004 | 24.937 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | B | 356 | GLY | 0 | 0.015 | 0.013 | 24.881 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | B | 357 | SER | 0 | -0.003 | -0.022 | 24.038 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | B | 358 | ILE | 0 | -0.040 | -0.012 | 21.884 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | B | 359 | ALA | 0 | 0.016 | -0.016 | 22.854 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | B | 360 | ASP | -1 | -0.904 | -0.945 | 25.087 | -0.144 | -0.144 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | B | 361 | PRO | 0 | -0.049 | -0.036 | 21.362 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | B | 362 | HIS | 0 | 0.014 | 0.027 | 24.113 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | B | 363 | ASP | -1 | -0.864 | -0.935 | 24.796 | -0.140 | -0.140 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | B | 364 | PRO | 0 | -0.089 | -0.041 | 24.405 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | B | 365 | GLY | 0 | 0.026 | 0.023 | 25.994 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | B | 366 | PRO | 0 | -0.068 | -0.036 | 23.741 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | B | 367 | ALA | 0 | -0.006 | -0.005 | 23.095 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |