FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2025-10-17
All entries: 77277
Number of unique PDB entries: 32023
FMODB ID: 942J2
Calculation Name: 5IOH-D-Xray372
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 5IOH
Chain ID: D
UniProt ID: Q69YH5
Base Structure: X-ray
Registration Date: 2023-06-26
Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.
Apendix: None
Modeling method
| Optimization | MOE:Amber10:EHT |
|---|---|
| Restraint | OptHSide |
| Protonation | MOE:Protonate 3D |
| Complement | MOE:Structure Preparation |
| Water | No |
| Procedure | Auto-FMO protocol ver. 2.20220422 |
| Remarks |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 30 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -84413.127624 |
|---|---|
| FMO2-HF: Nuclear repulsion | 73279.599299 |
| FMO2-HF: Total energy | -11133.528326 |
| FMO2-MP2: Total energy | -11166.585802 |
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(D:392:ARG)
Summations of interaction energy for
fragment #1(D:392:ARG)
| 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. |
| -49.092 | -45.914 | -0.009 | -1.52 | -1.649 | 0.004 |
Interaction energy analysis for fragmet #1(D:392:ARG)
| 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 | D | 394 | THR | 0 | -0.045 | -0.019 | 3.626 | -10.266 | -7.088 | -0.009 | -1.520 | -1.649 | 0.004 |
| 4 | D | 395 | PHE | 0 | 0.002 | -0.010 | 5.818 | 1.763 | 1.763 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | D | 396 | GLY | 0 | 0.002 | 0.009 | 9.071 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | D | 397 | GLU | -1 | -0.950 | -0.969 | 12.264 | -16.901 | -16.901 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | D | 398 | ASP | -1 | -0.914 | -0.950 | 15.229 | -17.950 | -17.950 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | D | 399 | LEU | 0 | -0.033 | -0.019 | 17.641 | 0.609 | 0.609 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | D | 400 | SER | 0 | -0.019 | -0.017 | 20.411 | 0.135 | 0.135 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | D | 401 | PRO | 0 | 0.032 | 0.031 | 24.095 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | D | 402 | GLU | -1 | -0.726 | -0.860 | 25.295 | -10.666 | -10.666 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | D | 403 | VAL | 0 | -0.080 | -0.029 | 28.002 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | D | 404 | PHE | 0 | 0.000 | -0.012 | 29.834 | 0.186 | 0.186 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | D | 405 | ASP | -1 | -0.803 | -0.879 | 33.615 | -8.203 | -8.203 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | D | 406 | GLU | -1 | -0.947 | -0.976 | 36.286 | -8.516 | -8.516 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | D | 407 | SER | 0 | -0.091 | -0.060 | 37.491 | 0.176 | 0.176 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | D | 408 | LEU | 0 | -0.052 | -0.027 | 38.281 | 0.218 | 0.218 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | D | 409 | PRO | 0 | 0.004 | -0.003 | 37.960 | -0.145 | -0.145 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | D | 410 | ALA | 0 | 0.046 | 0.022 | 33.365 | -0.152 | -0.152 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | D | 411 | ASN | 0 | -0.053 | -0.028 | 33.057 | -0.246 | -0.246 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | D | 412 | THR | 0 | -0.059 | -0.033 | 34.460 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | D | 413 | PRO | 0 | -0.009 | 0.016 | 31.221 | 0.119 | 0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | D | 414 | LEU | 0 | 0.014 | 0.002 | 33.929 | 0.116 | 0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | D | 415 | ARG | 1 | 0.899 | 0.943 | 29.778 | 10.197 | 10.197 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | D | 416 | LYS | 1 | 0.865 | 0.925 | 28.639 | 10.296 | 10.296 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | D | 417 | GLY | 0 | 0.014 | 0.007 | 25.780 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | D | 418 | GLY | 0 | -0.060 | -0.035 | 22.931 | 0.145 | 0.145 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | D | 419 | THR | 0 | -0.024 | -0.018 | 20.068 | -0.114 | -0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | D | 420 | PRO | 0 | -0.002 | 0.005 | 15.340 | -0.072 | -0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | D | 421 | VAL | 0 | 0.008 | 0.008 | 14.205 | 0.105 | 0.105 | 0.000 | 0.000 | 0.000 | 0.000 |