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: JVKG9
Calculation Name: 3A9J-C-Xray547
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 3A9J
Chain ID: C
UniProt ID: Q99K90
Base Structure: X-ray
Registration Date: 2025-10-05
Reference: Sci Data 11, 1164 (2024).
DOI: https://doi.org/10.1038/s41597-024-03999-2
Apendix: None
Modeling method
| Optimization | MOE:Amber10:EHT |
|---|---|
| Restraint | OptAll |
| Protonation | MOE:Protonate 3D |
| Complement | MOE:Homology Modeling |
| Water | No |
| Procedure | Manual calculation |
| Remarks |
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE. |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 32 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -127265.373689 |
|---|---|
| FMO2-HF: Nuclear repulsion | 112871.69188 |
| FMO2-HF: Total energy | -14393.681809 |
| FMO2-MP2: Total energy | -14430.609937 |
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:662:GLY)
Summations of interaction energy for
fragment #1(A:662:GLY)
| 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. |
| -7.312 | -6.393 | -0.004 | -0.395 | -0.521 | -0.001 |
Interaction energy analysis for fragmet #1(A:662:GLY)
| 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 | 664 | MET | 0 | 0.014 | 0.021 | 3.816 | -5.432 | -4.567 | -0.003 | -0.391 | -0.471 | -0.001 |
| 19 | A | 680 | ALA | 0 | -0.040 | -0.024 | 4.435 | -6.443 | -6.389 | -0.001 | -0.004 | -0.050 | 0.000 |
| 4 | A | 665 | GLY | 0 | 0.019 | -0.004 | 6.364 | 2.028 | 2.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 666 | ALA | 0 | 0.017 | 0.011 | 8.495 | 0.570 | 0.570 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 667 | GLN | 0 | 0.014 | -0.002 | 10.014 | -1.984 | -1.984 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 668 | TRP | 0 | -0.046 | -0.019 | 9.472 | 1.544 | 1.544 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 669 | ASN | 0 | -0.016 | -0.008 | 13.305 | -0.215 | -0.215 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 670 | CYS | 0 | -0.041 | -0.010 | 16.248 | -0.307 | -0.307 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 671 | THR | 0 | 0.002 | -0.005 | 17.069 | 0.896 | 0.896 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 672 | ALA | 0 | 0.026 | 0.018 | 19.632 | 0.756 | 0.756 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 673 | CYS | 0 | -0.001 | -0.001 | 20.282 | 0.316 | 0.316 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 674 | THR | 0 | -0.026 | -0.010 | 20.482 | 0.386 | 0.386 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 675 | PHE | 0 | 0.048 | 0.024 | 15.996 | -0.203 | -0.203 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 676 | LEU | 0 | 0.009 | 0.007 | 15.463 | -0.886 | -0.886 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 677 | ASN | 0 | 0.068 | 0.041 | 11.933 | 0.211 | 0.211 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 678 | HIS | 0 | 0.101 | 0.038 | 7.975 | -2.499 | -2.499 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 679 | PRO | 0 | -0.031 | -0.024 | 6.487 | -1.085 | -1.085 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 681 | LEU | 0 | 0.002 | 0.022 | 5.493 | -2.012 | -2.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 682 | ILE | 0 | -0.002 | -0.017 | 5.835 | 0.424 | 0.424 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 683 | ARG | 1 | 0.924 | 0.962 | 8.500 | 25.092 | 25.092 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 684 | CYS | 0 | -0.102 | -0.039 | 12.257 | -0.782 | -0.782 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 685 | GLU | -1 | -0.923 | -0.973 | 14.563 | -19.142 | -19.142 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 686 | GLN | 0 | 0.003 | -0.009 | 15.826 | 1.401 | 1.401 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 687 | CYS | 0 | 0.021 | 0.024 | 18.277 | 0.494 | 0.494 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 688 | GLU | -1 | -0.870 | -0.931 | 16.188 | -16.079 | -16.079 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 689 | MET | 0 | -0.022 | -0.017 | 16.018 | -0.739 | -0.739 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 690 | PRO | 0 | -0.034 | -0.032 | 13.060 | -1.271 | -1.271 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 691 | ARG | 1 | 0.864 | 0.956 | 7.735 | 33.231 | 33.231 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 692 | HIS | 0 | -0.048 | -0.032 | 6.987 | 2.407 | 2.407 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 693 | PHE | -1 | -0.900 | -0.938 | 12.497 | -17.989 | -17.989 | 0.000 | 0.000 | 0.000 | 0.000 |