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: 2GV2R
Calculation Name: 1N6J-G-Xray549
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 1N6J
Chain ID: G
UniProt ID: Q9Y6J0
Base Structure: X-ray
Registration Date: 2025-10-11
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 | OptH |
| Protonation | MOE:Protonate 3D |
| Complement | ac.sh, 23 2024 Oct |
| Water | No |
| Procedure | Manual calculation |
| Remarks |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 26 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -69662.649331 |
|---|---|
| FMO2-HF: Nuclear repulsion | 60401.701126 |
| FMO2-HF: Total energy | -9260.948205 |
| FMO2-MP2: Total energy | -9288.379616 |
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(G:101:SER)
Summations of interaction energy for
fragment #1(G:101:SER)
| 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. |
| 34.915 | 40.376 | 7.846 | -5.492 | -7.816 | -0.051 |
Interaction energy analysis for fragmet #1(G:101:SER)
| 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 | G | 103 | LYS | 1 | 1.001 | 0.999 | 3.867 | 34.095 | 35.145 | -0.009 | -0.435 | -0.606 | -0.001 |
| 4 | G | 104 | GLY | 0 | 0.060 | 0.041 | 2.497 | 5.606 | 6.698 | 1.285 | -1.024 | -1.353 | 0.005 |
| 5 | G | 105 | SER | 0 | -0.036 | -0.026 | 2.390 | -11.714 | -9.283 | 2.209 | -1.841 | -2.799 | -0.032 |
| 6 | G | 106 | ILE | 0 | 0.025 | 0.015 | 2.405 | -15.879 | -15.003 | 4.362 | -2.185 | -3.054 | -0.023 |
| 7 | G | 107 | SER | 0 | 0.040 | 0.026 | 4.281 | 3.665 | 3.677 | -0.001 | -0.007 | -0.004 | 0.000 |
| 8 | G | 108 | GLU | -1 | -0.772 | -0.890 | 6.310 | -24.593 | -24.593 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | G | 109 | GLU | -1 | -0.844 | -0.899 | 10.020 | -21.637 | -21.637 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | G | 110 | THR | 0 | -0.009 | -0.014 | 7.310 | 1.308 | 1.308 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | G | 111 | LYS | 1 | 0.861 | 0.911 | 9.138 | 28.863 | 28.863 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | G | 112 | GLN | 0 | 0.021 | 0.002 | 10.745 | 2.406 | 2.406 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | G | 113 | LYS | 1 | 0.887 | 0.950 | 12.758 | 22.342 | 22.342 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | G | 114 | LEU | 0 | 0.017 | 0.015 | 10.552 | 0.964 | 0.964 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | G | 115 | LYS | 1 | 0.967 | 0.983 | 14.175 | 17.174 | 17.174 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | G | 116 | SER | 0 | 0.004 | -0.017 | 16.386 | 1.212 | 1.212 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | G | 117 | ALA | 0 | -0.006 | 0.029 | 17.444 | 0.882 | 0.882 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | G | 118 | ILE | 0 | 0.008 | 0.008 | 16.201 | 0.586 | 0.586 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | G | 119 | LEU | 0 | -0.026 | -0.022 | 19.877 | 0.621 | 0.621 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | G | 120 | SER | 0 | -0.074 | -0.048 | 21.921 | 0.620 | 0.620 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | G | 121 | ALA | 0 | 0.003 | 0.010 | 23.547 | 0.407 | 0.407 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | G | 122 | GLN | 0 | -0.043 | -0.027 | 22.041 | 0.471 | 0.471 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | G | 123 | SER | 0 | -0.049 | -0.021 | 17.480 | -0.713 | -0.713 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | G | 124 | ALA | 0 | -0.004 | -0.005 | 18.563 | 0.543 | 0.543 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | G | 125 | ALA | 0 | -0.075 | -0.043 | 17.524 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | G | 126 | ASN | -1 | -0.905 | -0.944 | 19.678 | -12.401 | -12.401 | 0.000 | 0.000 | 0.000 | 0.000 |