FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-07-23
All entries: 37478
Number of unique PDB entries: 7783
FMODB ID: VRG91
Calculation Name: 1N6J-G-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1N6J
Chain ID: G
UniProt ID: Q9Y6J0
Base Structure: X-ray
Registration Date: 2023-06-20
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 |
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. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -69881.275817 |
|---|---|
| FMO2-HF: Nuclear repulsion | 60620.15695 |
| FMO2-HF: Total energy | -9261.118867 |
| FMO2-MP2: Total energy | -9288.581859 |
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. |
| -1.891 | 1.378 | 5.785 | -3.034 | -6.019 | -0.009 |
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 | 0.971 | 0.980 | 3.856 | 0.095 | 1.173 | -0.010 | -0.491 | -0.577 | 0.002 |
| 4 | G | 104 | GLY | 0 | 0.045 | 0.035 | 2.554 | -0.822 | 0.771 | 1.414 | -1.338 | -1.669 | 0.009 |
| 5 | G | 105 | SER | 0 | -0.061 | -0.025 | 2.819 | 1.426 | 1.317 | 1.103 | 0.319 | -1.313 | -0.004 |
| 6 | G | 106 | ILE | 0 | 0.038 | 0.025 | 2.461 | -2.616 | -1.919 | 3.279 | -1.516 | -2.460 | -0.016 |
| 7 | G | 107 | SER | 0 | 0.041 | 0.018 | 4.484 | -0.023 | -0.013 | -0.001 | -0.008 | 0.000 | 0.000 |
| 8 | G | 108 | GLU | -1 | -0.752 | -0.885 | 6.642 | -0.115 | -0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | G | 109 | GLU | -1 | -0.851 | -0.901 | 10.231 | 0.293 | 0.293 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | G | 110 | THR | 0 | 0.003 | -0.008 | 7.600 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | G | 111 | LYS | 1 | 0.852 | 0.908 | 9.328 | 0.171 | 0.171 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | G | 112 | GLN | 0 | 0.010 | -0.006 | 10.738 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | G | 113 | LYS | 1 | 0.890 | 0.951 | 13.033 | -0.244 | -0.244 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | G | 114 | LEU | 0 | 0.012 | 0.013 | 10.963 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | G | 115 | LYS | 1 | 0.981 | 0.994 | 14.292 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | G | 116 | SER | 0 | 0.013 | -0.004 | 16.638 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | G | 117 | ALA | 0 | 0.006 | 0.041 | 17.472 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | G | 118 | ILE | 0 | 0.011 | 0.003 | 16.772 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | G | 119 | LEU | 0 | 0.002 | 0.000 | 19.908 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | G | 120 | SER | 0 | -0.135 | -0.069 | 21.908 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | G | 121 | ALA | 0 | 0.011 | -0.010 | 23.507 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | G | 122 | GLN | 0 | -0.055 | -0.030 | 22.234 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | G | 123 | SER | 0 | -0.006 | 0.001 | 17.871 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | G | 124 | ALA | 0 | 0.010 | 0.003 | 19.535 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | G | 125 | ALA | 0 | -0.047 | -0.028 | 18.364 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | G | 126 | ASN | 0 | -0.011 | -0.003 | 20.515 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |