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: 14LMZ
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.
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 | 26 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -69774.302327 |
|---|---|
| FMO2-HF: Nuclear repulsion | 60513.059405 |
| FMO2-HF: Total energy | -9261.242922 |
| FMO2-MP2: Total energy | -9288.676518 |
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. |
| -0.893 | 4.659 | 3.77 | -3.273 | -6.047 | -0.017 |
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 | 0.953 | 0.978 | 3.816 | 0.602 | 2.471 | -0.011 | -0.918 | -0.940 | 0.001 |
| 4 | G | 104 | GLY | 0 | 0.037 | 0.028 | 2.776 | 0.366 | 1.753 | 0.552 | -0.728 | -1.210 | 0.004 |
| 5 | G | 105 | SER | 0 | -0.053 | -0.033 | 2.707 | 1.056 | 1.303 | 1.288 | -0.162 | -1.373 | -0.006 |
| 6 | G | 106 | ILE | 0 | 0.043 | 0.028 | 2.638 | -3.317 | -1.279 | 1.942 | -1.457 | -2.522 | -0.016 |
| 7 | G | 107 | SER | 0 | 0.045 | 0.031 | 4.249 | 0.085 | 0.096 | -0.001 | -0.008 | -0.002 | 0.000 |
| 8 | G | 108 | GLU | -1 | -0.758 | -0.886 | 6.694 | -0.375 | -0.375 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | G | 109 | GLU | -1 | -0.835 | -0.895 | 10.286 | 0.205 | 0.205 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | G | 110 | THR | 0 | 0.033 | 0.003 | 7.447 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | G | 111 | LYS | 1 | 0.834 | 0.900 | 9.322 | 0.483 | 0.483 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | G | 112 | GLN | 0 | 0.041 | 0.013 | 10.799 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | G | 113 | LYS | 1 | 0.862 | 0.945 | 12.719 | -0.172 | -0.172 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | G | 114 | LEU | 0 | 0.011 | 0.012 | 10.752 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | G | 115 | LYS | 1 | 0.940 | 0.963 | 14.067 | 0.092 | 0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | G | 116 | SER | 0 | -0.001 | -0.020 | 16.386 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | G | 117 | ALA | 0 | 0.000 | 0.028 | 17.395 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | G | 118 | ILE | 0 | -0.009 | 0.003 | 16.788 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | G | 119 | LEU | 0 | -0.022 | -0.019 | 19.802 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | G | 120 | SER | 0 | -0.072 | -0.038 | 21.892 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | G | 121 | ALA | 0 | -0.014 | -0.004 | 23.668 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | G | 122 | GLN | 0 | -0.029 | -0.018 | 22.265 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | G | 123 | SER | 0 | 0.000 | -0.006 | 17.723 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | G | 124 | ALA | 0 | 0.013 | 0.003 | 19.122 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | G | 125 | ALA | 0 | -0.031 | -0.009 | 18.160 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | G | 126 | ASN | 0 | -0.028 | -0.015 | 20.279 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |