FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-07-23
All entries: 37450
Number of unique PDB entries: 7783
FMODB ID: Q894Y
Calculation Name: 1N6J-G-Xray315
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: 2021-09-06
Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.
Modeling method
| Optimization | MOE:Amber10:EHT |
|---|---|
| Restraint | OptH |
| Protonation | MOE:Protonate 3D |
| Complement | MOE:Structure Preparation |
| Water | No |
| Procedure | Auto-FMO protocol ver. 1.20200129 |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 28 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver.1 Rev. 15 / 20190524 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -71971.496979 |
|---|---|
| FMO2-HF: Nuclear repulsion | 62539.556747 |
| FMO2-HF: Total energy | -9431.940232 |
| FMO2-MP2: Total energy | -9459.956707 |
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:100:ACE )
Summations of interaction energy for
fragment #1(G:100:ACE )
| 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. |
| 2.17 | 2.995 | -0.005 | -0.384 | -0.435 | 0 |
Interaction energy analysis for fragmet #1(G:100:ACE )
| 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 | 102 | PRO | 0 | 0.017 | 0.016 | 3.852 | 0.911 | 1.736 | -0.005 | -0.384 | -0.435 | 0.000 |
| 4 | G | 103 | LYS | 1 | 0.972 | 0.976 | 6.879 | 0.590 | 0.590 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | G | 104 | GLY | 0 | 0.057 | 0.044 | 6.925 | 0.188 | 0.188 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | G | 105 | SER | 0 | -0.079 | -0.032 | 7.877 | 0.091 | 0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | G | 106 | ILE | 0 | 0.037 | 0.026 | 6.748 | -0.598 | -0.598 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | G | 107 | SER | 0 | 0.037 | 0.010 | 7.103 | 0.187 | 0.187 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | G | 108 | GLU | -1 | -0.792 | -0.927 | 8.697 | -0.329 | -0.329 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | G | 109 | GLU | -1 | -0.908 | -0.941 | 10.824 | -0.152 | -0.152 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | G | 110 | THR | 0 | -0.008 | -0.009 | 8.261 | 0.102 | 0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | G | 111 | LYS | 1 | 0.902 | 0.948 | 10.972 | 0.572 | 0.572 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | G | 112 | GLN | 0 | 0.009 | -0.005 | 13.246 | 0.079 | 0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | G | 113 | LYS | 1 | 0.961 | 1.002 | 12.900 | 0.185 | 0.185 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | G | 114 | LEU | 0 | 0.015 | 0.012 | 13.873 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | G | 115 | LYS | 1 | 0.979 | 0.991 | 16.165 | 0.204 | 0.204 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | G | 116 | SER | 0 | 0.023 | 0.004 | 18.863 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | G | 117 | ALA | 0 | -0.004 | 0.045 | 18.827 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | G | 118 | ILE | 0 | -0.005 | -0.007 | 19.066 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | G | 119 | LEU | 0 | 0.013 | -0.003 | 22.099 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | G | 120 | SER | 0 | -0.133 | -0.077 | 23.242 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | G | 121 | ALA | 0 | 0.015 | -0.013 | 25.337 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | G | 122 | GLN | 0 | -0.048 | -0.023 | 22.866 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | G | 123 | SER | 0 | 0.003 | -0.002 | 19.536 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | G | 124 | ALA | 0 | 0.012 | 0.003 | 20.578 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | G | 125 | ALA | 0 | -0.051 | -0.036 | 20.415 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | G | 126 | ASN | 0 | -0.068 | -0.017 | 22.445 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | G | 127 | NME | 0 | 0.037 | 0.031 | 25.807 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |