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: 2L9KR
Calculation Name: 1N6J-G-Xray540
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: 2025-07-09
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 | OptAll |
| Protonation | MOE:Protonate 3D |
| Complement | MOE:Structure Preparation |
| Water | No |
| Procedure | Auto-FMO protocol ver. 2.20220422 |
| Remarks |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 50 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -69769.226801 |
|---|---|
| FMO2-HF: Nuclear repulsion | 60513.059405 |
| FMO2-HF: Total energy | -9256.167396 |
| FMO2-MP2: Total energy | -9283.476007 |
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. |
| 1.424 | 1.654 | 0.177 | 2.145 | -2.552 | -0.004 |
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]. |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 4 | G | 103 | LYS | 0 | 0.013 | 0.012 | 3.858 | -2.239 | -0.456 | -0.001 | -0.981 | -0.800 | 0.001 |
| 5 | G | 103 | LYS | 1 | 0.913 | 1.075 | 6.151 | 0.352 | 0.352 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | G | 104 | GLY | 0 | 0.043 | -0.090 | 3.425 | 1.023 | 1.116 | 0.021 | 0.146 | -0.261 | 0.001 |
| 7 | G | 105 | SER | 0 | -0.010 | -0.023 | 3.745 | -1.040 | -1.204 | 0.019 | 0.341 | -0.197 | -0.001 |
| 8 | G | 105 | SER | 0 | -0.020 | 0.085 | 3.937 | 0.354 | 0.394 | 0.000 | -0.016 | -0.023 | 0.000 |
| 9 | G | 106 | ILE | 0 | 0.106 | -0.070 | 2.917 | 1.908 | 0.362 | 0.141 | 2.661 | -1.257 | -0.005 |
| 10 | G | 106 | ILE | 0 | -0.066 | 0.113 | 5.021 | 0.066 | 0.079 | -0.001 | -0.003 | -0.008 | 0.000 |
| 11 | G | 107 | SER | 0 | 0.094 | -0.044 | 4.997 | 0.955 | 0.966 | -0.002 | -0.003 | -0.006 | 0.000 |
| 12 | G | 107 | SER | 0 | -0.010 | 0.082 | 6.564 | -0.157 | -0.157 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | G | 108 | GLU | 0 | 0.085 | -0.110 | 6.903 | -0.406 | -0.406 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | G | 108 | GLU | -1 | -0.841 | -0.776 | 9.927 | -0.077 | -0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | G | 109 | GLU | 0 | 0.076 | -0.081 | 10.442 | -0.147 | -0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | G | 109 | GLU | -1 | -0.882 | -0.786 | 10.879 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | G | 110 | THR | 0 | 0.016 | -0.110 | 9.259 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | G | 110 | THR | 0 | -0.029 | 0.058 | 8.429 | -0.119 | -0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | G | 111 | LYS | 0 | 0.145 | -0.052 | 10.377 | -0.097 | -0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | G | 111 | LYS | 1 | 0.721 | 0.993 | 9.860 | 0.410 | 0.410 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | G | 112 | GLN | 0 | 0.028 | -0.129 | 11.621 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | G | 112 | GLN | 0 | -0.016 | 0.125 | 14.132 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | G | 113 | LYS | 0 | 0.091 | -0.066 | 14.255 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | G | 113 | LYS | 1 | 0.781 | 1.015 | 13.218 | 0.092 | 0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | G | 114 | LEU | 0 | 0.132 | -0.053 | 13.618 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | G | 114 | LEU | 0 | -0.106 | 0.086 | 11.539 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | G | 115 | LYS | 0 | 0.153 | -0.065 | 14.951 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | G | 115 | LYS | 1 | 0.785 | 1.029 | 16.169 | 0.219 | 0.219 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | G | 116 | SER | 0 | 0.030 | -0.109 | 17.175 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | G | 116 | SER | 0 | -0.041 | 0.052 | 18.454 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | G | 117 | ALA | 0 | 0.135 | -0.041 | 18.557 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | G | 117 | ALA | 0 | -0.095 | 0.102 | 18.298 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | G | 118 | ILE | 0 | 0.071 | -0.072 | 19.220 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | G | 118 | ILE | 0 | -0.094 | 0.076 | 17.462 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | G | 119 | LEU | 0 | 0.038 | -0.093 | 20.918 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | G | 119 | LEU | 0 | -0.118 | 0.070 | 20.526 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | G | 120 | SER | 0 | 0.023 | -0.079 | 23.005 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | G | 120 | SER | 0 | -0.071 | 0.041 | 22.819 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | G | 121 | ALA | 0 | 0.117 | -0.080 | 24.506 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | G | 121 | ALA | 0 | -0.099 | 0.100 | 27.124 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | G | 122 | GLN | 0 | 0.020 | -0.102 | 23.587 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | G | 122 | GLN | 0 | -0.120 | 0.056 | 23.214 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | G | 123 | SER | 0 | 0.110 | -0.070 | 20.258 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | G | 123 | SER | 0 | -0.052 | 0.051 | 18.507 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | G | 124 | ALA | 0 | 0.105 | -0.065 | 20.380 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | G | 124 | ALA | 0 | -0.071 | 0.092 | 19.846 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | G | 125 | ALA | 0 | 0.051 | -0.100 | 19.627 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | G | 125 | ALA | 0 | -0.103 | 0.083 | 18.785 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | G | 126 | ASN | 0 | -0.113 | -0.138 | 20.920 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | G | 126 | ASN | 0 | 0.030 | 0.012 | 23.284 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |