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: 6GK3Z
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 | OptH |
| 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 | -69937.007089 |
|---|---|
| FMO2-HF: Nuclear repulsion | 60681.46432 |
| FMO2-HF: Total energy | -9255.542768 |
| FMO2-MP2: Total energy | -9282.895089 |
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. |
| 4.857 | -0.16 | 0.213 | 6.462 | -1.661 | 0.001 |
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 | 0.063 | 0.001 | 3.856 | -1.852 | -0.940 | -0.002 | -0.484 | -0.427 | 0.002 |
| 5 | G | 103 | LYS | 1 | 0.897 | 1.081 | 6.794 | 1.003 | 1.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | G | 104 | GLY | 0 | 0.035 | -0.077 | 3.264 | 1.546 | 1.215 | 0.034 | 0.515 | -0.218 | 0.001 |
| 7 | G | 105 | SER | 0 | -0.013 | -0.020 | 3.799 | -0.181 | -0.296 | 0.035 | 0.321 | -0.241 | 0.000 |
| 8 | G | 105 | SER | 0 | -0.014 | 0.082 | 4.853 | 0.498 | 0.498 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | G | 106 | ILE | 0 | 0.076 | -0.078 | 2.932 | 2.483 | -3.021 | 0.149 | 6.113 | -0.759 | -0.002 |
| 10 | G | 106 | ILE | 0 | -0.060 | 0.121 | 5.188 | 0.098 | 0.110 | -0.001 | -0.001 | -0.010 | 0.000 |
| 11 | G | 107 | SER | 0 | 0.086 | -0.052 | 5.199 | 0.690 | 0.699 | -0.002 | -0.002 | -0.006 | 0.000 |
| 12 | G | 107 | SER | 0 | -0.018 | 0.078 | 6.458 | -0.146 | -0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | G | 108 | GLU | 0 | 0.112 | -0.123 | 7.147 | -0.395 | -0.395 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | G | 108 | GLU | -1 | -0.899 | -0.796 | 10.226 | -0.133 | -0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | G | 109 | GLU | 0 | 0.111 | -0.111 | 10.671 | -0.161 | -0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | G | 109 | GLU | -1 | -0.977 | -0.833 | 11.234 | 0.457 | 0.457 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | G | 110 | THR | 0 | -0.044 | -0.101 | 9.341 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | G | 110 | THR | 0 | -0.013 | 0.055 | 8.460 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | G | 111 | LYS | 0 | 0.146 | -0.057 | 10.211 | -0.094 | -0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | G | 111 | LYS | 1 | 0.785 | 1.045 | 9.815 | 0.691 | 0.691 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | G | 112 | GLN | 0 | 0.026 | -0.136 | 11.558 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | G | 112 | GLN | 0 | -0.044 | 0.126 | 14.726 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | G | 113 | LYS | 0 | 0.095 | -0.092 | 14.146 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | G | 113 | LYS | 1 | 0.881 | 1.081 | 13.955 | -0.069 | -0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | G | 114 | LEU | 0 | 0.095 | -0.084 | 13.994 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | G | 114 | LEU | 0 | -0.106 | 0.102 | 12.010 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | G | 115 | LYS | 0 | 0.161 | -0.052 | 15.174 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | G | 115 | LYS | 1 | 0.861 | 1.064 | 16.309 | 0.260 | 0.260 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | G | 116 | SER | 0 | 0.023 | -0.097 | 17.438 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | G | 116 | SER | 0 | -0.031 | 0.068 | 18.592 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | G | 117 | ALA | 0 | 0.158 | -0.037 | 18.688 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | G | 117 | ALA | 0 | -0.099 | 0.110 | 18.448 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | G | 118 | ILE | 0 | 0.061 | -0.093 | 19.218 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | G | 118 | ILE | 0 | -0.089 | 0.073 | 17.287 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | G | 119 | LEU | 0 | 0.065 | -0.088 | 20.865 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | G | 119 | LEU | 0 | -0.118 | 0.086 | 21.028 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | G | 120 | SER | 0 | -0.035 | -0.093 | 22.932 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | G | 120 | SER | 0 | -0.052 | 0.019 | 22.758 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | G | 121 | ALA | 0 | 0.138 | -0.108 | 24.360 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | G | 121 | ALA | 0 | -0.109 | 0.107 | 26.935 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | G | 122 | GLN | 0 | 0.024 | -0.093 | 23.562 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | G | 122 | GLN | 0 | -0.125 | 0.053 | 22.946 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | G | 123 | SER | 0 | 0.079 | -0.051 | 20.405 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | G | 123 | SER | 0 | -0.056 | 0.037 | 18.711 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | G | 124 | ALA | 0 | 0.107 | -0.070 | 20.538 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | G | 124 | ALA | 0 | -0.055 | 0.095 | 20.309 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | G | 125 | ALA | 0 | 0.039 | -0.117 | 20.006 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | G | 125 | ALA | 0 | -0.108 | 0.089 | 19.088 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | G | 126 | ASN | 0 | -0.129 | -0.137 | 21.225 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | G | 126 | ASN | 0 | 0.043 | 0.036 | 23.304 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |