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: 6NGMZ
Calculation Name: 4N9G-C-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 4N9G
Chain ID: C
Base Structure: X-ray
Registration Date: 2023-06-22
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 |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 35 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -137218.582298 |
|---|---|
| FMO2-HF: Nuclear repulsion | 122949.982451 |
| FMO2-HF: Total energy | -14268.599848 |
| FMO2-MP2: Total energy | -14309.152597 |
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(C:63:ARG)
Summations of interaction energy for
fragment #1(C:63:ARG)
| 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. |
| -67.773 | -60.753 | 1.298 | -3.144 | -5.17 | -0.019 |
Interaction energy analysis for fragmet #1(C:63:ARG)
| 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 | C | 65 | SER | 0 | 0.019 | 0.002 | 3.340 | 1.525 | 3.532 | 0.037 | -0.703 | -1.340 | 0.002 |
| 4 | C | 66 | GLU | -1 | -0.937 | -0.956 | 2.687 | -30.484 | -29.235 | 0.211 | -0.441 | -1.020 | -0.003 |
| 5 | C | 67 | LEU | 0 | 0.081 | 0.039 | 4.166 | 3.422 | 3.821 | 0.000 | -0.087 | -0.311 | 0.000 |
| 6 | C | 68 | LEU | 0 | -0.027 | -0.024 | 5.897 | 3.684 | 3.684 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | C | 69 | SER | 0 | -0.056 | -0.048 | 6.809 | 3.164 | 3.164 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | C | 70 | LYS | 1 | 1.006 | 1.007 | 7.905 | 24.538 | 24.538 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | C | 71 | ILE | 0 | 0.011 | 0.008 | 9.431 | 1.741 | 1.741 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | C | 72 | ASN | 0 | -0.043 | -0.034 | 11.957 | 2.247 | 2.247 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | C | 73 | ASP | -1 | -0.914 | -0.954 | 13.030 | -17.830 | -17.830 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | C | 74 | MET | 0 | -0.039 | -0.003 | 13.102 | 1.061 | 1.061 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | C | 75 | PRO | 0 | -0.021 | -0.003 | 16.426 | 0.418 | 0.418 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | C | 76 | ILE | 0 | -0.015 | -0.008 | 16.325 | 0.518 | 0.518 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | C | 77 | THR | 0 | 0.032 | 0.005 | 20.593 | -0.205 | -0.205 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | C | 78 | ASN | 0 | 0.071 | 0.019 | 19.889 | -0.846 | -0.846 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | C | 79 | ASP | -1 | -0.851 | -0.953 | 19.225 | -14.753 | -14.753 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | C | 80 | GLN | 0 | 0.067 | 0.042 | 18.474 | -1.205 | -1.205 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | C | 81 | LYS | 1 | 0.917 | 0.992 | 15.370 | 14.931 | 14.931 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | C | 82 | LYS | 1 | 0.810 | 0.908 | 14.476 | 13.686 | 13.686 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | C | 83 | LEU | 0 | -0.029 | 0.011 | 14.572 | -1.020 | -1.020 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | C | 84 | MET | 0 | 0.068 | 0.033 | 12.214 | -0.711 | -0.711 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | C | 85 | SER | 0 | -0.020 | -0.025 | 10.571 | -2.677 | -2.677 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | C | 86 | ASN | 0 | -0.028 | -0.034 | 9.806 | -3.039 | -3.039 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | C | 87 | ASP | -1 | -0.918 | -0.964 | 10.134 | -23.224 | -23.224 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | C | 88 | VAL | 0 | -0.034 | -0.010 | 5.427 | -2.786 | -2.786 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | C | 89 | LEU | 0 | -0.023 | -0.028 | 5.213 | -6.676 | -6.676 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | C | 90 | LYS | 1 | 0.958 | 0.994 | 6.269 | 21.988 | 21.988 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | C | 91 | PHE | 0 | 0.041 | 0.023 | 4.886 | 0.479 | 0.479 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | C | 92 | ALA | 0 | -0.079 | -0.044 | 2.360 | -7.230 | -6.144 | 0.988 | -0.746 | -1.328 | -0.004 |
| 31 | C | 93 | ALA | 0 | 0.069 | 0.047 | 3.020 | 2.017 | 2.102 | 0.043 | 0.168 | -0.295 | -0.002 |
| 32 | C | 94 | GLU | -1 | -0.981 | -0.994 | 6.677 | -23.988 | -23.988 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | C | 95 | ALA | 0 | -0.070 | -0.044 | 4.272 | 2.930 | 3.007 | -0.001 | -0.006 | -0.069 | 0.000 |
| 34 | C | 96 | GLU | -1 | -0.964 | -0.971 | 3.199 | -59.759 | -57.642 | 0.020 | -1.329 | -0.807 | -0.012 |
| 35 | C | 97 | LYS | 1 | 0.857 | 0.952 | 6.809 | 30.311 | 30.311 | 0.000 | 0.000 | 0.000 | 0.000 |