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: R9YZ8
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 | 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 | 35 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -137192.549487 |
|---|---|
| FMO2-HF: Nuclear repulsion | 122923.544407 |
| FMO2-HF: Total energy | -14269.005079 |
| FMO2-MP2: Total energy | -14309.550909 |
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. |
| -139.844 | -142.054 | 30.895 | -15.284 | -13.4 | -0.169 |
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 | 0.058 | 0.017 | 3.422 | 2.821 | 4.304 | 0.027 | -0.477 | -1.032 | 0.002 |
| 4 | C | 66 | GLU | -1 | -0.839 | -0.895 | 1.884 | -25.906 | -25.677 | 2.874 | -1.292 | -1.811 | -0.007 |
| 5 | C | 67 | LEU | 0 | 0.051 | 0.031 | 3.870 | 3.312 | 3.838 | 0.002 | -0.172 | -0.356 | 0.000 |
| 6 | C | 68 | LEU | 0 | -0.004 | -0.006 | 5.967 | 3.354 | 3.354 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | C | 69 | SER | 0 | -0.048 | -0.032 | 6.841 | 2.943 | 2.943 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | C | 70 | LYS | 1 | 0.896 | 0.934 | 7.153 | 26.027 | 26.027 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | C | 71 | ILE | 0 | -0.027 | -0.005 | 9.224 | 1.573 | 1.573 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | C | 72 | ASN | 0 | -0.018 | -0.020 | 11.960 | 1.755 | 1.755 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | C | 73 | ASP | -1 | -0.898 | -0.942 | 12.589 | -16.990 | -16.990 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | C | 74 | MET | 0 | 0.013 | 0.016 | 13.513 | 1.244 | 1.244 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | C | 75 | PRO | 0 | -0.014 | 0.010 | 16.406 | 0.302 | 0.302 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | C | 76 | ILE | 0 | -0.023 | -0.014 | 16.169 | 0.455 | 0.455 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | C | 77 | THR | 0 | 0.054 | 0.012 | 20.421 | -0.237 | -0.237 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | C | 78 | ASN | 0 | 0.053 | 0.008 | 20.122 | -0.628 | -0.628 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | C | 79 | ASP | -1 | -0.843 | -0.901 | 19.722 | -14.284 | -14.284 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | C | 80 | GLN | 0 | 0.046 | 0.012 | 18.702 | -0.929 | -0.929 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | C | 81 | LYS | 1 | 0.809 | 0.920 | 15.758 | 14.776 | 14.776 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | C | 82 | LYS | 1 | 0.857 | 0.917 | 14.795 | 13.511 | 13.511 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | C | 83 | LEU | 0 | -0.027 | 0.006 | 15.139 | -1.066 | -1.066 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | C | 84 | MET | 0 | 0.044 | 0.004 | 12.485 | -0.807 | -0.807 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | C | 85 | SER | 0 | -0.010 | -0.019 | 10.611 | -2.381 | -2.381 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | C | 86 | ASN | 0 | 0.003 | -0.013 | 10.323 | -3.099 | -3.099 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | C | 87 | ASP | -1 | -0.812 | -0.895 | 11.056 | -23.545 | -23.545 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | C | 88 | VAL | 0 | -0.005 | 0.001 | 5.372 | -2.532 | -2.532 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | C | 89 | LEU | 0 | -0.022 | -0.013 | 6.292 | -5.950 | -5.950 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | C | 90 | LYS | 1 | 0.823 | 0.912 | 6.777 | 20.224 | 20.224 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | C | 91 | PHE | 0 | 0.009 | 0.000 | 5.662 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | C | 92 | ALA | 0 | -0.040 | -0.009 | 2.456 | -4.953 | -3.993 | 0.687 | -0.537 | -1.110 | 0.000 |
| 31 | C | 93 | ALA | 0 | 0.030 | 0.010 | 3.278 | -0.583 | -0.490 | 0.007 | 0.159 | -0.259 | -0.001 |
| 32 | C | 94 | GLU | -1 | -0.863 | -0.921 | 6.319 | -23.734 | -23.734 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | C | 95 | ALA | 0 | -0.033 | -0.009 | 3.515 | 3.718 | 3.886 | 0.002 | -0.034 | -0.136 | 0.000 |
| 34 | C | 96 | GLU | -1 | -0.842 | -0.897 | 1.734 | -140.778 | -146.447 | 27.296 | -12.931 | -8.696 | -0.163 |
| 35 | C | 97 | LYS | 1 | 0.745 | 0.869 | 5.872 | 32.623 | 32.623 | 0.000 | 0.000 | 0.000 | 0.000 |