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: 948L2
Calculation Name: 1FOD-4-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1FOD
Chain ID: 4
UniProt ID: P87677
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.
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 | 46 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -140346.669208 |
|---|---|
| FMO2-HF: Nuclear repulsion | 122383.206914 |
| FMO2-HF: Total energy | -17963.462294 |
| FMO2-MP2: Total energy | -18014.60878 |
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(4:15:SER)
Summations of interaction energy for
fragment #1(4:15: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. |
| -2.956 | -0.298 | 1.276 | -1.828 | -2.106 | -0.002 |
Interaction energy analysis for fragmet #1(4:15: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]. |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 3 | 4 | 17 | ASN | 0 | -0.028 | -0.007 | 3.876 | -1.887 | -0.161 | -0.015 | -0.955 | -0.756 | 0.004 |
| 4 | 4 | 18 | THR | 0 | -0.033 | -0.033 | 2.432 | -1.178 | -0.423 | 1.292 | -0.803 | -1.244 | -0.006 |
| 5 | 4 | 19 | GLY | 0 | 0.055 | 0.022 | 4.057 | -0.951 | -0.774 | -0.001 | -0.070 | -0.106 | 0.000 |
| 6 | 4 | 20 | SER | 0 | -0.035 | -0.011 | 6.707 | 0.194 | 0.194 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | 4 | 21 | ILE | 0 | 0.017 | 0.011 | 7.961 | 0.131 | 0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | 4 | 22 | ILE | 0 | -0.027 | -0.002 | 10.423 | 0.071 | 0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | 4 | 23 | ASN | 0 | -0.025 | -0.018 | 10.184 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | 4 | 24 | ASN | 0 | 0.007 | -0.010 | 9.262 | -0.087 | -0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | 4 | 25 | TYR | 0 | 0.021 | 0.022 | 11.553 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | 4 | 26 | TYR | 0 | -0.001 | 0.004 | 13.674 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | 4 | 27 | MET | 0 | 0.018 | 0.003 | 12.886 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | 4 | 28 | GLN | 0 | 0.064 | 0.018 | 7.455 | -0.136 | -0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | 4 | 29 | GLN | 0 | 0.009 | -0.016 | 11.115 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | 4 | 30 | TYR | 0 | -0.039 | -0.013 | 13.789 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | 4 | 31 | GLN | 0 | -0.041 | 0.000 | 8.966 | -0.113 | -0.113 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | 4 | 32 | ASN | 0 | -0.044 | -0.029 | 6.684 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | 4 | 33 | SER | 0 | 0.008 | 0.004 | 10.195 | -0.079 | -0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | 4 | 34 | MET | 0 | -0.047 | -0.016 | 10.724 | 0.116 | 0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | 4 | 35 | ASP | -1 | -0.852 | -0.909 | 9.692 | 1.036 | 1.036 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | 4 | 36 | THR | 0 | -0.042 | -0.030 | 12.997 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | 4 | 37 | GLN | 0 | -0.019 | -0.009 | 14.167 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | 4 | 38 | LEU | 0 | 0.016 | 0.006 | 17.840 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | 4 | 39 | GLY | 0 | -0.011 | 0.005 | 21.123 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | 4 | 65 | ASN | 0 | 0.046 | 0.019 | 9.889 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | 4 | 66 | ASP | -1 | -0.784 | -0.893 | 12.202 | 0.158 | 0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | 4 | 67 | TRP | 0 | 0.042 | 0.032 | 14.549 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | 4 | 68 | PHE | 0 | 0.052 | 0.016 | 15.895 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | 4 | 69 | SER | 0 | 0.010 | -0.003 | 13.490 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | 4 | 70 | LYS | 1 | 0.806 | 0.908 | 16.487 | -0.118 | -0.118 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | 4 | 71 | LEU | 0 | 0.003 | 0.010 | 19.547 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | 4 | 72 | ALA | 0 | 0.001 | 0.009 | 18.847 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | 4 | 73 | SER | 0 | -0.031 | -0.038 | 19.077 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | 4 | 74 | SER | 0 | -0.105 | -0.056 | 21.621 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | 4 | 75 | ALA | 0 | 0.011 | 0.013 | 24.399 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | 4 | 76 | PHE | 0 | -0.005 | -0.004 | 26.274 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | 4 | 77 | SER | 0 | -0.027 | -0.014 | 27.447 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | 4 | 78 | GLY | 0 | 0.003 | 0.004 | 29.949 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | 4 | 79 | LEU | 0 | -0.030 | -0.010 | 33.644 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | 4 | 80 | PHE | 0 | 0.008 | -0.004 | 37.275 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | 4 | 81 | GLY | 0 | 0.020 | 0.012 | 39.443 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | 4 | 82 | ALA | 0 | -0.013 | -0.008 | 42.174 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | 4 | 83 | LEU | 0 | 0.016 | 0.008 | 40.327 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | 4 | 84 | LEU | 0 | 0.015 | 0.021 | 43.837 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | 4 | 85 | ALA | 0 | -0.038 | -0.021 | 44.677 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |