FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2025-04-23
All entries: 37539
Number of unique PDB entries: 7791
FMODB ID: 66VGZ
Calculation Name: 3T5V-F-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3T5V
Chain ID: F
UniProt ID: P46674
Base Structure: X-ray
Registration Date: 2023-06-19
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 | OptHSide |
| 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 | 47 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -176624.202236 |
|---|---|
| FMO2-HF: Nuclear repulsion | 156265.223301 |
| FMO2-HF: Total energy | -20358.978934 |
| FMO2-MP2: Total energy | -20418.815041 |
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(F:30:GLU)
Summations of interaction energy for
fragment #1(F:30:GLU)
| 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. |
| 177.01 | 178.631 | 8.31 | -4.637 | -5.296 | -0.038 |
Interaction energy analysis for fragmet #1(F:30:GLU)
| 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 | F | 32 | ASP | -1 | -0.942 | -0.973 | 1.911 | 20.513 | 20.973 | 7.402 | -4.000 | -3.863 | -0.036 |
| 4 | F | 33 | ASP | -1 | -0.943 | -0.967 | 2.390 | 30.618 | 31.630 | 0.909 | -0.616 | -1.305 | -0.002 |
| 5 | F | 34 | GLU | -1 | -1.063 | -1.013 | 4.422 | 25.262 | 25.411 | -0.001 | -0.021 | -0.128 | 0.000 |
| 6 | F | 35 | PHE | 0 | -0.086 | -0.052 | 6.852 | -1.870 | -1.870 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | F | 36 | GLU | -1 | -0.917 | -0.949 | 10.448 | 18.307 | 18.307 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | F | 37 | ASP | -1 | -0.955 | -0.971 | 12.536 | 15.629 | 15.629 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | F | 38 | PHE | 0 | -0.046 | -0.029 | 15.797 | -0.566 | -0.566 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | F | 39 | PRO | 0 | -0.056 | -0.025 | 18.830 | -0.504 | -0.504 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | F | 53 | ALA | 0 | -0.034 | -0.028 | 30.781 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | F | 54 | VAL | 0 | 0.001 | -0.001 | 27.478 | -0.115 | -0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | F | 55 | THR | 0 | 0.001 | -0.001 | 29.920 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | F | 56 | GLN | 0 | 0.033 | 0.000 | 27.747 | 0.213 | 0.213 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | F | 57 | THR | 0 | -0.061 | -0.021 | 26.038 | 0.181 | 0.181 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | F | 58 | ASN | 0 | 0.019 | 0.003 | 26.364 | 0.547 | 0.547 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | F | 59 | ILE | 0 | -0.011 | 0.000 | 20.918 | -0.215 | -0.215 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | F | 60 | TRP | 0 | -0.041 | -0.009 | 19.005 | 0.423 | 0.423 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | F | 61 | GLU | -1 | -0.910 | -0.956 | 25.408 | 9.776 | 9.776 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | F | 62 | GLU | -1 | -0.973 | -0.996 | 27.904 | 9.385 | 9.385 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | F | 63 | ASN | 0 | -0.018 | -0.015 | 30.590 | -0.203 | -0.203 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | F | 64 | TRP | 0 | 0.018 | 0.008 | 26.630 | 0.125 | 0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | F | 65 | ASP | -1 | -0.930 | -0.969 | 30.829 | 9.146 | 9.146 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | F | 66 | ASP | -1 | -0.990 | -0.980 | 33.308 | 7.759 | 7.759 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | F | 67 | VAL | 0 | -0.134 | -0.062 | 33.995 | -0.311 | -0.311 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | F | 68 | GLU | -1 | -0.887 | -0.931 | 33.644 | 9.279 | 9.279 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | F | 69 | VAL | 0 | -0.103 | -0.057 | 34.280 | -0.281 | -0.281 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | F | 70 | ASP | -1 | -0.914 | -0.958 | 36.285 | 7.698 | 7.698 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | F | 71 | ASP | -1 | -0.739 | -0.858 | 33.595 | 9.385 | 9.385 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | F | 72 | ASP | -1 | -0.933 | -0.957 | 35.110 | 8.294 | 8.294 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | F | 73 | PHE | 0 | 0.033 | 0.022 | 32.174 | -0.155 | -0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | F | 74 | THR | 0 | -0.004 | -0.040 | 34.991 | -0.238 | -0.238 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | F | 75 | ASN | 0 | -0.065 | -0.043 | 37.055 | -0.325 | -0.325 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | F | 76 | GLU | -1 | -0.955 | -0.972 | 36.309 | 8.376 | 8.376 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | F | 77 | LEU | 0 | -0.023 | -0.006 | 34.959 | -0.209 | -0.209 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | F | 78 | LYS | 1 | 0.910 | 0.952 | 39.272 | -7.867 | -7.867 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | F | 79 | ALA | 0 | -0.027 | -0.012 | 42.466 | -0.215 | -0.215 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | F | 80 | GLU | -1 | -0.875 | -0.916 | 41.017 | 7.225 | 7.225 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | F | 81 | LEU | 0 | -0.011 | -0.009 | 41.694 | -0.173 | -0.173 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | F | 82 | ASP | -1 | -0.900 | -0.932 | 44.770 | 6.219 | 6.219 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | F | 83 | ARG | 1 | 0.833 | 0.893 | 42.538 | -7.461 | -7.461 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | F | 84 | TYR | 0 | 0.062 | 0.046 | 45.882 | -0.135 | -0.135 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | F | 85 | LYS | 1 | 0.978 | 0.983 | 47.960 | -6.312 | -6.312 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | F | 86 | ARG | 1 | 0.826 | 0.882 | 49.368 | -6.428 | -6.428 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | F | 87 | GLU | -1 | -0.962 | -0.970 | 49.123 | 6.438 | 6.438 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | F | 88 | ASN | 0 | -0.121 | -0.068 | 49.788 | -0.127 | -0.127 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | F | 89 | GLN | 0 | -0.093 | -0.024 | 53.180 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |