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: 6G82Z
Calculation Name: 3T5X-B-Xray540
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 3T5X
Chain ID: B
UniProt ID: Q5JVF3
Base Structure: X-ray
Registration Date: 2025-07-08
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 |
| Remarks |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 59 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -107108.232716 |
|---|---|
| FMO2-HF: Nuclear repulsion | 93919.916479 |
| FMO2-HF: Total energy | -13188.316237 |
| FMO2-MP2: Total energy | -13226.151021 |
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(B:38:VAL)
Summations of interaction energy for
fragment #1(B:38:VAL)
| 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. |
| 0.546 | 2.54 | -0.012 | -0.842 | -1.14 | -0.001 |
Interaction energy analysis for fragmet #1(B:38:VAL)
| 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 | B | 39 | TRP | 0 | -0.078 | 0.067 | 4.092 | -1.423 | -1.089 | 0.005 | 0.067 | -0.406 | -0.001 |
| 5 | B | 40 | GLU | 0 | 0.089 | -0.100 | 3.868 | 1.137 | 2.797 | -0.017 | -0.909 | -0.734 | 0.000 |
| 6 | B | 40 | GLU | -1 | -0.930 | -0.818 | 5.026 | 0.183 | 0.183 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | B | 41 | ASP | 0 | 0.062 | -0.090 | 6.513 | -0.357 | -0.357 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | B | 41 | ASP | -1 | -0.987 | -0.866 | 9.082 | 0.513 | 0.513 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | B | 42 | ASN | 0 | 0.036 | -0.062 | 9.567 | -0.111 | -0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | B | 42 | ASN | 0 | -0.126 | 0.017 | 8.371 | 0.217 | 0.217 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | B | 43 | TRP | 0 | 0.096 | -0.080 | 11.221 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | B | 43 | TRP | 0 | -0.140 | 0.058 | 9.674 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | B | 44 | ASP | 0 | 0.045 | -0.090 | 12.711 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | B | 44 | ASP | -1 | -1.022 | -0.881 | 14.570 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | B | 45 | ASP | 0 | 0.080 | -0.059 | 15.386 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | B | 45 | ASP | -1 | -0.945 | -0.862 | 15.772 | 0.253 | 0.253 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | B | 46 | ASP | 0 | 0.039 | -0.100 | 17.306 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | B | 46 | ASP | -1 | -1.036 | -0.896 | 21.377 | 0.129 | 0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | B | 47 | ASN | 0 | 0.046 | -0.099 | 18.984 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | B | 47 | ASN | 0 | -0.156 | 0.031 | 17.469 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | B | 48 | VAL | 0 | 0.096 | -0.065 | 20.001 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | B | 48 | VAL | 0 | -0.121 | 0.053 | 22.352 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | B | 49 | GLU | 0 | 0.068 | -0.108 | 20.877 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | B | 49 | GLU | -1 | -0.939 | -0.839 | 18.196 | 0.143 | 0.143 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | B | 50 | ASP | 0 | 0.061 | -0.075 | 19.352 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | B | 50 | ASP | -1 | -0.797 | -0.755 | 18.591 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | B | 51 | ASP | 0 | 0.089 | -0.109 | 20.486 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | B | 51 | ASP | -1 | -0.957 | -0.825 | 21.654 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | B | 52 | PHE | 0 | 0.113 | -0.074 | 21.544 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | B | 52 | PHE | 0 | -0.083 | 0.087 | 21.333 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | B | 53 | SER | 0 | 0.041 | -0.137 | 22.223 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | B | 53 | SER | 0 | -0.020 | 0.077 | 21.313 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | B | 54 | ASN | 0 | 0.025 | -0.090 | 23.935 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | B | 54 | ASN | 0 | -0.144 | 0.060 | 23.953 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | B | 55 | GLN | 0 | 0.071 | -0.115 | 26.135 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | B | 55 | GLN | 0 | -0.129 | 0.069 | 25.609 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | B | 56 | LEU | 0 | 0.119 | -0.096 | 26.729 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | B | 56 | LEU | 0 | -0.087 | 0.120 | 25.737 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | B | 57 | ARG | 0 | 0.093 | -0.104 | 27.947 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | B | 57 | ARG | 1 | 0.744 | 1.010 | 25.230 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | B | 58 | ALA | 0 | 0.117 | -0.104 | 29.812 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | B | 58 | ALA | 0 | -0.101 | 0.106 | 31.345 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | B | 59 | GLU | 0 | 0.052 | -0.112 | 31.371 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | B | 59 | GLU | -1 | -0.873 | -0.774 | 31.485 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | B | 60 | LEU | 0 | 0.046 | -0.104 | 32.137 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | B | 60 | LEU | 0 | -0.067 | 0.099 | 30.120 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | B | 61 | GLU | 0 | 0.120 | -0.088 | 33.753 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | B | 61 | GLU | -1 | -0.910 | -0.789 | 34.625 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | B | 62 | LYS | 0 | 0.041 | -0.121 | 35.780 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | B | 62 | LYS | 1 | 0.705 | 0.978 | 34.975 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | B | 63 | HIS | 0 | -0.018 | -0.114 | 37.191 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | B | 63 | HIS | 0 | -0.178 | 0.046 | 36.120 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | B | 64 | GLY | 0 | 0.016 | -0.121 | 38.785 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | B | 65 | TYR | 0 | 0.048 | -0.011 | 35.887 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | B | 65 | TYR | 0 | -0.132 | 0.092 | 35.176 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | B | 66 | LYS | 0 | 0.060 | -0.111 | 34.450 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | B | 66 | LYS | 1 | 0.797 | 1.003 | 35.373 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | B | 67 | MET | 0 | -0.068 | -0.128 | 33.238 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | B | 67 | MET | 0 | 0.052 | 0.045 | 32.209 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |