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: M386Z
Calculation Name: 1TII-C-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1TII
Chain ID: C
UniProt ID: P43528
Base Structure: X-ray
Registration Date: 2023-03-13
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 | 36 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -129917.893499 |
|---|---|
| FMO2-HF: Nuclear repulsion | 115171.944489 |
| FMO2-HF: Total energy | -14745.94901 |
| FMO2-MP2: Total energy | -14788.103221 |
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:195:THR)
Summations of interaction energy for
fragment #1(C:195:THR)
| 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. |
| -8.187 | -1.947 | 1.412 | -3.16 | -4.492 | 0 |
Interaction energy analysis for fragmet #1(C:195:THR)
| 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 | 197 | CYS | 0 | 0.089 | 0.029 | 2.969 | -1.486 | 1.833 | 0.204 | -1.821 | -1.701 | -0.001 |
| 4 | C | 198 | ALA | 0 | 0.029 | 0.034 | 5.525 | 0.840 | 0.840 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | C | 199 | SER | 0 | -0.008 | -0.014 | 2.283 | 0.020 | 0.563 | 0.936 | -0.461 | -1.019 | 0.000 |
| 6 | C | 200 | LEU | 0 | -0.002 | 0.003 | 2.949 | -1.467 | 0.565 | 0.267 | -0.818 | -1.481 | 0.001 |
| 7 | C | 201 | THR | 0 | 0.042 | 0.005 | 4.001 | -0.563 | -0.389 | 0.005 | -0.040 | -0.139 | 0.000 |
| 8 | C | 202 | ASN | 0 | 0.022 | 0.023 | 7.062 | -0.081 | -0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | C | 203 | LYS | 1 | 0.954 | 0.975 | 3.998 | -3.810 | -3.638 | 0.000 | -0.020 | -0.152 | 0.000 |
| 10 | C | 204 | LEU | 0 | 0.009 | 0.005 | 6.877 | -0.157 | -0.157 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | C | 205 | SER | 0 | 0.051 | 0.016 | 9.300 | -0.250 | -0.250 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | C | 206 | GLN | 0 | -0.066 | -0.045 | 10.282 | -0.174 | -0.174 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | C | 207 | HIS | 0 | -0.050 | -0.016 | 10.756 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | C | 208 | ASP | -1 | -0.836 | -0.921 | 12.458 | 0.656 | 0.656 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | C | 209 | LEU | 0 | -0.040 | -0.016 | 14.944 | -0.104 | -0.104 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | C | 210 | ALA | 0 | 0.008 | -0.004 | 15.076 | -0.076 | -0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | C | 211 | ASP | -1 | -0.816 | -0.888 | 16.658 | 0.552 | 0.552 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | C | 212 | PHE | 0 | 0.016 | 0.014 | 18.460 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | C | 213 | LYS | 1 | 0.952 | 0.971 | 18.116 | -0.430 | -0.430 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | C | 214 | LYS | 1 | 0.809 | 0.880 | 16.473 | -0.607 | -0.607 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | C | 215 | TYR | 0 | 0.031 | 0.024 | 22.376 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | C | 216 | ILE | 0 | 0.016 | 0.011 | 24.522 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | C | 217 | LYS | 1 | 0.965 | 0.983 | 24.524 | -0.270 | -0.270 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | C | 218 | ARG | 1 | 0.957 | 0.988 | 22.580 | -0.358 | -0.358 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | C | 219 | LYS | 1 | 0.957 | 0.982 | 28.182 | -0.206 | -0.206 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | C | 220 | PHE | 0 | 0.030 | 0.014 | 30.118 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | C | 221 | THR | 0 | -0.011 | -0.013 | 30.132 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | C | 222 | LEU | 0 | 0.000 | 0.002 | 32.305 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | C | 223 | MET | 0 | 0.001 | -0.003 | 34.187 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | C | 224 | THR | 0 | 0.004 | 0.006 | 35.161 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | C | 225 | LEU | 0 | -0.018 | -0.017 | 34.845 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | C | 226 | LEU | 0 | -0.024 | -0.008 | 38.279 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | C | 227 | SER | 0 | -0.031 | -0.019 | 40.115 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | C | 228 | ILE | 0 | -0.051 | -0.024 | 39.584 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | C | 229 | ASN | 0 | -0.074 | -0.030 | 40.392 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | C | 230 | ASN | 0 | 0.012 | 0.013 | 44.181 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |