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: LG2V9
Calculation Name: 7ML2-U-Other547
Preferred Name:
Target Type:
Ligand Name: iron/sulfur cluster
Ligand 3-letter code: SF4
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 7ML2
Chain ID: U
Base Structure: ElectronMicroscopy
Registration Date: 2025-10-05
Reference: Sci Data 11, 1164 (2024).
DOI: https://doi.org/10.1038/s41597-024-03999-2
Apendix: None
Modeling method
| Optimization | MOE:Amber10:EHT |
|---|---|
| Restraint | OptAll |
| Protonation | MOE:Protonate 3D |
| Complement | MOE:Homology Modeling |
| Water | No |
| Procedure | Manual calculation |
| Remarks |
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE. |
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. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -213480.150811 |
|---|---|
| FMO2-HF: Nuclear repulsion | 193934.858669 |
| FMO2-HF: Total energy | -19545.292142 |
| FMO2-MP2: Total energy | -19600.722469 |
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(A:241:GLU)
Summations of interaction energy for
fragment #1(A:241: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. |
| 3.239 | 5.225 | 2.463 | -1.639 | -2.808 | -0.008 |
Interaction energy analysis for fragmet #1(A:241: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 | A | 243 | LEU | 0 | -0.009 | 0.012 | 2.123 | -0.711 | 1.092 | 2.464 | -1.622 | -2.644 | -0.008 |
| 4 | A | 244 | MET | 0 | 0.001 | 0.014 | 4.702 | 1.920 | 2.103 | -0.001 | -0.017 | -0.164 | 0.000 |
| 5 | A | 245 | LEU | 0 | 0.003 | 0.006 | 7.370 | 0.524 | 0.524 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 246 | CYS | 0 | -0.078 | -0.015 | 10.535 | 0.772 | 0.772 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 247 | LEU | 0 | 0.037 | 0.029 | 14.260 | -0.063 | -0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 248 | TYR | 0 | 0.000 | -0.012 | 17.582 | 0.206 | 0.206 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 249 | ASP | -1 | -0.836 | -0.890 | 19.402 | -1.711 | -1.711 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 250 | LYS | 1 | 0.911 | 0.942 | 22.762 | 1.039 | 1.039 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 251 | VAL | 0 | 0.037 | 0.023 | 20.922 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 252 | THR | 0 | -0.060 | -0.035 | 23.569 | 0.102 | 0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 253 | ARG | 1 | 0.938 | 0.985 | 23.112 | 0.253 | 0.253 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 254 | THR | 0 | -0.021 | -0.017 | 26.331 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 255 | LYS | 1 | 0.945 | 0.951 | 27.260 | 0.240 | 0.240 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 256 | ALA | 0 | 0.065 | 0.062 | 25.675 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 257 | ARG | 1 | 0.920 | 0.978 | 22.575 | 0.115 | 0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 258 | TRP | 0 | -0.043 | -0.037 | 19.688 | -0.158 | -0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 259 | LYS | 1 | 0.861 | 0.935 | 21.261 | 0.420 | 0.420 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 260 | CYS | 0 | -0.010 | 0.005 | 17.352 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 261 | SER | 0 | -0.026 | -0.010 | 19.351 | -0.089 | -0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 262 | LEU | 0 | 0.024 | 0.004 | 14.783 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 263 | LYS | 1 | 0.872 | 0.904 | 18.921 | 2.070 | 2.070 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 264 | ASP | -1 | -0.810 | -0.903 | 18.782 | -2.271 | -2.271 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 265 | GLY | 0 | 0.004 | -0.001 | 14.675 | -0.267 | -0.267 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 266 | VAL | 0 | -0.007 | 0.015 | 10.125 | 0.394 | 0.394 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 267 | VAL | 0 | 0.006 | -0.024 | 10.037 | -0.740 | -0.740 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 268 | THR | 0 | -0.030 | -0.001 | 6.048 | -0.875 | -0.875 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 269 | ILE | 0 | 0.040 | 0.013 | 6.962 | -0.981 | -0.981 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 270 | ASN | 0 | -0.002 | -0.009 | 8.098 | 0.629 | 0.629 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 271 | ARG | 1 | 0.920 | 0.962 | 6.240 | 6.426 | 6.426 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 272 | ASN | 0 | 0.033 | 0.030 | 8.603 | -0.560 | -0.560 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 273 | ASP | -1 | -0.848 | -0.945 | 10.364 | -6.085 | -6.085 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 274 | TYR | 0 | -0.059 | -0.025 | 11.971 | 0.757 | 0.757 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 275 | THR | 0 | 0.030 | 0.014 | 14.424 | -0.233 | -0.233 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 276 | PHE | 0 | -0.029 | -0.019 | 13.836 | 0.490 | 0.490 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 277 | GLN | 0 | -0.006 | -0.001 | 18.332 | -0.068 | -0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 278 | LYS | 1 | 0.879 | 0.920 | 21.247 | 1.418 | 1.418 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 279 | ALA | 0 | 0.035 | 0.034 | 17.819 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 280 | GLN | 0 | 0.014 | -0.006 | 19.778 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 281 | VAL | 0 | 0.013 | 0.006 | 15.113 | 0.107 | 0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 282 | GLU | -1 | -0.874 | -0.942 | 17.819 | -0.398 | -0.398 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 283 | ALA | 0 | 0.011 | 0.024 | 16.202 | 0.149 | 0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 284 | GLU | -1 | -0.862 | -0.952 | 17.965 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 285 | TRP | 0 | -0.076 | -0.054 | 19.146 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 286 | VAL | -1 | -0.869 | -0.923 | 20.816 | 0.491 | 0.491 | 0.000 | 0.000 | 0.000 | 0.000 |