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: N6R8Q
Calculation Name: 2E74-H-Xray549
Preferred Name:
Target Type:
Ligand Name: chlorophyll a | protoporphyrin ix containing fe | (7r,17e)-4-hydroxy-n,n,n,7-tetramethyl-7-[(8e)-octadec-8-enoyloxy]-10-oxo-3,5,9-trioxa-4-phosphaheptacos-17-en-1-aminium 4-oxide | 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol | beta-carotene | undecyl-maltoside | fe2/s2 (inorganic) cluster | cadmium ion
Ligand 3-letter code: CLA | HEM | OPC | SQD | BCR | UMQ | FES | CD
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 2E74
Chain ID: H
UniProt ID: P83791
Base Structure: X-ray
Registration Date: 2025-10-11
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 | OptH |
| Protonation | MOE:Protonate 3D |
| Complement | ac.sh, 23 2024 Oct |
| Water | No |
| Procedure | Manual calculation |
| Remarks |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 29 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -91249.125178 |
|---|---|
| FMO2-HF: Nuclear repulsion | 79676.753712 |
| FMO2-HF: Total energy | -11572.371466 |
| FMO2-MP2: Total energy | -11605.400018 |
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(H:1:MET)
Summations of interaction energy for
fragment #1(H:1:MET)
| 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. |
| -52.286 | -45.611 | 9.454 | -8.145 | -7.984 | -0.092 |
Interaction energy analysis for fragmet #1(H:1:MET)
| 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 | H | 3 | ILE | 0 | 0.049 | 0.022 | 2.356 | 5.458 | 7.948 | 0.973 | -1.505 | -1.958 | -0.005 |
| 4 | H | 4 | ASP | -1 | -0.838 | -0.918 | 2.000 | -99.321 | -95.310 | 8.482 | -6.613 | -5.880 | -0.087 |
| 5 | H | 5 | VAL | 0 | -0.020 | -0.008 | 4.551 | 9.862 | 10.036 | -0.001 | -0.027 | -0.146 | 0.000 |
| 6 | H | 6 | LEU | 0 | 0.014 | 0.005 | 6.688 | 5.943 | 5.943 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | H | 7 | GLY | 0 | 0.024 | 0.014 | 7.385 | 4.173 | 4.173 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | H | 8 | TRP | 0 | -0.012 | -0.011 | 8.066 | 5.131 | 5.131 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | H | 9 | VAL | 0 | -0.004 | -0.006 | 10.692 | 2.770 | 2.770 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | H | 10 | ALA | 0 | 0.015 | 0.009 | 11.990 | 2.263 | 2.263 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | H | 11 | LEU | 0 | 0.007 | 0.013 | 13.674 | 1.786 | 1.786 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | H | 12 | LEU | 0 | 0.006 | -0.001 | 14.520 | 1.514 | 1.514 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | H | 13 | VAL | 0 | 0.006 | 0.017 | 16.449 | 1.350 | 1.350 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | H | 14 | VAL | 0 | 0.017 | 0.005 | 17.906 | 1.131 | 1.131 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | H | 15 | PHE | 0 | -0.014 | 0.014 | 19.725 | 1.007 | 1.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | H | 16 | THR | 0 | 0.002 | -0.018 | 20.650 | 0.873 | 0.873 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | H | 17 | TRP | 0 | 0.001 | -0.005 | 22.186 | 0.614 | 0.614 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | H | 18 | SER | 0 | -0.025 | -0.029 | 23.561 | 0.683 | 0.683 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | H | 19 | ILE | 0 | -0.024 | -0.001 | 25.603 | 0.578 | 0.578 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | H | 20 | ALA | 0 | 0.023 | 0.014 | 26.758 | 0.469 | 0.469 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | H | 21 | MET | 0 | 0.016 | 0.003 | 27.751 | 0.394 | 0.394 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | H | 22 | VAL | 0 | -0.053 | -0.013 | 29.647 | 0.466 | 0.466 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | H | 23 | VAL | 0 | -0.018 | -0.003 | 31.444 | 0.351 | 0.351 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | H | 24 | TRP | 0 | -0.012 | -0.010 | 30.899 | 0.232 | 0.232 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | H | 25 | GLY | 0 | 0.003 | 0.004 | 33.424 | 0.291 | 0.291 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | H | 26 | ARG | 1 | 0.880 | 0.933 | 35.195 | 8.785 | 8.785 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | H | 27 | ASN | 0 | -0.066 | -0.033 | 37.271 | 0.170 | 0.170 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | H | 28 | GLY | 0 | -0.056 | -0.022 | 36.546 | 0.193 | 0.193 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | H | 29 | LEU | -1 | -0.908 | -0.949 | 34.441 | -9.452 | -9.452 | 0.000 | 0.000 | 0.000 | 0.000 |