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: 3QZML
Calculation Name: 2C1T-C-Xray372
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 2C1T
Chain ID: C
UniProt ID: Q02821
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 |
| Remarks |
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 | -101972.525114 |
|---|---|
| FMO2-HF: Nuclear repulsion | 87270.443203 |
| FMO2-HF: Total energy | -14702.081911 |
| FMO2-MP2: Total energy | -14743.615554 |
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:2:ALA)
Summations of interaction energy for
fragment #1(C:2:ALA)
| 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. |
| -1.274 | 0.231 | 0.003 | -0.825 | -0.683 | 0 |
Interaction energy analysis for fragmet #1(C:2:ALA)
| 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 | 4 | ARG | 1 | 0.836 | 0.882 | 3.453 | -1.539 | -0.034 | 0.003 | -0.825 | -0.683 | 0.000 |
| 4 | C | 5 | VAL | 0 | 0.007 | 0.014 | 6.279 | 0.296 | 0.296 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | C | 6 | ALA | 0 | 0.008 | 0.002 | 9.439 | -0.143 | -0.143 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | C | 7 | ASP | -1 | -0.800 | -0.884 | 12.569 | -0.439 | -0.439 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | C | 8 | ALA | 0 | 0.016 | 0.012 | 13.799 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | C | 9 | GLN | 0 | -0.046 | -0.014 | 16.774 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | C | 10 | ILE | 0 | 0.012 | 0.015 | 18.399 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | C | 11 | GLN | 0 | -0.008 | -0.012 | 21.114 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | C | 12 | ARG | 1 | 0.872 | 0.915 | 24.490 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | C | 13 | GLU | -1 | -0.823 | -0.901 | 27.748 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | C | 14 | THR | 0 | -0.022 | -0.017 | 25.953 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | C | 15 | TYR | 0 | -0.040 | -0.009 | 22.097 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | C | 16 | ASP | -1 | -0.760 | -0.842 | 26.050 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | C | 17 | SER | 0 | -0.064 | -0.036 | 25.689 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | C | 18 | ASN | 0 | -0.143 | -0.092 | 27.054 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | C | 28 | THR | 0 | 0.030 | 0.002 | 20.469 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | C | 29 | LYS | 1 | 0.933 | 0.971 | 23.261 | 0.137 | 0.137 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | C | 30 | VAL | 0 | 0.067 | 0.041 | 24.096 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | C | 31 | ALA | 0 | -0.011 | -0.014 | 25.672 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | C | 32 | SER | 0 | 0.045 | 0.008 | 27.067 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | C | 33 | SER | 0 | 0.038 | 0.031 | 30.250 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | C | 34 | ALA | 0 | 0.050 | 0.015 | 32.164 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | C | 35 | VAL | 0 | -0.038 | -0.019 | 26.405 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | C | 36 | MET | 0 | -0.055 | -0.029 | 27.442 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | C | 37 | ASN | 0 | 0.078 | 0.040 | 30.300 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | C | 38 | ARG | 1 | 0.972 | 1.005 | 27.641 | 0.099 | 0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | C | 39 | ARG | 1 | 0.908 | 0.936 | 22.639 | 0.146 | 0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | C | 40 | LYS | 1 | 0.979 | 1.006 | 27.925 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | C | 41 | ILE | 0 | 0.021 | 0.011 | 27.588 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | C | 42 | ALA | 0 | -0.009 | -0.001 | 26.963 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | C | 43 | MET | 0 | 0.028 | 0.002 | 28.983 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | C | 44 | PRO | 0 | 0.026 | 0.017 | 28.390 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | C | 45 | LYS | 1 | 0.960 | 0.995 | 30.234 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | C | 46 | ARG | 1 | 0.977 | 0.984 | 32.179 | 0.091 | 0.091 | 0.000 | 0.000 | 0.000 | 0.000 |