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: 3MVVL
Calculation Name: 4DNN-A-Xray547
Preferred Name:
Target Type:
Ligand Name: calcium ion
Ligand 3-letter code: CA
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 4DNN
Chain ID: A
UniProt ID: Q9QYS9
Base Structure: X-ray
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 | 50 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -245057.832437 |
|---|---|
| FMO2-HF: Nuclear repulsion | 223714.653194 |
| FMO2-HF: Total energy | -21343.179243 |
| FMO2-MP2: Total energy | -21402.774695 |
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:-2:GLY)
Summations of interaction energy for
fragment #1(A:-2:GLY)
| 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. |
| -146.215 | -141.578 | 0.905 | -2.857 | -2.686 | -0.029 |
Interaction energy analysis for fragmet #1(A:-2:GLY)
| 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 | 14 | THR | 0 | -0.015 | -0.007 | 3.814 | 5.749 | 6.692 | -0.016 | -0.353 | -0.574 | -0.001 |
| 48 | A | 59 | ASP | -1 | -0.944 | -0.953 | 2.171 | -64.153 | -63.189 | 0.807 | -0.839 | -0.933 | -0.011 |
| 49 | A | 60 | THR | 0 | -0.140 | -0.085 | 2.933 | -24.760 | -22.030 | 0.114 | -1.665 | -1.179 | -0.017 |
| 4 | A | 15 | PRO | 0 | 0.034 | 0.003 | 7.079 | 1.240 | 1.240 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 16 | ASP | -1 | -0.844 | -0.922 | 9.953 | -23.823 | -23.823 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 17 | TYR | 0 | -0.011 | -0.032 | 11.953 | 2.117 | 2.117 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 18 | LEU | 0 | 0.033 | 0.013 | 12.233 | 1.810 | 1.810 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 19 | MET | 0 | -0.057 | -0.037 | 12.945 | 1.748 | 1.748 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 20 | GLN | 0 | -0.012 | 0.005 | 15.904 | 1.350 | 1.350 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 21 | LEU | 0 | 0.082 | 0.049 | 15.293 | 1.151 | 1.151 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 22 | MET | 0 | -0.019 | -0.022 | 17.192 | 0.644 | 0.644 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 23 | ASN | 0 | -0.030 | -0.009 | 19.647 | 1.002 | 1.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 24 | ASP | -1 | -0.835 | -0.912 | 21.973 | -13.544 | -13.544 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 25 | LYS | 1 | 0.769 | 0.860 | 22.352 | 13.287 | 13.287 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 26 | LYS | 1 | 0.854 | 0.930 | 21.047 | 15.045 | 15.045 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 27 | LEU | 0 | 0.013 | 0.024 | 25.914 | 0.589 | 0.589 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 28 | MET | 0 | -0.008 | -0.010 | 27.232 | 0.590 | 0.590 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 29 | SER | 0 | -0.015 | -0.016 | 27.175 | 0.395 | 0.395 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 30 | SER | 0 | -0.067 | -0.039 | 29.727 | 0.387 | 0.387 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 31 | LEU | 0 | -0.061 | -0.017 | 31.657 | 0.418 | 0.418 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 32 | PRO | 0 | 0.071 | 0.036 | 33.703 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 33 | ASN | 0 | -0.031 | -0.030 | 34.625 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 34 | PHE | 0 | -0.005 | -0.001 | 34.251 | 0.168 | 0.168 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 35 | SER | 0 | -0.013 | -0.048 | 30.555 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 36 | GLY | 0 | 0.008 | -0.002 | 32.915 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 37 | ILE | 0 | -0.039 | -0.004 | 35.838 | 0.247 | 0.247 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 38 | PHE | 0 | -0.044 | -0.024 | 32.385 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 39 | ASN | 0 | -0.034 | -0.019 | 33.600 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 40 | HIS | 0 | 0.052 | 0.020 | 28.919 | -0.306 | -0.306 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 41 | LEU | 0 | 0.009 | 0.020 | 27.093 | -0.403 | -0.403 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 42 | GLU | -1 | -0.742 | -0.831 | 26.293 | -11.854 | -11.854 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 43 | ARG | 1 | 0.861 | 0.912 | 25.062 | 11.416 | 11.416 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 44 | LEU | 0 | -0.012 | -0.012 | 23.603 | -0.491 | -0.491 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 45 | LEU | 0 | 0.009 | 0.020 | 20.323 | -0.774 | -0.774 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 46 | ASP | -1 | -0.803 | -0.895 | 20.274 | -14.172 | -14.172 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 47 | GLU | -1 | -0.870 | -0.919 | 19.902 | -14.097 | -14.097 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 48 | GLU | -1 | -0.783 | -0.851 | 16.071 | -20.466 | -20.466 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 49 | ILE | 0 | -0.020 | -0.013 | 15.714 | -1.644 | -1.644 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 50 | SER | 0 | -0.069 | -0.055 | 15.171 | -1.235 | -1.235 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 51 | ARG | 1 | 0.821 | 0.911 | 14.227 | 17.115 | 17.115 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 52 | VAL | 0 | 0.073 | 0.034 | 10.855 | -1.788 | -1.788 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 53 | ARG | 1 | 0.914 | 0.950 | 10.151 | 17.302 | 17.302 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 54 | LYS | 1 | 0.935 | 0.978 | 10.630 | 19.456 | 19.456 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 55 | ASP | -1 | -0.913 | -0.958 | 8.587 | -28.486 | -28.486 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 56 | MET | 0 | -0.038 | -0.029 | 5.844 | -3.239 | -3.239 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 57 | TYR | 0 | -0.013 | 0.005 | 5.585 | -5.871 | -5.871 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 58 | ASN | 0 | 0.034 | -0.001 | 7.308 | 0.198 | 0.198 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 61 | LEU | -1 | -0.990 | -0.970 | 5.807 | -28.515 | -28.515 | 0.000 | 0.000 | 0.000 | 0.000 |