FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2025-10-06
All entries: 70436
Number of unique PDB entries: 28101
FMODB ID: VVYM1
Calculation Name: 1CNN-A-Other547
Preferred Name:
Target Type:
Ligand Name: amino group
Ligand 3-letter code: NH2
Ligand of Interest (LOI):
PDB ID: 1CNN
Chain ID: A
UniProt ID: P37300
Base Structure: SolutionNMR
Registration Date: 2025-09-02
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 |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 23 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -83855.856811 |
|---|---|
| FMO2-HF: Nuclear repulsion | 72360.213883 |
| FMO2-HF: Total energy | -11495.642928 |
| FMO2-MP2: Total energy | -11522.549462 |
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:1:CYS)
Summations of interaction energy for
fragment #1(A:1:CYS)
| 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. |
| 66.225 | 67.478 | 20.542 | -9.646 | -12.148 | -0.012 |
Interaction energy analysis for fragmet #1(A:1:CYS)
| 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 | 3 | GLY | 0 | 0.106 | 0.049 | 1.800 | -10.248 | -14.715 | 13.032 | -3.746 | -4.819 | -0.045 |
| 4 | A | 4 | LYS | 1 | 1.008 | 0.974 | 4.138 | 28.722 | 28.960 | 0.001 | 0.004 | -0.242 | 0.000 |
| 8 | A | 8 | CYS | 0 | -0.054 | -0.006 | 4.326 | -2.377 | -2.224 | -0.001 | -0.052 | -0.101 | 0.000 |
| 13 | A | 13 | TYR | 0 | -0.008 | 0.009 | 5.018 | -2.664 | -2.493 | -0.002 | -0.006 | -0.163 | 0.000 |
| 14 | A | 14 | ASP | -1 | -0.763 | -0.874 | 3.522 | -64.550 | -60.954 | 0.016 | -1.774 | -1.838 | -0.009 |
| 17 | A | 18 | GLY | 0 | 0.042 | 0.031 | 1.936 | -5.899 | -4.356 | 7.468 | -4.482 | -4.529 | 0.040 |
| 18 | A | 19 | SER | 0 | 0.012 | -0.002 | 3.515 | -1.750 | -1.780 | 0.030 | 0.410 | -0.409 | 0.002 |
| 19 | A | 21 | GLY | 0 | 0.095 | 0.048 | 5.612 | 3.320 | 3.369 | -0.002 | 0.000 | -0.047 | 0.000 |
| 5 | A | 5 | GLY | 0 | 0.023 | 0.014 | 6.362 | 1.455 | 1.455 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | ALA | 0 | -0.033 | -0.010 | 6.164 | 2.285 | 2.285 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | PRO | 0 | 0.012 | -0.005 | 7.179 | -1.151 | -1.151 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | ARG | 1 | 0.852 | 0.882 | 6.017 | 41.788 | 41.788 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | LYS | 1 | 0.952 | 0.972 | 7.114 | 19.784 | 19.784 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | THR | 0 | -0.017 | -0.010 | 8.170 | 0.671 | 0.671 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | MET | 0 | 0.034 | 0.026 | 5.670 | 2.004 | 2.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 22 | ARG | 1 | 0.950 | 0.939 | 9.248 | 14.997 | 14.997 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 23 | ARG | 1 | 0.959 | 0.971 | 12.164 | 17.542 | 17.542 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 24 | GLY | 0 | 0.033 | 0.038 | 9.399 | 0.549 | 0.549 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 25 | LYS | 1 | 0.892 | 0.951 | 8.209 | 21.747 | 21.747 | 0.000 | 0.000 | 0.000 | 0.000 |