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: G82G1
Calculation Name: 1SCY-A-Other547
Preferred Name:
Target Type:
Ligand Name: amino group
Ligand 3-letter code: NH2
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 1SCY
Chain ID: A
UniProt ID: P16341
Base Structure: SolutionNMR
Registration Date: 2025-10-03
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 | 28 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -113675.931161 |
|---|---|
| FMO2-HF: Nuclear repulsion | 99986.741838 |
| FMO2-HF: Total energy | -13689.189323 |
| FMO2-MP2: Total energy | -13722.90976 |
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:ALA)
Summations of interaction energy for
fragment #1(A:1: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. |
| 11.561 | 15.35 | 3.264 | -3.548 | -3.504 | -0.033 |
Interaction energy analysis for fragmet #1(A:1: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 | A | 3 | CYS | 0 | -0.026 | -0.002 | 3.762 | 5.436 | 6.965 | 0.005 | -0.550 | -0.984 | 0.000 |
| 4 | A | 4 | ASN | 0 | 0.046 | 0.012 | 4.851 | 6.755 | 6.851 | -0.001 | -0.011 | -0.084 | 0.000 |
| 22 | A | 23 | GLY | 0 | -0.010 | -0.013 | 3.242 | -5.215 | -5.074 | 0.012 | -0.080 | -0.072 | 0.000 |
| 23 | A | 24 | ASP | -1 | -0.863 | -0.929 | 2.341 | -75.387 | -73.424 | 3.249 | -2.906 | -2.306 | -0.033 |
| 24 | A | 25 | LYS | 1 | 0.881 | 0.924 | 4.797 | 32.620 | 32.680 | -0.001 | -0.001 | -0.058 | 0.000 |
| 5 | A | 5 | LEU | 0 | 0.083 | 0.034 | 8.138 | 2.508 | 2.508 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | ARG | 1 | 0.989 | 1.002 | 10.715 | 19.925 | 19.925 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | MET | 0 | 0.001 | 0.010 | 10.821 | 0.764 | 0.764 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | CYS | 0 | 0.016 | 0.015 | 7.074 | 2.209 | 2.209 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | GLN | 0 | 0.007 | -0.001 | 12.428 | 2.524 | 2.524 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | LEU | 0 | -0.001 | 0.008 | 15.623 | 1.069 | 1.069 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | SER | 0 | -0.001 | -0.014 | 14.542 | 1.138 | 1.138 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | CYS | 0 | -0.030 | -0.007 | 12.751 | 0.185 | 0.185 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | ARG | 1 | 0.815 | 0.891 | 17.749 | 16.306 | 16.306 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | SER | 0 | -0.021 | -0.019 | 20.139 | 1.004 | 1.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | LEU | 0 | -0.029 | -0.006 | 19.624 | 0.589 | 0.589 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | GLY | 0 | -0.011 | -0.001 | 22.703 | 0.359 | 0.359 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | LEU | 0 | -0.006 | 0.007 | 19.471 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | LEU | 0 | 0.005 | 0.019 | 17.564 | -0.489 | -0.489 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | GLY | 0 | 0.013 | -0.008 | 14.773 | -0.552 | -0.552 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | LYS | 1 | 0.805 | 0.877 | 11.429 | 22.364 | 22.364 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 22 | ILE | 0 | 0.028 | 0.033 | 7.252 | -0.843 | -0.843 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 27 | GLU | -1 | -0.793 | -0.878 | 9.582 | -20.080 | -20.080 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 29 | VAL | 0 | 0.060 | 0.044 | 16.196 | 0.676 | 0.676 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 30 | LYS | 1 | 0.911 | 0.945 | 18.582 | 12.070 | 12.070 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 31 | HIS | -1 | -0.853 | -0.923 | 21.384 | -14.359 | -14.359 | 0.000 | 0.000 | 0.000 | 0.000 |