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: ZZN4N
Calculation Name: 2CWB-A-Other547
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 2CWB
Chain ID: A
UniProt ID: Q96S82
Base Structure: SolutionNMR
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 | 46 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -198849.159081 |
|---|---|
| FMO2-HF: Nuclear repulsion | 181626.766807 |
| FMO2-HF: Total energy | -17222.392274 |
| FMO2-MP2: Total energy | -17272.731124 |
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:63:GLY)
Summations of interaction energy for
fragment #1(A:63: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. |
| -128.607 | -122.294 | 4.018 | -5.437 | -4.893 | -0.052 |
Interaction energy analysis for fragmet #1(A:63: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 | 65 | GLN | 0 | -0.029 | -0.029 | 3.853 | 3.036 | 3.835 | -0.006 | -0.244 | -0.548 | 0.000 |
| 4 | A | 66 | TRP | 0 | 0.037 | 0.025 | 3.281 | 9.031 | 9.806 | 0.016 | -0.352 | -0.440 | -0.003 |
| 5 | A | 67 | GLN | 0 | 0.056 | 0.030 | 4.646 | 3.527 | 3.616 | -0.001 | -0.004 | -0.084 | 0.000 |
| 6 | A | 68 | PRO | 0 | -0.003 | -0.008 | 4.570 | 3.041 | 3.108 | -0.001 | -0.010 | -0.055 | 0.000 |
| 7 | A | 69 | GLN | 0 | 0.022 | 0.010 | 2.184 | -16.600 | -15.059 | 3.785 | -3.040 | -2.287 | -0.033 |
| 31 | A | 93 | GLY | 0 | -0.067 | -0.057 | 2.571 | -21.209 | -19.846 | 0.190 | -0.872 | -0.680 | -0.008 |
| 32 | A | 94 | ASP | -1 | -0.856 | -0.933 | 3.165 | -50.440 | -48.761 | 0.035 | -0.915 | -0.799 | -0.008 |
| 8 | A | 70 | LEU | 0 | 0.012 | 0.007 | 6.106 | 3.478 | 3.478 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 71 | GLN | 0 | 0.012 | 0.004 | 9.015 | 2.546 | 2.546 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 72 | GLN | 0 | -0.007 | 0.000 | 8.355 | 2.240 | 2.240 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 73 | LEU | 0 | 0.010 | 0.005 | 10.824 | 1.529 | 1.529 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 74 | ARG | 1 | 0.837 | 0.898 | 12.199 | 22.489 | 22.489 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 75 | ASP | -1 | -1.003 | -0.982 | 14.022 | -16.995 | -16.995 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 76 | MET | 0 | -0.042 | -0.023 | 15.277 | 0.653 | 0.653 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 77 | GLY | 0 | -0.009 | 0.009 | 17.322 | 0.780 | 0.780 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 78 | ILE | 0 | -0.078 | -0.033 | 15.520 | 0.606 | 0.606 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 79 | GLN | 0 | 0.044 | 0.014 | 16.515 | -0.401 | -0.401 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 80 | ASP | -1 | -0.902 | -0.946 | 16.883 | -16.143 | -16.143 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 81 | ASP | -1 | -0.815 | -0.916 | 13.240 | -22.835 | -22.835 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 82 | GLU | -1 | -0.847 | -0.881 | 12.873 | -19.949 | -19.949 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 83 | LEU | 0 | 0.039 | 0.021 | 14.398 | -0.905 | -0.905 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 84 | SER | 0 | 0.017 | 0.007 | 10.786 | -1.888 | -1.888 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 85 | LEU | 0 | -0.029 | -0.018 | 8.524 | -2.757 | -2.757 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 86 | ARG | 1 | 0.853 | 0.883 | 9.490 | 16.329 | 16.329 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 87 | ALA | 0 | 0.037 | 0.033 | 11.194 | -0.477 | -0.477 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 88 | LEU | 0 | -0.068 | -0.031 | 5.070 | -3.663 | -3.663 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 89 | GLN | 0 | -0.042 | -0.032 | 6.227 | -3.252 | -3.252 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 90 | ALA | 0 | -0.019 | -0.003 | 8.175 | -0.577 | -0.577 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 91 | THR | 0 | 0.031 | 0.018 | 7.327 | -1.283 | -1.283 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 92 | GLY | 0 | -0.031 | 0.004 | 5.594 | -0.150 | -0.150 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 95 | ILE | 0 | -0.007 | -0.017 | 5.908 | 2.563 | 2.563 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 96 | GLN | 0 | -0.041 | -0.013 | 8.809 | 4.014 | 4.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 97 | ALA | 0 | 0.098 | 0.047 | 9.663 | 1.668 | 1.668 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 98 | ALA | 0 | -0.038 | -0.013 | 9.172 | 1.441 | 1.441 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 99 | LEU | 0 | 0.003 | -0.012 | 11.114 | 1.898 | 1.898 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 100 | GLU | -1 | -0.912 | -0.950 | 14.189 | -18.705 | -18.705 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 101 | LEU | 0 | -0.020 | -0.011 | 12.072 | 1.135 | 1.135 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 102 | ILE | 0 | -0.053 | -0.030 | 13.198 | 0.989 | 0.989 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 103 | PHE | 0 | -0.073 | -0.030 | 16.522 | 1.242 | 1.242 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 104 | ALA | 0 | -0.003 | 0.002 | 18.319 | 0.895 | 0.895 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 105 | GLY | 0 | -0.029 | -0.004 | 18.709 | 0.744 | 0.744 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 106 | GLY | 0 | -0.064 | -0.049 | 17.711 | 0.224 | 0.224 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 107 | ALA | 0 | -0.061 | -0.037 | 16.300 | -1.276 | -1.276 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 108 | PRO | -1 | -0.919 | -0.938 | 15.780 | -15.200 | -15.200 | 0.000 | 0.000 | 0.000 | 0.000 |