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: 4JVMN
Calculation Name: 3CA7-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 3CA7
Chain ID: A
UniProt ID: Q01083
Base Structure: X-ray
Registration Date: 2023-09-23
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 | OptHSide |
| 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 | 47 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -243988.958904 |
|---|---|
| FMO2-HF: Nuclear repulsion | 222210.553047 |
| FMO2-HF: Total energy | -21778.405856 |
| FMO2-MP2: Total energy | -21836.395795 |
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:48:THR)
Summations of interaction energy for
fragment #1(A:48:THR)
| 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. |
| -2.699 | -0.041 | 0.372 | -1.279 | -1.751 | -0.008 |
Interaction energy analysis for fragmet #1(A:48:THR)
| 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 | 50 | PRO | 0 | 0.009 | 0.012 | 2.796 | -3.264 | -0.606 | 0.372 | -1.279 | -1.751 | -0.008 |
| 4 | A | 51 | THR | 0 | 0.019 | 0.003 | 4.934 | 0.541 | 0.541 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 52 | TYR | 0 | -0.048 | -0.026 | 7.100 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 53 | LYS | 1 | 0.869 | 0.914 | 10.874 | 0.350 | 0.350 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 54 | CYS | 0 | -0.042 | -0.020 | 14.150 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 55 | PRO | 0 | 0.030 | 0.012 | 15.963 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 56 | GLU | -1 | -0.872 | -0.942 | 19.409 | -0.149 | -0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 57 | THR | 0 | -0.014 | -0.003 | 22.219 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 58 | PHE | 0 | -0.026 | -0.024 | 18.371 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 59 | ASP | -1 | -0.849 | -0.910 | 17.825 | -0.213 | -0.213 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 60 | ALA | 0 | 0.004 | 0.025 | 19.690 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 61 | TRP | 0 | -0.011 | -0.024 | 23.038 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 62 | TYR | 0 | -0.045 | -0.023 | 16.908 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 63 | CYS | 0 | -0.023 | 0.021 | 13.352 | -0.055 | -0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 64 | LEU | 0 | 0.025 | 0.004 | 19.790 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 65 | ASN | 0 | -0.069 | -0.056 | 21.123 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 66 | ASP | -1 | -0.915 | -0.953 | 21.758 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 67 | ALA | 0 | -0.060 | -0.014 | 17.146 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 68 | HIS | 0 | 0.022 | 0.020 | 14.351 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 70 | PHE | 0 | -0.012 | -0.008 | 8.065 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 71 | ALA | 0 | 0.017 | -0.007 | 11.156 | 0.102 | 0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 72 | VAL | 0 | 0.036 | 0.027 | 6.509 | -0.261 | -0.261 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 73 | LYS | 1 | 0.828 | 0.898 | 9.182 | 0.511 | 0.511 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 74 | ILE | 0 | 0.006 | -0.001 | 8.651 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 75 | ALA | 0 | -0.012 | -0.011 | 11.024 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 76 | ASP | -1 | -0.830 | -0.907 | 13.772 | -0.222 | -0.222 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 77 | LEU | 0 | -0.004 | 0.005 | 14.556 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 78 | PRO | 0 | -0.035 | -0.020 | 13.641 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 79 | VAL | 0 | -0.006 | 0.007 | 11.877 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 80 | TYR | 0 | 0.004 | -0.012 | 12.092 | -0.098 | -0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 81 | SER | 0 | -0.035 | -0.017 | 11.200 | 0.105 | 0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 83 | GLU | -1 | -0.930 | -0.957 | 10.242 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 84 | CYS | 0 | -0.069 | -0.020 | 13.183 | -0.048 | -0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 85 | ALA | 0 | 0.082 | 0.053 | 15.860 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 86 | ILE | 0 | 0.017 | -0.020 | 17.951 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 87 | GLY | 0 | 0.010 | 0.010 | 19.543 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 88 | PHE | 0 | -0.020 | -0.010 | 20.182 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 89 | MET | 0 | 0.035 | 0.021 | 17.983 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 90 | GLY | 0 | 0.015 | 0.007 | 18.237 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 91 | GLN | 0 | -0.002 | 0.010 | 17.443 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 92 | ARG | 1 | 0.868 | 0.907 | 17.604 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 94 | GLU | -1 | -0.803 | -0.906 | 19.802 | 0.102 | 0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 95 | TYR | 0 | -0.039 | -0.014 | 22.562 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 96 | LYS | 1 | 0.852 | 0.940 | 23.049 | -0.079 | -0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 97 | GLU | -1 | -0.944 | -0.968 | 20.484 | 0.190 | 0.190 | 0.000 | 0.000 | 0.000 | 0.000 |