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: L74R9
Calculation Name: 1G3J-D-Xray540
Preferred Name: Catenin beta-1
Target Type: SINGLE PROTEIN
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 1G3J
Chain ID: D
ChEMBL ID: CHEMBL5866
UniProt ID: P35222
Base Structure: X-ray
Registration Date: 2025-07-10
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 | OptH |
| 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 | 63 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -83218.482576 |
|---|---|
| FMO2-HF: Nuclear repulsion | 70530.331028 |
| FMO2-HF: Total energy | -12688.151549 |
| FMO2-MP2: Total energy | -12725.31145 |
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(D:2:PRO)
Summations of interaction energy for
fragment #1(D:2:PRO)
| 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. |
| -1.255 | 2.096 | -0.013 | -1.593 | -1.745 | 0 |
Interaction energy analysis for fragmet #1(D:2:PRO)
| 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 | D | 3 | GLN | 0 | -0.059 | 0.107 | 3.393 | -1.236 | -0.355 | 0.020 | -0.268 | -0.633 | 0.000 |
| 4 | D | 4 | LEU | 0 | 0.068 | -0.130 | 3.795 | 0.408 | 2.878 | -0.033 | -1.325 | -1.112 | 0.000 |
| 5 | D | 4 | LEU | 0 | -0.070 | 0.137 | 7.061 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | D | 5 | ASN | 0 | 0.103 | -0.055 | 6.811 | -0.128 | -0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | D | 5 | ASN | 0 | -0.151 | 0.031 | 6.589 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | D | 6 | SER | 0 | 0.016 | -0.067 | 8.667 | -0.133 | -0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | D | 6 | SER | 0 | -0.054 | 0.061 | 12.931 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | D | 7 | GLY | 0 | 0.016 | -0.089 | 11.269 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | D | 8 | GLY | 0 | -0.031 | -0.030 | 12.148 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | D | 9 | GLY | 0 | 0.006 | -0.011 | 12.874 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | D | 10 | ASP | 0 | 0.015 | 0.000 | 14.249 | -0.048 | -0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | D | 10 | ASP | -1 | -0.875 | -0.819 | 15.677 | -0.110 | -0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | D | 11 | GLU | 0 | 0.032 | -0.109 | 16.745 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | D | 11 | GLU | -1 | -0.965 | -0.854 | 17.976 | -0.175 | -0.175 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | D | 12 | LEU | 0 | -0.063 | -0.156 | 19.850 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | D | 12 | LEU | 0 | -0.085 | 0.104 | 20.899 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | D | 13 | GLY | 0 | -0.021 | -0.124 | 20.194 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | D | 14 | ALA | 0 | 0.105 | 0.002 | 17.833 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | D | 14 | ALA | 0 | -0.094 | 0.086 | 18.670 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | D | 15 | ASN | 0 | 0.108 | -0.075 | 16.541 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | D | 15 | ASN | 0 | -0.160 | 0.049 | 13.911 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | D | 16 | ASP | 0 | 0.177 | -0.091 | 17.888 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | D | 16 | ASP | -1 | -1.044 | -0.852 | 20.999 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | D | 17 | GLU | 0 | -0.036 | -0.164 | 18.783 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | D | 17 | GLU | -1 | -0.901 | -0.798 | 16.031 | 0.188 | 0.188 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | D | 18 | LEU | 0 | 0.041 | -0.122 | 19.803 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | D | 18 | LEU | 0 | -0.107 | 0.086 | 20.742 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | D | 19 | ILE | 0 | 0.108 | -0.114 | 20.830 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | D | 19 | ILE | 0 | -0.045 | 0.147 | 23.222 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | D | 20 | ARG | 0 | 0.015 | -0.090 | 22.612 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | D | 20 | ARG | 1 | 0.821 | 1.044 | 18.671 | -0.138 | -0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | D | 21 | PHE | 0 | 0.150 | -0.108 | 23.901 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | D | 21 | PHE | 0 | -0.050 | 0.110 | 27.747 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | D | 22 | LYS | 0 | -0.026 | -0.099 | 27.493 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | D | 22 | LYS | 1 | 0.859 | 1.031 | 23.814 | -0.114 | -0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | D | 23 | ASP | 0 | 0.113 | -0.098 | 28.848 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | D | 23 | ASP | -1 | -1.001 | -0.851 | 31.994 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | D | 24 | GLU | 0 | -0.063 | -0.130 | 32.226 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | D | 24 | GLU | -1 | -0.900 | -0.931 | 33.689 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | D | 40 | ASP | 0 | 0.081 | 0.023 | 53.850 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | D | 40 | ASP | -1 | -0.955 | -0.891 | 52.295 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | D | 41 | LEU | 0 | 0.073 | -0.116 | 54.759 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | D | 41 | LEU | 0 | -0.078 | 0.118 | 51.459 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | D | 42 | ALA | 0 | 0.053 | -0.137 | 55.835 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | D | 42 | ALA | 0 | -0.035 | 0.129 | 59.215 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | D | 43 | ASP | 0 | 0.070 | -0.141 | 59.231 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | D | 43 | ASP | -1 | -0.919 | -0.805 | 59.797 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | D | 44 | VAL | 0 | 0.064 | -0.100 | 57.545 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | D | 44 | VAL | 0 | -0.056 | 0.103 | 55.926 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | D | 45 | LYS | 0 | 0.089 | -0.075 | 58.882 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | D | 45 | LYS | 1 | 0.858 | 1.047 | 56.148 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | D | 46 | SER | 0 | 0.036 | -0.074 | 59.933 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | D | 46 | SER | 0 | -0.054 | 0.071 | 62.776 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | D | 47 | SER | 0 | 0.038 | -0.092 | 63.153 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | D | 47 | SER | 0 | -0.026 | 0.079 | 62.634 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | D | 48 | LEU | 0 | 0.083 | -0.083 | 61.260 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | D | 48 | LEU | 0 | -0.149 | 0.081 | 58.674 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | D | 49 | VAL | 0 | -0.039 | -0.110 | 62.632 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | D | 49 | VAL | 0 | -0.133 | 0.066 | 62.861 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | D | 50 | ASN | 0 | 0.002 | -0.089 | 65.170 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | D | 50 | ASN | 0 | -0.002 | -0.003 | 67.732 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |