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: 7MZ9K
Calculation Name: 3AAE-W-Xray540
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 3AAE
Chain ID: W
UniProt ID: P14315
Base Structure: X-ray
Registration Date: 2025-07-08
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 | 48 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -74966.21989 |
|---|---|
| FMO2-HF: Nuclear repulsion | 64017.092978 |
| FMO2-HF: Total energy | -10949.126912 |
| FMO2-MP2: Total energy | -10981.67965 |
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(W:977:GLU)
Summations of interaction energy for
fragment #1(W:977:GLU)
| 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. |
| -1.435 | 0.562 | -0.014 | -1.071 | -0.914 | 0.004 |
Interaction energy analysis for fragmet #1(W:977:GLU)
| 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]. |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 4 | W | 978 | LEU | 0 | -0.087 | 0.120 | 4.170 | -0.030 | 0.444 | 0.002 | -0.252 | -0.225 | 0.000 |
| 5 | W | 979 | PRO | 0 | -0.034 | -0.106 | 3.790 | -0.004 | 1.519 | -0.016 | -0.819 | -0.689 | 0.004 |
| 6 | W | 980 | SER | 0 | 0.095 | 0.037 | 6.049 | 0.568 | 0.568 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | W | 980 | SER | 0 | -0.037 | 0.071 | 7.969 | 0.116 | 0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | W | 981 | GLU | 0 | 0.024 | -0.115 | 8.617 | -0.124 | -0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | W | 981 | GLU | -1 | -0.985 | -0.845 | 11.956 | -0.822 | -0.822 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | W | 982 | GLU | 0 | 0.061 | -0.121 | 11.853 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | W | 982 | GLU | -1 | -1.007 | -0.847 | 12.683 | -0.153 | -0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | W | 983 | GLY | 0 | -0.003 | -0.079 | 11.260 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | W | 984 | ARG | 0 | 0.054 | -0.038 | 12.274 | 0.111 | 0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | W | 984 | ARG | 1 | 0.853 | 1.062 | 16.874 | 0.163 | 0.163 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | W | 985 | ARG | 0 | 0.105 | -0.042 | 14.235 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | W | 985 | ARG | 1 | 0.795 | 1.011 | 15.231 | -0.188 | -0.188 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | W | 986 | LEU | 0 | 0.165 | -0.097 | 15.148 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | W | 986 | LEU | 0 | -0.052 | 0.151 | 15.450 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | W | 987 | GLU | 0 | -0.022 | -0.165 | 16.904 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | W | 987 | GLU | -1 | -0.954 | -0.833 | 19.946 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | W | 988 | HIS | 0 | 0.065 | -0.086 | 19.589 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | W | 988 | HIS | 0 | -0.110 | 0.085 | 15.870 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | W | 989 | PHE | 0 | 0.146 | -0.118 | 21.203 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | W | 989 | PHE | 0 | -0.019 | 0.146 | 24.984 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | W | 990 | THR | 0 | 0.017 | -0.091 | 24.361 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | W | 990 | THR | 0 | -0.034 | 0.055 | 24.003 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | W | 991 | LYS | 0 | 0.069 | -0.092 | 23.262 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | W | 991 | LYS | 1 | 0.904 | 1.072 | 18.940 | -0.353 | -0.353 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | W | 992 | LEU | 0 | -0.030 | -0.111 | 24.508 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | W | 992 | LEU | 0 | -0.020 | 0.124 | 25.020 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | W | 993 | ARG | 0 | 0.141 | -0.071 | 27.369 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | W | 993 | ARG | 1 | 0.846 | 1.058 | 27.772 | -0.168 | -0.168 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | W | 994 | PRO | 0 | 0.001 | -0.085 | 29.936 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | W | 995 | LYS | 0 | 0.049 | -0.011 | 31.383 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | W | 995 | LYS | 1 | 0.905 | 1.090 | 27.011 | -0.245 | -0.245 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | W | 996 | ARG | 0 | 0.133 | -0.085 | 32.076 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | W | 996 | ARG | 1 | 0.875 | 1.082 | 34.693 | -0.138 | -0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | W | 997 | ASN | 0 | 0.085 | -0.085 | 34.180 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | W | 997 | ASN | 0 | -0.104 | 0.083 | 34.501 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | W | 998 | LYS | 0 | 0.050 | -0.109 | 35.068 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | W | 998 | LYS | 1 | 0.946 | 1.080 | 31.955 | -0.205 | -0.205 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | W | 999 | LYS | 0 | 0.027 | -0.068 | 36.767 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | W | 999 | LYS | 1 | 0.896 | 1.076 | 40.742 | -0.122 | -0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | W | 1000 | GLN | 0 | 0.150 | -0.099 | 37.486 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | W | 1000 | GLN | 0 | -0.052 | 0.099 | 38.122 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | W | 1001 | GLN | 0 | 0.006 | -0.133 | 34.322 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | W | 1001 | GLN | 0 | -0.010 | 0.153 | 32.806 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | W | 1002 | PRO | 0 | -0.009 | -0.085 | 30.691 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |