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: 6GRMZ
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 | 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 | 48 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -74937.509523 |
|---|---|
| FMO2-HF: Nuclear repulsion | 63988.837511 |
| FMO2-HF: Total energy | -10948.672012 |
| FMO2-MP2: Total energy | -10981.245043 |
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. |
| -1.358 | 0.791 | -0.014 | -1.157 | -0.979 | 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 | -0.114 | 0.128 | 4.145 | -0.017 | 0.511 | 0.003 | -0.275 | -0.256 | 0.000 |
| 5 | W | 979 | PRO | 0 | -0.023 | -0.108 | 3.790 | 0.076 | 1.677 | -0.015 | -0.882 | -0.704 | 0.004 |
| 6 | W | 980 | SER | 0 | 0.129 | 0.063 | 5.974 | 0.566 | 0.586 | -0.002 | 0.000 | -0.019 | 0.000 |
| 7 | W | 980 | SER | 0 | -0.070 | 0.041 | 7.693 | 0.107 | 0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | W | 981 | GLU | 0 | 0.012 | -0.127 | 8.575 | -0.096 | -0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | W | 981 | GLU | -1 | -0.982 | -0.834 | 11.992 | -0.842 | -0.842 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | W | 982 | GLU | 0 | 0.064 | -0.128 | 11.825 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | W | 982 | GLU | -1 | -1.000 | -0.829 | 12.694 | -0.152 | -0.152 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | W | 983 | GLY | 0 | 0.002 | -0.083 | 11.262 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | W | 984 | ARG | 0 | 0.052 | -0.052 | 12.272 | 0.122 | 0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | W | 984 | ARG | 1 | 0.856 | 1.067 | 16.878 | 0.157 | 0.157 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | W | 985 | ARG | 0 | 0.121 | -0.047 | 14.198 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | W | 985 | ARG | 1 | 0.802 | 1.013 | 15.168 | -0.219 | -0.219 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | W | 986 | LEU | 0 | 0.160 | -0.100 | 15.121 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | W | 986 | LEU | 0 | -0.071 | 0.162 | 15.332 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | W | 987 | GLU | 0 | -0.026 | -0.182 | 16.875 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | W | 987 | GLU | -1 | -0.967 | -0.822 | 19.928 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | W | 988 | HIS | 0 | 0.071 | -0.098 | 19.563 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | W | 988 | HIS | 0 | -0.114 | 0.096 | 15.858 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | W | 989 | PHE | 0 | 0.156 | -0.128 | 21.184 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | W | 989 | PHE | 0 | -0.015 | 0.153 | 25.082 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | W | 990 | THR | 0 | -0.004 | -0.089 | 24.365 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | W | 990 | THR | 0 | -0.035 | 0.060 | 24.114 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | W | 991 | LYS | 0 | 0.064 | -0.093 | 23.234 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | W | 991 | LYS | 1 | 0.870 | 1.072 | 18.936 | -0.358 | -0.358 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | W | 992 | LEU | 0 | -0.015 | -0.116 | 24.497 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | W | 992 | LEU | 0 | -0.029 | 0.125 | 24.710 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | W | 993 | ARG | 0 | 0.129 | -0.085 | 27.354 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | W | 993 | ARG | 1 | 0.884 | 1.071 | 28.631 | -0.162 | -0.162 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | W | 994 | PRO | 0 | 0.018 | -0.086 | 29.927 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | W | 995 | LYS | 0 | 0.026 | -0.006 | 31.396 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | W | 995 | LYS | 1 | 0.926 | 1.092 | 26.795 | -0.257 | -0.257 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | W | 996 | ARG | 0 | 0.151 | -0.096 | 32.073 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | W | 996 | ARG | 1 | 0.872 | 1.098 | 34.668 | -0.141 | -0.141 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | W | 997 | ASN | 0 | 0.072 | -0.104 | 34.184 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | W | 997 | ASN | 0 | -0.092 | 0.096 | 34.486 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | W | 998 | LYS | 0 | 0.038 | -0.088 | 35.085 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | W | 998 | LYS | 1 | 0.928 | 1.071 | 31.795 | -0.203 | -0.203 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | W | 999 | LYS | 0 | 0.038 | -0.087 | 36.776 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | W | 999 | LYS | 1 | 0.897 | 1.083 | 40.685 | -0.124 | -0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | W | 1000 | GLN | 0 | 0.159 | -0.101 | 37.500 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | W | 1000 | GLN | 0 | -0.076 | 0.108 | 38.196 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | W | 1001 | GLN | 0 | 0.011 | -0.137 | 34.370 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | W | 1001 | GLN | 0 | -0.011 | 0.147 | 32.912 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | W | 1002 | PRO | 0 | 0.009 | -0.078 | 30.854 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |