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: 2L5YR
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 | OptAll |
| 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 | -74929.89031 |
|---|---|
| FMO2-HF: Nuclear repulsion | 63980.554522 |
| FMO2-HF: Total energy | -10949.335787 |
| FMO2-MP2: Total energy | -10981.866505 |
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. |
| -1.193 | 0.233 | -0.011 | -0.753 | -0.663 | 0.002 |
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 | -0.088 | 0.118 | 4.323 | 0.131 | 0.430 | 0.001 | -0.151 | -0.150 | 0.000 |
| 5 | W | 979 | PRO | 0 | -0.040 | -0.114 | 3.846 | -0.060 | 1.067 | -0.012 | -0.602 | -0.513 | 0.002 |
| 6 | W | 980 | SER | 0 | 0.057 | 0.027 | 6.229 | 0.609 | 0.609 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | W | 980 | SER | 0 | -0.061 | 0.032 | 9.098 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | W | 981 | GLU | 0 | 0.045 | -0.111 | 9.358 | -0.231 | -0.231 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | W | 981 | GLU | -1 | -0.986 | -0.841 | 12.643 | -0.711 | -0.711 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | W | 982 | GLU | 0 | 0.043 | -0.126 | 12.446 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | W | 982 | GLU | -1 | -0.949 | -0.816 | 12.569 | -0.188 | -0.188 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | W | 983 | GLY | 0 | -0.002 | -0.073 | 11.852 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | W | 984 | ARG | 0 | 0.053 | -0.034 | 12.883 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | W | 984 | ARG | 1 | 0.854 | 1.063 | 17.343 | 0.207 | 0.207 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | W | 985 | ARG | 0 | 0.105 | -0.068 | 14.576 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | W | 985 | ARG | 1 | 0.775 | 1.014 | 15.520 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | W | 986 | LEU | 0 | 0.149 | -0.079 | 15.324 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | W | 986 | LEU | 0 | -0.030 | 0.144 | 16.051 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | W | 987 | GLU | 0 | -0.031 | -0.149 | 17.214 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | W | 987 | GLU | -1 | -0.948 | -0.843 | 20.114 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | W | 988 | HIS | 0 | 0.070 | -0.076 | 19.925 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | W | 988 | HIS | 0 | -0.097 | 0.089 | 16.486 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | W | 989 | PHE | 0 | 0.158 | -0.113 | 21.776 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | W | 989 | PHE | 0 | 0.001 | 0.143 | 24.926 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | W | 990 | THR | 0 | 0.018 | -0.081 | 25.033 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | W | 990 | THR | 0 | -0.010 | 0.072 | 23.956 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | W | 991 | LYS | 0 | 0.040 | -0.110 | 23.722 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | W | 991 | LYS | 1 | 0.924 | 1.077 | 19.296 | -0.285 | -0.285 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | W | 992 | LEU | 0 | -0.022 | -0.102 | 25.020 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | W | 992 | LEU | 0 | -0.022 | 0.127 | 25.245 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | W | 993 | ARG | 0 | 0.124 | -0.075 | 27.835 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | W | 993 | ARG | 1 | 0.815 | 1.031 | 27.628 | -0.156 | -0.156 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | W | 994 | PRO | 0 | 0.003 | -0.082 | 30.549 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | W | 995 | LYS | 0 | 0.040 | -0.019 | 31.883 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | W | 995 | LYS | 1 | 0.906 | 1.089 | 27.384 | -0.209 | -0.209 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | W | 996 | ARG | 0 | 0.141 | -0.074 | 32.668 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | W | 996 | ARG | 1 | 0.864 | 1.077 | 35.210 | -0.127 | -0.127 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | W | 997 | ASN | 0 | 0.108 | -0.086 | 34.753 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | W | 997 | ASN | 0 | -0.094 | 0.081 | 34.439 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | W | 998 | LYS | 0 | 0.025 | -0.100 | 35.226 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | W | 998 | LYS | 1 | 0.920 | 1.080 | 32.260 | -0.203 | -0.203 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | W | 999 | LYS | 0 | 0.024 | -0.081 | 36.916 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | W | 999 | LYS | 1 | 0.912 | 1.075 | 40.861 | -0.114 | -0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | W | 1000 | GLN | 0 | 0.149 | -0.100 | 37.903 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | W | 1000 | GLN | 0 | -0.050 | 0.119 | 38.604 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | W | 1001 | GLN | 0 | 0.033 | -0.132 | 34.521 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | W | 1001 | GLN | 0 | -0.006 | 0.150 | 32.971 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | W | 1002 | PRO | 0 | -0.030 | -0.097 | 30.677 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |