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: 3Q13L
Calculation Name: 3MP7-B-Xray372
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 3MP7
Chain ID: B
UniProt ID: Q8TZK2
Base Structure: X-ray
Registration Date: 2023-06-20
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 | 54 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -203517.271594 |
|---|---|
| FMO2-HF: Nuclear repulsion | 182952.623525 |
| FMO2-HF: Total energy | -20564.648069 |
| FMO2-MP2: Total energy | -20626.265816 |
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(B:7:ILE)
Summations of interaction energy for
fragment #1(B:7:ILE)
| 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. |
| -12.083 | -7.08 | 0.46 | -2.167 | -3.295 | 0.009 |
Interaction energy analysis for fragmet #1(B:7:ILE)
| 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 | B | 9 | HIS | 0 | 0.020 | 0.008 | 3.251 | -7.547 | -3.766 | 0.148 | -1.824 | -2.105 | 0.011 |
| 4 | B | 10 | PHE | 0 | 0.082 | 0.055 | 2.669 | -1.891 | -0.669 | 0.312 | -0.343 | -1.190 | -0.002 |
| 5 | B | 11 | TRP | 0 | 0.045 | 0.014 | 6.420 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | B | 12 | LYS | 1 | 0.851 | 0.937 | 8.444 | -2.310 | -2.310 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | B | 13 | GLU | -1 | -0.842 | -0.943 | 9.206 | 1.241 | 1.241 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | B | 14 | SER | 0 | -0.042 | -0.015 | 10.489 | -0.169 | -0.169 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | B | 15 | ARG | 1 | 0.910 | 0.959 | 13.127 | -0.664 | -0.664 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | B | 16 | ARG | 1 | 1.002 | 1.000 | 14.967 | -0.395 | -0.395 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | B | 17 | ALA | 0 | 0.039 | 0.018 | 17.223 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | B | 18 | PHE | 0 | 0.042 | 0.007 | 18.996 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | B | 19 | LEU | 0 | -0.018 | -0.021 | 19.854 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | B | 20 | VAL | 0 | 0.008 | 0.023 | 22.062 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | B | 21 | THR | 0 | -0.063 | -0.011 | 23.355 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | B | 22 | LYN | 0 | 0.069 | 0.040 | 25.744 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | B | 23 | LYS | 1 | 0.902 | 0.978 | 24.065 | -0.097 | -0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | B | 24 | PRO | 0 | 0.022 | -0.009 | 29.306 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | B | 25 | ASN | 0 | 0.072 | 0.007 | 32.370 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | B | 26 | TRP | 0 | -0.007 | 0.000 | 31.440 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | B | 28 | ALA | 0 | -0.010 | 0.020 | 37.169 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | B | 29 | THR | 0 | 0.033 | -0.015 | 36.976 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | B | 30 | TYR | 0 | 0.008 | 0.016 | 33.379 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | B | 31 | LYS | 1 | 0.968 | 0.972 | 37.122 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | B | 32 | ARG | 1 | 0.954 | 0.989 | 40.186 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | B | 33 | ALA | 0 | 0.083 | 0.031 | 37.657 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | B | 34 | ALA | 0 | 0.028 | 0.028 | 37.871 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | B | 35 | LYS | 1 | 0.932 | 0.973 | 39.352 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | B | 36 | ILE | 0 | 0.024 | 0.022 | 41.763 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | B | 37 | THR | 0 | -0.012 | -0.024 | 37.692 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | B | 38 | GLY | 0 | 0.011 | 0.007 | 40.918 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | B | 39 | LEU | 0 | 0.001 | -0.017 | 42.308 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | B | 40 | GLY | 0 | 0.036 | 0.025 | 44.250 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | B | 41 | ILE | 0 | -0.015 | -0.019 | 39.827 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | B | 42 | ILE | 0 | -0.022 | -0.007 | 43.561 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | B | 43 | LEU | 0 | -0.002 | 0.005 | 46.478 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | B | 44 | ILE | 0 | -0.002 | -0.009 | 43.468 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | B | 45 | GLY | 0 | 0.034 | 0.027 | 46.851 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | B | 46 | LEU | 0 | 0.004 | 0.004 | 47.572 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | B | 47 | ILE | 0 | -0.010 | -0.006 | 50.932 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | B | 48 | GLY | 0 | 0.036 | 0.019 | 49.583 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | B | 49 | MET | 0 | -0.034 | -0.018 | 50.670 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | B | 50 | LEU | 0 | 0.003 | -0.002 | 52.091 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | B | 51 | ILE | 0 | 0.010 | 0.017 | 53.548 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | B | 52 | ARG | 1 | 0.944 | 0.975 | 49.864 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | B | 53 | ILE | 0 | -0.004 | -0.010 | 54.060 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | B | 54 | VAL | 0 | 0.032 | 0.013 | 56.854 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | B | 55 | GLY | 0 | 0.014 | 0.004 | 57.039 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | B | 56 | ILE | 0 | -0.051 | -0.030 | 54.968 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | B | 57 | LEU | 0 | -0.024 | -0.003 | 58.084 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | B | 58 | ILE | 0 | -0.028 | -0.008 | 61.408 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | B | 59 | LEU | 0 | -0.076 | -0.032 | 57.912 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | B | 60 | GLY | 0 | 0.016 | -0.005 | 60.112 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | B | 61 | GLY | 0 | -0.032 | 0.012 | 62.280 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |