FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-07-23
All entries: 37478
Number of unique PDB entries: 7783
FMODB ID: 3QK5L
Calculation Name: 1MZW-B-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1MZW
Chain ID: B
UniProt ID: O43447
Base Structure: X-ray
Registration Date: 2023-03-13
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 |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 31 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -117340.663489 |
|---|---|
| FMO2-HF: Nuclear repulsion | 105412.285496 |
| FMO2-HF: Total energy | -11928.377994 |
| FMO2-MP2: Total energy | -11964.246873 |
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:106:GLU)
Summations of interaction energy for
fragment #1(B:106: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. |
| -198.952 | -196.741 | 16.853 | -8.961 | -10.103 | 0.087 |
Interaction energy analysis for fragmet #1(B:106: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]. |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 3 | B | 108 | LYS | 1 | 0.929 | 0.954 | 1.794 | -90.058 | -90.027 | 15.812 | -8.084 | -7.760 | 0.084 |
| 4 | B | 109 | ALA | 0 | -0.020 | -0.021 | 2.123 | -14.555 | -13.259 | 1.036 | -0.591 | -1.741 | 0.003 |
| 5 | B | 110 | SER | 0 | 0.020 | 0.013 | 3.204 | -8.682 | -7.946 | 0.006 | -0.274 | -0.468 | 0.000 |
| 6 | B | 111 | LEU | 0 | 0.012 | 0.004 | 5.611 | -3.448 | -3.448 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | B | 112 | ARG | 1 | 0.932 | 0.983 | 5.062 | -41.148 | -41.148 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | B | 113 | ALA | 0 | -0.044 | -0.017 | 7.972 | -2.994 | -2.994 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | B | 114 | LEU | 0 | -0.024 | -0.009 | 9.756 | -2.018 | -2.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | B | 115 | GLY | 0 | -0.007 | 0.005 | 11.681 | -1.345 | -1.345 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | B | 116 | GLU | -1 | -0.921 | -0.953 | 11.116 | 20.306 | 20.306 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | B | 117 | PRO | 0 | 0.010 | 0.004 | 10.854 | 2.126 | 2.126 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | B | 118 | ILE | 0 | 0.017 | -0.002 | 6.254 | 2.344 | 2.344 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | B | 119 | THR | 0 | -0.059 | -0.032 | 7.140 | 7.637 | 7.637 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | B | 120 | LEU | 0 | 0.024 | 0.055 | 9.618 | -2.168 | -2.168 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | B | 121 | PHE | 0 | 0.020 | -0.014 | 12.888 | 1.062 | 1.062 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | B | 122 | GLY | 0 | 0.004 | -0.002 | 14.882 | -0.390 | -0.390 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | B | 123 | GLU | -1 | -0.752 | -0.814 | 10.162 | 30.075 | 30.075 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | B | 124 | GLY | 0 | 0.012 | 0.004 | 10.908 | 1.607 | 1.607 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | B | 125 | PRO | 0 | -0.077 | -0.067 | 7.300 | 2.304 | 2.304 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | B | 126 | ALA | 0 | 0.012 | -0.006 | 8.175 | 2.658 | 2.658 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | B | 127 | GLU | -1 | -0.793 | -0.884 | 10.555 | 22.804 | 22.804 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | B | 128 | ARG | 1 | 0.900 | 0.930 | 4.497 | -45.629 | -45.481 | -0.001 | -0.012 | -0.134 | 0.000 |
| 24 | B | 129 | ARG | 1 | 0.923 | 0.945 | 5.715 | -41.692 | -41.692 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | B | 130 | GLU | -1 | -0.863 | -0.933 | 8.272 | 21.500 | 21.500 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | B | 131 | ARG | 1 | 0.771 | 0.848 | 9.380 | -30.772 | -30.772 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | B | 132 | LEU | 0 | -0.002 | -0.006 | 6.362 | -0.429 | -0.429 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | B | 133 | ARG | 1 | 0.892 | 0.948 | 10.438 | -23.489 | -23.489 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | B | 134 | ASN | 0 | -0.044 | -0.026 | 11.832 | -2.296 | -2.296 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | B | 135 | ILE | 0 | -0.022 | 0.016 | 12.417 | -1.141 | -1.141 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | B | 136 | LEU | 0 | -0.050 | -0.014 | 8.564 | -1.121 | -1.121 | 0.000 | 0.000 | 0.000 | 0.000 |