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: LJQ29
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 | OptHSide |
| 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 | -117208.04158 |
|---|---|
| FMO2-HF: Nuclear repulsion | 105279.56775 |
| FMO2-HF: Total energy | -11928.47383 |
| FMO2-MP2: Total energy | -11964.319787 |
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. |
| -199.533 | -195.52 | 15.451 | -9.145 | -10.317 | 0.092 |
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 | 0.951 | 0.966 | 1.824 | -94.236 | -92.495 | 14.665 | -8.267 | -8.139 | 0.088 |
| 4 | B | 109 | ALA | 0 | -0.021 | -0.019 | 2.186 | -14.508 | -13.150 | 0.782 | -0.544 | -1.595 | 0.004 |
| 5 | B | 110 | SER | 0 | 0.017 | 0.008 | 3.343 | -8.790 | -8.015 | 0.005 | -0.322 | -0.457 | 0.000 |
| 6 | B | 111 | LEU | 0 | 0.012 | 0.007 | 5.711 | -3.231 | -3.231 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | B | 112 | ARG | 1 | 0.941 | 0.981 | 5.434 | -39.615 | -39.615 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | B | 113 | ALA | 0 | -0.049 | -0.017 | 8.033 | -2.923 | -2.923 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | B | 114 | LEU | 0 | -0.020 | -0.007 | 9.814 | -1.974 | -1.974 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | B | 115 | GLY | 0 | -0.016 | -0.002 | 11.752 | -1.333 | -1.333 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | B | 116 | GLU | -1 | -0.912 | -0.950 | 11.235 | 20.344 | 20.344 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | B | 117 | PRO | 0 | 0.007 | 0.005 | 10.932 | 2.074 | 2.074 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | B | 118 | ILE | 0 | 0.004 | -0.003 | 6.226 | 2.171 | 2.171 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | B | 119 | THR | 0 | -0.065 | -0.045 | 7.137 | 7.443 | 7.443 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | B | 120 | LEU | 0 | 0.026 | 0.043 | 9.609 | -2.240 | -2.240 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | B | 121 | PHE | 0 | 0.018 | -0.016 | 12.875 | 1.073 | 1.073 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | B | 122 | GLY | 0 | 0.009 | 0.001 | 14.873 | -0.403 | -0.403 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | B | 123 | GLU | -1 | -0.762 | -0.822 | 9.905 | 30.632 | 30.632 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | B | 124 | GLY | 0 | 0.038 | 0.011 | 10.896 | 1.716 | 1.716 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | B | 125 | PRO | 0 | -0.081 | -0.071 | 7.114 | 2.165 | 2.165 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | B | 126 | ALA | 0 | 0.004 | -0.002 | 8.087 | 2.538 | 2.538 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | B | 127 | GLU | -1 | -0.799 | -0.886 | 10.447 | 22.804 | 22.804 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | B | 128 | ARG | 1 | 0.884 | 0.944 | 4.500 | -43.404 | -43.265 | -0.001 | -0.012 | -0.126 | 0.000 |
| 24 | B | 129 | ARG | 1 | 0.924 | 0.946 | 5.490 | -41.920 | -41.920 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | B | 130 | GLU | -1 | -0.793 | -0.884 | 8.169 | 20.295 | 20.295 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | B | 131 | ARG | 1 | 0.786 | 0.855 | 9.382 | -30.488 | -30.488 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | B | 132 | LEU | 0 | -0.004 | -0.005 | 5.908 | -0.548 | -0.548 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | B | 133 | ARG | 1 | 0.836 | 0.906 | 10.299 | -22.596 | -22.596 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | B | 134 | ASN | 0 | -0.073 | -0.046 | 11.295 | -2.361 | -2.361 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | B | 135 | ILE | 0 | -0.016 | 0.018 | 12.459 | -1.107 | -1.107 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | B | 136 | LEU | 0 | -0.041 | -0.008 | 7.857 | -1.111 | -1.111 | 0.000 | 0.000 | 0.000 | 0.000 |