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: 63Q5Z
Calculation Name: 1MZW-B-Xray309
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: 2021-09-06
Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.
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. 1.20200116 |
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. 15 / 20190524 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -117259.959395 |
|---|---|
| FMO2-HF: Nuclear repulsion | 105332.19671 |
| FMO2-HF: Total energy | -11927.762685 |
| FMO2-MP2: Total energy | -11963.645133 |
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. |
| -178.179 | -176.217 | 17.155 | -8.978 | -10.141 | 0.084 |
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 | 0.927 | 0.953 | 1.794 | -89.551 | -89.690 | 15.953 | -8.067 | -7.747 | 0.082 |
| 4 | B | 109 | ALA | 0 | -0.023 | -0.024 | 2.077 | -14.881 | -13.656 | 1.194 | -0.627 | -1.793 | 0.002 |
| 5 | B | 110 | SER | 0 | 0.025 | 0.016 | 3.206 | -8.715 | -7.990 | 0.008 | -0.270 | -0.463 | 0.000 |
| 6 | B | 111 | LEU | 0 | 0.022 | 0.010 | 5.615 | -3.384 | -3.384 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | B | 112 | ARG | 1 | 0.920 | 0.978 | 5.071 | -41.218 | -41.218 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | B | 113 | ALA | 0 | -0.046 | -0.019 | 7.927 | -3.083 | -3.083 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | B | 114 | LEU | 0 | -0.010 | -0.001 | 9.761 | -2.059 | -2.059 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | B | 115 | GLY | 0 | -0.015 | 0.001 | 11.633 | -1.384 | -1.384 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | B | 116 | GLU | -1 | -0.914 | -0.950 | 11.059 | 20.277 | 20.277 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | B | 117 | PRO | 0 | 0.001 | -0.001 | 10.810 | 2.161 | 2.161 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | B | 118 | ILE | 0 | 0.014 | -0.002 | 6.252 | 2.472 | 2.472 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | B | 119 | THR | 0 | -0.056 | -0.031 | 7.135 | 7.552 | 7.552 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | B | 120 | LEU | 0 | 0.026 | 0.055 | 9.613 | -2.323 | -2.323 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | B | 121 | PHE | 0 | 0.016 | -0.016 | 12.881 | 1.005 | 1.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | B | 122 | GLY | 0 | -0.001 | -0.004 | 14.875 | -0.383 | -0.383 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | B | 123 | GLU | -1 | -0.751 | -0.813 | 10.155 | 30.060 | 30.060 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | B | 124 | GLY | 0 | 0.009 | 0.002 | 10.900 | 1.677 | 1.677 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | B | 125 | PRO | 0 | -0.081 | -0.069 | 7.291 | 2.373 | 2.373 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | B | 126 | ALA | 0 | 0.012 | -0.005 | 8.166 | 2.554 | 2.554 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | B | 127 | GLU | -1 | -0.796 | -0.885 | 10.565 | 22.730 | 22.730 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | B | 128 | ARG | 1 | 0.897 | 0.928 | 4.489 | -45.566 | -45.415 | 0.000 | -0.014 | -0.138 | 0.000 |
| 24 | B | 129 | ARG | 1 | 0.921 | 0.944 | 5.724 | -41.602 | -41.602 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | B | 130 | GLU | -1 | -0.866 | -0.934 | 8.283 | 21.361 | 21.361 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | B | 131 | ARG | 1 | 0.767 | 0.845 | 9.375 | -30.735 | -30.735 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | B | 132 | LEU | 0 | -0.004 | -0.010 | 6.369 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | B | 133 | ARG | 1 | 0.889 | 0.948 | 10.438 | -23.411 | -23.411 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | B | 134 | ASN | 0 | -0.050 | -0.030 | 11.832 | -2.314 | -2.314 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | B | 135 | ILE | 0 | -0.061 | -0.009 | 12.414 | -1.083 | -1.083 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | B | 136 | LEU | -1 | -0.969 | -0.969 | 8.574 | 19.299 | 19.299 | 0.000 | 0.000 | 0.000 | 0.000 |