FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-07-23
All entries: 37450
Number of unique PDB entries: 7783
FMODB ID: 9GL62
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.
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 |
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 | -117256.169332 |
|---|---|
| FMO2-HF: Nuclear repulsion | 105327.47264 |
| FMO2-HF: Total energy | -11928.696693 |
| FMO2-MP2: Total energy | -11964.529629 |
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. |
| -236.781 | -238.688 | 29.711 | -13.985 | -13.82 | 0.137 |
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 | 0.887 | 0.923 | 1.695 | -144.716 | -149.076 | 28.017 | -12.688 | -10.968 | 0.139 |
| 4 | B | 109 | ALA | 0 | -0.046 | -0.024 | 2.033 | -14.246 | -12.956 | 1.684 | -0.878 | -2.096 | -0.002 |
| 5 | B | 110 | SER | 0 | 0.014 | -0.004 | 3.336 | -8.493 | -7.437 | 0.011 | -0.416 | -0.652 | 0.000 |
| 6 | B | 111 | LEU | 0 | -0.010 | -0.004 | 5.563 | -3.091 | -3.091 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | B | 112 | ARG | 1 | 0.960 | 0.980 | 5.298 | -39.889 | -39.889 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | B | 113 | ALA | 0 | -0.040 | -0.016 | 7.901 | -2.806 | -2.806 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | B | 114 | LEU | 0 | -0.008 | 0.002 | 9.625 | -1.958 | -1.958 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | B | 115 | GLY | 0 | -0.017 | 0.001 | 11.566 | -1.475 | -1.475 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | B | 116 | GLU | -1 | -0.852 | -0.915 | 10.932 | 22.209 | 22.209 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | B | 117 | PRO | 0 | 0.000 | 0.000 | 10.512 | 2.328 | 2.328 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | B | 118 | ILE | 0 | -0.003 | -0.002 | 6.037 | 1.958 | 1.958 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | B | 119 | THR | 0 | -0.004 | -0.011 | 6.562 | 9.424 | 9.424 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | B | 120 | LEU | 0 | 0.027 | 0.035 | 9.176 | -2.619 | -2.619 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | B | 121 | PHE | 0 | -0.001 | -0.016 | 12.595 | 1.090 | 1.090 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | B | 122 | GLY | 0 | 0.026 | 0.014 | 14.372 | -0.783 | -0.783 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | B | 123 | GLU | -1 | -0.822 | -0.873 | 9.530 | 32.065 | 32.065 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | B | 124 | GLY | 0 | 0.093 | 0.040 | 10.196 | 2.934 | 2.934 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | B | 125 | PRO | 0 | -0.039 | -0.047 | 7.454 | 2.966 | 2.966 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | B | 126 | ALA | 0 | -0.019 | 0.013 | 7.983 | 3.113 | 3.113 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | B | 127 | GLU | -1 | -0.743 | -0.879 | 10.702 | 26.468 | 26.468 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | B | 128 | ARG | 1 | 0.813 | 0.913 | 4.970 | -43.302 | -43.195 | -0.001 | -0.003 | -0.104 | 0.000 |
| 24 | B | 129 | ARG | 1 | 0.865 | 0.917 | 6.053 | -39.259 | -39.259 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | B | 130 | GLU | -1 | -0.762 | -0.840 | 8.659 | 19.155 | 19.155 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | B | 131 | ARG | 1 | 0.771 | 0.842 | 9.468 | -30.225 | -30.225 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | B | 132 | LEU | 0 | 0.016 | 0.003 | 5.934 | -0.652 | -0.652 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | B | 133 | ARG | 1 | 0.764 | 0.845 | 10.445 | -22.297 | -22.297 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | B | 134 | ASN | 0 | -0.055 | -0.024 | 11.782 | -2.503 | -2.503 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | B | 135 | ILE | 0 | -0.023 | 0.007 | 12.834 | -1.046 | -1.046 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | B | 136 | LEU | 0 | -0.046 | -0.017 | 7.830 | -1.131 | -1.131 | 0.000 | 0.000 | 0.000 | 0.000 |