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: N9NGQ
Calculation Name: 1ZBA-4-Xray372
Preferred Name:
Target Type:
Ligand Name: 2-deoxy-6-o-sulfo-2-(sulfoamino)-alpha-d-glucopyranose
ligand 3-letter code: SGN
PDB ID: 1ZBA
Chain ID: 4
UniProt ID: P03306
Base Structure: X-ray
Registration Date: 2023-06-22
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 | 49 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -157116.328537 |
|---|---|
| FMO2-HF: Nuclear repulsion | 138000.571897 |
| FMO2-HF: Total energy | -19115.75664 |
| FMO2-MP2: Total energy | -19170.313677 |
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(4:15:SER)
Summations of interaction energy for
fragment #1(4:15:SER)
| 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. |
| -3.459 | 0.922 | 0.413 | -2.349 | -2.446 | 0.008 |
Interaction energy analysis for fragmet #1(4:15:SER)
| 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 | 4 | 17 | ASN | 0 | -0.047 | -0.012 | 3.804 | -0.783 | 2.008 | -0.024 | -1.524 | -1.244 | 0.004 |
| 4 | 4 | 18 | THR | 0 | 0.014 | 0.014 | 2.499 | -2.092 | -0.564 | 0.438 | -0.809 | -1.157 | 0.004 |
| 5 | 4 | 19 | GLY | 0 | 0.019 | 0.000 | 4.475 | -0.578 | -0.516 | -0.001 | -0.016 | -0.045 | 0.000 |
| 6 | 4 | 20 | SER | 0 | -0.035 | 0.001 | 6.971 | 0.123 | 0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | 4 | 21 | ILE | 0 | 0.032 | 0.008 | 8.030 | -0.101 | -0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | 4 | 22 | ILE | 0 | -0.033 | -0.017 | 10.577 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | 4 | 23 | ASN | 0 | 0.013 | 0.010 | 10.312 | -0.067 | -0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | 4 | 24 | ASN | 0 | 0.020 | 0.000 | 8.837 | 0.076 | 0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | 4 | 25 | TYR | 0 | 0.014 | 0.014 | 10.972 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | 4 | 26 | TYR | 0 | -0.008 | 0.008 | 12.991 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | 4 | 27 | MET | 0 | 0.032 | 0.010 | 12.578 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | 4 | 28 | GLN | 0 | 0.069 | 0.012 | 9.387 | 0.093 | 0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | 4 | 29 | GLN | 0 | -0.006 | -0.002 | 11.924 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | 4 | 30 | TYR | 0 | -0.056 | -0.022 | 14.008 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | 4 | 31 | GLN | 0 | -0.069 | -0.029 | 8.565 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | 4 | 32 | ASN | 0 | -0.011 | -0.001 | 7.422 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | 4 | 33 | SER | 0 | 0.005 | 0.017 | 11.022 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | 4 | 34 | MET | 0 | 0.024 | 0.001 | 12.296 | 0.086 | 0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | 4 | 35 | SER | 0 | -0.010 | -0.001 | 11.427 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | 4 | 36 | THR | 0 | -0.005 | 0.000 | 14.065 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | 4 | 37 | GLN | 0 | -0.012 | -0.015 | 14.586 | 0.066 | 0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | 4 | 38 | LEU | 0 | 0.023 | 0.006 | 18.700 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | 4 | 39 | GLY | 0 | -0.008 | 0.012 | 21.822 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | 4 | 62 | THR | 0 | -0.007 | -0.005 | 7.465 | -0.079 | -0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | 4 | 63 | GLN | 0 | 0.040 | 0.012 | 10.591 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | 4 | 64 | ASN | 0 | 0.034 | 0.014 | 12.164 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | 4 | 65 | ASN | 0 | -0.066 | -0.045 | 13.544 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | 4 | 66 | ASP | -1 | -0.820 | -0.906 | 12.168 | -0.252 | -0.252 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | 4 | 67 | TRP | 0 | -0.025 | -0.019 | 14.603 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | 4 | 68 | PHE | 0 | 0.084 | 0.016 | 16.626 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | 4 | 69 | SER | 0 | 0.028 | 0.045 | 13.871 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | 4 | 70 | LYS | 1 | 0.905 | 0.947 | 16.273 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | 4 | 71 | LEU | 0 | -0.020 | -0.010 | 19.194 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | 4 | 72 | ALA | 0 | 0.019 | 0.013 | 18.843 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | 4 | 73 | SER | 0 | -0.029 | -0.019 | 18.428 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | 4 | 74 | SER | 0 | -0.115 | -0.045 | 21.112 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | 4 | 75 | ALA | 0 | 0.004 | 0.012 | 24.050 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | 4 | 76 | PHE | 0 | -0.009 | -0.009 | 26.040 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | 4 | 77 | THR | 0 | 0.020 | -0.007 | 27.220 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | 4 | 78 | GLY | 0 | -0.064 | -0.015 | 29.796 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | 4 | 79 | LEU | 0 | 0.045 | 0.016 | 33.252 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | 4 | 80 | PHE | 0 | -0.015 | -0.005 | 36.639 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | 4 | 81 | GLY | 0 | 0.000 | 0.005 | 38.844 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | 4 | 82 | ALA | 0 | -0.016 | -0.005 | 41.649 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | 4 | 83 | LEU | 0 | 0.020 | 0.005 | 40.521 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | 4 | 84 | LEU | 0 | 0.006 | -0.002 | 43.599 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | 4 | 85 | ALA | 0 | -0.018 | 0.006 | 42.519 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |