FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-04-05
All entries: 36946
Number of unique PDB entries: 7781
FMODB ID: 7G93K
Calculation Name: 4DX9-w-Xray372
Preferred Name: Fibronectin receptor beta
Target Type: SINGLE PROTEIN
Ligand Name:
ligand 3-letter code:
PDB ID: 4DX9
Chain ID: w
ChEMBL ID: CHEMBL1905
UniProt ID: P05556
Base Structure: X-ray
Registration Date: 2023-06-20
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 | 51 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -236750.132002 |
|---|---|
| FMO2-HF: Nuclear repulsion | 215693.788857 |
| FMO2-HF: Total energy | -21056.343145 |
| FMO2-MP2: Total energy | -21114.312894 |
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(w:65:ILE)
Summations of interaction energy for
fragment #1(w:65:ILE)
| 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. |
| -26.315 | -13.288 | 13.404 | -8.942 | -17.49 | -0.038 |
Interaction energy analysis for fragmet #1(w:65:ILE)
| 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 | w | 67 | TYR | 0 | 0.009 | -0.017 | 3.662 | -0.138 | 2.615 | 0.009 | -1.279 | -1.483 | 0.003 |
| 4 | w | 68 | VAL | 0 | -0.019 | 0.002 | 5.025 | -0.029 | 0.038 | -0.001 | -0.003 | -0.062 | 0.000 |
| 5 | w | 69 | GLY | 0 | 0.038 | -0.002 | 7.994 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | w | 70 | ALA | 0 | -0.058 | -0.006 | 8.426 | 0.149 | 0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | w | 71 | ILE | 0 | -0.028 | -0.020 | 9.938 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | w | 99 | GLY | 0 | 0.025 | -0.001 | 18.267 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | w | 100 | LYS | 1 | 0.939 | 0.968 | 17.762 | -0.067 | -0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | w | 101 | LEU | 0 | -0.005 | -0.004 | 12.545 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | w | 102 | PRO | 0 | 0.016 | 0.030 | 11.830 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | w | 103 | PHE | 0 | -0.005 | -0.024 | 12.295 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | w | 104 | VAL | 0 | -0.026 | -0.009 | 11.452 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | w | 105 | PRO | 0 | -0.023 | 0.005 | 7.120 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | w | 106 | PRO | 0 | 0.033 | 0.008 | 8.792 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | w | 107 | GLU | -1 | -0.841 | -0.907 | 8.205 | -1.376 | -1.376 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | w | 108 | GLU | -1 | -0.972 | -0.972 | 7.158 | -1.760 | -1.760 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | w | 109 | GLU | -1 | -0.947 | -0.975 | 4.179 | -3.781 | -3.558 | -0.001 | -0.028 | -0.194 | 0.000 |
| 19 | w | 110 | PHE | 0 | -0.019 | -0.022 | 2.345 | 1.226 | 2.329 | 1.573 | -0.669 | -2.007 | 0.002 |
| 20 | w | 111 | ILE | 0 | -0.001 | 0.007 | 2.294 | -8.500 | -6.442 | 2.628 | -2.155 | -2.531 | -0.029 |
| 21 | w | 112 | MET | 0 | 0.001 | -0.015 | 2.418 | -3.901 | -1.396 | 1.820 | -1.194 | -3.132 | -0.001 |
| 22 | w | 113 | GLY | 0 | 0.021 | 0.011 | 3.946 | -0.185 | -0.036 | 0.004 | -0.036 | -0.117 | 0.000 |
| 23 | w | 114 | VAL | 0 | -0.035 | -0.015 | 7.535 | -0.129 | -0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | w | 115 | SER | 0 | -0.002 | 0.014 | 9.627 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | w | 140 | ARG | 1 | 0.988 | 0.993 | 13.837 | -0.447 | -0.447 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | w | 141 | MET | 0 | 0.006 | 0.017 | 6.834 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | w | 142 | VAL | 0 | -0.012 | -0.017 | 10.514 | -0.133 | -0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | w | 143 | CYS | 0 | 0.024 | 0.028 | 8.492 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | w | 153 | SER | 0 | 0.027 | 0.019 | 6.734 | 0.127 | 0.127 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | w | 154 | LEU | 0 | -0.032 | -0.044 | 6.522 | -0.103 | -0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | w | 155 | LEU | 0 | -0.003 | -0.007 | 2.504 | -0.644 | -0.129 | 0.497 | -0.215 | -0.797 | 0.002 |
| 32 | w | 156 | ALA | 0 | -0.003 | 0.007 | 6.208 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | w | 157 | LEU | 0 | 0.036 | 0.005 | 5.982 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | w | 158 | LYS | 1 | 0.874 | 0.934 | 9.743 | -0.427 | -0.427 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | w | 168 | SER | 0 | 0.058 | 0.027 | 13.971 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | w | 169 | LEU | 0 | -0.036 | -0.014 | 12.922 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | w | 170 | TRP | 0 | 0.049 | 0.028 | 7.913 | -0.149 | -0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | w | 171 | VAL | 0 | -0.001 | 0.001 | 7.737 | 0.167 | 0.167 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | w | 172 | TYR | 0 | 0.039 | 0.025 | 2.282 | -2.672 | -0.717 | 2.623 | -1.158 | -3.421 | -0.002 |
| 40 | w | 173 | GLN | 0 | 0.036 | 0.018 | 3.507 | -0.375 | 0.100 | 0.006 | -0.097 | -0.383 | 0.000 |
| 41 | w | 174 | CYS | 0 | -0.015 | 0.006 | 2.620 | -1.906 | -0.819 | 4.240 | -2.086 | -3.242 | -0.013 |
| 42 | w | 175 | ASN | 0 | 0.066 | 0.035 | 3.904 | -0.408 | -0.271 | 0.006 | -0.022 | -0.121 | 0.000 |
| 43 | w | 184 | CYS | 0 | 0.026 | -0.008 | 8.385 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | w | 185 | LYS | 1 | 0.987 | 0.996 | 9.648 | -0.962 | -0.962 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | w | 186 | VAL | 0 | 0.059 | 0.041 | 10.068 | -0.103 | -0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | w | 187 | LEU | 0 | 0.006 | 0.002 | 8.628 | -0.085 | -0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | w | 188 | SER | 0 | -0.020 | -0.024 | 11.452 | -0.123 | -0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | w | 189 | THR | 0 | -0.012 | -0.017 | 14.508 | -0.091 | -0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | w | 190 | ALA | 0 | -0.033 | -0.004 | 14.392 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | w | 191 | PHE | 0 | -0.096 | -0.040 | 13.240 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | w | 192 | ASP | -1 | -0.946 | -0.963 | 18.072 | 0.367 | 0.367 | 0.000 | 0.000 | 0.000 | 0.000 |