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: 9G3N2
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 | 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 | 51 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -235505.796329 |
|---|---|
| FMO2-HF: Nuclear repulsion | 214449.798343 |
| FMO2-HF: Total energy | -21055.997986 |
| FMO2-MP2: Total energy | -21113.941331 |
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. |
| -14.339 | -6.122 | 16.793 | -8.061 | -16.948 | -0.034 |
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 | 0.032 | -0.008 | 3.807 | -0.015 | 1.711 | -0.018 | -0.694 | -1.015 | 0.001 |
| 4 | w | 68 | VAL | 0 | -0.025 | 0.002 | 5.696 | 0.365 | 0.365 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | w | 69 | GLY | 0 | 0.036 | -0.006 | 7.935 | 0.080 | 0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | w | 70 | ALA | 0 | -0.046 | -0.005 | 8.281 | 0.096 | 0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | w | 71 | ILE | 0 | -0.019 | 0.012 | 9.741 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | w | 99 | GLY | 0 | 0.001 | -0.010 | 18.184 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | w | 100 | LYS | 1 | 0.960 | 0.975 | 17.556 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | w | 101 | LEU | 0 | -0.024 | -0.005 | 11.869 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | w | 102 | PRO | 0 | 0.043 | 0.033 | 12.329 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | w | 103 | PHE | 0 | 0.003 | -0.017 | 12.697 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | w | 104 | VAL | 0 | -0.034 | -0.015 | 11.111 | 0.076 | 0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | w | 105 | PRO | 0 | -0.026 | 0.002 | 6.989 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | w | 106 | PRO | 0 | 0.022 | 0.003 | 9.143 | 0.150 | 0.150 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | w | 107 | GLU | -1 | -0.903 | -0.959 | 8.138 | 0.263 | 0.263 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | w | 108 | GLU | -1 | -0.980 | -0.969 | 7.679 | -1.071 | -1.071 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | w | 109 | GLU | -1 | -0.954 | -0.981 | 4.689 | -0.369 | -0.245 | -0.001 | -0.009 | -0.113 | 0.000 |
| 19 | w | 110 | PHE | 0 | 0.003 | -0.015 | 2.532 | 0.084 | 0.958 | 0.409 | -0.228 | -1.054 | 0.001 |
| 20 | w | 111 | ILE | 0 | -0.008 | 0.009 | 3.083 | -4.176 | -2.714 | 0.069 | -0.745 | -0.786 | -0.006 |
| 21 | w | 112 | MET | 0 | -0.005 | -0.014 | 2.191 | -4.248 | -2.234 | 3.869 | -1.666 | -4.218 | -0.008 |
| 22 | w | 113 | GLY | 0 | 0.008 | 0.005 | 3.861 | 0.272 | 0.467 | 0.014 | -0.031 | -0.178 | 0.000 |
| 23 | w | 114 | VAL | 0 | -0.028 | -0.012 | 7.032 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | w | 115 | SER | 0 | 0.014 | 0.015 | 9.388 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | w | 140 | ARG | 1 | 0.957 | 0.957 | 12.738 | -0.171 | -0.171 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | w | 141 | MET | 0 | 0.038 | 0.049 | 6.740 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | w | 142 | VAL | 0 | -0.007 | -0.011 | 10.565 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | w | 143 | CYS | 0 | 0.021 | 0.023 | 8.311 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | w | 153 | SER | 0 | 0.007 | -0.011 | 6.386 | 0.120 | 0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | w | 154 | LEU | 0 | 0.012 | -0.007 | 6.314 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | w | 155 | LEU | 0 | 0.010 | 0.002 | 2.384 | -0.681 | -0.420 | 1.121 | -0.299 | -1.083 | 0.002 |
| 32 | w | 156 | ALA | 0 | -0.026 | -0.004 | 6.005 | -0.107 | -0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | w | 157 | LEU | 0 | 0.041 | 0.016 | 5.305 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | w | 158 | LYS | 1 | 0.990 | 1.006 | 9.453 | -0.144 | -0.144 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | w | 168 | SER | 0 | -0.024 | -0.028 | 13.378 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | w | 169 | LEU | 0 | -0.058 | -0.033 | 12.585 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | w | 170 | TRP | 0 | 0.039 | 0.013 | 7.102 | -0.109 | -0.109 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | w | 171 | VAL | 0 | 0.000 | -0.003 | 7.512 | 0.154 | 0.154 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | w | 172 | TYR | 0 | 0.029 | 0.021 | 2.075 | -1.879 | -1.462 | 6.332 | -1.893 | -4.856 | -0.006 |
| 40 | w | 173 | GLN | 0 | 0.021 | 0.016 | 3.950 | -0.125 | 0.430 | 0.006 | -0.127 | -0.434 | 0.000 |
| 41 | w | 174 | CYS | 0 | -0.005 | 0.003 | 2.375 | -1.774 | -1.247 | 4.987 | -2.360 | -3.154 | -0.018 |
| 42 | w | 175 | ASN | 0 | 0.042 | 0.029 | 3.776 | -0.730 | -0.668 | 0.005 | -0.009 | -0.057 | 0.000 |
| 43 | w | 184 | CYS | 0 | 0.014 | -0.010 | 7.835 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | w | 185 | LYS | 1 | 0.987 | 0.987 | 9.498 | -0.578 | -0.578 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | w | 186 | VAL | 0 | 0.070 | 0.045 | 9.765 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | w | 187 | LEU | 0 | -0.004 | -0.008 | 8.389 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | w | 188 | SER | 0 | -0.035 | -0.036 | 11.160 | -0.055 | -0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | w | 189 | THR | 0 | -0.008 | -0.006 | 14.197 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | w | 190 | ALA | 0 | -0.040 | -0.006 | 14.325 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | w | 191 | PHE | 0 | -0.080 | -0.032 | 13.041 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | w | 192 | ASP | -1 | -0.932 | -0.949 | 18.053 | 0.136 | 0.136 | 0.000 | 0.000 | 0.000 | 0.000 |