FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2025-10-17
All entries: 77277
Number of unique PDB entries: 32023
FMODB ID: 8G3VY
Calculation Name: 2DA0-A-Other547
Preferred Name: Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1
Target Type: SINGLE PROTEIN
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 2DA0
Chain ID: A
ChEMBL ID: CHEMBL2146311
UniProt ID: Q9ULH1
Base Structure: SolutionNMR
Registration Date: 2025-10-03
Reference: Sci Data 11, 1164 (2024).
DOI: https://doi.org/10.1038/s41597-024-03999-2
Apendix: None
Modeling method
| Optimization | MOE:Amber10:EHT |
|---|---|
| Restraint | OptAll |
| Protonation | MOE:Protonate 3D |
| Complement | MOE:Homology Modeling |
| Water | No |
| Procedure | Manual calculation |
| Remarks |
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE. |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 114 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -855592.96511 |
|---|---|
| FMO2-HF: Nuclear repulsion | 811321.955196 |
| FMO2-HF: Total energy | -44271.009914 |
| FMO2-MP2: Total energy | -44400.141242 |
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(A:1:GLY)
Summations of interaction energy for
fragment #1(A:1:GLY)
| 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. |
| 46.816 | 47.512 | -0.003 | -0.231 | -0.462 | 0 |
Interaction energy analysis for fragmet #1(A:1:GLY)
| 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 | A | 3 | SER | 0 | 0.030 | 0.024 | 3.834 | -0.377 | 0.319 | -0.003 | -0.231 | -0.462 | 0.000 |
| 4 | A | 4 | GLY | 0 | 0.040 | 0.027 | 6.088 | 3.677 | 3.677 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 5 | SER | 0 | 0.024 | 0.008 | 8.941 | -1.165 | -1.165 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | SER | 0 | 0.011 | -0.001 | 7.025 | 0.450 | 0.450 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | GLY | 0 | 0.007 | 0.004 | 9.067 | 0.176 | 0.176 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | TYR | 0 | -0.029 | -0.016 | 9.427 | 0.705 | 0.705 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | GLY | 0 | 0.063 | 0.045 | 12.825 | 1.504 | 1.504 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | SER | 0 | 0.024 | -0.019 | 13.282 | -1.654 | -1.654 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | GLU | -1 | -0.900 | -0.916 | 15.187 | -15.718 | -15.718 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | LYS | 1 | 0.887 | 0.948 | 14.752 | 18.199 | 18.199 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | LYS | 1 | 0.907 | 0.948 | 18.092 | 12.734 | 12.734 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | GLY | 0 | 0.029 | 0.016 | 20.794 | 0.100 | 0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | TYR | 0 | -0.044 | -0.043 | 20.856 | 0.776 | 0.776 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | LEU | 0 | 0.053 | 0.044 | 15.571 | -0.538 | -0.538 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | LEU | 0 | 0.022 | 0.029 | 19.191 | 1.034 | 1.034 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | LYS | 1 | 0.890 | 0.940 | 19.278 | 12.323 | 12.323 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | LYS | 1 | 0.905 | 0.984 | 20.915 | 14.667 | 14.667 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | SER | 0 | -0.035 | -0.051 | 23.057 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | ASP | -1 | -0.917 | -0.928 | 25.940 | -10.523 | -10.523 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | GLY | 0 | 0.053 | 0.023 | 27.509 | -0.247 | -0.247 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | ILE | 0 | -0.024 | 0.006 | 28.512 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | ARG | 1 | 0.977 | 0.988 | 30.037 | 9.777 | 9.777 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | LYS | 1 | 0.974 | 0.979 | 25.201 | 11.456 | 11.456 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | VAL | 0 | 0.009 | 0.002 | 25.400 | -0.311 | -0.311 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | TRP | 0 | 0.055 | 0.015 | 18.126 | -0.208 | -0.208 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | GLN | 0 | 0.015 | 0.008 | 24.205 | 0.347 | 0.347 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | ARG | 1 | 1.002 | 1.018 | 23.825 | 11.347 | 11.347 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | ARG | 1 | 0.856 | 0.922 | 23.508 | 11.507 | 11.507 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | LYS | 1 | 0.903 | 0.962 | 23.235 | 11.728 | 11.728 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 32 | CYS | 0 | 0.022 | 0.020 | 19.455 | 0.448 | 0.448 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 33 | SER | 0 | -0.071 | -0.058 | 20.419 | 0.457 | 0.457 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 34 | VAL | 0 | 0.053 | 0.039 | 15.520 | 0.437 | 0.437 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 35 | LYS | 1 | 0.993 | 0.986 | 18.744 | 12.353 | 12.353 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 36 | ASN | 0 | 0.014 | 0.012 | 20.052 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 37 | GLY | 0 | 0.164 | 0.100 | 16.638 | 0.262 | 0.262 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 38 | ILE | 0 | -0.102 | -0.047 | 17.680 | 0.102 | 0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 39 | LEU | 0 | 0.023 | 0.017 | 17.018 | -0.068 | -0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 40 | THR | 0 | -0.069 | -0.043 | 19.559 | 0.797 | 0.797 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 41 | ILE | 0 | 0.021 | 0.000 | 20.746 | -0.305 | -0.305 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 42 | SER | 0 | 0.001 | -0.001 | 24.071 | 0.523 | 0.523 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 43 | HIS | 0 | 0.056 | 0.019 | 27.466 | -0.333 | -0.333 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 44 | ALA | 0 | -0.054 | -0.035 | 30.034 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 45 | THR | 0 | 0.043 | 0.024 | 31.804 | 0.165 | 0.165 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 46 | SER | 0 | 0.019 | 0.012 | 33.708 | 0.260 | 0.260 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 47 | ASN | 0 | -0.031 | -0.013 | 34.215 | -0.421 | -0.421 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 48 | ARG | 1 | 1.012 | 1.017 | 34.453 | 8.879 | 8.879 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 49 | GLN | 0 | 0.025 | -0.011 | 32.190 | -0.087 | -0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 50 | PRO | 0 | -0.035 | 0.000 | 27.322 | -0.067 | -0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 51 | ALA | 0 | 0.013 | 0.009 | 25.551 | 0.153 | 0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 52 | LYS | 1 | 0.935 | 0.956 | 23.684 | 10.962 | 10.962 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 53 | LEU | 0 | 0.014 | 0.008 | 19.587 | 0.193 | 0.193 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 54 | ASN | 0 | 0.048 | 0.024 | 19.856 | -0.164 | -0.164 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 55 | LEU | 0 | 0.021 | 0.000 | 14.169 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 56 | LEU | 0 | 0.037 | 0.027 | 14.943 | -0.919 | -0.919 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 57 | THR | 0 | -0.061 | -0.020 | 17.097 | 0.208 | 0.208 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 58 | CYS | 0 | -0.068 | -0.023 | 16.037 | 0.309 | 0.309 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 59 | GLN | 0 | 0.048 | 0.022 | 11.804 | -1.327 | -1.327 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 60 | VAL | 0 | 0.013 | -0.003 | 9.267 | 1.040 | 1.040 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 61 | LYS | 1 | 0.893 | 0.954 | 9.121 | 22.609 | 22.609 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 62 | PRO | 0 | 0.009 | 0.000 | 5.221 | 2.893 | 2.893 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | A | 63 | ASN | 0 | 0.023 | 0.004 | 8.216 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 64 | ALA | 0 | -0.014 | 0.003 | 7.982 | -3.461 | -3.461 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | A | 65 | GLU | -1 | -0.865 | -0.933 | 9.138 | -27.383 | -27.383 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | A | 66 | ASP | -1 | -0.930 | -0.958 | 11.952 | -19.618 | -19.618 | 0.000 | 0.000 | 0.000 | 0.000 |
| 67 | A | 67 | LYS | 1 | 0.928 | 0.955 | 7.856 | 32.727 | 32.727 | 0.000 | 0.000 | 0.000 | 0.000 |
| 68 | A | 68 | LYS | 1 | 0.856 | 0.955 | 11.564 | 19.116 | 19.116 | 0.000 | 0.000 | 0.000 | 0.000 |
| 69 | A | 69 | SER | 0 | 0.019 | 0.001 | 12.058 | 2.307 | 2.307 | 0.000 | 0.000 | 0.000 | 0.000 |
| 70 | A | 70 | PHE | 0 | -0.026 | -0.025 | 10.545 | -2.308 | -2.308 | 0.000 | 0.000 | 0.000 | 0.000 |
| 71 | A | 71 | ASP | -1 | -0.803 | -0.868 | 12.157 | -16.816 | -16.816 | 0.000 | 0.000 | 0.000 | 0.000 |
| 72 | A | 72 | LEU | 0 | -0.056 | -0.038 | 12.808 | -1.502 | -1.502 | 0.000 | 0.000 | 0.000 | 0.000 |
| 73 | A | 73 | ILE | 0 | 0.037 | 0.017 | 14.227 | 1.324 | 1.324 | 0.000 | 0.000 | 0.000 | 0.000 |
| 74 | A | 74 | SER | 0 | 0.007 | -0.031 | 16.745 | -0.173 | -0.173 | 0.000 | 0.000 | 0.000 | 0.000 |
| 75 | A | 75 | HIS | 0 | 0.051 | 0.031 | 19.559 | -0.331 | -0.331 | 0.000 | 0.000 | 0.000 | 0.000 |
| 76 | A | 76 | ASN | 0 | -0.009 | 0.002 | 22.596 | 0.158 | 0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
| 77 | A | 77 | ARG | 1 | 0.957 | 0.975 | 22.106 | 12.122 | 12.122 | 0.000 | 0.000 | 0.000 | 0.000 |
| 78 | A | 78 | THR | 0 | -0.007 | -0.009 | 17.695 | -0.829 | -0.829 | 0.000 | 0.000 | 0.000 | 0.000 |
| 79 | A | 79 | TYR | 0 | -0.044 | -0.002 | 18.520 | 1.025 | 1.025 | 0.000 | 0.000 | 0.000 | 0.000 |
| 80 | A | 80 | HIS | 0 | -0.012 | -0.023 | 17.278 | 0.097 | 0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
| 81 | A | 81 | PHE | 0 | -0.040 | -0.045 | 15.292 | 1.490 | 1.490 | 0.000 | 0.000 | 0.000 | 0.000 |
| 82 | A | 82 | GLN | 0 | 0.014 | 0.019 | 15.599 | -0.621 | -0.621 | 0.000 | 0.000 | 0.000 | 0.000 |
| 83 | A | 83 | ALA | 0 | -0.007 | -0.002 | 14.384 | 0.648 | 0.648 | 0.000 | 0.000 | 0.000 | 0.000 |
| 84 | A | 84 | GLU | -1 | -0.899 | -0.958 | 16.390 | -13.421 | -13.421 | 0.000 | 0.000 | 0.000 | 0.000 |
| 85 | A | 85 | ASP | -1 | -0.787 | -0.917 | 17.648 | -16.742 | -16.742 | 0.000 | 0.000 | 0.000 | 0.000 |
| 86 | A | 86 | GLU | -1 | -0.939 | -0.985 | 12.520 | -23.719 | -23.719 | 0.000 | 0.000 | 0.000 | 0.000 |
| 87 | A | 87 | GLN | 0 | -0.002 | -0.003 | 12.726 | -1.833 | -1.833 | 0.000 | 0.000 | 0.000 | 0.000 |
| 88 | A | 88 | ASP | -1 | -0.826 | -0.901 | 13.576 | -18.491 | -18.491 | 0.000 | 0.000 | 0.000 | 0.000 |
| 89 | A | 89 | TYR | 0 | -0.010 | -0.006 | 7.897 | -1.623 | -1.623 | 0.000 | 0.000 | 0.000 | 0.000 |
| 90 | A | 90 | VAL | 0 | 0.003 | 0.005 | 8.391 | -1.990 | -1.990 | 0.000 | 0.000 | 0.000 | 0.000 |
| 91 | A | 91 | ALA | 0 | -0.001 | 0.006 | 9.020 | -1.948 | -1.948 | 0.000 | 0.000 | 0.000 | 0.000 |
| 92 | A | 92 | TRP | 0 | -0.055 | -0.050 | 11.118 | -0.254 | -0.254 | 0.000 | 0.000 | 0.000 | 0.000 |
| 93 | A | 93 | ILE | 0 | 0.003 | 0.007 | 5.431 | 0.145 | 0.145 | 0.000 | 0.000 | 0.000 | 0.000 |
| 94 | A | 94 | SER | 0 | -0.002 | 0.023 | 7.204 | -2.197 | -2.197 | 0.000 | 0.000 | 0.000 | 0.000 |
| 95 | A | 95 | VAL | 0 | 0.003 | 0.004 | 8.110 | 0.616 | 0.616 | 0.000 | 0.000 | 0.000 | 0.000 |
| 96 | A | 96 | LEU | 0 | -0.052 | -0.035 | 10.307 | 1.311 | 1.311 | 0.000 | 0.000 | 0.000 | 0.000 |
| 97 | A | 97 | THR | 0 | -0.028 | -0.024 | 5.726 | 0.603 | 0.603 | 0.000 | 0.000 | 0.000 | 0.000 |
| 98 | A | 98 | ASN | 0 | -0.009 | -0.003 | 8.743 | -0.606 | -0.606 | 0.000 | 0.000 | 0.000 | 0.000 |
| 99 | A | 99 | SER | 0 | -0.036 | -0.052 | 10.487 | 1.792 | 1.792 | 0.000 | 0.000 | 0.000 | 0.000 |
| 100 | A | 100 | LYS | 1 | 0.757 | 0.887 | 11.014 | 25.748 | 25.748 | 0.000 | 0.000 | 0.000 | 0.000 |
| 101 | A | 101 | GLU | -1 | -0.788 | -0.895 | 8.970 | -25.518 | -25.518 | 0.000 | 0.000 | 0.000 | 0.000 |
| 102 | A | 102 | GLU | -1 | -0.915 | -0.962 | 12.192 | -19.264 | -19.264 | 0.000 | 0.000 | 0.000 | 0.000 |
| 103 | A | 103 | ALA | 0 | -0.025 | -0.018 | 14.701 | 1.244 | 1.244 | 0.000 | 0.000 | 0.000 | 0.000 |
| 104 | A | 104 | LEU | 0 | -0.057 | -0.037 | 13.833 | 0.801 | 0.801 | 0.000 | 0.000 | 0.000 | 0.000 |
| 105 | A | 105 | THR | 0 | -0.018 | 0.000 | 14.787 | 0.865 | 0.865 | 0.000 | 0.000 | 0.000 | 0.000 |
| 106 | A | 106 | MET | 0 | -0.054 | -0.010 | 16.813 | 0.958 | 0.958 | 0.000 | 0.000 | 0.000 | 0.000 |
| 107 | A | 107 | ALA | 0 | -0.046 | -0.015 | 19.624 | 0.821 | 0.821 | 0.000 | 0.000 | 0.000 | 0.000 |
| 108 | A | 108 | PHE | 0 | 0.006 | -0.006 | 21.070 | -0.255 | -0.255 | 0.000 | 0.000 | 0.000 | 0.000 |
| 109 | A | 109 | SER | 0 | 0.003 | -0.002 | 19.535 | -0.158 | -0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
| 110 | A | 110 | GLY | 0 | -0.015 | -0.010 | 21.387 | -0.208 | -0.208 | 0.000 | 0.000 | 0.000 | 0.000 |
| 111 | A | 111 | PRO | 0 | -0.059 | -0.018 | 24.818 | 0.107 | 0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
| 112 | A | 112 | SER | 0 | 0.004 | -0.003 | 28.500 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
| 113 | A | 113 | SER | 0 | -0.072 | -0.038 | 31.258 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 114 | A | 114 | GLY | -1 | -0.878 | -0.923 | 33.709 | -9.037 | -9.037 | 0.000 | 0.000 | 0.000 | 0.000 |