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: 3MK3L
Calculation Name: 2DOC-A-Other547
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 2DOC
Chain ID: A
UniProt ID: O15394
Base Structure: SolutionNMR
Registration Date: 2025-10-05
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 | 119 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -829865.231531 |
|---|---|
| FMO2-HF: Nuclear repulsion | 785914.752922 |
| FMO2-HF: Total energy | -43950.478609 |
| FMO2-MP2: Total energy | -44080.892165 |
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. |
| -31.444 | -30.667 | -0.013 | -0.317 | -0.447 | 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 | -0.012 | -0.004 | 3.825 | -2.375 | -1.598 | -0.013 | -0.317 | -0.447 | 0.000 |
| 4 | A | 4 | GLY | 0 | 0.047 | 0.028 | 6.879 | 2.162 | 2.162 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 5 | SER | 0 | -0.043 | -0.022 | 9.222 | -0.934 | -0.934 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | SER | 0 | 0.041 | 0.017 | 7.378 | -0.572 | -0.572 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | GLY | 0 | -0.005 | -0.009 | 9.311 | -0.337 | -0.337 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | GLN | 0 | -0.016 | -0.004 | 10.155 | -0.393 | -0.393 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | GLU | -1 | -0.871 | -0.950 | 11.021 | -24.325 | -24.325 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | TYR | 0 | -0.041 | -0.015 | 12.426 | 0.528 | 0.528 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | ILE | 0 | 0.044 | 0.014 | 13.366 | 0.554 | 0.554 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | LEU | 0 | -0.018 | -0.009 | 17.094 | 0.653 | 0.653 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | ALA | 0 | -0.010 | -0.006 | 14.805 | 0.838 | 0.838 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | LEU | 0 | -0.051 | -0.011 | 13.916 | 0.155 | 0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | ALA | 0 | -0.009 | 0.005 | 17.948 | 0.506 | 0.506 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | ASP | -1 | -0.865 | -0.928 | 21.519 | -12.915 | -12.915 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | VAL | 0 | 0.000 | -0.005 | 24.871 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | PRO | 0 | -0.073 | -0.046 | 28.154 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | SER | 0 | 0.012 | 0.004 | 30.834 | 0.115 | 0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | SER | 0 | 0.016 | 0.015 | 33.751 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | PRO | 0 | -0.056 | -0.036 | 37.296 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | TYR | 0 | 0.064 | 0.021 | 39.538 | 0.252 | 0.252 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | GLY | 0 | -0.020 | -0.022 | 42.585 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | VAL | 0 | -0.058 | -0.024 | 44.911 | 0.090 | 0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | LYS | 1 | 0.987 | 1.004 | 46.735 | 6.361 | 6.361 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | ILE | 0 | -0.003 | -0.004 | 50.308 | -0.084 | -0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | ILE | 0 | -0.056 | -0.029 | 51.640 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | GLU | -1 | -0.823 | -0.889 | 54.320 | -5.656 | -5.656 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | LEU | 0 | -0.028 | -0.010 | 55.607 | -0.123 | -0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | SER | 0 | 0.012 | 0.005 | 57.902 | 0.114 | 0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | GLN | 0 | 0.015 | 0.014 | 60.174 | -0.099 | -0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 32 | THR | 0 | 0.021 | 0.009 | 59.551 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 33 | THR | 0 | -0.014 | -0.013 | 55.435 | -0.085 | -0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 34 | ALA | 0 | 0.073 | 0.035 | 53.400 | 0.083 | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 35 | LYS | 1 | 0.812 | 0.893 | 51.018 | 5.863 | 5.863 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 36 | VAL | 0 | 0.032 | 0.025 | 46.682 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 37 | SER | 0 | -0.031 | -0.021 | 47.265 | -0.105 | -0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 38 | PHE | 0 | 0.033 | 0.016 | 40.468 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 39 | ASN | 0 | -0.011 | 0.012 | 42.269 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 40 | LYS | 1 | 0.973 | 0.972 | 36.226 | 8.198 | 8.198 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 41 | PRO | 0 | -0.006 | 0.003 | 34.635 | 0.178 | 0.178 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 42 | ASP | -1 | -0.862 | -0.895 | 35.241 | -8.957 | -8.957 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 43 | SER | 0 | 0.019 | 0.000 | 31.143 | -0.173 | -0.173 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 44 | HIS | 0 | -0.062 | -0.033 | 26.619 | 0.260 | 0.260 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 45 | GLY | 0 | 0.077 | 0.044 | 27.486 | -0.164 | -0.164 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 46 | GLY | 0 | 0.015 | 0.013 | 23.845 | -0.452 | -0.452 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 47 | VAL | 0 | -0.053 | -0.041 | 22.863 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 48 | PRO | 0 | -0.003 | -0.005 | 25.334 | 0.363 | 0.363 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 49 | ILE | 0 | -0.018 | -0.021 | 28.871 | -0.137 | -0.137 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 50 | HIS | 0 | -0.019 | 0.000 | 30.614 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 51 | HIS | 0 | -0.026 | -0.006 | 32.603 | 0.186 | 0.186 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 52 | TYR | 0 | 0.042 | 0.018 | 35.591 | -0.198 | -0.198 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 53 | GLN | 0 | -0.022 | -0.017 | 36.853 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 54 | VAL | 0 | 0.002 | 0.006 | 39.459 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 55 | ASP | -1 | -0.801 | -0.901 | 42.765 | -7.328 | -7.328 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 56 | VAL | 0 | -0.006 | -0.005 | 44.693 | 0.067 | 0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 57 | LYS | 1 | 0.866 | 0.936 | 48.508 | 6.293 | 6.293 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 58 | GLU | -1 | -0.888 | -0.941 | 51.146 | -5.658 | -5.658 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 59 | VAL | 0 | -0.024 | -0.019 | 53.872 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 60 | ALA | 0 | -0.013 | 0.000 | 55.368 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 61 | SER | 0 | 0.004 | 0.013 | 54.129 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 62 | GLU | -1 | -0.921 | -0.972 | 50.297 | -6.360 | -6.360 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | A | 63 | ILE | 0 | -0.059 | -0.031 | 49.669 | -0.166 | -0.166 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 64 | TRP | 0 | -0.028 | -0.003 | 45.629 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | A | 65 | LYS | 1 | 0.925 | 0.968 | 46.978 | 6.458 | 6.458 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | A | 66 | ILE | 0 | 0.011 | 0.007 | 40.548 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
| 67 | A | 67 | VAL | 0 | -0.007 | -0.007 | 43.834 | 0.086 | 0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
| 68 | A | 68 | ARG | 1 | 0.893 | 0.939 | 35.737 | 8.411 | 8.411 | 0.000 | 0.000 | 0.000 | 0.000 |
| 69 | A | 69 | SER | 0 | -0.005 | -0.011 | 39.655 | 0.145 | 0.145 | 0.000 | 0.000 | 0.000 | 0.000 |
| 70 | A | 70 | HIS | 0 | -0.016 | -0.010 | 40.154 | -0.280 | -0.280 | 0.000 | 0.000 | 0.000 | 0.000 |
| 71 | A | 71 | GLY | 0 | 0.055 | 0.034 | 37.399 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 72 | A | 72 | VAL | 0 | -0.009 | 0.003 | 34.290 | 0.124 | 0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
| 73 | A | 73 | GLN | 0 | -0.047 | -0.028 | 37.441 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 74 | A | 74 | THR | 0 | -0.028 | -0.032 | 40.161 | -0.097 | -0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
| 75 | A | 75 | MET | 0 | -0.012 | 0.002 | 42.504 | 0.178 | 0.178 | 0.000 | 0.000 | 0.000 | 0.000 |
| 76 | A | 76 | VAL | 0 | -0.004 | 0.003 | 43.842 | -0.077 | -0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
| 77 | A | 77 | VAL | 0 | -0.027 | -0.011 | 46.934 | 0.107 | 0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
| 78 | A | 78 | LEU | 0 | 0.002 | 0.012 | 47.693 | -0.092 | -0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
| 79 | A | 79 | ASN | 0 | 0.005 | -0.023 | 51.190 | 0.095 | 0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
| 80 | A | 80 | ASN | 0 | -0.030 | -0.014 | 53.479 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 81 | A | 81 | LEU | 0 | -0.006 | 0.017 | 53.256 | -0.064 | -0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
| 82 | A | 82 | GLU | -1 | -0.852 | -0.919 | 57.208 | -5.163 | -5.163 | 0.000 | 0.000 | 0.000 | 0.000 |
| 83 | A | 83 | PRO | 0 | 0.038 | 0.028 | 60.384 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
| 84 | A | 84 | ASN | 0 | -0.081 | -0.030 | 63.032 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 85 | A | 85 | THR | 0 | 0.044 | 0.035 | 58.650 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
| 86 | A | 86 | THR | 0 | -0.040 | -0.027 | 56.382 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
| 87 | A | 87 | TYR | 0 | -0.014 | -0.024 | 53.062 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 88 | A | 88 | GLU | -1 | -0.844 | -0.912 | 49.703 | -6.288 | -6.288 | 0.000 | 0.000 | 0.000 | 0.000 |
| 89 | A | 89 | ILE | 0 | -0.027 | -0.029 | 46.880 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
| 90 | A | 90 | ARG | 1 | 0.855 | 0.934 | 42.692 | 7.427 | 7.427 | 0.000 | 0.000 | 0.000 | 0.000 |
| 91 | A | 91 | VAL | 0 | 0.019 | 0.011 | 40.789 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
| 92 | A | 92 | ALA | 0 | 0.085 | 0.051 | 36.740 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
| 93 | A | 93 | ALA | 0 | 0.001 | 0.001 | 34.235 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
| 94 | A | 94 | VAL | 0 | 0.010 | -0.002 | 32.061 | -0.164 | -0.164 | 0.000 | 0.000 | 0.000 | 0.000 |
| 95 | A | 95 | ASN | 0 | 0.015 | 0.007 | 27.096 | 0.083 | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
| 96 | A | 96 | GLY | 0 | -0.011 | -0.010 | 25.846 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
| 97 | A | 97 | LYS | 1 | 0.857 | 0.949 | 21.093 | 13.865 | 13.865 | 0.000 | 0.000 | 0.000 | 0.000 |
| 98 | A | 98 | GLY | 0 | 0.048 | 0.028 | 25.882 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
| 99 | A | 99 | GLN | 0 | -0.035 | -0.037 | 29.511 | 0.247 | 0.247 | 0.000 | 0.000 | 0.000 | 0.000 |
| 100 | A | 100 | GLY | 0 | 0.002 | 0.013 | 31.694 | -0.114 | -0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
| 101 | A | 101 | ASP | -1 | -0.875 | -0.923 | 32.527 | -9.037 | -9.037 | 0.000 | 0.000 | 0.000 | 0.000 |
| 102 | A | 102 | TYR | 0 | -0.072 | -0.052 | 35.886 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
| 103 | A | 103 | SER | 0 | -0.024 | -0.032 | 39.464 | 0.098 | 0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
| 104 | A | 104 | LYS | 1 | 0.841 | 0.905 | 41.645 | 6.797 | 6.797 | 0.000 | 0.000 | 0.000 | 0.000 |
| 105 | A | 105 | ILE | 0 | 0.005 | 0.002 | 44.548 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
| 106 | A | 106 | GLU | -1 | -0.846 | -0.904 | 46.890 | -6.413 | -6.413 | 0.000 | 0.000 | 0.000 | 0.000 |
| 107 | A | 107 | ILE | 0 | 0.006 | -0.011 | 49.555 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 108 | A | 108 | PHE | 0 | -0.035 | -0.009 | 51.439 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 109 | A | 109 | GLN | 0 | 0.014 | 0.001 | 55.408 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
| 110 | A | 110 | THR | 0 | -0.034 | -0.032 | 57.903 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 111 | A | 111 | LEU | 0 | -0.005 | -0.006 | 60.006 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
| 112 | A | 112 | PRO | 0 | 0.033 | 0.009 | 63.329 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 113 | A | 113 | VAL | 0 | -0.021 | -0.023 | 66.422 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 114 | A | 114 | SER | 0 | -0.014 | 0.011 | 68.137 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
| 115 | A | 115 | GLY | 0 | 0.038 | -0.003 | 70.063 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
| 116 | A | 116 | PRO | 0 | -0.036 | -0.013 | 69.155 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
| 117 | A | 117 | SER | 0 | -0.034 | -0.011 | 70.217 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 118 | A | 118 | SER | 0 | -0.044 | -0.019 | 70.563 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
| 119 | A | 119 | GLY | -1 | -0.908 | -0.948 | 71.823 | -4.383 | -4.383 | 0.000 | 0.000 | 0.000 | 0.000 |