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: 4YLMN
Calculation Name: 2DHM-A-Other547
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 2DHM
Chain ID: A
UniProt ID: P0ABE2
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 | 107 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -735745.765745 |
|---|---|
| FMO2-HF: Nuclear repulsion | 693042.287563 |
| FMO2-HF: Total energy | -42703.478182 |
| FMO2-MP2: Total energy | -42827.031774 |
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. |
| -54.211 | -53.512 | 0 | -0.301 | -0.397 | 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 | 0.065 | 0.026 | 3.827 | -4.489 | -3.822 | 0.001 | -0.297 | -0.370 | 0.000 |
| 6 | A | 6 | SER | 0 | -0.050 | -0.020 | 5.165 | -6.522 | -6.490 | -0.001 | -0.004 | -0.027 | 0.000 |
| 4 | A | 4 | GLY | 0 | 0.009 | 0.014 | 6.520 | 2.138 | 2.138 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 5 | SER | 0 | -0.030 | -0.017 | 6.219 | 3.193 | 3.193 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | GLY | 0 | 0.079 | 0.041 | 7.088 | 3.465 | 3.465 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | MET | 0 | -0.039 | -0.030 | 9.792 | -0.798 | -0.798 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | MET | 0 | 0.011 | 0.019 | 12.069 | 2.312 | 2.312 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | ILE | 0 | 0.052 | 0.018 | 13.596 | -1.079 | -1.079 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | ARG | 1 | 0.835 | 0.903 | 12.948 | 20.594 | 20.594 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | GLU | -1 | -0.919 | -0.950 | 9.308 | -30.784 | -30.784 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | ARG | 1 | 0.958 | 0.970 | 11.742 | 23.198 | 23.198 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | ILE | 0 | 0.002 | 0.003 | 12.669 | 0.417 | 0.417 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | GLU | -1 | -0.823 | -0.915 | 12.312 | -21.276 | -21.276 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | GLU | -1 | -0.963 | -0.995 | 7.195 | -37.484 | -37.484 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | LYS | 1 | 0.872 | 0.936 | 10.660 | 21.511 | 21.511 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | LEU | 0 | 0.020 | 0.008 | 13.747 | 0.860 | 0.860 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | ARG | 1 | 0.931 | 0.955 | 9.900 | 27.594 | 27.594 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | ALA | 0 | -0.011 | -0.005 | 12.690 | 0.395 | 0.395 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | ALA | 0 | -0.041 | -0.016 | 14.532 | 1.066 | 1.066 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | PHE | 0 | -0.040 | -0.033 | 17.787 | 1.076 | 1.076 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | GLN | 0 | -0.066 | -0.006 | 15.806 | 0.444 | 0.444 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | PRO | 0 | -0.018 | 0.005 | 16.800 | 0.673 | 0.673 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | VAL | 0 | 0.009 | -0.004 | 18.257 | -0.670 | -0.670 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | PHE | 0 | -0.018 | -0.011 | 18.874 | -0.392 | -0.392 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | LEU | 0 | -0.024 | -0.021 | 14.033 | 0.210 | 0.210 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | GLU | -1 | -0.805 | -0.870 | 17.038 | -15.207 | -15.207 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | VAL | 0 | 0.025 | 0.009 | 16.903 | 0.689 | 0.689 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | VAL | 0 | -0.026 | -0.007 | 18.396 | -0.522 | -0.522 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | ASP | -1 | -0.899 | -0.969 | 18.875 | -15.905 | -15.905 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 32 | GLU | -1 | -0.897 | -0.940 | 20.894 | -11.401 | -11.401 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 33 | SER | 0 | 0.036 | 0.031 | 21.575 | -0.190 | -0.190 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 34 | TYR | 0 | 0.006 | -0.013 | 23.293 | 0.345 | 0.345 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 35 | ARG | 1 | 0.856 | 0.934 | 26.496 | 10.661 | 10.661 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 36 | HIS | 0 | -0.019 | -0.014 | 29.048 | 0.096 | 0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 37 | ASN | 0 | 0.018 | 0.002 | 30.704 | -0.210 | -0.210 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 38 | VAL | 0 | -0.006 | 0.002 | 32.602 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 39 | PRO | 0 | -0.006 | -0.002 | 32.344 | -0.230 | -0.230 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 40 | ALA | 0 | 0.010 | 0.006 | 30.788 | 0.275 | 0.275 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 41 | GLY | 0 | 0.021 | 0.004 | 31.207 | -0.323 | -0.323 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 42 | SER | 0 | -0.079 | -0.029 | 33.145 | 0.265 | 0.265 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 43 | GLU | -1 | -0.923 | -0.962 | 32.090 | -9.720 | -9.720 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 44 | SER | 0 | -0.002 | -0.019 | 26.622 | -0.191 | -0.191 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 45 | HIS | 0 | -0.010 | 0.019 | 25.818 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 46 | PHE | 0 | 0.035 | 0.007 | 19.173 | -0.518 | -0.518 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 47 | LYS | 1 | 0.837 | 0.910 | 22.701 | 13.894 | 13.894 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 48 | VAL | 0 | 0.013 | 0.013 | 19.848 | -0.653 | -0.653 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 49 | VAL | 0 | -0.023 | -0.012 | 21.063 | 0.850 | 0.850 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 50 | LEU | 0 | -0.009 | -0.008 | 19.348 | -0.841 | -0.841 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 51 | VAL | 0 | -0.013 | 0.005 | 21.749 | 0.669 | 0.669 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 52 | SER | 0 | -0.007 | -0.019 | 22.646 | -0.506 | -0.506 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 53 | ASP | -1 | -0.834 | -0.927 | 24.959 | -11.733 | -11.733 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 54 | ARG | 1 | 0.956 | 0.969 | 25.786 | 11.979 | 11.979 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 55 | PHE | 0 | -0.030 | -0.015 | 24.330 | 0.235 | 0.235 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 56 | THR | 0 | 0.009 | 0.011 | 29.761 | 0.230 | 0.230 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 57 | GLY | 0 | -0.003 | 0.003 | 32.739 | 0.265 | 0.265 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 58 | GLU | -1 | -0.971 | -0.957 | 32.187 | -9.161 | -9.161 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 59 | ARG | 1 | 0.915 | 0.928 | 33.875 | 8.874 | 8.874 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 60 | PHE | 0 | 0.072 | 0.033 | 33.376 | -0.304 | -0.304 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 61 | LEU | 0 | 0.038 | 0.018 | 32.941 | -0.213 | -0.213 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 62 | ASN | 0 | 0.016 | -0.016 | 31.420 | -0.181 | -0.181 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | A | 63 | ARG | 1 | 0.935 | 0.973 | 28.266 | 10.053 | 10.053 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 64 | HIS | 0 | 0.015 | 0.016 | 26.989 | -0.148 | -0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | A | 65 | ARG | 1 | 0.928 | 0.972 | 26.979 | 9.777 | 9.777 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | A | 66 | MET | 0 | -0.028 | -0.004 | 25.045 | -0.166 | -0.166 | 0.000 | 0.000 | 0.000 | 0.000 |
| 67 | A | 67 | ILE | 0 | 0.057 | 0.033 | 21.474 | -0.496 | -0.496 | 0.000 | 0.000 | 0.000 | 0.000 |
| 68 | A | 68 | TYR | 0 | 0.020 | -0.014 | 22.420 | -0.521 | -0.521 | 0.000 | 0.000 | 0.000 | 0.000 |
| 69 | A | 69 | SER | 0 | -0.050 | -0.028 | 23.897 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
| 70 | A | 70 | THR | 0 | -0.054 | -0.019 | 18.175 | -0.304 | -0.304 | 0.000 | 0.000 | 0.000 | 0.000 |
| 71 | A | 71 | LEU | 0 | -0.032 | -0.018 | 16.586 | -0.783 | -0.783 | 0.000 | 0.000 | 0.000 | 0.000 |
| 72 | A | 72 | ALA | 0 | 0.006 | 0.032 | 20.370 | 0.155 | 0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
| 73 | A | 73 | GLU | -1 | -0.846 | -0.948 | 22.155 | -12.718 | -12.718 | 0.000 | 0.000 | 0.000 | 0.000 |
| 74 | A | 74 | GLU | -1 | -0.871 | -0.912 | 15.714 | -20.403 | -20.403 | 0.000 | 0.000 | 0.000 | 0.000 |
| 75 | A | 75 | LEU | 0 | -0.043 | -0.017 | 19.572 | -0.277 | -0.277 | 0.000 | 0.000 | 0.000 | 0.000 |
| 76 | A | 76 | SER | 0 | -0.001 | -0.001 | 21.662 | 0.249 | 0.249 | 0.000 | 0.000 | 0.000 | 0.000 |
| 77 | A | 77 | THR | 0 | -0.054 | -0.032 | 20.564 | 0.329 | 0.329 | 0.000 | 0.000 | 0.000 | 0.000 |
| 78 | A | 78 | THR | 0 | -0.078 | -0.042 | 21.218 | 0.343 | 0.343 | 0.000 | 0.000 | 0.000 | 0.000 |
| 79 | A | 79 | VAL | 0 | 0.005 | 0.025 | 21.823 | 0.353 | 0.353 | 0.000 | 0.000 | 0.000 | 0.000 |
| 80 | A | 80 | HIS | 0 | 0.019 | 0.008 | 24.573 | 0.142 | 0.142 | 0.000 | 0.000 | 0.000 | 0.000 |
| 81 | A | 81 | ALA | 0 | 0.015 | 0.004 | 27.789 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
| 82 | A | 82 | LEU | 0 | 0.005 | -0.005 | 22.678 | -0.380 | -0.380 | 0.000 | 0.000 | 0.000 | 0.000 |
| 83 | A | 83 | ALA | 0 | -0.003 | 0.006 | 26.624 | 0.305 | 0.305 | 0.000 | 0.000 | 0.000 | 0.000 |
| 84 | A | 84 | LEU | 0 | -0.005 | 0.000 | 24.057 | -0.377 | -0.377 | 0.000 | 0.000 | 0.000 | 0.000 |
| 85 | A | 85 | HIS | 0 | -0.043 | -0.021 | 25.350 | 0.927 | 0.927 | 0.000 | 0.000 | 0.000 | 0.000 |
| 86 | A | 86 | THR | 0 | -0.023 | -0.010 | 25.133 | -0.329 | -0.329 | 0.000 | 0.000 | 0.000 | 0.000 |
| 87 | A | 87 | TYR | 0 | 0.022 | 0.011 | 26.155 | 0.429 | 0.429 | 0.000 | 0.000 | 0.000 | 0.000 |
| 88 | A | 88 | THR | 0 | -0.001 | -0.029 | 26.975 | -0.484 | -0.484 | 0.000 | 0.000 | 0.000 | 0.000 |
| 89 | A | 89 | ILE | 0 | 0.021 | -0.009 | 26.511 | -0.112 | -0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
| 90 | A | 90 | LYS | 1 | 0.867 | 0.919 | 28.730 | 9.260 | 9.260 | 0.000 | 0.000 | 0.000 | 0.000 |
| 91 | A | 91 | GLU | -1 | -0.833 | -0.901 | 31.688 | -9.298 | -9.298 | 0.000 | 0.000 | 0.000 | 0.000 |
| 92 | A | 92 | TRP | 0 | -0.044 | -0.021 | 24.541 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
| 93 | A | 93 | GLU | -1 | -0.891 | -0.928 | 29.405 | -9.745 | -9.745 | 0.000 | 0.000 | 0.000 | 0.000 |
| 94 | A | 94 | GLY | 0 | -0.001 | 0.005 | 31.287 | 0.132 | 0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
| 95 | A | 95 | LEU | 0 | -0.056 | -0.001 | 29.621 | 0.201 | 0.201 | 0.000 | 0.000 | 0.000 | 0.000 |
| 96 | A | 96 | GLN | 0 | -0.045 | -0.031 | 33.141 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
| 97 | A | 97 | ASP | -1 | -0.918 | -0.955 | 34.979 | -8.124 | -8.124 | 0.000 | 0.000 | 0.000 | 0.000 |
| 98 | A | 98 | THR | 0 | -0.019 | -0.013 | 36.554 | -0.114 | -0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
| 99 | A | 99 | VAL | 0 | 0.038 | 0.018 | 38.572 | 0.234 | 0.234 | 0.000 | 0.000 | 0.000 | 0.000 |
| 100 | A | 100 | PHE | 0 | 0.011 | 0.007 | 41.067 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 101 | A | 101 | ALA | 0 | -0.028 | -0.020 | 41.883 | 0.142 | 0.142 | 0.000 | 0.000 | 0.000 | 0.000 |
| 102 | A | 102 | SER | 0 | -0.009 | -0.001 | 43.879 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
| 103 | A | 103 | PRO | 0 | -0.032 | -0.008 | 45.313 | 0.144 | 0.144 | 0.000 | 0.000 | 0.000 | 0.000 |
| 104 | A | 104 | PRO | 0 | -0.002 | 0.002 | 48.178 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
| 105 | A | 105 | CYS | 0 | -0.017 | -0.010 | 50.535 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
| 106 | A | 106 | ARG | 1 | 0.896 | 0.931 | 51.160 | 6.244 | 6.244 | 0.000 | 0.000 | 0.000 | 0.000 |
| 107 | A | 107 | GLY | -1 | -0.881 | -0.924 | 54.052 | -5.916 | -5.916 | 0.000 | 0.000 | 0.000 | 0.000 |