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: 3M7RL
Calculation Name: 2CTX-A-Xray547
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 2CTX
Chain ID: A
UniProt ID: P25671
Base Structure: X-ray
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 | 66 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -406108.665279 |
|---|---|
| FMO2-HF: Nuclear repulsion | 376359.001678 |
| FMO2-HF: Total energy | -29749.663602 |
| FMO2-MP2: Total energy | -29828.167081 |
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:ILE)
Summations of interaction energy for
fragment #1(A:1: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. |
| -123.563 | -106.719 | 20.035 | -13.281 | -23.595 | -0.131 |
Interaction energy analysis for fragmet #1(A:1: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 | A | 3 | CYS | 0 | 0.003 | 0.022 | 2.775 | -6.748 | -3.435 | 5.003 | -2.315 | -6.001 | -0.015 |
| 4 | A | 4 | PHE | 0 | 0.033 | 0.010 | 4.939 | 1.772 | 1.833 | -0.001 | -0.011 | -0.049 | 0.000 |
| 13 | A | 13 | ASP | -1 | -0.849 | -0.921 | 3.802 | -67.830 | -67.523 | 0.000 | -0.167 | -0.141 | -0.001 |
| 14 | A | 14 | CYS | 0 | -0.031 | -0.006 | 2.608 | 10.980 | 12.878 | 0.391 | -0.718 | -1.570 | 0.000 |
| 15 | A | 15 | PRO | 0 | 0.051 | 0.030 | 1.946 | -35.284 | -34.209 | 6.154 | -3.895 | -3.334 | -0.045 |
| 16 | A | 16 | ASN | 0 | -0.018 | -0.014 | 4.105 | 0.263 | 0.460 | -0.001 | -0.006 | -0.189 | 0.000 |
| 17 | A | 17 | GLY | 0 | -0.013 | 0.006 | 2.853 | 9.433 | 9.798 | 0.227 | -0.103 | -0.489 | 0.000 |
| 18 | A | 18 | HIS | 0 | -0.076 | -0.061 | 2.558 | -20.997 | -18.860 | 2.632 | -1.908 | -2.860 | -0.022 |
| 19 | A | 19 | VAL | 0 | -0.031 | -0.018 | 2.793 | -0.078 | 1.823 | 0.981 | -0.803 | -2.079 | -0.009 |
| 20 | A | 21 | TYR | 0 | -0.046 | -0.051 | 4.084 | 3.114 | 3.247 | 0.000 | -0.012 | -0.121 | 0.000 |
| 39 | A | 42 | ALA | 0 | 0.019 | 0.005 | 4.420 | 4.118 | 4.195 | -0.001 | -0.004 | -0.071 | 0.000 |
| 40 | A | 43 | ALA | 0 | 0.066 | 0.040 | 4.607 | -5.048 | -4.946 | -0.001 | -0.005 | -0.097 | 0.000 |
| 53 | A | 57 | CYS | 0 | -0.031 | 0.005 | 4.434 | 4.644 | 4.920 | 0.005 | -0.028 | -0.253 | 0.000 |
| 54 | A | 58 | SER | 0 | 0.066 | 0.025 | 2.618 | -2.339 | -1.988 | 1.131 | -0.484 | -0.998 | 0.000 |
| 55 | A | 59 | THR | 0 | 0.002 | 0.008 | 2.895 | -2.439 | -2.328 | 0.821 | 0.234 | -1.165 | -0.003 |
| 56 | A | 60 | ASP | -1 | -0.787 | -0.909 | 2.581 | -76.615 | -72.145 | 2.684 | -3.152 | -4.002 | -0.036 |
| 57 | A | 61 | ASN | 0 | 0.005 | 0.002 | 3.678 | 4.333 | 4.403 | 0.010 | 0.096 | -0.176 | 0.000 |
| 5 | A | 5 | ILE | 0 | -0.007 | -0.011 | 6.597 | -1.295 | -1.295 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | THR | 0 | -0.027 | 0.009 | 9.718 | 1.404 | 1.404 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | PRO | 0 | -0.007 | -0.015 | 13.415 | -0.270 | -0.270 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | ASP | -1 | -0.902 | -0.950 | 12.895 | -19.244 | -19.244 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | ILE | 0 | -0.016 | -0.016 | 13.296 | -1.015 | -1.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | THR | 0 | -0.003 | -0.005 | 12.779 | -0.482 | -0.482 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | SER | 0 | -0.056 | -0.028 | 7.283 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | LYS | 1 | 0.876 | 0.938 | 7.461 | 26.480 | 26.480 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 22 | THR | 0 | 0.052 | 0.018 | 7.789 | -0.472 | -0.472 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 23 | LYS | 1 | 0.830 | 0.932 | 11.281 | 20.693 | 20.693 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 24 | THR | 0 | 0.026 | -0.013 | 14.497 | 0.556 | 0.556 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 25 | TRP | 0 | 0.011 | 0.011 | 17.493 | 0.353 | 0.353 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 26 | CYS | 0 | -0.017 | 0.008 | 21.433 | -0.221 | -0.221 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 27 | ASP | 0 | 0.007 | -0.001 | 25.022 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 28 | ALA | 0 | 0.057 | 0.016 | 27.796 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 29 | PHE | 0 | 0.037 | 0.014 | 29.362 | 0.157 | 0.157 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 31 | SER | 0 | 0.022 | 0.002 | 27.472 | -0.309 | -0.309 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 32 | ILE | 0 | -0.016 | 0.000 | 30.135 | 0.084 | 0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 33 | ARG | 1 | 0.913 | 0.958 | 26.612 | 10.356 | 10.356 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 34 | GLY | 0 | 0.060 | 0.051 | 24.195 | -0.292 | -0.292 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 35 | LYS | 1 | 0.851 | 0.904 | 19.567 | 13.645 | 13.645 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 36 | ARG | 1 | 0.920 | 0.970 | 21.229 | 12.715 | 12.715 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 37 | VAL | 0 | 0.069 | 0.035 | 14.963 | -0.104 | -0.104 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 38 | ASP | -1 | -0.842 | -0.906 | 13.450 | -19.815 | -19.815 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 39 | LEU | 0 | -0.016 | 0.004 | 10.214 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 40 | GLY | 0 | 0.071 | 0.030 | 8.086 | 0.864 | 0.864 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 44 | THR | 0 | 0.010 | 0.007 | 6.892 | 0.169 | 0.169 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 45 | CYS | 0 | -0.027 | -0.028 | 7.680 | -1.281 | -1.281 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 46 | PRO | 0 | -0.007 | 0.004 | 9.476 | 1.299 | 1.299 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 47 | THR | 0 | 0.033 | 0.004 | 12.324 | 0.392 | 0.392 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 48 | VAL | 0 | -0.002 | 0.010 | 15.873 | -0.148 | -0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 49 | LYS | 1 | 0.951 | 0.975 | 18.146 | 12.766 | 12.766 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 50 | THR | 0 | 0.072 | 0.017 | 21.658 | -0.290 | -0.290 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 51 | GLY | 0 | 0.009 | 0.012 | 23.704 | 0.211 | 0.211 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 52 | VAL | 0 | -0.087 | -0.041 | 17.642 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 53 | ASP | -1 | -0.871 | -0.930 | 17.545 | -14.118 | -14.118 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 54 | ILE | 0 | 0.044 | -0.004 | 11.177 | -0.343 | -0.343 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 55 | GLN | 0 | 0.008 | 0.020 | 10.116 | 0.803 | 0.803 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 63 | ASN | 0 | -0.016 | -0.005 | 6.216 | 0.242 | 0.242 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 64 | PRO | 0 | 0.043 | 0.026 | 8.472 | 0.296 | 0.296 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 65 | PHE | 0 | 0.000 | -0.015 | 11.663 | 0.181 | 0.181 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 66 | PRO | 0 | 0.004 | 0.042 | 14.016 | 0.396 | 0.396 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 67 | THR | 0 | -0.014 | -0.037 | 16.259 | 0.569 | 0.569 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | A | 68 | ARG | 1 | 0.935 | 0.982 | 20.038 | 11.541 | 11.541 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 69 | LYS | 0 | -0.093 | -0.040 | 17.869 | 0.318 | 0.318 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | A | 70 | ARG | 1 | 0.872 | 0.909 | 16.874 | 13.930 | 13.930 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | A | 71 | PRO | -1 | -0.828 | -0.895 | 16.342 | -15.605 | -15.605 | 0.000 | 0.000 | 0.000 | 0.000 |