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: 1VNLZ
Calculation Name: 5IT7-A-Other547
Preferred Name:
Target Type:
Ligand Name: phosphomethylphosphonic acid guanylate ester | (2s)-1-amino-n,n,n-trimethyl-1-oxobutan-2-aminium
Ligand 3-letter code: GCP | 6EM
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 5IT7
Chain ID: A
UniProt ID: P38665
Base Structure: ElectronMicroscopy
Registration Date: 2025-10-06
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 | 51 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -249754.098303 |
|---|---|
| FMO2-HF: Nuclear repulsion | 228245.269763 |
| FMO2-HF: Total energy | -21508.82854 |
| FMO2-MP2: Total energy | -21568.325822 |
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:78:ILE)
Summations of interaction energy for
fragment #1(A:78: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. |
| 215.906 | 220.572 | 2.213 | -1.787 | -5.091 | -0.01 |
Interaction energy analysis for fragmet #1(A:78: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 | 80 | PRO | 0 | -0.015 | -0.017 | 2.885 | -1.286 | 1.282 | 0.260 | -1.271 | -1.557 | -0.008 |
| 4 | A | 81 | SER | 0 | 0.065 | 0.035 | 5.229 | 1.047 | 1.182 | -0.001 | -0.007 | -0.126 | 0.000 |
| 5 | A | 82 | LEU | 0 | 0.092 | 0.045 | 2.943 | 3.501 | 4.030 | 0.059 | -0.126 | -0.462 | 0.000 |
| 6 | A | 83 | LYS | 1 | 0.946 | 0.975 | 2.352 | 39.311 | 41.009 | 1.804 | -0.750 | -2.752 | -0.002 |
| 7 | A | 84 | ALA | 0 | -0.001 | 0.016 | 3.389 | 4.945 | 4.681 | 0.091 | 0.367 | -0.194 | 0.000 |
| 8 | A | 85 | LEU | 0 | 0.008 | 0.009 | 6.518 | 2.875 | 2.875 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 86 | ALA | 0 | 0.048 | 0.010 | 5.102 | 2.758 | 2.758 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 87 | SER | 0 | -0.030 | -0.029 | 6.279 | 2.538 | 2.538 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 88 | LYS | 1 | 0.950 | 0.985 | 8.447 | 22.536 | 22.536 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 89 | TYR | 0 | 0.010 | 0.012 | 10.587 | 2.011 | 2.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 90 | ASN | 0 | -0.097 | -0.034 | 9.011 | 2.873 | 2.873 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 91 | CYS | -1 | -0.778 | -0.904 | 10.501 | -20.451 | -20.451 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 92 | GLU | -1 | -0.938 | -0.965 | 11.044 | -19.549 | -19.549 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 93 | LYS | 1 | 0.803 | 0.886 | 14.045 | 17.474 | 17.474 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 94 | SER | 0 | 0.026 | 0.014 | 17.051 | -0.071 | -0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 95 | VAL | 0 | -0.044 | -0.032 | 19.520 | -0.333 | -0.333 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 96 | CYS | 0 | -0.045 | -0.003 | 22.215 | 0.446 | 0.446 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 97 | ARG | 1 | 0.900 | 0.933 | 25.790 | 10.191 | 10.191 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 98 | LYS | 1 | 0.945 | 0.977 | 27.298 | 8.624 | 8.624 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 99 | CYS | 0 | -0.003 | -0.019 | 28.331 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 100 | TYR | 0 | 0.041 | 0.025 | 23.503 | -0.324 | -0.324 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 101 | ALA | 0 | -0.014 | -0.002 | 22.637 | -0.520 | -0.520 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 102 | ARG | 1 | 0.981 | 0.988 | 15.767 | 16.032 | 16.032 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 103 | LEU | 0 | -0.038 | -0.023 | 20.593 | 0.335 | 0.335 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 104 | PRO | 0 | 0.027 | 0.008 | 19.767 | -0.675 | -0.675 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 105 | PRO | 0 | 0.005 | -0.005 | 17.798 | 0.538 | 0.538 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 106 | ARG | 1 | 1.000 | 1.003 | 18.893 | 13.520 | 13.520 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 107 | ALA | 0 | -0.048 | -0.002 | 23.868 | 0.383 | 0.383 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 108 | THR | 0 | 0.086 | 0.030 | 25.894 | -0.172 | -0.172 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 109 | ASN | 0 | 0.006 | 0.003 | 28.911 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 110 | CYS | 0 | -0.095 | -0.032 | 27.413 | -0.444 | -0.444 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 111 | ARG | 1 | 1.008 | 0.997 | 22.505 | 11.980 | 11.980 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 112 | LYS | 1 | 0.967 | 0.966 | 25.425 | 11.034 | 11.034 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 113 | ARG | 1 | 1.093 | 1.046 | 30.239 | 7.789 | 7.789 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 114 | LYS | 1 | 0.941 | 0.971 | 29.932 | 9.582 | 9.582 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 115 | CYS | 0 | -0.049 | -0.018 | 31.220 | -0.120 | -0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 116 | GLY | 0 | 0.080 | 0.045 | 33.516 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 117 | HIS | 0 | 0.022 | 0.003 | 32.196 | 0.158 | 0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 118 | THR | 0 | 0.037 | 0.038 | 30.873 | -0.058 | -0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 119 | ASN | 0 | 0.130 | 0.055 | 30.535 | -0.287 | -0.287 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 120 | GLN | 0 | 0.034 | 0.032 | 30.218 | -0.068 | -0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 121 | LEU | 0 | -0.011 | -0.001 | 25.251 | -0.253 | -0.253 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 122 | ARG | 1 | 0.921 | 0.962 | 19.662 | 12.853 | 12.853 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 123 | PRO | 0 | 0.099 | 0.041 | 19.351 | -0.216 | -0.216 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 124 | LYS | 1 | 0.861 | 0.946 | 13.394 | 17.849 | 17.849 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 125 | LYS | 1 | 0.948 | 0.966 | 16.301 | 12.419 | 12.419 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 126 | LYS | 1 | 0.900 | 0.948 | 11.735 | 17.335 | 17.335 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 127 | LEU | 0 | 0.016 | 0.006 | 7.247 | 0.692 | 0.692 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 128 | LYS | 0 | 0.080 | 0.057 | 7.411 | 7.053 | 7.053 | 0.000 | 0.000 | 0.000 | 0.000 |