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: 8GQ1Y
Calculation Name: 1D6T-A-Other547
Preferred Name: Ribonuclease P protein component
Target Type: SINGLE PROTEIN
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 1D6T
Chain ID: A
ChEMBL ID: CHEMBL4295710
UniProt ID: P0A0H5
Base Structure: SolutionNMR
Registration Date: 2025-09-02
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 | 117 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -1033328.354842 |
|---|---|
| FMO2-HF: Nuclear repulsion | 986284.692569 |
| FMO2-HF: Total energy | -47043.662273 |
| FMO2-MP2: Total energy | -47183.255468 |
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:MET)
Summations of interaction energy for
fragment #1(A:1:MET)
| 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. |
| 135.389 | 137.095 | -0.024 | -0.753 | -0.929 | 0 |
Interaction energy analysis for fragmet #1(A:1:MET)
| 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 | LEU | 0 | 0.038 | 0.036 | 3.843 | 2.469 | 4.175 | -0.024 | -0.753 | -0.929 | 0.000 |
| 4 | A | 4 | GLU | -1 | -0.765 | -0.879 | 7.066 | -24.519 | -24.519 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 5 | LYS | 1 | 0.846 | 0.887 | 9.814 | 21.662 | 21.662 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | ALA | 0 | 0.051 | 0.036 | 11.214 | 1.440 | 1.440 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | TYR | 0 | 0.004 | 0.002 | 11.765 | 0.946 | 0.946 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | ARG | 0 | -0.052 | -0.013 | 13.812 | 1.633 | 1.633 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | ILE | 0 | 0.023 | 0.027 | 17.234 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | LYS | 1 | 0.885 | 0.932 | 19.977 | 14.595 | 14.595 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | LYS | 1 | 0.966 | 0.987 | 22.145 | 13.296 | 13.296 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | ASN | 0 | 0.034 | 0.013 | 24.153 | -0.083 | -0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | ALA | 0 | 0.069 | 0.034 | 24.274 | 0.123 | 0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | ASP | -1 | -0.837 | -0.916 | 19.778 | -14.751 | -14.751 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | PHE | 0 | -0.013 | -0.020 | 22.776 | -0.120 | -0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | GLN | 0 | -0.018 | -0.001 | 25.643 | 0.513 | 0.513 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | ARG | 0 | 0.117 | 0.072 | 21.248 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | ILE | 0 | 0.020 | 0.000 | 23.407 | 0.319 | 0.319 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | TYR | 0 | -0.074 | -0.030 | 26.317 | 0.345 | 0.345 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | LYS | 0 | 0.011 | 0.053 | 28.781 | 0.331 | 0.331 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | LYS | 1 | 0.881 | 0.895 | 28.361 | 9.970 | 9.970 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | GLY | 0 | 0.040 | 0.045 | 26.781 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | HIS | 0 | -0.015 | 0.009 | 26.938 | 0.427 | 0.427 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | SER | 0 | -0.013 | -0.012 | 27.507 | -0.336 | -0.336 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | VAL | 0 | -0.002 | 0.003 | 29.111 | 0.294 | 0.294 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | ALA | 0 | 0.015 | -0.022 | 31.708 | -0.092 | -0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | ASN | 0 | -0.057 | 0.001 | 32.599 | 0.194 | 0.194 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | ARG | 1 | 0.967 | 0.977 | 34.145 | 9.120 | 9.120 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | GLN | 0 | -0.051 | -0.043 | 36.617 | 0.102 | 0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | PHE | 0 | -0.014 | -0.018 | 28.168 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | VAL | 0 | 0.022 | 0.011 | 31.329 | 0.164 | 0.164 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 32 | VAL | 0 | -0.022 | -0.011 | 26.132 | -0.265 | -0.265 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 33 | TYR | 0 | 0.021 | 0.002 | 26.420 | 0.359 | 0.359 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 34 | THR | 0 | -0.083 | -0.030 | 22.775 | -0.553 | -0.553 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 35 | CYS | -1 | -0.692 | -0.827 | 22.362 | -11.556 | -11.556 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 36 | ASN | 0 | -0.062 | -0.067 | 20.322 | -0.323 | -0.323 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 37 | ASN | 0 | -0.050 | -0.037 | 20.183 | -0.607 | -0.607 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 38 | LYS | 1 | 0.881 | 0.922 | 15.439 | 15.527 | 15.527 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 39 | GLU | -1 | -0.856 | -0.910 | 17.668 | -13.225 | -13.225 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 40 | ILE | 0 | -0.012 | 0.016 | 14.902 | -0.067 | -0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 41 | ASP | -1 | -0.879 | -0.937 | 8.866 | -26.810 | -26.810 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 42 | HIS | 0 | -0.026 | -0.040 | 9.829 | -1.119 | -1.119 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 43 | PHE | 0 | -0.025 | -0.010 | 11.315 | 1.529 | 1.529 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 44 | ARG | 1 | 0.754 | 0.832 | 15.068 | 15.361 | 15.361 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 45 | LEU | 0 | 0.011 | 0.018 | 17.181 | 1.069 | 1.069 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 46 | GLY | 0 | 0.017 | 0.003 | 19.062 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 47 | ILE | 0 | -0.020 | -0.027 | 22.642 | 0.276 | 0.276 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 48 | SER | 0 | -0.026 | -0.015 | 25.722 | 0.230 | 0.230 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 49 | VAL | 0 | -0.035 | -0.031 | 29.350 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 50 | SER | 0 | 0.026 | 0.029 | 32.935 | 0.131 | 0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 51 | LYS | 1 | 1.025 | 0.995 | 36.519 | 7.855 | 7.855 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 52 | LYS | 1 | 0.990 | 1.001 | 39.149 | 7.203 | 7.203 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 53 | LEU | 0 | -0.059 | -0.004 | 35.784 | 0.090 | 0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 54 | GLY | 0 | 0.071 | 0.022 | 39.860 | 0.095 | 0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 55 | ASN | 0 | 0.089 | 0.050 | 40.292 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 56 | ALA | 0 | 0.063 | 0.024 | 35.931 | -0.214 | -0.214 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 57 | VAL | 0 | 0.034 | 0.014 | 34.992 | -0.346 | -0.346 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 58 | LEU | 0 | -0.005 | 0.007 | 35.191 | -0.261 | -0.261 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 59 | ARG | 0 | -0.009 | -0.026 | 34.132 | -0.329 | -0.329 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 60 | ASN | 0 | 0.013 | 0.018 | 30.613 | -0.725 | -0.725 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 61 | LYS | 1 | 0.925 | 0.983 | 30.434 | 8.893 | 8.893 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 62 | ILE | 0 | 0.059 | 0.014 | 30.671 | -0.343 | -0.343 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | A | 63 | LYS | 1 | 0.971 | 0.994 | 27.208 | 10.373 | 10.373 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 64 | ARG | 1 | 0.845 | 0.919 | 26.112 | 10.131 | 10.131 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | A | 65 | ALA | 0 | 0.055 | 0.036 | 26.055 | -0.400 | -0.400 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | A | 66 | ILE | 0 | 0.007 | 0.009 | 24.455 | -0.257 | -0.257 | 0.000 | 0.000 | 0.000 | 0.000 |
| 67 | A | 67 | ARG | 1 | 0.884 | 0.931 | 21.923 | 12.138 | 12.138 | 0.000 | 0.000 | 0.000 | 0.000 |
| 68 | A | 68 | GLU | -1 | -0.897 | -0.943 | 21.446 | -14.018 | -14.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 69 | A | 69 | ASN | 0 | 0.004 | -0.008 | 22.413 | -0.515 | -0.515 | 0.000 | 0.000 | 0.000 | 0.000 |
| 70 | A | 70 | PHE | 0 | 0.022 | -0.011 | 19.374 | -0.345 | -0.345 | 0.000 | 0.000 | 0.000 | 0.000 |
| 71 | A | 71 | LYS | 1 | 0.940 | 0.980 | 16.696 | 16.764 | 16.764 | 0.000 | 0.000 | 0.000 | 0.000 |
| 72 | A | 72 | VAL | 0 | 0.028 | 0.022 | 17.258 | -1.177 | -1.177 | 0.000 | 0.000 | 0.000 | 0.000 |
| 73 | A | 73 | HIS | 0 | 0.037 | 0.002 | 17.968 | -1.285 | -1.285 | 0.000 | 0.000 | 0.000 | 0.000 |
| 74 | A | 74 | LYS | 1 | 0.952 | 0.991 | 11.353 | 24.831 | 24.831 | 0.000 | 0.000 | 0.000 | 0.000 |
| 75 | A | 75 | SER | 0 | -0.017 | -0.015 | 12.040 | -1.548 | -1.548 | 0.000 | 0.000 | 0.000 | 0.000 |
| 76 | A | 76 | HIS | 0 | -0.055 | -0.010 | 14.153 | 0.727 | 0.727 | 0.000 | 0.000 | 0.000 | 0.000 |
| 77 | A | 77 | ILE | 0 | -0.031 | -0.026 | 15.551 | 0.892 | 0.892 | 0.000 | 0.000 | 0.000 | 0.000 |
| 78 | A | 78 | LEU | 0 | -0.041 | -0.008 | 13.945 | -1.214 | -1.214 | 0.000 | 0.000 | 0.000 | 0.000 |
| 79 | A | 79 | ALA | 0 | -0.014 | -0.008 | 12.625 | 0.791 | 0.791 | 0.000 | 0.000 | 0.000 | 0.000 |
| 80 | A | 80 | LYS | 1 | 0.826 | 0.915 | 14.710 | 13.782 | 13.782 | 0.000 | 0.000 | 0.000 | 0.000 |
| 81 | A | 81 | ASP | -1 | -0.767 | -0.859 | 18.036 | -13.864 | -13.864 | 0.000 | 0.000 | 0.000 | 0.000 |
| 82 | A | 82 | ILE | 0 | 0.005 | 0.003 | 18.134 | 0.530 | 0.530 | 0.000 | 0.000 | 0.000 | 0.000 |
| 83 | A | 83 | ILE | 0 | 0.002 | 0.019 | 21.064 | -0.235 | -0.235 | 0.000 | 0.000 | 0.000 | 0.000 |
| 84 | A | 84 | VAL | 0 | -0.032 | -0.007 | 24.013 | 0.376 | 0.376 | 0.000 | 0.000 | 0.000 | 0.000 |
| 85 | A | 85 | ILE | 0 | 0.008 | -0.009 | 26.749 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 86 | A | 86 | ALA | 0 | -0.038 | -0.014 | 30.260 | 0.221 | 0.221 | 0.000 | 0.000 | 0.000 | 0.000 |
| 87 | A | 87 | ARG | 1 | 0.938 | 0.976 | 33.410 | 8.185 | 8.185 | 0.000 | 0.000 | 0.000 | 0.000 |
| 88 | A | 88 | GLN | 0 | 0.044 | -0.012 | 36.296 | 0.210 | 0.210 | 0.000 | 0.000 | 0.000 | 0.000 |
| 89 | A | 89 | PRO | 0 | 0.020 | 0.002 | 39.070 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
| 90 | A | 90 | ALA | 0 | 0.074 | 0.019 | 35.240 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
| 91 | A | 91 | LYS | 1 | 0.922 | 0.973 | 36.992 | 7.180 | 7.180 | 0.000 | 0.000 | 0.000 | 0.000 |
| 92 | A | 92 | ASP | -1 | -0.836 | -0.911 | 38.996 | -8.016 | -8.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 93 | A | 93 | MET | 0 | -0.058 | 0.007 | 33.834 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
| 94 | A | 94 | THR | 0 | 0.067 | 0.023 | 36.298 | -0.216 | -0.216 | 0.000 | 0.000 | 0.000 | 0.000 |
| 95 | A | 95 | THR | 0 | -0.006 | -0.042 | 30.230 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
| 96 | A | 96 | LEU | 0 | 0.067 | 0.062 | 31.623 | -0.355 | -0.355 | 0.000 | 0.000 | 0.000 | 0.000 |
| 97 | A | 97 | GLN | 0 | 0.068 | 0.025 | 33.188 | -0.171 | -0.171 | 0.000 | 0.000 | 0.000 | 0.000 |
| 98 | A | 98 | ILE | 0 | -0.008 | -0.002 | 29.997 | -0.125 | -0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
| 99 | A | 99 | GLN | 0 | -0.002 | 0.003 | 27.294 | -0.640 | -0.640 | 0.000 | 0.000 | 0.000 | 0.000 |
| 100 | A | 100 | ASN | 0 | 0.080 | 0.036 | 29.476 | -0.386 | -0.386 | 0.000 | 0.000 | 0.000 | 0.000 |
| 101 | A | 101 | SER | 0 | -0.057 | -0.031 | 31.364 | 0.344 | 0.344 | 0.000 | 0.000 | 0.000 | 0.000 |
| 102 | A | 102 | LEU | 0 | -0.026 | -0.008 | 24.881 | 0.099 | 0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
| 103 | A | 103 | GLU | -1 | -0.814 | -0.901 | 27.664 | -10.724 | -10.724 | 0.000 | 0.000 | 0.000 | 0.000 |
| 104 | A | 104 | HIS | 0 | -0.054 | -0.021 | 29.095 | 0.361 | 0.361 | 0.000 | 0.000 | 0.000 | 0.000 |
| 105 | A | 105 | VAL | 0 | -0.028 | -0.031 | 28.355 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
| 106 | A | 106 | LEU | 0 | 0.028 | 0.021 | 22.519 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 107 | A | 107 | LYS | 1 | 0.954 | 0.980 | 25.299 | 9.570 | 9.570 | 0.000 | 0.000 | 0.000 | 0.000 |
| 108 | A | 108 | ILE | 0 | -0.048 | -0.023 | 27.195 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 109 | A | 109 | ALA | 0 | -0.007 | 0.005 | 24.537 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 110 | A | 110 | LYS | 1 | 0.983 | 0.994 | 23.307 | 11.132 | 11.132 | 0.000 | 0.000 | 0.000 | 0.000 |
| 111 | A | 111 | VAL | 0 | -0.008 | 0.009 | 19.799 | -0.400 | -0.400 | 0.000 | 0.000 | 0.000 | 0.000 |
| 112 | A | 112 | PHE | 0 | 0.032 | -0.013 | 19.763 | -0.422 | -0.422 | 0.000 | 0.000 | 0.000 | 0.000 |
| 113 | A | 113 | ASN | 0 | -0.004 | 0.001 | 15.248 | 0.555 | 0.555 | 0.000 | 0.000 | 0.000 | 0.000 |
| 114 | A | 114 | LYS | 1 | 0.963 | 0.969 | 19.400 | 12.045 | 12.045 | 0.000 | 0.000 | 0.000 | 0.000 |
| 115 | A | 115 | LYS | 1 | 0.798 | 0.927 | 22.323 | 11.663 | 11.663 | 0.000 | 0.000 | 0.000 | 0.000 |
| 116 | A | 116 | ILE | 0 | 0.040 | 0.022 | 21.217 | 0.358 | 0.358 | 0.000 | 0.000 | 0.000 | 0.000 |
| 117 | A | 117 | LYS | 0 | 0.064 | 0.037 | 24.580 | -1.276 | -1.276 | 0.000 | 0.000 | 0.000 | 0.000 |