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: JKV19
Calculation Name: 6N1D-A-Xray547
Preferred Name:
Target Type:
Ligand Name: 2-amino-7-deaza-(2'',3''-dihydroxy-cyclopentylamino)-guanosine-5'-monophosphate | 2-methylthio-n6-isopentenyl-adenosine-5'-monophosphate | 5-(carboxymethoxy) uridine-5'-monophosphate | n7-methyl-guanosine-5'-monophosphate | n6-methyladenosine-5'-monophosphate | pseudouridine-5'-monophosphate | 5-methyluridine 5'-monophosphate | 4-thiouridine-5'-monophosphate | iron/sulfur cluster | magnesium ion
Ligand 3-letter code: QUO | MIA | CM0 | G7M | 6MZ | PSU | 5MU | 4SU | SF4 | MG
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 6N1D
Chain ID: A
UniProt ID: P60493
Base Structure: X-ray
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 | 101 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -622477.611993 |
|---|---|
| FMO2-HF: Nuclear repulsion | 584776.696154 |
| FMO2-HF: Total energy | -37700.915839 |
| FMO2-MP2: Total energy | -37813.495416 |
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. |
| -11.98 | -3.076 | 7.669 | -7.231 | -9.339 | -0.071 |
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 | ALA | 0 | 0.091 | 0.052 | 3.842 | 0.077 | 1.453 | -0.013 | -0.540 | -0.822 | 0.002 |
| 15 | A | 15 | GLU | -1 | -0.843 | -0.913 | 3.472 | -60.000 | -59.571 | 0.002 | -0.109 | -0.321 | 0.000 |
| 16 | A | 16 | PRO | 0 | -0.026 | -0.015 | 3.681 | 5.276 | 5.659 | 0.005 | -0.057 | -0.331 | 0.000 |
| 42 | A | 42 | GLY | 0 | -0.147 | -0.047 | 2.097 | 2.472 | 2.266 | 2.998 | -1.879 | -0.913 | 0.004 |
| 43 | A | 43 | GLU | -1 | -0.808 | -0.923 | 2.347 | -92.398 | -85.932 | 4.581 | -4.540 | -6.507 | -0.076 |
| 44 | A | 44 | LYS | 1 | 0.898 | 0.953 | 5.256 | 33.417 | 33.435 | -0.001 | -0.002 | -0.015 | 0.000 |
| 99 | A | 99 | ILE | 0 | -0.055 | -0.033 | 3.084 | 0.453 | 0.891 | 0.097 | -0.104 | -0.430 | -0.001 |
| 4 | A | 4 | ILE | 0 | -0.041 | -0.009 | 6.081 | 2.453 | 2.453 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 5 | VAL | 0 | 0.044 | 0.024 | 9.772 | 0.590 | 0.590 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | LYS | 1 | 0.953 | 0.973 | 12.441 | 16.729 | 16.729 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | THR | 0 | 0.036 | 0.016 | 16.188 | 0.941 | 0.941 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | GLY | 0 | 0.065 | 0.033 | 18.710 | 0.077 | 0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | GLY | 0 | -0.021 | -0.015 | 22.166 | 0.377 | 0.377 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | LYS | 1 | 0.801 | 0.906 | 19.743 | 13.676 | 13.676 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | GLN | 0 | 0.028 | 0.002 | 15.397 | 0.193 | 0.193 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | TYR | 0 | -0.007 | -0.004 | 13.940 | 0.894 | 0.894 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | ARG | 1 | 0.880 | 0.944 | 5.711 | 39.941 | 39.941 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | VAL | 0 | -0.016 | -0.017 | 7.680 | 1.812 | 1.812 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | GLY | 0 | 0.064 | 0.025 | 6.489 | 0.127 | 0.127 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | LEU | 0 | -0.042 | -0.011 | 9.556 | 2.204 | 2.204 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | LYS | 1 | 0.968 | 0.984 | 12.614 | 15.447 | 15.447 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | LEU | 0 | -0.018 | -0.005 | 13.983 | -0.233 | -0.233 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | ARG | 1 | 0.868 | 0.945 | 16.493 | 14.425 | 14.425 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | VAL | 0 | 0.037 | 0.028 | 17.462 | -0.328 | -0.328 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | GLU | -1 | -0.813 | -0.902 | 20.564 | -11.566 | -11.566 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | LYS | 1 | 0.908 | 0.960 | 23.058 | 9.909 | 9.909 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | LEU | 0 | 0.033 | 0.010 | 21.904 | -0.105 | -0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | ASP | -1 | -0.940 | -0.960 | 25.657 | -10.073 | -10.073 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | ALA | 0 | -0.020 | -0.008 | 24.678 | -0.099 | -0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | GLU | -1 | -0.874 | -0.938 | 26.591 | -10.765 | -10.765 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | PRO | 0 | -0.045 | -0.042 | 25.450 | -0.418 | -0.418 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | GLY | 0 | 0.001 | 0.017 | 24.701 | -0.390 | -0.390 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | ALA | 0 | 0.050 | 0.024 | 23.022 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 32 | THR | 0 | -0.031 | -0.037 | 16.819 | -0.844 | -0.844 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 33 | VAL | 0 | -0.043 | -0.015 | 17.343 | 0.619 | 0.619 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 34 | GLU | -1 | -0.881 | -0.946 | 15.307 | -17.696 | -17.696 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 35 | LEU | 0 | -0.074 | -0.043 | 13.502 | 0.956 | 0.956 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 36 | PRO | 0 | 0.122 | 0.050 | 13.151 | -1.596 | -1.596 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 37 | VAL | 0 | -0.083 | -0.025 | 14.623 | -0.087 | -0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 38 | LEU | 0 | 0.009 | 0.008 | 7.214 | -0.352 | -0.352 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 39 | LEU | 0 | -0.056 | -0.040 | 10.557 | 1.570 | 1.570 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 40 | LEU | 0 | -0.005 | -0.017 | 7.806 | -2.676 | -2.676 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 41 | GLY | 0 | 0.105 | 0.051 | 4.929 | 0.173 | 0.173 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 45 | THR | 0 | 0.034 | 0.024 | 7.352 | 0.912 | 0.912 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 46 | VAL | 0 | -0.020 | -0.016 | 9.004 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 47 | VAL | 0 | -0.003 | 0.005 | 12.006 | 0.201 | 0.201 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 48 | GLY | 0 | 0.025 | 0.018 | 14.502 | 0.499 | 0.499 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 49 | THR | 0 | 0.001 | -0.014 | 17.578 | 0.783 | 0.783 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 50 | PRO | 0 | -0.038 | -0.029 | 17.605 | -0.707 | -0.707 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 51 | VAL | 0 | -0.025 | -0.014 | 15.844 | -0.893 | -0.893 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 52 | VAL | 0 | 0.019 | 0.028 | 11.023 | 0.504 | 0.504 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 53 | GLU | -1 | -0.924 | -0.962 | 14.277 | -15.811 | -15.811 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 54 | GLY | 0 | -0.022 | -0.013 | 15.153 | -0.297 | -0.297 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 55 | ALA | 0 | 0.011 | 0.021 | 9.793 | -0.095 | -0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 56 | SER | 0 | -0.047 | -0.031 | 10.648 | 1.150 | 1.150 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 57 | VAL | 0 | -0.035 | -0.022 | 8.658 | -2.588 | -2.588 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 58 | VAL | 0 | 0.001 | 0.009 | 10.327 | 2.099 | 2.099 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 59 | ALA | 0 | -0.030 | -0.028 | 12.048 | -1.514 | -1.514 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 60 | GLU | -1 | -0.868 | -0.920 | 14.495 | -15.013 | -15.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 61 | VAL | 0 | -0.076 | -0.025 | 17.346 | -0.447 | -0.447 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 62 | LEU | 0 | 0.006 | 0.002 | 20.297 | -0.219 | -0.219 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | A | 63 | GLY | 0 | 0.087 | 0.041 | 22.747 | 0.613 | 0.613 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 64 | HIS | 0 | -0.016 | -0.015 | 24.658 | -0.258 | -0.258 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | A | 65 | GLY | 0 | 0.048 | 0.014 | 27.290 | 0.360 | 0.360 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | A | 66 | ARG | 1 | 0.834 | 0.913 | 29.441 | 9.517 | 9.517 | 0.000 | 0.000 | 0.000 | 0.000 |
| 67 | A | 67 | GLY | 0 | 0.106 | 0.074 | 28.563 | -0.112 | -0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
| 68 | A | 68 | LYS | 1 | 0.970 | 0.971 | 29.167 | 9.992 | 9.992 | 0.000 | 0.000 | 0.000 | 0.000 |
| 69 | A | 69 | LYS | 1 | 0.916 | 0.968 | 32.021 | 7.996 | 7.996 | 0.000 | 0.000 | 0.000 | 0.000 |
| 70 | A | 70 | ILE | 0 | 0.034 | 0.018 | 32.428 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
| 71 | A | 71 | LEU | 0 | -0.023 | -0.013 | 35.651 | 0.129 | 0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
| 72 | A | 72 | VAL | 0 | 0.038 | 0.012 | 37.095 | -0.070 | -0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
| 73 | A | 73 | SER | 0 | -0.061 | -0.048 | 39.807 | 0.212 | 0.212 | 0.000 | 0.000 | 0.000 | 0.000 |
| 74 | A | 74 | LYS | 1 | 0.951 | 0.974 | 41.798 | 7.507 | 7.507 | 0.000 | 0.000 | 0.000 | 0.000 |
| 75 | A | 75 | PHE | 0 | 0.046 | 0.010 | 45.145 | 0.146 | 0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
| 76 | A | 76 | LYS | 1 | 0.926 | 0.970 | 47.594 | 6.540 | 6.540 | 0.000 | 0.000 | 0.000 | 0.000 |
| 77 | A | 77 | ALA | 0 | 0.084 | 0.043 | 50.199 | 0.103 | 0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
| 78 | A | 78 | LYS | 1 | 0.994 | 1.000 | 52.481 | 5.692 | 5.692 | 0.000 | 0.000 | 0.000 | 0.000 |
| 79 | A | 79 | VAL | 0 | 0.011 | 0.007 | 54.916 | 0.084 | 0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
| 80 | A | 80 | GLN | 0 | 0.058 | 0.024 | 55.704 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 81 | A | 81 | TYR | 0 | -0.038 | -0.015 | 47.641 | -0.100 | -0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
| 82 | A | 82 | ARG | 1 | 1.012 | 1.000 | 50.028 | 5.810 | 5.810 | 0.000 | 0.000 | 0.000 | 0.000 |
| 83 | A | 83 | ARG | 1 | 0.938 | 0.974 | 46.886 | 6.497 | 6.497 | 0.000 | 0.000 | 0.000 | 0.000 |
| 84 | A | 84 | LYS | 1 | 1.028 | 1.039 | 44.462 | 6.863 | 6.863 | 0.000 | 0.000 | 0.000 | 0.000 |
| 85 | A | 85 | LYS | 1 | 0.975 | 0.973 | 41.452 | 7.309 | 7.309 | 0.000 | 0.000 | 0.000 | 0.000 |
| 86 | A | 86 | GLY | 0 | 0.035 | 0.015 | 39.079 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
| 87 | A | 87 | HIS | 0 | 0.003 | 0.025 | 32.625 | 0.421 | 0.421 | 0.000 | 0.000 | 0.000 | 0.000 |
| 88 | A | 88 | ARG | 1 | 0.937 | 0.952 | 32.869 | 8.943 | 8.943 | 0.000 | 0.000 | 0.000 | 0.000 |
| 89 | A | 89 | GLN | 0 | 0.024 | 0.013 | 27.851 | 0.534 | 0.534 | 0.000 | 0.000 | 0.000 | 0.000 |
| 90 | A | 90 | PRO | 0 | -0.041 | -0.023 | 29.004 | -0.128 | -0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
| 91 | A | 91 | TYR | 0 | -0.113 | -0.091 | 22.772 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
| 92 | A | 92 | THR | 0 | 0.011 | 0.000 | 21.232 | 0.266 | 0.266 | 0.000 | 0.000 | 0.000 | 0.000 |
| 93 | A | 93 | GLU | -1 | -0.872 | -0.914 | 20.981 | -12.848 | -12.848 | 0.000 | 0.000 | 0.000 | 0.000 |
| 94 | A | 94 | LEU | 0 | 0.037 | 0.021 | 16.141 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 95 | A | 95 | LEU | 0 | -0.008 | -0.004 | 13.329 | -0.441 | -0.441 | 0.000 | 0.000 | 0.000 | 0.000 |
| 96 | A | 96 | ILE | 0 | -0.018 | -0.008 | 9.134 | 0.323 | 0.323 | 0.000 | 0.000 | 0.000 | 0.000 |
| 97 | A | 97 | LYS | 1 | 0.910 | 0.963 | 10.876 | 20.067 | 20.067 | 0.000 | 0.000 | 0.000 | 0.000 |
| 98 | A | 98 | GLU | -1 | -0.921 | -0.968 | 7.986 | -25.184 | -25.184 | 0.000 | 0.000 | 0.000 | 0.000 |
| 100 | A | 100 | ARG | 1 | 0.980 | 1.001 | 6.980 | 17.934 | 17.934 | 0.000 | 0.000 | 0.000 | 0.000 |
| 101 | A | 101 | GLY | -1 | -0.873 | -0.918 | 9.609 | -20.486 | -20.486 | 0.000 | 0.000 | 0.000 | 0.000 |