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: 1VK7Z
Calculation Name: 1J34-C-Xray549
Preferred Name:
Target Type:
Ligand Name: gamma-carboxy-glutamic acid
Ligand 3-letter code: CGU
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 1J34
Chain ID: C
UniProt ID: P00741
Base Structure: X-ray
Registration Date: 2025-10-11
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 | OptH |
| Protonation | MOE:Protonate 3D |
| Complement | ac.sh, 23 2024 Oct |
| Water | No |
| Procedure | Manual calculation |
| Remarks |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 45 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -231495.10634 |
|---|---|
| FMO2-HF: Nuclear repulsion | 212726.136314 |
| FMO2-HF: Total energy | -18768.970026 |
| FMO2-MP2: Total energy | -18824.099363 |
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(C:401:TYR)
Summations of interaction energy for
fragment #1(C:401:TYR)
| 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. |
| 101.66 | 114.239 | 17.803 | -11.875 | -18.506 | -0.107 |
Interaction energy analysis for fragmet #1(C:401:TYR)
| 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 | C | 403 | SER | 0 | 0.048 | 0.020 | 2.632 | 0.075 | 4.571 | 1.567 | -1.882 | -4.182 | 0.003 |
| 4 | C | 404 | GLY | 0 | 0.021 | 0.021 | 3.592 | 3.852 | 3.884 | 0.026 | 0.307 | -0.365 | 0.001 |
| 17 | C | 417 | LEU | 0 | -0.030 | -0.023 | 2.889 | -7.379 | -6.598 | 0.123 | -0.250 | -0.654 | -0.001 |
| 18 | C | 418 | CYS | 0 | -0.116 | -0.056 | 1.928 | -65.168 | -61.062 | 10.074 | -6.853 | -7.327 | -0.084 |
| 19 | C | 419 | LYS | 1 | 0.989 | 1.009 | 5.077 | 30.072 | 30.114 | -0.001 | -0.001 | -0.040 | 0.000 |
| 21 | C | 421 | LEU | 0 | -0.025 | -0.009 | 2.249 | -10.363 | -9.775 | 5.501 | -2.205 | -3.884 | -0.017 |
| 22 | C | 422 | LYS | 1 | 1.039 | 1.033 | 3.167 | 38.677 | 40.147 | 0.053 | -0.520 | -1.003 | -0.003 |
| 23 | C | 424 | SER | 0 | 0.061 | 0.026 | 3.678 | 8.503 | 8.699 | 0.005 | -0.064 | -0.136 | -0.001 |
| 26 | C | 427 | LEU | 0 | -0.027 | -0.007 | 2.354 | -2.243 | -1.375 | 0.455 | -0.407 | -0.915 | -0.005 |
| 5 | C | 405 | LYS | 1 | 0.927 | 0.952 | 6.350 | 28.747 | 28.747 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | C | 406 | LEU | 0 | 0.096 | 0.050 | 9.175 | -0.834 | -0.834 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | C | 407 | LEU | 0 | -0.041 | -0.019 | 4.896 | 0.174 | 0.174 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | C | 408 | LEU | 0 | -0.044 | -0.027 | 5.970 | -2.034 | -2.034 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | C | 409 | PHE | 0 | 0.049 | 0.031 | 9.553 | 1.396 | 1.396 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | C | 410 | VAL | 0 | -0.005 | 0.013 | 10.053 | 1.462 | 1.462 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | C | 411 | ARG | 1 | 1.005 | 1.003 | 10.555 | 17.011 | 17.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | C | 412 | GLY | 0 | 0.043 | 0.029 | 8.090 | -2.310 | -2.310 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | C | 413 | ASN | 0 | 0.024 | -0.006 | 7.516 | 1.642 | 1.642 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | C | 414 | LEU | 0 | 0.060 | 0.029 | 7.169 | -5.041 | -5.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | C | 415 | LEU | 0 | 0.049 | 0.031 | 7.785 | -2.930 | -2.930 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | C | 416 | ARG | 1 | 0.934 | 0.950 | 5.660 | 33.456 | 33.456 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | C | 420 | LEU | 0 | 0.040 | 0.026 | 6.742 | 1.874 | 1.874 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | C | 425 | PHE | 0 | 0.098 | 0.037 | 6.609 | -1.062 | -1.062 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | C | 426 | LEU | 0 | 0.023 | 0.005 | 9.029 | 0.965 | 0.965 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | C | 428 | ALA | 0 | 0.064 | 0.030 | 6.407 | 1.683 | 1.683 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | C | 429 | ARG | 1 | 0.927 | 0.975 | 8.634 | 23.857 | 23.857 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | C | 430 | LEU | 0 | -0.035 | -0.024 | 8.374 | 2.154 | 2.154 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | C | 431 | VAL | 0 | -0.081 | -0.026 | 8.304 | 0.634 | 0.634 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | C | 432 | PHE | 0 | -0.016 | -0.021 | 10.979 | 1.798 | 1.798 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | C | 433 | LEU | 0 | -0.024 | 0.001 | 13.637 | 1.504 | 1.504 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | C | 434 | ASN | 0 | 0.083 | 0.044 | 15.578 | 0.902 | 0.902 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | C | 435 | THR | 0 | 0.061 | 0.028 | 16.139 | -1.193 | -1.193 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | C | 436 | LEU | 0 | 0.062 | 0.061 | 17.143 | -0.591 | -0.591 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | C | 437 | LYS | 1 | 0.961 | 0.971 | 16.746 | 15.521 | 15.521 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | C | 438 | THR | 0 | -0.017 | -0.023 | 11.654 | -1.064 | -1.064 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | C | 439 | THR | 0 | -0.020 | -0.024 | 14.039 | -0.956 | -0.956 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | C | 440 | LEU | 0 | -0.056 | -0.029 | 16.581 | 0.131 | 0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | C | 441 | PHE | 0 | 0.019 | 0.003 | 8.597 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | C | 442 | TRP | 0 | 0.031 | -0.006 | 8.218 | -1.522 | -1.522 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | C | 443 | LYS | 1 | 0.959 | 0.969 | 13.450 | 14.770 | 14.770 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | C | 444 | GLN | 0 | -0.038 | -0.011 | 15.336 | 1.141 | 1.141 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | C | 445 | TYR | 0 | -0.106 | -0.054 | 5.906 | -3.910 | -3.910 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | C | 446 | VAL | -1 | -0.903 | -0.930 | 11.664 | -21.761 | -21.761 | 0.000 | 0.000 | 0.000 | 0.000 |