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: 7MLKK
Calculation Name: 2XV5-A-Xray540
Preferred Name: Prelamin-A/C
Target Type: SINGLE PROTEIN
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 2XV5
Chain ID: A
ChEMBL ID: CHEMBL1293235
UniProt ID: P02545
Base Structure: X-ray
Registration Date: 2025-07-10
Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.
Apendix: None
Modeling method
| Optimization | MOE:Amber10:EHT |
|---|---|
| Restraint | OptAll |
| Protonation | MOE:Protonate 3D |
| Complement | MOE:Structure Preparation |
| Water | No |
| Procedure | Auto-FMO protocol ver. 2.20220422 |
| Remarks |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 112 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -251086.878356 |
|---|---|
| FMO2-HF: Nuclear repulsion | 226420.617765 |
| FMO2-HF: Total energy | -24666.260591 |
| FMO2-MP2: Total energy | -24735.325363 |
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:326:GLY)
Summations of interaction energy for
fragment #1(A:326:GLY)
| 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. |
| -23.534 | -26.673 | 13.965 | -5.585 | -5.24 | 0.028 |
Interaction energy analysis for fragmet #1(A:326:GLY)
| 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 | 327 | SER | 0 | -0.009 | 0.088 | 4.326 | 0.698 | 0.877 | 0.000 | -0.068 | -0.111 | 0.000 |
| 4 | A | 328 | ALA | 0 | 0.094 | -0.108 | 3.623 | 0.837 | 2.179 | -0.004 | -0.652 | -0.686 | -0.001 |
| 5 | A | 328 | ALA | 0 | -0.065 | 0.106 | 3.929 | 0.005 | 0.064 | -0.001 | -0.014 | -0.044 | 0.000 |
| 6 | A | 329 | ARG | 0 | 0.032 | -0.105 | 3.746 | 0.052 | 0.389 | -0.001 | -0.119 | -0.217 | 0.000 |
| 7 | A | 329 | ARG | 1 | 0.890 | 1.044 | 1.943 | -23.767 | -29.538 | 13.960 | -4.435 | -3.753 | 0.031 |
| 8 | A | 330 | GLU | 0 | 0.071 | -0.092 | 4.644 | 0.885 | 1.015 | -0.002 | -0.026 | -0.102 | 0.000 |
| 9 | A | 330 | GLU | -1 | -0.856 | -0.785 | 3.707 | -4.808 | -4.223 | 0.013 | -0.271 | -0.327 | -0.002 |
| 10 | A | 331 | ARG | 0 | 0.107 | -0.056 | 6.450 | 0.543 | 0.543 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 331 | ARG | 1 | 0.855 | 1.061 | 7.721 | 1.493 | 1.493 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 332 | ASP | 0 | 0.072 | -0.082 | 8.296 | 0.147 | 0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 332 | ASP | -1 | -0.827 | -0.763 | 8.774 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 333 | THR | 0 | 0.009 | -0.106 | 9.170 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 333 | THR | 0 | -0.048 | 0.057 | 8.377 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 334 | SER | 0 | 0.119 | -0.035 | 10.421 | 0.101 | 0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 334 | SER | 0 | -0.055 | 0.059 | 11.139 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 335 | ARG | 0 | 0.114 | -0.068 | 12.367 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 335 | ARG | 1 | 0.741 | 0.985 | 13.035 | 0.145 | 0.145 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 336 | ARG | 0 | 0.011 | -0.099 | 13.827 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 336 | ARG | 1 | 0.785 | 0.990 | 11.913 | -0.202 | -0.202 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 337 | LEU | 0 | 0.130 | -0.074 | 14.858 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 337 | LEU | 0 | -0.071 | 0.103 | 13.252 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 338 | LEU | 0 | 0.086 | -0.103 | 16.388 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 338 | LEU | 0 | -0.099 | 0.095 | 15.862 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 339 | ALA | 0 | 0.135 | -0.075 | 18.150 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 339 | ALA | 0 | -0.109 | 0.083 | 18.935 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 340 | GLU | 0 | 0.070 | -0.117 | 19.503 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 340 | GLU | -1 | -0.962 | -0.815 | 19.676 | 0.090 | 0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 341 | LYS | 0 | 0.125 | -0.078 | 20.628 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 341 | LYS | 1 | 0.709 | 0.973 | 20.774 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 342 | GLU | 0 | 0.008 | -0.117 | 22.439 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 342 | GLU | -1 | -0.846 | -0.760 | 22.868 | -0.084 | -0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 343 | ARG | 0 | 0.057 | -0.088 | 24.124 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 343 | ARG | 1 | 0.820 | 1.012 | 22.598 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 344 | GLU | 0 | 0.198 | -0.046 | 25.849 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 344 | GLU | -1 | -0.996 | -0.849 | 26.368 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 345 | MET | 0 | 0.097 | -0.110 | 26.987 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 345 | MET | 0 | -0.124 | 0.081 | 26.655 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 346 | ALA | 0 | 0.073 | -0.094 | 28.322 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 346 | ALA | 0 | -0.091 | 0.093 | 28.569 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 347 | GLU | 0 | 0.040 | -0.139 | 30.133 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 347 | GLU | -1 | -0.906 | -0.800 | 30.289 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 348 | MET | 0 | 0.091 | -0.092 | 31.648 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 348 | MET | 0 | -0.097 | 0.118 | 31.805 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 349 | ARG | 0 | 0.045 | -0.092 | 32.615 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 349 | ARG | 1 | 0.751 | 0.961 | 27.337 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 350 | ALA | 0 | 0.139 | -0.058 | 34.282 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 350 | ALA | 0 | -0.101 | 0.089 | 34.977 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 351 | ARG | 0 | 0.058 | -0.075 | 36.092 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 351 | ARG | 1 | 0.760 | 0.980 | 32.527 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 352 | MET | 0 | 0.146 | -0.079 | 37.287 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 352 | MET | 0 | -0.123 | 0.077 | 37.088 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 353 | GLN | 0 | 0.093 | -0.076 | 38.438 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 353 | GLN | 0 | -0.175 | 0.033 | 38.487 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 354 | GLN | 0 | 0.141 | -0.065 | 40.189 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 354 | GLN | 0 | -0.166 | 0.037 | 41.280 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 355 | GLN | 0 | 0.096 | -0.086 | 42.008 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 355 | GLN | 0 | -0.119 | 0.058 | 40.517 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 356 | LEU | 0 | 0.050 | -0.103 | 42.980 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 356 | LEU | 0 | -0.110 | 0.083 | 41.088 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 357 | ASP | 0 | 0.118 | -0.090 | 44.365 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | A | 357 | ASP | -1 | -0.964 | -0.820 | 43.532 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 358 | GLU | 0 | 0.102 | -0.107 | 46.242 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | A | 358 | GLU | -1 | -0.957 | -0.809 | 46.233 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | A | 359 | TYR | 0 | 0.081 | -0.072 | 47.670 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 67 | A | 359 | TYR | 0 | -0.122 | 0.062 | 47.761 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 68 | A | 360 | GLN | 0 | 0.081 | -0.107 | 48.580 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 69 | A | 360 | GLN | 0 | -0.155 | 0.054 | 48.350 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 70 | A | 361 | GLU | 0 | 0.112 | -0.108 | 50.190 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 71 | A | 361 | GLU | -1 | -1.011 | -0.853 | 50.993 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 72 | A | 362 | LEU | 0 | 0.090 | -0.100 | 52.273 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 73 | A | 362 | LEU | 0 | -0.125 | 0.090 | 52.853 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 74 | A | 363 | LEU | 0 | 0.048 | -0.127 | 53.255 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 75 | A | 363 | LEU | 0 | -0.086 | 0.099 | 51.365 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 76 | A | 364 | ASP | 0 | 0.105 | -0.105 | 54.296 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 77 | A | 364 | ASP | -1 | -0.956 | -0.812 | 53.114 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 78 | A | 365 | ILE | 0 | 0.066 | -0.099 | 56.036 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 79 | A | 365 | ILE | 0 | -0.087 | 0.103 | 55.997 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 80 | A | 366 | LYS | 0 | 0.117 | -0.087 | 57.886 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 81 | A | 366 | LYS | 1 | 0.671 | 0.963 | 58.213 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 82 | A | 367 | LEU | 0 | 0.043 | -0.128 | 58.758 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 83 | A | 367 | LEU | 0 | -0.075 | 0.103 | 56.719 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 84 | A | 368 | ALA | 0 | 0.092 | -0.107 | 60.130 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 85 | A | 368 | ALA | 0 | -0.065 | 0.120 | 60.506 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 86 | A | 369 | LEU | 0 | 0.136 | -0.080 | 62.006 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 87 | A | 369 | LEU | 0 | -0.102 | 0.105 | 63.149 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 88 | A | 370 | ASP | 0 | 0.097 | -0.115 | 63.512 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 89 | A | 370 | ASP | -1 | -0.901 | -0.785 | 62.838 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 90 | A | 371 | MET | 0 | 0.056 | -0.111 | 64.643 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 91 | A | 371 | MET | 0 | -0.103 | 0.095 | 61.738 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 92 | A | 372 | GLU | 0 | 0.055 | -0.134 | 66.247 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 93 | A | 372 | GLU | -1 | -0.992 | -0.832 | 65.969 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 94 | A | 373 | ILE | 0 | 0.073 | -0.099 | 68.030 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 95 | A | 373 | ILE | 0 | -0.093 | 0.105 | 67.240 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 96 | A | 374 | HIS | 0 | 0.075 | -0.083 | 69.211 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 97 | A | 374 | HIS | 0 | -0.103 | 0.058 | 69.383 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 98 | A | 375 | ALA | 0 | 0.077 | -0.119 | 70.445 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 99 | A | 375 | ALA | 0 | -0.072 | 0.116 | 70.614 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 100 | A | 376 | TYR | 0 | 0.073 | -0.101 | 72.148 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 101 | A | 376 | TYR | 0 | -0.071 | 0.101 | 72.703 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 102 | A | 377 | ARG | 0 | 0.103 | -0.072 | 73.715 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 103 | A | 377 | ARG | 1 | 0.751 | 0.986 | 74.255 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 104 | A | 378 | LYS | 0 | 0.012 | -0.126 | 74.991 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 105 | A | 378 | LYS | 1 | 0.776 | 1.017 | 74.586 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 106 | A | 379 | LEU | 0 | 0.090 | -0.097 | 76.449 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 107 | A | 379 | LEU | 0 | -0.113 | 0.094 | 76.581 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 108 | A | 380 | LEU | 0 | -0.029 | -0.130 | 78.313 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 109 | A | 380 | LEU | 0 | -0.071 | 0.103 | 78.181 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 110 | A | 381 | GLU | 0 | 0.090 | -0.095 | 80.275 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 111 | A | 381 | GLU | -1 | -0.855 | -0.772 | 78.674 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 112 | A | 382 | GLY | 0 | -0.068 | -0.116 | 81.740 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |