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: Q58GY
Calculation Name: 1MCT-I-Xray547
Preferred Name:
Target Type:
Ligand Name: calcium ion
Ligand 3-letter code: CA
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 1MCT
Chain ID: I
UniProt ID: P30709
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 | 25 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -100643.01404 |
|---|---|
| FMO2-HF: Nuclear repulsion | 87532.413842 |
| FMO2-HF: Total energy | -13110.600198 |
| FMO2-MP2: Total energy | -13141.409916 |
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(I:1:ARG)
Summations of interaction energy for
fragment #1(I:1:ARG)
| 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. |
| -238.347 | -248.605 | 60.488 | -23.363 | -26.868 | -0.274 |
Interaction energy analysis for fragmet #1(I:1:ARG)
| 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 | I | 3 | CYS | 0 | -0.075 | -0.010 | 1.875 | -56.706 | -60.994 | 25.247 | -10.911 | -10.048 | -0.097 |
| 4 | I | 4 | PRO | 0 | 0.010 | -0.004 | 4.378 | 5.816 | 5.913 | 0.000 | -0.025 | -0.072 | 0.000 |
| 10 | I | 10 | CYS | 0 | -0.062 | -0.025 | 4.728 | 0.423 | 0.537 | -0.002 | -0.009 | -0.104 | 0.000 |
| 19 | I | 19 | LYS | 0 | 0.046 | 0.047 | 2.297 | -12.151 | -10.098 | 5.365 | -3.349 | -4.069 | -0.025 |
| 20 | I | 21 | ILE | 0 | 0.011 | 0.008 | 2.517 | 9.058 | 8.834 | 2.193 | 1.909 | -3.878 | -0.005 |
| 21 | I | 23 | VAL | 0 | -0.011 | -0.001 | 4.621 | 3.727 | 3.820 | -0.001 | -0.003 | -0.089 | 0.000 |
| 25 | I | 28 | GLY | -1 | -0.780 | -0.854 | 1.846 | -186.814 | -194.917 | 27.686 | -10.975 | -8.608 | -0.147 |
| 5 | I | 5 | ARG | 1 | 0.958 | 0.983 | 7.255 | 62.619 | 62.619 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | I | 6 | ILE | 0 | 0.002 | 0.004 | 9.035 | 4.732 | 4.732 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | I | 7 | TRP | 0 | -0.004 | 0.003 | 9.551 | -3.752 | -3.752 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | I | 8 | MET | 0 | 0.019 | -0.002 | 9.581 | 1.136 | 1.136 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | I | 9 | GLU | -1 | -0.902 | -0.953 | 10.551 | -36.878 | -36.878 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | I | 11 | THR | 0 | -0.060 | -0.032 | 12.160 | 2.089 | 2.089 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | I | 12 | ARG | 1 | 0.923 | 0.955 | 11.894 | 37.267 | 37.267 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | I | 13 | ASP | -1 | -0.810 | -0.914 | 6.781 | -66.415 | -66.415 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | I | 14 | SER | 0 | -0.058 | -0.033 | 8.227 | -2.568 | -2.568 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | I | 15 | ASP | -1 | -0.760 | -0.876 | 10.766 | -39.496 | -39.496 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | I | 16 | CYS | 0 | -0.027 | 0.002 | 5.922 | -1.476 | -1.476 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | I | 17 | MET | 0 | 0.016 | 0.007 | 7.712 | 0.771 | 0.771 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | I | 18 | ALA | 0 | -0.006 | -0.017 | 5.735 | -10.206 | -10.206 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | I | 24 | ALA | 0 | -0.024 | -0.021 | 7.645 | 3.144 | 3.144 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | I | 25 | GLY | 0 | 0.042 | 0.029 | 11.409 | 2.314 | 2.314 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | I | 26 | HIS | 1 | 0.849 | 0.912 | 9.608 | 45.019 | 45.019 | 0.000 | 0.000 | 0.000 | 0.000 |