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: 865RY
Calculation Name: 3K6T-D-Xray549
Preferred Name: Female germline-specific tumor suppressor gld-1
Target Type: SINGLE PROTEIN
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 3K6T
Chain ID: D
ChEMBL ID: CHEMBL1293302
UniProt ID: Q17339
Base Structure: X-ray
Registration Date: 2025-10-12
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 | 46 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -220817.461991 |
|---|---|
| FMO2-HF: Nuclear repulsion | 202121.154098 |
| FMO2-HF: Total energy | -18696.307893 |
| FMO2-MP2: Total energy | -18751.547324 |
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(D:-1:SER)
Summations of interaction energy for
fragment #1(D:-1:SER)
| 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. |
| -89.181 | -85.095 | 0.694 | -1.946 | -2.833 | -0.012 |
Interaction energy analysis for fragmet #1(D:-1:SER)
| 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 | D | 144 | GLU | -1 | -0.858 | -0.916 | 3.827 | -34.510 | -33.208 | -0.001 | -0.564 | -0.736 | -0.001 |
| 36 | D | 177 | GLU | -1 | -0.792 | -0.844 | 3.794 | -59.756 | -58.967 | 0.006 | -0.423 | -0.372 | -0.003 |
| 39 | D | 180 | ARG | 1 | 0.797 | 0.860 | 2.962 | 52.538 | 54.533 | 0.689 | -0.959 | -1.725 | -0.008 |
| 4 | D | 145 | ALA | 0 | 0.006 | 0.015 | 6.544 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | D | 146 | THR | 0 | 0.017 | -0.011 | 8.344 | 1.157 | 1.157 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | D | 147 | VAL | 0 | 0.038 | 0.012 | 11.583 | -0.392 | -0.392 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | D | 148 | GLU | -1 | -0.841 | -0.911 | 14.135 | -19.471 | -19.471 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | D | 149 | TYR | 0 | -0.015 | -0.036 | 4.847 | 0.446 | 0.446 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | D | 150 | LEU | 0 | -0.010 | -0.006 | 11.013 | -0.074 | -0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | D | 151 | ALA | 0 | -0.014 | -0.010 | 11.884 | 0.894 | 0.894 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | D | 152 | ASP | -1 | -0.905 | -0.950 | 12.480 | -19.356 | -19.356 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | D | 153 | LEU | 0 | 0.003 | 0.000 | 7.566 | 0.841 | 0.841 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | D | 154 | VAL | 0 | -0.020 | -0.021 | 12.093 | 1.217 | 1.217 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | D | 155 | LYS | 1 | 0.871 | 0.928 | 15.161 | 16.361 | 16.361 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | D | 156 | GLU | -1 | -0.917 | -0.964 | 13.472 | -20.377 | -20.377 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | D | 157 | LYS | 1 | 0.852 | 0.912 | 14.922 | 17.925 | 17.925 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | D | 158 | LYS | 1 | 0.891 | 0.955 | 16.550 | 14.850 | 14.850 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | D | 159 | HIS | 0 | 0.012 | 0.023 | 19.137 | 0.508 | 0.508 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | D | 160 | LEU | 0 | 0.035 | 0.017 | 15.495 | 0.570 | 0.570 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | D | 161 | THR | 0 | -0.034 | -0.034 | 18.739 | 0.651 | 0.651 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | D | 162 | LEU | 0 | -0.038 | -0.003 | 21.159 | 0.600 | 0.600 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | D | 163 | PHE | 0 | -0.044 | -0.021 | 22.467 | 0.615 | 0.615 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | D | 164 | PRO | 0 | 0.103 | 0.045 | 21.841 | -0.260 | -0.260 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | D | 165 | HIS | 0 | -0.069 | -0.047 | 22.581 | -0.528 | -0.528 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | D | 166 | MET | 0 | -0.062 | -0.012 | 22.697 | 0.231 | 0.231 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | D | 167 | PHE | 0 | 0.022 | 0.002 | 18.302 | -0.449 | -0.449 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | D | 168 | SER | 0 | 0.065 | 0.055 | 17.803 | -1.217 | -1.217 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | D | 169 | ASN | 0 | -0.011 | -0.016 | 15.592 | -1.109 | -1.109 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | D | 170 | VAL | 0 | 0.000 | 0.004 | 13.661 | -1.391 | -1.391 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | D | 171 | GLU | -1 | -0.837 | -0.937 | 13.244 | -16.132 | -16.132 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | D | 172 | ARG | 1 | 0.911 | 0.955 | 12.096 | 20.028 | 20.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | D | 173 | LEU | 0 | -0.014 | -0.008 | 9.054 | -1.022 | -1.022 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | D | 174 | LEU | 0 | -0.013 | 0.011 | 8.995 | -2.862 | -2.862 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | D | 175 | ASP | -1 | -0.821 | -0.899 | 10.485 | -19.022 | -19.022 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | D | 176 | ASP | -1 | -0.892 | -0.949 | 9.132 | -24.248 | -24.248 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | D | 178 | ILE | 0 | -0.037 | -0.023 | 7.050 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | D | 179 | GLY | 0 | -0.029 | -0.014 | 10.135 | 1.088 | 1.088 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | D | 181 | VAL | 0 | -0.016 | -0.013 | 6.043 | 0.238 | 0.238 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | D | 182 | ARG | 1 | 0.952 | 0.972 | 8.165 | 20.626 | 20.626 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | D | 183 | VAL | 0 | -0.025 | -0.010 | 10.094 | 1.523 | 1.523 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | D | 184 | ALA | 0 | 0.006 | -0.009 | 7.292 | 0.858 | 0.858 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | D | 185 | LEU | 0 | -0.060 | -0.015 | 9.316 | 0.195 | 0.195 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | D | 186 | PHE | 0 | -0.102 | -0.044 | 12.164 | 1.496 | 1.496 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | D | 187 | GLN | -1 | -0.935 | -0.946 | 11.264 | -22.345 | -22.345 | 0.000 | 0.000 | 0.000 | 0.000 |