FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-07-23
All entries: 37478
Number of unique PDB entries: 7783
FMODB ID: GN2G1
Calculation Name: 1OR7-C-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1OR7
Chain ID: C
UniProt ID: P0AGB6
Base Structure: X-ray
Registration Date: 2023-06-20
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 |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 66 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -363546.118341 |
|---|---|
| FMO2-HF: Nuclear repulsion | 335649.061446 |
| FMO2-HF: Total energy | -27897.056895 |
| FMO2-MP2: Total energy | -27974.852797 |
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:1:MET)
Summations of interaction energy for
fragment #1(C: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. |
| -17.639 | -10.576 | 23.742 | -7.31 | -23.491 | -0.027 |
Interaction energy analysis for fragmet #1(C: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 | C | 3 | LYS | 1 | 0.857 | 0.887 | 2.889 | -2.230 | 0.011 | 0.787 | -1.152 | -1.876 | -0.002 |
| 4 | C | 4 | GLU | -1 | -0.962 | -0.966 | 4.360 | 0.017 | 0.212 | -0.001 | -0.007 | -0.186 | 0.000 |
| 5 | C | 5 | GLN | 0 | 0.041 | 0.007 | 2.698 | -1.666 | 0.103 | 0.893 | -0.909 | -1.753 | -0.008 |
| 6 | C | 6 | LEU | 0 | 0.003 | 0.006 | 2.497 | -3.543 | -2.435 | 4.513 | -1.512 | -4.109 | 0.005 |
| 7 | C | 7 | SER | 0 | 0.001 | 0.001 | 3.217 | 0.008 | -0.230 | 0.049 | 0.476 | -0.287 | 0.000 |
| 8 | C | 8 | ALA | 0 | 0.019 | 0.006 | 6.321 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | C | 9 | LEU | 0 | -0.022 | -0.004 | 2.456 | -0.545 | -0.231 | 0.797 | -0.175 | -0.935 | -0.001 |
| 10 | C | 10 | MET | 0 | -0.047 | -0.018 | 5.627 | 0.215 | 0.215 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | C | 11 | ASP | -1 | -0.903 | -0.942 | 7.999 | -0.079 | -0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | C | 12 | GLY | 0 | -0.028 | 0.003 | 9.179 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | C | 13 | GLU | -1 | -0.951 | -0.972 | 10.085 | -0.286 | -0.286 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | C | 14 | THR | 0 | -0.074 | -0.043 | 5.721 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | C | 15 | LEU | 0 | 0.016 | -0.003 | 8.062 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | C | 16 | ASP | -1 | -0.888 | -0.934 | 6.233 | -0.946 | -0.946 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | C | 17 | SER | 0 | 0.002 | -0.018 | 6.327 | -0.351 | -0.351 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | C | 18 | GLU | -1 | -0.836 | -0.907 | 6.639 | -0.660 | -0.660 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | C | 19 | LEU | 0 | -0.055 | -0.025 | 2.354 | -1.201 | -1.590 | 4.807 | -0.657 | -3.761 | -0.001 |
| 20 | C | 20 | LEU | 0 | 0.013 | 0.001 | 2.523 | -1.262 | -1.790 | 2.681 | -0.336 | -1.817 | -0.017 |
| 21 | C | 21 | ASN | 0 | -0.038 | -0.023 | 4.721 | 0.530 | 0.613 | -0.001 | -0.002 | -0.080 | 0.000 |
| 22 | C | 22 | GLU | -1 | -0.860 | -0.918 | 2.272 | -2.242 | -2.665 | 4.518 | -1.304 | -2.791 | -0.002 |
| 23 | C | 23 | LEU | 0 | -0.033 | -0.030 | 2.234 | 0.082 | 1.509 | 1.274 | -0.679 | -2.022 | -0.004 |
| 24 | C | 24 | ALA | 0 | -0.057 | -0.028 | 4.132 | -0.114 | -0.034 | 0.021 | 0.027 | -0.127 | 0.000 |
| 25 | C | 25 | HIS | 0 | -0.058 | -0.029 | 7.373 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | C | 26 | ASN | 0 | -0.025 | -0.005 | 4.100 | 0.173 | 0.330 | 0.000 | -0.036 | -0.121 | 0.000 |
| 27 | C | 27 | PRO | 0 | 0.059 | 0.014 | 6.848 | 0.465 | 0.465 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | C | 28 | GLU | -1 | -0.858 | -0.901 | 7.082 | -0.143 | -0.143 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | C | 29 | MET | 0 | -0.012 | 0.017 | 2.649 | -2.394 | -1.194 | 3.405 | -1.028 | -3.577 | 0.003 |
| 30 | C | 30 | GLN | 0 | 0.048 | 0.023 | 5.202 | -0.155 | -0.088 | -0.001 | -0.016 | -0.049 | 0.000 |
| 31 | C | 31 | LYS | 1 | 0.853 | 0.913 | 7.803 | -0.476 | -0.476 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | C | 32 | THR | 0 | -0.040 | -0.038 | 6.628 | -0.307 | -0.307 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | C | 33 | TRP | 0 | 0.074 | 0.028 | 5.694 | -0.248 | -0.248 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | C | 34 | GLU | -1 | -0.880 | -0.921 | 8.168 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | C | 35 | SER | 0 | -0.050 | -0.037 | 11.473 | -0.093 | -0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | C | 36 | TYR | 0 | 0.004 | -0.010 | 7.675 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | C | 37 | HIS | 0 | 0.023 | 0.018 | 8.774 | -0.094 | -0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | C | 38 | LEU | 0 | 0.042 | 0.036 | 13.069 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | C | 39 | ILE | 0 | -0.037 | -0.018 | 14.386 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | C | 40 | ARG | 1 | 0.815 | 0.883 | 11.498 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | C | 41 | ASP | -1 | -0.881 | -0.948 | 16.485 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | C | 42 | SER | 0 | -0.028 | -0.030 | 18.800 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | C | 43 | MET | 0 | -0.109 | -0.052 | 18.708 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | C | 44 | ARG | 1 | 0.843 | 0.933 | 16.728 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | C | 45 | GLY | 0 | 0.003 | 0.010 | 22.560 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | C | 46 | ASP | -1 | -0.902 | -0.928 | 20.298 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | C | 47 | THR | 0 | -0.050 | -0.039 | 21.366 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | C | 48 | PRO | 0 | -0.031 | -0.015 | 23.762 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | C | 49 | GLU | -1 | -0.946 | -0.977 | 26.761 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | C | 50 | VAL | 0 | -0.023 | -0.009 | 28.613 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | C | 51 | LEU | 0 | 0.013 | 0.013 | 21.571 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | C | 52 | HIS | 0 | -0.065 | -0.036 | 23.336 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | C | 53 | PHE | 0 | 0.001 | -0.015 | 19.578 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | C | 54 | ASP | -1 | -0.794 | -0.877 | 19.879 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | C | 55 | ILE | 0 | 0.027 | 0.018 | 20.409 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | C | 56 | SER | 0 | 0.028 | 0.022 | 15.926 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | C | 57 | SER | 0 | -0.019 | -0.023 | 18.003 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | C | 58 | ARG | 1 | 0.870 | 0.911 | 19.664 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | C | 59 | VAL | 0 | -0.016 | 0.000 | 19.397 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | C | 60 | MET | 0 | -0.030 | -0.008 | 16.340 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | C | 61 | ALA | 0 | 0.026 | 0.008 | 19.628 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | C | 62 | ALA | 0 | -0.039 | -0.011 | 22.973 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | C | 63 | ILE | 0 | -0.020 | -0.010 | 19.538 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | C | 64 | GLU | -1 | -0.927 | -0.980 | 19.690 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | C | 65 | GLU | -1 | -1.000 | -0.984 | 23.075 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | C | 66 | GLU | -1 | -1.094 | -1.036 | 24.774 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |