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: Z63GN
Calculation Name: 1YRN-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1YRN
Chain ID: A
UniProt ID: P0CY10
Base Structure: X-ray
Registration Date: 2023-09-20
Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.
Modeling method
| Optimization | MOE:Amber10:EHT |
|---|---|
| Restraint | OptHSide |
| 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 | 49 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -266329.937227 |
|---|---|
| FMO2-HF: Nuclear repulsion | 245951.819129 |
| FMO2-HF: Total energy | -20378.118098 |
| FMO2-MP2: Total energy | -20437.602014 |
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:77:ILE)
Summations of interaction energy for
fragment #1(A:77:ILE)
| 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. |
| -18.312 | -10.819 | 11.526 | -5.598 | -13.419 | -0.013 |
Interaction energy analysis for fragmet #1(A:77:ILE)
| 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 | 79 | PRO | 0 | 0.084 | 0.032 | 2.748 | -2.943 | -0.233 | 0.477 | -1.461 | -1.726 | -0.010 |
| 4 | A | 80 | GLN | 0 | 0.080 | 0.034 | 5.319 | -0.073 | 0.047 | -0.001 | -0.010 | -0.108 | 0.000 |
| 5 | A | 81 | ALA | 0 | 0.014 | 0.007 | 2.250 | 0.912 | -0.720 | 3.981 | -0.786 | -1.563 | -0.002 |
| 6 | A | 82 | ARG | 1 | 0.890 | 0.917 | 2.225 | -12.895 | -10.003 | 4.029 | -2.164 | -4.756 | 0.006 |
| 7 | A | 83 | ALA | 0 | 0.038 | 0.037 | 3.599 | 0.047 | 0.101 | 0.040 | 0.070 | -0.163 | 0.000 |
| 8 | A | 84 | PHE | 0 | 0.038 | 0.006 | 6.323 | 0.067 | 0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 85 | LEU | 0 | 0.013 | 0.006 | 2.359 | -0.508 | -0.285 | 1.198 | -0.294 | -1.127 | -0.002 |
| 10 | A | 86 | GLU | -1 | -0.785 | -0.879 | 6.394 | 0.165 | 0.165 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 87 | GLN | 0 | 0.023 | 0.033 | 8.681 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 88 | VAL | 0 | -0.009 | 0.007 | 9.659 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 89 | PHE | 0 | 0.024 | -0.001 | 9.813 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 90 | ARG | 1 | 0.874 | 0.928 | 11.650 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 91 | ARG | 1 | 0.852 | 0.911 | 14.176 | 0.129 | 0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 92 | LYS | 1 | 0.828 | 0.893 | 14.549 | 0.139 | 0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 93 | GLN | 0 | 0.078 | 0.048 | 13.750 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 94 | SER | 0 | -0.023 | -0.009 | 13.862 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 95 | LEU | 0 | 0.004 | 0.007 | 10.987 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 96 | ASN | 0 | 0.055 | 0.029 | 15.222 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 97 | SER | 0 | 0.040 | -0.005 | 15.665 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 98 | LYS | 1 | 1.003 | 1.013 | 15.793 | 0.121 | 0.121 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 99 | GLU | -1 | -0.721 | -0.838 | 14.561 | -0.171 | -0.171 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 100 | LYS | 1 | 0.860 | 0.926 | 10.953 | 0.198 | 0.198 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 101 | GLU | -1 | -0.851 | -0.916 | 11.130 | -0.385 | -0.385 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 102 | GLU | -1 | -0.888 | -0.946 | 12.096 | -0.241 | -0.241 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 103 | VAL | 0 | -0.017 | -0.023 | 7.703 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 104 | ALA | 0 | -0.011 | -0.003 | 7.473 | -0.093 | -0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 105 | LYS | 1 | 0.897 | 0.940 | 7.857 | 0.217 | 0.217 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 106 | LYS | 1 | 0.929 | 0.973 | 9.368 | 0.321 | 0.321 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 107 | CYS | 0 | -0.104 | -0.039 | 3.743 | -0.143 | 0.015 | 0.001 | -0.032 | -0.127 | 0.000 |
| 32 | A | 108 | GLY | 0 | 0.021 | 0.019 | 4.639 | -0.367 | -0.271 | -0.001 | -0.007 | -0.088 | 0.000 |
| 33 | A | 109 | ILE | 0 | -0.063 | -0.021 | 2.291 | -1.721 | -0.548 | 1.690 | -0.529 | -2.334 | -0.004 |
| 34 | A | 110 | THR | 0 | 0.041 | -0.002 | 5.550 | 0.181 | 0.181 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 111 | PRO | 0 | 0.118 | 0.020 | 6.833 | -0.102 | -0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 112 | LEU | 0 | -0.012 | 0.008 | 8.398 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 113 | GLN | 0 | 0.081 | 0.051 | 3.152 | -0.537 | 0.121 | 0.032 | -0.151 | -0.539 | 0.000 |
| 38 | A | 114 | VAL | 0 | 0.032 | 0.031 | 4.860 | -0.187 | -0.064 | -0.001 | -0.004 | -0.118 | 0.000 |
| 39 | A | 115 | ARG | 1 | 0.933 | 0.968 | 6.325 | 0.269 | 0.269 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 116 | VAL | 0 | 0.017 | -0.008 | 5.058 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 117 | TRP | 0 | 0.002 | 0.030 | 2.940 | -0.962 | -0.044 | 0.081 | -0.230 | -0.770 | -0.001 |
| 42 | A | 118 | PHE | 0 | 0.012 | -0.010 | 6.053 | 0.136 | 0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 119 | ILE | 0 | -0.024 | 0.005 | 9.339 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 120 | ASN | 0 | -0.012 | -0.026 | 7.680 | 0.119 | 0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 121 | LYS | 1 | 0.812 | 0.916 | 8.715 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 122 | ARG | 1 | 0.904 | 0.933 | 10.443 | 0.098 | 0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 123 | MET | 0 | -0.023 | -0.016 | 13.055 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 124 | ARG | 1 | 0.876 | 0.938 | 9.264 | -0.307 | -0.307 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 125 | SER | 0 | -0.021 | 0.018 | 13.790 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |