FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-04-05
All entries: 36946
Number of unique PDB entries: 7781
FMODB ID: R9RK8
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 | 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 | 49 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -264931.807697 |
|---|---|
| FMO2-HF: Nuclear repulsion | 244553.424038 |
| FMO2-HF: Total energy | -20378.383659 |
| FMO2-MP2: Total energy | -20437.800029 |
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. |
| -27.228 | -23.245 | 16.071 | -7.047 | -13.009 | -0.003 |
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 | 0.075 | 0.032 | 2.634 | -2.823 | -0.289 | 0.748 | -1.440 | -1.843 | -0.013 |
| 4 | A | 80 | GLN | 0 | 0.098 | 0.035 | 5.208 | -0.078 | 0.016 | -0.001 | -0.008 | -0.085 | 0.000 |
| 5 | A | 81 | ALA | 0 | 0.021 | 0.018 | 2.319 | 0.113 | -0.188 | 1.901 | -0.479 | -1.120 | -0.002 |
| 6 | A | 82 | ARG | 1 | 0.874 | 0.904 | 2.021 | -21.306 | -23.095 | 11.778 | -4.191 | -5.798 | 0.016 |
| 7 | A | 83 | ALA | 0 | 0.046 | 0.030 | 3.902 | -0.002 | 0.132 | 0.010 | -0.026 | -0.118 | 0.000 |
| 8 | A | 84 | PHE | 0 | 0.033 | 0.002 | 6.580 | 0.094 | 0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 85 | LEU | 0 | 0.022 | -0.002 | 2.490 | -0.647 | -0.148 | 0.648 | -0.230 | -0.918 | -0.002 |
| 10 | A | 86 | GLU | -1 | -0.785 | -0.877 | 6.539 | 0.338 | 0.338 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 87 | GLN | 0 | 0.007 | 0.027 | 9.192 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 88 | VAL | 0 | 0.005 | 0.019 | 9.782 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 89 | PHE | 0 | 0.041 | 0.005 | 10.128 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 90 | ARG | 1 | 0.885 | 0.930 | 11.950 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 91 | ARG | 1 | 0.852 | 0.922 | 14.479 | 0.131 | 0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 92 | LYS | 1 | 0.820 | 0.880 | 14.887 | 0.156 | 0.156 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 93 | GLN | 0 | 0.083 | 0.049 | 14.179 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 94 | SER | 0 | 0.006 | -0.006 | 14.358 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 95 | LEU | 0 | 0.003 | 0.026 | 11.160 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 96 | ASN | 0 | 0.076 | 0.042 | 15.240 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 97 | SER | 0 | 0.027 | -0.003 | 15.432 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 98 | LYS | 1 | 0.941 | 0.967 | 15.606 | 0.179 | 0.179 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 99 | GLU | -1 | -0.720 | -0.851 | 14.498 | -0.207 | -0.207 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 100 | LYS | 1 | 0.822 | 0.910 | 10.701 | 0.233 | 0.233 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 101 | GLU | -1 | -0.822 | -0.907 | 11.081 | -0.517 | -0.517 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 102 | GLU | -1 | -0.847 | -0.916 | 12.142 | -0.309 | -0.309 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 103 | VAL | 0 | -0.018 | -0.016 | 7.696 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 104 | ALA | 0 | -0.013 | -0.003 | 7.492 | -0.130 | -0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 105 | LYS | 1 | 0.915 | 0.951 | 7.668 | 0.282 | 0.282 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 106 | LYS | 1 | 0.892 | 0.958 | 9.575 | 0.413 | 0.413 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 107 | CYS | 0 | -0.089 | -0.040 | 4.006 | -0.095 | 0.022 | 0.000 | -0.017 | -0.100 | 0.000 |
| 32 | A | 108 | GLY | 0 | 0.011 | 0.018 | 4.302 | -0.569 | -0.443 | -0.001 | -0.021 | -0.104 | 0.000 |
| 33 | A | 109 | ILE | 0 | -0.075 | -0.031 | 2.356 | -1.703 | -0.435 | 0.959 | -0.409 | -1.819 | -0.002 |
| 34 | A | 110 | THR | 0 | 0.071 | 0.008 | 5.748 | 0.251 | 0.251 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 111 | PRO | 0 | 0.061 | 0.005 | 7.111 | -0.112 | -0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 112 | LEU | 0 | 0.006 | 0.011 | 8.316 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 113 | GLN | 0 | 0.088 | 0.058 | 3.446 | -0.323 | 0.171 | 0.015 | -0.091 | -0.418 | 0.000 |
| 38 | A | 114 | VAL | 0 | 0.041 | 0.032 | 4.646 | -0.170 | -0.029 | -0.001 | -0.008 | -0.132 | 0.000 |
| 39 | A | 115 | ARG | 1 | 0.945 | 0.978 | 6.024 | 0.360 | 0.360 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 116 | VAL | 0 | 0.004 | -0.008 | 4.963 | 0.096 | 0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 117 | TRP | 0 | 0.012 | 0.029 | 3.496 | -0.794 | -0.128 | 0.015 | -0.127 | -0.554 | 0.000 |
| 42 | A | 118 | PHE | 0 | 0.007 | -0.014 | 5.957 | 0.183 | 0.183 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 119 | ILE | 0 | -0.040 | -0.011 | 9.304 | 0.063 | 0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 120 | ASN | 0 | -0.006 | -0.008 | 7.558 | 0.132 | 0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 121 | LYS | 1 | 0.800 | 0.905 | 8.801 | -0.115 | -0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 122 | ARG | 1 | 0.890 | 0.933 | 10.543 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 123 | MET | 0 | 0.001 | 0.000 | 13.000 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 124 | ARG | 1 | 0.858 | 0.927 | 10.026 | -0.473 | -0.473 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 125 | SER | 0 | -0.027 | 0.002 | 14.423 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |