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: 6N9RZ
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 | OptH |
| 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 | -266439.217121 |
|---|---|
| FMO2-HF: Nuclear repulsion | 246061.671305 |
| FMO2-HF: Total energy | -20377.545816 |
| FMO2-MP2: Total energy | -20437.105493 |
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. |
| -17.009 | -13.654 | 18.863 | -7.073 | -15.147 | -0.016 |
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 | 0.095 | 0.035 | 2.550 | -3.498 | -0.657 | 1.030 | -1.785 | -2.086 | -0.017 |
| 4 | A | 80 | GLN | 0 | 0.094 | 0.038 | 5.083 | 0.005 | 0.159 | -0.001 | -0.010 | -0.143 | 0.000 |
| 5 | A | 81 | ALA | 0 | -0.003 | -0.003 | 2.232 | 1.144 | -0.916 | 4.774 | -0.989 | -1.726 | -0.002 |
| 6 | A | 82 | ARG | 1 | 0.890 | 0.913 | 1.989 | -10.793 | -12.022 | 10.504 | -3.233 | -6.043 | 0.009 |
| 7 | A | 83 | ALA | 0 | 0.049 | 0.046 | 3.500 | 0.153 | 0.110 | 0.071 | 0.178 | -0.205 | 0.000 |
| 8 | A | 84 | PHE | 0 | 0.019 | 0.003 | 6.420 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 85 | LEU | 0 | 0.015 | 0.005 | 2.445 | -0.618 | -0.091 | 0.666 | -0.235 | -0.958 | -0.002 |
| 10 | A | 86 | GLU | -1 | -0.834 | -0.920 | 6.447 | 0.280 | 0.280 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 87 | GLN | 0 | 0.028 | 0.030 | 8.544 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 88 | VAL | 0 | -0.015 | 0.008 | 9.747 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 89 | PHE | 0 | 0.030 | 0.000 | 9.780 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 90 | ARG | 1 | 0.867 | 0.928 | 11.660 | 0.092 | 0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 91 | ARG | 1 | 0.854 | 0.914 | 14.176 | 0.154 | 0.154 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 92 | LYS | 1 | 0.864 | 0.916 | 14.606 | 0.141 | 0.141 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 93 | GLN | 0 | 0.068 | 0.038 | 13.859 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 94 | SER | 0 | -0.036 | -0.022 | 13.872 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 95 | LEU | 0 | 0.014 | 0.005 | 10.900 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 96 | ASN | 0 | 0.022 | 0.040 | 15.099 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 97 | SER | 0 | 0.038 | -0.009 | 15.481 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 98 | LYS | 1 | 0.980 | 1.002 | 15.591 | 0.120 | 0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 99 | GLU | -1 | -0.738 | -0.861 | 14.934 | -0.180 | -0.180 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 100 | LYS | 1 | 0.894 | 0.946 | 10.822 | 0.175 | 0.175 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 101 | GLU | -1 | -0.916 | -0.950 | 10.999 | -0.411 | -0.411 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 102 | GLU | -1 | -0.875 | -0.953 | 12.245 | -0.275 | -0.275 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 103 | VAL | 0 | -0.020 | -0.026 | 7.680 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 104 | ALA | 0 | -0.009 | -0.002 | 7.541 | -0.123 | -0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 105 | LYS | 1 | 0.981 | 0.993 | 8.112 | 0.210 | 0.210 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 106 | LYS | 1 | 0.924 | 0.963 | 9.424 | 0.393 | 0.393 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 107 | CYS | 0 | -0.116 | -0.041 | 3.814 | -0.152 | 0.010 | 0.000 | -0.035 | -0.128 | 0.000 |
| 32 | A | 108 | GLY | 0 | 0.020 | 0.021 | 4.884 | -0.422 | -0.333 | -0.001 | -0.003 | -0.084 | 0.000 |
| 33 | A | 109 | ILE | 0 | -0.061 | -0.016 | 2.200 | -1.679 | -0.610 | 1.365 | -0.458 | -1.977 | -0.003 |
| 34 | A | 110 | THR | 0 | 0.040 | 0.007 | 5.330 | 0.177 | 0.197 | -0.001 | -0.001 | -0.018 | 0.000 |
| 35 | A | 111 | PRO | 0 | 0.137 | 0.023 | 6.832 | -0.115 | -0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 112 | LEU | 0 | -0.005 | 0.007 | 8.339 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 113 | GLN | 0 | 0.058 | 0.027 | 2.609 | -1.052 | -0.114 | 0.430 | -0.321 | -1.047 | 0.000 |
| 38 | A | 114 | VAL | 0 | 0.046 | 0.045 | 4.643 | -0.133 | -0.001 | -0.001 | -0.008 | -0.123 | 0.000 |
| 39 | A | 115 | ARG | 1 | 0.911 | 0.955 | 6.196 | 0.236 | 0.236 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 116 | VAL | 0 | 0.020 | -0.002 | 5.437 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 117 | TRP | 0 | -0.020 | 0.009 | 3.261 | -0.812 | -0.057 | 0.027 | -0.173 | -0.609 | -0.001 |
| 42 | A | 118 | PHE | 0 | 0.008 | -0.009 | 6.209 | 0.112 | 0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 119 | ILE | 0 | -0.025 | -0.005 | 9.420 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 120 | ASN | 0 | 0.018 | -0.004 | 7.175 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 121 | LYS | 1 | 0.828 | 0.944 | 8.793 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 122 | ARG | 1 | 0.898 | 0.939 | 10.660 | 0.062 | 0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 123 | MET | 0 | -0.013 | -0.015 | 13.329 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 124 | ARG | 1 | 0.907 | 0.956 | 8.939 | -0.432 | -0.432 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 125 | SER | 0 | -0.012 | 0.026 | 13.577 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |