![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: KRNL3
Calculation Name: 6UFA-A-Xray303
Preferred Name:
Target Type:
Ligand Name: d-histidine
ligand 3-letter code: DHI
PDB ID: 6UFA
Chain ID: A
Base Structure: X-ray
Registration Date: 2021-08-02
Reference: C. Watanabe, T. Honma et. al., Interaction energy analysis of high resolution X-ray structure dataset on FMODB, To be pubulished.
Modeling method
Optimization | BaseStructure_original |
---|---|
Restraint | BaseStructure_original |
Protonation | MOE:AddH |
Complement | MOE:AddH |
Water | All crystal waters in PDB. |
Procedure | Manual calculation |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Manual |
Number of fragment | 60 |
LigandCharge | Null |
Software | ABINIT-MP |
Total energy (hartree)
FMO2-HF: Electronic energy | -127317.204244 |
---|---|
FMO2-HF: Nuclear repulsion | 113039.990633 |
FMO2-HF: Total energy | -14277.213611 |
FMO2-MP2: Total energy | -14313.567646 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F015062/ligand_interaction/ligand_F015062.png)
Ligand Interaction
![ligand interaction](./Kdata/F015062/ligand_interaction/ligand_interaction_F015062.png)
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:1:LYS)
Summations of interaction energy for
fragment #1(A:1:LYS)
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. |
-9469.762 | -9339.668 | -91.084 | 22.224 | -61.237 | 6.643 |
Interaction energy analysis for fragmet #1(A:1:LYS)
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 | 3 | DGN | 0 | -0.046 | 0.006 | 2.166 | -15.067 | -9.462 | 6.037 | -5.424 | -6.217 | 0.061 |
4 | A | 4 | DGL | -1 | -0.837 | -0.942 | 3.826 | -25.850 | -25.644 | 0.004 | 0.008 | -0.218 | 0.001 |
5 | A | 5 | AIB | 0 | 0.002 | 0.008 | 6.913 | -0.392 | -0.392 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | HIS | 0 | 0.007 | -0.014 | 4.689 | -0.102 | -0.012 | -0.002 | -0.017 | -0.071 | 0.000 |
7 | A | 7 | DLY | 1 | 0.923 | 0.868 | 5.651 | 22.002 | 21.994 | -0.002 | 0.000 | 0.010 | 0.000 |
8 | A | 6 | HIS | 2 | 1.479 | 2.278 | 1.542 | 190.526 | 75.813 | 18.260 | 102.458 | -6.004 | 0.093 |
9 | A | 8 | DLE | 0 | 0.008 | 0.018 | 8.030 | 0.814 | 0.814 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 9 | GLN | 0 | 0.000 | 0.002 | 7.630 | -1.124 | -1.124 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 10 | GLU | -1 | -0.791 | -0.882 | 9.157 | -15.059 | -15.059 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 11 | AIB | 0 | 0.012 | 0.006 | 10.577 | -0.179 | -0.179 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 12 | DHI | 0 | 0.004 | -0.017 | 7.120 | -0.081 | -0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 13 | LYS | 1 | 0.945 | 0.879 | 7.517 | 14.049 | 14.049 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 14 | LEU | 0 | 0.020 | 0.023 | 9.560 | 0.128 | 0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 15 | DGN | 0 | -0.004 | -0.001 | 4.888 | 2.399 | 2.518 | -0.002 | -0.002 | -0.115 | 0.000 |
17 | A | 16 | DGL | -1 | -0.846 | -0.946 | 8.072 | -22.163 | -22.163 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 17 | AIB | 0 | -0.011 | -0.008 | 5.174 | -0.791 | -0.791 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 18 | HIS | 0 | 0.017 | -0.010 | 4.369 | -1.948 | -1.887 | 0.000 | 0.013 | -0.075 | 0.000 |
20 | A | 19 | DLY | 1 | 0.885 | 0.842 | 5.819 | 20.516 | 20.513 | -0.002 | 0.001 | 0.004 | 0.000 |
21 | A | 20 | DLE | 0 | 0.013 | 0.020 | 6.802 | 1.838 | 1.838 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 21 | GLN | 0 | -0.028 | 0.013 | 4.985 | -1.272 | -1.162 | -0.001 | -0.005 | -0.103 | 0.000 |
23 | A | 22 | GLU | -1 | -0.793 | -0.898 | 1.993 | -125.448 | -121.391 | 4.910 | -4.398 | -4.569 | -0.069 |
24 | A | 23 | AIB | 0 | -0.030 | -0.007 | 1.962 | -21.036 | -17.748 | 6.519 | -4.720 | -5.087 | -0.052 |
26 | A | 201 | HOH | 0 | -0.032 | -0.040 | 14.002 | -0.148 | -0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 202 | HOH | 0 | -0.051 | -0.045 | 2.933 | 3.443 | 3.871 | 0.008 | -0.231 | -0.206 | -0.001 |
28 | A | 203 | HOH | 0 | -0.030 | -0.029 | 12.982 | 0.278 | 0.278 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 204 | HOH | 0 | -0.018 | -0.019 | 13.310 | 0.254 | 0.254 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 205 | HOH | 0 | 0.034 | 0.014 | 2.508 | 3.127 | 4.418 | 0.964 | -0.959 | -1.296 | -0.008 |
31 | A | 206 | HOH | 0 | 0.035 | 0.013 | 9.691 | -0.467 | -0.467 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 207 | HOH | 0 | 0.002 | -0.005 | 6.161 | -0.161 | -0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 208 | HOH | 0 | -0.015 | -0.029 | 7.047 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 209 | HOH | 0 | 0.032 | 0.020 | 7.014 | -0.244 | -0.244 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 210 | HOH | 0 | -0.053 | -0.042 | 5.201 | 2.951 | 2.951 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 211 | HOH | 0 | -0.021 | -0.034 | 3.464 | 3.044 | 3.285 | 0.003 | -0.106 | -0.139 | 0.000 |
37 | A | 212 | HOH | 0 | 0.032 | 0.014 | 1.928 | -19.347 | -21.099 | 6.058 | -2.046 | -2.261 | -0.029 |
38 | A | 213 | HOH | 0 | 0.024 | 0.007 | 15.681 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 214 | HOH | 0 | -0.011 | -0.015 | 4.361 | -2.485 | -2.429 | -0.001 | -0.004 | -0.052 | 0.000 |
40 | A | 215 | HOH | 0 | -0.036 | -0.031 | 9.316 | 0.363 | 0.363 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 216 | HOH | 0 | 0.014 | 0.005 | 12.958 | -0.283 | -0.283 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 217 | HOH | 0 | 0.033 | 0.031 | 8.387 | -0.872 | -0.872 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 218 | HOH | 0 | 0.033 | 0.010 | 7.281 | 0.415 | 0.415 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 219 | HOH | 0 | 0.013 | 0.009 | 7.374 | 0.123 | 0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 220 | HOH | 0 | 0.006 | -0.003 | 6.538 | -0.760 | -0.760 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 221 | HOH | 0 | 0.040 | 0.023 | 7.360 | -0.404 | -0.404 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 222 | HOH | 0 | 0.019 | 0.007 | 16.277 | -0.366 | -0.366 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 223 | HOH | 0 | 0.033 | 0.020 | 13.296 | -0.272 | -0.272 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 224 | HOH | 0 | 0.016 | 0.017 | 6.288 | 0.961 | 0.961 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 225 | HOH | 0 | 0.008 | 0.001 | 2.673 | -14.188 | -12.988 | 0.787 | -0.881 | -1.106 | -0.012 |
51 | A | 226 | HOH | 0 | 0.049 | 0.039 | 11.238 | -1.142 | -1.142 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 227 | HOH | 0 | 0.024 | 0.008 | 10.281 | -0.105 | -0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 228 | HOH | 0 | -0.026 | -0.020 | 14.196 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 229 | HOH | 0 | -0.056 | -0.051 | 8.931 | -0.380 | -0.380 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 230 | HOH | 0 | -0.005 | -0.007 | 15.014 | -0.134 | -0.134 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 231 | HOH | 0 | 0.052 | 0.039 | 2.437 | -2.304 | -1.435 | 0.986 | -0.717 | -1.138 | -0.011 |
57 | A | 232 | HOH | 0 | 0.025 | 0.010 | 10.506 | -0.514 | -0.514 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 233 | HOH | 0 | 0.005 | 0.001 | 6.971 | 1.454 | 1.454 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 234 | HOH | 0 | 0.018 | 0.022 | 8.588 | -0.986 | -0.986 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 235 | HOH | 0 | -0.013 | -0.009 | 7.021 | -0.070 | -0.070 | 0.000 | 0.000 | 0.000 | 0.000 |