![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 949Y2
Calculation Name: 4HRN-C-Xray372
Preferred Name: Receptor protein-tyrosine kinase erbB-2
Target Type: SINGLE PROTEIN
Ligand Name:
ligand 3-letter code:
PDB ID: 4HRN
Chain ID: C
ChEMBL ID: CHEMBL1824
UniProt ID: P04626
Base Structure: X-ray
Registration Date: 2023-09-19
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 | 66 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -406918.01812 |
---|---|
FMO2-HF: Nuclear repulsion | 376485.91939 |
FMO2-HF: Total energy | -30432.09873 |
FMO2-MP2: Total energy | -30511.598225 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F029416/ligand_interaction/ligand_F029416.png)
Ligand Interaction
![ligand interaction](./Kdata/F029416/ligand_interaction/ligand_interaction_F029416.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(C:9:CYS)
Summations of interaction energy for
fragment #1(C:9:CYS)
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. |
-29.294 | -21.133 | 18.926 | -10.68 | -16.407 | 0.059 |
Interaction energy analysis for fragmet #1(C:9:CYS)
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 | 11 | GLN | 0 | -0.039 | -0.027 | 2.535 | -5.887 | -6.596 | 10.438 | -4.062 | -5.667 | 0.023 |
4 | C | 12 | PHE | 0 | -0.010 | -0.005 | 3.979 | -2.415 | -2.683 | 0.198 | 0.902 | -0.833 | -0.002 |
5 | C | 13 | LEU | 0 | 0.027 | 0.018 | 2.694 | -2.963 | 2.671 | 2.205 | -2.876 | -4.962 | -0.003 |
6 | C | 14 | ARG | 1 | 0.860 | 0.930 | 1.924 | -16.354 | -17.220 | 6.044 | -2.868 | -2.310 | 0.037 |
7 | C | 15 | GLY | 0 | 0.008 | 0.015 | 3.471 | -3.823 | -3.413 | 0.087 | -0.075 | -0.422 | 0.001 |
8 | C | 16 | GLN | 0 | -0.033 | -0.030 | 3.822 | 0.959 | 2.207 | -0.016 | -0.487 | -0.744 | -0.003 |
11 | C | 20 | GLU | -1 | -0.863 | -0.948 | 3.786 | 0.645 | 3.357 | -0.030 | -1.214 | -1.469 | 0.006 |
12 | C | 21 | GLU | -1 | -0.952 | -0.983 | 6.801 | 1.930 | 1.930 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | C | 22 | CYS | 0 | -0.107 | -0.041 | 6.241 | -0.752 | -0.752 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | C | 23 | ARG | 1 | 0.920 | 0.957 | 9.328 | -0.918 | -0.918 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | C | 24 | VAL | 0 | 0.022 | 0.014 | 12.181 | -0.165 | -0.165 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | C | 25 | LEU | 0 | 0.033 | -0.001 | 14.980 | -0.132 | -0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | C | 26 | GLN | 0 | 0.018 | 0.026 | 13.541 | -0.132 | -0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | C | 27 | GLY | 0 | 0.003 | 0.003 | 14.195 | 0.127 | 0.127 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | C | 28 | LEU | 0 | -0.038 | -0.002 | 14.630 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | C | 29 | PRO | 0 | 0.025 | -0.008 | 12.944 | -0.123 | -0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | C | 30 | ARG | 1 | 0.890 | 0.921 | 13.229 | -0.397 | -0.397 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | C | 31 | GLU | -1 | -0.787 | -0.891 | 9.109 | 2.665 | 2.665 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | C | 32 | TYR | 0 | 0.023 | 0.012 | 13.198 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | C | 33 | VAL | 0 | 0.002 | -0.009 | 10.208 | 0.260 | 0.260 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | C | 34 | ASN | 0 | 0.000 | -0.011 | 11.442 | -0.367 | -0.367 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | C | 35 | ALA | 0 | 0.051 | 0.036 | 10.575 | 0.298 | 0.298 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | C | 36 | ARG | 1 | 0.859 | 0.925 | 6.020 | -3.995 | -3.995 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | C | 37 | HIS | 0 | 0.008 | 0.008 | 6.613 | 1.477 | 1.477 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | C | 39 | LEU | 0 | -0.003 | -0.007 | 7.964 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | C | 40 | PRO | 0 | 0.004 | 0.011 | 10.734 | -0.085 | -0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | C | 41 | CYS | 0 | -0.035 | -0.016 | 13.207 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | C | 42 | HIS | 0 | 0.094 | 0.058 | 16.767 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | C | 43 | PRO | 0 | -0.022 | -0.034 | 19.212 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | C | 44 | GLU | -1 | -0.819 | -0.912 | 20.705 | 0.111 | 0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | C | 45 | CYS | 0 | -0.111 | -0.026 | 20.814 | 0.067 | 0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | C | 46 | GLN | 0 | 0.056 | 0.009 | 22.371 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | C | 47 | PRO | 0 | -0.053 | -0.013 | 20.183 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | C | 48 | GLN | 0 | -0.077 | -0.044 | 21.365 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | C | 49 | ASP | -1 | -0.857 | -0.921 | 21.694 | 0.344 | 0.344 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | C | 50 | GLY | 0 | -0.059 | -0.025 | 23.279 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | C | 51 | SER | 0 | -0.062 | -0.068 | 23.015 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | C | 52 | VAL | 0 | 0.057 | 0.044 | 18.762 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | C | 53 | THR | 0 | 0.045 | 0.034 | 18.445 | -0.099 | -0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | C | 55 | PHE | 0 | -0.041 | -0.021 | 19.173 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | C | 56 | GLY | 0 | -0.016 | -0.010 | 17.652 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | C | 57 | PRO | 0 | -0.033 | -0.013 | 16.238 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | C | 58 | GLU | -1 | -0.893 | -0.935 | 17.934 | 0.300 | 0.300 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | C | 59 | ALA | 0 | -0.006 | -0.016 | 21.688 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | C | 60 | ASP | -1 | -0.908 | -0.950 | 24.393 | 0.331 | 0.331 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | C | 61 | GLN | 0 | 0.004 | 0.001 | 21.286 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | C | 63 | VAL | 0 | -0.010 | 0.008 | 22.916 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | C | 64 | ALA | 0 | 0.005 | -0.020 | 25.175 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | C | 65 | CYS | 0 | -0.088 | -0.008 | 25.613 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | C | 66 | ALA | 0 | 0.003 | 0.011 | 25.010 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | C | 67 | HIS | 0 | -0.104 | -0.062 | 26.807 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | C | 68 | TYR | 0 | -0.033 | -0.007 | 30.352 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | C | 69 | LYS | 1 | 0.940 | 0.966 | 30.447 | -0.231 | -0.231 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | C | 70 | ASP | -1 | -0.945 | -0.970 | 32.229 | 0.111 | 0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | C | 71 | PRO | 0 | -0.091 | -0.012 | 33.094 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | C | 72 | PRO | 0 | 0.006 | -0.008 | 30.407 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | C | 73 | PHE | 0 | 0.070 | 0.009 | 27.303 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | C | 75 | VAL | 0 | 0.024 | 0.002 | 27.559 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | C | 76 | ALA | 0 | 0.087 | 0.040 | 28.404 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | C | 77 | ARG | 1 | 0.891 | 0.928 | 29.877 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | C | 78 | CYS | 0 | 0.016 | 0.020 | 33.586 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | C | 79 | PRO | 0 | 0.018 | 0.018 | 36.056 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |