![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: MVYMZ
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 | 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 | 66 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -406783.861542 |
---|---|
FMO2-HF: Nuclear repulsion | 376351.474797 |
FMO2-HF: Total energy | -30432.386745 |
FMO2-MP2: Total energy | -30511.856508 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F029415/ligand_interaction/ligand_F029415.png)
Ligand Interaction
![ligand interaction](./Kdata/F029415/ligand_interaction/ligand_interaction_F029415.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. |
-30.875 | -19.062 | 15.815 | -11.062 | -16.568 | 0.058 |
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 | -0.037 | -0.027 | 2.640 | -7.299 | -4.410 | 6.197 | -3.890 | -5.196 | 0.025 |
4 | C | 12 | PHE | 0 | 0.006 | 0.001 | 4.037 | -2.664 | -2.713 | 0.195 | 0.637 | -0.783 | -0.002 |
5 | C | 13 | LEU | 0 | 0.032 | 0.020 | 2.587 | -3.085 | 2.456 | 3.334 | -3.177 | -5.699 | -0.006 |
6 | C | 14 | ARG | 1 | 0.824 | 0.897 | 1.923 | -16.980 | -17.903 | 6.051 | -2.849 | -2.279 | 0.037 |
7 | C | 15 | GLY | 0 | 0.017 | 0.018 | 3.471 | -3.750 | -3.344 | 0.087 | -0.073 | -0.420 | 0.001 |
8 | C | 16 | GLN | 0 | -0.035 | -0.029 | 3.822 | 1.468 | 2.735 | -0.016 | -0.496 | -0.755 | -0.003 |
11 | C | 20 | GLU | -1 | -0.868 | -0.950 | 3.786 | 0.517 | 3.199 | -0.033 | -1.214 | -1.436 | 0.006 |
12 | C | 21 | GLU | -1 | -0.917 | -0.966 | 6.942 | 1.666 | 1.666 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | C | 22 | CYS | 0 | -0.116 | -0.052 | 6.372 | -0.815 | -0.815 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | C | 23 | ARG | 1 | 0.918 | 0.945 | 9.328 | -1.284 | -1.284 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | C | 24 | VAL | 0 | -0.005 | -0.004 | 12.181 | -0.151 | -0.151 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | C | 25 | LEU | 0 | 0.029 | 0.003 | 14.980 | -0.134 | -0.134 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | C | 26 | GLN | 0 | -0.016 | 0.010 | 13.918 | -0.128 | -0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | C | 27 | GLY | 0 | 0.008 | 0.004 | 14.195 | 0.133 | 0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | C | 28 | LEU | 0 | -0.035 | 0.000 | 14.614 | 0.062 | 0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | C | 29 | PRO | 0 | 0.017 | -0.008 | 12.691 | -0.122 | -0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | C | 30 | ARG | 1 | 0.897 | 0.926 | 13.229 | -0.407 | -0.407 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | C | 31 | GLU | -1 | -0.744 | -0.831 | 9.329 | 2.656 | 2.656 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | C | 32 | TYR | 0 | 0.036 | 0.015 | 13.198 | -0.078 | -0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | C | 33 | VAL | 0 | 0.001 | -0.016 | 10.143 | 0.280 | 0.280 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | C | 34 | ASN | 0 | -0.008 | -0.013 | 11.444 | -0.395 | -0.395 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | C | 35 | ALA | 0 | 0.065 | 0.043 | 10.688 | 0.333 | 0.333 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | C | 36 | ARG | 1 | 0.844 | 0.920 | 6.224 | -3.311 | -3.311 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | C | 37 | HIS | 0 | -0.001 | 0.001 | 6.557 | 1.685 | 1.685 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | C | 39 | LEU | 0 | 0.000 | -0.003 | 7.964 | 0.062 | 0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | C | 40 | PRO | 0 | 0.000 | 0.006 | 10.734 | -0.115 | -0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | C | 41 | CYS | 0 | -0.054 | -0.026 | 13.207 | -0.083 | -0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | C | 42 | HIS | 0 | 0.095 | 0.048 | 16.767 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | C | 43 | PRO | 0 | -0.019 | -0.031 | 19.061 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | C | 44 | GLU | -1 | -0.801 | -0.891 | 20.705 | 0.170 | 0.170 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | C | 45 | CYS | 0 | -0.119 | -0.029 | 20.805 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | C | 46 | GLN | 0 | 0.025 | 0.002 | 22.371 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | C | 47 | PRO | 0 | -0.033 | -0.018 | 20.083 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | C | 48 | GLN | 0 | -0.071 | -0.027 | 21.353 | -0.068 | -0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | C | 49 | ASP | -1 | -0.859 | -0.930 | 21.694 | 0.371 | 0.371 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | C | 50 | GLY | 0 | -0.050 | -0.017 | 23.279 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | C | 51 | SER | 0 | -0.046 | -0.044 | 23.009 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | C | 52 | VAL | 0 | 0.054 | 0.037 | 18.311 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | C | 53 | THR | 0 | 0.025 | 0.014 | 18.409 | -0.094 | -0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | C | 55 | PHE | 0 | -0.028 | -0.014 | 19.173 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | C | 56 | GLY | 0 | -0.004 | -0.003 | 17.647 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | C | 57 | PRO | 0 | -0.031 | -0.015 | 16.158 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | C | 58 | GLU | -1 | -0.895 | -0.939 | 17.934 | 0.392 | 0.392 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | C | 59 | ALA | 0 | -0.007 | -0.012 | 21.688 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | C | 60 | ASP | -1 | -0.909 | -0.955 | 24.393 | 0.364 | 0.364 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | C | 61 | GLN | 0 | -0.005 | -0.002 | 21.053 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | C | 63 | VAL | 0 | -0.006 | 0.009 | 23.023 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | C | 64 | ALA | 0 | 0.002 | -0.016 | 25.175 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | C | 65 | CYS | 0 | -0.098 | -0.015 | 25.613 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | C | 66 | ALA | 0 | 0.006 | 0.006 | 24.984 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | C | 67 | HIS | 0 | -0.105 | -0.073 | 26.434 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | C | 68 | TYR | 0 | -0.024 | -0.001 | 30.352 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | C | 69 | LYS | 1 | 0.923 | 0.960 | 29.920 | -0.268 | -0.268 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | C | 70 | ASP | -1 | -0.923 | -0.965 | 32.229 | 0.138 | 0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | C | 71 | PRO | 0 | -0.082 | -0.004 | 33.065 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | C | 72 | PRO | 0 | 0.008 | -0.009 | 30.430 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | C | 73 | PHE | 0 | 0.061 | 0.002 | 27.489 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | C | 75 | VAL | 0 | 0.025 | 0.002 | 27.559 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | C | 76 | ALA | 0 | 0.086 | 0.046 | 28.354 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | C | 77 | ARG | 1 | 0.879 | 0.925 | 29.877 | -0.081 | -0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | C | 78 | CYS | 0 | 0.035 | 0.030 | 33.586 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | C | 79 | PRO | 0 | -0.004 | 0.008 | 35.902 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |