
FMODB ID: KGRZ3
Calculation Name: 3PH0-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3PH0
Chain ID: A
UniProt ID: Q1EHA4
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.
Apendix: None
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 | 65 |
LigandResidueName | |
LigandFragmentNumber | 0 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -346577.998158 |
---|---|
FMO2-HF: Nuclear repulsion | 320700.711941 |
FMO2-HF: Total energy | -25877.286217 |
FMO2-MP2: Total energy | -25952.762532 |
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:1:MET)
Summations of interaction energy for
fragment #1(A:1:MET)
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. |
-2.044 | -0.705 | -0.007 | -0.693 | -0.639 | 0.001 |
Interaction energy analysis for fragmet #1(A:1:MET)
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 | THR | 0 | -0.016 | -0.009 | 3.765 | -0.488 | 0.851 | -0.007 | -0.693 | -0.639 | 0.001 |
4 | A | 4 | ASN | 0 | 0.027 | -0.005 | 6.391 | 0.357 | 0.357 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 5 | LEU | 0 | 0.024 | 0.021 | 9.458 | 0.100 | 0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | GLU | -1 | -0.772 | -0.897 | 5.654 | -2.596 | -2.596 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 7 | THR | 0 | -0.030 | -0.013 | 8.819 | 0.206 | 0.206 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | ARG | 1 | 0.812 | 0.893 | 11.503 | 0.360 | 0.360 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | LEU | 0 | 0.008 | -0.003 | 12.591 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | SER | 0 | -0.042 | -0.022 | 11.574 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | GLY | 0 | -0.010 | 0.000 | 14.093 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | ALA | 0 | -0.034 | -0.014 | 15.600 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | ASP | -1 | -0.751 | -0.868 | 17.582 | -0.175 | -0.175 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | PRO | 0 | 0.010 | 0.002 | 19.241 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | VAL | 0 | -0.055 | -0.019 | 22.051 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | PHE | 0 | 0.041 | 0.017 | 15.482 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | ALA | 0 | 0.020 | -0.001 | 18.193 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | ARG | 1 | 0.887 | 0.941 | 19.284 | 0.145 | 0.145 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | GLU | -1 | -0.906 | -0.949 | 22.112 | -0.193 | -0.193 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | LEU | 0 | 0.019 | 0.014 | 15.861 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | HIS | 0 | 0.012 | 0.002 | 19.843 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | ALA | 0 | 0.025 | 0.011 | 21.254 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | GLN | 0 | -0.003 | -0.012 | 21.631 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | LEU | 0 | 0.004 | 0.010 | 17.399 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | VAL | 0 | 0.008 | -0.005 | 22.001 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | GLN | 0 | -0.082 | -0.039 | 24.827 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | ALA | 0 | 0.030 | 0.014 | 23.691 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | LEU | 0 | -0.005 | -0.002 | 23.013 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | GLY | 0 | 0.018 | 0.010 | 25.534 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | ASP | -1 | -0.828 | -0.894 | 28.499 | -0.138 | -0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | VAL | 0 | -0.030 | 0.003 | 25.406 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | LYS | 1 | 0.810 | 0.878 | 25.494 | 0.224 | 0.224 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | ARG | 1 | 0.812 | 0.891 | 29.981 | 0.142 | 0.142 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | ARG | 1 | 0.798 | 0.880 | 27.666 | 0.165 | 0.165 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | LEU | 0 | -0.001 | 0.006 | 28.508 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | LEU | 0 | -0.003 | 0.004 | 33.031 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | ARG | 1 | 0.845 | 0.901 | 35.621 | 0.111 | 0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | GLY | 0 | 0.026 | 0.024 | 32.845 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | GLY | 0 | -0.001 | 0.023 | 33.907 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | THR | 0 | 0.027 | -0.016 | 31.268 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | GLN | 0 | 0.009 | -0.022 | 30.668 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | GLN | 0 | 0.074 | 0.055 | 33.382 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | GLN | 0 | 0.000 | -0.001 | 32.152 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | TYR | 0 | -0.030 | 0.001 | 31.101 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | GLN | 0 | 0.015 | 0.004 | 26.044 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | GLN | 0 | 0.021 | 0.022 | 26.674 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | TRP | 0 | 0.032 | 0.003 | 25.933 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | GLN | 0 | -0.049 | -0.031 | 25.147 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | GLN | 0 | 0.029 | 0.021 | 20.698 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | GLU | -1 | -0.847 | -0.893 | 21.558 | -0.204 | -0.204 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 51 | ALA | 0 | 0.004 | -0.011 | 21.991 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 52 | ASP | -1 | -0.837 | -0.912 | 20.668 | -0.254 | -0.254 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 53 | ALA | 0 | -0.027 | -0.011 | 17.627 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | ILE | 0 | -0.004 | 0.004 | 17.271 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | GLU | -1 | -0.786 | -0.882 | 18.873 | -0.267 | -0.267 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | ALA | 0 | -0.011 | -0.007 | 15.132 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | GLY | 0 | 0.016 | 0.002 | 14.358 | -0.067 | -0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | LEU | 0 | -0.004 | -0.018 | 15.126 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | ASN | 0 | -0.031 | -0.018 | 15.563 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 60 | ILE | 0 | -0.018 | 0.000 | 10.029 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | ILE | 0 | 0.016 | 0.015 | 12.637 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | GLU | -1 | -0.861 | -0.925 | 14.504 | -0.329 | -0.329 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 63 | LYS | 1 | 0.844 | 0.925 | 12.717 | 0.575 | 0.575 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 64 | ILE | 0 | -0.020 | 0.003 | 8.724 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 65 | LYS | 1 | 0.784 | 0.898 | 11.827 | 0.414 | 0.414 | 0.000 | 0.000 | 0.000 | 0.000 |