![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: QVV8Y
Calculation Name: 3PH0-C-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3PH0
Chain ID: C
UniProt ID: Q1EHA4
Base Structure: X-ray
Registration Date: 2023-09-21
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 | 53 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -258719.090669 |
---|---|
FMO2-HF: Nuclear repulsion | 236947.263794 |
FMO2-HF: Total energy | -21771.826876 |
FMO2-MP2: Total energy | -21830.706439 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F033409/ligand_interaction/ligand_F033409.png)
Ligand Interaction
![ligand interaction](./Kdata/F033409/ligand_interaction/ligand_interaction_F033409.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:1:MET)
Summations of interaction energy for
fragment #1(C: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. |
-6.019 | -1.417 | 3.666 | -2.76 | -5.509 | 0.013 |
Interaction energy analysis for fragmet #1(C: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 | C | 3 | VAL | 0 | 0.078 | 0.023 | 3.616 | -0.221 | 1.071 | -0.001 | -0.653 | -0.639 | 0.003 |
4 | C | 4 | GLN | 0 | 0.027 | 0.006 | 6.198 | 0.271 | 0.271 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | C | 5 | LEU | 0 | 0.028 | 0.030 | 2.058 | -1.068 | -0.650 | 3.163 | -1.037 | -2.543 | 0.001 |
6 | C | 6 | LYS | 1 | 0.829 | 0.897 | 3.181 | -2.889 | -1.551 | 0.212 | -0.505 | -1.045 | 0.005 |
7 | C | 7 | LYS | 1 | 0.919 | 0.951 | 4.617 | -1.063 | -0.971 | -0.001 | -0.017 | -0.074 | 0.000 |
8 | C | 8 | GLN | 0 | -0.017 | 0.002 | 6.802 | -0.136 | -0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | C | 9 | LEU | 0 | 0.010 | 0.006 | 3.983 | -0.331 | -0.119 | 0.002 | -0.036 | -0.178 | 0.000 |
10 | C | 10 | ALA | 0 | 0.017 | 0.015 | 7.770 | -0.134 | -0.134 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | C | 11 | GLU | -1 | -0.926 | -0.958 | 10.346 | 0.066 | 0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | C | 12 | LEU | 0 | -0.003 | -0.001 | 10.371 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | C | 13 | ALA | 0 | 0.000 | -0.007 | 11.704 | -0.048 | -0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | C | 14 | LEU | 0 | -0.023 | -0.017 | 13.378 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | C | 15 | ALA | 0 | 0.000 | 0.002 | 15.428 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | C | 16 | GLY | 0 | 0.026 | 0.012 | 15.960 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | C | 17 | THR | 0 | -0.049 | -0.037 | 17.368 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | C | 18 | GLY | 0 | -0.018 | 0.005 | 19.673 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | C | 19 | HIS | 0 | -0.088 | -0.054 | 20.201 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | C | 20 | HIS | 0 | 0.020 | 0.020 | 22.176 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | C | 21 | CYS | 0 | -0.048 | -0.012 | 17.511 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | C | 22 | HIS | 0 | 0.029 | -0.015 | 17.634 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | C | 23 | GLN | 0 | -0.040 | -0.008 | 17.576 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | C | 24 | GLU | -1 | -0.820 | -0.918 | 14.084 | -0.182 | -0.182 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | C | 25 | ALA | 0 | 0.021 | 0.006 | 13.230 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | C | 26 | ALA | 0 | -0.013 | 0.003 | 13.893 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | C | 27 | SER | 0 | -0.013 | -0.007 | 12.289 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | C | 28 | ILE | 0 | -0.053 | -0.026 | 8.434 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | C | 29 | ALA | 0 | -0.013 | -0.016 | 10.187 | 0.150 | 0.150 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | C | 30 | ASP | -1 | -0.832 | -0.912 | 12.765 | 0.067 | 0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | C | 31 | TRP | 0 | -0.040 | -0.008 | 3.123 | -1.194 | 0.056 | 0.291 | -0.512 | -1.030 | 0.004 |
32 | C | 32 | LEU | 0 | -0.029 | -0.027 | 7.048 | 0.159 | 0.159 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | C | 33 | ALA | 0 | -0.006 | 0.005 | 9.653 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | C | 34 | GLN | 0 | -0.077 | -0.032 | 9.557 | -0.071 | -0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | C | 35 | GLU | -1 | -0.871 | -0.922 | 7.659 | 0.662 | 0.662 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | C | 36 | GLU | -1 | -0.888 | -0.945 | 11.283 | 0.120 | 0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | C | 37 | CYS | 0 | -0.082 | -0.040 | 11.453 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | C | 38 | MET | 0 | -0.012 | -0.013 | 9.663 | 0.096 | 0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | C | 39 | ALA | 0 | 0.041 | 0.031 | 13.021 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | C | 40 | GLU | -1 | -0.844 | -0.942 | 16.375 | 0.118 | 0.118 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | C | 41 | CYS | 0 | -0.049 | -0.016 | 12.917 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | C | 42 | VAL | 0 | 0.016 | 0.008 | 13.639 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | C | 43 | THR | 0 | -0.007 | 0.004 | 15.157 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | C | 44 | LEU | 0 | 0.023 | 0.018 | 17.871 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | C | 45 | ILE | 0 | 0.009 | 0.019 | 12.910 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | C | 46 | ARG | 1 | 0.921 | 0.932 | 16.504 | -0.108 | -0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | C | 47 | LEU | 0 | -0.006 | 0.003 | 19.438 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | C | 48 | SER | 0 | 0.025 | 0.013 | 19.933 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | C | 49 | SER | 0 | -0.013 | -0.008 | 19.532 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | C | 50 | LEU | 0 | -0.063 | -0.044 | 21.587 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | C | 51 | MET | 0 | -0.072 | -0.030 | 24.689 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | C | 52 | ASN | 0 | -0.054 | -0.023 | 23.620 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | C | 53 | GLN | 0 | -0.049 | 0.005 | 23.605 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |