![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 98RK2
Calculation Name: 3CJH-B-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3CJH
Chain ID: B
UniProt ID: P53299
Base Structure: X-ray
Registration Date: 2023-09-23
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 | 57 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -287043.160189 |
---|---|
FMO2-HF: Nuclear repulsion | 262276.923299 |
FMO2-HF: Total energy | -24766.23689 |
FMO2-MP2: Total energy | -24834.699392 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F035216/ligand_interaction/ligand_F035216.png)
Ligand Interaction
![ligand interaction](./Kdata/F035216/ligand_interaction/ligand_interaction_F035216.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(B:28:ASN)
Summations of interaction energy for
fragment #1(B:28:ASN)
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. |
-17.535 | -12.429 | 0.747 | -2.164 | -3.69 | 0.015 |
Interaction energy analysis for fragmet #1(B:28:ASN)
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 | B | 30 | LYS | 1 | 1.023 | 1.003 | 2.760 | -9.076 | -4.468 | 0.729 | -2.054 | -3.283 | 0.014 |
4 | B | 31 | GLN | 0 | 0.056 | 0.026 | 3.922 | -2.540 | -2.348 | 0.017 | -0.057 | -0.153 | 0.001 |
5 | B | 32 | LYS | 1 | 0.972 | 0.969 | 5.763 | -1.911 | -1.911 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | B | 33 | VAL | 0 | -0.002 | 0.010 | 3.789 | -1.204 | -0.898 | 0.001 | -0.053 | -0.254 | 0.000 |
7 | B | 34 | GLN | 0 | 0.027 | 0.016 | 5.622 | -0.993 | -0.993 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | B | 35 | MET | 0 | -0.032 | -0.008 | 9.194 | -0.458 | -0.458 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | B | 36 | SER | 0 | 0.027 | 0.008 | 8.379 | -0.341 | -0.341 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | B | 37 | ILE | 0 | 0.051 | 0.041 | 9.253 | -0.223 | -0.223 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | B | 38 | HIS | 0 | 0.043 | 0.045 | 11.798 | -0.214 | -0.214 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | B | 39 | GLN | 0 | -0.025 | -0.008 | 14.158 | -0.198 | -0.198 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | B | 40 | PHE | 0 | 0.009 | -0.024 | 11.144 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | B | 41 | THR | 0 | 0.019 | 0.002 | 15.176 | -0.088 | -0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | B | 42 | ASN | 0 | -0.009 | -0.005 | 17.497 | -0.085 | -0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | B | 43 | ILE | 0 | -0.073 | -0.033 | 17.987 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | B | 44 | CYS | 0 | -0.070 | -0.045 | 19.282 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | B | 45 | PHE | 0 | 0.044 | 0.035 | 21.058 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | B | 46 | LYS | 1 | 0.930 | 0.964 | 22.836 | -0.317 | -0.317 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | B | 47 | LYS | 1 | 0.901 | 0.951 | 23.664 | -0.234 | -0.234 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | B | 48 | CYS | 0 | -0.104 | -0.041 | 22.816 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | B | 49 | VAL | 0 | 0.029 | 0.036 | 24.782 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | B | 50 | GLU | -1 | -0.940 | -0.964 | 27.452 | 0.160 | 0.160 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | B | 51 | SER | 0 | -0.081 | -0.047 | 30.879 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | B | 52 | VAL | 0 | 0.000 | 0.004 | 29.746 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | B | 53 | ASN | 0 | -0.025 | -0.009 | 32.326 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | B | 54 | ASP | -1 | -0.876 | -0.934 | 32.983 | 0.164 | 0.164 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | B | 55 | SER | 0 | -0.053 | -0.044 | 29.657 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | B | 56 | ASN | 0 | -0.075 | -0.032 | 28.471 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | B | 57 | LEU | 0 | 0.023 | 0.030 | 22.712 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | B | 58 | SER | 0 | -0.014 | -0.034 | 27.326 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | B | 59 | SER | 0 | 0.052 | -0.016 | 27.497 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | B | 60 | GLN | 0 | -0.012 | 0.008 | 27.117 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | B | 61 | GLU | -1 | -0.814 | -0.885 | 26.193 | 0.212 | 0.212 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | B | 62 | GLU | -1 | -0.906 | -0.951 | 22.120 | 0.255 | 0.255 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | B | 63 | GLN | 0 | -0.027 | -0.007 | 22.031 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | B | 65 | LEU | 0 | 0.059 | 0.019 | 20.003 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | B | 66 | SER | 0 | 0.026 | 0.012 | 17.945 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | B | 67 | ASN | 0 | 0.013 | 0.002 | 18.209 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | B | 69 | VAL | 0 | 0.039 | 0.016 | 13.579 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | B | 70 | ASN | 0 | -0.058 | -0.035 | 15.918 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | B | 71 | ARG | 1 | 0.934 | 0.964 | 16.977 | -0.126 | -0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | B | 72 | PHE | 0 | -0.018 | -0.002 | 16.609 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | B | 73 | LEU | 0 | 0.011 | 0.008 | 11.674 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | B | 74 | ASP | -1 | -0.843 | -0.920 | 15.423 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | B | 75 | THR | 0 | -0.064 | -0.041 | 18.327 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | B | 76 | ASN | 0 | -0.023 | -0.012 | 15.388 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | B | 77 | ILE | 0 | 0.041 | 0.017 | 14.698 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | B | 78 | ARG | 1 | 0.940 | 0.968 | 17.107 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | B | 79 | ILE | 0 | -0.006 | -0.005 | 19.971 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | B | 80 | VAL | 0 | -0.004 | 0.012 | 15.864 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | B | 81 | ASN | 0 | -0.028 | -0.024 | 18.816 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | B | 82 | GLY | 0 | -0.038 | -0.024 | 20.579 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | B | 83 | LEU | 0 | -0.017 | -0.012 | 21.026 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | B | 84 | GLN | 0 | -0.044 | -0.011 | 18.700 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | B | 85 | ASN | 0 | -0.029 | -0.017 | 23.391 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | B | 86 | THR | 0 | -0.019 | 0.016 | 26.083 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |