![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 2NM8R
Calculation Name: 3CJH-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3CJH
Chain ID: A
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 | 50 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -239857.972829 |
---|---|
FMO2-HF: Nuclear repulsion | 217874.22742 |
FMO2-HF: Total energy | -21983.745409 |
FMO2-MP2: Total energy | -22044.215336 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F035213/ligand_interaction/ligand_F035213.png)
Ligand Interaction
![ligand interaction](./Kdata/F035213/ligand_interaction/ligand_interaction_F035213.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(A:46:ALA)
Summations of interaction energy for
fragment #1(A:46:ALA)
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. |
-3.78 | -0.195 | 0.234 | -1.565 | -2.255 | 0.004 |
Interaction energy analysis for fragmet #1(A:46:ALA)
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 | 48 | GLU | -1 | -0.915 | -0.958 | 2.703 | -4.138 | -1.185 | 0.229 | -1.427 | -1.755 | 0.004 |
4 | A | 49 | LEU | 0 | 0.055 | 0.024 | 3.204 | -0.798 | -0.284 | 0.006 | -0.126 | -0.394 | 0.000 |
5 | A | 50 | VAL | 0 | 0.001 | 0.000 | 4.960 | 0.355 | 0.473 | -0.001 | -0.012 | -0.106 | 0.000 |
6 | A | 51 | ASN | 0 | 0.030 | 0.013 | 7.447 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 52 | LYS | 1 | 1.044 | 1.030 | 7.668 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 53 | ILE | 0 | -0.032 | 0.005 | 8.959 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 54 | SER | 0 | -0.028 | -0.021 | 11.249 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 55 | GLU | -1 | -0.918 | -0.952 | 12.731 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 56 | ASN | 0 | -0.039 | -0.033 | 12.452 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 57 | CYS | 0 | -0.090 | -0.060 | 15.166 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 58 | PHE | 0 | -0.012 | 0.004 | 16.776 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 59 | GLU | -1 | -0.934 | -0.972 | 18.356 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 60 | LYS | 1 | 0.865 | 0.936 | 19.186 | 0.125 | 0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 61 | CYS | 0 | -0.094 | -0.029 | 21.278 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 62 | LEU | 0 | -0.011 | 0.008 | 21.275 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 63 | THR | 0 | 0.042 | 0.025 | 24.279 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 64 | SER | 0 | -0.011 | -0.005 | 26.979 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 65 | PRO | 0 | 0.002 | -0.023 | 28.813 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 66 | TYR | 0 | -0.021 | 0.000 | 24.218 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 67 | ALA | 0 | 0.000 | 0.021 | 27.709 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 68 | THR | 0 | 0.005 | -0.010 | 29.230 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 69 | ARG | 1 | 0.991 | 0.994 | 24.070 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 70 | ASN | 0 | -0.015 | -0.024 | 24.481 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 71 | ASP | -1 | -0.835 | -0.931 | 21.657 | -0.122 | -0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 72 | ALA | 0 | 0.008 | 0.012 | 21.871 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 74 | ILE | 0 | 0.043 | 0.022 | 17.240 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 75 | ASP | -1 | -0.865 | -0.925 | 17.922 | -0.214 | -0.214 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 76 | GLN | 0 | -0.052 | -0.024 | 18.395 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 78 | LEU | 0 | 0.071 | 0.035 | 11.947 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 79 | ALA | 0 | -0.014 | -0.011 | 14.620 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 80 | LYS | 1 | 0.908 | 0.928 | 16.599 | 0.147 | 0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 81 | TYR | 0 | 0.041 | 0.029 | 9.625 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 82 | MET | 0 | 0.022 | 0.003 | 9.410 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 83 | ARG | 1 | 0.912 | 0.954 | 13.305 | 0.219 | 0.219 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 84 | SER | 0 | -0.015 | -0.008 | 15.081 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 85 | TRP | 0 | 0.019 | 0.018 | 7.559 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 86 | ASN | 0 | 0.014 | 0.000 | 12.899 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 87 | VAL | 0 | -0.015 | -0.001 | 15.033 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 88 | ILE | 0 | 0.019 | 0.016 | 13.856 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 89 | SER | 0 | -0.005 | 0.008 | 12.933 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 90 | LYS | 1 | 1.002 | 1.000 | 14.608 | 0.179 | 0.179 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 91 | ALA | 0 | -0.039 | -0.022 | 18.160 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 92 | TYR | 0 | -0.021 | -0.016 | 14.379 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 93 | ILE | 0 | 0.051 | 0.009 | 15.039 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 94 | SER | 0 | -0.046 | -0.026 | 18.476 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 95 | ARG | 1 | 0.912 | 0.961 | 20.821 | 0.089 | 0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 96 | ILE | 0 | -0.065 | -0.012 | 17.220 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 97 | GLN | 0 | -0.009 | 0.010 | 21.484 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |