![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: ZVZ1N
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 | 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 | 50 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -241187.896242 |
---|---|
FMO2-HF: Nuclear repulsion | 219203.596893 |
FMO2-HF: Total energy | -21984.299349 |
FMO2-MP2: Total energy | -22044.751749 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F035211/ligand_interaction/ligand_F035211.png)
Ligand Interaction
![ligand interaction](./Kdata/F035211/ligand_interaction/ligand_interaction_F035211.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. |
-2.561 | 0.592 | 0.093 | -1.32 | -1.925 | 0.001 |
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 | -0.874 | -0.940 | 2.837 | -4.621 | -1.997 | 0.091 | -1.221 | -1.494 | 0.001 |
4 | A | 49 | LEU | 0 | 0.064 | 0.043 | 3.545 | 0.028 | 0.438 | 0.003 | -0.085 | -0.328 | 0.000 |
5 | A | 50 | VAL | 0 | 0.007 | 0.000 | 5.383 | 0.477 | 0.596 | -0.001 | -0.014 | -0.103 | 0.000 |
6 | A | 51 | ASN | 0 | -0.016 | -0.002 | 7.396 | 0.350 | 0.350 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 52 | LYS | 1 | 0.903 | 0.954 | 7.234 | 0.411 | 0.411 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 53 | ILE | 0 | -0.026 | -0.012 | 8.378 | 0.120 | 0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 54 | SER | 0 | -0.025 | -0.028 | 11.311 | 0.113 | 0.113 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 55 | GLU | -1 | -0.861 | -0.919 | 11.691 | -0.160 | -0.160 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 56 | ASN | 0 | -0.020 | -0.009 | 13.041 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 57 | CYS | 0 | -0.054 | -0.037 | 15.426 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 58 | PHE | 0 | 0.014 | 0.012 | 17.098 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 59 | GLU | -1 | -0.869 | -0.944 | 18.474 | -0.149 | -0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 60 | LYS | 1 | 0.766 | 0.877 | 17.616 | 0.215 | 0.215 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 61 | CYS | 0 | -0.096 | -0.012 | 21.172 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 62 | LEU | 0 | -0.002 | 0.020 | 21.017 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 63 | THR | 0 | 0.008 | -0.005 | 24.309 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 64 | SER | 0 | -0.005 | 0.008 | 26.840 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 65 | PRO | 0 | 0.006 | -0.007 | 29.026 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 66 | TYR | 0 | -0.002 | -0.012 | 24.375 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 67 | ALA | 0 | -0.005 | 0.010 | 27.618 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 68 | THR | 0 | -0.024 | -0.009 | 28.877 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 69 | ARG | 1 | 0.971 | 0.994 | 23.785 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 70 | ASN | 0 | 0.014 | -0.017 | 23.950 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 71 | ASP | -1 | -0.861 | -0.932 | 21.645 | -0.112 | -0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 72 | ALA | 0 | 0.070 | 0.035 | 21.448 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 74 | ILE | 0 | 0.027 | 0.008 | 16.961 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 75 | ASP | -1 | -0.868 | -0.926 | 17.575 | -0.209 | -0.209 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 76 | GLN | 0 | -0.076 | -0.054 | 18.257 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 78 | LEU | 0 | 0.066 | 0.033 | 11.671 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 79 | ALA | 0 | -0.007 | -0.006 | 14.323 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 80 | LYS | 1 | 0.930 | 0.959 | 16.654 | 0.178 | 0.178 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 81 | TYR | 0 | 0.040 | 0.038 | 9.499 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 82 | MET | 0 | 0.028 | 0.009 | 8.722 | -0.055 | -0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 83 | ARG | 1 | 0.922 | 0.960 | 12.896 | 0.222 | 0.222 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 84 | SER | 0 | -0.015 | -0.023 | 15.322 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 85 | TRP | 0 | 0.021 | 0.014 | 8.110 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 86 | ASN | 0 | 0.013 | 0.011 | 12.810 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 87 | VAL | 0 | -0.034 | -0.006 | 14.703 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 88 | ILE | 0 | 0.018 | 0.007 | 14.153 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 89 | SER | 0 | -0.005 | -0.007 | 12.303 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 90 | LYS | 1 | 0.992 | 0.997 | 14.391 | 0.195 | 0.195 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 91 | ALA | 0 | -0.015 | 0.003 | 17.844 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 92 | TYR | 0 | 0.010 | -0.002 | 15.198 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 93 | ILE | 0 | 0.017 | -0.005 | 14.598 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 94 | SER | 0 | -0.038 | -0.034 | 18.408 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 95 | ARG | 1 | 0.890 | 0.950 | 21.128 | 0.125 | 0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 96 | ILE | 0 | -0.043 | -0.008 | 17.589 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 97 | GLN | 0 | -0.028 | 0.005 | 21.826 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |