![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: MNLJZ
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 | 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 | 57 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -287176.405947 |
---|---|
FMO2-HF: Nuclear repulsion | 262409.684314 |
FMO2-HF: Total energy | -24766.721633 |
FMO2-MP2: Total energy | -24835.116621 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F035215/ligand_interaction/ligand_F035215.png)
Ligand Interaction
![ligand interaction](./Kdata/F035215/ligand_interaction/ligand_interaction_F035215.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. |
-17.379 | -12.213 | 0.527 | -2.15 | -3.543 | 0.013 |
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 | 1.019 | 1.003 | 2.878 | -9.230 | -4.546 | 0.515 | -2.042 | -3.157 | 0.013 |
4 | B | 31 | GLN | 0 | 0.054 | 0.032 | 4.033 | -2.292 | -2.110 | 0.010 | -0.058 | -0.134 | 0.000 |
5 | B | 32 | LYS | 1 | 0.971 | 0.968 | 5.984 | -1.829 | -1.829 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | B | 33 | VAL | 0 | 0.003 | 0.002 | 3.911 | -1.156 | -0.856 | 0.002 | -0.050 | -0.252 | 0.000 |
7 | B | 34 | GLN | 0 | 0.013 | 0.016 | 5.743 | -1.025 | -1.025 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | B | 35 | MET | 0 | -0.017 | -0.009 | 9.312 | -0.426 | -0.426 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | B | 36 | SER | 0 | 0.007 | 0.007 | 8.661 | -0.334 | -0.334 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | B | 37 | ILE | 0 | 0.052 | 0.038 | 9.340 | -0.213 | -0.213 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | B | 38 | HIS | 0 | 0.050 | 0.042 | 11.885 | -0.236 | -0.236 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | B | 39 | GLN | 0 | -0.015 | -0.004 | 14.275 | -0.173 | -0.173 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | B | 40 | PHE | 0 | 0.015 | -0.017 | 10.945 | -0.075 | -0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | B | 41 | THR | 0 | 0.032 | 0.016 | 15.278 | -0.091 | -0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | B | 42 | ASN | 0 | 0.022 | 0.011 | 17.572 | -0.096 | -0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | B | 43 | ILE | 0 | -0.084 | -0.039 | 18.271 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | B | 44 | CYS | 0 | -0.060 | -0.033 | 19.319 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | B | 45 | PHE | 0 | 0.048 | 0.034 | 21.123 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | B | 46 | LYS | 1 | 0.885 | 0.934 | 22.900 | -0.339 | -0.339 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | B | 47 | LYS | 1 | 0.911 | 0.959 | 23.743 | -0.231 | -0.231 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | B | 48 | CYS | 0 | -0.095 | -0.048 | 22.805 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | B | 49 | VAL | 0 | 0.019 | 0.035 | 24.821 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | B | 50 | GLU | -1 | -0.928 | -0.931 | 27.500 | 0.153 | 0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | B | 51 | SER | 0 | -0.058 | -0.060 | 30.931 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | B | 52 | VAL | 0 | -0.006 | -0.001 | 29.684 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | B | 53 | ASN | 0 | -0.042 | -0.019 | 32.377 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | B | 54 | ASP | -1 | -0.833 | -0.917 | 32.923 | 0.148 | 0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | B | 55 | SER | 0 | -0.028 | -0.021 | 29.817 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | B | 56 | ASN | 0 | -0.138 | -0.068 | 28.495 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | B | 57 | LEU | 0 | 0.013 | 0.026 | 22.912 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | B | 58 | SER | 0 | -0.019 | -0.047 | 27.336 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | B | 59 | SER | 0 | 0.048 | -0.012 | 27.492 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | B | 60 | GLN | 0 | -0.009 | 0.003 | 27.099 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | B | 61 | GLU | -1 | -0.793 | -0.873 | 25.991 | 0.195 | 0.195 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | B | 62 | GLU | -1 | -0.909 | -0.942 | 22.267 | 0.224 | 0.224 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | B | 63 | GLN | 0 | -0.011 | -0.009 | 22.021 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | B | 65 | LEU | 0 | 0.058 | 0.024 | 19.923 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | B | 66 | SER | 0 | 0.005 | 0.007 | 17.937 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | B | 67 | ASN | 0 | 0.016 | 0.005 | 18.200 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | B | 69 | VAL | 0 | 0.033 | 0.010 | 13.610 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | B | 70 | ASN | 0 | -0.068 | -0.042 | 15.939 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | B | 71 | ARG | 1 | 0.914 | 0.942 | 16.972 | -0.115 | -0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | B | 72 | PHE | 0 | -0.034 | -0.004 | 16.459 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | B | 73 | LEU | 0 | 0.006 | -0.001 | 11.697 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | B | 74 | ASP | -1 | -0.823 | -0.903 | 15.448 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | B | 75 | THR | 0 | -0.060 | -0.043 | 18.331 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | B | 76 | ASN | 0 | -0.021 | -0.009 | 15.465 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | B | 77 | ILE | 0 | 0.037 | 0.026 | 14.081 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | B | 78 | ARG | 1 | 0.968 | 0.987 | 17.109 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | B | 79 | ILE | 0 | -0.010 | -0.008 | 20.083 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | B | 80 | VAL | 0 | 0.010 | 0.008 | 15.696 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | B | 81 | ASN | 0 | -0.067 | -0.048 | 17.817 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | B | 82 | GLY | 0 | -0.025 | -0.018 | 20.579 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | B | 83 | LEU | 0 | -0.008 | -0.009 | 20.953 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | B | 84 | GLN | 0 | -0.018 | 0.010 | 18.556 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | B | 85 | ASN | 0 | -0.029 | 0.002 | 23.391 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | B | 86 | THR | 0 | -0.061 | -0.028 | 26.081 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |