![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: Q1GYY
Calculation Name: 3PC7-A-Xray372
Preferred Name: DNA ligase 3
Target Type: SINGLE PROTEIN
Ligand Name:
ligand 3-letter code:
PDB ID: 3PC7
Chain ID: A
ChEMBL ID: CHEMBL4295773
UniProt ID: P49916
Base Structure: X-ray
Registration Date: 2023-06-19
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 | 81 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -538239.516071 |
---|---|
FMO2-HF: Nuclear repulsion | 506064.290558 |
FMO2-HF: Total energy | -32175.225513 |
FMO2-MP2: Total energy | -32270.076231 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F021254/ligand_interaction/ligand_F021254.png)
Ligand Interaction
![ligand interaction](./Kdata/F021254/ligand_interaction/ligand_interaction_F021254.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:842:SER)
Summations of interaction energy for
fragment #1(A:842:SER)
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. |
-1.661 | -0.238 | -0.005 | -0.607 | -0.811 | 0.003 |
Interaction energy analysis for fragmet #1(A:842:SER)
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 | 844 | THR | 0 | 0.027 | 0.006 | 3.859 | 0.226 | 1.451 | -0.006 | -0.562 | -0.657 | 0.003 |
4 | A | 845 | LYS | 1 | 0.875 | 0.920 | 3.901 | -2.738 | -2.540 | 0.001 | -0.045 | -0.154 | 0.000 |
5 | A | 846 | VAL | 0 | 0.018 | 0.026 | 8.670 | 0.131 | 0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 847 | LEU | 0 | -0.028 | -0.006 | 11.499 | -0.163 | -0.163 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 848 | LEU | 0 | -0.017 | -0.019 | 12.341 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 849 | ASP | -1 | -0.830 | -0.908 | 15.733 | -0.183 | -0.183 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 850 | ILE | 0 | -0.134 | -0.058 | 17.890 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 851 | PHE | 0 | -0.047 | -0.046 | 20.849 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 852 | THR | 0 | 0.049 | 0.014 | 22.799 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 853 | GLY | 0 | -0.029 | -0.006 | 24.860 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 854 | VAL | 0 | -0.080 | -0.040 | 27.512 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 855 | ARG | 1 | 0.811 | 0.896 | 29.501 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 856 | LEU | 0 | -0.017 | -0.012 | 30.390 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 857 | TYR | 0 | -0.022 | -0.038 | 33.179 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 858 | LEU | 0 | -0.038 | -0.022 | 30.254 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 859 | PRO | 0 | 0.043 | 0.023 | 34.394 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 860 | PRO | 0 | 0.050 | 0.025 | 35.941 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 861 | SER | 0 | -0.008 | 0.005 | 36.713 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 862 | THR | 0 | -0.058 | -0.035 | 33.726 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 863 | PRO | 0 | 0.034 | 0.009 | 34.543 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 864 | ASP | -1 | -0.769 | -0.879 | 28.188 | -0.084 | -0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 865 | PHE | 0 | 0.035 | 0.034 | 29.753 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 866 | SER | 0 | -0.008 | -0.002 | 28.716 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 867 | ARG | 1 | 0.846 | 0.882 | 24.573 | 0.086 | 0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 868 | LEU | 0 | 0.023 | 0.014 | 25.228 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 869 | ARG | 1 | 1.003 | 1.000 | 26.491 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 870 | ARG | 1 | 0.892 | 0.955 | 18.704 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 871 | TYR | 0 | -0.004 | -0.027 | 18.240 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 872 | PHE | 0 | 0.002 | 0.026 | 22.074 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 873 | VAL | 0 | 0.032 | 0.018 | 23.474 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 874 | ALA | 0 | -0.070 | -0.033 | 18.723 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 875 | PHE | 0 | -0.056 | -0.046 | 15.780 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 876 | ASP | -1 | -0.773 | -0.868 | 20.214 | -0.108 | -0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 877 | GLY | 0 | 0.007 | 0.011 | 22.718 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 878 | ASP | -1 | -0.863 | -0.921 | 25.948 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 879 | LEU | 0 | -0.038 | -0.027 | 28.769 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 880 | VAL | 0 | 0.029 | 0.021 | 31.290 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 881 | GLN | 0 | -0.022 | -0.017 | 34.040 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 882 | GLU | -1 | -0.836 | -0.899 | 37.208 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 883 | PHE | 0 | -0.021 | -0.028 | 38.912 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 884 | ASP | -1 | -0.797 | -0.874 | 37.339 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 885 | MET | 0 | -0.010 | 0.008 | 38.861 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 886 | THR | 0 | -0.018 | -0.014 | 39.941 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 887 | SER | 0 | -0.057 | -0.032 | 38.424 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 888 | ALA | 0 | -0.026 | 0.002 | 35.791 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 889 | THR | 0 | 0.031 | -0.002 | 32.843 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 890 | HIS | 0 | -0.003 | 0.013 | 31.436 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 891 | VAL | 0 | 0.021 | -0.002 | 34.915 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 892 | LEU | 0 | 0.004 | 0.016 | 33.175 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 893 | GLY | 0 | -0.003 | 0.001 | 37.224 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 894 | SER | 0 | -0.036 | -0.050 | 40.718 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 895 | ARG | 1 | 0.897 | 0.940 | 40.997 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 896 | ASP | -1 | -0.882 | -0.909 | 43.444 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 897 | LYS | 1 | 0.925 | 0.958 | 43.680 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 898 | ASN | 0 | -0.026 | -0.018 | 39.765 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 899 | PRO | 0 | 0.039 | 0.022 | 42.315 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 900 | ALA | 0 | 0.001 | 0.013 | 41.618 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 901 | ALA | 0 | 0.006 | 0.030 | 37.849 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 902 | GLN | 0 | -0.049 | -0.042 | 34.485 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 903 | GLN | 0 | -0.015 | -0.024 | 36.141 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 904 | VAL | 0 | -0.014 | 0.003 | 32.166 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 905 | SER | 0 | -0.004 | -0.020 | 33.284 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 906 | PRO | 0 | 0.054 | 0.009 | 30.833 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 907 | GLU | -1 | -0.838 | -0.897 | 29.229 | -0.102 | -0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 908 | TRP | 0 | 0.000 | -0.002 | 28.644 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 909 | ILE | 0 | 0.046 | 0.037 | 25.828 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 910 | TRP | 0 | 0.011 | -0.010 | 22.505 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 911 | ALA | 0 | -0.057 | -0.028 | 23.877 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 912 | CYS | 0 | 0.014 | 0.020 | 23.714 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 913 | ILE | 0 | -0.014 | 0.005 | 19.296 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 914 | ARG | 1 | 0.891 | 0.949 | 19.250 | 0.145 | 0.145 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 915 | LYS | 1 | 0.919 | 0.962 | 19.955 | 0.219 | 0.219 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 916 | ARG | 1 | 0.912 | 0.963 | 10.952 | 0.788 | 0.788 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 917 | ARG | 1 | 0.946 | 0.981 | 18.419 | 0.279 | 0.279 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 918 | LEU | 0 | 0.078 | 0.044 | 21.342 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 919 | VAL | 0 | -0.036 | -0.032 | 24.857 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 920 | ALA | 0 | 0.039 | 0.023 | 27.318 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 921 | PRO | 0 | 0.011 | 0.012 | 31.141 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 922 | SER | 0 | -0.012 | -0.023 | 31.680 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |