![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: ZY56N
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 | 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 | 81 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -537278.314839 |
---|---|
FMO2-HF: Nuclear repulsion | 505103.396112 |
FMO2-HF: Total energy | -32174.918727 |
FMO2-MP2: Total energy | -32269.769261 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F021256/ligand_interaction/ligand_F021256.png)
Ligand Interaction
![ligand interaction](./Kdata/F021256/ligand_interaction/ligand_interaction_F021256.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. |
2.391 | 3.985 | -0.016 | -0.681 | -0.897 | 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 | 0.022 | 0.002 | 3.785 | -1.505 | -0.035 | -0.015 | -0.668 | -0.787 | 0.003 |
4 | A | 845 | LYS | 1 | 0.947 | 0.966 | 3.918 | 3.454 | 3.578 | -0.001 | -0.013 | -0.110 | 0.000 |
5 | A | 846 | VAL | 0 | 0.001 | 0.010 | 8.294 | 0.247 | 0.247 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 847 | LEU | 0 | -0.038 | -0.010 | 11.490 | -0.070 | -0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 848 | LEU | 0 | -0.037 | -0.032 | 12.921 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 849 | ASP | -1 | -0.814 | -0.897 | 15.525 | -0.321 | -0.321 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 850 | ILE | 0 | -0.141 | -0.061 | 17.834 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 851 | PHE | 0 | -0.072 | -0.060 | 20.882 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 852 | THR | 0 | 0.081 | 0.024 | 22.694 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 853 | GLY | 0 | -0.038 | -0.014 | 24.843 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 854 | VAL | 0 | -0.085 | -0.036 | 27.472 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 855 | ARG | 1 | 0.879 | 0.931 | 29.282 | 0.097 | 0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 856 | LEU | 0 | 0.000 | -0.004 | 30.335 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 857 | TYR | 0 | 0.039 | 0.027 | 32.733 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 858 | LEU | 0 | -0.026 | -0.016 | 29.704 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 859 | PRO | 0 | 0.044 | 0.021 | 33.787 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 860 | PRO | 0 | 0.055 | 0.047 | 35.073 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 861 | SER | 0 | -0.033 | -0.007 | 36.021 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 862 | THR | 0 | -0.054 | -0.055 | 33.089 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 863 | PRO | 0 | 0.054 | 0.019 | 34.224 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 864 | ASP | -1 | -0.800 | -0.913 | 28.315 | -0.089 | -0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 865 | PHE | 0 | 0.019 | 0.026 | 29.233 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 866 | SER | 0 | -0.014 | -0.003 | 27.494 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 867 | ARG | 1 | 0.888 | 0.920 | 24.131 | 0.071 | 0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 868 | LEU | 0 | 0.051 | 0.029 | 24.499 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 869 | ARG | 1 | 1.004 | 1.005 | 25.831 | 0.127 | 0.127 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 870 | ARG | 1 | 0.904 | 0.959 | 17.481 | 0.186 | 0.186 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 871 | TYR | 0 | -0.017 | -0.027 | 18.088 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 872 | PHE | 0 | -0.013 | 0.010 | 21.599 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 873 | VAL | 0 | 0.017 | 0.008 | 22.290 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 874 | ALA | 0 | -0.064 | -0.024 | 17.910 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 875 | PHE | 0 | -0.065 | -0.047 | 15.488 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 876 | ASP | -1 | -0.758 | -0.857 | 20.048 | -0.230 | -0.230 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 877 | GLY | 0 | -0.023 | 0.002 | 22.434 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 878 | ASP | -1 | -0.864 | -0.923 | 25.750 | -0.136 | -0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 879 | LEU | 0 | -0.047 | -0.043 | 28.231 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 880 | VAL | 0 | 0.011 | 0.018 | 30.563 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 881 | GLN | 0 | 0.008 | -0.018 | 33.339 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 882 | GLU | -1 | -0.901 | -0.958 | 36.472 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 883 | PHE | 0 | -0.033 | -0.022 | 38.040 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 884 | ASP | -1 | -0.844 | -0.927 | 37.853 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 885 | MET | 0 | -0.067 | -0.015 | 38.654 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 886 | THR | 0 | -0.051 | -0.029 | 39.729 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 887 | SER | 0 | 0.000 | 0.014 | 38.086 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 888 | ALA | 0 | -0.052 | -0.014 | 35.843 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 889 | THR | 0 | 0.060 | 0.002 | 32.859 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 890 | HIS | 0 | -0.009 | 0.027 | 31.294 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 891 | VAL | 0 | 0.018 | 0.002 | 34.790 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 892 | LEU | 0 | 0.001 | 0.020 | 32.923 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 893 | GLY | 0 | 0.005 | 0.001 | 36.830 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 894 | SER | 0 | -0.006 | -0.010 | 40.308 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 895 | ARG | 1 | 0.924 | 0.951 | 40.750 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 896 | ASP | -1 | -0.880 | -0.939 | 43.234 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 897 | LYS | 1 | 0.899 | 0.946 | 43.978 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 898 | ASN | 0 | -0.034 | -0.024 | 39.590 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 899 | PRO | 0 | 0.047 | 0.028 | 42.195 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 900 | ALA | 0 | 0.014 | 0.014 | 41.347 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 901 | ALA | 0 | 0.003 | 0.033 | 37.841 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 902 | GLN | 0 | -0.017 | -0.016 | 33.903 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 903 | GLN | 0 | -0.043 | -0.031 | 35.964 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 904 | VAL | 0 | -0.006 | -0.002 | 31.734 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 905 | SER | 0 | -0.005 | -0.016 | 32.450 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 906 | PRO | 0 | 0.066 | 0.015 | 30.496 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 907 | GLU | -1 | -0.871 | -0.945 | 28.938 | -0.073 | -0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 908 | TRP | 0 | -0.029 | -0.010 | 28.348 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 909 | ILE | 0 | 0.047 | 0.030 | 25.468 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 910 | TRP | 0 | 0.018 | -0.002 | 22.494 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 911 | ALA | 0 | -0.054 | -0.029 | 23.354 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 912 | CYS | 0 | 0.020 | 0.030 | 23.397 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 913 | ILE | 0 | -0.015 | 0.003 | 18.880 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 914 | ARG | 1 | 0.900 | 0.952 | 18.781 | 0.066 | 0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 915 | LYS | 1 | 0.901 | 0.953 | 18.911 | 0.076 | 0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 916 | ARG | 1 | 0.920 | 0.971 | 11.176 | 0.496 | 0.496 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 917 | ARG | 1 | 0.976 | 0.988 | 18.201 | 0.128 | 0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 918 | LEU | 0 | 0.071 | 0.034 | 21.274 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 919 | VAL | 0 | -0.057 | -0.035 | 24.754 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 920 | ALA | 0 | 0.024 | 0.010 | 27.029 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 921 | PRO | 0 | 0.005 | -0.002 | 30.804 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 922 | SER | 0 | 0.033 | 0.029 | 31.243 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |