![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 4NMQN
Calculation Name: 3PC7-A-Xray313
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: 2021-09-06
Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.
Modeling method
Optimization | MOE:Amber10:EHT |
---|---|
Restraint | OptH |
Protonation | MOE:Protonate 3D |
Complement | MOE:Structure Preparation |
Water | No |
Procedure | Auto-FMO protocol ver. 1.20200116 |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 82 |
LigandCharge | |
Software | ABINIT-MP - Open Ver.1 Rev. 15 / 20190524 |
Total energy (hartree)
FMO2-HF: Electronic energy | -539520.649721 |
---|---|
FMO2-HF: Nuclear repulsion | 507194.411736 |
FMO2-HF: Total energy | -32326.237985 |
FMO2-MP2: Total energy | -32421.519044 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F015721/ligand_interaction/ligand_F015721.png)
Ligand Interaction
![ligand interaction](./Kdata/F015721/ligand_interaction/ligand_interaction_F015721.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:841:ACE )
Summations of interaction energy for
fragment #1(A:841:ACE )
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. |
-0.711 | 1.472 | 0.446 | -1.348 | -1.281 | -0.007 |
Interaction energy analysis for fragmet #1(A:841:ACE )
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 | 843 | GLN | 0 | -0.001 | 0.032 | 2.946 | -1.446 | 0.696 | 0.446 | -1.341 | -1.247 | -0.007 |
4 | A | 844 | THR | 0 | 0.022 | 0.002 | 5.719 | -0.149 | -0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 845 | LYS | 1 | 0.944 | 0.964 | 4.241 | 0.944 | 0.985 | 0.000 | -0.007 | -0.034 | 0.000 |
6 | A | 846 | VAL | 0 | 0.001 | 0.010 | 9.494 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 847 | LEU | 0 | -0.038 | -0.010 | 13.052 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 848 | LEU | 0 | -0.037 | -0.032 | 15.662 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 849 | ASP | -1 | -0.816 | -0.898 | 18.059 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 850 | ILE | 0 | -0.140 | -0.061 | 20.518 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 851 | PHE | 0 | -0.064 | -0.055 | 23.711 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 852 | THR | 0 | 0.075 | 0.021 | 25.060 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 853 | GLY | 0 | -0.040 | -0.016 | 27.264 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 854 | VAL | 0 | -0.078 | -0.032 | 29.752 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 855 | ARG | 1 | 0.874 | 0.928 | 30.908 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 856 | LEU | 0 | 0.002 | -0.001 | 31.387 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 857 | TYR | 0 | 0.033 | 0.023 | 33.738 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 858 | LEU | 0 | -0.016 | -0.010 | 30.482 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 859 | PRO | 0 | 0.042 | 0.020 | 34.584 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 860 | PRO | 0 | 0.051 | 0.045 | 35.500 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 861 | SER | 0 | -0.037 | -0.009 | 36.388 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 862 | THR | 0 | -0.051 | -0.053 | 33.820 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 863 | PRO | 0 | 0.055 | 0.019 | 34.687 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 864 | ASP | -1 | -0.799 | -0.912 | 28.784 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 865 | PHE | 0 | 0.017 | 0.027 | 29.689 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 866 | SER | 0 | -0.015 | -0.005 | 27.582 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 867 | ARG | 1 | 0.884 | 0.916 | 24.392 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 868 | LEU | 0 | 0.060 | 0.034 | 25.057 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 869 | ARG | 1 | 1.002 | 1.004 | 26.076 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 870 | ARG | 1 | 0.900 | 0.956 | 17.591 | -0.111 | -0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 871 | TYR | 0 | -0.019 | -0.027 | 18.607 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 872 | PHE | 0 | -0.008 | 0.013 | 22.595 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 873 | VAL | 0 | 0.013 | 0.006 | 23.016 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 874 | ALA | 0 | -0.066 | -0.025 | 18.786 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 875 | PHE | 0 | -0.068 | -0.048 | 17.022 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 876 | ASP | -1 | -0.757 | -0.857 | 21.399 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 877 | GLY | 0 | -0.019 | 0.004 | 23.799 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 878 | ASP | -1 | -0.866 | -0.924 | 27.029 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 879 | LEU | 0 | -0.048 | -0.042 | 28.934 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 880 | VAL | 0 | 0.012 | 0.018 | 31.498 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 881 | GLN | 0 | 0.006 | -0.021 | 33.951 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 882 | GLU | -1 | -0.899 | -0.957 | 37.216 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 883 | PHE | 0 | -0.037 | -0.024 | 38.692 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 884 | ASP | -1 | -0.845 | -0.928 | 38.837 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 885 | MET | 0 | -0.065 | -0.014 | 39.680 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 886 | THR | 0 | -0.052 | -0.029 | 40.747 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 887 | SER | 0 | -0.004 | 0.012 | 39.243 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 888 | ALA | 0 | -0.053 | -0.015 | 37.333 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 889 | THR | 0 | 0.055 | -0.002 | 35.095 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 890 | HIS | 0 | -0.001 | 0.033 | 34.090 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 891 | VAL | 0 | 0.010 | -0.004 | 36.785 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 892 | LEU | 0 | 0.007 | 0.027 | 34.042 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 893 | GLY | 0 | 0.004 | 0.000 | 38.114 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 894 | SER | 0 | -0.010 | -0.012 | 41.613 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 895 | ARG | 1 | 0.925 | 0.953 | 43.179 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 896 | ASP | -1 | -0.882 | -0.940 | 45.069 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 897 | LYS | 1 | 0.894 | 0.944 | 44.979 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 898 | ASN | 0 | -0.032 | -0.025 | 41.335 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 899 | PRO | 0 | 0.041 | 0.026 | 44.204 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 900 | ALA | 0 | 0.011 | 0.012 | 44.005 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 901 | ALA | 0 | 0.000 | 0.031 | 39.876 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 902 | GLN | 0 | -0.017 | -0.017 | 36.778 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 903 | GLN | 0 | -0.059 | -0.040 | 38.199 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 904 | VAL | 0 | 0.001 | 0.006 | 33.878 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 905 | SER | 0 | 0.032 | -0.007 | 34.494 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 906 | PRO | 0 | 0.025 | -0.006 | 31.596 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 907 | GLU | -1 | -0.881 | -0.950 | 30.291 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 908 | TRP | 0 | -0.005 | 0.005 | 30.344 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 909 | ILE | 0 | 0.030 | 0.021 | 26.694 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 910 | TRP | 0 | 0.008 | -0.008 | 23.290 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 911 | ALA | 0 | -0.050 | -0.026 | 25.441 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 912 | CYS | 0 | -0.004 | 0.023 | 26.253 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 913 | ILE | 0 | 0.008 | 0.009 | 20.613 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 914 | ARG | 1 | 0.895 | 0.950 | 21.403 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 915 | LYS | 1 | 0.898 | 0.952 | 22.004 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 916 | ARG | 1 | 0.910 | 0.967 | 15.073 | 0.110 | 0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 917 | ARG | 1 | 0.969 | 0.985 | 21.741 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 918 | LEU | 0 | 0.070 | 0.033 | 25.007 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 919 | VAL | 0 | -0.057 | -0.037 | 28.207 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 920 | ALA | 0 | 0.003 | -0.002 | 30.657 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 921 | PRO | 0 | -0.014 | -0.014 | 34.211 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 922 | SER | -1 | -0.838 | -0.905 | 34.522 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |