![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 6NLKZ
Calculation Name: 4HDV-A-Xray372
Preferred Name:
Target Type:
Ligand Name: 2,6-diaminopurine nucleotide
ligand 3-letter code: 1AP
PDB ID: 4HDV
Chain ID: A
UniProt ID: Q9UTN9
Base Structure: X-ray
Registration Date: 2023-06-21
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 | 108 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -910890.099608 |
---|---|
FMO2-HF: Nuclear repulsion | 865756.642428 |
FMO2-HF: Total energy | -45133.457181 |
FMO2-MP2: Total energy | -45262.859973 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F024237/ligand_interaction/ligand_F024237.png)
Ligand Interaction
![ligand interaction](./Kdata/F024237/ligand_interaction/ligand_interaction_F024237.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:1:MET)
Summations of interaction energy for
fragment #1(A:1:MET)
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. |
-19.103 | -19.998 | 27.736 | -11.275 | -15.566 | -0.003 |
Interaction energy analysis for fragmet #1(A:1:MET)
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 | 3 | MET | 0 | 0.041 | 0.004 | 2.725 | -3.282 | -0.939 | 0.596 | -1.266 | -1.673 | -0.005 |
4 | A | 4 | ASP | -1 | -0.799 | -0.885 | 5.000 | 0.017 | 0.198 | -0.001 | -0.011 | -0.168 | 0.000 |
5 | A | 5 | GLU | -1 | -0.796 | -0.884 | 2.339 | 0.113 | 2.811 | 2.093 | -1.688 | -3.104 | -0.018 |
6 | A | 6 | PHE | 0 | -0.007 | -0.003 | 2.435 | 0.381 | 2.505 | 0.924 | -0.697 | -2.351 | -0.001 |
7 | A | 7 | TYR | 0 | -0.009 | -0.025 | 3.815 | -0.294 | -0.111 | 0.016 | 0.083 | -0.282 | 0.000 |
8 | A | 8 | THR | 0 | -0.029 | -0.016 | 7.185 | -0.063 | -0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | LYS | 1 | 0.907 | 0.929 | 2.108 | -12.608 | -22.065 | 20.086 | -6.206 | -4.422 | 0.033 |
10 | A | 10 | VAL | 0 | -0.019 | -0.008 | 5.915 | -0.585 | -0.585 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | TYR | 0 | -0.059 | -0.059 | 7.932 | -0.108 | -0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | ASP | -1 | -0.844 | -0.916 | 9.303 | 1.130 | 1.130 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | ALA | 0 | 0.012 | -0.001 | 8.875 | -0.120 | -0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | VAL | 0 | -0.048 | -0.046 | 10.833 | -0.086 | -0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | CYS | 0 | -0.059 | -0.044 | 13.377 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | GLU | -1 | -0.859 | -0.890 | 12.809 | 0.249 | 0.249 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | ILE | 0 | -0.067 | -0.007 | 14.765 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | PRO | 0 | -0.003 | 0.002 | 17.614 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | TYR | 0 | -0.002 | -0.020 | 21.321 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | GLY | 0 | 0.053 | 0.034 | 24.281 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | LYS | 1 | 0.797 | 0.914 | 21.566 | 0.058 | 0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | VAL | 0 | 0.009 | 0.002 | 20.010 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | SER | 0 | 0.054 | 0.013 | 14.434 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | THR | 0 | 0.006 | -0.001 | 15.445 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | TYR | 0 | -0.023 | -0.022 | 12.955 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | GLY | 0 | 0.000 | -0.017 | 11.285 | -0.132 | -0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | GLU | -1 | -0.843 | -0.890 | 11.367 | -0.544 | -0.544 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | ILE | 0 | 0.030 | 0.012 | 8.807 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | ALA | 0 | 0.001 | -0.001 | 7.008 | -0.110 | -0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | ARG | 1 | 0.806 | 0.877 | 6.438 | 0.190 | 0.190 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | TYR | 0 | -0.070 | -0.049 | 7.893 | -0.155 | -0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | VAL | 0 | -0.024 | -0.003 | 3.539 | -0.045 | 0.246 | 0.006 | -0.043 | -0.254 | 0.000 |
33 | A | 33 | GLY | 0 | 0.011 | 0.014 | 2.920 | -3.620 | -2.358 | 0.154 | -0.652 | -0.765 | -0.008 |
34 | A | 34 | MET | 0 | -0.056 | -0.028 | 2.554 | -1.981 | -2.501 | 3.862 | -0.795 | -2.547 | -0.004 |
35 | A | 35 | PRO | 0 | 0.037 | -0.003 | 5.437 | 0.442 | 0.442 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | SER | 0 | -0.002 | 0.007 | 9.045 | 0.120 | 0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | TYR | 0 | -0.013 | -0.001 | 5.283 | 0.301 | 0.301 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | ALA | 0 | 0.035 | 0.013 | 8.386 | 0.119 | 0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | ARG | 1 | 0.940 | 0.958 | 11.368 | 0.757 | 0.757 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | GLN | 0 | 0.065 | 0.037 | 7.944 | 0.147 | 0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | VAL | 0 | 0.027 | 0.029 | 8.357 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | GLY | 0 | 0.013 | 0.009 | 10.129 | 0.155 | 0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | GLN | 0 | -0.041 | -0.030 | 11.521 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | ALA | 0 | 0.055 | 0.041 | 9.448 | 0.100 | 0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | MET | 0 | -0.008 | 0.010 | 11.610 | 0.141 | 0.141 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | LYS | 1 | 0.804 | 0.890 | 14.710 | 0.334 | 0.334 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | HIS | 0 | -0.073 | -0.049 | 13.861 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | LEU | 0 | -0.051 | 0.006 | 14.819 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | HIS | 0 | 0.041 | 0.028 | 17.155 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | PRO | 0 | -0.052 | -0.034 | 20.437 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 51 | GLU | -1 | -0.858 | -0.942 | 23.339 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 52 | THR | 0 | -0.062 | -0.018 | 17.857 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 53 | HIS | 0 | 0.017 | 0.000 | 20.646 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | VAL | 0 | 0.015 | 0.016 | 14.636 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | PRO | 0 | -0.007 | 0.012 | 16.691 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | TRP | 0 | 0.039 | -0.013 | 16.827 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | HIS | 0 | -0.034 | -0.016 | 17.839 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | ARG | 1 | 0.846 | 0.925 | 18.914 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | VAL | 0 | 0.025 | 0.010 | 14.055 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 60 | ILE | 0 | 0.012 | 0.030 | 17.354 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | ASN | 0 | -0.007 | -0.026 | 17.508 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | SER | 0 | 0.045 | -0.004 | 17.933 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 63 | ARG | 1 | 0.754 | 0.853 | 20.156 | 0.257 | 0.257 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 64 | GLY | 0 | 0.025 | 0.014 | 22.705 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 65 | THR | 0 | -0.063 | -0.045 | 23.718 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 66 | ILE | 0 | 0.009 | 0.018 | 22.919 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 67 | SER | 0 | -0.007 | -0.001 | 19.855 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 68 | LYS | 1 | 0.881 | 0.934 | 22.852 | 0.179 | 0.179 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 69 | ARG | 1 | 0.810 | 0.886 | 20.212 | 0.214 | 0.214 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 70 | ASP | -1 | -0.824 | -0.898 | 23.036 | -0.239 | -0.239 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 71 | ILE | 0 | 0.027 | 0.018 | 25.885 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 72 | SER | 0 | -0.008 | -0.026 | 26.920 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 73 | ALA | 0 | 0.054 | 0.022 | 28.796 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 74 | GLY | 0 | -0.016 | -0.004 | 24.582 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 75 | GLU | -1 | -0.793 | -0.872 | 24.813 | -0.171 | -0.171 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 76 | GLN | 0 | 0.005 | -0.011 | 26.162 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 77 | ARG | 1 | 0.948 | 0.977 | 22.557 | 0.113 | 0.113 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 78 | GLN | 0 | -0.038 | -0.027 | 20.089 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 79 | LYS | 1 | 0.800 | 0.879 | 25.020 | 0.092 | 0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 80 | ASP | -1 | -0.785 | -0.873 | 28.054 | -0.077 | -0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 81 | ARG | 1 | 0.936 | 0.963 | 22.403 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 82 | LEU | 0 | -0.050 | -0.022 | 23.075 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 83 | GLU | -1 | -0.804 | -0.896 | 26.969 | -0.077 | -0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 84 | GLU | -1 | -0.942 | -0.964 | 29.336 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 85 | GLU | -1 | -0.846 | -0.895 | 24.447 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 86 | GLY | 0 | -0.001 | 0.001 | 28.570 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 87 | VAL | 0 | -0.059 | -0.030 | 25.877 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 88 | GLU | -1 | -0.906 | -0.950 | 29.310 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 89 | ILE | 0 | -0.097 | -0.042 | 27.240 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 90 | TYR | 0 | 0.010 | 0.011 | 30.753 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 91 | GLN | 0 | -0.031 | -0.031 | 31.876 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 92 | THR | 0 | -0.044 | -0.017 | 31.621 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 93 | SER | 0 | 0.050 | 0.007 | 34.321 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 94 | LEU | 0 | -0.029 | -0.012 | 33.086 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 95 | GLY | 0 | 0.038 | 0.033 | 33.456 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 96 | GLU | -1 | -0.791 | -0.843 | 26.629 | -0.221 | -0.221 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 97 | TYR | 0 | 0.043 | 0.016 | 28.473 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 98 | LYS | 1 | 0.880 | 0.947 | 27.569 | 0.146 | 0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 99 | LEU | 0 | 0.101 | 0.068 | 24.068 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 100 | ASN | 0 | -0.004 | -0.024 | 27.871 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 101 | LEU | 0 | 0.037 | 0.008 | 20.944 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 102 | PRO | 0 | -0.016 | -0.013 | 24.233 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 103 | GLU | -1 | -0.845 | -0.885 | 25.896 | -0.075 | -0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 104 | TYR | 0 | -0.018 | -0.036 | 24.477 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 105 | MET | 0 | -0.066 | -0.001 | 16.430 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 106 | TRP | 0 | 0.034 | 0.006 | 13.436 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 107 | LYS | 1 | 0.855 | 0.918 | 18.269 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 108 | PRO | 0 | 0.019 | 0.032 | 14.605 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |