![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 723QK
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 | 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 | 108 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -907567.932329 |
---|---|
FMO2-HF: Nuclear repulsion | 862435.601939 |
FMO2-HF: Total energy | -45132.33039 |
FMO2-MP2: Total energy | -45261.775223 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F024239/ligand_interaction/ligand_F024239.png)
Ligand Interaction
![ligand interaction](./Kdata/F024239/ligand_interaction/ligand_interaction_F024239.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. |
-10.792 | -5.53 | 13.096 | -5.588 | -12.77 | -0.001 |
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 | 0.037 | 0.004 | 2.555 | -4.150 | -1.436 | 0.875 | -1.478 | -2.110 | -0.010 |
4 | A | 4 | ASP | -1 | -0.810 | -0.889 | 5.039 | -1.038 | -0.864 | -0.001 | -0.007 | -0.166 | 0.000 |
5 | A | 5 | GLU | -1 | -0.854 | -0.930 | 2.389 | -4.588 | -2.330 | 0.837 | -1.184 | -1.911 | -0.007 |
6 | A | 6 | PHE | 0 | -0.027 | -0.020 | 3.034 | -2.286 | -0.165 | 1.394 | -0.958 | -2.558 | 0.001 |
7 | A | 7 | TYR | 0 | -0.045 | -0.035 | 3.841 | -0.219 | -0.447 | 0.042 | 0.424 | -0.238 | 0.001 |
8 | A | 8 | THR | 0 | 0.006 | 0.008 | 6.092 | 0.162 | 0.162 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | LYS | 1 | 0.995 | 1.001 | 1.982 | 1.979 | -0.819 | 7.751 | -1.618 | -3.335 | 0.015 |
10 | A | 10 | VAL | 0 | -0.029 | -0.006 | 5.624 | 0.165 | 0.165 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | TYR | 0 | -0.069 | -0.072 | 7.420 | 0.058 | 0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | ASP | -1 | -0.857 | -0.920 | 8.390 | -0.531 | -0.531 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | ALA | 0 | 0.009 | 0.000 | 8.555 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | VAL | 0 | -0.058 | -0.045 | 10.382 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | CYS | 0 | -0.061 | -0.044 | 13.035 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | GLU | -1 | -0.893 | -0.931 | 11.912 | -0.215 | -0.215 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | ILE | 0 | -0.090 | -0.029 | 14.542 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | PRO | 0 | -0.006 | 0.010 | 17.211 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | TYR | 0 | 0.027 | -0.001 | 20.822 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | GLY | 0 | 0.053 | 0.040 | 23.552 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | LYS | 1 | 0.862 | 0.935 | 21.049 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | VAL | 0 | 0.017 | 0.005 | 19.801 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | SER | 0 | 0.044 | 0.009 | 14.519 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | THR | 0 | -0.014 | -0.008 | 15.477 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | TYR | 0 | 0.011 | 0.012 | 13.164 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | GLY | 0 | -0.007 | -0.018 | 11.741 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | GLU | -1 | -0.854 | -0.937 | 11.879 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | ILE | 0 | 0.048 | 0.031 | 8.660 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | ALA | 0 | 0.007 | -0.002 | 7.548 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | ARG | 1 | 0.842 | 0.916 | 7.169 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | TYR | 0 | -0.049 | -0.008 | 8.160 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | VAL | 0 | -0.015 | -0.003 | 3.649 | -0.265 | -0.063 | 0.002 | -0.028 | -0.176 | 0.000 |
33 | A | 33 | GLY | 0 | -0.018 | 0.004 | 3.580 | -0.803 | -0.413 | 0.010 | -0.174 | -0.226 | -0.001 |
34 | A | 34 | MET | 0 | -0.054 | -0.035 | 3.581 | 1.084 | 1.513 | 2.186 | -0.565 | -2.050 | 0.000 |
35 | A | 35 | PRO | 0 | 0.051 | 0.009 | 6.439 | -0.197 | -0.197 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | SER | 0 | -0.020 | -0.005 | 9.783 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | TYR | 0 | -0.028 | -0.010 | 6.134 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | ALA | 0 | 0.049 | 0.019 | 9.449 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | ARG | 1 | 0.958 | 0.959 | 12.198 | -0.097 | -0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | GLN | 0 | 0.061 | 0.033 | 8.835 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | VAL | 0 | 0.055 | 0.046 | 8.615 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | GLY | 0 | -0.006 | -0.006 | 10.641 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | GLN | 0 | -0.049 | -0.034 | 12.058 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | ALA | 0 | 0.038 | 0.030 | 9.995 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | MET | 0 | 0.000 | 0.021 | 11.954 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | LYS | 1 | 0.920 | 0.961 | 15.000 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | HIS | 0 | -0.076 | -0.052 | 13.333 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | LEU | 0 | -0.003 | 0.030 | 14.265 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | HIS | 0 | 0.048 | 0.033 | 16.867 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | PRO | 0 | -0.025 | -0.027 | 19.995 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 51 | GLU | -1 | -0.919 | -0.968 | 22.866 | -0.110 | -0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 52 | THR | 0 | -0.054 | -0.001 | 16.901 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 53 | HIS | 0 | 0.023 | 0.004 | 19.151 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | VAL | 0 | 0.007 | 0.001 | 13.988 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | PRO | 0 | -0.008 | 0.014 | 16.216 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | TRP | 0 | 0.037 | -0.011 | 16.514 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | HIS | 0 | -0.071 | -0.043 | 17.522 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | ARG | 1 | 0.869 | 0.941 | 18.321 | 0.093 | 0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | VAL | 0 | 0.001 | 0.010 | 14.271 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 60 | ILE | 0 | 0.009 | 0.020 | 17.281 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | ASN | 0 | -0.017 | -0.030 | 17.941 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | SER | 0 | 0.042 | -0.007 | 18.202 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 63 | ARG | 1 | 0.842 | 0.936 | 20.162 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 64 | GLY | 0 | 0.024 | 0.023 | 22.594 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 65 | THR | 0 | -0.003 | 0.003 | 23.893 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 66 | ILE | 0 | 0.014 | 0.010 | 23.170 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 67 | SER | 0 | -0.039 | -0.024 | 19.964 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 68 | LYS | 1 | 0.919 | 0.975 | 23.112 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 69 | ARG | 1 | 0.752 | 0.869 | 21.166 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 70 | ASP | -1 | -0.845 | -0.900 | 24.851 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 71 | ILE | 0 | -0.024 | -0.006 | 26.852 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 72 | SER | 0 | 0.059 | 0.001 | 28.503 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 73 | ALA | 0 | 0.028 | 0.009 | 28.916 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 74 | GLY | 0 | -0.020 | -0.015 | 24.940 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 75 | GLU | -1 | -0.836 | -0.935 | 25.490 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 76 | GLN | 0 | 0.021 | 0.024 | 26.409 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 77 | ARG | 1 | 0.965 | 0.986 | 23.267 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 78 | GLN | 0 | -0.040 | -0.018 | 20.261 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 79 | LYS | 1 | 0.938 | 0.972 | 25.133 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 80 | ASP | -1 | -0.839 | -0.916 | 28.024 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 81 | ARG | 1 | 0.925 | 0.963 | 22.490 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 82 | LEU | 0 | -0.040 | -0.023 | 22.829 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 83 | GLU | -1 | -0.874 | -0.943 | 26.619 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 84 | GLU | -1 | -0.972 | -0.977 | 29.466 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 85 | GLU | -1 | -0.888 | -0.938 | 24.321 | -0.067 | -0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 86 | GLY | 0 | -0.027 | -0.010 | 28.534 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 87 | VAL | 0 | -0.060 | -0.026 | 25.624 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 88 | GLU | -1 | -0.914 | -0.959 | 29.065 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 89 | ILE | 0 | -0.082 | -0.029 | 27.368 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 90 | TYR | 0 | 0.011 | 0.003 | 31.147 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 91 | GLN | 0 | -0.010 | -0.011 | 32.332 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 92 | THR | 0 | -0.023 | -0.003 | 32.327 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 93 | SER | 0 | 0.072 | 0.025 | 34.961 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 94 | LEU | 0 | -0.053 | -0.027 | 33.744 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 95 | GLY | 0 | 0.027 | 0.019 | 34.311 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 96 | GLU | -1 | -0.922 | -0.992 | 28.760 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 97 | TYR | 0 | -0.020 | -0.012 | 28.310 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 98 | LYS | 1 | 0.929 | 0.969 | 27.807 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 99 | LEU | 0 | 0.095 | 0.061 | 24.337 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 100 | ASN | 0 | 0.012 | -0.005 | 27.949 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 101 | LEU | 0 | 0.042 | 0.011 | 21.249 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 102 | PRO | 0 | -0.038 | -0.034 | 24.413 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 103 | GLU | -1 | -0.918 | -0.937 | 26.062 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 104 | TYR | 0 | 0.035 | 0.014 | 24.495 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 105 | MET | 0 | -0.079 | -0.014 | 17.018 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 106 | TRP | 0 | 0.006 | -0.008 | 13.432 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 107 | LYS | 1 | 0.922 | 0.958 | 18.011 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 108 | PRO | 0 | 0.024 | 0.028 | 14.763 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |