![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 2J79R
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 | OptHSide |
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 | -908009.15514 |
---|---|
FMO2-HF: Nuclear repulsion | 862876.003437 |
FMO2-HF: Total energy | -45133.151703 |
FMO2-MP2: Total energy | -45262.59387 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F024238/ligand_interaction/ligand_F024238.png)
Ligand Interaction
![ligand interaction](./Kdata/F024238/ligand_interaction/ligand_interaction_F024238.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. |
-17.798 | -18.939 | 27.335 | -11.162 | -15.033 | 0.011 |
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 | 0.053 | 0.010 | 2.604 | -4.011 | -1.566 | 0.942 | -1.397 | -1.990 | -0.005 |
4 | A | 4 | ASP | -1 | -0.822 | -0.903 | 4.924 | 0.157 | 0.358 | -0.001 | -0.011 | -0.188 | 0.000 |
5 | A | 5 | GLU | -1 | -0.796 | -0.893 | 2.343 | -0.584 | 2.554 | 1.689 | -1.795 | -3.032 | -0.018 |
6 | A | 6 | PHE | 0 | -0.028 | -0.019 | 2.383 | 0.421 | 2.334 | 1.146 | -0.665 | -2.394 | 0.000 |
7 | A | 7 | TYR | 0 | -0.009 | -0.025 | 3.867 | -0.230 | -0.058 | 0.014 | 0.066 | -0.253 | 0.000 |
8 | A | 8 | THR | 0 | -0.006 | -0.005 | 7.174 | -0.074 | -0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | LYS | 1 | 0.912 | 0.942 | 2.103 | -12.856 | -21.596 | 19.313 | -6.315 | -4.258 | 0.040 |
10 | A | 10 | VAL | 0 | -0.023 | -0.006 | 6.041 | -0.497 | -0.497 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | TYR | 0 | -0.063 | -0.062 | 8.169 | -0.124 | -0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | ASP | -1 | -0.856 | -0.918 | 9.697 | 1.111 | 1.111 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | ALA | 0 | 0.002 | -0.003 | 9.356 | -0.117 | -0.117 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | VAL | 0 | -0.041 | -0.043 | 11.300 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | CYS | 0 | -0.071 | -0.043 | 13.816 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | GLU | -1 | -0.846 | -0.884 | 13.133 | 0.362 | 0.362 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | ILE | 0 | -0.087 | -0.026 | 15.073 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | PRO | 0 | 0.001 | 0.015 | 17.964 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | TYR | 0 | 0.014 | -0.005 | 21.633 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | GLY | 0 | 0.057 | 0.036 | 24.349 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | LYS | 1 | 0.787 | 0.898 | 21.632 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | VAL | 0 | 0.022 | 0.005 | 20.204 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | SER | 0 | 0.058 | 0.008 | 15.415 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | THR | 0 | -0.027 | -0.016 | 15.389 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | TYR | 0 | -0.016 | -0.006 | 13.025 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | GLY | 0 | -0.003 | -0.011 | 11.442 | -0.096 | -0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | GLU | -1 | -0.825 | -0.892 | 11.427 | -0.374 | -0.374 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | ILE | 0 | 0.050 | 0.024 | 8.987 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | ALA | 0 | 0.006 | 0.000 | 7.194 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | ARG | 1 | 0.816 | 0.880 | 6.641 | 0.133 | 0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | TYR | 0 | -0.102 | -0.064 | 8.416 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | VAL | 0 | -0.013 | -0.001 | 3.790 | 0.018 | 0.190 | 0.000 | -0.020 | -0.153 | 0.000 |
33 | A | 33 | GLY | 0 | -0.003 | 0.011 | 3.613 | -1.098 | -0.651 | 0.007 | -0.202 | -0.252 | -0.001 |
34 | A | 34 | MET | 0 | -0.060 | -0.035 | 2.461 | -1.919 | -2.826 | 4.226 | -0.823 | -2.495 | -0.005 |
35 | A | 35 | PRO | 0 | 0.056 | 0.011 | 5.358 | 0.301 | 0.319 | -0.001 | 0.000 | -0.018 | 0.000 |
36 | A | 36 | SER | 0 | -0.023 | -0.004 | 8.701 | 0.132 | 0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | TYR | 0 | -0.037 | -0.013 | 5.661 | 0.146 | 0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | ALA | 0 | 0.055 | 0.021 | 8.401 | 0.103 | 0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | ARG | 1 | 0.958 | 0.963 | 11.399 | 0.705 | 0.705 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | GLN | 0 | 0.055 | 0.030 | 7.829 | 0.177 | 0.177 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | VAL | 0 | 0.044 | 0.037 | 8.423 | 0.081 | 0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | GLY | 0 | 0.000 | 0.001 | 10.071 | 0.151 | 0.151 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | GLN | 0 | -0.042 | -0.031 | 11.253 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | ALA | 0 | 0.055 | 0.041 | 9.374 | 0.091 | 0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | MET | 0 | 0.009 | 0.023 | 11.495 | 0.127 | 0.127 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | LYS | 1 | 0.855 | 0.926 | 14.765 | 0.330 | 0.330 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | HIS | 0 | -0.086 | -0.051 | 13.671 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | LEU | 0 | -0.029 | 0.019 | 14.824 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | HIS | 0 | 0.045 | 0.026 | 16.884 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | PRO | 0 | -0.037 | -0.031 | 20.271 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 51 | GLU | -1 | -0.904 | -0.956 | 23.126 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 52 | THR | 0 | -0.042 | -0.008 | 17.691 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 53 | HIS | 0 | 0.002 | -0.004 | 20.294 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | VAL | 0 | 0.013 | 0.007 | 14.778 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | PRO | 0 | -0.005 | 0.017 | 17.196 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | TRP | 0 | 0.065 | -0.005 | 17.039 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | HIS | 0 | -0.065 | -0.035 | 18.055 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | ARG | 1 | 0.861 | 0.918 | 19.126 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | VAL | 0 | 0.012 | 0.018 | 14.275 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 60 | ILE | 0 | 0.006 | 0.022 | 17.517 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | ASN | 0 | 0.003 | -0.022 | 17.831 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | SER | 0 | 0.023 | -0.010 | 17.469 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 63 | ARG | 1 | 0.764 | 0.858 | 19.772 | 0.229 | 0.229 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 64 | GLY | 0 | 0.017 | 0.014 | 22.335 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 65 | THR | 0 | -0.050 | -0.036 | 23.712 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 66 | ILE | 0 | -0.006 | -0.002 | 23.015 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 67 | SER | 0 | -0.015 | -0.011 | 19.576 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 68 | LYS | 1 | 0.887 | 0.935 | 22.656 | 0.166 | 0.166 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 69 | ARG | 1 | 0.763 | 0.876 | 20.400 | 0.184 | 0.184 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 70 | ASP | -1 | -0.827 | -0.903 | 23.452 | -0.221 | -0.221 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 71 | ILE | 0 | 0.001 | 0.005 | 25.932 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 72 | SER | 0 | 0.034 | 0.002 | 27.658 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 73 | ALA | 0 | 0.039 | 0.017 | 28.368 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 74 | GLY | 0 | -0.001 | -0.005 | 24.509 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 75 | GLU | -1 | -0.808 | -0.905 | 25.249 | -0.148 | -0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 76 | GLN | 0 | 0.012 | 0.003 | 26.128 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 77 | ARG | 1 | 0.945 | 0.975 | 22.856 | 0.096 | 0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 78 | GLN | 0 | -0.040 | -0.021 | 20.355 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 79 | LYS | 1 | 0.818 | 0.899 | 25.355 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 80 | ASP | -1 | -0.780 | -0.870 | 28.291 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 81 | ARG | 1 | 0.932 | 0.966 | 22.739 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 82 | LEU | 0 | -0.038 | -0.022 | 23.241 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 83 | GLU | -1 | -0.802 | -0.899 | 27.080 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 84 | GLU | -1 | -0.967 | -0.970 | 29.885 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 85 | GLU | -1 | -0.875 | -0.910 | 24.887 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 86 | GLY | 0 | -0.015 | -0.004 | 29.183 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 87 | VAL | 0 | -0.079 | -0.037 | 26.069 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 88 | GLU | -1 | -0.901 | -0.947 | 29.473 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 89 | ILE | 0 | -0.088 | -0.033 | 27.639 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 90 | TYR | 0 | 0.015 | 0.005 | 31.197 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 91 | GLN | 0 | -0.011 | -0.012 | 32.297 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 92 | THR | 0 | -0.038 | -0.028 | 32.116 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 93 | SER | 0 | 0.055 | 0.028 | 34.741 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 94 | LEU | 0 | -0.016 | -0.013 | 33.316 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 95 | GLY | 0 | 0.018 | 0.015 | 33.769 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 96 | GLU | -1 | -0.813 | -0.868 | 26.833 | -0.193 | -0.193 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 97 | TYR | 0 | 0.024 | 0.011 | 28.335 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 98 | LYS | 1 | 0.941 | 0.977 | 27.714 | 0.117 | 0.117 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 99 | LEU | 0 | 0.071 | 0.055 | 24.440 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 100 | ASN | 0 | -0.020 | -0.024 | 27.898 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 101 | LEU | 0 | 0.064 | 0.017 | 21.031 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 102 | PRO | 0 | -0.008 | -0.013 | 24.496 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 103 | GLU | -1 | -0.853 | -0.897 | 26.085 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 104 | TYR | 0 | 0.010 | -0.019 | 24.844 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 105 | MET | 0 | -0.070 | -0.004 | 16.920 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 106 | TRP | 0 | 0.006 | -0.006 | 13.844 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 107 | LYS | 1 | 0.874 | 0.937 | 18.312 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 108 | PRO | 0 | 0.035 | 0.035 | 15.050 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |