
FMODB ID: 9RVV2
Calculation Name: 5DN6-I-Xray547
Preferred Name:
Target Type:
Ligand Name: adenosine-5'-triphosphate | adenosine-5'-diphosphate
Ligand 3-letter code: ATP | ADP
Ligand of Interest (LOI):
PDB ID: 5DN6
Chain ID: I
UniProt ID: A1B619
Base Structure: X-ray
Registration Date: 2025-10-05
Reference: Sci Data 11, 1164 (2024).
DOI: https://doi.org/10.1038/s41597-024-03999-2
Apendix: None
Modeling method
Optimization | MOE:Amber10:EHT |
---|---|
Restraint | OptAll |
Protonation | MOE:Protonate 3D |
Complement | MOE:Homology Modeling |
Water | No |
Procedure | Manual calculation |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 75 |
LigandResidueName | |
LigandFragmentNumber | 0 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
FMO2-HF: Electronic energy | -388334.321554 |
---|---|
FMO2-HF: Nuclear repulsion | 361547.639379 |
FMO2-HF: Total energy | -26786.682176 |
FMO2-MP2: Total energy | -26865.45568 |
3D Structure
Ligand structure

Ligand Interaction

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:9:VAL)
Summations of interaction energy for
fragment #1(A:9:VAL)
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. |
-183.967 | -175.475 | 18.026 | -11.832 | -14.685 | -0.123 |
Interaction energy analysis for fragmet #1(A:9:VAL)
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 | 11 | PRO | 0 | 0.020 | -0.005 | 2.949 | -0.415 | 2.043 | 0.259 | -1.166 | -1.551 | -0.005 |
4 | A | 12 | GLU | -1 | -0.861 | -0.890 | 5.154 | -23.204 | -23.101 | -0.001 | -0.004 | -0.097 | 0.000 |
5 | A | 13 | ARG | 1 | 0.954 | 0.973 | 4.374 | 34.868 | 35.110 | -0.001 | -0.061 | -0.181 | 0.000 |
6 | A | 14 | ASN | 0 | 0.018 | -0.012 | 1.925 | -36.547 | -33.079 | 6.637 | -5.265 | -4.840 | -0.040 |
7 | A | 15 | LEU | 0 | -0.025 | -0.009 | 2.583 | 8.823 | 8.347 | 0.318 | 1.079 | -0.921 | -0.003 |
8 | A | 16 | VAL | 0 | 0.044 | 0.019 | 3.476 | 7.739 | 8.083 | 0.010 | -0.089 | -0.265 | 0.000 |
9 | A | 17 | SER | 0 | -0.039 | -0.022 | 4.231 | -8.610 | -8.403 | -0.001 | -0.030 | -0.175 | 0.000 |
69 | A | 77 | THR | 0 | -0.043 | -0.015 | 3.889 | -3.469 | -3.282 | 0.000 | -0.025 | -0.162 | 0.000 |
70 | A | 78 | LEU | 0 | 0.013 | 0.012 | 4.050 | 2.740 | 3.359 | -0.001 | -0.273 | -0.346 | -0.001 |
71 | A | 79 | LEU | 0 | -0.038 | -0.017 | 1.829 | -49.260 | -48.346 | 10.780 | -6.085 | -5.609 | -0.074 |
72 | A | 80 | ALA | 0 | 0.019 | 0.003 | 3.404 | 11.275 | 11.701 | 0.026 | 0.087 | -0.538 | 0.000 |
10 | A | 18 | VAL | 0 | 0.003 | 0.009 | 6.940 | 3.636 | 3.636 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 19 | PRO | 0 | 0.032 | 0.014 | 9.858 | -1.341 | -1.341 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 20 | VAL | 0 | -0.015 | 0.002 | 9.983 | 0.358 | 0.358 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 21 | ARG | 1 | 0.945 | 0.984 | 12.666 | 16.002 | 16.002 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 22 | GLU | -1 | -0.875 | -0.961 | 14.226 | -17.277 | -17.277 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 23 | VAL | 0 | -0.051 | -0.007 | 8.813 | -1.091 | -1.091 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 24 | ARG | 1 | 0.875 | 0.904 | 12.018 | 18.253 | 18.253 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 25 | LEU | 0 | -0.017 | -0.009 | 8.801 | -1.570 | -1.570 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 26 | PRO | 0 | 0.010 | 0.009 | 12.591 | 1.309 | 1.309 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 27 | GLY | 0 | 0.050 | 0.015 | 14.269 | -0.897 | -0.897 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 28 | ALA | 0 | -0.065 | -0.038 | 15.208 | 1.027 | 1.027 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 29 | ASP | -1 | -0.931 | -0.967 | 17.469 | -15.739 | -15.739 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 30 | GLY | 0 | -0.035 | -0.020 | 18.630 | 1.037 | 1.037 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 31 | ASP | -1 | -0.894 | -0.917 | 17.574 | -18.341 | -18.341 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 32 | LEU | 0 | 0.009 | 0.014 | 12.858 | 0.595 | 0.595 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 33 | THR | 0 | -0.004 | 0.003 | 14.848 | -1.060 | -1.060 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 34 | ALA | 0 | -0.024 | -0.009 | 12.529 | 0.699 | 0.699 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 35 | MET | 0 | 0.036 | 0.013 | 14.177 | -0.697 | -0.697 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 36 | PRO | 0 | -0.011 | -0.021 | 15.313 | -0.069 | -0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 37 | GLY | 0 | -0.007 | 0.002 | 16.760 | 1.070 | 1.070 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 38 | HIS | 0 | -0.016 | 0.004 | 16.518 | 0.620 | 0.620 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 39 | ALA | 0 | -0.024 | -0.017 | 17.020 | -0.354 | -0.354 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 40 | PRO | 0 | -0.040 | -0.033 | 14.832 | -0.802 | -0.802 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 41 | ALA | 0 | -0.025 | 0.001 | 13.695 | 1.210 | 1.210 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 42 | ILE | 0 | 0.009 | 0.002 | 10.422 | -1.756 | -1.756 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 43 | VAL | 0 | -0.010 | 0.004 | 11.364 | 1.816 | 1.816 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 44 | ASN | 0 | 0.010 | 0.008 | 11.162 | -3.728 | -3.728 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 45 | LEU | 0 | 0.001 | 0.004 | 9.503 | 1.103 | 1.103 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 46 | ARG | 1 | 0.936 | 0.977 | 12.627 | 16.620 | 16.620 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 47 | PRO | 0 | 0.001 | -0.004 | 13.695 | -0.917 | -0.917 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 48 | GLY | 0 | -0.048 | -0.028 | 13.355 | 1.850 | 1.850 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 49 | LEU | 0 | -0.052 | -0.005 | 12.818 | -1.510 | -1.510 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 50 | VAL | 0 | -0.001 | -0.002 | 7.684 | -0.222 | -0.222 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 51 | THR | 0 | 0.023 | 0.025 | 10.993 | 0.446 | 0.446 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 52 | VAL | 0 | -0.008 | -0.019 | 9.148 | -0.849 | -0.849 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 53 | VAL | 0 | 0.021 | 0.027 | 11.898 | 0.993 | 0.993 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 54 | ALA | 0 | 0.040 | 0.005 | 12.637 | -0.471 | -0.471 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 55 | GLY | 0 | -0.013 | -0.023 | 13.938 | 1.372 | 1.372 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 56 | ASP | -1 | -0.946 | -0.966 | 16.428 | -14.757 | -14.757 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 57 | GLY | 0 | -0.060 | -0.036 | 18.597 | 0.700 | 0.700 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 58 | SER | 0 | -0.036 | -0.010 | 16.879 | 0.579 | 0.579 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 59 | GLU | -1 | -0.922 | -0.965 | 15.808 | -18.695 | -18.695 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 60 | THR | 0 | -0.080 | -0.034 | 12.394 | -0.209 | -0.209 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 61 | GLU | -1 | -0.865 | -0.948 | 12.809 | -19.251 | -19.251 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 62 | PHE | 0 | -0.027 | -0.015 | 7.384 | 0.139 | 0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 63 | ALA | 0 | 0.002 | 0.011 | 11.273 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 64 | VAL | 0 | -0.028 | -0.016 | 7.370 | -2.078 | -2.078 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 65 | THR | 0 | -0.029 | -0.053 | 10.020 | 1.293 | 1.293 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 66 | GLY | 0 | 0.069 | 0.031 | 10.224 | 2.460 | 2.460 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 67 | GLY | 0 | 0.016 | 0.016 | 7.939 | -4.249 | -4.249 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 68 | PHE | 0 | 0.005 | -0.007 | 7.106 | 3.534 | 3.534 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 69 | ALA | 0 | 0.001 | 0.004 | 6.402 | -6.986 | -6.986 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 70 | GLU | -1 | -0.950 | -0.971 | 7.105 | -25.052 | -25.052 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 71 | ILE | 0 | 0.006 | 0.001 | 8.414 | -2.776 | -2.776 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 72 | ASN | 0 | 0.012 | -0.012 | 11.041 | 2.932 | 2.932 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 73 | ASN | 0 | 0.014 | 0.008 | 13.276 | -0.284 | -0.284 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 74 | GLU | -1 | -0.951 | -0.956 | 13.765 | -20.255 | -20.255 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 75 | SER | 0 | -0.017 | -0.003 | 8.997 | -1.758 | -1.758 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 76 | VAL | 0 | 0.046 | 0.011 | 8.511 | 1.223 | 1.223 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 81 | GLU | -1 | -0.940 | -0.972 | 5.629 | -28.458 | -28.458 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 82 | ARG | 1 | 0.774 | 0.859 | 8.455 | 24.293 | 24.293 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 83 | GLY | -1 | -0.819 | -0.874 | 10.914 | -21.549 | -21.549 | 0.000 | 0.000 | 0.000 | 0.000 |