
FMODB ID: 7KMYK
Calculation Name: 2B3A-A-Other547
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
PDB ID: 2B3A
Chain ID: A
UniProt ID: Q12967
Base Structure: SolutionNMR
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 | 87 |
LigandResidueName | |
LigandFragmentNumber | 0 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
FMO2-HF: Electronic energy | -623319.791855 |
---|---|
FMO2-HF: Nuclear repulsion | 587356.954063 |
FMO2-HF: Total energy | -35962.837792 |
FMO2-MP2: Total energy | -36065.116514 |
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:11:ASP)
Summations of interaction energy for
fragment #1(A:11:ASP)
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. |
-51.236 | -59.527 | 31.738 | -13.473 | -9.975 | 0.097 |
Interaction energy analysis for fragmet #1(A:11:ASP)
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 | 13 | CYS | 0 | 0.022 | 0.025 | 3.823 | -2.321 | -0.232 | -0.024 | -1.012 | -1.053 | -0.001 |
23 | A | 33 | THR | 0 | 0.022 | -0.009 | 2.961 | -4.296 | -1.461 | 0.559 | -1.633 | -1.761 | 0.015 |
24 | A | 34 | SER | 0 | -0.024 | -0.046 | 1.689 | -28.004 | -43.090 | 30.849 | -10.129 | -5.634 | 0.080 |
25 | A | 35 | GLN | 0 | -0.072 | -0.029 | 3.622 | -8.032 | -7.555 | 0.047 | -0.144 | -0.380 | 0.004 |
70 | A | 80 | PHE | 0 | 0.003 | -0.015 | 3.100 | 0.466 | 1.860 | 0.307 | -0.555 | -1.147 | -0.001 |
4 | A | 14 | ILE | 0 | 0.015 | 0.009 | 6.548 | 0.222 | 0.222 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 15 | ILE | 0 | 0.001 | 0.006 | 10.326 | 0.194 | 0.194 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 16 | ARG | 1 | 0.848 | 0.921 | 12.869 | -0.547 | -0.547 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 17 | VAL | 0 | 0.004 | -0.010 | 15.853 | 0.224 | 0.224 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 18 | SER | 0 | -0.039 | -0.029 | 18.451 | -0.167 | -0.167 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 19 | LEU | 0 | 0.008 | 0.001 | 22.229 | 0.122 | 0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 20 | ASP | -1 | -0.974 | -0.987 | 25.094 | 0.573 | 0.573 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 21 | VAL | 0 | 0.009 | -0.001 | 27.570 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 22 | ASP | -1 | -0.861 | -0.899 | 28.781 | 0.280 | 0.280 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 23 | ASN | 0 | -0.021 | -0.006 | 27.893 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 24 | GLY | 0 | 0.094 | 0.045 | 25.510 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 25 | ASN | 0 | -0.009 | -0.009 | 24.645 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 26 | MET | 0 | -0.060 | -0.066 | 20.345 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 27 | TYR | 0 | -0.065 | -0.016 | 21.733 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 28 | LYS | 1 | 0.865 | 0.931 | 18.664 | -0.531 | -0.531 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 29 | SER | 0 | -0.011 | -0.004 | 15.146 | 0.129 | 0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 30 | ILE | 0 | -0.015 | -0.001 | 11.554 | -0.149 | -0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 31 | LEU | 0 | -0.016 | 0.000 | 6.530 | -0.162 | -0.162 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 32 | VAL | 0 | 0.016 | 0.011 | 6.533 | 0.330 | 0.330 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 36 | ASP | -1 | -0.813 | -0.877 | 6.161 | 1.637 | 1.637 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 37 | LYS | 1 | 0.952 | 0.971 | 8.268 | -5.744 | -5.744 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 38 | ALA | 0 | 0.070 | 0.038 | 10.501 | -0.484 | -0.484 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 39 | PRO | 0 | 0.036 | 0.022 | 13.031 | -0.236 | -0.236 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 40 | ALA | 0 | -0.049 | -0.015 | 12.268 | -0.368 | -0.368 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 41 | VAL | 0 | -0.004 | -0.009 | 10.090 | -0.327 | -0.327 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 42 | ILE | 0 | 0.006 | 0.007 | 13.379 | -0.312 | -0.312 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 43 | ARG | 1 | 1.017 | 1.016 | 17.024 | -2.208 | -2.208 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 44 | LYS | 1 | 0.803 | 0.875 | 11.770 | -3.645 | -3.645 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 45 | ALA | 0 | 0.001 | -0.004 | 15.851 | -0.258 | -0.258 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 46 | MET | 0 | 0.013 | 0.031 | 17.184 | -0.132 | -0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 47 | ASP | -1 | -0.737 | -0.832 | 18.770 | 1.034 | 1.034 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 48 | LYS | 1 | 0.783 | 0.864 | 16.234 | -1.285 | -1.285 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 49 | HIS | 0 | -0.098 | -0.076 | 19.729 | -0.232 | -0.232 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 50 | ASN | 0 | -0.036 | -0.022 | 22.950 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 51 | LEU | 0 | 0.013 | 0.028 | 23.819 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 52 | GLU | -1 | -1.002 | -1.008 | 22.550 | 0.789 | 0.789 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 53 | GLU | -1 | -0.967 | -0.985 | 24.250 | 0.685 | 0.685 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 54 | GLU | -1 | -0.813 | -0.880 | 25.925 | 0.646 | 0.646 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 55 | GLU | -1 | -0.887 | -0.949 | 24.673 | 0.990 | 0.990 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 56 | PRO | 0 | -0.066 | -0.071 | 20.832 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 57 | GLU | -1 | -1.005 | -0.988 | 23.228 | 1.000 | 1.000 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 58 | ASP | -1 | -0.830 | -0.863 | 26.451 | 0.675 | 0.675 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 59 | TYR | 0 | -0.037 | -0.053 | 24.316 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 60 | GLU | -1 | -0.764 | -0.865 | 21.743 | 1.212 | 1.212 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 61 | LEU | 0 | -0.012 | -0.011 | 15.547 | -0.058 | -0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 62 | LEU | 0 | -0.049 | -0.032 | 19.740 | 0.095 | 0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 63 | GLN | 0 | 0.027 | 0.037 | 15.145 | -0.078 | -0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 64 | ILE | 0 | -0.001 | -0.015 | 18.989 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 65 | LEU | 0 | -0.008 | 0.019 | 18.903 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 66 | SER | 0 | -0.012 | -0.046 | 21.450 | -0.109 | -0.109 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 67 | ASP | -1 | -0.878 | -0.915 | 25.033 | 0.385 | 0.385 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 68 | ASP | -1 | -0.862 | -0.925 | 27.505 | 0.545 | 0.545 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 69 | ARG | 1 | 0.909 | 0.944 | 23.119 | -0.758 | -0.758 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 70 | LYS | 1 | 0.901 | 0.966 | 22.840 | -0.570 | -0.570 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 71 | LEU | 0 | -0.031 | -0.013 | 18.455 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 72 | LYS | 1 | 0.949 | 0.965 | 20.001 | -0.904 | -0.904 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 73 | ILE | 0 | -0.029 | -0.010 | 14.758 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 74 | PRO | 0 | 0.018 | 0.018 | 17.570 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 75 | GLU | -1 | -0.849 | -0.945 | 16.604 | 2.213 | 2.213 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 76 | ASN | 0 | -0.048 | -0.028 | 15.983 | 0.351 | 0.351 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 77 | ALA | 0 | -0.002 | 0.014 | 14.594 | 0.077 | 0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 78 | ASN | 0 | 0.006 | -0.006 | 9.153 | 0.544 | 0.544 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 79 | VAL | 0 | 0.090 | 0.034 | 8.148 | -0.393 | -0.393 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 81 | TYR | 0 | -0.043 | -0.013 | 7.751 | -0.716 | -0.716 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 82 | ALA | 0 | 0.000 | 0.008 | 11.257 | -0.633 | -0.633 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 83 | MET | 0 | -0.049 | 0.001 | 9.587 | -0.686 | -0.686 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 84 | ASN | 0 | -0.016 | -0.051 | 12.492 | -0.234 | -0.234 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 85 | SER | 0 | 0.027 | 0.003 | 10.938 | -0.227 | -0.227 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 86 | THR | 0 | -0.077 | -0.040 | 13.309 | -0.280 | -0.280 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 87 | ALA | 0 | -0.023 | -0.002 | 16.765 | -0.111 | -0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 88 | ASN | 0 | 0.005 | -0.005 | 18.176 | -0.203 | -0.203 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 89 | TYR | 0 | 0.000 | 0.026 | 13.711 | 0.145 | 0.145 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 90 | ASP | -1 | -0.826 | -0.902 | 15.741 | 0.663 | 0.663 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 91 | PHE | 0 | -0.018 | -0.024 | 12.884 | 0.215 | 0.215 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 92 | VAL | 0 | 0.036 | 0.024 | 18.343 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 93 | LEU | 0 | 0.015 | 0.003 | 20.534 | 0.129 | 0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 94 | LYS | 1 | 0.818 | 0.899 | 22.390 | -1.127 | -1.127 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 95 | LYS | 1 | 0.850 | 0.923 | 25.663 | -0.573 | -0.573 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 96 | ARG | 1 | 0.718 | 0.834 | 26.769 | -0.945 | -0.945 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 97 | THR | -1 | -0.874 | -0.920 | 29.694 | 0.607 | 0.607 | 0.000 | 0.000 | 0.000 | 0.000 |