FMODB ID: YZ1Y2
Calculation Name: 1VJQ-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1VJQ
Chain ID: A
Base Structure: X-ray
Registration Date: 2023-06-22
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 | 73 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -446991.10001 |
---|---|
FMO2-HF: Nuclear repulsion | 418327.754399 |
FMO2-HF: Total energy | -28663.345611 |
FMO2-MP2: Total energy | -28747.511588 |
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:1:LYS)
Summations of interaction energy for
fragment #1(A:1:LYS)
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. |
-301.258 | -298.845 | 28.336 | -16.576 | -14.175 | -0.167 |
Interaction energy analysis for fragmet #1(A:1:LYS)
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 | ILE | 0 | 0.026 | 0.030 | 3.878 | -0.854 | 1.490 | -0.020 | -1.312 | -1.012 | 0.004 |
4 | A | 4 | PHE | 0 | 0.009 | 0.009 | 6.322 | 2.080 | 2.080 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 5 | VAL | 0 | -0.015 | -0.012 | 9.884 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | ILE | 0 | 0.028 | 0.005 | 12.861 | 0.846 | 0.846 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 7 | VAL | 0 | -0.019 | -0.008 | 15.571 | 0.134 | 0.134 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | PRO | 0 | 0.002 | 0.025 | 19.247 | 0.369 | 0.369 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | THR | 0 | -0.031 | -0.042 | 21.797 | 0.382 | 0.382 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | ASN | 0 | -0.017 | -0.022 | 25.388 | 0.066 | 0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | GLU | -1 | -0.779 | -0.905 | 25.716 | -10.689 | -10.689 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | GLU | -1 | -0.906 | -0.952 | 26.204 | -10.095 | -10.095 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | GLN | 0 | -0.025 | 0.001 | 22.163 | -0.463 | -0.463 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | VAL | 0 | 0.029 | 0.019 | 21.653 | -0.653 | -0.653 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | ALA | 0 | 0.051 | 0.019 | 21.805 | -0.444 | -0.444 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | PHE | 0 | -0.010 | -0.015 | 19.134 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | LEU | 0 | 0.032 | 0.008 | 16.198 | -0.431 | -0.431 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | GLU | -1 | -0.847 | -0.899 | 17.909 | -12.238 | -12.238 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | ALA | 0 | -0.042 | -0.021 | 20.220 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | LEU | 0 | -0.026 | -0.012 | 15.888 | -0.073 | -0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | ALA | 0 | 0.023 | 0.008 | 15.444 | -0.441 | -0.441 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | LYS | 1 | 0.758 | 0.866 | 16.494 | 11.951 | 11.951 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | GLN | 0 | -0.090 | -0.041 | 16.458 | 0.731 | 0.731 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | ASP | -1 | -0.932 | -0.956 | 15.209 | -17.725 | -17.725 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | GLU | -1 | -0.968 | -0.979 | 12.307 | -19.030 | -19.030 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | LEU | 0 | 0.005 | -0.012 | 10.912 | -1.319 | -1.319 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | ASN | 0 | -0.027 | -0.023 | 6.227 | -1.674 | -1.674 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | PHE | 0 | -0.010 | -0.004 | 6.343 | -3.591 | -3.591 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | ASP | -1 | -0.874 | -0.923 | 6.969 | -24.429 | -24.429 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | TRP | 0 | 0.021 | -0.004 | 8.561 | -1.210 | -1.210 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | GLN | 0 | -0.070 | -0.043 | 8.643 | 0.829 | 0.829 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | ASN | 0 | -0.066 | -0.042 | 11.660 | 0.252 | 0.252 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | PRO | 0 | 0.013 | 0.020 | 15.122 | -0.364 | -0.364 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | PRO | 0 | 0.005 | -0.017 | 17.362 | 0.068 | 0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | THR | 0 | -0.044 | -0.026 | 19.793 | 0.269 | 0.269 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | GLU | -1 | -0.884 | -0.932 | 23.274 | -9.908 | -9.908 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | PRO | 0 | -0.023 | -0.016 | 23.753 | -0.570 | -0.570 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | GLY | 0 | -0.050 | -0.022 | 23.762 | 0.226 | 0.226 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | GLN | 0 | -0.039 | -0.015 | 21.341 | -0.224 | -0.224 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | PRO | 0 | -0.024 | -0.023 | 16.499 | -0.277 | -0.277 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | VAL | 0 | -0.006 | 0.010 | 14.513 | 0.254 | 0.254 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | VAL | 0 | -0.015 | -0.003 | 9.635 | -0.703 | -0.703 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | ILE | 0 | -0.013 | -0.003 | 8.087 | 0.443 | 0.443 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | LEU | 0 | -0.011 | 0.001 | 2.465 | -3.712 | -3.301 | 0.964 | -0.421 | -0.954 | -0.001 |
45 | A | 45 | ILE | 0 | 0.015 | 0.014 | 3.961 | 3.017 | 3.275 | -0.001 | -0.050 | -0.208 | 0.000 |
46 | A | 46 | PRO | 0 | 0.014 | 0.002 | 2.469 | -13.652 | -10.664 | 0.915 | -2.124 | -1.779 | -0.020 |
47 | A | 47 | SER | 0 | 0.005 | -0.026 | 2.462 | -2.491 | -1.105 | 1.851 | -1.077 | -2.160 | -0.016 |
48 | A | 48 | ASP | -1 | -0.934 | -0.975 | 3.992 | -29.406 | -29.218 | 0.005 | -0.035 | -0.159 | 0.000 |
49 | A | 49 | MET | 0 | -0.013 | 0.009 | 6.583 | 3.825 | 3.825 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | VAL | 0 | -0.014 | 0.002 | 6.164 | 1.888 | 1.888 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 51 | GLU | -1 | -0.898 | -0.954 | 8.871 | -17.276 | -17.276 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 52 | TRP | 0 | 0.019 | -0.016 | 11.278 | 1.356 | 1.356 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 53 | PHE | 0 | 0.023 | 0.019 | 10.702 | 1.122 | 1.122 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | LEU | 0 | 0.002 | 0.002 | 12.160 | 0.903 | 0.903 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | GLU | -1 | -0.796 | -0.884 | 14.101 | -13.877 | -13.877 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | MET | 0 | -0.044 | -0.010 | 14.610 | 1.304 | 1.304 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | LEU | 0 | -0.015 | -0.001 | 13.862 | 0.932 | 0.932 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | LYS | 1 | 0.830 | 0.885 | 18.010 | 15.422 | 15.422 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | ALA | 0 | -0.051 | -0.017 | 20.218 | 0.716 | 0.716 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 60 | LYS | 1 | 0.829 | 0.933 | 21.274 | 12.930 | 12.930 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | GLY | 0 | 0.000 | 0.001 | 23.081 | 0.247 | 0.247 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | ILE | 0 | -0.030 | -0.009 | 19.009 | 0.351 | 0.351 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 63 | PRO | 0 | -0.014 | -0.004 | 19.396 | -0.579 | -0.579 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 64 | PHE | 0 | 0.004 | -0.005 | 13.912 | -0.440 | -0.440 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 65 | THR | 0 | -0.036 | -0.003 | 13.828 | 0.341 | 0.341 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 66 | VAL | 0 | 0.017 | 0.003 | 9.052 | -0.663 | -0.663 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 67 | TYR | 0 | -0.010 | 0.002 | 8.546 | 1.621 | 1.621 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 68 | VAL | 0 | 0.021 | 0.000 | 5.862 | -3.576 | -3.576 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 69 | GLU | -1 | -0.838 | -0.901 | 1.747 | -141.032 | -146.194 | 24.622 | -11.557 | -7.903 | -0.134 |
70 | A | 70 | GLU | -1 | -0.977 | -0.977 | 5.551 | -22.961 | -22.961 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 71 | GLY | 0 | -0.011 | -0.011 | 7.697 | 2.485 | 2.485 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 72 | GLY | 0 | 0.005 | 0.005 | 7.637 | -3.252 | -3.252 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 73 | SER | 0 | -0.044 | -0.011 | 8.939 | 1.758 | 1.758 | 0.000 | 0.000 | 0.000 | 0.000 |