![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 1N59Z
Calculation Name: 2VXQ-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2VXQ
Chain ID: A
UniProt ID: P01857
Base Structure: X-ray
Registration Date: 2023-09-22
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 | 92 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -662242.178874 |
---|---|
FMO2-HF: Nuclear repulsion | 625785.705281 |
FMO2-HF: Total energy | -36456.473593 |
FMO2-MP2: Total energy | -36562.714003 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F034363/ligand_interaction/ligand_F034363.png)
Ligand Interaction
![ligand interaction](./Kdata/F034363/ligand_interaction/ligand_interaction_F034363.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:3:LYS)
Summations of interaction energy for
fragment #1(A:3: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. |
-167.143 | -166.229 | 23.877 | -11.968 | -12.822 | -0.128 |
Interaction energy analysis for fragmet #1(A:3: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 | 5 | THR | 0 | -0.053 | -0.012 | 3.880 | 6.546 | 8.434 | -0.017 | -0.957 | -0.914 | -0.001 |
4 | A | 6 | PHE | 0 | 0.083 | 0.026 | 6.300 | -1.307 | -1.307 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 7 | THR | 0 | 0.018 | 0.020 | 10.116 | 0.858 | 0.858 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 8 | VAL | 0 | 0.023 | 0.029 | 12.598 | 0.139 | 0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 9 | GLU | -1 | -0.838 | -0.930 | 15.983 | -15.960 | -15.960 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 10 | LYS | 1 | 0.903 | 0.939 | 18.491 | 12.139 | 12.139 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 11 | GLY | 0 | 0.005 | -0.002 | 22.117 | 0.149 | 0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 12 | SER | 0 | -0.030 | 0.000 | 20.353 | 0.258 | 0.258 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 13 | ASN | 0 | -0.056 | -0.042 | 22.895 | 0.547 | 0.547 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 14 | GLU | -1 | -0.852 | -0.933 | 24.953 | -10.102 | -10.102 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 15 | LYS | 1 | 0.809 | 0.910 | 27.253 | 9.411 | 9.411 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 16 | HIS | 0 | -0.057 | -0.042 | 23.543 | -0.407 | -0.407 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 17 | LEU | 0 | -0.014 | 0.003 | 18.175 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 18 | ALA | 0 | 0.039 | 0.021 | 19.208 | -0.353 | -0.353 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 19 | VAL | 0 | -0.011 | -0.014 | 13.519 | -0.120 | -0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 20 | LEU | 0 | 0.001 | 0.015 | 11.964 | -0.523 | -0.523 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 21 | VAL | 0 | -0.022 | -0.002 | 8.772 | -1.256 | -1.256 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 22 | LYS | 1 | 0.831 | 0.912 | 6.371 | 39.475 | 39.475 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 23 | TYR | 0 | 0.077 | 0.026 | 2.066 | -27.566 | -28.717 | 11.870 | -4.732 | -5.988 | -0.053 |
22 | A | 24 | GLU | -1 | -0.845 | -0.912 | 2.606 | -41.715 | -39.376 | 0.701 | -1.005 | -2.035 | -0.003 |
23 | A | 25 | GLY | 0 | 0.018 | 0.008 | 1.790 | -37.658 | -40.116 | 11.325 | -5.261 | -3.605 | -0.071 |
24 | A | 26 | ASP | -1 | -0.850 | -0.928 | 4.572 | -35.708 | -35.564 | -0.001 | -0.008 | -0.134 | 0.000 |
25 | A | 27 | THR | 0 | 0.021 | 0.016 | 6.046 | -0.355 | -0.355 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 28 | MET | 0 | -0.028 | 0.001 | 6.414 | -1.145 | -1.145 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 29 | ALA | 0 | 0.024 | 0.013 | 9.995 | 2.135 | 2.135 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 30 | GLU | -1 | -0.912 | -0.975 | 12.380 | -16.816 | -16.816 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 31 | VAL | 0 | -0.017 | -0.020 | 11.285 | -2.602 | -2.602 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 32 | GLU | -1 | -0.799 | -0.872 | 13.821 | -15.449 | -15.449 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 33 | LEU | 0 | -0.004 | -0.008 | 15.148 | -1.468 | -1.468 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 34 | ARG | 1 | 0.855 | 0.927 | 17.421 | 15.491 | 15.491 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 35 | GLU | -1 | -0.803 | -0.898 | 19.074 | -12.877 | -12.877 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 36 | HIS | 0 | -0.090 | -0.057 | 20.000 | 0.727 | 0.727 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 37 | GLY | 0 | -0.004 | -0.011 | 21.647 | 0.096 | 0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 38 | SER | 0 | -0.058 | -0.015 | 23.188 | 0.649 | 0.649 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 39 | ASP | -1 | -0.902 | -0.954 | 23.433 | -11.671 | -11.671 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 40 | GLU | -1 | -0.969 | -0.982 | 23.623 | -11.941 | -11.941 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 41 | TRP | 0 | -0.056 | -0.036 | 15.503 | -0.733 | -0.733 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 42 | VAL | 0 | 0.026 | 0.014 | 20.432 | 0.461 | 0.461 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 43 | ALA | 0 | 0.018 | 0.005 | 18.855 | -0.868 | -0.868 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 44 | MET | 0 | -0.054 | -0.010 | 16.815 | 0.090 | 0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 45 | THR | 0 | -0.014 | -0.008 | 18.564 | -0.302 | -0.302 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 46 | LYS | 1 | 0.801 | 0.918 | 14.425 | 20.298 | 20.298 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 47 | GLY | 0 | 0.035 | 0.011 | 17.629 | 1.123 | 1.123 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 48 | GLU | -1 | -0.911 | -0.968 | 17.783 | -16.231 | -16.231 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 49 | GLY | 0 | -0.041 | -0.016 | 16.852 | -0.361 | -0.361 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 50 | GLY | 0 | -0.009 | -0.002 | 13.330 | -1.100 | -1.100 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 51 | VAL | 0 | -0.026 | -0.018 | 13.655 | -1.265 | -1.265 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 52 | TRP | 0 | -0.024 | -0.005 | 12.673 | 0.295 | 0.295 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 53 | THR | 0 | -0.023 | -0.023 | 17.022 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 54 | PHE | 0 | 0.020 | 0.010 | 20.274 | -0.356 | -0.356 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 55 | ASP | -1 | -0.836 | -0.902 | 22.262 | -12.474 | -12.474 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 56 | SER | 0 | -0.016 | -0.019 | 26.045 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 57 | GLU | -1 | -0.891 | -0.947 | 28.156 | -9.541 | -9.541 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 58 | GLU | -1 | -0.876 | -0.944 | 30.302 | -8.729 | -8.729 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 59 | PRO | 0 | -0.079 | -0.031 | 29.132 | -0.412 | -0.412 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 60 | LEU | 0 | 0.013 | 0.026 | 23.128 | -0.128 | -0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 61 | GLN | 0 | -0.096 | -0.063 | 25.163 | 0.169 | 0.169 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 62 | GLY | 0 | -0.003 | 0.007 | 21.082 | -0.256 | -0.256 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 63 | PRO | 0 | -0.065 | -0.064 | 17.990 | 0.597 | 0.597 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 64 | PHE | 0 | -0.005 | 0.007 | 16.835 | 0.311 | 0.311 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 65 | ASN | 0 | -0.017 | 0.018 | 14.742 | -1.316 | -1.316 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 66 | PHE | 0 | 0.025 | -0.002 | 11.739 | 0.399 | 0.399 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 67 | ARG | 1 | 0.793 | 0.878 | 11.650 | 16.195 | 16.195 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 68 | PHE | 0 | 0.036 | 0.009 | 5.661 | -1.093 | -1.093 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 69 | LEU | 0 | 0.002 | 0.012 | 10.599 | -1.021 | -1.021 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 70 | THR | 0 | -0.047 | -0.042 | 5.477 | 1.125 | 1.125 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 71 | GLU | -1 | -0.836 | -0.930 | 8.853 | -20.144 | -20.144 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 72 | LYS | 1 | 0.816 | 0.916 | 7.259 | 39.351 | 39.351 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 73 | GLY | 0 | 0.019 | 0.018 | 10.597 | 0.949 | 0.949 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 74 | MET | 0 | -0.049 | -0.008 | 5.428 | 3.126 | 3.126 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 75 | LYS | 1 | 0.927 | 0.950 | 8.572 | 23.796 | 23.796 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 76 | ASN | 0 | -0.074 | -0.045 | 5.919 | -6.915 | -6.915 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 77 | VAL | 0 | 0.048 | 0.021 | 9.336 | 1.140 | 1.140 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 78 | PHE | 0 | -0.069 | -0.038 | 5.302 | -2.077 | -2.077 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 79 | ASP | -1 | -0.764 | -0.897 | 10.579 | -17.543 | -17.543 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 80 | ASP | -1 | -0.870 | -0.935 | 13.155 | -15.808 | -15.808 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 81 | VAL | 0 | -0.048 | -0.006 | 9.724 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 82 | VAL | 0 | -0.016 | 0.003 | 12.539 | -0.093 | -0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 83 | PRO | 0 | 0.020 | 0.008 | 14.846 | 0.579 | 0.579 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 84 | GLU | -1 | -0.757 | -0.859 | 18.122 | -11.115 | -11.115 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 85 | LYS | 1 | 0.785 | 0.880 | 21.663 | 11.062 | 11.062 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 86 | TYR | 0 | 0.004 | 0.024 | 17.940 | -0.246 | -0.246 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 87 | THR | 0 | -0.042 | -0.040 | 18.098 | 0.834 | 0.834 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 88 | ILE | 0 | -0.019 | -0.001 | 17.819 | -0.658 | -0.658 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 89 | GLY | 0 | -0.010 | -0.005 | 17.146 | 0.518 | 0.518 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 90 | ALA | 0 | -0.035 | -0.010 | 15.013 | -0.478 | -0.478 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 91 | THR | 0 | -0.039 | -0.036 | 8.500 | -0.211 | -0.211 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 92 | TYR | 0 | 0.021 | 0.016 | 10.180 | 1.041 | 1.041 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 93 | ALA | 0 | 0.014 | -0.011 | 5.145 | -2.370 | -2.370 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 94 | PRO | 0 | -0.013 | 0.019 | 5.247 | 1.655 | 1.807 | -0.001 | -0.005 | -0.146 | 0.000 |