![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: KR613
Calculation Name: 2ZV3-A-Xray311
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2ZV3
Chain ID: A
UniProt ID: Q60363
Base Structure: X-ray
Registration Date: 2021-09-06
Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.
Modeling method
Optimization | MOE:Amber10:EHT |
---|---|
Restraint | OptH |
Protonation | MOE:Protonate 3D |
Complement | MOE:Structure Preparation |
Water | No |
Procedure | Auto-FMO protocol ver. 1.20200116 |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 110 |
LigandCharge | |
Software | ABINIT-MP - Open Ver.1 Rev. 15 / 20190524 |
Total energy (hartree)
FMO2-HF: Electronic energy | -849584.098568 |
---|---|
FMO2-HF: Nuclear repulsion | 807347.874577 |
FMO2-HF: Total energy | -42236.22399 |
FMO2-MP2: Total energy | -42358.309911 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F015582/ligand_interaction/ligand_F015582.png)
Ligand Interaction
![ligand interaction](./Kdata/F015582/ligand_interaction/ligand_interaction_F015582.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. |
-114.481 | -104.649 | 22.743 | -8.685 | -23.895 | -0.151 |
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 | 0.031 | 0.032 | 3.762 | 2.507 | 4.859 | -0.030 | -1.236 | -1.087 | -0.002 |
4 | A | 4 | VAL | 0 | -0.046 | -0.014 | 6.606 | 0.323 | 0.323 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 5 | VAL | 0 | 0.000 | -0.011 | 9.934 | 1.399 | 1.399 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | VAL | 0 | -0.001 | -0.008 | 13.140 | 0.420 | 0.420 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 7 | ILE | 0 | 0.019 | -0.002 | 16.287 | 0.802 | 0.802 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | ARG | 1 | 0.779 | 0.868 | 19.566 | 11.999 | 11.999 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | ASN | 0 | -0.002 | -0.016 | 23.038 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | ASP | -1 | -0.795 | -0.875 | 25.109 | -11.230 | -11.230 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | LEU | 0 | -0.047 | -0.025 | 25.518 | 0.374 | 0.374 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | GLY | 0 | 0.023 | 0.030 | 28.823 | 0.306 | 0.306 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | MET | 0 | -0.063 | -0.023 | 23.056 | 0.268 | 0.268 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | GLY | 0 | 0.084 | 0.041 | 27.541 | -0.086 | -0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | LYS | 1 | 1.002 | 0.976 | 25.173 | 11.274 | 11.274 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | GLY | 0 | 0.036 | 0.020 | 24.239 | -0.473 | -0.473 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | LYS | 1 | 0.897 | 0.949 | 24.662 | 10.717 | 10.717 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | MET | 0 | 0.037 | 0.023 | 21.594 | -0.380 | -0.380 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | VAL | 0 | 0.001 | 0.009 | 19.742 | -0.753 | -0.753 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | ALA | 0 | 0.004 | 0.006 | 19.750 | -0.584 | -0.584 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | GLN | 0 | 0.020 | 0.040 | 20.650 | -0.442 | -0.442 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | GLY | 0 | 0.074 | 0.026 | 17.389 | -0.496 | -0.496 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | GLY | 0 | -0.017 | 0.004 | 16.009 | -1.136 | -1.136 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | HIS | 0 | 0.011 | -0.004 | 16.558 | -0.798 | -0.798 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | ALA | 0 | 0.014 | 0.005 | 15.132 | -0.356 | -0.356 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | ILE | 0 | 0.008 | -0.016 | 11.296 | -1.231 | -1.231 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | ILE | 0 | -0.009 | 0.005 | 11.757 | -1.252 | -1.252 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | GLU | -1 | -0.874 | -0.951 | 13.229 | -15.843 | -15.843 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | ALA | 0 | -0.041 | 0.003 | 9.593 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | PHE | 0 | 0.029 | 0.006 | 8.203 | -1.052 | -1.052 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | LEU | 0 | -0.030 | -0.018 | 9.043 | -0.224 | -0.224 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | ASP | -1 | -0.805 | -0.908 | 10.533 | -18.750 | -18.750 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | ALA | 0 | 0.024 | -0.007 | 5.299 | 0.168 | 0.168 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | LYS | 1 | 0.923 | 0.961 | 7.437 | 19.740 | 19.740 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | ARG | 1 | 0.915 | 0.950 | 8.688 | 16.809 | 16.809 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | LYS | 1 | 0.866 | 0.954 | 8.578 | 20.250 | 20.250 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | ASN | 0 | 0.014 | 0.002 | 5.475 | 0.859 | 0.859 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | PRO | 0 | 0.048 | 0.018 | 5.870 | -2.543 | -2.543 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | ARG | 1 | 0.998 | 0.998 | 7.549 | 20.675 | 20.675 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | ALA | 0 | 0.018 | 0.014 | 2.215 | -1.917 | -1.660 | 1.430 | -0.390 | -1.297 | 0.001 |
41 | A | 41 | VAL | 0 | -0.018 | -0.004 | 3.415 | -5.353 | -3.864 | 0.952 | -0.811 | -1.631 | -0.013 |
42 | A | 42 | ASP | -1 | -0.898 | -0.955 | 4.784 | -24.574 | -24.566 | 0.000 | -0.007 | -0.001 | 0.000 |
43 | A | 43 | GLU | -1 | -0.989 | -1.011 | 3.312 | -52.908 | -50.345 | 0.317 | -1.099 | -1.781 | -0.009 |
44 | A | 44 | TRP | 0 | -0.038 | -0.007 | 2.736 | -2.607 | -0.245 | 0.879 | -0.846 | -2.396 | 0.000 |
45 | A | 45 | LEU | 0 | -0.038 | -0.027 | 3.568 | 0.489 | 0.525 | 0.031 | 0.082 | -0.150 | 0.001 |
46 | A | 46 | ARG | 1 | 0.906 | 0.975 | 6.955 | 33.398 | 33.398 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | GLU | -1 | -0.956 | -0.970 | 2.831 | -82.756 | -79.500 | 0.185 | -1.838 | -1.602 | -0.018 |
48 | A | 48 | GLY | 0 | 0.019 | 0.016 | 6.437 | -0.730 | -0.730 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | GLN | 0 | -0.020 | -0.013 | 5.773 | 2.916 | 2.916 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | LYS | 1 | 1.013 | 1.009 | 5.048 | 47.770 | 47.770 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 51 | LYS | 1 | 0.872 | 0.924 | 6.494 | 26.159 | 26.159 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 52 | VAL | 0 | -0.010 | -0.002 | 8.772 | 1.111 | 1.111 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 53 | VAL | 0 | 0.000 | 0.005 | 11.021 | 0.107 | 0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | VAL | 0 | 0.024 | 0.025 | 13.449 | 0.722 | 0.722 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | LYS | 1 | 0.939 | 0.978 | 16.097 | 14.184 | 14.184 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | VAL | 0 | -0.007 | -0.002 | 19.103 | -0.215 | -0.215 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | ASN | 0 | -0.046 | -0.050 | 21.550 | 0.313 | 0.313 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | SER | 0 | 0.050 | 0.027 | 24.774 | 0.591 | 0.591 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | GLU | -1 | -0.839 | -0.930 | 24.648 | -11.407 | -11.407 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 60 | LYS | 1 | 0.986 | 0.992 | 24.472 | 10.850 | 10.850 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | GLU | -1 | -0.854 | -0.923 | 21.426 | -14.117 | -14.117 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | LEU | 0 | -0.025 | -0.003 | 19.037 | -0.701 | -0.701 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 63 | ILE | 0 | 0.015 | -0.007 | 19.594 | -0.742 | -0.742 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 64 | ASP | -1 | -0.921 | -0.951 | 20.590 | -12.930 | -12.930 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 65 | ILE | 0 | -0.040 | -0.016 | 15.572 | -0.554 | -0.554 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 66 | TYR | 0 | 0.037 | 0.024 | 15.812 | -1.074 | -1.074 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 67 | ASN | 0 | 0.027 | 0.006 | 16.434 | -0.585 | -0.585 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 68 | LYS | 1 | 0.949 | 0.985 | 16.376 | 14.949 | 14.949 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 69 | ALA | 0 | 0.042 | 0.023 | 12.154 | -0.560 | -0.560 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 70 | ARG | 1 | 0.873 | 0.923 | 13.034 | 16.661 | 16.661 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 71 | SER | 0 | -0.086 | -0.040 | 15.253 | 0.251 | 0.251 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 72 | GLU | -1 | -0.858 | -0.924 | 12.055 | -18.841 | -18.841 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 73 | GLY | 0 | -0.031 | 0.001 | 12.052 | -0.730 | -0.730 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 74 | LEU | 0 | -0.059 | -0.029 | 7.476 | -1.422 | -1.422 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 75 | PRO | 0 | -0.042 | -0.011 | 5.868 | 1.830 | 1.830 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 76 | CYS | 0 | -0.046 | -0.022 | 9.000 | -0.958 | -0.958 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 77 | SER | 0 | -0.032 | -0.008 | 11.562 | 1.089 | 1.089 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 78 | ILE | 0 | 0.050 | 0.008 | 14.765 | -0.344 | -0.344 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 79 | ILE | 0 | -0.016 | 0.010 | 17.482 | 0.491 | 0.491 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 80 | ARG | 1 | 0.969 | 0.977 | 20.414 | 10.520 | 10.520 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 81 | ASP | -1 | -0.875 | -0.941 | 24.213 | -10.915 | -10.915 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 82 | ALA | 0 | -0.035 | -0.012 | 26.444 | 0.266 | 0.266 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 83 | NME | 0 | 0.025 | 0.014 | 29.663 | 0.205 | 0.205 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 89 | ACE | 0 | 0.008 | -0.007 | 34.256 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 90 | GLY | 0 | 0.027 | 0.016 | 30.461 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 91 | THR | 0 | -0.067 | -0.024 | 27.106 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 92 | LEU | 0 | 0.021 | 0.020 | 22.827 | -0.232 | -0.232 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 93 | THR | 0 | -0.013 | -0.056 | 22.455 | -0.147 | -0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 94 | ALA | 0 | 0.021 | 0.001 | 17.984 | -0.216 | -0.216 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 95 | VAL | 0 | 0.005 | 0.015 | 14.236 | 0.396 | 0.396 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 96 | ALA | 0 | -0.022 | 0.012 | 11.274 | -0.600 | -0.600 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 97 | ILE | 0 | 0.006 | -0.001 | 8.341 | 0.942 | 0.942 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 98 | GLY | 0 | 0.017 | 0.035 | 5.504 | -3.254 | -3.254 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 99 | PRO | 0 | -0.054 | -0.052 | 2.470 | 2.695 | 3.409 | 0.469 | -0.226 | -0.958 | 0.000 |
95 | A | 100 | GLU | -1 | -0.845 | -0.959 | 2.051 | -32.409 | -35.365 | 8.020 | -1.585 | -3.479 | -0.011 |
96 | A | 101 | LYS | 1 | 0.924 | 0.954 | 2.334 | 25.536 | 22.796 | 4.175 | 3.283 | -4.719 | -0.033 |
97 | A | 102 | ASP | -1 | -0.848 | -0.934 | 2.153 | -98.978 | -96.652 | 6.313 | -3.970 | -4.669 | -0.067 |
98 | A | 103 | GLU | -1 | -0.789 | -0.905 | 4.184 | -36.992 | -36.827 | 0.002 | -0.042 | -0.125 | 0.000 |
99 | A | 104 | LYS | 1 | 0.909 | 0.957 | 6.381 | 31.695 | 31.695 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 105 | ILE | 0 | -0.011 | 0.001 | 5.167 | 3.662 | 3.662 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 106 | ASP | -1 | -0.811 | -0.891 | 7.983 | -31.607 | -31.607 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 107 | LYS | 1 | 0.837 | 0.929 | 9.953 | 22.213 | 22.213 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 108 | ILE | 0 | -0.078 | -0.041 | 11.703 | 2.061 | 2.061 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 109 | THR | 0 | -0.011 | -0.032 | 11.054 | 0.998 | 0.998 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 110 | GLY | 0 | 0.036 | 0.034 | 12.659 | 0.225 | 0.225 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 111 | HIS | 0 | -0.030 | -0.008 | 13.387 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 112 | LEU | 0 | -0.053 | -0.016 | 15.415 | 1.044 | 1.044 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 113 | LYS | 1 | 0.932 | 0.962 | 16.749 | 14.056 | 14.056 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 114 | LEU | 0 | 0.019 | -0.005 | 14.355 | -0.385 | -0.385 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 115 | LEU | -1 | -0.937 | -0.969 | 17.840 | -14.403 | -14.403 | 0.000 | 0.000 | 0.000 | 0.000 |