![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 3QM3L
Calculation Name: 2ZV3-A-Xray372
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: 2023-03-14
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 | 108 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -844986.742494 |
---|---|
FMO2-HF: Nuclear repulsion | 802920.643919 |
FMO2-HF: Total energy | -42066.098576 |
FMO2-MP2: Total energy | -42187.667444 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F019213/ligand_interaction/ligand_F019213.png)
Ligand Interaction
![ligand interaction](./Kdata/F019213/ligand_interaction/ligand_interaction_F019213.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. |
-34.221 | -33.912 | 42.897 | -15.584 | -27.622 | -0.043 |
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 | -0.013 | 0.013 | 3.852 | -1.689 | 1.364 | -0.025 | -1.707 | -1.321 | 0.007 |
4 | A | 4 | VAL | 0 | -0.015 | -0.004 | 6.962 | -0.085 | -0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 5 | VAL | 0 | -0.004 | -0.008 | 9.757 | 0.211 | 0.211 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | VAL | 0 | 0.004 | 0.002 | 13.341 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 7 | ILE | 0 | 0.002 | -0.010 | 16.328 | 0.068 | 0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | ARG | 1 | 0.823 | 0.883 | 19.853 | 0.305 | 0.305 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | ASN | 0 | -0.014 | -0.026 | 23.299 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | ASP | -1 | -0.800 | -0.881 | 25.190 | -0.290 | -0.290 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | LEU | 0 | -0.026 | -0.005 | 26.097 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | GLY | 0 | 0.010 | 0.020 | 28.943 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | MET | 0 | -0.044 | -0.016 | 23.709 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | GLY | 0 | 0.085 | 0.040 | 27.337 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | LYS | 1 | 0.978 | 0.968 | 25.390 | 0.381 | 0.381 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | GLY | 0 | 0.050 | 0.031 | 24.402 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | LYS | 1 | 0.868 | 0.924 | 24.838 | 0.266 | 0.266 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | MET | 0 | -0.002 | 0.004 | 22.041 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | VAL | 0 | 0.002 | 0.003 | 20.103 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | ALA | 0 | 0.003 | 0.009 | 20.044 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | GLN | 0 | -0.002 | 0.005 | 20.988 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | GLY | 0 | 0.065 | 0.024 | 17.781 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | GLY | 0 | -0.009 | 0.002 | 16.349 | -0.079 | -0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | HIS | 0 | 0.021 | 0.001 | 16.627 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | ALA | 0 | 0.014 | 0.014 | 15.551 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | ILE | 0 | 0.017 | 0.001 | 11.600 | -0.058 | -0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | ILE | 0 | 0.003 | 0.007 | 12.028 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | GLU | -1 | -0.731 | -0.848 | 13.522 | -0.258 | -0.258 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | ALA | 0 | -0.052 | -0.002 | 10.205 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | PHE | 0 | 0.028 | 0.001 | 8.534 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | LEU | 0 | -0.009 | -0.003 | 9.277 | 0.112 | 0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | ASP | -1 | -0.778 | -0.878 | 11.380 | -0.155 | -0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | ALA | 0 | 0.022 | 0.012 | 5.784 | 0.122 | 0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | LYS | 1 | 0.760 | 0.862 | 7.878 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | ARG | 1 | 0.792 | 0.855 | 9.135 | 0.326 | 0.326 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | LYS | 1 | 0.845 | 0.937 | 9.254 | 0.160 | 0.160 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | ASN | 0 | 0.004 | -0.010 | 6.112 | 0.228 | 0.228 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | PRO | 0 | 0.056 | 0.024 | 6.267 | -0.074 | -0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | ARG | 1 | 1.019 | 1.004 | 7.219 | -1.994 | -1.994 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | ALA | 0 | 0.016 | 0.016 | 2.180 | 0.600 | 0.737 | 1.226 | -0.269 | -1.095 | 0.002 |
41 | A | 41 | VAL | 0 | 0.008 | 0.010 | 2.576 | -2.091 | -0.854 | 1.115 | -1.004 | -1.349 | -0.016 |
42 | A | 42 | ASP | -1 | -0.810 | -0.895 | 4.855 | 0.478 | 0.491 | -0.001 | -0.005 | -0.008 | 0.000 |
43 | A | 43 | GLU | -1 | -0.855 | -0.924 | 2.701 | 8.440 | 9.323 | 4.154 | -1.710 | -3.328 | -0.014 |
44 | A | 44 | TRP | 0 | -0.017 | -0.014 | 2.859 | -2.415 | -0.457 | 0.335 | -0.571 | -1.721 | 0.000 |
45 | A | 45 | LEU | 0 | -0.051 | -0.035 | 4.063 | -1.164 | -0.997 | 0.007 | -0.026 | -0.148 | 0.000 |
46 | A | 46 | ARG | 1 | 0.787 | 0.889 | 6.308 | -2.757 | -2.757 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | GLU | -1 | -0.897 | -0.928 | 3.599 | -1.464 | -0.626 | 0.012 | -0.312 | -0.537 | -0.002 |
48 | A | 48 | GLY | 0 | 0.009 | 0.004 | 6.233 | -0.861 | -0.861 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | GLN | 0 | 0.010 | 0.014 | 6.363 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | LYS | 1 | 0.877 | 0.944 | 3.085 | 8.160 | 8.737 | 0.005 | -0.212 | -0.370 | 0.001 |
51 | A | 51 | LYS | 1 | 0.852 | 0.914 | 6.529 | 1.229 | 1.229 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 52 | VAL | 0 | 0.020 | 0.015 | 8.323 | 0.130 | 0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 53 | VAL | 0 | -0.001 | 0.004 | 11.055 | 0.079 | 0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | VAL | 0 | 0.010 | 0.012 | 13.728 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | LYS | 1 | 0.860 | 0.937 | 16.156 | 0.509 | 0.509 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | VAL | 0 | 0.006 | 0.010 | 19.115 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | ASN | 0 | -0.070 | -0.064 | 21.685 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | SER | 0 | 0.046 | 0.026 | 24.972 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | GLU | -1 | -0.800 | -0.872 | 24.914 | -0.250 | -0.250 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 60 | LYS | 1 | 0.902 | 0.925 | 25.008 | 0.176 | 0.176 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | GLU | -1 | -0.795 | -0.889 | 21.600 | -0.372 | -0.372 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | LEU | 0 | -0.013 | -0.005 | 19.446 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 63 | ILE | 0 | 0.017 | 0.004 | 20.105 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 64 | ASP | -1 | -0.862 | -0.907 | 20.941 | -0.204 | -0.204 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 65 | ILE | 0 | -0.051 | -0.019 | 15.471 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 66 | TYR | 0 | 0.049 | 0.031 | 15.915 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 67 | ASN | 0 | 0.025 | -0.002 | 16.556 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 68 | LYS | 1 | 0.956 | 0.999 | 16.387 | 0.295 | 0.295 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 69 | ALA | 0 | 0.041 | 0.023 | 12.356 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 70 | ARG | 1 | 0.824 | 0.890 | 13.049 | 0.335 | 0.335 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 71 | SER | 0 | -0.077 | -0.040 | 15.385 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 72 | GLU | -1 | -0.819 | -0.893 | 12.230 | 0.200 | 0.200 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 73 | GLY | 0 | -0.009 | -0.001 | 11.898 | 0.086 | 0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 74 | LEU | 0 | -0.035 | -0.011 | 7.773 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 75 | PRO | 0 | -0.008 | 0.001 | 6.050 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 76 | CYS | 0 | -0.065 | -0.039 | 9.202 | -0.163 | -0.163 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 77 | SER | 0 | -0.051 | -0.028 | 11.783 | 0.106 | 0.106 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 78 | ILE | 0 | 0.036 | 0.000 | 14.988 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 79 | ILE | 0 | -0.025 | 0.009 | 18.125 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 80 | ARG | 1 | 0.891 | 0.940 | 20.959 | 0.194 | 0.194 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 81 | ASP | -1 | -0.793 | -0.868 | 24.785 | -0.261 | -0.261 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 82 | ALA | 0 | 0.026 | 0.011 | 27.089 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 90 | GLY | 0 | 0.005 | 0.012 | 30.465 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 91 | THR | 0 | -0.054 | -0.049 | 27.956 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 92 | LEU | 0 | 0.027 | 0.001 | 23.417 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 93 | THR | 0 | -0.016 | -0.033 | 23.267 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 94 | ALA | 0 | 0.009 | -0.004 | 18.505 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 95 | VAL | 0 | 0.000 | 0.006 | 14.986 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 96 | ALA | 0 | -0.017 | -0.001 | 11.609 | -0.088 | -0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 97 | ILE | 0 | 0.013 | 0.004 | 8.960 | 0.178 | 0.178 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 98 | GLY | 0 | 0.018 | 0.026 | 5.982 | -0.447 | -0.447 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 99 | PRO | 0 | -0.041 | -0.038 | 3.098 | 0.012 | 0.442 | 0.041 | -0.091 | -0.379 | 0.000 |
93 | A | 100 | GLU | -1 | -0.797 | -0.913 | 2.078 | 0.961 | 1.168 | 4.105 | -1.599 | -2.713 | -0.012 |
94 | A | 101 | LYS | 1 | 0.849 | 0.899 | 2.011 | -25.641 | -33.457 | 28.179 | -8.818 | -11.544 | 0.026 |
95 | A | 102 | ASP | -1 | -0.724 | -0.859 | 2.124 | -14.882 | -16.529 | 3.743 | 0.773 | -2.869 | -0.035 |
96 | A | 103 | GLU | -1 | -0.782 | -0.911 | 4.118 | 1.823 | 2.030 | 0.002 | -0.030 | -0.179 | 0.000 |
97 | A | 104 | LYS | 1 | 0.861 | 0.923 | 5.826 | -1.526 | -1.526 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 105 | ILE | 0 | -0.019 | -0.004 | 4.756 | -0.125 | -0.060 | -0.001 | -0.003 | -0.061 | 0.000 |
99 | A | 106 | ASP | -1 | -0.837 | -0.913 | 7.990 | -1.592 | -1.592 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 107 | LYS | 1 | 0.798 | 0.891 | 10.106 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 108 | ILE | 0 | -0.066 | -0.023 | 11.361 | 0.066 | 0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 109 | THR | 0 | 0.020 | -0.018 | 11.293 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 110 | GLY | 0 | 0.002 | 0.009 | 12.920 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 111 | HIS | 0 | -0.020 | 0.003 | 13.585 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 112 | LEU | 0 | -0.041 | -0.014 | 15.559 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 113 | LYS | 1 | 0.931 | 0.960 | 17.026 | 0.423 | 0.423 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 114 | LEU | 0 | 0.060 | 0.021 | 13.958 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 115 | LEU | 0 | -0.033 | -0.018 | 17.628 | 0.097 | 0.097 | 0.000 | 0.000 | 0.000 | 0.000 |