![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: N1LVQ
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 | OptH |
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 | -844207.243345 |
---|---|
FMO2-HF: Nuclear repulsion | 802142.001428 |
FMO2-HF: Total energy | -42065.241917 |
FMO2-MP2: Total energy | -42186.790785 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F019215/ligand_interaction/ligand_F019215.png)
Ligand Interaction
![ligand interaction](./Kdata/F019215/ligand_interaction/ligand_interaction_F019215.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. |
-26.662 | -18.186 | 23.523 | -7.655 | -24.345 | -0.082 |
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 | -0.001 | 0.013 | 3.762 | -4.157 | 1.652 | -0.050 | -3.265 | -2.494 | 0.019 |
4 | A | 4 | VAL | 0 | -0.046 | -0.017 | 6.611 | -0.294 | -0.294 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 5 | VAL | 0 | -0.009 | -0.014 | 9.927 | 0.208 | 0.208 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | VAL | 0 | 0.003 | -0.009 | 13.145 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 7 | ILE | 0 | 0.009 | -0.006 | 16.295 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | ARG | 1 | 0.788 | 0.872 | 19.572 | 0.097 | 0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | ASN | 0 | -0.023 | -0.028 | 23.046 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | ASP | -1 | -0.792 | -0.875 | 25.106 | -0.125 | -0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | LEU | 0 | -0.038 | -0.020 | 25.522 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | GLY | 0 | 0.022 | 0.030 | 28.829 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | MET | 0 | -0.057 | -0.020 | 23.059 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | GLY | 0 | 0.081 | 0.041 | 27.543 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | LYS | 1 | 0.993 | 0.971 | 25.171 | 0.228 | 0.228 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | GLY | 0 | 0.039 | 0.021 | 24.236 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | LYS | 1 | 0.902 | 0.953 | 24.658 | 0.097 | 0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | MET | 0 | 0.029 | 0.017 | 21.594 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | VAL | 0 | -0.002 | 0.008 | 19.734 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | ALA | 0 | 0.009 | 0.010 | 19.745 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | GLN | 0 | 0.024 | 0.041 | 20.662 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | GLY | 0 | 0.064 | 0.022 | 17.397 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | GLY | 0 | -0.016 | 0.005 | 16.019 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | HIS | 0 | 0.014 | -0.002 | 16.573 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | ALA | 0 | 0.008 | 0.003 | 15.138 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | ILE | 0 | 0.007 | -0.016 | 11.307 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | ILE | 0 | -0.004 | 0.007 | 11.773 | 0.076 | 0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | GLU | -1 | -0.876 | -0.952 | 13.215 | 0.218 | 0.218 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | ALA | 0 | -0.048 | 0.000 | 9.606 | 0.071 | 0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | PHE | 0 | 0.040 | 0.012 | 8.187 | 0.154 | 0.154 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | LEU | 0 | -0.031 | -0.019 | 9.033 | 0.182 | 0.182 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | ASP | -1 | -0.808 | -0.910 | 10.527 | 0.505 | 0.505 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | ALA | 0 | 0.029 | -0.003 | 5.293 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | LYS | 1 | 0.926 | 0.963 | 7.433 | -0.525 | -0.525 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | ARG | 1 | 0.914 | 0.948 | 8.683 | -0.333 | -0.333 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | LYS | 1 | 0.860 | 0.950 | 8.584 | -0.598 | -0.598 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | ASN | 0 | 0.015 | 0.004 | 5.485 | 0.083 | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | PRO | 0 | 0.041 | 0.016 | 5.874 | 0.350 | 0.350 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | ARG | 1 | 0.994 | 0.994 | 7.548 | -1.307 | -1.307 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | ALA | 0 | 0.024 | 0.018 | 2.229 | -0.449 | -0.135 | 1.413 | -0.399 | -1.328 | 0.002 |
41 | A | 41 | VAL | 0 | -0.019 | -0.004 | 3.415 | 1.150 | 2.359 | 1.065 | -0.673 | -1.600 | -0.011 |
42 | A | 42 | ASP | -1 | -0.905 | -0.960 | 4.775 | 1.035 | 1.040 | -0.001 | -0.007 | 0.003 | 0.000 |
43 | A | 43 | GLU | -1 | -0.985 | -1.009 | 3.314 | 0.140 | 2.503 | 0.322 | -0.921 | -1.764 | -0.007 |
44 | A | 44 | TRP | 0 | -0.010 | 0.007 | 2.750 | -4.355 | -1.640 | 0.891 | -1.062 | -2.544 | 0.004 |
45 | A | 45 | LEU | 0 | -0.053 | -0.035 | 3.589 | -2.020 | -1.958 | 0.029 | 0.071 | -0.162 | 0.001 |
46 | A | 46 | ARG | 1 | 0.894 | 0.968 | 6.953 | -1.645 | -1.645 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | GLU | -1 | -0.944 | -0.962 | 2.747 | -8.460 | -6.039 | 0.293 | -1.297 | -1.418 | -0.014 |
48 | A | 48 | GLY | 0 | 0.011 | 0.012 | 6.415 | -0.508 | -0.508 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | GLN | 0 | -0.018 | -0.011 | 5.796 | 0.088 | 0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | LYS | 1 | 1.015 | 1.011 | 5.156 | 3.900 | 3.900 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 51 | LYS | 1 | 0.870 | 0.924 | 6.488 | 0.817 | 0.817 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 52 | VAL | 0 | -0.006 | 0.001 | 8.709 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 53 | VAL | 0 | -0.003 | 0.004 | 11.021 | 0.122 | 0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | VAL | 0 | 0.027 | 0.022 | 13.455 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | LYS | 1 | 0.912 | 0.963 | 16.100 | 0.341 | 0.341 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | VAL | 0 | 0.011 | 0.010 | 19.100 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | ASN | 0 | -0.057 | -0.055 | 21.548 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | SER | 0 | 0.056 | 0.031 | 24.769 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | GLU | -1 | -0.840 | -0.929 | 24.647 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 60 | LYS | 1 | 0.990 | 0.994 | 24.472 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | GLU | -1 | -0.856 | -0.925 | 21.421 | -0.183 | -0.183 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | LEU | 0 | -0.030 | -0.005 | 19.035 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 63 | ILE | 0 | 0.016 | -0.006 | 19.593 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 64 | ASP | -1 | -0.918 | -0.950 | 20.589 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 65 | ILE | 0 | -0.046 | -0.019 | 15.564 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 66 | TYR | 0 | 0.042 | 0.026 | 15.816 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 67 | ASN | 0 | 0.026 | 0.006 | 16.434 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 68 | LYS | 1 | 0.946 | 0.983 | 16.383 | 0.071 | 0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 69 | ALA | 0 | 0.046 | 0.026 | 12.153 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 70 | ARG | 1 | 0.877 | 0.925 | 13.036 | -0.166 | -0.166 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 71 | SER | 0 | -0.092 | -0.043 | 15.253 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 72 | GLU | -1 | -0.859 | -0.925 | 12.058 | 0.254 | 0.254 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 73 | GLY | 0 | -0.030 | 0.001 | 12.051 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 74 | LEU | 0 | -0.053 | -0.025 | 7.479 | 0.136 | 0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 75 | PRO | 0 | -0.034 | -0.007 | 5.869 | -0.112 | -0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 76 | CYS | 0 | -0.046 | -0.023 | 8.999 | -0.116 | -0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 77 | SER | 0 | -0.031 | -0.008 | 11.569 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 78 | ILE | 0 | 0.044 | 0.006 | 14.774 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 79 | ILE | 0 | -0.012 | 0.011 | 17.494 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 80 | ARG | 1 | 0.964 | 0.975 | 20.424 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 81 | ASP | -1 | -0.872 | -0.934 | 24.223 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 82 | ALA | 0 | -0.014 | -0.005 | 26.455 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 90 | GLY | 0 | 0.020 | 0.006 | 30.463 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 91 | THR | 0 | -0.046 | -0.020 | 27.114 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 92 | LEU | 0 | 0.021 | 0.020 | 22.832 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 93 | THR | 0 | -0.010 | -0.056 | 22.464 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 94 | ALA | 0 | 0.013 | -0.005 | 17.989 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 95 | VAL | 0 | 0.003 | 0.015 | 14.239 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 96 | ALA | 0 | -0.022 | 0.011 | 11.281 | -0.083 | -0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 97 | ILE | 0 | 0.003 | -0.003 | 8.338 | 0.118 | 0.118 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 98 | GLY | 0 | 0.027 | 0.042 | 5.508 | -0.295 | -0.295 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 99 | PRO | 0 | -0.058 | -0.056 | 2.488 | -0.953 | -0.176 | 0.429 | -0.231 | -0.975 | 0.001 |
93 | A | 100 | GLU | -1 | -0.869 | -0.969 | 2.052 | 3.810 | 0.737 | 8.143 | -1.553 | -3.518 | -0.008 |
94 | A | 101 | LYS | 1 | 0.962 | 0.975 | 2.331 | -1.593 | -5.187 | 4.344 | 3.889 | -4.639 | -0.027 |
95 | A | 102 | ASP | -1 | -0.856 | -0.933 | 2.168 | -11.455 | -12.168 | 6.644 | -2.171 | -3.760 | -0.042 |
96 | A | 103 | GLU | -1 | -0.801 | -0.913 | 4.198 | 0.631 | 0.812 | 0.001 | -0.036 | -0.146 | 0.000 |
97 | A | 104 | LYS | 1 | 0.905 | 0.954 | 6.389 | -1.007 | -1.007 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 105 | ILE | 0 | -0.009 | 0.002 | 5.157 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 106 | ASP | -1 | -0.815 | -0.894 | 7.988 | -1.331 | -1.331 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 107 | LYS | 1 | 0.834 | 0.927 | 9.961 | -0.088 | -0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 108 | ILE | 0 | -0.077 | -0.040 | 11.702 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 109 | THR | 0 | -0.017 | -0.034 | 11.053 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 110 | GLY | 0 | 0.041 | 0.038 | 12.670 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 111 | HIS | 0 | -0.029 | -0.008 | 13.398 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 112 | LEU | 0 | -0.051 | -0.013 | 15.415 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 113 | LYS | 1 | 0.940 | 0.967 | 16.759 | 0.284 | 0.284 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 114 | LEU | 0 | 0.055 | 0.017 | 14.307 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 115 | LEU | 0 | -0.031 | -0.018 | 17.831 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |