![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: JQ669
Calculation Name: 1SV4-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1SV4
Chain ID: A
UniProt ID: Q01842
Base Structure: X-ray
Registration Date: 2023-09-20
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 | 78 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -536015.024784 |
---|---|
FMO2-HF: Nuclear repulsion | 503893.632845 |
FMO2-HF: Total energy | -32121.391939 |
FMO2-MP2: Total energy | -32213.140268 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F031799/ligand_interaction/ligand_F031799.png)
Ligand Interaction
![ligand interaction](./Kdata/F031799/ligand_interaction/ligand_interaction_F031799.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:42:GLN)
Summations of interaction energy for
fragment #1(A:42:GLN)
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. |
-41.972 | -41.374 | 21.158 | -10.525 | -11.231 | -0.113 |
Interaction energy analysis for fragmet #1(A:42:GLN)
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 | 44 | PRO | 0 | -0.022 | -0.007 | 3.861 | -0.858 | 0.380 | -0.004 | -0.493 | -0.741 | 0.003 |
4 | A | 45 | PRO | 0 | 0.027 | -0.006 | 5.409 | 0.334 | 0.334 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 46 | SER | 0 | -0.026 | -0.001 | 8.124 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 47 | LEU | 0 | -0.051 | -0.011 | 8.381 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 48 | PRO | 0 | 0.004 | 0.004 | 11.530 | 0.102 | 0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 49 | SER | 0 | 0.044 | 0.021 | 12.232 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 50 | ASP | -1 | -0.801 | -0.899 | 13.288 | -0.048 | -0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 51 | PRO | 0 | 0.034 | 0.006 | 13.263 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 52 | ARG | 1 | 0.847 | 0.916 | 15.791 | 0.122 | 0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 53 | LEU | 0 | -0.058 | -0.038 | 18.291 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 54 | TRP | 0 | -0.046 | -0.006 | 11.435 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 55 | SER | 0 | 0.028 | -0.019 | 17.435 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 56 | ARG | 1 | 0.892 | 0.922 | 18.373 | 0.210 | 0.210 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 57 | GLU | -1 | -0.866 | -0.935 | 17.640 | -0.314 | -0.314 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 58 | ASP | -1 | -0.751 | -0.852 | 14.048 | -0.318 | -0.318 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 59 | VAL | 0 | -0.006 | 0.004 | 13.404 | -0.125 | -0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 60 | LEU | 0 | -0.010 | 0.000 | 14.351 | -0.135 | -0.135 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 61 | VAL | 0 | -0.020 | -0.017 | 9.929 | -0.177 | -0.177 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 62 | PHE | 0 | 0.059 | 0.025 | 9.362 | -0.394 | -0.394 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 63 | LEU | 0 | 0.012 | 0.007 | 9.792 | -0.327 | -0.327 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 64 | ARG | 1 | 0.906 | 0.949 | 10.585 | 0.665 | 0.665 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 65 | PHE | 0 | -0.008 | -0.001 | 2.523 | -0.703 | 0.168 | 0.270 | -0.286 | -0.855 | 0.002 |
25 | A | 66 | CYS | 0 | -0.012 | -0.011 | 6.907 | -0.886 | -0.886 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 67 | VAL | 0 | -0.033 | -0.032 | 8.609 | -0.286 | -0.286 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 68 | ARG | 1 | 0.789 | 0.892 | 2.338 | 8.943 | 9.783 | 0.551 | -0.415 | -0.975 | 0.001 |
28 | A | 69 | GLU | -1 | -0.772 | -0.854 | 1.823 | -47.283 | -49.726 | 20.342 | -9.330 | -8.570 | -0.119 |
29 | A | 70 | PHE | 0 | -0.028 | -0.024 | 5.332 | -0.001 | 0.091 | -0.001 | -0.001 | -0.090 | 0.000 |
30 | A | 71 | ASP | -1 | -0.917 | -0.942 | 8.611 | -2.295 | -2.295 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 72 | LEU | 0 | -0.055 | -0.008 | 10.619 | 0.475 | 0.475 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 73 | PRO | 0 | 0.008 | -0.012 | 13.452 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 74 | LYS | 1 | 0.910 | 0.947 | 16.091 | 0.624 | 0.624 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 75 | LEU | 0 | 0.041 | 0.034 | 14.849 | 0.071 | 0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 76 | ASP | -1 | -0.884 | -0.939 | 18.069 | -0.434 | -0.434 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 77 | PHE | 0 | 0.029 | -0.025 | 14.186 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 78 | ASP | -1 | -0.824 | -0.890 | 19.637 | -0.327 | -0.327 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 79 | LEU | 0 | -0.050 | -0.017 | 22.248 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 80 | PHE | 0 | -0.023 | -0.026 | 18.793 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 81 | GLN | 0 | 0.005 | 0.016 | 20.609 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 82 | MET | 0 | -0.131 | -0.063 | 20.823 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 83 | ASN | 0 | 0.033 | 0.017 | 20.142 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 84 | GLY | 0 | 0.072 | 0.039 | 18.173 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 85 | LYS | 1 | 0.963 | 0.989 | 19.031 | 0.114 | 0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 86 | ARG | 1 | 0.885 | 0.942 | 22.356 | 0.250 | 0.250 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 87 | LEU | 0 | 0.058 | 0.025 | 15.448 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 88 | CYS | 0 | -0.021 | -0.008 | 17.958 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 89 | LEU | 0 | -0.087 | -0.045 | 19.783 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 90 | LEU | 0 | -0.045 | 0.005 | 19.904 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 91 | THR | 0 | -0.004 | -0.020 | 21.713 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 92 | ARG | 1 | 0.890 | 0.893 | 21.113 | 0.429 | 0.429 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 93 | ALA | 0 | 0.018 | 0.003 | 22.165 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 94 | ASP | -1 | -0.815 | -0.866 | 23.273 | -0.323 | -0.323 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 95 | PHE | 0 | 0.035 | 0.005 | 16.180 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 96 | GLY | 0 | -0.015 | 0.003 | 20.656 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 97 | HIS | 0 | -0.059 | -0.055 | 22.731 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 98 | ARG | 1 | 0.817 | 0.910 | 21.295 | 0.388 | 0.388 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 99 | CYS | 0 | -0.014 | -0.002 | 16.876 | -0.048 | -0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 100 | PRO | 0 | 0.026 | 0.011 | 20.398 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 101 | GLY | 0 | -0.003 | 0.009 | 20.672 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 102 | ALA | 0 | 0.014 | -0.003 | 15.391 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 103 | GLY | 0 | 0.016 | 0.014 | 16.198 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 104 | ASP | -1 | -0.807 | -0.872 | 17.253 | -0.549 | -0.549 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 105 | VAL | 0 | 0.036 | 0.026 | 11.624 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 106 | LEU | 0 | -0.002 | -0.001 | 12.341 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 107 | HIS | 0 | -0.008 | 0.000 | 13.733 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 108 | ASN | 0 | 0.003 | -0.008 | 13.307 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 109 | VAL | 0 | 0.039 | 0.016 | 8.302 | 0.119 | 0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 110 | LEU | 0 | 0.001 | 0.002 | 11.270 | 0.161 | 0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 111 | GLN | 0 | -0.012 | -0.015 | 13.317 | 0.106 | 0.106 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 112 | MET | 0 | -0.033 | -0.013 | 10.491 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 113 | LEU | 0 | 0.042 | 0.032 | 7.932 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 114 | ILE | 0 | -0.043 | -0.021 | 12.018 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 115 | ILE | 0 | -0.032 | -0.011 | 15.766 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 116 | GLU | -1 | -0.913 | -0.949 | 9.916 | 0.657 | 0.657 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 117 | SER | 0 | -0.027 | -0.020 | 14.214 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 118 | HIS | 0 | -0.066 | -0.026 | 15.771 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 119 | SER | 0 | -0.125 | -0.063 | 16.575 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |