![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: NNVVQ
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 | OptHSide |
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 | -534780.834167 |
---|---|
FMO2-HF: Nuclear repulsion | 502659.64286 |
FMO2-HF: Total energy | -32121.191307 |
FMO2-MP2: Total energy | -32212.946911 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F031800/ligand_interaction/ligand_F031800.png)
Ligand Interaction
![ligand interaction](./Kdata/F031800/ligand_interaction/ligand_interaction_F031800.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. |
-42.305 | -37.879 | 11.427 | -8.007 | -7.844 | -0.086 |
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 | -0.018 | -0.014 | 3.832 | -0.484 | 0.791 | -0.004 | -0.487 | -0.784 | 0.002 |
4 | A | 45 | PRO | 0 | 0.044 | 0.009 | 5.446 | 0.300 | 0.300 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 46 | SER | 0 | -0.049 | -0.014 | 8.002 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 47 | LEU | 0 | -0.033 | 0.000 | 8.545 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 48 | PRO | 0 | 0.000 | 0.006 | 11.220 | 0.118 | 0.118 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 49 | SER | 0 | 0.066 | 0.032 | 11.959 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 50 | ASP | -1 | -0.812 | -0.905 | 13.000 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 51 | PRO | 0 | 0.064 | 0.012 | 13.234 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 52 | ARG | 1 | 0.868 | 0.935 | 15.628 | 0.113 | 0.113 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 53 | LEU | 0 | -0.070 | -0.040 | 18.081 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 54 | TRP | 0 | -0.058 | -0.011 | 11.134 | -0.074 | -0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 55 | SER | 0 | 0.021 | -0.015 | 17.533 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 56 | ARG | 1 | 0.943 | 0.950 | 18.295 | 0.181 | 0.181 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 57 | GLU | -1 | -0.870 | -0.942 | 17.818 | -0.275 | -0.275 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 58 | ASP | -1 | -0.769 | -0.851 | 14.523 | -0.243 | -0.243 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 59 | VAL | 0 | 0.002 | 0.001 | 13.657 | -0.132 | -0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 60 | LEU | 0 | -0.035 | -0.003 | 14.173 | -0.154 | -0.154 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 61 | VAL | 0 | -0.009 | -0.016 | 9.993 | -0.192 | -0.192 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 62 | PHE | 0 | 0.040 | 0.023 | 9.096 | -0.385 | -0.385 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 63 | LEU | 0 | 0.024 | 0.005 | 9.684 | -0.405 | -0.405 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 64 | ARG | 1 | 0.912 | 0.956 | 10.625 | 0.566 | 0.566 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 65 | PHE | 0 | -0.011 | -0.007 | 2.380 | -0.041 | 0.986 | 0.432 | -0.414 | -1.044 | 0.001 |
25 | A | 66 | CYS | 0 | -0.001 | 0.004 | 6.921 | -0.954 | -0.954 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 67 | VAL | 0 | -0.029 | -0.024 | 8.764 | -0.253 | -0.253 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 68 | ARG | 1 | 0.934 | 0.967 | 3.930 | 4.448 | 4.641 | -0.001 | -0.019 | -0.173 | 0.000 |
28 | A | 69 | GLU | -1 | -0.880 | -0.921 | 1.814 | -44.351 | -42.420 | 11.000 | -7.087 | -5.843 | -0.089 |
29 | A | 70 | PHE | 0 | -0.050 | -0.038 | 5.665 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 71 | ASP | -1 | -0.924 | -0.942 | 8.718 | -2.262 | -2.262 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 72 | LEU | 0 | -0.078 | -0.020 | 10.720 | 0.491 | 0.491 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 73 | PRO | 0 | 0.006 | -0.015 | 13.466 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 74 | LYS | 1 | 0.913 | 0.955 | 15.996 | 0.631 | 0.631 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 75 | LEU | 0 | 0.047 | 0.027 | 15.007 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 76 | ASP | -1 | -0.863 | -0.936 | 18.257 | -0.439 | -0.439 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 77 | PHE | 0 | 0.005 | -0.034 | 14.349 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 78 | ASP | -1 | -0.824 | -0.886 | 19.771 | -0.324 | -0.324 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 79 | LEU | 0 | -0.076 | -0.022 | 22.342 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 80 | PHE | 0 | -0.024 | -0.025 | 18.748 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 81 | GLN | 0 | -0.041 | -0.009 | 20.304 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 82 | MET | 0 | -0.115 | -0.058 | 20.752 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 83 | ASN | 0 | 0.027 | 0.009 | 20.407 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 84 | GLY | 0 | 0.090 | 0.036 | 18.013 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 85 | LYS | 1 | 0.962 | 0.988 | 18.818 | 0.110 | 0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 86 | ARG | 1 | 0.903 | 0.946 | 21.936 | 0.247 | 0.247 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 87 | LEU | 0 | 0.053 | 0.033 | 15.240 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 88 | CYS | 0 | -0.035 | -0.019 | 17.847 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 89 | LEU | 0 | -0.093 | -0.047 | 19.473 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 90 | LEU | 0 | -0.063 | -0.006 | 19.892 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 91 | THR | 0 | 0.005 | -0.028 | 21.614 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 92 | ARG | 1 | 0.886 | 0.898 | 20.811 | 0.480 | 0.480 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 93 | ALA | 0 | 0.019 | -0.001 | 21.852 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 94 | ASP | -1 | -0.839 | -0.873 | 23.325 | -0.339 | -0.339 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 95 | PHE | 0 | 0.003 | -0.011 | 16.238 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 96 | GLY | 0 | -0.007 | -0.003 | 20.801 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 97 | HIS | 0 | -0.068 | -0.050 | 22.723 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 98 | ARG | 1 | 0.860 | 0.937 | 21.438 | 0.418 | 0.418 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 99 | CYS | 0 | -0.024 | 0.003 | 17.216 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 100 | PRO | 0 | 0.023 | 0.010 | 20.681 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 101 | GLY | 0 | -0.029 | 0.001 | 20.417 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 102 | ALA | 0 | 0.047 | -0.002 | 15.626 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 103 | GLY | 0 | 0.033 | 0.023 | 16.209 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 104 | ASP | -1 | -0.815 | -0.890 | 17.146 | -0.620 | -0.620 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 105 | VAL | 0 | 0.044 | 0.035 | 11.587 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 106 | LEU | 0 | -0.007 | 0.005 | 12.405 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 107 | HIS | 0 | 0.001 | 0.001 | 13.453 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 108 | ASN | 0 | 0.000 | -0.009 | 13.263 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 109 | VAL | 0 | 0.042 | 0.009 | 8.110 | 0.123 | 0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 110 | LEU | 0 | 0.003 | -0.001 | 11.015 | 0.181 | 0.181 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 111 | GLN | 0 | -0.013 | -0.012 | 12.929 | 0.138 | 0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 112 | MET | 0 | -0.019 | -0.007 | 10.018 | 0.121 | 0.121 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 113 | LEU | 0 | 0.040 | 0.037 | 7.785 | 0.089 | 0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 114 | ILE | 0 | -0.026 | -0.020 | 11.818 | 0.080 | 0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 115 | ILE | 0 | -0.054 | -0.027 | 15.354 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 116 | GLU | -1 | -0.945 | -0.973 | 9.275 | 0.922 | 0.922 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 117 | SER | 0 | -0.066 | -0.027 | 13.697 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 118 | HIS | 0 | -0.067 | -0.031 | 15.417 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 119 | SER | 0 | -0.063 | -0.020 | 16.495 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |