![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: LZ7J9
Calculation Name: 3GPV-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3GPV
Chain ID: A
UniProt ID: Q6HKH9
Base Structure: X-ray
Registration Date: 2023-06-22
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 | 114 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -924384.643411 |
---|---|
FMO2-HF: Nuclear repulsion | 876055.562476 |
FMO2-HF: Total energy | -48329.080935 |
FMO2-MP2: Total energy | -48467.55692 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F026042/ligand_interaction/ligand_F026042.png)
Ligand Interaction
![ligand interaction](./Kdata/F026042/ligand_interaction/ligand_interaction_F026042.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:20:MET)
Summations of interaction energy for
fragment #1(A:20: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. |
-5.304 | 0.374 | 4.317 | -2.761 | -7.236 | -0.012 |
Interaction energy analysis for fragmet #1(A:20: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 | 22 | TYR | 0 | 0.000 | 0.012 | 2.553 | -4.450 | 0.337 | 4.291 | -2.596 | -6.483 | -0.013 |
4 | A | 23 | THR | 0 | 0.065 | 0.029 | 3.987 | 0.403 | 0.516 | 0.002 | -0.011 | -0.104 | 0.000 |
5 | A | 24 | ILE | 0 | 0.069 | 0.023 | 7.298 | -0.075 | -0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 25 | GLY | 0 | -0.016 | -0.013 | 10.093 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 26 | GLN | 0 | 0.019 | 0.010 | 3.029 | -0.584 | -0.238 | 0.023 | -0.092 | -0.278 | 0.001 |
8 | A | 27 | VAL | 0 | 0.073 | 0.036 | 7.611 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 28 | ALA | 0 | -0.033 | -0.019 | 9.551 | 0.094 | 0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 29 | LYS | 1 | 0.941 | 0.978 | 10.446 | 0.356 | 0.356 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 30 | MET | 0 | -0.044 | -0.025 | 5.570 | 0.115 | 0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 31 | GLN | 0 | 0.001 | 0.005 | 11.391 | 0.126 | 0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 32 | HIS | 0 | -0.054 | -0.002 | 14.719 | 0.098 | 0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 33 | LEU | 0 | -0.003 | 0.006 | 15.914 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 34 | THR | 0 | 0.019 | -0.017 | 16.332 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 35 | ILE | 0 | 0.038 | -0.002 | 13.741 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 36 | SER | 0 | -0.006 | -0.011 | 16.213 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 37 | GLN | 0 | 0.065 | 0.058 | 18.942 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 38 | ILE | 0 | 0.050 | 0.037 | 13.033 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 39 | ARG | 1 | 0.989 | 0.983 | 14.953 | 0.298 | 0.298 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 40 | TYR | 0 | -0.028 | 0.000 | 17.885 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 41 | TYR | 0 | 0.056 | 0.020 | 17.778 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 42 | ASP | -1 | -0.803 | -0.880 | 16.065 | -0.556 | -0.556 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 43 | LYS | 1 | 0.942 | 0.974 | 18.428 | 0.254 | 0.254 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 44 | GLN | 0 | -0.050 | -0.027 | 21.881 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 45 | GLY | 0 | 0.003 | -0.003 | 21.601 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 46 | LEU | 0 | -0.035 | -0.016 | 19.354 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 47 | PHE | 0 | -0.013 | -0.015 | 14.917 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 48 | PRO | 0 | 0.005 | 0.011 | 16.459 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 49 | PHE | 0 | 0.070 | 0.026 | 12.583 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 50 | LEU | 0 | -0.077 | -0.016 | 11.402 | -0.150 | -0.150 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 51 | GLN | 0 | 0.073 | 0.048 | 7.915 | -0.191 | -0.191 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 52 | ARG | 1 | 0.877 | 0.919 | 11.684 | 0.288 | 0.288 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 53 | ASN | 0 | 0.027 | 0.021 | 7.375 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 54 | GLU | -1 | -0.827 | -0.931 | 9.780 | 0.247 | 0.247 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 55 | LYS | 1 | 0.891 | 0.950 | 9.181 | -0.701 | -0.701 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 56 | GLY | 0 | 0.012 | 0.013 | 13.054 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 57 | ASP | -1 | -0.926 | -0.965 | 9.538 | -0.497 | -0.497 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 58 | ARG | 1 | 0.800 | 0.885 | 11.197 | 0.407 | 0.407 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 59 | ILE | 0 | -0.059 | -0.026 | 6.816 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 60 | PHE | 0 | 0.043 | -0.007 | 6.921 | 0.197 | 0.197 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 61 | ASN | 0 | 0.048 | 0.034 | 4.926 | -0.998 | -0.998 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 62 | GLU | -1 | -0.808 | -0.940 | 3.753 | -3.022 | -2.590 | 0.001 | -0.062 | -0.371 | 0.000 |
44 | A | 63 | GLU | -1 | -0.874 | -0.920 | 6.113 | -0.604 | -0.604 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 64 | ALA | 0 | -0.002 | 0.003 | 8.773 | 0.279 | 0.279 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 65 | LEU | 0 | -0.030 | -0.016 | 5.789 | 0.329 | 0.329 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 66 | LYS | 1 | 0.935 | 0.973 | 8.180 | 1.980 | 1.980 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 67 | TYR | 0 | -0.033 | -0.024 | 12.389 | 0.213 | 0.213 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 68 | LEU | 0 | -0.058 | -0.031 | 11.848 | 0.143 | 0.143 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 69 | GLU | -1 | -0.939 | -0.966 | 13.642 | -0.692 | -0.692 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 70 | MET | 0 | 0.037 | 0.023 | 15.332 | 0.123 | 0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 71 | ILE | 0 | -0.025 | -0.007 | 16.326 | 0.083 | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 72 | LEU | 0 | -0.024 | -0.018 | 15.870 | 0.077 | 0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 73 | CYS | 0 | 0.029 | 0.028 | 19.410 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 74 | LEU | 0 | 0.020 | 0.005 | 21.365 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 75 | LYS | 1 | 0.897 | 0.949 | 22.199 | 0.393 | 0.393 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 76 | ASN | 0 | -0.077 | -0.048 | 21.454 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 77 | THR | 0 | -0.041 | -0.024 | 24.994 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 78 | GLY | 0 | 0.015 | 0.008 | 27.444 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 79 | MET | 0 | -0.021 | 0.024 | 26.226 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 80 | PRO | 0 | -0.006 | -0.013 | 27.401 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 81 | ILE | 0 | 0.072 | 0.023 | 24.776 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 82 | GLN | 0 | 0.028 | 0.006 | 25.920 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 83 | LYS | 1 | 0.913 | 0.959 | 27.722 | 0.240 | 0.240 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 84 | ILE | 0 | 0.012 | 0.008 | 21.768 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 85 | LYS | 1 | 0.871 | 0.929 | 22.926 | 0.301 | 0.301 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 86 | GLN | 0 | 0.038 | 0.042 | 23.871 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 87 | PHE | 0 | 0.000 | -0.010 | 19.902 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 88 | ILE | 0 | -0.029 | -0.019 | 18.471 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 89 | ASP | -1 | -0.892 | -0.951 | 20.379 | -0.413 | -0.413 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 90 | TRP | 0 | -0.015 | -0.029 | 22.511 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 91 | SER | 0 | -0.069 | -0.047 | 18.539 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 92 | MET | 0 | -0.023 | 0.005 | 17.221 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 93 | GLU | -1 | -0.916 | -0.952 | 19.247 | -0.295 | -0.295 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 94 | GLY | 0 | 0.056 | 0.040 | 20.911 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 95 | ASP | -1 | -0.977 | -0.995 | 21.924 | -0.290 | -0.290 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 96 | SER | 0 | 0.053 | 0.025 | 23.898 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 97 | THR | 0 | -0.009 | 0.000 | 24.113 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 98 | ILE | 0 | -0.005 | 0.000 | 22.941 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 99 | LEU | 0 | 0.021 | 0.001 | 25.830 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 100 | HIS | 0 | 0.013 | 0.011 | 27.931 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 101 | ARG | 1 | 0.892 | 0.942 | 20.397 | 0.425 | 0.425 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 102 | LEU | 0 | 0.006 | 0.019 | 26.169 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 103 | LYS | 1 | 0.967 | 0.983 | 27.606 | 0.204 | 0.204 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 104 | LEU | 0 | -0.025 | -0.013 | 26.347 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 105 | MET | 0 | 0.005 | 0.002 | 24.097 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 106 | LYS | 1 | 0.993 | 1.001 | 27.277 | 0.217 | 0.217 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 107 | GLN | 0 | -0.012 | 0.006 | 30.620 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 108 | GLN | 0 | 0.019 | 0.004 | 26.764 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 109 | GLU | -1 | -0.908 | -0.942 | 28.982 | -0.230 | -0.230 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 110 | ALA | 0 | 0.004 | -0.003 | 30.202 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 111 | ASN | 0 | -0.049 | -0.040 | 31.429 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 112 | VAL | 0 | -0.017 | -0.013 | 27.878 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 113 | LEU | 0 | 0.006 | 0.007 | 31.302 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 114 | GLN | 0 | -0.037 | -0.023 | 33.954 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 115 | LEU | 0 | 0.028 | 0.018 | 30.921 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 116 | ILE | 0 | -0.005 | 0.018 | 30.679 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 117 | GLN | 0 | 0.041 | 0.031 | 34.556 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 118 | ASP | -1 | -0.868 | -0.938 | 37.786 | -0.134 | -0.134 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 119 | THR | 0 | -0.113 | -0.079 | 34.212 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 120 | GLU | -1 | -0.904 | -0.950 | 36.952 | -0.137 | -0.137 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 121 | LYS | 1 | 0.927 | 0.969 | 39.026 | 0.111 | 0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 122 | ASN | 0 | -0.005 | -0.018 | 39.190 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 123 | LEU | 0 | 0.038 | 0.034 | 37.451 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 124 | LYS | 1 | 0.991 | 0.995 | 40.523 | 0.098 | 0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 125 | LYS | 1 | 0.891 | 0.946 | 43.844 | 0.116 | 0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 126 | ILE | 0 | -0.011 | -0.007 | 40.684 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 127 | GLN | 0 | 0.044 | 0.008 | 40.917 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 128 | GLN | 0 | -0.013 | -0.006 | 44.618 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 129 | LYS | 1 | 0.892 | 0.961 | 46.477 | 0.084 | 0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 130 | ILE | 0 | 0.017 | 0.004 | 42.527 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 131 | ALA | 0 | -0.008 | 0.006 | 47.127 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 132 | LYS | 1 | 0.895 | 0.948 | 49.946 | 0.067 | 0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 133 | TYR | 0 | -0.016 | 0.002 | 47.013 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |