![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 7GQRK
Calculation Name: 3LR3-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3LR3
Chain ID: A
UniProt ID: Q63T74
Base Structure: X-ray
Registration Date: 2023-06-19
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 | -948843.340815 |
---|---|
FMO2-HF: Nuclear repulsion | 903652.853067 |
FMO2-HF: Total energy | -45190.487747 |
FMO2-MP2: Total energy | -45325.891529 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F021159/ligand_interaction/ligand_F021159.png)
Ligand Interaction
![ligand interaction](./Kdata/F021159/ligand_interaction/ligand_interaction_F021159.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:37:GLU)
Summations of interaction energy for
fragment #1(A:37:GLU)
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. |
-23.68 | -18.507 | 12.072 | -8.043 | -9.202 | 0.067 |
Interaction energy analysis for fragmet #1(A:37:GLU)
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 | 39 | ARG | 1 | 0.953 | 0.968 | 3.767 | -34.096 | -32.382 | -0.004 | -0.735 | -0.975 | 0.003 |
4 | A | 40 | ALA | 0 | -0.008 | -0.003 | 2.847 | -5.820 | -4.951 | 0.195 | -0.302 | -0.761 | -0.001 |
5 | A | 41 | GLN | 0 | 0.050 | 0.013 | 1.837 | -38.955 | -39.028 | 9.543 | -4.765 | -4.705 | 0.061 |
6 | A | 42 | ARG | 1 | 0.839 | 0.925 | 4.879 | -33.711 | -33.568 | -0.001 | -0.015 | -0.127 | 0.000 |
7 | A | 43 | VAL | 0 | 0.001 | -0.011 | 7.882 | -3.484 | -3.484 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 44 | ALA | 0 | 0.030 | 0.033 | 7.618 | -3.027 | -3.027 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 45 | LEU | 0 | 0.003 | -0.004 | 7.519 | -3.576 | -3.576 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 46 | GLN | 0 | -0.015 | -0.006 | 10.432 | -1.261 | -1.261 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 47 | LEU | 0 | 0.033 | 0.018 | 12.381 | -1.706 | -1.706 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 48 | VAL | 0 | 0.010 | 0.005 | 11.498 | -1.544 | -1.544 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 49 | ALA | 0 | -0.055 | -0.021 | 14.439 | -1.560 | -1.560 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 50 | ILE | 0 | 0.074 | 0.037 | 16.431 | -1.093 | -1.093 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 51 | VAL | 0 | 0.028 | 0.035 | 17.755 | -1.072 | -1.072 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 52 | LYS | 1 | 0.933 | 0.959 | 16.374 | -19.134 | -19.134 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 53 | LEU | 0 | -0.008 | 0.017 | 19.920 | -0.843 | -0.843 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 54 | THR | 0 | 0.044 | 0.016 | 22.181 | -0.841 | -0.841 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 55 | ARG | 1 | 0.925 | 0.971 | 20.142 | -15.330 | -15.330 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 56 | THR | 0 | -0.072 | -0.058 | 23.176 | -0.546 | -0.546 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 57 | ALA | 0 | 0.028 | 0.015 | 25.731 | -0.481 | -0.481 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 58 | LEU | 0 | 0.003 | 0.001 | 27.826 | -0.466 | -0.466 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 59 | LEU | 0 | -0.023 | 0.002 | 27.038 | -0.380 | -0.380 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 60 | TYR | 0 | -0.044 | -0.030 | 27.368 | -0.379 | -0.379 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 61 | SER | 0 | -0.044 | -0.006 | 31.831 | -0.386 | -0.386 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 62 | ASP | -1 | -0.826 | -0.922 | 33.882 | 7.908 | 7.908 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 63 | PRO | 0 | -0.035 | -0.032 | 37.597 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 64 | ASP | -1 | -0.928 | -0.952 | 38.702 | 7.397 | 7.397 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 65 | LEU | 0 | -0.017 | -0.008 | 37.795 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 66 | ARG | 1 | 0.871 | 0.943 | 34.050 | -9.104 | -9.104 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 67 | ARG | 1 | 0.968 | 0.960 | 34.812 | -8.396 | -8.396 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 68 | ALA | 0 | 0.024 | 0.015 | 36.346 | 0.093 | 0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 69 | LEU | 0 | 0.034 | 0.015 | 30.615 | 0.100 | 0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 70 | LEU | 0 | -0.042 | -0.021 | 30.442 | 0.235 | 0.235 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 71 | GLN | 0 | -0.028 | -0.011 | 32.062 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 72 | ASP | -1 | -0.873 | -0.900 | 32.645 | 9.579 | 9.579 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 73 | LEU | 0 | 0.009 | -0.001 | 26.767 | 0.230 | 0.230 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 74 | GLU | -1 | -0.862 | -0.909 | 28.500 | 10.334 | 10.334 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 75 | SER | 0 | -0.070 | -0.050 | 29.462 | 0.079 | 0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 76 | ASN | 0 | -0.098 | -0.068 | 30.850 | -0.115 | -0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 77 | GLU | -1 | -0.933 | -0.962 | 25.884 | 11.292 | 11.292 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 78 | GLY | 0 | -0.031 | 0.005 | 25.120 | 0.580 | 0.580 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 79 | VAL | 0 | -0.087 | -0.051 | 23.281 | 0.585 | 0.585 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 80 | ARG | 1 | 0.860 | 0.925 | 25.557 | -10.539 | -10.539 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 81 | VAL | 0 | -0.004 | -0.005 | 26.213 | 0.506 | 0.506 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 82 | TYR | 0 | -0.020 | -0.017 | 27.762 | -0.693 | -0.693 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 83 | PRO | 0 | 0.017 | 0.016 | 28.849 | 0.393 | 0.393 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 84 | ARG | 1 | 0.935 | 0.967 | 23.793 | -12.751 | -12.751 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 85 | GLU | -1 | -0.890 | -0.944 | 29.522 | 9.308 | 9.308 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 86 | LYS | 1 | 0.851 | 0.897 | 30.325 | -10.169 | -10.169 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 87 | THR | 0 | -0.020 | -0.015 | 30.862 | 0.074 | 0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 88 | ASP | -1 | -0.795 | -0.855 | 28.767 | 10.469 | 10.469 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 89 | LYS | 1 | 0.906 | 0.948 | 28.537 | -9.489 | -9.489 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 90 | PHE | 0 | 0.043 | 0.015 | 21.551 | 0.145 | 0.145 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 91 | LYS | 1 | 0.916 | 0.973 | 22.125 | -12.791 | -12.791 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 92 | LEU | 0 | 0.029 | 0.013 | 17.834 | 0.334 | 0.334 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 93 | GLN | 0 | 0.015 | 0.001 | 13.083 | -1.224 | -1.224 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 94 | PRO | 0 | 0.024 | 0.021 | 15.329 | 0.150 | 0.150 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 95 | ASP | -1 | -0.865 | -0.933 | 12.451 | 22.719 | 22.719 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 96 | GLU | -1 | -0.922 | -0.960 | 12.174 | 16.504 | 16.504 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 97 | SER | 0 | -0.005 | -0.008 | 8.976 | 1.980 | 1.980 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 98 | VAL | 0 | 0.015 | -0.005 | 3.768 | 1.161 | 1.295 | 0.000 | -0.025 | -0.110 | 0.000 |
63 | A | 99 | ASN | 0 | -0.039 | -0.015 | 6.616 | 3.231 | 3.231 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 100 | ARG | 1 | 0.827 | 0.890 | 9.765 | -19.944 | -19.944 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 101 | LEU | 0 | -0.019 | -0.001 | 2.127 | -5.537 | -3.341 | 2.340 | -2.194 | -2.343 | 0.004 |
66 | A | 102 | ILE | 0 | 0.016 | 0.007 | 6.524 | 2.515 | 2.515 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 103 | GLU | -1 | -0.804 | -0.893 | 7.835 | 21.150 | 21.150 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 104 | HIS | 0 | -0.055 | -0.018 | 5.944 | -5.885 | -5.885 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 105 | ASP | -1 | -0.804 | -0.916 | 4.856 | 62.431 | 62.621 | -0.001 | -0.007 | -0.181 | 0.000 |
70 | A | 106 | ILE | 0 | -0.005 | -0.011 | 7.698 | -2.859 | -2.859 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 107 | ARG | 1 | 0.906 | 0.957 | 11.167 | -22.551 | -22.551 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 108 | SER | 0 | -0.006 | 0.018 | 8.911 | -1.731 | -1.731 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 109 | ARG | 1 | 0.792 | 0.889 | 9.576 | -28.575 | -28.575 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 110 | LEU | 0 | -0.053 | -0.035 | 12.660 | -1.697 | -1.697 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 111 | GLY | 0 | 0.020 | 0.022 | 15.012 | -1.479 | -1.479 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 112 | ASP | -1 | -0.905 | -0.966 | 14.931 | 22.019 | 22.019 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 113 | ASP | -1 | -0.928 | -0.945 | 16.695 | 14.908 | 14.908 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 114 | THR | 0 | -0.119 | -0.055 | 16.535 | -0.839 | -0.839 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 115 | VAL | 0 | -0.029 | -0.014 | 17.755 | 0.750 | 0.750 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 116 | ILE | 0 | 0.009 | 0.000 | 13.581 | 0.132 | 0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 117 | ALA | 0 | -0.058 | -0.025 | 17.531 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 118 | GLN | 0 | 0.002 | -0.012 | 18.708 | -0.369 | -0.369 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 119 | SER | 0 | -0.023 | -0.014 | 20.018 | -0.361 | -0.361 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 120 | VAL | 0 | 0.055 | 0.027 | 23.728 | 0.309 | 0.309 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 121 | ASN | 0 | -0.059 | -0.043 | 26.306 | -0.273 | -0.273 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 122 | ASP | -1 | -0.952 | -0.975 | 27.918 | 10.192 | 10.192 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 123 | ILE | 0 | -0.019 | 0.001 | 27.410 | -0.146 | -0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 124 | PRO | 0 | -0.007 | -0.019 | 24.088 | 0.446 | 0.446 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 125 | GLY | 0 | 0.010 | 0.012 | 22.210 | -0.345 | -0.345 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 126 | VAL | 0 | -0.038 | -0.009 | 16.265 | 0.525 | 0.525 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 127 | TRP | 0 | -0.005 | 0.001 | 19.157 | -0.388 | -0.388 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 128 | ILE | 0 | 0.005 | -0.008 | 15.922 | 0.970 | 0.970 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 129 | SER | 0 | -0.008 | 0.017 | 19.606 | -0.695 | -0.695 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 130 | PHE | 0 | -0.058 | -0.040 | 20.325 | 0.926 | 0.926 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 131 | LYS | 1 | 0.878 | 0.950 | 22.469 | -12.329 | -12.329 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 132 | ILE | 0 | -0.029 | -0.026 | 24.944 | 0.472 | 0.472 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 133 | ASP | -1 | -0.875 | -0.928 | 27.737 | 10.208 | 10.208 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 134 | ASP | -1 | -0.915 | -0.968 | 28.558 | 10.718 | 10.718 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 135 | ASP | -1 | -0.896 | -0.911 | 30.513 | 9.707 | 9.707 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 136 | ASP | -1 | -0.891 | -0.949 | 27.192 | 12.156 | 12.156 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 137 | TYR | 0 | -0.065 | -0.055 | 26.180 | -0.461 | -0.461 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 138 | TRP | 0 | -0.050 | -0.053 | 22.384 | 0.974 | 0.974 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 139 | VAL | 0 | 0.014 | 0.008 | 21.487 | -0.460 | -0.460 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 140 | ALA | 0 | -0.034 | -0.022 | 22.371 | 0.493 | 0.493 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 141 | LEU | 0 | 0.011 | 0.001 | 18.363 | -0.230 | -0.230 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 142 | ASP | -1 | -0.762 | -0.891 | 21.685 | 12.713 | 12.713 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 143 | ARG | 1 | 0.836 | 0.903 | 12.981 | -17.672 | -17.672 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 144 | ASP | -1 | -0.875 | -0.939 | 18.701 | 13.468 | 13.468 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 145 | GLN | 0 | 0.001 | -0.007 | 20.440 | 0.241 | 0.241 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 146 | LEU | 0 | -0.004 | -0.002 | 15.192 | 0.434 | 0.434 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 147 | ASP | -1 | -0.851 | -0.909 | 15.590 | 18.521 | 18.521 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 148 | THR | 0 | -0.106 | -0.044 | 16.515 | 0.295 | 0.295 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 149 | VAL | 0 | -0.009 | 0.004 | 17.591 | 0.174 | 0.174 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 150 | THR | 0 | -0.073 | -0.042 | 12.204 | 2.856 | 2.856 | 0.000 | 0.000 | 0.000 | 0.000 |