![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 2291R
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 | 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 | 114 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -951410.555534 |
---|---|
FMO2-HF: Nuclear repulsion | 906219.758833 |
FMO2-HF: Total energy | -45190.796701 |
FMO2-MP2: Total energy | -45326.167342 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F021158/ligand_interaction/ligand_F021158.png)
Ligand Interaction
![ligand interaction](./Kdata/F021158/ligand_interaction/ligand_interaction_F021158.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. |
-28.055 | -23.999 | 14.074 | -8.445 | -9.683 | 0.08 |
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 | 0.936 | 0.964 | 3.591 | -33.940 | -32.350 | 0.004 | -0.634 | -0.960 | 0.003 |
4 | A | 40 | ALA | 0 | 0.006 | 0.008 | 3.081 | -5.598 | -4.787 | 0.065 | -0.260 | -0.615 | 0.000 |
5 | A | 41 | GLN | 0 | 0.032 | 0.003 | 1.809 | -41.309 | -42.279 | 12.046 | -5.556 | -5.519 | 0.073 |
6 | A | 42 | ARG | 1 | 0.833 | 0.911 | 4.612 | -35.141 | -34.969 | -0.001 | -0.032 | -0.139 | 0.000 |
7 | A | 43 | VAL | 0 | 0.008 | -0.003 | 7.865 | -3.602 | -3.602 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 44 | ALA | 0 | 0.027 | 0.024 | 7.400 | -3.235 | -3.235 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 45 | LEU | 0 | -0.005 | -0.012 | 7.275 | -3.864 | -3.864 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 46 | GLN | 0 | -0.023 | -0.014 | 10.134 | -1.298 | -1.298 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 47 | LEU | 0 | 0.036 | 0.021 | 12.464 | -1.821 | -1.821 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 48 | VAL | 0 | -0.003 | 0.001 | 11.255 | -1.631 | -1.631 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 49 | ALA | 0 | -0.041 | -0.017 | 14.117 | -1.470 | -1.470 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 50 | ILE | 0 | 0.068 | 0.038 | 16.118 | -1.148 | -1.148 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 51 | VAL | 0 | 0.024 | 0.027 | 17.452 | -1.103 | -1.103 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 52 | LYS | 1 | 0.933 | 0.965 | 15.886 | -19.732 | -19.732 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 53 | LEU | 0 | -0.011 | 0.013 | 19.574 | -0.858 | -0.858 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 54 | THR | 0 | 0.023 | 0.003 | 21.893 | -0.863 | -0.863 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 55 | ARG | 1 | 0.940 | 0.979 | 19.590 | -15.642 | -15.642 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 56 | THR | 0 | -0.066 | -0.050 | 22.841 | -0.533 | -0.533 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 57 | ALA | 0 | 0.015 | 0.004 | 25.424 | -0.513 | -0.513 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 58 | LEU | 0 | 0.004 | -0.001 | 27.436 | -0.457 | -0.457 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 59 | LEU | 0 | -0.016 | 0.003 | 27.228 | -0.403 | -0.403 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 60 | TYR | 0 | -0.030 | -0.030 | 27.082 | -0.438 | -0.438 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 61 | SER | 0 | -0.038 | 0.000 | 31.543 | -0.385 | -0.385 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 62 | ASP | -1 | -0.828 | -0.916 | 33.490 | 7.978 | 7.978 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 63 | PRO | 0 | -0.023 | -0.034 | 37.152 | 0.083 | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 64 | ASP | -1 | -0.949 | -0.951 | 38.432 | 7.505 | 7.505 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 65 | LEU | 0 | 0.013 | -0.006 | 37.551 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 66 | ARG | 1 | 0.848 | 0.935 | 33.609 | -9.326 | -9.326 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 67 | ARG | 1 | 0.938 | 0.951 | 34.660 | -8.425 | -8.425 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 68 | ALA | 0 | 0.039 | 0.028 | 36.323 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 69 | LEU | 0 | 0.041 | 0.027 | 30.298 | 0.134 | 0.134 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 70 | LEU | 0 | -0.040 | -0.024 | 29.974 | 0.276 | 0.276 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 71 | GLN | 0 | -0.081 | -0.045 | 32.281 | -0.182 | -0.182 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 72 | ASP | -1 | -0.900 | -0.921 | 32.507 | 9.582 | 9.582 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 73 | LEU | 0 | 0.021 | 0.006 | 26.561 | 0.189 | 0.189 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 74 | GLU | -1 | -0.852 | -0.893 | 28.327 | 10.441 | 10.441 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 75 | SER | 0 | -0.065 | -0.051 | 29.814 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 76 | ASN | 0 | -0.086 | -0.042 | 30.626 | -0.159 | -0.159 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 77 | GLU | -1 | -0.905 | -0.966 | 25.110 | 11.530 | 11.530 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 78 | GLY | 0 | -0.025 | 0.007 | 25.066 | 0.541 | 0.541 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 79 | VAL | 0 | -0.087 | -0.051 | 23.076 | 0.506 | 0.506 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 80 | ARG | 1 | 0.863 | 0.919 | 25.583 | -10.549 | -10.549 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 81 | VAL | 0 | -0.011 | -0.017 | 26.066 | 0.541 | 0.541 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 82 | TYR | 0 | -0.027 | -0.006 | 27.720 | -0.694 | -0.694 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 83 | PRO | 0 | 0.041 | 0.021 | 28.604 | 0.385 | 0.385 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 84 | ARG | 1 | 0.920 | 0.955 | 23.777 | -12.842 | -12.842 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 85 | GLU | -1 | -0.873 | -0.935 | 29.275 | 9.322 | 9.322 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 86 | LYS | 1 | 0.846 | 0.900 | 30.478 | -10.145 | -10.145 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 87 | THR | 0 | -0.020 | -0.012 | 31.216 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 88 | ASP | -1 | -0.811 | -0.875 | 28.446 | 10.596 | 10.596 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 89 | LYS | 1 | 0.919 | 0.958 | 28.343 | -9.449 | -9.449 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 90 | PHE | 0 | 0.027 | 0.012 | 21.809 | 0.153 | 0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 91 | LYS | 1 | 0.914 | 0.970 | 21.883 | -12.824 | -12.824 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 92 | LEU | 0 | 0.054 | 0.029 | 17.694 | 0.309 | 0.309 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 93 | GLN | 0 | 0.009 | 0.000 | 12.819 | -1.056 | -1.056 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 94 | PRO | 0 | 0.020 | 0.017 | 15.107 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 95 | ASP | -1 | -0.809 | -0.904 | 12.959 | 21.841 | 21.841 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 96 | GLU | -1 | -0.917 | -0.962 | 12.006 | 16.898 | 16.898 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 97 | SER | 0 | -0.027 | -0.019 | 8.564 | 2.046 | 2.046 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 98 | VAL | 0 | 0.020 | 0.004 | 3.612 | 1.209 | 1.371 | 0.002 | -0.032 | -0.131 | 0.000 |
63 | A | 99 | ASN | 0 | -0.040 | -0.012 | 6.564 | 3.471 | 3.471 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 100 | ARG | 1 | 0.787 | 0.863 | 9.723 | -19.898 | -19.898 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 101 | LEU | 0 | -0.032 | 0.006 | 2.196 | -5.364 | -3.240 | 1.959 | -1.926 | -2.158 | 0.004 |
66 | A | 102 | ILE | 0 | 0.032 | 0.016 | 6.611 | 1.664 | 1.664 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 103 | GLU | -1 | -0.805 | -0.901 | 8.063 | 20.410 | 20.410 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 104 | HIS | 0 | -0.051 | -0.027 | 5.993 | -5.840 | -5.840 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 105 | ASP | -1 | -0.788 | -0.897 | 5.010 | 61.624 | 61.791 | -0.001 | -0.005 | -0.161 | 0.000 |
70 | A | 106 | ILE | 0 | 0.003 | -0.005 | 7.672 | -2.675 | -2.675 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 107 | ARG | 1 | 0.878 | 0.951 | 11.170 | -22.604 | -22.604 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 108 | SER | 0 | -0.007 | -0.003 | 8.917 | -1.551 | -1.551 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 109 | ARG | 1 | 0.787 | 0.878 | 9.417 | -28.674 | -28.674 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 110 | LEU | 0 | -0.073 | -0.031 | 12.676 | -1.633 | -1.633 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 111 | GLY | 0 | 0.037 | 0.033 | 15.271 | -1.432 | -1.432 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 112 | ASP | -1 | -0.886 | -0.950 | 14.438 | 22.167 | 22.167 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 113 | ASP | -1 | -0.950 | -0.965 | 16.662 | 15.117 | 15.117 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 114 | THR | 0 | -0.095 | -0.051 | 16.383 | -0.782 | -0.782 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 115 | VAL | 0 | 0.003 | 0.007 | 17.612 | 0.925 | 0.925 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 116 | ILE | 0 | -0.008 | -0.008 | 13.881 | 0.105 | 0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 117 | ALA | 0 | -0.055 | -0.025 | 17.722 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 118 | GLN | 0 | 0.000 | -0.011 | 18.638 | -0.385 | -0.385 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 119 | SER | 0 | -0.015 | -0.008 | 20.038 | -0.333 | -0.333 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 120 | VAL | 0 | 0.038 | 0.013 | 23.761 | 0.321 | 0.321 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 121 | ASN | 0 | -0.061 | -0.054 | 26.241 | -0.318 | -0.318 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 122 | ASP | -1 | -0.948 | -0.972 | 27.660 | 10.383 | 10.383 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 123 | ILE | 0 | -0.012 | 0.014 | 27.660 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 124 | PRO | 0 | -0.001 | -0.019 | 24.402 | 0.458 | 0.458 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 125 | GLY | 0 | 0.008 | 0.015 | 22.308 | -0.308 | -0.308 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 126 | VAL | 0 | -0.033 | -0.013 | 16.117 | 0.549 | 0.549 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 127 | TRP | 0 | -0.011 | -0.004 | 19.227 | -0.337 | -0.337 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 128 | ILE | 0 | 0.003 | -0.012 | 15.748 | 0.982 | 0.982 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 129 | SER | 0 | -0.032 | 0.004 | 19.665 | -0.738 | -0.738 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 130 | PHE | 0 | -0.051 | -0.039 | 20.399 | 0.889 | 0.889 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 131 | LYS | 1 | 0.828 | 0.911 | 22.442 | -12.264 | -12.264 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 132 | ILE | 0 | -0.018 | -0.024 | 24.925 | 0.447 | 0.447 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 133 | ASP | -1 | -0.884 | -0.930 | 27.713 | 10.304 | 10.304 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 134 | ASP | -1 | -0.873 | -0.943 | 28.369 | 10.582 | 10.582 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 135 | ASP | -1 | -0.883 | -0.896 | 30.356 | 9.891 | 9.891 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 136 | ASP | -1 | -0.884 | -0.939 | 27.078 | 12.222 | 12.222 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 137 | TYR | 0 | -0.067 | -0.062 | 26.088 | -0.468 | -0.468 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 138 | TRP | 0 | -0.060 | -0.051 | 22.149 | 0.919 | 0.919 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 139 | VAL | 0 | 0.005 | 0.004 | 21.079 | -0.456 | -0.456 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 140 | ALA | 0 | -0.030 | -0.018 | 22.446 | 0.444 | 0.444 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 141 | LEU | 0 | 0.015 | 0.010 | 18.584 | -0.218 | -0.218 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 142 | ASP | -1 | -0.747 | -0.884 | 21.878 | 12.890 | 12.890 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 143 | ARG | 1 | 0.818 | 0.900 | 13.277 | -17.572 | -17.572 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 144 | ASP | -1 | -0.872 | -0.934 | 18.619 | 13.707 | 13.707 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 145 | GLN | 0 | 0.012 | -0.006 | 20.173 | 0.269 | 0.269 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 146 | LEU | 0 | 0.015 | 0.018 | 15.204 | 0.509 | 0.509 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 147 | ASP | -1 | -0.824 | -0.887 | 15.186 | 19.117 | 19.117 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 148 | THR | 0 | -0.112 | -0.046 | 16.156 | 0.523 | 0.523 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 149 | VAL | 0 | 0.005 | 0.019 | 17.296 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 150 | THR | 0 | -0.115 | -0.079 | 12.023 | 3.279 | 3.279 | 0.000 | 0.000 | 0.000 | 0.000 |