![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: VR821
Calculation Name: 3LR3-A-Xray317
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: 2021-09-07
Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.
Modeling method
Optimization | MOE:Amber10:EHT |
---|---|
Restraint | OptH |
Protonation | MOE:Protonate 3D |
Complement | MOE:Structure Preparation |
Water | No |
Procedure | Auto-FMO protocol ver. 1.20200129 |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 116 |
LigandCharge | |
Software | ABINIT-MP - Open Ver.1 Rev. 15 / 20190524 |
Total energy (hartree)
FMO2-HF: Electronic energy | -954171.273806 |
---|---|
FMO2-HF: Nuclear repulsion | 908810.330549 |
FMO2-HF: Total energy | -45360.943256 |
FMO2-MP2: Total energy | -45496.883602 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F016038/ligand_interaction/ligand_F016038.png)
Ligand Interaction
![ligand interaction](./Kdata/F016038/ligand_interaction/ligand_interaction_F016038.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:36:ACE )
Summations of interaction energy for
fragment #1(A:36:ACE )
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. |
0.256 | 2.025 | 0.42 | -0.999 | -1.191 | -0.003 |
Interaction energy analysis for fragmet #1(A:36:ACE )
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 | 38 | PRO | 0 | 0.049 | 0.035 | 3.556 | 0.660 | 1.847 | 0.005 | -0.595 | -0.597 | -0.001 |
4 | A | 39 | ARG | 1 | 0.916 | 0.954 | 4.931 | -0.372 | -0.372 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 40 | ALA | 0 | -0.001 | 0.002 | 4.123 | 0.097 | 0.164 | 0.000 | -0.020 | -0.048 | 0.000 |
6 | A | 41 | GLN | 0 | 0.054 | 0.027 | 5.811 | 0.453 | 0.453 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 42 | ARG | 1 | 0.836 | 0.924 | 8.425 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 43 | VAL | 0 | -0.002 | -0.007 | 9.149 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 44 | ALA | 0 | 0.044 | 0.034 | 10.071 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 45 | LEU | 0 | -0.002 | -0.007 | 11.915 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 46 | GLN | 0 | -0.037 | -0.020 | 13.675 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 47 | LEU | 0 | 0.036 | 0.017 | 13.336 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 48 | VAL | 0 | 0.012 | 0.005 | 15.804 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 49 | ALA | 0 | -0.049 | -0.017 | 17.929 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 50 | ILE | 0 | 0.062 | 0.030 | 19.348 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 51 | VAL | 0 | 0.029 | 0.036 | 20.152 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 52 | LYS | 1 | 0.921 | 0.949 | 21.287 | 0.133 | 0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 53 | LEU | 0 | 0.000 | 0.018 | 23.559 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 54 | THR | 0 | 0.046 | 0.019 | 24.774 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 55 | ARG | 1 | 0.931 | 0.973 | 24.687 | 0.091 | 0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 56 | THR | 0 | -0.071 | -0.053 | 27.586 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 57 | ALA | 0 | 0.038 | 0.019 | 29.730 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 58 | LEU | 0 | 0.009 | -0.003 | 31.134 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 59 | LEU | 0 | -0.033 | -0.001 | 31.503 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 60 | TYR | 0 | -0.046 | -0.030 | 32.438 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 61 | SER | 0 | -0.044 | 0.001 | 35.919 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 62 | ASP | -1 | -0.819 | -0.924 | 37.491 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 63 | PRO | 0 | -0.034 | -0.033 | 40.786 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 64 | ASP | -1 | -0.940 | -0.959 | 42.006 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 65 | LEU | 0 | -0.009 | -0.001 | 40.661 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 66 | ARG | 1 | 0.880 | 0.948 | 36.735 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 67 | ARG | 1 | 0.944 | 0.948 | 36.871 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 68 | ALA | 0 | 0.032 | 0.019 | 37.814 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 69 | LEU | 0 | 0.030 | 0.014 | 32.864 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 70 | LEU | 0 | -0.045 | -0.028 | 32.260 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 71 | GLN | 0 | -0.018 | -0.005 | 33.078 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 72 | ASP | -1 | -0.897 | -0.922 | 33.989 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 73 | LEU | 0 | 0.030 | 0.004 | 28.674 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 74 | GLU | -1 | -0.913 | -0.951 | 29.287 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 75 | SER | 0 | -0.064 | -0.038 | 30.011 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 76 | ASN | 0 | -0.096 | -0.055 | 31.575 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 77 | GLU | -1 | -0.939 | -0.968 | 27.074 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 78 | GLY | 0 | -0.018 | 0.013 | 25.871 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 79 | VAL | 0 | -0.089 | -0.055 | 24.093 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 80 | ARG | 1 | 0.906 | 0.968 | 26.204 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 81 | VAL | 0 | -0.002 | -0.006 | 27.004 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 82 | TYR | 0 | -0.034 | -0.022 | 28.216 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 83 | PRO | 0 | 0.020 | 0.018 | 30.209 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 84 | ARG | 1 | 0.944 | 0.975 | 26.309 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 85 | GLU | -1 | -0.891 | -0.952 | 30.776 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 86 | LYS | 1 | 0.842 | 0.900 | 31.456 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 87 | THR | 0 | -0.021 | -0.020 | 31.930 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 88 | ASP | -1 | -0.802 | -0.865 | 29.338 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 89 | LYS | 1 | 0.918 | 0.955 | 28.722 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 90 | PHE | 0 | 0.059 | 0.022 | 21.984 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 91 | LYS | 1 | 0.937 | 0.987 | 21.450 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 92 | LEU | 0 | 0.022 | 0.009 | 17.452 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 93 | GLN | 0 | 0.023 | 0.022 | 13.372 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 94 | PRO | 0 | 0.030 | 0.020 | 14.510 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 95 | ASP | -1 | -0.959 | -0.975 | 10.911 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 96 | GLU | -1 | -0.871 | -0.944 | 11.036 | 0.266 | 0.266 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 97 | SER | 0 | -0.047 | -0.020 | 7.441 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 98 | VAL | 0 | 0.022 | -0.006 | 2.651 | -0.205 | 0.132 | 0.397 | -0.300 | -0.434 | -0.002 |
64 | A | 99 | ASN | 0 | -0.017 | -0.009 | 5.728 | -0.313 | -0.313 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 100 | ARG | 1 | 0.883 | 0.927 | 9.270 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 101 | LEU | 0 | -0.006 | 0.007 | 3.591 | -0.334 | -0.156 | 0.018 | -0.084 | -0.112 | 0.000 |
67 | A | 102 | ILE | 0 | 0.005 | 0.003 | 7.081 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 103 | GLU | -1 | -0.798 | -0.906 | 9.047 | -0.081 | -0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 104 | HIS | 0 | -0.021 | 0.003 | 10.419 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 105 | ASP | -1 | -0.823 | -0.930 | 8.473 | -0.971 | -0.971 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 106 | ILE | 0 | -0.033 | -0.022 | 11.773 | 0.071 | 0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 107 | ARG | 1 | 0.884 | 0.934 | 14.479 | 0.203 | 0.203 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 108 | SER | 0 | -0.031 | 0.003 | 14.338 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 109 | ARG | 1 | 0.861 | 0.929 | 15.735 | 0.297 | 0.297 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 110 | LEU | 0 | -0.063 | -0.047 | 18.170 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 111 | GLY | 0 | 0.012 | 0.020 | 19.633 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 112 | ASP | -1 | -0.907 | -0.962 | 19.268 | -0.227 | -0.227 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 113 | ASP | -1 | -0.915 | -0.937 | 20.663 | -0.108 | -0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 114 | THR | 0 | -0.125 | -0.063 | 19.213 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 115 | VAL | 0 | -0.020 | -0.003 | 19.893 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 116 | ILE | 0 | 0.006 | -0.003 | 15.072 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 117 | ALA | 0 | -0.072 | -0.033 | 18.321 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 118 | GLN | 0 | -0.028 | -0.036 | 18.204 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 119 | SER | 0 | -0.038 | -0.016 | 19.748 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 120 | VAL | 0 | 0.061 | 0.023 | 23.520 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 121 | ASN | 0 | -0.054 | -0.030 | 26.308 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 122 | ASP | -1 | -0.939 | -0.965 | 27.594 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 123 | ILE | 0 | -0.028 | -0.006 | 27.183 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 124 | PRO | 0 | 0.003 | -0.014 | 23.812 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 125 | GLY | 0 | 0.008 | 0.008 | 22.007 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 126 | VAL | 0 | -0.028 | -0.005 | 16.734 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 127 | TRP | 0 | -0.014 | 0.001 | 19.322 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 128 | ILE | 0 | 0.000 | -0.014 | 17.144 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 129 | SER | 0 | -0.007 | 0.021 | 20.769 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 130 | PHE | 0 | -0.049 | -0.041 | 22.763 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 131 | LYS | 1 | 0.927 | 0.972 | 25.350 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 132 | ILE | 0 | -0.039 | -0.030 | 28.684 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 133 | ASP | -1 | -0.884 | -0.927 | 31.664 | -0.048 | -0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 134 | ASP | -1 | -0.956 | -0.990 | 32.626 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 135 | ASP | -1 | -0.944 | -0.950 | 33.794 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 136 | ASP | -1 | -0.898 | -0.951 | 29.537 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 137 | TYR | 0 | 0.002 | -0.008 | 28.482 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 138 | TRP | 0 | -0.055 | -0.055 | 23.318 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 139 | VAL | 0 | 0.011 | 0.008 | 22.447 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 140 | ALA | 0 | -0.031 | -0.021 | 23.152 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 141 | LEU | 0 | 0.000 | -0.004 | 19.088 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 142 | ASP | -1 | -0.776 | -0.882 | 21.856 | 0.062 | 0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 143 | ARG | 1 | 0.904 | 0.947 | 12.534 | -0.158 | -0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 144 | ASP | -1 | -0.853 | -0.921 | 18.537 | 0.114 | 0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 145 | GLN | 0 | -0.008 | -0.021 | 20.293 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 146 | LEU | 0 | -0.019 | -0.010 | 15.498 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 147 | ASP | -1 | -0.908 | -0.961 | 15.666 | 0.164 | 0.164 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 148 | THR | 0 | -0.100 | -0.047 | 16.485 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 149 | VAL | 0 | -0.012 | 0.005 | 18.174 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 150 | THR | 0 | -0.049 | -0.026 | 12.680 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 151 | NME | 0 | 0.003 | 0.003 | 12.479 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |