![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: LZY19
Calculation Name: 3KG5-A-Xray372
Preferred Name: B-cell antigen receptor complex-associated protein beta chain
Target Type: SINGLE PROTEIN
Ligand Name:
ligand 3-letter code:
PDB ID: 3KG5
Chain ID: A
ChEMBL ID: CHEMBL3712852
UniProt ID: P40259
Base Structure: X-ray
Registration Date: 2023-09-19
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 | 101 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -820571.010962 |
---|---|
FMO2-HF: Nuclear repulsion | 776383.132705 |
FMO2-HF: Total energy | -44187.878257 |
FMO2-MP2: Total energy | -44309.683988 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F028917/ligand_interaction/ligand_F028917.png)
Ligand Interaction
![ligand interaction](./Kdata/F028917/ligand_interaction/ligand_interaction_F028917.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:43:CYS)
Summations of interaction energy for
fragment #1(A:43:CYS)
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. |
-59.947 | -37.914 | 33.483 | -20.425 | -35.091 | -0.051 |
Interaction energy analysis for fragmet #1(A:43:CYS)
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 | 45 | ARG | 1 | 0.902 | 0.970 | 3.885 | -1.061 | 1.852 | -0.019 | -1.668 | -1.226 | 0.006 |
4 | A | 46 | ILE | 0 | 0.031 | 0.029 | 5.769 | 0.374 | 0.374 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 47 | TRP | 0 | -0.025 | -0.020 | 8.389 | -0.445 | -0.445 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 48 | GLN | 0 | 0.040 | 0.014 | 12.111 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 49 | SER | 0 | -0.033 | 0.005 | 14.952 | -0.058 | -0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 50 | PRO | 0 | 0.044 | 0.016 | 18.442 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 51 | ARG | 1 | 1.003 | 0.978 | 19.565 | 0.327 | 0.327 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 52 | PHE | 0 | -0.007 | 0.000 | 21.222 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 53 | ILE | 0 | -0.018 | 0.006 | 22.509 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 54 | ALA | 0 | 0.062 | 0.035 | 26.265 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 55 | ARG | 1 | 0.887 | 0.930 | 27.598 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 56 | LYS | 1 | 0.919 | 0.970 | 31.400 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 57 | ARG | 1 | 0.996 | 0.997 | 32.425 | 0.109 | 0.109 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 58 | GLY | 0 | -0.018 | -0.007 | 32.335 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 59 | PHE | 0 | -0.017 | -0.004 | 30.901 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 60 | THR | 0 | -0.003 | 0.008 | 27.255 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 61 | VAL | 0 | -0.010 | -0.009 | 22.715 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 62 | LYS | 1 | 0.898 | 0.944 | 20.739 | -0.169 | -0.169 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 63 | MET | 0 | -0.034 | 0.003 | 18.074 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 64 | HIS | 0 | 0.010 | 0.009 | 16.210 | 0.079 | 0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 65 | CYS | 0 | -0.025 | -0.001 | 10.218 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 66 | TYR | 0 | 0.022 | 0.023 | 11.572 | 0.246 | 0.246 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 67 | MET | 0 | -0.072 | -0.021 | 6.589 | 0.199 | 0.199 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 68 | ASN | 0 | 0.061 | 0.015 | 3.053 | 0.499 | 1.377 | 0.039 | -0.278 | -0.639 | -0.002 |
27 | A | 69 | SER | 0 | 0.026 | 0.006 | 5.981 | 0.204 | 0.204 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 70 | ALA | 0 | -0.002 | 0.016 | 3.936 | -0.224 | -0.005 | 0.006 | -0.058 | -0.167 | 0.000 |
29 | A | 71 | SER | 0 | -0.008 | -0.026 | 3.379 | 4.803 | 6.604 | 0.133 | -0.589 | -1.346 | -0.002 |
30 | A | 72 | GLY | 0 | -0.047 | -0.023 | 2.583 | -5.115 | -2.728 | 1.121 | -1.528 | -1.979 | 0.013 |
31 | A | 73 | ASN | 0 | -0.075 | -0.056 | 3.606 | -6.041 | -6.114 | 0.006 | 0.216 | -0.149 | 0.001 |
32 | A | 74 | VAL | 0 | 0.004 | 0.006 | 6.552 | -0.994 | -0.994 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 75 | SER | 0 | 0.000 | 0.024 | 7.200 | -0.313 | -0.313 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 76 | TRP | 0 | -0.020 | -0.031 | 9.342 | -0.071 | -0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 77 | LEU | 0 | -0.023 | -0.006 | 10.636 | -0.120 | -0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 78 | TRP | 0 | -0.046 | -0.022 | 13.788 | 0.130 | 0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 79 | LYS | 1 | 0.810 | 0.915 | 17.437 | 0.602 | 0.602 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 80 | GLN | 0 | -0.025 | 0.006 | 19.905 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 81 | GLU | -1 | -0.917 | -0.955 | 23.272 | -0.364 | -0.364 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 82 | MET | 0 | -0.035 | -0.044 | 22.929 | -0.059 | -0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 83 | ASP | -1 | -0.875 | -0.934 | 23.153 | -0.470 | -0.470 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 84 | GLU | -1 | -0.774 | -0.868 | 21.391 | -0.667 | -0.667 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 85 | ASN | 0 | -0.020 | -0.030 | 15.748 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 86 | PRO | 0 | -0.062 | -0.034 | 14.160 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 87 | GLN | 0 | -0.009 | 0.007 | 15.359 | -0.126 | -0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 88 | GLN | 0 | 0.005 | -0.022 | 10.577 | 0.213 | 0.213 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 89 | LEU | 0 | 0.019 | 0.031 | 14.579 | 0.131 | 0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 90 | LYS | 1 | 0.940 | 0.966 | 16.544 | 0.502 | 0.502 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 91 | LEU | 0 | 0.020 | 0.017 | 17.361 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 92 | GLU | -1 | -0.709 | -0.839 | 20.540 | -0.216 | -0.216 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 93 | LYS | 1 | 0.877 | 0.920 | 24.361 | 0.187 | 0.187 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 94 | GLY | 0 | 0.015 | 0.004 | 26.536 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 95 | ARG | 1 | 0.730 | 0.848 | 25.612 | 0.201 | 0.201 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 96 | MET | 0 | -0.042 | -0.018 | 20.517 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 97 | GLU | -1 | -0.908 | -0.948 | 19.719 | 0.095 | 0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 98 | GLU | -1 | -0.874 | -0.944 | 12.780 | -0.360 | -0.360 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 99 | SER | 0 | 0.025 | 0.017 | 15.898 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 100 | GLN | 0 | -0.016 | -0.034 | 8.661 | -0.142 | -0.142 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 101 | ASN | 0 | 0.029 | 0.021 | 13.260 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 102 | GLU | -1 | -0.847 | -0.903 | 11.480 | 1.680 | 1.680 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 103 | SER | 0 | 0.006 | 0.000 | 10.026 | 0.502 | 0.502 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 104 | LEU | 0 | -0.044 | -0.023 | 11.112 | -0.132 | -0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 105 | ALA | 0 | 0.022 | 0.008 | 10.958 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 106 | THR | 0 | -0.020 | -0.042 | 12.938 | -0.130 | -0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 107 | LEU | 0 | 0.023 | 0.046 | 15.745 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 108 | THR | 0 | -0.022 | -0.009 | 17.303 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 109 | ILE | 0 | 0.026 | 0.021 | 20.882 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 110 | GLN | 0 | 0.001 | -0.015 | 23.683 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 111 | GLY | 0 | 0.018 | 0.008 | 27.408 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 112 | ILE | 0 | -0.065 | -0.023 | 26.476 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 113 | ARG | 1 | 0.848 | 0.884 | 27.724 | 0.202 | 0.202 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 114 | PHE | 0 | -0.016 | -0.016 | 29.071 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 115 | GLU | -1 | -0.836 | -0.939 | 28.598 | -0.207 | -0.207 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 116 | ASP | -1 | -0.735 | -0.817 | 24.887 | -0.225 | -0.225 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 117 | ASN | 0 | 0.012 | 0.016 | 24.196 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 118 | GLY | 0 | 0.069 | 0.043 | 23.010 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 119 | ILE | 0 | -0.067 | -0.037 | 18.079 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 120 | TYR | 0 | 0.012 | -0.004 | 16.815 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 121 | PHE | 0 | -0.024 | -0.017 | 12.582 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 123 | GLN | 0 | 0.024 | -0.018 | 5.798 | -0.534 | -0.534 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 124 | GLN | 0 | 0.005 | 0.007 | 2.097 | -14.852 | -11.467 | 3.928 | -3.512 | -3.801 | 0.031 |
84 | A | 128 | ASN | 0 | 0.012 | -0.015 | 2.541 | -11.536 | -8.308 | 9.677 | -4.750 | -8.155 | -0.002 |
85 | A | 129 | THR | 0 | 0.011 | -0.024 | 2.707 | -1.987 | -1.568 | 4.722 | -1.574 | -3.567 | -0.011 |
86 | A | 130 | SER | 0 | -0.036 | -0.001 | 3.310 | -3.157 | -2.274 | 0.100 | -0.027 | -0.957 | -0.002 |
87 | A | 131 | GLU | -1 | -0.827 | -0.886 | 2.448 | -4.692 | -1.599 | 1.836 | -1.534 | -3.395 | -0.015 |
88 | A | 132 | VAL | 0 | -0.023 | -0.021 | 2.221 | -10.589 | -10.624 | 4.282 | -1.326 | -2.921 | -0.029 |
89 | A | 133 | TYR | 0 | -0.030 | -0.026 | 2.157 | -6.140 | -3.205 | 7.652 | -3.797 | -6.789 | -0.039 |
90 | A | 134 | GLN | 0 | 0.041 | 0.006 | 5.483 | -0.425 | -0.425 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 135 | GLY | 0 | 0.007 | 0.018 | 8.836 | 0.195 | 0.195 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 136 | CYS | 0 | -0.060 | -0.052 | 11.779 | -0.134 | -0.134 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 137 | GLY | 0 | 0.017 | 0.014 | 14.829 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 138 | THR | 0 | -0.074 | -0.040 | 16.517 | 0.076 | 0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 139 | GLU | -1 | -0.842 | -0.896 | 19.247 | -0.284 | -0.284 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 140 | LEU | 0 | -0.032 | -0.014 | 22.337 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 141 | ARG | 1 | 0.860 | 0.903 | 24.623 | 0.199 | 0.199 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 142 | VAL | 0 | 0.014 | 0.002 | 28.058 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 143 | MET | 0 | -0.003 | 0.000 | 30.490 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 144 | GLY | 0 | 0.022 | 0.000 | 34.214 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 145 | PHE | 0 | 0.002 | 0.002 | 37.397 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |