![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 899JY
Calculation Name: 3QQN-A-Xray372
Preferred Name: Basigin
Target Type: SINGLE PROTEIN
Ligand Name:
ligand 3-letter code:
PDB ID: 3QQN
Chain ID: A
ChEMBL ID: CHEMBL3580492
UniProt ID: P35613
Base Structure: X-ray
Registration Date: 2023-09-21
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 | 116 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -927549.611138 |
---|---|
FMO2-HF: Nuclear repulsion | 881235.936522 |
FMO2-HF: Total energy | -46313.674616 |
FMO2-MP2: Total energy | -46448.516169 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F033421/ligand_interaction/ligand_F033421.png)
Ligand Interaction
![ligand interaction](./Kdata/F033421/ligand_interaction/ligand_interaction_F033421.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:1:MET)
Summations of interaction energy for
fragment #1(A:1: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. |
-9.249 | -8.268 | 7.284 | -3.696 | -4.568 | 0 |
Interaction energy analysis for fragmet #1(A:1: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 | 3 | GLY | 0 | -0.011 | -0.005 | 3.851 | -1.331 | 0.226 | -0.011 | -0.688 | -0.858 | 0.001 |
4 | A | 4 | PHE | 0 | -0.026 | -0.023 | 5.366 | 0.375 | 0.426 | -0.001 | -0.004 | -0.046 | 0.000 |
5 | A | 5 | VAL | 0 | -0.006 | -0.002 | 9.005 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | GLN | 0 | -0.019 | -0.013 | 11.276 | 0.155 | 0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 7 | ALA | 0 | 0.017 | 0.020 | 13.869 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | PRO | 0 | 0.029 | 0.027 | 15.169 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | LEU | 0 | 0.011 | 0.001 | 18.591 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | SER | 0 | 0.037 | 0.003 | 21.362 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | GLN | 0 | -0.048 | -0.021 | 23.859 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | GLN | 0 | 0.024 | 0.026 | 27.436 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | ARG | 1 | 0.831 | 0.913 | 28.767 | 0.146 | 0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | TRP | 0 | 0.035 | 0.013 | 33.153 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | VAL | 0 | 0.047 | 0.019 | 36.343 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | GLY | 0 | -0.040 | -0.015 | 37.499 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | GLY | 0 | -0.052 | -0.021 | 35.904 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | SER | 0 | 0.005 | 0.004 | 31.934 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | VAL | 0 | -0.038 | -0.027 | 26.930 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | GLU | -1 | -0.864 | -0.922 | 25.132 | -0.156 | -0.156 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | LEU | 0 | -0.063 | -0.011 | 21.369 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | HIS | 1 | 0.813 | 0.862 | 18.589 | 0.307 | 0.307 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | CYS | 0 | -0.029 | 0.009 | 14.056 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | GLU | -1 | -0.803 | -0.884 | 13.752 | -0.340 | -0.340 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | ALA | 0 | -0.001 | -0.014 | 8.615 | -0.149 | -0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | VAL | 0 | 0.015 | 0.013 | 6.295 | 0.322 | 0.322 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | GLY | 0 | 0.058 | 0.011 | 4.505 | -1.390 | -1.392 | -0.001 | -0.044 | 0.047 | 0.000 |
28 | A | 28 | SER | 0 | -0.051 | -0.010 | 3.632 | -0.293 | 0.009 | 0.000 | -0.078 | -0.224 | 0.000 |
29 | A | 29 | PRO | 0 | 0.032 | -0.018 | 4.178 | 0.852 | 1.119 | 0.001 | -0.033 | -0.234 | 0.000 |
30 | A | 30 | VAL | 0 | 0.001 | 0.020 | 6.089 | 0.334 | 0.334 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | PRO | 0 | -0.076 | -0.020 | 5.848 | 0.222 | 0.222 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | GLU | -1 | -0.751 | -0.861 | 7.728 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | ILE | 0 | 0.002 | -0.028 | 9.712 | -0.176 | -0.176 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | GLN | 0 | -0.028 | -0.006 | 12.321 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | TRP | 0 | 0.038 | 0.000 | 14.836 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | TRP | 0 | -0.041 | -0.025 | 15.572 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | PHE | 0 | 0.034 | 0.000 | 19.233 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | GLU | -1 | -0.840 | -0.921 | 22.534 | -0.174 | -0.174 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | GLY | 0 | 0.046 | 0.043 | 24.636 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | GLN | 0 | 0.017 | -0.005 | 27.645 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | GLY | 0 | 0.029 | 0.018 | 30.005 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | PRO | 0 | -0.005 | -0.019 | 30.023 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | ASN | 0 | -0.106 | -0.047 | 30.978 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | ASP | -1 | -0.884 | -0.933 | 28.240 | -0.098 | -0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | ILE | 0 | -0.029 | -0.012 | 24.471 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | MET | 0 | -0.077 | -0.024 | 18.943 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | SER | 0 | -0.062 | -0.032 | 21.309 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | GLN | 0 | -0.030 | -0.017 | 17.235 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | LEU | 0 | -0.022 | -0.014 | 20.357 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | TRP | 0 | -0.028 | -0.021 | 20.825 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 51 | ASP | -1 | -0.854 | -0.932 | 23.014 | -0.096 | -0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 52 | GLY | 0 | 0.087 | 0.043 | 24.686 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 53 | ALA | 0 | -0.061 | -0.022 | 26.221 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | ARG | 1 | 0.805 | 0.874 | 26.745 | 0.128 | 0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | LEU | 0 | -0.026 | -0.030 | 31.106 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | ASP | -1 | -0.860 | -0.928 | 30.917 | -0.067 | -0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | ARG | 1 | 0.838 | 0.946 | 31.499 | 0.090 | 0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | VAL | 0 | -0.031 | 0.002 | 25.046 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | HIS | 1 | 0.852 | 0.920 | 26.163 | 0.100 | 0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 60 | ILE | 0 | -0.024 | -0.022 | 19.462 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | HIS | 0 | 0.031 | 0.033 | 22.021 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | ALA | 0 | -0.020 | -0.021 | 16.648 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 63 | THR | 0 | -0.025 | -0.002 | 17.488 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 64 | TYR | 0 | 0.011 | -0.006 | 12.362 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 65 | HIS | 0 | 0.034 | 0.024 | 14.475 | 0.063 | 0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 66 | GLN | 0 | -0.012 | -0.001 | 12.762 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 67 | HIS | 0 | -0.069 | -0.032 | 11.178 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 68 | ALA | 0 | 0.007 | 0.005 | 10.849 | 0.093 | 0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 69 | ALA | 0 | 0.006 | 0.011 | 12.602 | -0.102 | -0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 70 | SER | 0 | 0.013 | 0.000 | 15.851 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 71 | THR | 0 | 0.011 | 0.009 | 17.605 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 72 | ILE | 0 | -0.015 | 0.017 | 21.013 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 73 | SER | 0 | 0.001 | -0.022 | 22.728 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 74 | ILE | 0 | -0.036 | -0.018 | 26.105 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 75 | ASP | -1 | -0.841 | -0.922 | 29.159 | -0.092 | -0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 76 | THR | 0 | -0.047 | -0.033 | 32.809 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 77 | LEU | 0 | -0.038 | -0.014 | 30.635 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 78 | VAL | 0 | 0.044 | 0.020 | 34.150 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 79 | GLU | -1 | -0.840 | -0.926 | 34.226 | -0.085 | -0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 80 | GLU | -1 | -0.898 | -0.947 | 33.393 | -0.088 | -0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 81 | ASP | -1 | -0.812 | -0.888 | 30.075 | -0.113 | -0.113 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 82 | THR | 0 | -0.024 | 0.000 | 29.037 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 83 | GLY | 0 | 0.011 | 0.002 | 27.189 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 84 | THR | 0 | -0.036 | -0.020 | 20.709 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 85 | TYR | 0 | -0.010 | -0.024 | 21.509 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 86 | GLU | -1 | -0.738 | -0.855 | 15.663 | -0.398 | -0.398 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 88 | ARG | 1 | 0.805 | 0.891 | 11.515 | 0.226 | 0.226 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 89 | ALA | 0 | 0.045 | 0.015 | 8.182 | 0.093 | 0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 90 | SER | 0 | -0.016 | -0.018 | 5.256 | -0.212 | -0.212 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 91 | ASN | 0 | 0.010 | 0.001 | 2.133 | -8.118 | -9.312 | 7.296 | -2.849 | -3.253 | -0.001 |
91 | A | 92 | ASP | -1 | -0.864 | -0.933 | 5.453 | 0.945 | 0.945 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 93 | PRO | 0 | -0.013 | -0.016 | 6.255 | -0.216 | -0.216 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 94 | ASP | -1 | -0.882 | -0.940 | 9.629 | 0.198 | 0.198 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 95 | ARG | 1 | 0.725 | 0.848 | 8.144 | -0.387 | -0.387 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 96 | ASN | 0 | -0.049 | -0.025 | 10.823 | -0.094 | -0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 97 | HIS | 0 | -0.014 | -0.009 | 14.189 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 98 | LEU | 0 | 0.047 | 0.053 | 13.403 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 99 | THR | 0 | -0.022 | -0.019 | 17.030 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 100 | ARG | 1 | 0.931 | 0.941 | 17.891 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 101 | ALA | 0 | 0.066 | 0.040 | 15.484 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 102 | PRO | 0 | -0.050 | -0.024 | 15.084 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 103 | ARG | 1 | 0.947 | 0.956 | 10.988 | -0.085 | -0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 104 | VAL | 0 | 0.017 | 0.051 | 7.541 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 105 | LYS | 1 | 0.913 | 0.961 | 8.571 | 0.125 | 0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 106 | TRP | 0 | 0.034 | 0.016 | 7.404 | -0.111 | -0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 107 | VAL | 0 | -0.030 | -0.003 | 5.214 | 0.138 | 0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 108 | ARG | 1 | 0.902 | 0.930 | 8.380 | 0.497 | 0.497 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 109 | ALA | 0 | -0.009 | 0.002 | 11.682 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 110 | GLN | 0 | -0.057 | -0.046 | 13.839 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 111 | ALA | 0 | 0.003 | 0.025 | 17.613 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 112 | VAL | 0 | -0.004 | -0.003 | 20.870 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 113 | VAL | 0 | -0.008 | -0.008 | 24.326 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 114 | LEU | 0 | -0.005 | 0.001 | 27.211 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 115 | VAL | 0 | -0.019 | -0.012 | 30.729 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 116 | LEU | 0 | 0.004 | 0.008 | 33.644 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 117 | GLU | -1 | -0.923 | -0.953 | 36.957 | -0.070 | -0.070 | 0.000 | 0.000 | 0.000 | 0.000 |