![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: NNN3Q
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 | 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 | 116 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -928280.048339 |
---|---|
FMO2-HF: Nuclear repulsion | 881966.031677 |
FMO2-HF: Total energy | -46314.016661 |
FMO2-MP2: Total energy | -46448.841939 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F033420/ligand_interaction/ligand_F033420.png)
Ligand Interaction
![ligand interaction](./Kdata/F033420/ligand_interaction/ligand_interaction_F033420.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. |
-12.794 | -15.109 | 12.652 | -5.015 | -5.319 | 0.001 |
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 | -0.004 | 3.362 | -2.313 | -0.060 | 0.086 | -1.154 | -1.185 | -0.002 |
4 | A | 4 | PHE | 0 | -0.022 | -0.023 | 4.920 | 0.349 | 0.403 | -0.001 | -0.006 | -0.046 | 0.000 |
5 | A | 5 | VAL | 0 | -0.024 | -0.016 | 8.531 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | GLN | 0 | -0.016 | -0.006 | 10.958 | 0.168 | 0.168 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 7 | ALA | 0 | 0.031 | 0.023 | 13.475 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | PRO | 0 | 0.022 | 0.018 | 14.554 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | LEU | 0 | 0.001 | -0.002 | 18.047 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | SER | 0 | 0.043 | 0.009 | 21.004 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | GLN | 0 | -0.048 | -0.008 | 23.428 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | GLN | 0 | -0.016 | -0.009 | 27.010 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | ARG | 1 | 0.809 | 0.896 | 28.308 | 0.161 | 0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | TRP | 0 | 0.044 | 0.031 | 33.104 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | VAL | 0 | 0.061 | 0.027 | 36.131 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | GLY | 0 | -0.043 | -0.013 | 37.834 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | GLY | 0 | -0.033 | -0.010 | 35.786 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | SER | 0 | 0.015 | 0.009 | 31.960 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | VAL | 0 | -0.035 | -0.022 | 26.618 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | GLU | -1 | -0.865 | -0.912 | 24.501 | -0.190 | -0.190 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | LEU | 0 | -0.059 | -0.014 | 20.686 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | HIS | 1 | 0.829 | 0.885 | 18.410 | 0.363 | 0.363 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | CYS | 0 | -0.018 | 0.011 | 14.019 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | GLU | -1 | -0.798 | -0.873 | 13.446 | -0.435 | -0.435 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | ALA | 0 | 0.005 | -0.006 | 8.500 | -0.141 | -0.141 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | VAL | 0 | 0.020 | 0.014 | 6.360 | 0.361 | 0.361 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | GLY | 0 | 0.052 | 0.005 | 4.578 | -1.491 | -1.485 | -0.001 | -0.041 | 0.036 | 0.000 |
28 | A | 28 | SER | 0 | -0.023 | 0.004 | 3.647 | -0.480 | -0.163 | 0.000 | -0.073 | -0.244 | 0.000 |
29 | A | 29 | PRO | 0 | 0.007 | -0.017 | 4.289 | 1.860 | 2.105 | 0.000 | -0.023 | -0.222 | 0.000 |
30 | A | 30 | VAL | 0 | -0.005 | 0.016 | 6.493 | 0.089 | 0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | PRO | 0 | -0.071 | -0.020 | 6.192 | 0.249 | 0.249 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | GLU | -1 | -0.739 | -0.845 | 8.008 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | ILE | 0 | -0.007 | -0.029 | 10.004 | -0.194 | -0.194 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | GLN | 0 | -0.039 | -0.006 | 12.702 | 0.077 | 0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | TRP | 0 | 0.036 | -0.001 | 15.105 | -0.090 | -0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | TRP | 0 | -0.035 | -0.008 | 16.143 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | PHE | 0 | 0.047 | 0.007 | 19.689 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | GLU | -1 | -0.835 | -0.918 | 22.359 | -0.176 | -0.176 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | GLY | 0 | 0.059 | 0.040 | 24.299 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | GLN | 0 | -0.007 | -0.014 | 27.680 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | GLY | 0 | 0.055 | 0.021 | 29.427 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | PRO | 0 | -0.050 | -0.036 | 29.822 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | ASN | 0 | -0.107 | -0.048 | 30.979 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | ASP | -1 | -0.875 | -0.913 | 27.885 | -0.097 | -0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | ILE | 0 | -0.029 | -0.026 | 24.201 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | MET | 0 | -0.096 | -0.032 | 18.455 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | SER | 0 | -0.056 | -0.033 | 21.264 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | GLN | 0 | -0.036 | -0.032 | 16.937 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | LEU | 0 | -0.010 | -0.008 | 20.903 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | TRP | 0 | -0.023 | -0.024 | 21.235 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 51 | ASP | -1 | -0.846 | -0.921 | 23.446 | -0.113 | -0.113 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 52 | GLY | 0 | 0.074 | 0.036 | 25.387 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 53 | ALA | 0 | -0.049 | -0.019 | 26.510 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | ARG | 1 | 0.796 | 0.867 | 27.069 | 0.137 | 0.137 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | LEU | 0 | -0.012 | -0.014 | 31.472 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | ASP | -1 | -0.865 | -0.943 | 31.230 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | ARG | 1 | 0.776 | 0.896 | 31.842 | 0.100 | 0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | VAL | 0 | -0.026 | -0.001 | 25.570 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | HIS | 1 | 0.860 | 0.920 | 26.720 | 0.114 | 0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 60 | ILE | 0 | -0.042 | -0.031 | 20.059 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | HIS | 0 | 0.050 | 0.039 | 22.149 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | ALA | 0 | -0.017 | -0.011 | 16.907 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 63 | THR | 0 | -0.033 | -0.004 | 17.513 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 64 | TYR | 0 | 0.033 | 0.008 | 12.653 | -0.064 | -0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 65 | HIS | 0 | 0.037 | 0.027 | 14.311 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 66 | GLN | 0 | -0.003 | -0.006 | 12.720 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 67 | HIS | 0 | -0.078 | -0.036 | 11.461 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 68 | ALA | 0 | 0.000 | 0.005 | 10.942 | 0.119 | 0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 69 | ALA | 0 | -0.004 | -0.001 | 12.808 | -0.110 | -0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 70 | SER | 0 | -0.006 | -0.020 | 16.069 | 0.063 | 0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 71 | THR | 0 | -0.014 | -0.005 | 18.019 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 72 | ILE | 0 | 0.000 | 0.031 | 21.239 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 73 | SER | 0 | 0.000 | -0.039 | 23.044 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 74 | ILE | 0 | -0.045 | -0.021 | 26.567 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 75 | ASP | -1 | -0.821 | -0.902 | 29.714 | -0.107 | -0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 76 | THR | 0 | -0.037 | -0.029 | 33.377 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 77 | LEU | 0 | -0.029 | 0.002 | 30.645 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 78 | VAL | 0 | 0.031 | 0.013 | 34.314 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 79 | GLU | -1 | -0.870 | -0.931 | 34.086 | -0.090 | -0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 80 | GLU | -1 | -0.880 | -0.943 | 33.049 | -0.094 | -0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 81 | ASP | -1 | -0.777 | -0.860 | 30.073 | -0.122 | -0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 82 | THR | 0 | -0.032 | -0.002 | 28.791 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 83 | GLY | 0 | 0.012 | -0.007 | 26.777 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 84 | THR | 0 | -0.033 | -0.009 | 20.304 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 85 | TYR | 0 | -0.003 | -0.014 | 21.139 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 86 | GLU | -1 | -0.737 | -0.851 | 15.323 | -0.412 | -0.412 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 88 | ARG | 1 | 0.788 | 0.887 | 11.841 | 0.250 | 0.250 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 89 | ALA | 0 | 0.051 | 0.017 | 8.649 | 0.068 | 0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 90 | SER | 0 | -0.016 | -0.018 | 5.565 | -0.173 | -0.173 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 91 | ASN | 0 | 0.036 | 0.003 | 1.959 | -10.936 | -16.204 | 12.569 | -3.713 | -3.587 | 0.003 |
91 | A | 92 | ASP | -1 | -0.889 | -0.933 | 5.116 | 1.424 | 1.424 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 93 | PRO | 0 | -0.004 | -0.013 | 5.987 | -0.405 | -0.405 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 94 | ASP | -1 | -0.870 | -0.934 | 9.387 | 0.298 | 0.298 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 95 | ARG | 1 | 0.709 | 0.834 | 8.284 | -0.528 | -0.528 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 96 | ASN | 0 | 0.007 | -0.006 | 10.648 | -0.124 | -0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 97 | HIS | 0 | 0.002 | 0.013 | 14.216 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 98 | LEU | 0 | 0.012 | 0.023 | 13.280 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 99 | THR | 0 | 0.037 | 0.023 | 16.642 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 100 | ARG | 1 | 0.864 | 0.902 | 17.768 | -0.099 | -0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 101 | ALA | 0 | 0.084 | 0.041 | 15.458 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 102 | PRO | 0 | -0.050 | 0.001 | 14.829 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 103 | ARG | 1 | 0.907 | 0.934 | 10.339 | -0.241 | -0.241 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 104 | VAL | 0 | 0.027 | 0.029 | 7.901 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 105 | LYS | 1 | 0.906 | 0.953 | 8.301 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 106 | TRP | 0 | 0.023 | 0.019 | 7.290 | -0.110 | -0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 107 | VAL | 0 | -0.032 | -0.002 | 4.741 | 0.043 | 0.121 | -0.001 | -0.005 | -0.071 | 0.000 |
107 | A | 108 | ARG | 1 | 0.886 | 0.910 | 7.974 | 0.533 | 0.533 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 109 | ALA | 0 | -0.007 | 0.001 | 11.048 | -0.081 | -0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 110 | GLN | 0 | -0.045 | -0.042 | 13.339 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 111 | ALA | 0 | -0.002 | 0.011 | 17.077 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 112 | VAL | 0 | -0.001 | -0.001 | 20.521 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 113 | VAL | 0 | -0.003 | 0.002 | 23.988 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 114 | LEU | 0 | -0.004 | -0.005 | 26.860 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 115 | VAL | 0 | -0.005 | -0.004 | 30.435 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 116 | LEU | 0 | 0.005 | 0.008 | 33.479 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 117 | GLU | -1 | -0.919 | -0.961 | 36.899 | -0.074 | -0.074 | 0.000 | 0.000 | 0.000 | 0.000 |