![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: G55Q1
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 | OptH |
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 | -926921.526951 |
---|---|
FMO2-HF: Nuclear repulsion | 880608.469634 |
FMO2-HF: Total energy | -46313.057317 |
FMO2-MP2: Total energy | -46447.946058 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F033422/ligand_interaction/ligand_F033422.png)
Ligand Interaction
![ligand interaction](./Kdata/F033422/ligand_interaction/ligand_interaction_F033422.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. |
-11.502 | -10.07 | 7.316 | -4.095 | -4.653 | 0.009 |
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 | -0.008 | -0.004 | 3.843 | -1.485 | 0.101 | -0.016 | -0.716 | -0.853 | 0.002 |
4 | A | 4 | PHE | 0 | -0.034 | -0.026 | 5.722 | 0.418 | 0.418 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 5 | VAL | 0 | -0.007 | -0.005 | 9.365 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | GLN | 0 | 0.002 | -0.004 | 11.605 | 0.130 | 0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 7 | ALA | 0 | 0.001 | 0.016 | 14.246 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | PRO | 0 | 0.027 | 0.028 | 15.530 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | LEU | 0 | 0.012 | -0.002 | 18.953 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | SER | 0 | 0.043 | 0.005 | 21.719 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | GLN | 0 | -0.073 | -0.037 | 24.208 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | GLN | 0 | 0.036 | 0.027 | 27.790 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | ARG | 1 | 0.857 | 0.933 | 29.641 | 0.127 | 0.127 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | TRP | 0 | 0.034 | 0.017 | 33.510 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | VAL | 0 | 0.049 | 0.023 | 36.516 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | GLY | 0 | -0.050 | -0.022 | 37.473 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | GLY | 0 | -0.053 | -0.022 | 36.046 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | SER | 0 | 0.004 | 0.002 | 31.894 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | VAL | 0 | -0.041 | -0.026 | 27.077 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | GLU | -1 | -0.917 | -0.957 | 25.304 | -0.126 | -0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | LEU | 0 | -0.053 | -0.010 | 21.591 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | HIS | 1 | 0.804 | 0.860 | 18.562 | 0.246 | 0.246 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | CYS | 0 | -0.034 | 0.007 | 13.921 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | GLU | -1 | -0.811 | -0.891 | 13.800 | -0.254 | -0.254 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | ALA | 0 | 0.002 | -0.013 | 8.543 | -0.148 | -0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | VAL | 0 | 0.016 | 0.017 | 6.208 | 0.310 | 0.310 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | GLY | 0 | 0.055 | 0.004 | 4.538 | -1.272 | -1.263 | -0.001 | -0.047 | 0.039 | 0.000 |
28 | A | 28 | SER | 0 | -0.047 | -0.007 | 3.594 | -0.626 | -0.263 | 0.001 | -0.116 | -0.248 | 0.001 |
29 | A | 29 | PRO | 0 | 0.037 | -0.017 | 4.080 | 0.679 | 0.995 | 0.002 | -0.051 | -0.268 | 0.000 |
30 | A | 30 | VAL | 0 | 0.000 | 0.019 | 5.931 | 0.587 | 0.587 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | PRO | 0 | -0.080 | -0.023 | 5.827 | 0.176 | 0.176 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | GLU | -1 | -0.797 | -0.895 | 7.684 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | ILE | 0 | 0.005 | -0.019 | 9.676 | -0.161 | -0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | GLN | 0 | -0.007 | 0.012 | 12.283 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | TRP | 0 | 0.036 | -0.001 | 14.806 | -0.076 | -0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | TRP | 0 | -0.066 | -0.030 | 15.373 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | PHE | 0 | 0.027 | -0.006 | 19.211 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | GLU | -1 | -0.908 | -0.947 | 22.515 | -0.175 | -0.175 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | GLY | 0 | 0.019 | 0.031 | 24.622 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | GLN | 0 | 0.044 | 0.007 | 28.035 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | GLY | 0 | 0.034 | 0.023 | 30.402 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | PRO | 0 | 0.009 | -0.011 | 30.374 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | ASN | 0 | -0.067 | -0.034 | 31.298 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | ASP | -1 | -0.913 | -0.938 | 28.120 | -0.102 | -0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | ILE | 0 | -0.018 | -0.015 | 24.537 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | MET | 0 | -0.058 | -0.016 | 18.955 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | SER | 0 | -0.049 | -0.030 | 21.286 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | GLN | 0 | -0.040 | -0.022 | 17.784 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | LEU | 0 | -0.020 | -0.014 | 20.324 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | TRP | 0 | -0.021 | -0.013 | 20.798 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 51 | ASP | -1 | -0.871 | -0.952 | 22.985 | -0.070 | -0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 52 | GLY | 0 | 0.098 | 0.047 | 24.653 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 53 | ALA | 0 | -0.068 | -0.027 | 26.163 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | ARG | 1 | 0.806 | 0.883 | 26.843 | 0.116 | 0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | LEU | 0 | -0.034 | -0.035 | 31.079 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | ASP | -1 | -0.851 | -0.922 | 30.900 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | ARG | 1 | 0.876 | 0.966 | 31.455 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | VAL | 0 | -0.022 | 0.006 | 24.956 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | HIS | 1 | 0.878 | 0.948 | 26.126 | 0.081 | 0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 60 | ILE | 0 | -0.017 | -0.011 | 19.450 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | HIS | 0 | 0.032 | 0.035 | 21.977 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | ALA | 0 | -0.018 | -0.020 | 16.593 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 63 | THR | 0 | -0.030 | -0.007 | 17.426 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 64 | TYR | 0 | 0.007 | -0.007 | 12.322 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 65 | HIS | 0 | 0.037 | 0.023 | 14.371 | 0.071 | 0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 66 | GLN | 0 | -0.013 | 0.001 | 12.769 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 67 | HIS | 0 | -0.061 | -0.032 | 11.183 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 68 | ALA | 0 | 0.009 | 0.007 | 10.861 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 69 | ALA | 0 | 0.016 | 0.021 | 12.550 | -0.103 | -0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 70 | SER | 0 | 0.012 | -0.007 | 15.856 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 71 | THR | 0 | 0.025 | 0.015 | 17.559 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 72 | ILE | 0 | -0.007 | 0.021 | 20.969 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 73 | SER | 0 | 0.024 | 0.007 | 22.688 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 74 | ILE | 0 | -0.041 | -0.023 | 26.034 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 75 | ASP | -1 | -0.848 | -0.939 | 29.123 | -0.076 | -0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 76 | THR | 0 | -0.069 | -0.043 | 32.771 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 77 | LEU | 0 | -0.037 | -0.013 | 30.735 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 78 | VAL | 0 | 0.040 | 0.025 | 34.117 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 79 | GLU | -1 | -0.823 | -0.926 | 34.198 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 80 | GLU | -1 | -0.909 | -0.958 | 33.306 | -0.083 | -0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 81 | ASP | -1 | -0.843 | -0.913 | 30.051 | -0.103 | -0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 82 | THR | 0 | -0.025 | 0.005 | 29.011 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 83 | GLY | 0 | 0.018 | 0.006 | 27.482 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 84 | THR | 0 | -0.030 | -0.014 | 21.111 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 85 | TYR | 0 | -0.023 | -0.037 | 21.484 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 86 | GLU | -1 | -0.800 | -0.903 | 15.771 | -0.403 | -0.403 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 88 | ARG | 1 | 0.831 | 0.892 | 11.480 | 0.225 | 0.225 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 89 | ALA | 0 | 0.049 | 0.021 | 8.091 | 0.100 | 0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 90 | SER | 0 | -0.020 | -0.022 | 5.228 | -0.229 | -0.229 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 91 | ASN | 0 | -0.012 | -0.008 | 2.101 | -9.933 | -10.775 | 7.330 | -3.165 | -3.323 | 0.006 |
91 | A | 92 | ASP | -1 | -0.862 | -0.929 | 5.427 | 0.545 | 0.545 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 93 | PRO | 0 | -0.014 | -0.013 | 6.260 | -0.126 | -0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 94 | ASP | -1 | -0.882 | -0.942 | 9.441 | 0.134 | 0.134 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 95 | ARG | 1 | 0.746 | 0.845 | 8.245 | -0.404 | -0.404 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 96 | ASN | 0 | -0.050 | -0.022 | 10.826 | -0.088 | -0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 97 | HIS | 0 | -0.026 | -0.007 | 14.185 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 98 | LEU | 0 | 0.080 | 0.057 | 13.439 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 99 | THR | 0 | -0.042 | -0.021 | 17.044 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 100 | ARG | 1 | 0.930 | 0.939 | 17.912 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 101 | ALA | 0 | 0.074 | 0.043 | 15.384 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 102 | PRO | 0 | -0.041 | -0.017 | 15.113 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 103 | ARG | 1 | 0.943 | 0.956 | 11.303 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 104 | VAL | 0 | 0.004 | 0.044 | 7.587 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 105 | LYS | 1 | 0.920 | 0.964 | 8.737 | 0.230 | 0.230 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 106 | TRP | 0 | 0.040 | 0.023 | 7.415 | -0.133 | -0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 107 | VAL | 0 | -0.029 | -0.004 | 5.859 | 0.106 | 0.106 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 108 | ARG | 1 | 0.959 | 0.964 | 8.599 | 0.539 | 0.539 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 109 | ALA | 0 | -0.004 | 0.010 | 12.113 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 110 | GLN | 0 | -0.039 | -0.028 | 14.226 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 111 | ALA | 0 | -0.004 | 0.018 | 18.036 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 112 | VAL | 0 | 0.009 | 0.005 | 21.213 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 113 | VAL | 0 | -0.015 | -0.012 | 24.691 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 114 | LEU | 0 | -0.011 | -0.001 | 27.555 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 115 | VAL | 0 | -0.022 | -0.015 | 31.069 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 116 | LEU | 0 | 0.006 | 0.008 | 33.989 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 117 | GLU | -1 | -0.935 | -0.955 | 37.302 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |