FMODB ID: MV7QZ
Calculation Name: 3O6U-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3O6U
Chain ID: A
UniProt ID: Q8XI95
Base Structure: X-ray
Registration Date: 2023-09-20
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 | 122 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -992201.867435 |
---|---|
FMO2-HF: Nuclear repulsion | 944861.871891 |
FMO2-HF: Total energy | -47339.995544 |
FMO2-MP2: Total energy | -47477.949722 |
3D Structure
Ligand structure
Ligand Interaction
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:28:MET)
Summations of interaction energy for
fragment #1(A:28: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. |
-20.057 | -18.582 | 13.108 | -6.558 | -8.025 | -0.055 |
Interaction energy analysis for fragmet #1(A:28: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 | 30 | LYS | 1 | 0.830 | 0.911 | 2.267 | -3.710 | -4.331 | 6.317 | -2.011 | -3.685 | 0.006 |
4 | A | 31 | ASP | -1 | -0.762 | -0.878 | 5.146 | 0.208 | 0.287 | -0.001 | -0.004 | -0.074 | 0.000 |
5 | A | 32 | GLY | 0 | -0.017 | -0.002 | 8.473 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 33 | ASP | -1 | -0.838 | -0.897 | 11.616 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 34 | TYR | 0 | 0.007 | 0.006 | 8.353 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 35 | THR | 0 | -0.046 | -0.030 | 14.373 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 36 | VAL | 0 | -0.029 | 0.003 | 15.779 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 37 | GLU | -1 | -0.813 | -0.894 | 17.836 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 38 | THR | 0 | 0.058 | 0.041 | 21.377 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 39 | ALA | 0 | -0.025 | -0.027 | 23.615 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 40 | LYS | 1 | 0.807 | 0.889 | 25.141 | 0.090 | 0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 41 | ALA | 0 | 0.010 | -0.006 | 27.702 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 42 | ASP | -1 | -0.753 | -0.884 | 29.423 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 43 | ASP | -1 | -0.907 | -0.964 | 30.947 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 44 | HIS | 0 | -0.103 | -0.045 | 33.857 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 45 | GLY | 0 | 0.006 | 0.019 | 34.186 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 46 | TYR | 0 | -0.055 | -0.051 | 30.362 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 47 | LYS | 1 | 0.848 | 0.955 | 26.405 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 48 | ALA | 0 | 0.007 | 0.000 | 23.879 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 49 | LYS | 1 | 0.867 | 0.923 | 21.514 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 50 | LEU | 0 | -0.015 | 0.000 | 15.200 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 51 | SER | 0 | -0.027 | -0.033 | 17.111 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 52 | ILE | 0 | -0.010 | -0.007 | 10.691 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 53 | LYS | 1 | 0.840 | 0.915 | 13.778 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 54 | VAL | 0 | -0.011 | 0.001 | 7.079 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 55 | SER | 0 | -0.037 | -0.025 | 10.357 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 56 | ASP | -1 | -0.857 | -0.919 | 9.408 | 0.296 | 0.296 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 57 | GLY | 0 | 0.007 | 0.006 | 5.504 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 58 | LYS | 1 | 0.759 | 0.866 | 5.946 | 0.079 | 0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 59 | ILE | 0 | -0.028 | -0.012 | 8.758 | -0.142 | -0.142 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 60 | THR | 0 | -0.020 | -0.025 | 11.046 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 61 | GLU | -1 | -0.928 | -0.955 | 14.146 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 62 | ALA | 0 | -0.007 | -0.015 | 15.434 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 63 | LYS | 1 | 0.868 | 0.941 | 17.715 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 64 | TYR | 0 | -0.049 | -0.059 | 20.032 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 65 | ASN | 0 | -0.028 | -0.018 | 21.832 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 66 | GLU | -1 | -0.678 | -0.790 | 25.185 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 67 | PHE | 0 | -0.013 | -0.018 | 25.493 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 68 | ASN | 0 | -0.006 | 0.025 | 29.911 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 69 | GLY | 0 | 0.009 | 0.004 | 30.971 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 70 | GLU | -1 | -0.940 | -0.977 | 31.983 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 71 | THR | 0 | -0.064 | -0.059 | 34.776 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 72 | ASN | 0 | -0.057 | -0.019 | 29.683 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 73 | ALA | 0 | 0.030 | 0.029 | 32.250 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 74 | MET | 0 | -0.001 | 0.006 | 28.611 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 75 | LYS | 1 | 0.866 | 0.926 | 29.918 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 76 | ARG | 1 | 0.786 | 0.861 | 24.690 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 77 | GLU | -1 | -0.947 | -0.977 | 31.460 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 78 | ASP | -1 | -0.876 | -0.930 | 34.576 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 79 | LYS | 1 | 0.817 | 0.893 | 36.832 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 80 | ASP | -1 | -0.818 | -0.892 | 39.094 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 81 | TYR | 0 | 0.011 | -0.004 | 33.623 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 82 | ASN | 0 | -0.038 | -0.051 | 33.729 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 83 | GLU | -1 | -0.848 | -0.904 | 36.482 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 84 | LYS | 1 | 0.862 | 0.941 | 35.991 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 85 | MET | 0 | -0.047 | -0.012 | 32.515 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 86 | THR | 0 | -0.008 | -0.020 | 35.682 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 87 | GLY | 0 | -0.018 | -0.004 | 37.215 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 88 | VAL | 0 | -0.077 | -0.038 | 37.784 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 89 | SER | 0 | -0.066 | -0.038 | 33.708 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 90 | GLY | 0 | 0.006 | 0.009 | 35.238 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 91 | ILE | 0 | -0.063 | -0.019 | 29.484 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 92 | GLY | 0 | 0.047 | 0.023 | 32.905 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 93 | PRO | 0 | 0.003 | -0.005 | 29.301 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 94 | ALA | 0 | -0.011 | -0.016 | 29.022 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 95 | GLU | -1 | -0.871 | -0.914 | 30.224 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 96 | TYR | 0 | 0.016 | -0.019 | 26.273 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 97 | GLU | -1 | -0.792 | -0.882 | 24.560 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 98 | PRO | 0 | -0.029 | -0.004 | 23.565 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 99 | GLN | 0 | 0.017 | 0.008 | 23.825 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 100 | LEU | 0 | -0.009 | -0.002 | 20.826 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 101 | GLU | -1 | -0.780 | -0.866 | 19.198 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 102 | LYS | 1 | 0.884 | 0.937 | 18.286 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 103 | ALA | 0 | 0.033 | 0.021 | 18.330 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 104 | LEU | 0 | -0.011 | -0.001 | 12.322 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 105 | ILE | 0 | -0.006 | -0.003 | 13.600 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 106 | GLU | -1 | -0.949 | -0.964 | 14.307 | 0.109 | 0.109 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 107 | LYS | 1 | 0.796 | 0.877 | 14.076 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 108 | GLN | 0 | -0.066 | -0.021 | 9.390 | 0.139 | 0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 109 | SER | 0 | -0.013 | -0.022 | 9.148 | 0.096 | 0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 110 | SER | 0 | 0.038 | 0.013 | 10.810 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 111 | ASP | -1 | -0.881 | -0.909 | 13.069 | -0.138 | -0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 112 | ILE | 0 | 0.006 | 0.006 | 15.083 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 113 | ASP | -1 | -0.836 | -0.906 | 17.804 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 114 | VAL | 0 | -0.047 | -0.029 | 21.384 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 115 | ILE | 0 | 0.038 | 0.017 | 23.712 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 116 | THR | 0 | 0.002 | -0.017 | 26.450 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 117 | GLY | 0 | 0.045 | 0.029 | 30.042 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 118 | ALA | 0 | 0.043 | 0.021 | 27.985 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 119 | THR | 0 | 0.003 | 0.008 | 26.556 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 120 | SER | 0 | 0.034 | 0.020 | 25.769 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 121 | SER | 0 | 0.021 | -0.014 | 25.195 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 122 | SER | 0 | -0.017 | -0.012 | 22.546 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 123 | ASN | 0 | -0.033 | -0.023 | 21.068 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 124 | GLN | 0 | 0.015 | 0.015 | 20.873 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 125 | PHE | 0 | 0.022 | 0.002 | 17.006 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 126 | LYS | 1 | 0.782 | 0.887 | 16.625 | 0.115 | 0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 127 | LYS | 1 | 0.946 | 0.977 | 15.576 | 0.131 | 0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 128 | LEU | 0 | -0.024 | -0.006 | 16.036 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 129 | ALA | 0 | 0.039 | 0.005 | 13.369 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 130 | GLU | -1 | -0.917 | -0.984 | 11.634 | -0.306 | -0.306 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 131 | LYN | 0 | -0.001 | 0.026 | 10.857 | -0.144 | -0.144 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 132 | VAL | 0 | -0.005 | -0.011 | 11.310 | -0.081 | -0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 133 | LEU | 0 | 0.021 | 0.014 | 7.358 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 134 | LYS | 1 | 0.852 | 0.918 | 6.668 | 0.158 | 0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 135 | ASN | 0 | -0.012 | -0.018 | 7.725 | -0.230 | -0.230 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 136 | ALA | 0 | 0.072 | 0.038 | 7.136 | 0.122 | 0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 137 | GLU | -1 | -0.906 | -0.943 | 1.976 | -18.184 | -16.404 | 6.793 | -4.525 | -4.049 | -0.061 |
111 | A | 138 | GLU | -1 | -0.936 | -0.970 | 4.570 | 0.715 | 0.952 | -0.001 | -0.018 | -0.217 | 0.000 |
112 | A | 139 | GLY | 0 | -0.039 | -0.007 | 7.297 | 0.601 | 0.601 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 140 | LYS | 1 | 0.842 | 0.941 | 8.243 | 0.317 | 0.317 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 141 | THR | 0 | 0.010 | -0.010 | 11.777 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 142 | GLU | -1 | -0.912 | -0.946 | 14.300 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 143 | ALA | 0 | 0.007 | -0.002 | 16.427 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | A | 144 | THR | 0 | -0.046 | -0.011 | 15.611 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | A | 145 | LEU | 0 | -0.012 | -0.011 | 18.249 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
119 | A | 146 | VAL | 0 | 0.020 | 0.003 | 17.224 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
120 | A | 147 | ASP | -1 | -0.837 | -0.914 | 20.311 | -0.078 | -0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
121 | A | 148 | LEU | 0 | -0.036 | -0.018 | 20.772 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
122 | A | 149 | GLU | -1 | -0.965 | -0.965 | 24.208 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |