FMODB ID: 2N2GR
Calculation Name: 1NXV-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1NXV
Chain ID: A
UniProt ID: Q9S1K0
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 | 118 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -1015644.610973 |
---|---|
FMO2-HF: Nuclear repulsion | 969245.10789 |
FMO2-HF: Total energy | -46399.503083 |
FMO2-MP2: Total energy | -46535.758684 |
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:2:LYS)
Summations of interaction energy for
fragment #1(A:2:LYS)
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. |
-264.312 | -258.948 | 23.781 | -14.117 | -15.026 | -0.141 |
Interaction energy analysis for fragmet #1(A:2:LYS)
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 | 4 | ILE | 0 | -0.049 | -0.025 | 3.812 | -3.367 | -1.013 | -0.016 | -1.140 | -1.197 | 0.003 |
4 | A | 5 | LEU | 0 | 0.007 | 0.011 | 6.112 | 2.219 | 2.219 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 6 | ILE | 0 | -0.046 | -0.034 | 9.649 | 0.219 | 0.219 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 7 | VAL | 0 | -0.008 | -0.015 | 12.104 | 0.735 | 0.735 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 8 | ASP | -1 | -0.787 | -0.896 | 15.456 | -14.657 | -14.657 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 9 | ASP | -1 | -0.875 | -0.941 | 18.337 | -12.410 | -12.410 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 10 | GLU | -1 | -0.856 | -0.901 | 21.456 | -12.001 | -12.001 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 11 | LYS | 1 | 0.811 | 0.873 | 19.669 | 13.200 | 13.200 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 12 | PRO | 0 | 0.009 | -0.017 | 20.600 | -0.420 | -0.420 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 13 | ILE | 0 | 0.008 | 0.015 | 18.130 | -0.250 | -0.250 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 14 | SER | 0 | 0.060 | 0.031 | 16.489 | -0.999 | -0.999 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 15 | ASP | -1 | -0.841 | -0.902 | 15.763 | -15.140 | -15.140 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 16 | ILE | 0 | -0.015 | 0.003 | 16.461 | -0.430 | -0.430 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 17 | ILE | 0 | 0.030 | 0.015 | 11.817 | -0.567 | -0.567 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 18 | LYS | 1 | 1.007 | 1.018 | 11.838 | 16.781 | 16.781 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 19 | PHE | 0 | -0.017 | 0.001 | 11.543 | -0.924 | -0.924 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 20 | ASN | 0 | -0.067 | -0.054 | 12.710 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 21 | MET | 0 | 0.012 | 0.013 | 7.730 | -1.216 | -1.216 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 22 | THR | 0 | -0.021 | -0.020 | 7.663 | -1.692 | -1.692 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 23 | LYS | 1 | 0.869 | 0.934 | 8.823 | 16.074 | 16.074 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 24 | GLU | -1 | -0.824 | -0.876 | 7.212 | -23.631 | -23.631 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 25 | GLY | 0 | -0.029 | 0.000 | 5.977 | -0.839 | -0.839 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 26 | TYR | 0 | -0.081 | -0.051 | 2.250 | -4.166 | -2.874 | 0.969 | -0.540 | -1.721 | -0.002 |
26 | A | 27 | GLU | -1 | -0.913 | -0.953 | 3.582 | -28.659 | -28.134 | 0.000 | -0.117 | -0.408 | 0.000 |
27 | A | 28 | VAL | 0 | -0.045 | -0.033 | 5.656 | -1.566 | -1.566 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 29 | VAL | 0 | 0.005 | 0.025 | 8.743 | 1.942 | 1.942 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 30 | THR | 0 | -0.010 | -0.013 | 11.119 | -0.642 | -0.642 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 31 | ALA | 0 | -0.009 | 0.001 | 14.136 | 0.271 | 0.271 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 32 | PHE | 0 | -0.027 | -0.029 | 16.752 | -0.228 | -0.228 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 33 | ASN | 0 | -0.006 | -0.017 | 19.814 | 0.621 | 0.621 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 34 | GLY | 0 | 0.108 | 0.054 | 19.684 | -0.788 | -0.788 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 35 | ARG | 1 | 0.804 | 0.890 | 20.305 | 11.634 | 11.634 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 36 | GLU | -1 | -0.783 | -0.885 | 18.763 | -14.848 | -14.848 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 37 | ALA | 0 | -0.053 | -0.027 | 16.009 | -0.994 | -0.994 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 38 | LEU | 0 | 0.007 | -0.007 | 15.666 | -1.339 | -1.339 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 39 | GLU | -1 | -0.906 | -0.949 | 17.378 | -14.748 | -14.748 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 40 | GLN | 0 | -0.008 | -0.017 | 13.413 | -0.992 | -0.992 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 41 | PHE | 0 | -0.043 | -0.025 | 11.733 | -2.092 | -2.092 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 42 | GLU | -1 | -0.969 | -0.985 | 12.630 | -18.973 | -18.973 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 43 | ALA | 0 | -0.049 | -0.023 | 14.290 | -0.599 | -0.599 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 44 | GLU | -1 | -0.873 | -0.931 | 9.505 | -25.448 | -25.448 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 45 | GLN | 0 | -0.090 | -0.026 | 8.649 | -3.330 | -3.330 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 46 | PRO | 0 | -0.016 | 0.001 | 6.528 | -4.495 | -4.495 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 47 | ASP | -1 | -0.795 | -0.888 | 1.700 | -131.950 | -132.369 | 22.287 | -11.992 | -9.876 | -0.140 |
47 | A | 48 | ILE | 0 | -0.047 | -0.031 | 4.252 | 1.099 | 1.319 | -0.001 | -0.020 | -0.199 | 0.000 |
48 | A | 49 | ILE | 0 | 0.008 | 0.016 | 6.627 | 0.865 | 0.865 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 50 | ILE | 0 | -0.055 | -0.011 | 9.652 | 0.693 | 0.693 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 51 | LEU | 0 | 0.013 | 0.004 | 11.962 | 0.394 | 0.394 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 52 | ASP | -1 | -0.785 | -0.894 | 15.250 | -14.529 | -14.529 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 53 | LEU | 0 | 0.000 | -0.016 | 18.469 | 0.091 | 0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 54 | MET | 0 | -0.092 | -0.048 | 21.498 | 0.626 | 0.626 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 55 | LEU | 0 | 0.067 | 0.052 | 18.831 | -0.195 | -0.195 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 56 | PRO | 0 | -0.014 | -0.011 | 23.407 | 0.403 | 0.403 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 57 | GLU | -1 | -0.880 | -0.913 | 24.506 | -11.574 | -11.574 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 58 | ILE | 0 | -0.051 | -0.035 | 22.431 | 0.323 | 0.323 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 59 | ASP | -1 | -0.820 | -0.898 | 23.084 | -13.073 | -13.073 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 60 | GLY | 0 | 0.088 | 0.030 | 20.076 | -0.454 | -0.454 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 61 | LEU | 0 | 0.000 | 0.002 | 20.150 | -0.716 | -0.716 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 62 | GLU | -1 | -0.840 | -0.909 | 21.860 | -13.501 | -13.501 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 63 | VAL | 0 | 0.009 | 0.020 | 17.132 | -0.454 | -0.454 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 64 | ALA | 0 | 0.021 | 0.007 | 17.231 | -0.759 | -0.759 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 65 | LYS | 1 | 0.839 | 0.907 | 17.933 | 12.657 | 12.657 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 66 | THR | 0 | -0.095 | -0.083 | 20.182 | -0.158 | -0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 67 | ILE | 0 | 0.023 | 0.020 | 13.657 | -0.185 | -0.185 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 68 | ARG | 1 | 0.801 | 0.888 | 12.014 | 22.532 | 22.532 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 69 | LYS | 1 | 0.820 | 0.934 | 16.728 | 14.461 | 14.461 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 70 | THR | 0 | -0.019 | -0.014 | 16.329 | 0.114 | 0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 71 | SER | 0 | 0.024 | 0.028 | 10.889 | -1.610 | -1.610 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 72 | SER | 0 | 0.004 | -0.004 | 9.812 | 1.529 | 1.529 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 73 | VAL | 0 | -0.035 | 0.010 | 7.201 | -1.536 | -1.536 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 74 | PRO | 0 | 0.028 | 0.017 | 6.340 | 3.805 | 3.805 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 75 | ILE | 0 | 0.006 | -0.007 | 9.304 | -1.004 | -1.004 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 76 | LEU | 0 | -0.032 | -0.003 | 11.755 | 1.011 | 1.011 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 77 | MET | 0 | -0.010 | 0.005 | 13.297 | 0.558 | 0.558 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 78 | LEU | 0 | 0.010 | -0.005 | 15.599 | 0.242 | 0.242 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 79 | SER | 0 | 0.017 | 0.002 | 17.948 | 0.516 | 0.516 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 80 | ALA | 0 | 0.045 | 0.028 | 21.663 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 81 | LYS | 1 | 0.791 | 0.895 | 24.842 | 11.234 | 11.234 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 82 | ASP | -1 | -0.848 | -0.930 | 24.877 | -11.301 | -11.301 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 83 | SER | 0 | -0.015 | -0.017 | 26.800 | 0.216 | 0.216 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 84 | GLU | -1 | -0.929 | -0.976 | 27.618 | -10.422 | -10.422 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 85 | PHE | 0 | 0.035 | 0.017 | 28.059 | -0.314 | -0.314 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 86 | ASP | -1 | -0.791 | -0.859 | 25.599 | -11.314 | -11.314 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 87 | LYS | 1 | 0.871 | 0.937 | 23.147 | 11.602 | 11.602 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 88 | VAL | 0 | 0.004 | 0.002 | 23.211 | -0.599 | -0.599 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 89 | ILE | 0 | 0.035 | 0.031 | 24.297 | -0.313 | -0.313 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 90 | GLY | 0 | 0.028 | -0.001 | 21.670 | -0.380 | -0.380 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 91 | LEU | 0 | -0.046 | -0.030 | 18.404 | -0.652 | -0.652 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 92 | GLU | -1 | -0.963 | -0.968 | 19.965 | -12.282 | -12.282 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 93 | LEU | 0 | -0.107 | -0.076 | 21.622 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 94 | GLY | 0 | -0.011 | 0.012 | 17.737 | -0.377 | -0.377 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 95 | ALA | 0 | -0.018 | -0.010 | 15.736 | -1.360 | -1.360 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 96 | ASP | -1 | -0.825 | -0.916 | 12.247 | -24.433 | -24.433 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 97 | ASP | -1 | -0.860 | -0.935 | 14.552 | -18.209 | -18.209 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 98 | TYR | 0 | -0.016 | -0.027 | 16.224 | -0.068 | -0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 99 | VAL | 0 | -0.053 | -0.019 | 15.804 | 0.416 | 0.416 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 100 | THR | 0 | 0.015 | 0.002 | 18.781 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 101 | LYS | 1 | 0.675 | 0.847 | 19.376 | 13.986 | 13.986 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 102 | PRO | 0 | 0.003 | -0.018 | 22.442 | 0.395 | 0.395 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 103 | PHE | 0 | 0.076 | 0.032 | 17.099 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 104 | SER | 0 | -0.005 | 0.000 | 19.601 | 0.183 | 0.183 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 105 | ASN | 0 | 0.047 | 0.001 | 15.904 | -0.984 | -0.984 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 106 | ARG | 1 | 0.981 | 0.981 | 14.663 | 13.266 | 13.266 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 107 | GLU | -1 | -0.836 | -0.898 | 14.809 | -15.815 | -15.815 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 108 | LEU | 0 | 0.028 | 0.005 | 11.955 | -0.970 | -0.970 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 109 | GLN | 0 | -0.036 | -0.024 | 10.360 | -0.414 | -0.414 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 110 | ALA | 0 | -0.039 | -0.007 | 10.143 | -1.754 | -1.754 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 111 | ARG | 1 | 0.799 | 0.870 | 11.548 | 15.828 | 15.828 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 112 | VAL | 0 | 0.050 | 0.026 | 6.475 | -1.328 | -1.328 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 113 | LYS | 1 | 0.838 | 0.905 | 6.880 | 21.639 | 21.639 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 114 | ALA | 0 | -0.071 | -0.043 | 7.849 | -2.071 | -2.071 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 115 | LEU | 0 | 0.051 | 0.019 | 8.870 | -0.716 | -0.716 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 116 | LEU | 0 | 0.016 | 0.017 | 2.505 | -4.321 | -2.994 | 0.543 | -0.308 | -1.562 | -0.002 |
116 | A | 117 | ARG | 1 | 0.878 | 0.949 | 5.030 | 21.084 | 21.149 | -0.001 | 0.000 | -0.063 | 0.000 |
117 | A | 118 | ARG | 1 | 0.894 | 0.956 | 7.145 | 25.027 | 25.027 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | A | 119 | SER | 0 | 0.013 | 0.014 | 5.024 | -0.311 | -0.311 | 0.000 | 0.000 | 0.000 | 0.000 |