FMODB ID: YZMQ2
Calculation Name: 4IDL-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 4IDL
Chain ID: A
Base Structure: X-ray
Registration Date: 2023-06-26
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 | -975682.938555 |
---|---|
FMO2-HF: Nuclear repulsion | 928262.268631 |
FMO2-HF: Total energy | -47420.669924 |
FMO2-MP2: Total energy | -47558.169452 |
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:1:LYS)
Summations of interaction energy for
fragment #1(A:1: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. |
-36.795 | -31.956 | 25.158 | -13.621 | -16.377 | -0.16 |
Interaction energy analysis for fragmet #1(A:1: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 | 3 | GLN | 0 | 0.014 | 0.028 | 2.146 | -31.082 | -26.885 | 3.933 | -3.603 | -4.527 | -0.034 |
4 | A | 4 | LEU | 0 | 0.028 | 0.010 | 5.276 | 3.980 | 4.071 | -0.001 | -0.005 | -0.085 | 0.000 |
5 | A | 5 | GLN | 0 | 0.000 | 0.005 | 8.356 | 1.818 | 1.818 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | GLN | 0 | -0.002 | -0.010 | 11.850 | -1.907 | -1.907 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 7 | SER | 0 | 0.013 | 0.008 | 14.692 | 1.044 | 1.044 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | GLY | 0 | 0.043 | 0.015 | 18.518 | -0.339 | -0.339 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | GLY | 0 | 0.004 | -0.002 | 21.281 | 0.223 | 0.223 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | GLY | 0 | -0.010 | -0.002 | 22.409 | 0.356 | 0.356 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | ALA | 0 | -0.021 | -0.020 | 26.093 | -0.223 | -0.223 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | VAL | 0 | -0.005 | 0.010 | 29.039 | 0.237 | 0.237 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | GLN | 0 | 0.039 | 0.022 | 31.585 | 0.077 | 0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | THR | 0 | -0.011 | -0.052 | 33.376 | -0.244 | -0.244 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | GLY | 0 | -0.033 | -0.010 | 33.386 | 0.289 | 0.289 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | GLY | 0 | -0.014 | 0.005 | 32.595 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | SER | 0 | -0.028 | -0.061 | 28.872 | -0.085 | -0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | LEU | 0 | -0.046 | -0.021 | 24.503 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | LYS | 1 | 0.885 | 0.933 | 20.588 | 15.228 | 15.228 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | LEU | 0 | -0.007 | 0.018 | 17.992 | -0.295 | -0.295 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | THR | 0 | 0.018 | 0.006 | 17.101 | 0.455 | 0.455 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | CYS | 0 | -0.036 | -0.005 | 10.875 | -0.970 | -0.970 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | LEU | 0 | 0.015 | 0.020 | 12.642 | 0.778 | 0.778 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | ALA | 0 | 0.020 | 0.005 | 8.306 | -2.665 | -2.665 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | SER | 0 | 0.011 | 0.007 | 7.436 | 2.923 | 2.923 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | GLY | 0 | 0.030 | 0.013 | 4.392 | -6.310 | -6.277 | -0.001 | -0.042 | 0.010 | 0.000 |
27 | A | 27 | ASN | 0 | 0.024 | 0.003 | 4.096 | 4.913 | 5.459 | -0.001 | -0.205 | -0.341 | 0.001 |
28 | A | 28 | THR | 0 | 0.016 | -0.003 | 5.856 | -2.898 | -2.898 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | ALA | 0 | 0.044 | 0.027 | 8.637 | 0.325 | 0.325 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | SER | 0 | -0.075 | -0.031 | 6.146 | -1.363 | -1.363 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | ILE | 0 | -0.014 | 0.004 | 6.824 | -1.964 | -1.964 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | ARG | 1 | 0.775 | 0.874 | 8.951 | 32.088 | 32.088 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | ALA | 0 | 0.009 | 0.003 | 9.988 | 3.073 | 3.073 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | MET | 0 | -0.037 | -0.007 | 9.395 | -3.386 | -3.386 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | GLY | 0 | 0.074 | 0.040 | 10.983 | 2.673 | 2.673 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | TRP | 0 | -0.034 | -0.012 | 12.327 | -1.550 | -1.550 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | TYR | 0 | 0.053 | 0.028 | 11.524 | 1.932 | 1.932 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | ARG | 1 | 0.787 | 0.882 | 15.595 | 13.774 | 13.774 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | ARG | 1 | 0.930 | 0.973 | 17.796 | 16.077 | 16.077 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | ALA | 0 | 0.067 | 0.035 | 19.673 | 0.196 | 0.196 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | PRO | 0 | 0.005 | -0.015 | 23.448 | -0.235 | -0.235 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | GLY | 0 | 0.004 | 0.010 | 25.239 | 0.277 | 0.277 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | LYS | 1 | 0.815 | 0.917 | 22.475 | 13.111 | 13.111 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | GLN | 0 | 0.015 | 0.005 | 19.012 | -0.450 | -0.450 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | ARG | 1 | 0.822 | 0.924 | 10.068 | 26.626 | 26.626 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | GLU | -1 | -0.746 | -0.843 | 17.169 | -13.965 | -13.965 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | TRP | 0 | 0.020 | -0.012 | 15.095 | -0.155 | -0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | VAL | 0 | -0.063 | -0.027 | 17.157 | 1.124 | 1.124 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | ALA | 0 | 0.047 | 0.013 | 17.101 | 1.058 | 1.058 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | SER | 0 | 0.004 | 0.004 | 14.789 | -1.794 | -1.794 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 51 | LEU | 0 | 0.031 | 0.033 | 14.677 | 1.271 | 1.271 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 52 | THR | 0 | 0.050 | 0.027 | 14.371 | -1.797 | -1.797 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 53 | THR | 0 | -0.053 | -0.060 | 12.684 | 0.393 | 0.393 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | THR | 0 | -0.015 | -0.005 | 15.489 | 0.331 | 0.331 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | GLY | 0 | 0.006 | 0.010 | 18.321 | 0.915 | 0.915 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | THR | 0 | -0.031 | -0.009 | 19.253 | 0.418 | 0.418 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | ALA | 0 | 0.005 | 0.001 | 18.681 | -1.112 | -1.112 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | ASP | -1 | -0.897 | -0.936 | 19.020 | -14.785 | -14.785 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | TYR | 0 | 0.020 | -0.015 | 19.724 | -0.873 | -0.873 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 60 | GLY | 0 | 0.053 | 0.037 | 21.509 | 0.287 | 0.287 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | ASP | -1 | -0.858 | -0.932 | 22.715 | -12.039 | -12.039 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | PHE | 0 | -0.042 | -0.020 | 21.149 | 0.705 | 0.705 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 63 | VAL | 0 | -0.020 | 0.006 | 22.574 | 0.324 | 0.324 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 64 | LYS | 1 | 0.875 | 0.914 | 25.916 | 11.029 | 11.029 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 65 | GLY | 0 | 0.044 | 0.020 | 27.480 | 0.359 | 0.359 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 66 | ARG | 1 | 0.723 | 0.848 | 27.375 | 11.485 | 11.485 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 67 | PHE | 0 | -0.019 | -0.011 | 22.461 | -0.146 | -0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 68 | THR | 0 | -0.003 | -0.003 | 23.420 | 0.267 | 0.267 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 69 | ILE | 0 | -0.037 | -0.003 | 15.289 | -0.279 | -0.279 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 70 | SER | 0 | -0.002 | -0.014 | 18.662 | 0.525 | 0.525 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 71 | ARG | 1 | 0.847 | 0.896 | 12.579 | 22.204 | 22.204 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 72 | ASP | -1 | -0.799 | -0.868 | 16.428 | -14.985 | -14.985 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 73 | ASN | 0 | 0.026 | -0.004 | 16.203 | -1.450 | -1.450 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 74 | ALA | 0 | -0.016 | 0.008 | 16.817 | -0.444 | -0.444 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 75 | ASN | 0 | -0.062 | -0.060 | 17.427 | -0.232 | -0.232 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 76 | ASN | 0 | -0.038 | 0.000 | 12.087 | -2.368 | -2.368 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 77 | ALA | 0 | 0.016 | 0.013 | 12.649 | -2.027 | -2.027 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 78 | ALA | 0 | 0.018 | 0.000 | 13.240 | 0.158 | 0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 79 | THR | 0 | -0.033 | -0.026 | 14.970 | 0.566 | 0.566 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 80 | LEU | 0 | -0.001 | 0.006 | 17.958 | -0.188 | -0.188 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 81 | GLN | 0 | -0.004 | -0.007 | 19.821 | -0.136 | -0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 82 | MET | 0 | -0.043 | -0.024 | 22.453 | -0.332 | -0.332 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 83 | ASP | -1 | -0.723 | -0.822 | 25.322 | -10.937 | -10.937 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 84 | SER | 0 | 0.007 | 0.000 | 29.136 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 85 | LEU | 0 | -0.015 | 0.010 | 25.711 | -0.064 | -0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 86 | LYS | 1 | 0.867 | 0.910 | 29.452 | 11.238 | 11.238 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 87 | PRO | 0 | 0.041 | 0.020 | 29.596 | -0.397 | -0.397 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 88 | GLU | -1 | -0.864 | -0.919 | 28.116 | -11.226 | -11.226 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 89 | ASP | -1 | -0.755 | -0.841 | 25.599 | -12.329 | -12.329 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 90 | THR | 0 | 0.017 | 0.026 | 24.791 | -0.564 | -0.564 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 91 | ALA | 0 | -0.018 | -0.019 | 21.130 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 92 | VAL | 0 | -0.038 | 0.000 | 17.162 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 93 | TYR | 0 | 0.052 | -0.006 | 17.380 | -0.486 | -0.486 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 94 | TYR | 0 | -0.022 | -0.025 | 12.067 | 0.130 | 0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 96 | ASN | 0 | -0.043 | -0.059 | 7.805 | -0.428 | -0.428 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 97 | ALA | 0 | 0.022 | -0.002 | 5.509 | 2.969 | 2.969 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 98 | ASP | -1 | -0.817 | -0.876 | 4.966 | -45.464 | -45.418 | -0.001 | -0.001 | -0.044 | 0.000 |
98 | A | 99 | GLY | 0 | 0.077 | 0.013 | 6.198 | 3.818 | 3.818 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 100 | ARG | 1 | 0.884 | 0.936 | 7.095 | 24.209 | 24.209 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 101 | ARG | 1 | 0.960 | 0.994 | 2.958 | 38.392 | 39.167 | 0.094 | -0.158 | -0.712 | 0.000 |
101 | A | 102 | PHE | 0 | 0.046 | 0.034 | 6.971 | 0.439 | 0.439 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 103 | ASP | -1 | -0.861 | -0.949 | 7.280 | -26.622 | -26.622 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 104 | GLY | 0 | 0.035 | 0.023 | 8.343 | 0.084 | 0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 105 | ALA | 0 | -0.007 | 0.002 | 11.157 | 1.418 | 1.418 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 106 | ARG | 1 | 0.879 | 0.931 | 11.934 | 23.427 | 23.427 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 107 | TRP | 0 | 0.043 | 0.026 | 9.796 | -2.314 | -2.314 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 108 | ARG | 1 | 0.848 | 0.912 | 7.634 | 28.258 | 28.258 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 109 | GLU | -1 | -0.818 | -0.884 | 7.362 | -30.465 | -30.465 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 110 | TYR | 0 | -0.092 | -0.061 | 2.308 | -10.573 | -8.904 | 2.954 | -1.630 | -2.994 | -0.021 |
110 | A | 111 | GLU | -1 | -0.695 | -0.825 | 3.706 | -33.837 | -33.359 | 0.002 | -0.207 | -0.273 | -0.001 |
111 | A | 112 | SER | 0 | -0.095 | -0.064 | 1.791 | -68.966 | -72.281 | 18.122 | -7.694 | -7.112 | -0.103 |
112 | A | 113 | TRP | 0 | 0.011 | -0.014 | 3.258 | 13.150 | 13.469 | 0.057 | -0.076 | -0.299 | -0.002 |
113 | A | 114 | GLY | 0 | 0.025 | 0.028 | 6.871 | -1.841 | -1.841 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 115 | GLN | 0 | 0.000 | -0.017 | 9.850 | -0.933 | -0.933 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 116 | GLY | 0 | 0.014 | 0.013 | 12.250 | 1.235 | 1.235 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 117 | THR | 0 | -0.072 | -0.029 | 15.143 | 0.214 | 0.214 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | A | 118 | GLN | 0 | -0.016 | 0.006 | 18.200 | 0.480 | 0.480 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | A | 119 | VAL | 0 | 0.062 | 0.042 | 21.542 | 0.169 | 0.169 | 0.000 | 0.000 | 0.000 | 0.000 |
119 | A | 120 | THR | 0 | -0.046 | -0.037 | 23.973 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
120 | A | 121 | ILE | 0 | 0.014 | 0.020 | 26.937 | 0.124 | 0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
121 | A | 122 | SER | 0 | 0.041 | 0.028 | 30.485 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
122 | A | 123 | SER | 0 | 0.021 | 0.028 | 34.120 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |