
FMODB ID: K9233
Calculation Name: 3F27-D-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3F27
Chain ID: D
UniProt ID: Q61473
Base Structure: X-ray
Registration Date: 2023-06-22
Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.
Apendix: None
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 | 74 |
LigandResidueName | |
LigandFragmentNumber | 0 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -469444.328555 |
---|---|
FMO2-HF: Nuclear repulsion | 437595.654186 |
FMO2-HF: Total energy | -31848.674369 |
FMO2-MP2: Total energy | -31940.561662 |
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(D:68:ILE)
Summations of interaction energy for
fragment #1(D:68:ILE)
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. |
-12.65 | -3.536 | 7.03 | -4.733 | -11.409 | -0.024 |
Interaction energy analysis for fragmet #1(D:68:ILE)
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 | D | 70 | ARG | 1 | 0.967 | 0.980 | 3.322 | -2.575 | 0.111 | 0.046 | -1.288 | -1.444 | 0.000 |
4 | D | 71 | PRO | 0 | 0.043 | 0.047 | 4.964 | 0.097 | 0.189 | -0.001 | -0.003 | -0.087 | 0.000 |
5 | D | 72 | MET | 0 | -0.031 | -0.011 | 7.097 | 0.120 | 0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | D | 73 | ASN | 0 | 0.054 | 0.028 | 10.584 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | D | 74 | ALA | 0 | 0.109 | 0.022 | 13.335 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | D | 75 | PHE | 0 | 0.000 | 0.023 | 16.865 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | D | 76 | MET | 0 | -0.043 | -0.030 | 12.808 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | D | 77 | VAL | 0 | 0.033 | 0.012 | 14.028 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | D | 78 | TRP | 0 | 0.032 | 0.030 | 16.125 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | D | 79 | ALA | 0 | -0.037 | -0.032 | 18.020 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | D | 80 | LYS | 1 | 0.787 | 0.889 | 15.784 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | D | 81 | ASP | -1 | -0.823 | -0.890 | 17.895 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | D | 82 | GLU | -1 | -0.716 | -0.836 | 21.178 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | D | 83 | ARG | 1 | 0.860 | 0.928 | 19.581 | -0.140 | -0.140 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | D | 84 | LYS | 1 | 0.950 | 0.982 | 21.941 | -0.086 | -0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | D | 85 | ARG | 1 | 0.807 | 0.875 | 23.798 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | D | 86 | LEU | 0 | 0.007 | -0.027 | 26.061 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | D | 87 | ALA | 0 | 0.010 | 0.005 | 25.558 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | D | 88 | GLN | 0 | -0.043 | -0.017 | 26.889 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | D | 89 | GLN | 0 | -0.061 | -0.037 | 29.799 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | D | 90 | ASN | 0 | -0.046 | -0.030 | 30.722 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | D | 91 | PRO | 0 | -0.013 | 0.005 | 30.124 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | D | 92 | ASP | -1 | -0.890 | -0.941 | 31.002 | 0.081 | 0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | D | 93 | LEU | 0 | -0.006 | 0.007 | 30.487 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | D | 94 | HIS | 0 | 0.078 | 0.040 | 25.575 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | D | 95 | ASN | 0 | 0.077 | 0.027 | 20.656 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | D | 96 | ALA | 0 | 0.016 | 0.006 | 24.750 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | D | 97 | GLU | -1 | -0.792 | -0.893 | 25.715 | 0.071 | 0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | D | 98 | LEU | 0 | 0.066 | 0.032 | 24.707 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | D | 99 | SER | 0 | -0.034 | -0.027 | 21.401 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | D | 100 | LYS | 1 | 0.812 | 0.913 | 23.883 | -0.092 | -0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | D | 101 | MET | 0 | -0.011 | 0.005 | 26.961 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | D | 102 | LEU | 0 | 0.018 | 0.027 | 21.637 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | D | 103 | GLY | 0 | 0.004 | -0.003 | 24.120 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | D | 104 | LYS | 1 | 0.927 | 0.948 | 24.996 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | D | 105 | SER | 0 | 0.016 | -0.009 | 27.717 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | D | 106 | TRP | 0 | 0.046 | 0.036 | 20.355 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | D | 107 | LYS | 1 | 0.927 | 0.958 | 25.563 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | D | 108 | ALA | 0 | -0.021 | -0.006 | 27.788 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | D | 109 | LEU | 0 | 0.011 | 0.035 | 25.717 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | D | 110 | THR | 0 | 0.028 | 0.005 | 28.265 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | D | 111 | LEU | 0 | -0.019 | -0.020 | 25.676 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | D | 112 | ALA | 0 | 0.027 | 0.007 | 26.562 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | D | 113 | GLU | -1 | -0.819 | -0.897 | 27.672 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | D | 114 | LYS | 1 | 0.801 | 0.882 | 23.072 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | D | 115 | ARG | 1 | 0.904 | 0.945 | 22.674 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | D | 116 | PRO | 0 | 0.030 | 0.022 | 22.208 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | D | 117 | PHE | 0 | 0.023 | 0.010 | 19.465 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | D | 118 | VAL | 0 | -0.036 | -0.009 | 18.052 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | D | 119 | GLU | -1 | -0.816 | -0.904 | 17.575 | -0.129 | -0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | D | 120 | GLU | -1 | -0.852 | -0.910 | 16.250 | -0.130 | -0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | D | 121 | ALA | 0 | -0.048 | -0.045 | 13.795 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | D | 122 | GLU | -1 | -0.803 | -0.863 | 12.801 | -0.360 | -0.360 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | D | 123 | ARG | 1 | 0.865 | 0.933 | 13.737 | 0.105 | 0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | D | 124 | LEU | 0 | 0.010 | 0.006 | 10.475 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | D | 125 | ARG | 1 | 0.756 | 0.842 | 9.296 | 0.257 | 0.257 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | D | 126 | VAL | 0 | 0.019 | -0.011 | 9.595 | -0.120 | -0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | D | 127 | GLN | 0 | -0.034 | -0.026 | 9.530 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | D | 128 | HIS | 0 | -0.017 | -0.020 | 2.438 | -0.763 | -0.036 | 0.822 | -0.396 | -1.153 | -0.001 |
62 | D | 129 | MET | 0 | -0.058 | -0.018 | 6.302 | -0.291 | -0.291 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | D | 130 | GLN | 0 | -0.026 | 0.003 | 8.293 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | D | 131 | ASP | -1 | -0.864 | -0.915 | 6.086 | -1.016 | -1.016 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | D | 132 | HIS | 0 | -0.094 | -0.057 | 2.589 | -5.630 | -1.864 | 1.273 | -1.721 | -3.317 | -0.021 |
66 | D | 133 | PRO | 0 | 0.065 | 0.043 | 4.734 | 0.076 | 0.130 | -0.001 | -0.002 | -0.050 | 0.000 |
67 | D | 134 | ASN | 0 | -0.013 | -0.016 | 5.658 | 0.119 | 0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | D | 135 | TYR | 0 | -0.014 | 0.003 | 2.280 | -2.396 | -0.748 | 4.889 | -1.307 | -5.231 | -0.002 |
69 | D | 136 | LYS | 1 | 0.977 | 0.989 | 4.093 | 0.190 | 0.331 | 0.002 | -0.016 | -0.127 | 0.000 |
70 | D | 137 | TYR | 0 | 0.018 | -0.005 | 5.578 | 0.097 | 0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | D | 138 | ARG | 1 | 0.964 | 0.978 | 6.157 | 0.261 | 0.261 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | D | 139 | PRO | 0 | 0.011 | 0.019 | 7.662 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | D | 140 | ARG | 1 | 0.939 | 0.955 | 8.716 | -0.224 | -0.224 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | D | 141 | ARG | 1 | 1.032 | 1.033 | 12.481 | -0.087 | -0.087 | 0.000 | 0.000 | 0.000 | 0.000 |