![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: N9V3Q
Calculation Name: 3H9W-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3H9W
Chain ID: A
UniProt ID: A1U4R9
Base Structure: X-ray
Registration Date: 2023-06-21
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 | 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 | 109 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -928755.695057 |
---|---|
FMO2-HF: Nuclear repulsion | 883427.83807 |
FMO2-HF: Total energy | -45327.856987 |
FMO2-MP2: Total energy | -45459.368129 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F024025/ligand_interaction/ligand_F024025.png)
Ligand Interaction
![ligand interaction](./Kdata/F024025/ligand_interaction/ligand_interaction_F024025.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:23:LYS)
Summations of interaction energy for
fragment #1(A:23: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. |
-173.091 | -165.377 | 3.933 | -4.306 | -7.342 | -0.044 |
Interaction energy analysis for fragmet #1(A:23: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 | 25 | ILE | 0 | -0.011 | -0.002 | 3.386 | 3.858 | 5.135 | 0.018 | -0.400 | -0.895 | 0.001 |
4 | A | 26 | PRO | 0 | -0.012 | 0.010 | 6.495 | 1.117 | 1.117 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 27 | TRP | 0 | -0.022 | -0.041 | 9.356 | 2.068 | 2.068 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 28 | LYS | 1 | 0.806 | 0.899 | 12.835 | 14.023 | 14.023 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 29 | ILE | 0 | -0.016 | 0.001 | 16.475 | 0.340 | 0.340 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 30 | ASN | 0 | 0.015 | 0.006 | 19.051 | 0.529 | 0.529 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 31 | TRP | 0 | 0.031 | 0.001 | 22.652 | -0.181 | -0.181 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 32 | GLN | 0 | -0.027 | -0.013 | 24.356 | 0.418 | 0.418 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 33 | THR | 0 | -0.055 | -0.049 | 25.834 | 0.268 | 0.268 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 34 | MET | 0 | 0.002 | 0.018 | 23.084 | -0.261 | -0.261 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 35 | ALA | 0 | 0.036 | 0.022 | 22.209 | -0.488 | -0.488 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 36 | PHE | 0 | -0.032 | -0.028 | 14.655 | -0.347 | -0.347 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 37 | GLU | -1 | -0.819 | -0.890 | 19.179 | -13.205 | -13.205 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 38 | TYR | 0 | -0.062 | -0.030 | 12.745 | 0.512 | 0.512 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 39 | ILE | 0 | 0.049 | 0.027 | 11.017 | -0.617 | -0.617 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 40 | GLY | 0 | -0.003 | 0.021 | 8.724 | 1.073 | 1.073 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 41 | PRO | 0 | 0.023 | 0.001 | 8.856 | -0.710 | -0.710 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 42 | GLN | 0 | -0.013 | -0.029 | 3.612 | 3.576 | 3.851 | 0.005 | -0.044 | -0.236 | 0.000 |
21 | A | 43 | ILE | 0 | 0.043 | 0.028 | 6.066 | -1.798 | -1.798 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 44 | GLU | -1 | -0.895 | -0.921 | 8.750 | -17.090 | -17.090 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 45 | ALA | 0 | -0.052 | -0.031 | 6.405 | 0.707 | 0.707 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 46 | LEU | 0 | -0.023 | 0.000 | 4.870 | -0.079 | -0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 47 | LEU | 0 | 0.016 | -0.006 | 7.771 | 0.966 | 0.966 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 48 | GLY | 0 | 0.005 | 0.011 | 11.454 | 1.789 | 1.789 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 49 | TRP | 0 | -0.049 | -0.052 | 13.583 | 1.834 | 1.834 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 50 | PRO | 0 | 0.026 | 0.012 | 13.945 | -0.832 | -0.832 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 51 | GLN | 0 | 0.016 | 0.017 | 12.175 | 0.644 | 0.644 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 52 | GLY | 0 | 0.002 | -0.001 | 14.052 | 0.150 | 0.150 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 53 | SER | 0 | -0.079 | -0.063 | 16.693 | 0.734 | 0.734 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 54 | TRP | 0 | 0.016 | 0.020 | 13.449 | 0.290 | 0.290 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 55 | LYS | 1 | 0.871 | 0.925 | 17.578 | 13.398 | 13.398 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 56 | SER | 0 | 0.016 | 0.017 | 20.632 | 0.269 | 0.269 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 57 | VAL | 0 | 0.079 | 0.022 | 19.254 | -0.678 | -0.678 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 58 | GLU | -1 | -0.905 | -0.942 | 20.338 | -12.045 | -12.045 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 59 | ASP | -1 | -0.822 | -0.886 | 18.636 | -14.446 | -14.446 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 60 | TRP | 0 | -0.057 | -0.043 | 13.864 | 0.455 | 0.455 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 61 | ALA | 0 | 0.027 | 0.025 | 17.006 | -0.495 | -0.495 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 62 | THR | 0 | -0.015 | -0.022 | 19.705 | 0.205 | 0.205 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 63 | ARG | 1 | 0.721 | 0.854 | 16.035 | 16.388 | 16.388 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 64 | MET | 0 | 0.000 | 0.008 | 15.186 | -1.323 | -1.323 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 65 | HIS | 0 | 0.008 | 0.000 | 16.909 | 0.871 | 0.871 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 66 | PRO | 0 | 0.016 | 0.007 | 18.838 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 67 | GLU | -1 | -0.809 | -0.891 | 20.629 | -14.187 | -14.187 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 68 | ASP | -1 | -0.776 | -0.872 | 16.056 | -18.233 | -18.233 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 69 | GLN | 0 | -0.038 | -0.026 | 19.009 | 0.491 | 0.491 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 70 | GLU | -1 | -0.959 | -0.968 | 21.120 | -11.713 | -11.713 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 71 | TRP | 0 | -0.079 | -0.036 | 15.405 | 0.431 | 0.431 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 72 | VAL | 0 | 0.005 | 0.007 | 15.503 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 73 | VAL | 0 | 0.031 | 0.005 | 18.523 | -0.092 | -0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 74 | ASN | 0 | -0.035 | -0.022 | 20.717 | 0.388 | 0.388 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 75 | PHE | 0 | -0.015 | -0.007 | 17.033 | 0.521 | 0.521 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 76 | CYS | 0 | 0.020 | 0.011 | 16.138 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 77 | VAL | 0 | 0.036 | 0.050 | 19.470 | 0.194 | 0.194 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 78 | LYS | 1 | 0.818 | 0.908 | 22.883 | 11.820 | 11.820 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 79 | GLN | 0 | 0.021 | 0.013 | 20.149 | 0.733 | 0.733 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 80 | SER | 0 | 0.010 | -0.019 | 20.746 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 81 | GLU | -1 | -0.859 | -0.923 | 22.686 | -10.962 | -10.962 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 82 | CYS | 0 | -0.129 | -0.061 | 25.396 | 0.596 | 0.596 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 83 | GLY | 0 | 0.044 | 0.011 | 23.802 | 0.238 | 0.238 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 84 | VAL | 0 | -0.069 | -0.020 | 21.137 | 0.102 | 0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 85 | ASP | -1 | -0.763 | -0.858 | 16.873 | -17.071 | -17.071 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 86 | HIS | 0 | -0.102 | -0.062 | 16.422 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 87 | GLU | -1 | -0.909 | -0.963 | 11.359 | -28.704 | -28.704 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 88 | ALA | 0 | 0.004 | -0.003 | 11.999 | 1.753 | 1.753 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 89 | ASP | -1 | -0.803 | -0.875 | 10.209 | -31.217 | -31.217 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 90 | TYR | 0 | -0.055 | -0.065 | 10.858 | 1.962 | 1.962 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 91 | ARG | 1 | 0.716 | 0.822 | 11.303 | 14.679 | 14.679 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 92 | ALA | 0 | 0.056 | 0.036 | 11.018 | 1.520 | 1.520 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 93 | LEU | 0 | -0.016 | -0.007 | 13.063 | 0.077 | 0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 94 | HIS | 0 | 0.037 | 0.029 | 11.683 | 0.421 | 0.421 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 95 | ARG | 1 | 0.929 | 0.981 | 14.688 | 15.838 | 15.838 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 96 | ASP | -1 | -0.935 | -0.956 | 16.300 | -16.364 | -16.364 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 97 | GLY | 0 | 0.025 | 0.020 | 18.255 | 0.809 | 0.809 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 98 | HIS | 1 | 0.778 | 0.871 | 12.139 | 20.122 | 20.122 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 99 | TYR | 0 | 0.047 | 0.013 | 14.780 | -0.338 | -0.338 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 100 | VAL | 0 | -0.047 | -0.031 | 8.346 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 101 | TRP | 0 | 0.015 | 0.008 | 9.356 | 0.863 | 0.863 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 102 | ILE | 0 | 0.019 | -0.003 | 6.630 | -4.622 | -4.622 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 103 | ARG | 1 | 0.795 | 0.865 | 6.004 | 38.359 | 38.359 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 104 | ASP | -1 | -0.766 | -0.881 | 6.959 | -29.627 | -29.627 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 105 | VAL | 0 | 0.010 | 0.000 | 8.469 | 1.639 | 1.639 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 106 | VAL | 0 | -0.013 | -0.005 | 11.095 | -0.451 | -0.451 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 107 | HIS | 0 | -0.068 | -0.055 | 14.345 | 0.928 | 0.928 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 108 | VAL | 0 | -0.025 | -0.019 | 16.758 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 109 | VAL | 0 | 0.003 | 0.011 | 19.597 | 0.457 | 0.457 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 110 | ARG | 1 | 0.819 | 0.904 | 22.147 | 12.222 | 12.222 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 111 | ASP | -1 | -0.785 | -0.865 | 25.942 | -10.477 | -10.477 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 112 | ASP | -1 | -0.942 | -0.981 | 28.911 | -10.026 | -10.026 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 113 | SER | 0 | -0.112 | -0.075 | 31.887 | 0.363 | 0.363 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 114 | GLY | 0 | -0.057 | -0.020 | 30.046 | 0.195 | 0.195 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 115 | GLU | -1 | -0.969 | -0.978 | 29.616 | -9.910 | -9.910 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 116 | VAL | 0 | -0.013 | -0.009 | 23.955 | -0.299 | -0.299 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 117 | GLU | -1 | -0.860 | -0.919 | 23.897 | -12.628 | -12.628 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 118 | ALA | 0 | -0.049 | -0.049 | 20.809 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 119 | LEU | 0 | 0.013 | 0.025 | 17.654 | -0.095 | -0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 120 | ILE | 0 | 0.008 | -0.003 | 15.438 | -0.137 | -0.137 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 121 | GLY | 0 | 0.058 | 0.023 | 12.265 | 0.133 | 0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 122 | PHE | 0 | -0.059 | -0.031 | 6.686 | -0.591 | -0.591 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 123 | MET | 0 | 0.023 | 0.047 | 7.215 | -0.187 | -0.187 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 124 | PHE | 0 | -0.041 | -0.041 | 2.223 | -13.896 | -12.051 | 1.370 | -0.992 | -2.224 | -0.008 |
103 | A | 125 | ASP | -1 | -0.810 | -0.886 | 2.597 | -42.158 | -40.488 | 0.440 | -0.595 | -1.515 | -0.006 |
104 | A | 126 | ILE | 0 | -0.012 | 0.001 | 2.375 | -23.074 | -20.448 | 2.101 | -2.274 | -2.453 | -0.031 |
105 | A | 127 | SER | 0 | -0.014 | -0.043 | 5.132 | 7.589 | 7.610 | -0.001 | -0.001 | -0.019 | 0.000 |
106 | A | 128 | LEU | 0 | -0.051 | -0.032 | 4.845 | 3.631 | 3.631 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 129 | GLU | -1 | -0.872 | -0.905 | 6.165 | -38.946 | -38.946 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 130 | HIS | 1 | 0.808 | 0.908 | 9.275 | 28.758 | 28.758 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 131 | HIS | 0 | -0.018 | 0.020 | 9.866 | 3.022 | 3.022 | 0.000 | 0.000 | 0.000 | 0.000 |