![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: KGZQ3
Calculation Name: 1WMI-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1WMI
Chain ID: A
UniProt ID: O73966
Base Structure: X-ray
Registration Date: 2023-09-23
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 | 88 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -682240.200274 |
---|---|
FMO2-HF: Nuclear repulsion | 646158.420391 |
FMO2-HF: Total energy | -36081.779883 |
FMO2-MP2: Total energy | -36190.169188 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F035968/ligand_interaction/ligand_F035968.png)
Ligand Interaction
![ligand interaction](./Kdata/F035968/ligand_interaction/ligand_interaction_F035968.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:1:MET)
Summations of interaction energy for
fragment #1(A:1: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. |
-13.097 | -5.493 | 2.398 | -4.375 | -5.63 | -0.029 |
Interaction energy analysis for fragmet #1(A:1: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 | 3 | TYR | 0 | -0.004 | 0.013 | 3.783 | 0.616 | 1.892 | 0.002 | -0.475 | -0.804 | 0.002 |
4 | A | 4 | ARG | 1 | 0.997 | 1.002 | 3.498 | -1.435 | -1.014 | 0.027 | -0.183 | -0.266 | -0.001 |
5 | A | 5 | VAL | 0 | 0.034 | 0.024 | 5.449 | 0.755 | 0.755 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | LYS | 1 | 0.897 | 0.948 | 7.846 | 0.700 | 0.700 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 7 | ILE | 0 | 0.032 | 0.010 | 11.196 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | HIS | 0 | 0.049 | 0.036 | 14.377 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | LYS | 1 | 1.013 | 0.995 | 17.998 | 0.289 | 0.289 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | GLN | 0 | 0.049 | 0.005 | 20.138 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | VAL | 0 | -0.024 | 0.011 | 17.474 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | VAL | 0 | 0.007 | 0.000 | 16.623 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | LYS | 1 | 0.962 | 0.988 | 19.243 | 0.232 | 0.232 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | ALA | 0 | -0.011 | -0.006 | 22.628 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | LEU | 0 | 0.001 | -0.001 | 16.870 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | GLN | 0 | -0.008 | 0.003 | 21.206 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | SER | 0 | -0.031 | -0.016 | 23.428 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | LEU | 0 | -0.075 | -0.025 | 20.795 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | PRO | 0 | 0.052 | 0.027 | 24.536 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | LYN | 0 | 0.107 | 0.072 | 22.485 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | ALA | 0 | 0.002 | -0.002 | 21.276 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | HIS | 0 | -0.012 | -0.028 | 20.625 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | TYR | 0 | 0.037 | 0.024 | 16.506 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | ARG | 1 | 0.959 | 0.948 | 16.996 | 0.331 | 0.331 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | ARG | 1 | 0.940 | 0.968 | 15.736 | 0.316 | 0.316 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | PHE | 0 | -0.006 | -0.002 | 13.891 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | LEU | 0 | -0.042 | -0.013 | 12.483 | -0.110 | -0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | GLU | -1 | -0.754 | -0.864 | 10.879 | -0.788 | -0.788 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | PHE | 0 | 0.012 | -0.004 | 10.622 | -0.111 | -0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | ARG | 1 | 0.811 | 0.872 | 7.717 | 1.563 | 1.563 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | ASP | -1 | -0.798 | -0.880 | 6.458 | -2.225 | -2.225 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | ILE | 0 | -0.006 | 0.001 | 5.842 | -0.316 | -0.316 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | LEU | 0 | -0.019 | -0.006 | 6.900 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | GLU | -1 | -0.966 | -0.978 | 2.352 | -8.939 | -5.998 | 1.618 | -2.050 | -2.510 | -0.018 |
35 | A | 35 | TYR | 0 | -0.054 | -0.037 | 2.977 | -5.620 | -2.684 | 0.752 | -1.665 | -2.023 | -0.012 |
36 | A | 36 | GLU | -1 | -0.839 | -0.911 | 5.042 | -0.031 | -0.001 | -0.001 | -0.002 | -0.027 | 0.000 |
37 | A | 37 | PRO | 0 | 0.022 | 0.012 | 8.506 | -0.119 | -0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | VAL | 0 | -0.030 | -0.013 | 10.238 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | PRO | 0 | 0.018 | 0.033 | 11.736 | 0.094 | 0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | ARG | 1 | 0.890 | 0.914 | 13.632 | 0.232 | 0.232 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | GLU | -1 | -0.838 | -0.932 | 17.409 | -0.231 | -0.231 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | LYS | 1 | 0.787 | 0.905 | 14.146 | 0.532 | 0.532 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | PHE | 0 | 0.001 | -0.008 | 13.099 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | ASP | -1 | -0.760 | -0.868 | 18.152 | -0.239 | -0.239 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | VAL | 0 | -0.009 | 0.020 | 15.715 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | ILE | 0 | -0.011 | -0.007 | 19.106 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | LYS | 1 | 0.855 | 0.924 | 19.172 | 0.172 | 0.172 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | LEU | 0 | -0.110 | -0.063 | 21.508 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | GLU | -1 | -0.807 | -0.895 | 22.719 | -0.123 | -0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | GLY | 0 | -0.041 | -0.040 | 21.773 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 51 | THR | 0 | 0.008 | -0.001 | 22.500 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 52 | GLY | 0 | 0.010 | 0.025 | 21.235 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 53 | ASP | -1 | -0.899 | -0.943 | 19.274 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | LEU | 0 | -0.086 | -0.065 | 17.375 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | ASP | -1 | -0.712 | -0.801 | 17.230 | -0.214 | -0.214 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | LEU | 0 | -0.043 | -0.037 | 17.866 | -0.055 | -0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | TYR | 0 | 0.047 | -0.004 | 16.039 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | ARG | 1 | 0.782 | 0.877 | 19.039 | 0.245 | 0.245 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | ALA | 0 | 0.066 | 0.054 | 16.826 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 60 | ARG | 1 | 0.784 | 0.866 | 18.881 | 0.262 | 0.262 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | LEU | 0 | 0.044 | 0.032 | 15.893 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | GLY | 0 | 0.022 | 0.012 | 20.005 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 63 | ASP | -1 | -0.820 | -0.905 | 23.679 | -0.221 | -0.221 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 64 | TYR | 0 | -0.065 | -0.045 | 19.080 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 65 | ARG | 1 | 0.870 | 0.928 | 21.486 | 0.232 | 0.232 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 66 | VAL | 0 | -0.010 | -0.005 | 16.399 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 67 | ILE | 0 | 0.001 | 0.005 | 19.181 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 68 | TYR | 0 | -0.077 | -0.066 | 13.208 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 69 | SER | 0 | 0.004 | 0.011 | 15.241 | 0.063 | 0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 70 | VAL | 0 | 0.030 | 0.012 | 11.806 | -0.131 | -0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 71 | ASN | 0 | -0.036 | -0.022 | 13.179 | 0.112 | 0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 72 | TRP | 0 | 0.052 | 0.000 | 12.232 | -0.117 | -0.117 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 73 | LYS | 1 | 0.902 | 0.944 | 13.007 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 74 | ASP | -1 | -0.860 | -0.902 | 11.894 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 75 | LYS | 1 | 0.894 | 0.949 | 5.785 | 0.118 | 0.118 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 76 | VAL | 0 | -0.046 | -0.014 | 7.803 | -0.440 | -0.440 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 77 | ILE | 0 | 0.050 | 0.030 | 7.883 | 0.199 | 0.199 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 78 | LYS | 1 | 0.915 | 0.951 | 10.633 | 0.329 | 0.329 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 79 | ILE | 0 | 0.043 | 0.013 | 12.497 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 80 | LEU | 0 | -0.026 | -0.011 | 15.262 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 81 | LYS | 1 | 0.916 | 0.936 | 18.856 | 0.271 | 0.271 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 82 | LEU | 0 | 0.067 | 0.054 | 19.232 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 83 | LYS | 1 | 0.897 | 0.943 | 22.157 | 0.263 | 0.263 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 84 | PRO | 0 | 0.088 | 0.038 | 25.025 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 85 | ARG | 1 | 0.922 | 0.977 | 26.863 | 0.214 | 0.214 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 86 | GLY | 0 | 0.004 | -0.015 | 27.735 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 87 | ARG | 1 | 0.901 | 0.954 | 30.247 | 0.155 | 0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 88 | ALA | 0 | 0.089 | 0.068 | 32.828 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |