![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 7GKMK
Calculation Name: 3D33-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3D33
Chain ID: A
UniProt ID: A6KX32
Base Structure: X-ray
Registration Date: 2023-03-14
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 | 94 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -666341.172578 |
---|---|
FMO2-HF: Nuclear repulsion | 629350.662046 |
FMO2-HF: Total energy | -36990.510532 |
FMO2-MP2: Total energy | -37097.958961 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F019309/ligand_interaction/ligand_F019309.png)
Ligand Interaction
![ligand interaction](./Kdata/F019309/ligand_interaction/ligand_interaction_F019309.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:34:PRO)
Summations of interaction energy for
fragment #1(A:34:PRO)
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. |
-3.406 | -1.742 | 0.02 | -0.866 | -0.819 | 0 |
Interaction energy analysis for fragmet #1(A:34:PRO)
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 | 36 | LYS | 1 | 0.881 | 0.948 | 3.447 | -0.543 | 1.121 | 0.020 | -0.866 | -0.819 | 0.000 |
4 | A | 37 | ASP | -1 | -0.843 | -0.938 | 5.803 | -0.436 | -0.436 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 38 | VAL | 0 | -0.115 | -0.062 | 7.719 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 39 | GLU | -1 | -0.885 | -0.931 | 11.409 | -0.521 | -0.521 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 40 | LEU | 0 | -0.062 | -0.034 | 13.258 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 41 | ASP | -1 | -0.870 | -0.915 | 16.864 | -0.333 | -0.333 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 42 | GLY | 0 | -0.039 | -0.033 | 20.163 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 43 | ARG | 1 | 0.740 | 0.827 | 23.412 | 0.145 | 0.145 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 44 | TRP | 0 | 0.026 | -0.006 | 23.369 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 45 | ASP | -1 | -0.803 | -0.854 | 25.338 | -0.128 | -0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 46 | ASP | -1 | -0.923 | -0.948 | 27.095 | -0.094 | -0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 54 | ASN | 0 | 0.014 | -0.003 | 15.574 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 55 | CYS | 0 | -0.023 | 0.004 | 17.760 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 56 | PRO | 0 | 0.027 | 0.021 | 17.830 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 57 | ILE | 0 | 0.006 | 0.008 | 17.355 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 58 | THR | 0 | -0.006 | -0.007 | 12.208 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 59 | VAL | 0 | 0.025 | -0.005 | 12.472 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 60 | PHE | 0 | -0.013 | 0.005 | 7.569 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 61 | THR | 0 | -0.011 | -0.015 | 8.584 | 0.351 | 0.351 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 62 | ASP | -1 | -0.911 | -0.957 | 6.511 | -1.185 | -1.185 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 63 | GLY | 0 | 0.015 | 0.003 | 7.672 | 0.369 | 0.369 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 64 | TYR | 0 | -0.064 | -0.041 | 9.616 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 65 | LEU | 0 | -0.020 | -0.011 | 11.782 | 0.102 | 0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 66 | LEU | 0 | 0.030 | 0.026 | 11.480 | -0.135 | -0.135 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 67 | THR | 0 | -0.032 | -0.026 | 11.522 | 0.180 | 0.180 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 68 | LEU | 0 | 0.033 | 0.028 | 12.931 | -0.092 | -0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 69 | LYS | 1 | 0.897 | 0.936 | 11.878 | 0.154 | 0.154 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 70 | ASN | 0 | 0.079 | 0.043 | 15.969 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 71 | ALA | 0 | -0.036 | -0.021 | 17.293 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 72 | SER | 0 | -0.066 | -0.052 | 19.086 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 73 | PRO | 0 | -0.029 | -0.015 | 22.161 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 74 | ASP | -1 | -0.803 | -0.868 | 24.622 | -0.115 | -0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 75 | ARG | 1 | 0.774 | 0.862 | 26.786 | 0.131 | 0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 76 | ASP | -1 | -0.861 | -0.919 | 27.414 | -0.092 | -0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 77 | MET | 0 | -0.052 | -0.031 | 21.532 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 78 | THR | 0 | -0.045 | -0.026 | 26.214 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 79 | ILE | 0 | -0.032 | -0.002 | 19.836 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 80 | ARG | 1 | 0.860 | 0.903 | 22.879 | 0.194 | 0.194 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 81 | ILE | 0 | -0.005 | 0.001 | 19.055 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 82 | THR | 0 | -0.047 | -0.029 | 22.512 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 83 | ASP | -1 | -0.755 | -0.873 | 23.149 | -0.252 | -0.252 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 84 | MET | 0 | 0.010 | -0.002 | 21.724 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 85 | ALA | 0 | -0.024 | 0.006 | 24.849 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 86 | LYS | 1 | 0.797 | 0.880 | 27.664 | 0.183 | 0.183 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 87 | GLY | 0 | 0.019 | 0.029 | 28.138 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 88 | GLY | 0 | -0.036 | -0.017 | 28.626 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 89 | VAL | 0 | -0.009 | -0.014 | 26.703 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 90 | VAL | 0 | -0.028 | -0.007 | 22.799 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 91 | TYR | 0 | -0.012 | -0.017 | 22.961 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 92 | GLU | -1 | -0.858 | -0.916 | 25.007 | -0.168 | -0.168 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 93 | ASN | 0 | -0.032 | -0.014 | 24.287 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 94 | ASP | -1 | -0.840 | -0.888 | 26.303 | -0.143 | -0.143 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 95 | ILE | 0 | -0.048 | -0.033 | 23.063 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 96 | PRO | 0 | 0.019 | 0.006 | 27.135 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 97 | GLU | -1 | -0.869 | -0.922 | 27.175 | -0.074 | -0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 98 | VAL | 0 | -0.041 | -0.024 | 26.421 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 99 | GLN | 0 | -0.061 | -0.041 | 25.109 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 100 | SER | 0 | -0.042 | -0.037 | 23.182 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 101 | ALA | 0 | 0.017 | 0.017 | 20.838 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 102 | TYR | 0 | -0.054 | -0.040 | 14.440 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 103 | ILE | 0 | 0.017 | 0.028 | 17.504 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 104 | THR | 0 | -0.022 | -0.004 | 14.856 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 105 | ILE | 0 | -0.008 | -0.004 | 16.300 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 106 | SER | 0 | -0.016 | -0.009 | 16.391 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 107 | ILE | 0 | 0.042 | 0.023 | 13.543 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 108 | ALA | 0 | 0.001 | 0.004 | 17.112 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 109 | ASN | 0 | -0.031 | -0.029 | 17.930 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 110 | PHE | 0 | 0.023 | 0.024 | 19.318 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 111 | PRO | 0 | 0.006 | -0.004 | 20.896 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 112 | ALA | 0 | -0.005 | 0.013 | 19.480 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 113 | GLU | -1 | -0.868 | -0.917 | 19.565 | -0.274 | -0.274 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 114 | GLU | -1 | -0.912 | -0.961 | 17.843 | -0.572 | -0.572 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 115 | TYR | 0 | -0.053 | -0.047 | 18.694 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 116 | LYS | 1 | 0.905 | 0.953 | 18.634 | 0.202 | 0.202 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 117 | LEU | 0 | -0.047 | -0.022 | 16.110 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 118 | GLU | -1 | -0.826 | -0.910 | 19.755 | -0.233 | -0.233 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 119 | ILE | 0 | -0.010 | -0.008 | 18.065 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 120 | THR | 0 | 0.015 | 0.000 | 22.359 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 121 | GLY | 0 | 0.004 | 0.002 | 25.858 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 122 | THR | 0 | -0.035 | 0.013 | 27.926 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 123 | PRO | 0 | -0.010 | -0.024 | 31.668 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 124 | SER | 0 | -0.034 | -0.032 | 30.971 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 125 | GLY | 0 | 0.064 | 0.038 | 26.815 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 126 | HIS | 0 | -0.087 | -0.050 | 25.091 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 127 | LEU | 0 | 0.024 | 0.029 | 19.602 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 128 | THR | 0 | -0.003 | -0.014 | 20.737 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 129 | GLY | 0 | 0.064 | 0.043 | 16.582 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 130 | TYR | 0 | -0.002 | -0.009 | 15.726 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 131 | PHE | 0 | -0.020 | -0.026 | 13.453 | -0.119 | -0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 132 | THR | 0 | 0.042 | 0.013 | 14.697 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 133 | LYS | 1 | 0.739 | 0.898 | 14.102 | 0.223 | 0.223 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 134 | GLU | -1 | -0.888 | -0.945 | 13.516 | -0.318 | -0.318 | 0.000 | 0.000 | 0.000 | 0.000 |