![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 82J2Y
Calculation Name: 4EMO-A-Xray321
Preferred Name: Sharpin/RBCK1/RNF31
Target Type: PROTEIN COMPLEX
Ligand Name:
ligand 3-letter code:
PDB ID: 4EMO
Chain ID: A
ChEMBL ID: CHEMBL4296109
UniProt ID: Q9H0F6
Base Structure: X-ray
Registration Date: 2021-09-07
Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.
Modeling method
Optimization | MOE:Amber10:EHT |
---|---|
Restraint | OptH |
Protonation | MOE:Protonate 3D |
Complement | MOE:Structure Preparation |
Water | No |
Procedure | Auto-FMO protocol ver. 1.20200129 |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 106 |
LigandCharge | |
Software | ABINIT-MP - Open Ver.1 Rev. 15 / 20190524 |
Total energy (hartree)
FMO2-HF: Electronic energy | -735397.93942 |
---|---|
FMO2-HF: Nuclear repulsion | 696780.663114 |
FMO2-HF: Total energy | -38617.276306 |
FMO2-MP2: Total energy | -38731.524773 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F016455/ligand_interaction/ligand_F016455.png)
Ligand Interaction
![ligand interaction](./Kdata/F016455/ligand_interaction/ligand_interaction_F016455.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:17:ACE )
Summations of interaction energy for
fragment #1(A:17:ACE )
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. |
5.87 | 0.9 | 6.932 | 0.306 | -2.267 | -0.009 |
Interaction energy analysis for fragmet #1(A:17:ACE )
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 | 19 | ALA | 0 | -0.018 | 0.008 | 3.813 | 0.653 | 1.697 | -0.006 | -0.477 | -0.560 | -0.001 |
4 | A | 20 | VAL | 0 | 0.030 | 0.008 | 5.991 | 0.167 | 0.167 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 21 | LEU | 0 | -0.019 | -0.001 | 9.502 | 0.090 | 0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 22 | MET | 0 | -0.046 | -0.028 | 10.964 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 23 | ALA | 0 | 0.028 | 0.007 | 14.238 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 24 | VAL | 0 | -0.048 | -0.013 | 16.476 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 25 | HIS | 0 | 0.010 | -0.007 | 20.093 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 26 | ALA | 0 | 0.009 | 0.003 | 22.848 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 27 | ALA | 0 | 0.012 | 0.015 | 25.138 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 28 | VAL | 0 | -0.009 | -0.009 | 23.186 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 29 | ARG | 1 | 0.966 | 0.979 | 26.617 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 30 | PRO | 0 | 0.038 | 0.015 | 27.985 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 31 | LEU | 0 | -0.002 | -0.017 | 29.103 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 32 | GLY | 0 | -0.043 | -0.009 | 30.621 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 33 | ALA | 0 | -0.023 | -0.006 | 32.120 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 34 | GLY | 0 | 0.043 | 0.026 | 34.190 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 35 | PRO | 0 | -0.084 | -0.057 | 36.066 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 36 | ASP | -1 | -0.879 | -0.950 | 37.756 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 37 | ALA | 0 | -0.042 | 0.012 | 32.868 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 38 | GLU | -1 | -0.911 | -0.959 | 32.225 | -0.071 | -0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 39 | ALA | 0 | -0.064 | -0.045 | 30.362 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 40 | GLN | 0 | 0.033 | 0.020 | 27.526 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 41 | LEU | 0 | -0.016 | -0.003 | 25.889 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 42 | ARG | 1 | 0.880 | 0.944 | 21.498 | 0.133 | 0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 43 | ARG | 1 | 0.947 | 0.982 | 16.904 | 0.196 | 0.196 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 44 | LEU | 0 | 0.017 | 0.015 | 17.298 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 45 | GLN | 0 | -0.026 | -0.039 | 12.316 | 0.081 | 0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 46 | LEU | 0 | 0.016 | 0.019 | 11.640 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 47 | SER | 0 | -0.023 | -0.008 | 6.797 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 48 | ALA | 0 | 0.028 | 0.010 | 3.411 | -0.023 | 0.173 | 0.029 | -0.087 | -0.138 | 0.000 |
33 | A | 49 | ASP | -1 | -0.804 | -0.892 | 4.342 | -0.871 | -0.926 | 0.001 | -0.041 | 0.095 | 0.000 |
34 | A | 50 | PRO | 0 | -0.070 | -0.021 | 2.211 | 4.339 | -0.199 | 6.725 | -0.788 | -1.399 | -0.005 |
35 | A | 51 | GLU | -1 | -0.937 | -0.956 | 2.954 | 1.668 | 0.051 | 0.183 | 1.699 | -0.265 | -0.003 |
36 | A | 52 | ARG | 1 | 0.763 | 0.875 | 5.901 | -0.153 | -0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 53 | PRO | 0 | 0.044 | 0.020 | 5.998 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 54 | GLY | 0 | -0.016 | -0.007 | 6.780 | -0.247 | -0.247 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 55 | ARG | 1 | 0.930 | 0.986 | 8.088 | -0.328 | -0.328 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 56 | PHE | 0 | 0.011 | -0.001 | 7.328 | 0.081 | 0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 57 | ARG | 1 | 0.917 | 0.961 | 6.079 | 1.263 | 1.263 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 58 | LEU | 0 | 0.004 | 0.001 | 10.109 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 59 | GLU | -1 | -0.796 | -0.887 | 9.626 | -0.718 | -0.718 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 60 | LEU | 0 | -0.048 | -0.020 | 13.908 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 61 | LEU | 0 | -0.011 | -0.014 | 14.589 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 62 | GLY | 0 | 0.052 | 0.020 | 18.091 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 63 | ALA | 0 | -0.045 | -0.033 | 21.136 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 64 | GLY | 0 | 0.043 | 0.028 | 23.950 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 65 | PRO | 0 | -0.005 | -0.005 | 21.912 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 66 | GLY | 0 | 0.001 | -0.005 | 21.165 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 67 | ALA | 0 | -0.051 | -0.003 | 22.030 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 68 | VAL | 0 | 0.013 | 0.001 | 18.363 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 69 | ASN | 0 | 0.020 | 0.010 | 14.768 | 0.066 | 0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 70 | LEU | 0 | -0.021 | -0.005 | 16.355 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 71 | GLU | -1 | -0.874 | -0.948 | 10.477 | -0.700 | -0.700 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 72 | TRP | 0 | -0.026 | -0.022 | 13.624 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 73 | PRO | 0 | 0.034 | 0.015 | 11.644 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 74 | LEU | 0 | -0.010 | -0.002 | 12.349 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 75 | GLU | -1 | -0.803 | -0.936 | 13.760 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 76 | SER | 0 | -0.109 | -0.037 | 16.045 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 77 | VAL | 0 | -0.014 | -0.001 | 17.295 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 78 | SER | 0 | -0.027 | 0.004 | 19.535 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 79 | TYR | 0 | -0.019 | -0.040 | 20.327 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 80 | THR | 0 | -0.021 | -0.018 | 22.604 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 81 | ILE | 0 | -0.002 | -0.011 | 24.585 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 82 | ARG | 1 | 0.948 | 0.979 | 27.694 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 83 | GLY | 0 | 0.021 | 0.004 | 30.358 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 84 | PRO | 0 | -0.012 | -0.009 | 30.175 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 85 | THR | 0 | 0.001 | 0.001 | 29.393 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 86 | GLN | 0 | 0.029 | 0.022 | 29.198 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 87 | HIS | 0 | 0.012 | 0.044 | 23.924 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 88 | GLU | -1 | -0.940 | -0.971 | 26.011 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 89 | LEU | 0 | 0.024 | 0.021 | 19.136 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 90 | GLN | 0 | 0.006 | -0.006 | 23.371 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 91 | PRO | 0 | 0.009 | 0.008 | 20.568 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 92 | PRO | 0 | 0.022 | 0.010 | 19.132 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 93 | PRO | 0 | -0.002 | -0.019 | 22.235 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 94 | GLY | 0 | 0.006 | 0.010 | 23.778 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 95 | GLY | 0 | -0.004 | 0.015 | 22.624 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 96 | PRO | 0 | -0.030 | -0.020 | 22.165 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 97 | GLY | 0 | 0.029 | 0.021 | 25.064 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 98 | THR | 0 | 0.004 | -0.019 | 25.430 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 99 | LEU | 0 | -0.023 | 0.005 | 22.543 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 100 | SER | 0 | 0.028 | 0.031 | 26.336 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 101 | MET | 0 | -0.010 | -0.023 | 21.078 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 102 | HIS | 0 | 0.010 | 0.013 | 26.522 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 103 | PHE | 0 | -0.018 | -0.025 | 22.636 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 104 | LEU | 0 | 0.063 | 0.024 | 27.388 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 105 | ASN | 0 | -0.050 | -0.035 | 28.507 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 106 | PRO | 0 | 0.058 | 0.011 | 28.650 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 107 | GLN | 0 | 0.019 | 0.022 | 27.065 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 108 | GLU | -1 | -0.914 | -0.942 | 24.366 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 109 | ALA | 0 | 0.042 | 0.022 | 23.577 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 110 | GLN | 0 | -0.004 | 0.000 | 24.263 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 111 | ARG | 1 | 0.957 | 0.981 | 20.736 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 112 | TRP | 0 | 0.027 | 0.004 | 15.608 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 113 | ALA | 0 | 0.014 | 0.007 | 19.657 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 114 | VAL | 0 | -0.092 | -0.050 | 20.993 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 115 | LEU | 0 | 0.022 | 0.023 | 14.466 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 116 | VAL | 0 | 0.015 | 0.004 | 16.479 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 117 | ARG | 1 | 0.925 | 0.953 | 17.187 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 118 | GLY | 0 | -0.027 | -0.009 | 17.529 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 119 | ALA | 0 | -0.033 | -0.021 | 12.710 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 120 | THR | 0 | -0.046 | -0.008 | 13.580 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 121 | VAL | 0 | -0.031 | -0.017 | 13.695 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 122 | NME | 0 | -0.022 | -0.008 | 16.634 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |