![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 4J9JN
Calculation Name: 2OMO-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2OMO
Chain ID: A
UniProt ID: Q82WP3
Base Structure: X-ray
Registration Date: 2023-09-21
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 | 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 | 105 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -824033.310245 |
---|---|
FMO2-HF: Nuclear repulsion | 781117.75533 |
FMO2-HF: Total energy | -42915.554915 |
FMO2-MP2: Total energy | -43040.371727 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F033067/ligand_interaction/ligand_F033067.png)
Ligand Interaction
![ligand interaction](./Kdata/F033067/ligand_interaction/ligand_interaction_F033067.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:-6:ASN)
Summations of interaction energy for
fragment #1(A:-6:ASN)
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. |
-16.323 | -11.962 | 6.078 | -4.585 | -5.853 | 0.044 |
Interaction energy analysis for fragmet #1(A:-6:ASN)
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 | -4 | TYR | 0 | -0.023 | 0.011 | 2.078 | -13.311 | -8.949 | 6.076 | -4.654 | -5.784 | 0.043 |
4 | A | -3 | PHE | 0 | 0.004 | 0.002 | 3.754 | -2.574 | -2.575 | 0.002 | 0.069 | -0.069 | 0.001 |
5 | A | -2 | GLN | 0 | -0.009 | -0.010 | 6.670 | 0.389 | 0.389 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | -1 | GLY | 0 | -0.016 | -0.001 | 7.874 | 0.207 | 0.207 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 0 | HIS | 0 | -0.024 | -0.017 | 10.623 | -0.229 | -0.229 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 1 | MET | 0 | -0.004 | -0.001 | 14.210 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 2 | TYR | 0 | -0.041 | -0.015 | 13.135 | 0.143 | 0.143 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 3 | VAL | 0 | 0.046 | 0.016 | 15.393 | -0.073 | -0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 4 | THR | 0 | -0.053 | -0.020 | 16.439 | 0.125 | 0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 5 | ILE | 0 | 0.014 | 0.015 | 18.712 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 6 | VAL | 0 | -0.029 | -0.021 | 20.875 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 7 | TYR | 0 | 0.008 | 0.004 | 20.355 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 8 | ALA | 0 | 0.000 | -0.018 | 25.751 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 9 | SER | 0 | 0.026 | 0.002 | 29.336 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 10 | VAL | 0 | -0.055 | -0.007 | 32.105 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 11 | LYS | 1 | 0.877 | 0.919 | 35.411 | -0.173 | -0.173 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 12 | THR | 0 | 0.087 | 0.027 | 38.822 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 13 | ASP | -1 | -0.880 | -0.927 | 40.972 | 0.130 | 0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 14 | LYS | 1 | 0.820 | 0.903 | 39.791 | -0.138 | -0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 15 | THR | 0 | 0.023 | 0.002 | 38.163 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 16 | GLU | -1 | -0.796 | -0.876 | 38.921 | 0.139 | 0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 17 | ALA | 0 | 0.049 | 0.034 | 40.992 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 18 | PHE | 0 | 0.032 | 0.004 | 31.431 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 19 | LYS | 1 | 0.828 | 0.912 | 36.437 | -0.137 | -0.137 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 20 | GLU | -1 | -0.957 | -0.960 | 37.421 | 0.106 | 0.106 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 21 | ALA | 0 | 0.024 | 0.006 | 37.211 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 22 | THR | 0 | -0.026 | -0.038 | 31.923 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 23 | ARG | 1 | 0.860 | 0.918 | 33.970 | -0.100 | -0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 24 | MET | 0 | -0.003 | 0.005 | 35.854 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 25 | ASN | 0 | 0.021 | 0.003 | 29.739 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 26 | HIS | 0 | -0.026 | -0.016 | 30.825 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 27 | GLU | -1 | -0.829 | -0.894 | 32.164 | 0.095 | 0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 28 | GLN | 0 | -0.030 | -0.019 | 33.685 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 29 | SER | 0 | 0.004 | -0.010 | 28.177 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 30 | ILE | 0 | -0.053 | -0.020 | 28.694 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 31 | ARG | 1 | 0.890 | 0.962 | 30.146 | -0.077 | -0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 32 | GLU | -1 | -0.749 | -0.816 | 26.618 | 0.147 | 0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 33 | PRO | 0 | 0.044 | 0.011 | 26.334 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 34 | GLY | 0 | -0.007 | -0.005 | 23.322 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 35 | ASN | 0 | -0.006 | -0.004 | 22.796 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 36 | MET | 0 | -0.097 | -0.044 | 20.447 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 37 | ARG | 1 | 0.934 | 0.967 | 22.715 | -0.200 | -0.200 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 38 | PHE | 0 | 0.053 | 0.028 | 24.748 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 39 | ASP | -1 | -0.863 | -0.910 | 26.520 | 0.201 | 0.201 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 40 | ILE | 0 | -0.018 | -0.014 | 27.884 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 41 | LEU | 0 | -0.018 | -0.008 | 26.685 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 42 | GLN | 0 | -0.009 | -0.025 | 30.665 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 43 | SER | 0 | -0.019 | -0.006 | 31.176 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 44 | ALA | 0 | 0.006 | -0.008 | 32.450 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 45 | ASP | -1 | -0.908 | -0.942 | 33.191 | 0.201 | 0.201 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 46 | ASP | -1 | -0.832 | -0.902 | 34.123 | 0.204 | 0.204 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 47 | PRO | 0 | 0.030 | 0.022 | 34.781 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 48 | THR | 0 | -0.031 | -0.032 | 35.900 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 49 | ARG | 1 | 0.824 | 0.916 | 30.719 | -0.241 | -0.241 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 50 | PHE | 0 | 0.022 | -0.005 | 30.694 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 51 | VAL | 0 | -0.019 | -0.015 | 24.644 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 52 | LEU | 0 | -0.019 | 0.006 | 26.189 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 53 | TYR | 0 | -0.005 | -0.002 | 19.526 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 54 | GLU | -1 | -0.838 | -0.929 | 22.411 | 0.260 | 0.260 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 55 | ALA | 0 | -0.017 | -0.011 | 19.873 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 56 | TYR | 0 | -0.017 | -0.046 | 19.225 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 57 | LYS | 1 | 0.938 | 0.958 | 18.350 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 58 | THR | 0 | -0.034 | -0.034 | 16.422 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 59 | ARG | 1 | 0.967 | 0.968 | 10.479 | -0.503 | -0.503 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 60 | LYS | 1 | 0.958 | 0.976 | 14.615 | 0.098 | 0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 61 | ASP | -1 | -0.744 | -0.846 | 19.209 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 62 | ALA | 0 | -0.003 | 0.000 | 18.660 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 63 | ALA | 0 | -0.096 | -0.053 | 19.459 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 64 | ALA | 0 | 0.074 | 0.040 | 21.262 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 65 | HIS | 1 | 0.828 | 0.915 | 24.057 | -0.212 | -0.212 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 66 | LYS | 1 | 0.895 | 0.942 | 21.837 | -0.344 | -0.344 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 67 | GLU | -1 | -0.920 | -0.954 | 26.209 | 0.097 | 0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 68 | THR | 0 | -0.076 | -0.023 | 28.696 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 69 | ALA | 0 | 0.067 | 0.016 | 31.012 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 70 | HIS | 0 | 0.004 | 0.005 | 30.145 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 71 | TYR | 0 | 0.007 | 0.010 | 27.167 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 72 | LEU | 0 | -0.005 | -0.003 | 30.895 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 73 | THR | 0 | 0.018 | -0.007 | 33.050 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 74 | TRP | 0 | -0.039 | -0.012 | 28.915 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 75 | ARG | 1 | 0.780 | 0.855 | 30.459 | -0.165 | -0.165 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 76 | ASP | -1 | -0.822 | -0.892 | 32.851 | 0.159 | 0.159 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 77 | THR | 0 | -0.039 | -0.015 | 36.242 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 78 | VAL | 0 | -0.040 | -0.024 | 33.006 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 79 | ALA | 0 | 0.004 | 0.018 | 34.562 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 80 | ASP | -1 | -0.852 | -0.928 | 35.615 | 0.160 | 0.160 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 81 | TRP | 0 | -0.042 | -0.031 | 37.280 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 82 | MET | 0 | -0.009 | 0.036 | 32.350 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 83 | ALA | 0 | -0.013 | -0.020 | 34.434 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 84 | GLU | -1 | -0.866 | -0.907 | 29.905 | 0.297 | 0.297 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 85 | PRO | 0 | -0.025 | -0.018 | 27.900 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 86 | ARG | 1 | 0.915 | 0.953 | 26.783 | -0.245 | -0.245 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 87 | LYS | 1 | 0.932 | 0.972 | 18.186 | -0.687 | -0.687 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 88 | GLY | 0 | 0.028 | 0.026 | 21.049 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 89 | VAL | 0 | -0.073 | -0.044 | 15.828 | 0.063 | 0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 90 | ILE | 0 | -0.006 | 0.002 | 12.814 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 91 | TYR | 0 | 0.034 | 0.008 | 12.524 | 0.193 | 0.193 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 92 | GLY | 0 | -0.006 | 0.004 | 10.926 | -0.142 | -0.142 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 93 | GLY | 0 | -0.023 | -0.010 | 11.973 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 94 | LEU | 0 | 0.040 | 0.011 | 9.897 | -0.059 | -0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 95 | TYR | 0 | 0.017 | 0.009 | 13.656 | -0.144 | -0.144 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 96 | PRO | 0 | -0.004 | -0.009 | 17.443 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 97 | THR | 0 | 0.037 | 0.013 | 15.899 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 98 | GLY | 0 | -0.024 | 0.005 | 17.737 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |