![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 223ZR
Calculation Name: 1UB9-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1UB9
Chain ID: A
UniProt ID: O58788
Base Structure: X-ray
Registration Date: 2023-06-20
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 | OptH |
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 | 100 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -727106.636365 |
---|---|
FMO2-HF: Nuclear repulsion | 687321.626846 |
FMO2-HF: Total energy | -39785.009519 |
FMO2-MP2: Total energy | -39900.983658 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F021578/ligand_interaction/ligand_F021578.png)
Ligand Interaction
![ligand interaction](./Kdata/F021578/ligand_interaction/ligand_interaction_F021578.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. |
-1.824 | 3.428 | 1.556 | -1.94 | -4.87 | -0.005 |
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 | GLU | -1 | -0.809 | -0.913 | 3.220 | -5.285 | -2.484 | -0.001 | -1.215 | -1.586 | -0.004 |
4 | A | 4 | LEU | 0 | -0.018 | -0.002 | 2.414 | -0.377 | 0.935 | 1.521 | -0.536 | -2.297 | -0.002 |
5 | A | 5 | LYS | 1 | 0.949 | 0.954 | 3.205 | 2.364 | 3.308 | 0.038 | -0.179 | -0.804 | 0.001 |
6 | A | 6 | GLU | -1 | -0.933 | -0.950 | 5.297 | -0.529 | -0.429 | -0.001 | -0.004 | -0.095 | 0.000 |
7 | A | 7 | ILE | 0 | 0.005 | 0.010 | 7.904 | 0.380 | 0.380 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | MET | 0 | -0.049 | -0.029 | 5.384 | 0.081 | 0.176 | -0.001 | -0.006 | -0.088 | 0.000 |
9 | A | 9 | LYS | 1 | 0.919 | 0.966 | 8.969 | 0.799 | 0.799 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | SER | 0 | 0.000 | 0.024 | 11.219 | 0.113 | 0.113 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | HIS | 0 | 0.028 | 0.009 | 13.881 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | ILE | 0 | -0.067 | -0.039 | 16.150 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | LEU | 0 | 0.032 | -0.012 | 17.265 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | GLY | 0 | 0.074 | 0.049 | 15.062 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | ASN | 0 | -0.059 | -0.024 | 15.941 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | PRO | 0 | 0.090 | 0.035 | 17.900 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | VAL | 0 | 0.019 | 0.017 | 20.063 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | ARG | 1 | 0.870 | 0.927 | 20.624 | 0.176 | 0.176 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | LEU | 0 | 0.043 | 0.043 | 17.473 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | GLY | 0 | 0.057 | 0.028 | 21.193 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | ILE | 0 | -0.026 | -0.017 | 24.128 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | MET | 0 | -0.034 | -0.011 | 22.901 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | ILE | 0 | 0.017 | 0.014 | 20.784 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | PHE | 0 | -0.031 | -0.016 | 24.830 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | LEU | 0 | -0.004 | -0.018 | 28.222 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | LEU | 0 | -0.013 | 0.016 | 22.804 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | PRO | 0 | -0.031 | -0.013 | 27.371 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | ARG | 1 | 0.930 | 0.960 | 30.015 | 0.105 | 0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | ARG | 1 | 0.845 | 0.957 | 31.268 | 0.125 | 0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | LYS | 1 | 0.955 | 0.947 | 32.622 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | ALA | 0 | 0.014 | 0.015 | 34.666 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | PRO | 0 | -0.025 | -0.008 | 36.359 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | PHE | 0 | 0.077 | 0.029 | 34.247 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | SER | 0 | -0.009 | -0.019 | 36.274 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | GLN | 0 | -0.005 | -0.005 | 37.478 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | ILE | 0 | 0.038 | 0.027 | 31.370 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | GLN | 0 | -0.037 | -0.029 | 33.305 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | LYS | 1 | 0.935 | 0.966 | 34.681 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | VAL | 0 | -0.021 | 0.000 | 32.988 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | LEU | 0 | -0.051 | -0.031 | 28.441 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | ASP | -1 | -0.926 | -0.946 | 30.587 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | LEU | 0 | 0.018 | 0.025 | 28.037 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | THR | 0 | 0.034 | 0.009 | 32.135 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | PRO | 0 | 0.036 | -0.009 | 33.480 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | GLY | 0 | 0.048 | 0.026 | 34.466 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | ASN | 0 | 0.025 | 0.004 | 29.257 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | LEU | 0 | -0.015 | 0.013 | 29.603 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | ASP | -1 | -0.822 | -0.895 | 30.666 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | SER | 0 | -0.015 | -0.006 | 28.913 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | HIS | 0 | 0.020 | 0.006 | 23.780 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 51 | ILE | 0 | 0.011 | 0.008 | 27.008 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 52 | ARG | 1 | 0.907 | 0.927 | 29.442 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 53 | VAL | 0 | -0.078 | -0.026 | 23.381 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | LEU | 0 | 0.022 | 0.006 | 23.489 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | GLU | -1 | -0.805 | -0.874 | 26.121 | -0.105 | -0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | ARG | 1 | 0.908 | 0.956 | 25.980 | 0.124 | 0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | ASN | 0 | -0.066 | -0.042 | 23.385 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | GLY | 0 | 0.061 | 0.041 | 25.237 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | LEU | 0 | 0.001 | 0.017 | 21.910 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 60 | VAL | 0 | -0.017 | -0.024 | 26.224 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | LYS | 1 | 0.923 | 0.976 | 29.506 | 0.106 | 0.106 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | THR | 0 | -0.080 | -0.066 | 33.059 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 63 | TYR | 0 | 0.003 | -0.013 | 35.772 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 64 | LYS | 1 | 0.880 | 0.941 | 39.536 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 65 | VAL | 0 | 0.032 | 0.015 | 42.404 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 66 | ILE | 0 | -0.005 | -0.023 | 44.907 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 67 | ALA | 0 | 0.005 | 0.047 | 48.278 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 68 | ASP | -1 | -0.857 | -0.967 | 50.294 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 69 | ARG | 1 | 0.915 | 0.944 | 48.351 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 70 | PRO | 0 | -0.019 | -0.008 | 47.126 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 71 | ARG | 1 | 0.955 | 0.987 | 42.637 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 72 | THR | 0 | 0.018 | 0.022 | 37.638 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 73 | VAL | 0 | -0.047 | -0.004 | 37.277 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 74 | VAL | 0 | 0.035 | 0.018 | 31.456 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 75 | GLU | -1 | -0.872 | -0.942 | 33.491 | -0.092 | -0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 76 | ILE | 0 | 0.015 | 0.020 | 25.671 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 77 | THR | 0 | -0.025 | -0.031 | 28.455 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 78 | ASP | -1 | -0.816 | -0.928 | 28.103 | -0.131 | -0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 79 | PHE | 0 | 0.029 | 0.023 | 22.241 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 80 | GLY | 0 | 0.045 | 0.010 | 23.962 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 81 | MET | 0 | -0.091 | -0.055 | 23.515 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 82 | GLU | -1 | -0.918 | -0.964 | 22.171 | -0.212 | -0.212 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 83 | GLU | -1 | -0.860 | -0.915 | 19.390 | -0.360 | -0.360 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 84 | ALA | 0 | -0.016 | -0.006 | 18.463 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 85 | LYS | 1 | 0.947 | 0.971 | 18.627 | 0.165 | 0.165 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 86 | ARG | 1 | 0.913 | 0.965 | 15.763 | 0.282 | 0.282 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 87 | PHE | 0 | 0.039 | 0.016 | 12.642 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 88 | LEU | 0 | -0.033 | -0.036 | 13.995 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 89 | SER | 0 | -0.050 | -0.026 | 14.636 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 90 | SER | 0 | 0.034 | 0.018 | 9.942 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 91 | LEU | 0 | -0.004 | -0.021 | 9.799 | -0.128 | -0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 92 | LYS | 1 | 0.889 | 0.957 | 11.603 | 0.294 | 0.294 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 93 | ALA | 0 | 0.037 | 0.030 | 9.316 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 94 | VAL | 0 | -0.012 | -0.008 | 6.318 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 95 | ILE | 0 | -0.046 | -0.031 | 8.226 | 0.139 | 0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 96 | ASP | -1 | -0.909 | -0.964 | 11.549 | -0.241 | -0.241 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 97 | GLY | 0 | -0.023 | 0.000 | 8.621 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 98 | LEU | 0 | -0.103 | -0.057 | 8.731 | 0.112 | 0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 99 | ASP | -1 | -0.927 | -0.939 | 10.919 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 100 | LEU | 0 | -0.082 | -0.038 | 14.121 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |