![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: Q1JKY
Calculation Name: 1KPT-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1KPT
Chain ID: A
UniProt ID: Q90121
Base Structure: X-ray
Registration Date: 2023-06-19
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 | 100 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -747062.418471 |
---|---|
FMO2-HF: Nuclear repulsion | 705569.311116 |
FMO2-HF: Total energy | -41493.107355 |
FMO2-MP2: Total energy | -41605.143339 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F020514/ligand_interaction/ligand_F020514.png)
Ligand Interaction
![ligand interaction](./Kdata/F020514/ligand_interaction/ligand_interaction_F020514.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:LEU)
Summations of interaction energy for
fragment #1(A:1:LEU)
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. |
-20.956 | -9.823 | 9.727 | -7.731 | -13.128 | -0.053 |
Interaction energy analysis for fragmet #1(A:1:LEU)
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 | ILE | 0 | 0.014 | 0.008 | 2.845 | -3.986 | 0.097 | 0.364 | -2.320 | -2.127 | -0.002 |
4 | A | 4 | ASN | 0 | -0.082 | -0.046 | 2.655 | -0.304 | 1.526 | 1.039 | -0.731 | -2.138 | -0.006 |
5 | A | 5 | CYS | 0 | -0.030 | -0.014 | 4.698 | -0.227 | -0.172 | -0.002 | -0.007 | -0.045 | 0.000 |
6 | A | 6 | ARG | 1 | 0.936 | 0.983 | 2.515 | -5.173 | -4.000 | 2.379 | -0.612 | -2.941 | 0.000 |
7 | A | 7 | GLY | 0 | 0.058 | 0.017 | 6.406 | -0.243 | -0.243 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | SER | 0 | -0.001 | 0.006 | 9.072 | 0.120 | 0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | SER | 0 | 0.075 | 0.023 | 12.167 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | GLN | 0 | 0.017 | 0.015 | 14.630 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | CYS | 0 | -0.088 | -0.036 | 10.564 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | GLY | 0 | -0.010 | -0.005 | 15.192 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | LEU | 0 | -0.003 | 0.006 | 16.688 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | SER | 0 | -0.006 | 0.020 | 18.662 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | GLY | 0 | 0.055 | 0.043 | 20.250 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | GLY | 0 | 0.026 | 0.002 | 22.345 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | ASN | 0 | 0.026 | 0.017 | 18.456 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | LEU | 0 | 0.021 | -0.007 | 18.202 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | MET | 0 | 0.033 | 0.036 | 12.084 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | VAL | 0 | 0.016 | 0.002 | 17.017 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | ARG | 1 | 0.962 | 0.992 | 20.001 | 0.096 | 0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | ILE | 0 | -0.009 | -0.006 | 16.775 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | ARG | 1 | 0.869 | 0.923 | 17.963 | 0.229 | 0.229 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | ASP | -1 | -0.810 | -0.906 | 19.456 | -0.200 | -0.200 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | GLN | 0 | -0.046 | -0.023 | 22.338 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | ALA | 0 | -0.009 | -0.007 | 19.776 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | CYS | 0 | -0.093 | -0.038 | 16.566 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | GLY | 0 | 0.045 | 0.039 | 23.260 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | ASN | 0 | -0.039 | -0.025 | 25.205 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | GLN | 0 | -0.015 | -0.018 | 23.209 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | GLY | 0 | 0.025 | 0.030 | 25.107 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | GLN | 0 | -0.022 | 0.009 | 23.398 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | THR | 0 | 0.002 | -0.008 | 22.548 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | TRP | 0 | -0.027 | -0.029 | 16.783 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | CYS | 0 | 0.012 | 0.001 | 17.331 | -0.071 | -0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | PRO | 0 | 0.008 | -0.014 | 15.727 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | GLY | 0 | -0.020 | -0.003 | 15.779 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | GLU | -1 | -0.824 | -0.870 | 17.246 | -0.291 | -0.291 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | ARG | 1 | 0.813 | 0.897 | 17.513 | 0.170 | 0.170 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | ARG | 1 | 0.820 | 0.880 | 19.459 | 0.346 | 0.346 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | ALA | 0 | 0.017 | 0.031 | 19.150 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | LYS | 1 | 0.917 | 0.946 | 19.084 | 0.156 | 0.156 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | VAL | 0 | -0.004 | 0.008 | 20.428 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 105 | CYS | 0 | -0.079 | -0.025 | 21.485 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | GLY | 0 | 0.071 | 0.052 | 23.962 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | THR | 0 | -0.017 | -0.023 | 25.281 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | GLY | 0 | 0.033 | 0.018 | 26.419 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | ASN | 0 | -0.047 | -0.018 | 21.103 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | SER | 0 | -0.014 | -0.023 | 20.348 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | ILE | 0 | 0.040 | 0.046 | 15.306 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 51 | SER | 0 | -0.026 | -0.029 | 16.107 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 52 | ALA | 0 | 0.040 | 0.026 | 14.378 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 53 | TYR | 0 | -0.038 | -0.023 | 10.989 | 0.084 | 0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | VAL | 0 | 0.068 | 0.051 | 12.837 | -0.099 | -0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | GLN | 0 | 0.031 | 0.011 | 9.070 | 0.185 | 0.185 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | SER | 0 | 0.003 | -0.002 | 8.225 | -0.187 | -0.187 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | THR | 0 | 0.045 | 0.018 | 10.567 | -0.067 | -0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | ASN | 0 | 0.008 | 0.007 | 13.726 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | ASN | 0 | -0.031 | -0.011 | 16.087 | 0.130 | 0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 61 | ILE | 0 | -0.010 | 0.005 | 15.087 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 62 | SER | 0 | 0.018 | -0.023 | 19.016 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 63 | GLY | 0 | 0.072 | 0.017 | 20.036 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 64 | THR | 0 | 0.002 | -0.008 | 21.075 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 65 | GLU | -1 | -0.847 | -0.891 | 17.090 | -0.622 | -0.622 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 66 | ALA | 0 | 0.005 | 0.004 | 16.225 | -0.069 | -0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 68 | ARG | 1 | 0.943 | 0.959 | 13.957 | 0.811 | 0.811 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 69 | HIS | 0 | -0.039 | -0.007 | 11.461 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 70 | LEU | 0 | 0.001 | -0.006 | 12.961 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 71 | THR | 0 | -0.019 | -0.021 | 14.992 | 0.074 | 0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 72 | ASN | 0 | -0.062 | -0.034 | 11.975 | 0.172 | 0.172 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 73 | LEU | 0 | 0.015 | 0.004 | 8.690 | 0.058 | 0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 74 | VAL | 0 | -0.059 | -0.026 | 12.246 | 0.094 | 0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 75 | ASN | 0 | -0.036 | -0.032 | 15.210 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 76 | HIS | 0 | -0.006 | 0.007 | 6.897 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 77 | GLY | 0 | 0.022 | 0.021 | 11.890 | 0.090 | 0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 79 | ARG | 1 | 0.867 | 0.917 | 12.136 | -0.072 | -0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 80 | VAL | 0 | -0.057 | -0.044 | 13.950 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 82 | GLY | 0 | 0.055 | 0.032 | 7.630 | 0.107 | 0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 83 | SER | 0 | -0.024 | -0.019 | 5.367 | 0.155 | 0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 84 | ASP | -1 | -0.751 | -0.867 | 6.222 | -1.684 | -1.684 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 85 | PRO | 0 | -0.003 | 0.009 | 5.350 | 0.094 | 0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 86 | LEU | 0 | -0.013 | -0.013 | 7.599 | 0.404 | 0.404 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 87 | TYR | 0 | -0.007 | 0.007 | 10.430 | 0.263 | 0.263 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 88 | ALA | 0 | 0.055 | 0.013 | 9.675 | -0.334 | -0.334 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 89 | GLY | 0 | 0.003 | 0.004 | 8.355 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 90 | ASN | 0 | -0.054 | -0.027 | 6.728 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 91 | ASP | -1 | -0.755 | -0.835 | 2.141 | -16.899 | -14.500 | 4.261 | -3.321 | -3.339 | -0.042 |
88 | A | 92 | VAL | 0 | -0.007 | -0.022 | 2.387 | 1.222 | 2.605 | 1.687 | -0.723 | -2.346 | -0.003 |
89 | A | 93 | SER | 0 | -0.090 | -0.072 | 4.402 | 1.962 | 2.172 | -0.001 | -0.017 | -0.192 | 0.000 |
90 | A | 94 | ARG | 1 | 0.893 | 0.934 | 6.180 | 2.413 | 2.413 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 95 | GLY | 0 | 0.008 | 0.014 | 8.415 | 0.414 | 0.414 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 96 | GLN | 0 | -0.021 | -0.025 | 5.150 | -0.552 | -0.552 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 97 | LEU | 0 | -0.020 | 0.010 | 8.905 | 0.320 | 0.320 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 98 | THR | 0 | -0.017 | -0.023 | 8.540 | -0.215 | -0.215 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 99 | VAL | 0 | 0.035 | 0.021 | 10.106 | 0.108 | 0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 100 | ASN | 0 | 0.050 | -0.005 | 10.387 | 0.116 | 0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 101 | TYR | 0 | 0.021 | -0.012 | 12.336 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 102 | VAL | 0 | -0.029 | -0.007 | 14.886 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 103 | ASN | 0 | 0.004 | 0.004 | 17.577 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 104 | SER | 0 | 0.112 | 0.059 | 20.773 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |