![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 2KZGR
Calculation Name: 1KPT-A-Xray315
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: 2021-09-06
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 | 100 |
LigandCharge | |
Software | ABINIT-MP - Open Ver.1 Rev. 15 / 20190524 |
Total energy (hartree)
FMO2-HF: Electronic energy | -746738.930679 |
---|---|
FMO2-HF: Nuclear repulsion | 705246.027296 |
FMO2-HF: Total energy | -41492.903383 |
FMO2-MP2: Total energy | -41604.980843 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F015787/ligand_interaction/ligand_F015787.png)
Ligand Interaction
![ligand interaction](./Kdata/F015787/ligand_interaction/ligand_interaction_F015787.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. |
-1.735 | 10.56 | 14.399 | -11.857 | -14.836 | -0.135 |
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 | 0.038 | 0.027 | 2.870 | -4.743 | -1.628 | 0.338 | -1.674 | -1.778 | -0.010 |
4 | A | 4 | ASN | 0 | -0.090 | -0.045 | 2.497 | 1.475 | 3.403 | 1.425 | -0.929 | -2.424 | -0.010 |
5 | A | 78 | CYS | 0 | -0.026 | -0.010 | 4.732 | 1.655 | 1.701 | 0.000 | -0.007 | -0.038 | 0.000 |
6 | A | 6 | ARG | 1 | 0.933 | 0.976 | 2.600 | 40.201 | 42.004 | 1.276 | -0.579 | -2.500 | -0.003 |
7 | A | 7 | GLY | 0 | 0.060 | 0.018 | 6.383 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | SER | 0 | -0.004 | 0.005 | 9.079 | 0.519 | 0.519 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | SER | 0 | 0.074 | 0.019 | 12.167 | -0.141 | -0.141 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | GLN | 0 | 0.021 | 0.019 | 14.600 | 0.837 | 0.837 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 81 | CYS | 0 | -0.071 | -0.031 | 10.604 | 1.059 | 1.059 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | GLY | 0 | -0.020 | -0.012 | 15.196 | 0.383 | 0.383 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | LEU | 0 | -0.004 | 0.007 | 16.663 | 0.538 | 0.538 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | SER | 0 | -0.009 | 0.015 | 18.679 | 0.614 | 0.614 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | GLY | 0 | 0.053 | 0.035 | 20.273 | -0.256 | -0.256 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | GLY | 0 | 0.026 | 0.002 | 22.362 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | ASN | 0 | 0.031 | 0.014 | 18.444 | -0.949 | -0.949 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | LEU | 0 | 0.021 | -0.003 | 18.176 | 0.233 | 0.233 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | MET | 0 | 0.037 | 0.038 | 12.040 | 0.301 | 0.301 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | VAL | 0 | 0.004 | 0.000 | 17.083 | -0.048 | -0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | ARG | 1 | 0.973 | 0.992 | 20.059 | 11.657 | 11.657 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | ILE | 0 | 0.008 | 0.002 | 16.878 | 0.317 | 0.317 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | ARG | 1 | 0.928 | 0.966 | 18.059 | 14.011 | 14.011 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | ASP | -1 | -0.882 | -0.952 | 19.436 | -12.073 | -12.073 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | GLN | 0 | -0.059 | -0.034 | 22.343 | 0.185 | 0.185 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | ALA | 0 | -0.009 | -0.007 | 19.747 | 0.263 | 0.263 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 67 | CYS | 0 | -0.088 | -0.035 | 16.573 | -0.510 | -0.510 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | GLY | 0 | 0.042 | 0.041 | 23.260 | 0.382 | 0.382 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | ASN | 0 | -0.031 | -0.017 | 25.203 | 0.581 | 0.581 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | GLN | 0 | -0.028 | -0.036 | 23.443 | -0.477 | -0.477 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | GLY | 0 | 0.025 | 0.028 | 25.119 | -0.180 | -0.180 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | GLN | 0 | -0.028 | -0.001 | 23.407 | 0.252 | 0.252 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | THR | 0 | 0.000 | -0.012 | 22.264 | -0.401 | -0.401 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | TRP | 0 | -0.050 | -0.034 | 16.980 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 60 | CYS | 0 | 0.021 | 0.016 | 17.468 | -0.966 | -0.966 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | PRO | 0 | -0.006 | -0.018 | 15.950 | -0.245 | -0.245 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | GLY | 0 | -0.016 | -0.005 | 15.885 | 0.793 | 0.793 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | GLU | -1 | -0.841 | -0.907 | 17.346 | -12.766 | -12.766 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | ARG | 1 | 0.830 | 0.907 | 17.655 | 12.792 | 12.792 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | ARG | 1 | 0.849 | 0.922 | 19.576 | 13.388 | 13.388 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | ALA | 0 | 0.020 | 0.035 | 19.199 | 0.469 | 0.469 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | LYS | 1 | 0.872 | 0.922 | 19.184 | 11.156 | 11.156 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | VAL | 0 | -0.011 | 0.007 | 20.509 | 0.645 | 0.645 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 105 | CYS | -1 | -0.891 | -0.937 | 21.549 | -12.396 | -12.396 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | GLY | 0 | 0.053 | 0.039 | 24.027 | 0.208 | 0.208 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | THR | 0 | -0.030 | -0.028 | 25.329 | 0.284 | 0.284 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | GLY | 0 | 0.024 | 0.012 | 26.473 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | ASN | 0 | -0.052 | -0.012 | 21.129 | -0.284 | -0.284 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | SER | 0 | 0.021 | 0.002 | 20.324 | 0.132 | 0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | ILE | 0 | 0.029 | 0.040 | 15.387 | -0.625 | -0.625 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 51 | SER | 0 | -0.015 | -0.025 | 16.186 | 0.813 | 0.813 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 52 | ALA | 0 | 0.018 | 0.016 | 14.483 | -1.112 | -1.112 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 53 | TYR | 0 | -0.018 | -0.016 | 11.803 | 1.193 | 1.193 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | VAL | 0 | 0.054 | 0.047 | 12.941 | -1.697 | -1.697 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | GLN | 0 | 0.013 | -0.001 | 9.028 | 0.377 | 0.377 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | SER | 0 | 0.010 | 0.004 | 8.422 | -1.790 | -1.790 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | THR | 0 | 0.029 | 0.018 | 10.688 | -0.517 | -0.517 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | ASN | 0 | 0.023 | 0.016 | 13.788 | 0.611 | 0.611 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | ASN | 0 | -0.048 | -0.022 | 15.953 | 1.809 | 1.809 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 61 | ILE | 0 | -0.005 | 0.003 | 15.212 | -0.281 | -0.281 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 62 | SER | 0 | 0.026 | 0.009 | 19.050 | 0.823 | 0.823 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 63 | GLY | 0 | 0.083 | 0.025 | 20.061 | -0.698 | -0.698 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 64 | THR | 0 | 0.010 | 0.005 | 21.090 | -0.194 | -0.194 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 65 | GLU | -1 | -0.878 | -0.941 | 17.246 | -16.941 | -16.941 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 66 | ALA | 0 | 0.021 | 0.012 | 16.240 | -1.109 | -1.109 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 68 | ARG | 1 | 0.986 | 0.997 | 13.990 | 19.911 | 19.911 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 69 | HIS | 0 | -0.058 | -0.039 | 11.723 | 0.325 | 0.325 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 70 | LEU | 0 | 0.017 | 0.000 | 12.966 | -0.857 | -0.857 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 71 | THR | 0 | -0.027 | -0.018 | 14.986 | 0.511 | 0.511 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 72 | ASN | 0 | -0.059 | -0.027 | 11.917 | 1.673 | 1.673 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 73 | LEU | 0 | 0.000 | -0.003 | 8.652 | -0.428 | -0.428 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 74 | VAL | 0 | -0.051 | -0.017 | 12.259 | 0.310 | 0.310 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 75 | ASN | 0 | -0.029 | -0.032 | 15.183 | 0.828 | 0.828 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 76 | HIS | 0 | -0.008 | 0.005 | 7.252 | 0.853 | 0.853 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 77 | GLY | 0 | 0.020 | 0.019 | 11.889 | -0.238 | -0.238 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 79 | ARG | 1 | 0.875 | 0.926 | 12.174 | 14.834 | 14.834 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 80 | VAL | 0 | -0.050 | -0.032 | 14.002 | 0.741 | 0.741 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 82 | GLY | 0 | 0.048 | 0.026 | 7.669 | -0.105 | -0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 83 | SER | 0 | -0.024 | -0.015 | 5.353 | 2.079 | 2.079 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 84 | ASP | -1 | -0.763 | -0.890 | 6.208 | -32.257 | -32.257 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 85 | PRO | 0 | -0.031 | -0.007 | 5.302 | 0.921 | 0.921 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 86 | LEU | 0 | -0.008 | -0.001 | 7.652 | 2.686 | 2.686 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 87 | TYR | 0 | -0.001 | 0.006 | 10.345 | 2.182 | 2.182 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 88 | ALA | 0 | 0.055 | 0.013 | 9.818 | -3.124 | -3.124 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 89 | GLY | 0 | 0.010 | 0.014 | 8.439 | -0.295 | -0.295 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 90 | ASN | 0 | -0.053 | -0.028 | 6.879 | -2.079 | -2.079 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 91 | ASP | -1 | -0.788 | -0.886 | 1.867 | -124.716 | -121.078 | 9.678 | -7.795 | -5.522 | -0.105 |
88 | A | 92 | VAL | 0 | 0.012 | -0.014 | 2.258 | 11.419 | 12.978 | 1.682 | -0.857 | -2.384 | -0.007 |
89 | A | 93 | SER | 0 | -0.061 | -0.026 | 4.393 | 12.170 | 12.376 | 0.000 | -0.016 | -0.190 | 0.000 |
90 | A | 94 | ARG | 1 | 0.917 | 0.943 | 6.141 | 39.287 | 39.287 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 95 | GLY | 0 | 0.022 | 0.022 | 8.328 | 3.712 | 3.712 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 96 | GLN | 0 | -0.028 | -0.033 | 5.583 | -4.859 | -4.859 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 97 | LEU | 0 | -0.004 | 0.017 | 8.930 | 2.676 | 2.676 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 98 | THR | 0 | -0.015 | -0.019 | 8.472 | -2.496 | -2.496 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 99 | VAL | 0 | 0.044 | 0.025 | 10.222 | 2.101 | 2.101 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 100 | ASN | 0 | 0.058 | 0.003 | 10.575 | -0.490 | -0.490 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 101 | TYR | 0 | 0.017 | -0.007 | 12.403 | 0.928 | 0.928 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 102 | VAL | 0 | -0.032 | -0.009 | 14.946 | -0.604 | -0.604 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 103 | ASN | 0 | -0.018 | -0.021 | 17.644 | 0.791 | 0.791 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 104 | SER | 0 | 0.065 | 0.036 | 20.830 | 0.437 | 0.437 | 0.000 | 0.000 | 0.000 | 0.000 |