![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 7J89K
Calculation Name: 2OKU-A-Xray316
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2OKU
Chain ID: A
UniProt ID: Q7MW70
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 | 123 |
LigandCharge | |
Software | ABINIT-MP - Open Ver.1 Rev. 15 / 20190524 |
Total energy (hartree)
FMO2-HF: Electronic energy | -1043197.708072 |
---|---|
FMO2-HF: Nuclear repulsion | 993503.573331 |
FMO2-HF: Total energy | -49694.134741 |
FMO2-MP2: Total energy | -49839.019478 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F015928/ligand_interaction/ligand_F015928.png)
Ligand Interaction
![ligand interaction](./Kdata/F015928/ligand_interaction/ligand_interaction_F015928.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:443:GLN )
Summations of interaction energy for
fragment #1(A:443:GLN )
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. |
-12.563 | -11.274 | 7.374 | -3.296 | -5.367 | 0.013 |
Interaction energy analysis for fragmet #1(A:443:GLN )
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 | 445 | VAL | 0 | 0.060 | 0.029 | 2.019 | 3.695 | 2.542 | 5.768 | -1.824 | -2.792 | 0.002 |
4 | A | 446 | ALA | 0 | -0.061 | -0.026 | 2.576 | -5.836 | -4.324 | 1.598 | -1.117 | -1.993 | 0.010 |
5 | A | 447 | ALA | 0 | -0.018 | -0.012 | 3.789 | -2.909 | -2.048 | 0.008 | -0.349 | -0.520 | 0.001 |
6 | A | 448 | ILE | 0 | -0.011 | -0.001 | 5.694 | -1.150 | -1.150 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 449 | ARG | 1 | 0.992 | 1.000 | 7.817 | -2.473 | -2.473 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 450 | HIS | 0 | 0.020 | 0.007 | 9.205 | -0.336 | -0.336 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 451 | ILE | 0 | -0.020 | -0.003 | 11.559 | -0.265 | -0.265 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 452 | THR | 0 | 0.003 | -0.008 | 9.902 | -0.213 | -0.213 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 453 | THR | 0 | -0.040 | -0.014 | 12.667 | -0.186 | -0.186 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 454 | GLY | 0 | 0.053 | 0.040 | 14.705 | -0.127 | -0.127 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 455 | THR | 0 | -0.038 | -0.035 | 15.669 | -0.074 | -0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 456 | TYR | 0 | 0.000 | -0.012 | 15.462 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 457 | ILE | 0 | 0.026 | 0.025 | 19.052 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 458 | ALA | 0 | 0.054 | 0.033 | 21.012 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 459 | ARG | 1 | 0.874 | 0.933 | 22.195 | -0.588 | -0.588 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 460 | ILE | 0 | -0.040 | -0.017 | 22.893 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 461 | ARG | 1 | 0.785 | 0.865 | 23.810 | -0.433 | -0.433 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 462 | GLU | -1 | -0.946 | -0.966 | 25.579 | 0.420 | 0.420 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 463 | GLU | -1 | -0.849 | -0.916 | 27.381 | 0.419 | 0.419 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 464 | TYR | 0 | -0.028 | -0.019 | 23.926 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 465 | GLN | 0 | -0.058 | -0.049 | 29.313 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 466 | GLN | 0 | -0.066 | -0.034 | 31.354 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 467 | THR | 0 | -0.045 | -0.022 | 32.452 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 468 | GLU | -1 | -0.969 | -0.965 | 35.020 | 0.180 | 0.180 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 469 | VAL | 0 | 0.005 | 0.005 | 36.274 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 470 | LYS | 1 | 0.972 | 0.984 | 39.419 | -0.164 | -0.164 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 471 | PRO | 0 | 0.024 | -0.012 | 41.420 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 472 | GLU | -1 | -0.927 | -0.959 | 42.013 | 0.160 | 0.160 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 473 | LEU | 0 | 0.036 | 0.018 | 36.306 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 474 | GLN | 0 | -0.048 | -0.021 | 37.260 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 475 | PRO | 0 | 0.022 | 0.009 | 37.333 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 476 | MET | 0 | -0.031 | 0.002 | 31.361 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 477 | LYS | 1 | 0.932 | 0.961 | 33.104 | -0.230 | -0.230 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 478 | GLU | -1 | -0.875 | -0.925 | 32.514 | 0.199 | 0.199 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 479 | ALA | 0 | -0.071 | -0.041 | 32.497 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 480 | LEU | 0 | 0.008 | 0.006 | 27.880 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 481 | ALA | 0 | 0.046 | 0.044 | 27.885 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 482 | ARG | 1 | 0.960 | 0.981 | 28.055 | -0.184 | -0.184 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 483 | MET | 0 | -0.044 | -0.012 | 25.607 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 484 | THR | 0 | 0.007 | -0.009 | 23.442 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 485 | ASP | -1 | -0.860 | -0.926 | 23.194 | 0.331 | 0.331 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 486 | ARG | 1 | 0.798 | 0.900 | 23.888 | -0.212 | -0.212 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 487 | ALA | 0 | 0.001 | -0.005 | 19.613 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 488 | GLU | -1 | -0.811 | -0.882 | 19.147 | 0.446 | 0.446 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 489 | ALA | 0 | 0.010 | 0.002 | 19.600 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 490 | LEU | 0 | -0.058 | -0.022 | 18.000 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 491 | ILE | 0 | 0.013 | 0.000 | 14.078 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 492 | ALA | 0 | 0.004 | 0.014 | 15.613 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 493 | PHE | 0 | -0.002 | -0.003 | 17.960 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 494 | VAL | 0 | 0.004 | 0.012 | 12.609 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 495 | THR | 0 | -0.062 | -0.042 | 11.992 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 496 | GLU | -1 | -0.941 | -0.975 | 14.039 | 0.209 | 0.209 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 497 | GLN | 0 | -0.064 | -0.039 | 15.623 | -0.089 | -0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 498 | LYS | 1 | 0.851 | 0.931 | 13.554 | -0.147 | -0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 499 | ASP | -1 | -0.806 | -0.895 | 12.565 | -0.438 | -0.438 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 500 | GLN | 0 | -0.055 | -0.060 | 5.425 | 0.504 | 0.504 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 501 | GLU | -1 | -0.869 | -0.934 | 7.877 | -1.649 | -1.649 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 502 | LEU | 0 | -0.011 | 0.009 | 9.723 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 503 | LEU | 0 | -0.053 | -0.032 | 7.582 | 0.145 | 0.145 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 504 | ASP | -1 | -0.855 | -0.934 | 4.851 | -1.399 | -1.330 | 0.000 | -0.006 | -0.062 | 0.000 |
63 | A | 505 | PHE | 0 | -0.064 | -0.022 | 7.159 | 0.098 | 0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 506 | GLN | 0 | 0.035 | 0.007 | 10.587 | 0.138 | 0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 507 | ALA | 0 | 0.010 | 0.018 | 7.812 | 0.179 | 0.179 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 508 | ARG | 1 | 0.948 | 0.957 | 9.752 | -0.255 | -0.255 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 509 | ARG | 1 | 0.985 | 1.000 | 11.196 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 510 | LEU | 0 | 0.044 | 0.028 | 11.701 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 511 | VAL | 0 | -0.010 | -0.004 | 10.458 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 512 | GLU | -1 | -0.940 | -0.978 | 13.784 | 0.386 | 0.386 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 513 | MET | 0 | -0.032 | 0.012 | 16.584 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 514 | THR | 0 | 0.020 | 0.009 | 16.511 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 515 | ALA | 0 | -0.009 | -0.004 | 17.238 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 516 | HIS | 0 | 0.024 | 0.011 | 19.091 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 517 | ALA | 0 | 0.006 | 0.017 | 22.069 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 518 | VAL | 0 | 0.005 | 0.002 | 19.886 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 519 | PHE | 0 | -0.014 | -0.021 | 19.311 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 520 | GLY | 0 | 0.045 | 0.020 | 24.075 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 521 | HIS | 0 | 0.016 | -0.006 | 26.114 | -0.048 | -0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 522 | LEU | 0 | -0.025 | -0.004 | 23.145 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 523 | LEU | 0 | -0.022 | -0.010 | 27.645 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 524 | MET | 0 | -0.011 | -0.003 | 30.181 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 525 | LEU | 0 | -0.015 | -0.017 | 28.956 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 526 | ALA | 0 | 0.035 | 0.024 | 31.778 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 527 | ALA | 0 | -0.042 | -0.024 | 33.493 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 528 | ASN | 0 | -0.038 | -0.035 | 35.622 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 529 | ASP | -1 | -0.953 | -0.956 | 35.122 | 0.250 | 0.250 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 530 | ASP | -1 | -0.897 | -0.941 | 37.835 | 0.170 | 0.170 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 531 | ASP | -1 | -0.817 | -0.914 | 38.942 | 0.172 | 0.172 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 532 | SER | 0 | -0.043 | -0.020 | 40.974 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 533 | PHE | 0 | -0.079 | -0.044 | 35.856 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 534 | ARG | 1 | 0.871 | 0.940 | 36.539 | -0.154 | -0.154 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 535 | GLN | 0 | 0.010 | 0.005 | 37.162 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 536 | SER | 0 | 0.008 | -0.012 | 34.902 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 537 | ALA | 0 | 0.020 | 0.011 | 32.744 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 538 | GLU | -1 | -0.880 | -0.942 | 32.628 | 0.185 | 0.185 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 539 | VAL | 0 | -0.029 | -0.016 | 33.327 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 540 | TYR | 0 | -0.011 | -0.012 | 27.835 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 541 | LEU | 0 | -0.003 | 0.005 | 29.023 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 542 | ARG | 1 | 0.866 | 0.935 | 29.723 | -0.182 | -0.182 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 543 | TYR | 0 | 0.011 | 0.013 | 24.238 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 544 | GLY | 0 | 0.063 | 0.029 | 25.288 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 545 | GLN | 0 | 0.014 | -0.006 | 25.573 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 546 | ALA | 0 | -0.008 | -0.002 | 27.445 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 547 | GLU | -1 | -0.859 | -0.924 | 22.696 | 0.208 | 0.208 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 548 | GLN | 0 | -0.025 | -0.045 | 22.246 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 549 | GLU | -1 | -0.883 | -0.922 | 23.672 | 0.150 | 0.150 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 550 | LYS | 1 | 0.829 | 0.903 | 23.838 | -0.188 | -0.188 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 551 | ILE | 0 | -0.032 | -0.010 | 18.403 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 552 | ASP | -1 | -0.812 | -0.921 | 20.819 | 0.192 | 0.192 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 553 | SER | 0 | -0.002 | 0.001 | 22.449 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 554 | TYR | 0 | -0.042 | -0.017 | 17.400 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 555 | VAL | 0 | -0.027 | -0.028 | 17.040 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 556 | ARG | 1 | 0.835 | 0.910 | 19.326 | -0.218 | -0.218 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 557 | ALA | 0 | -0.029 | 0.000 | 22.017 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 558 | PHE | 0 | -0.040 | -0.008 | 16.178 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | A | 559 | ARG | 1 | 0.971 | 0.986 | 20.383 | 0.153 | 0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | A | 560 | PRO | 0 | 0.059 | 0.024 | 16.626 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
119 | A | 561 | GLU | -1 | -0.931 | -0.979 | 17.306 | -0.229 | -0.229 | 0.000 | 0.000 | 0.000 | 0.000 |
120 | A | 562 | GLU | -1 | -1.019 | -0.999 | 18.815 | -0.213 | -0.213 | 0.000 | 0.000 | 0.000 | 0.000 |
121 | A | 563 | LEU | 0 | -0.071 | -0.018 | 12.650 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
122 | A | 564 | THR | 0 | -0.034 | -0.024 | 15.073 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
123 | A | 1 | NME | 0 | 0.005 | 0.010 | 13.152 | -0.093 | -0.093 | 0.000 | 0.000 | 0.000 | 0.000 |