![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: ZY8ZN
Calculation Name: 2OKU-A-Xray372
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: 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 | OptAll |
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 | 122 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -1046874.18565 |
---|---|
FMO2-HF: Nuclear repulsion | 997198.568893 |
FMO2-HF: Total energy | -49675.616757 |
FMO2-MP2: Total energy | -49820.40615 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F021756/ligand_interaction/ligand_F021756.png)
Ligand Interaction
![ligand interaction](./Kdata/F021756/ligand_interaction/ligand_interaction_F021756.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. |
-15.393 | -9.883 | 2.61 | -3.443 | -4.677 | -0.002 |
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 | 0.030 | 0.001 | 2.186 | 1.935 | 3.399 | 1.884 | -1.281 | -2.067 | 0.001 |
4 | A | 446 | ALA | 0 | -0.053 | -0.024 | 2.654 | -3.291 | -1.643 | 0.677 | -0.783 | -1.542 | 0.006 |
5 | A | 447 | ALA | 0 | -0.022 | -0.014 | 4.010 | -2.252 | -1.704 | 0.001 | -0.194 | -0.355 | 0.001 |
6 | A | 448 | ILE | 0 | -0.006 | 0.009 | 5.970 | -0.986 | -0.986 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 449 | ARG | 1 | 1.007 | 1.017 | 7.763 | -2.911 | -2.911 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 450 | HIS | 0 | 0.027 | 0.025 | 9.310 | -0.260 | -0.260 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 451 | ILE | 0 | 0.006 | 0.018 | 11.810 | -0.263 | -0.263 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 452 | THR | 0 | 0.038 | 0.007 | 9.389 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 453 | THR | 0 | -0.105 | -0.061 | 12.444 | -0.136 | -0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 454 | GLY | 0 | 0.051 | 0.033 | 14.840 | -0.095 | -0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 455 | THR | 0 | -0.063 | -0.057 | 15.704 | -0.076 | -0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 456 | TYR | 0 | 0.005 | -0.008 | 15.216 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 457 | ILE | 0 | 0.002 | 0.011 | 19.041 | -0.058 | -0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 458 | ALA | 0 | 0.032 | 0.028 | 21.183 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 459 | ARG | 1 | 0.838 | 0.882 | 22.325 | -0.559 | -0.559 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 460 | ILE | 0 | -0.030 | -0.016 | 22.789 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 461 | ARG | 1 | 0.779 | 0.842 | 23.718 | -0.410 | -0.410 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 462 | GLU | -1 | -0.925 | -0.964 | 25.330 | 0.467 | 0.467 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 463 | GLU | -1 | -0.824 | -0.872 | 27.329 | 0.421 | 0.421 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 464 | TYR | 0 | -0.029 | -0.016 | 24.385 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 465 | GLN | 0 | -0.019 | -0.034 | 29.450 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 466 | GLN | 0 | -0.062 | -0.030 | 31.550 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 467 | THR | 0 | -0.062 | -0.031 | 32.430 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 468 | GLU | -1 | -0.944 | -0.955 | 35.029 | 0.164 | 0.164 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 469 | VAL | 0 | -0.001 | -0.003 | 36.179 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 470 | LYS | 1 | 0.902 | 0.949 | 39.425 | -0.136 | -0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 471 | PRO | 0 | 0.009 | -0.010 | 41.462 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 472 | GLU | -1 | -0.828 | -0.908 | 42.374 | 0.126 | 0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 473 | LEU | 0 | -0.011 | -0.006 | 35.911 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 474 | GLN | 0 | -0.029 | -0.020 | 37.322 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 475 | PRO | 0 | 0.037 | 0.010 | 37.046 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 476 | MET | 0 | -0.062 | -0.011 | 31.608 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 477 | LYS | 1 | 0.916 | 0.952 | 32.975 | -0.212 | -0.212 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 478 | GLU | -1 | -0.870 | -0.911 | 32.319 | 0.169 | 0.169 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 479 | ALA | 0 | -0.068 | -0.037 | 32.398 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 480 | LEU | 0 | 0.015 | 0.010 | 28.122 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 481 | ALA | 0 | 0.031 | 0.033 | 27.693 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 482 | ARG | 1 | 0.960 | 0.979 | 27.602 | -0.140 | -0.140 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 483 | MET | 0 | -0.029 | 0.002 | 25.437 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 484 | THR | 0 | 0.006 | -0.003 | 23.226 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 485 | ASP | -1 | -0.859 | -0.923 | 22.900 | 0.302 | 0.302 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 486 | ARG | 1 | 0.698 | 0.807 | 23.606 | -0.120 | -0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 487 | ALA | 0 | 0.030 | 0.006 | 19.462 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 488 | GLU | -1 | -0.807 | -0.873 | 18.880 | 0.434 | 0.434 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 489 | ALA | 0 | 0.023 | 0.012 | 19.300 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 490 | LEU | 0 | -0.061 | -0.013 | 17.403 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 491 | ILE | 0 | 0.005 | -0.005 | 13.798 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 492 | ALA | 0 | 0.009 | 0.028 | 15.073 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 493 | PHE | 0 | 0.011 | 0.011 | 17.113 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 494 | VAL | 0 | 0.008 | 0.018 | 12.046 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 495 | THR | 0 | -0.036 | -0.040 | 11.294 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 496 | GLU | -1 | -0.921 | -0.965 | 13.570 | 0.241 | 0.241 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 497 | GLN | 0 | -0.055 | -0.038 | 15.241 | -0.071 | -0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 498 | LYS | 1 | 0.813 | 0.902 | 12.909 | -0.235 | -0.235 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 499 | ASP | -1 | -0.805 | -0.889 | 11.946 | -0.504 | -0.504 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 500 | GLN | 0 | -0.013 | -0.037 | 4.825 | 0.603 | 0.603 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 501 | GLU | -1 | -0.852 | -0.901 | 7.399 | -1.813 | -1.813 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 502 | LEU | 0 | -0.010 | -0.008 | 9.349 | -0.092 | -0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 503 | LEU | 0 | -0.027 | -0.010 | 7.145 | 0.090 | 0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 504 | ASP | -1 | -0.806 | -0.911 | 3.179 | -6.256 | -4.406 | 0.048 | -1.185 | -0.713 | -0.010 |
63 | A | 505 | PHE | 0 | -0.024 | -0.001 | 6.347 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 506 | GLN | 0 | 0.048 | 0.017 | 9.920 | 0.110 | 0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 507 | ALA | 0 | 0.002 | 0.012 | 7.377 | 0.188 | 0.188 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 508 | ARG | 1 | 0.936 | 0.959 | 9.463 | 0.389 | 0.389 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 509 | ARG | 1 | 0.934 | 0.980 | 11.315 | 0.409 | 0.409 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 510 | LEU | 0 | 0.055 | 0.033 | 11.372 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 511 | VAL | 0 | -0.028 | -0.001 | 10.908 | 0.086 | 0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 512 | GLU | -1 | -0.919 | -0.972 | 14.159 | 0.074 | 0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 513 | MET | 0 | -0.034 | 0.014 | 16.868 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 514 | THR | 0 | 0.007 | -0.003 | 16.286 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 515 | ALA | 0 | -0.024 | -0.011 | 17.463 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 516 | HIS | 0 | 0.010 | 0.005 | 19.384 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 517 | ALA | 0 | 0.021 | 0.024 | 22.302 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 518 | VAL | 0 | -0.003 | 0.003 | 20.083 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 519 | PHE | 0 | -0.011 | -0.024 | 19.208 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 520 | GLY | 0 | 0.045 | 0.022 | 24.530 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 521 | HIS | 0 | 0.033 | 0.002 | 26.101 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 522 | LEU | 0 | -0.028 | -0.007 | 23.933 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 523 | LEU | 0 | -0.017 | -0.012 | 28.219 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 524 | MET | 0 | -0.015 | -0.006 | 30.589 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 525 | LEU | 0 | -0.018 | -0.010 | 29.453 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 526 | ALA | 0 | 0.047 | 0.026 | 32.503 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 527 | ALA | 0 | -0.042 | -0.023 | 34.316 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 528 | ASN | 0 | -0.024 | -0.026 | 36.212 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 529 | ASP | -1 | -0.962 | -0.964 | 35.613 | 0.212 | 0.212 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 530 | ASP | -1 | -0.868 | -0.920 | 38.610 | 0.126 | 0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 531 | ASP | -1 | -0.762 | -0.850 | 39.351 | 0.132 | 0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 532 | SER | 0 | -0.071 | -0.053 | 41.056 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 533 | PHE | 0 | -0.050 | -0.022 | 35.901 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 534 | ARG | 1 | 0.791 | 0.862 | 36.609 | -0.122 | -0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 535 | GLN | 0 | 0.003 | 0.005 | 37.051 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 536 | SER | 0 | 0.012 | -0.010 | 35.131 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 537 | ALA | 0 | 0.032 | 0.017 | 32.693 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 538 | GLU | -1 | -0.832 | -0.919 | 32.586 | 0.130 | 0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 539 | VAL | 0 | -0.042 | -0.013 | 33.394 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 540 | TYR | 0 | -0.015 | -0.014 | 27.697 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 541 | LEU | 0 | -0.012 | 0.012 | 29.052 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 542 | ARG | 1 | 0.844 | 0.916 | 30.000 | -0.126 | -0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 543 | TYR | 0 | -0.008 | 0.004 | 24.092 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 544 | GLY | 0 | 0.059 | 0.024 | 25.585 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 545 | GLN | 0 | 0.027 | -0.010 | 25.825 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 546 | ALA | 0 | 0.008 | 0.012 | 27.571 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 547 | GLU | -1 | -0.838 | -0.909 | 22.982 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 548 | GLN | 0 | -0.020 | -0.045 | 22.023 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 549 | GLU | -1 | -0.839 | -0.866 | 23.284 | 0.074 | 0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 550 | LYS | 1 | 0.789 | 0.873 | 23.824 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 551 | ILE | 0 | -0.009 | -0.002 | 18.193 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 552 | ASP | -1 | -0.740 | -0.855 | 20.045 | 0.113 | 0.113 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 553 | SER | 0 | -0.001 | 0.005 | 21.757 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 554 | TYR | 0 | -0.022 | -0.014 | 16.962 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 555 | VAL | 0 | -0.038 | -0.035 | 16.151 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 556 | ARG | 1 | 0.767 | 0.847 | 18.548 | -0.148 | -0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 557 | ALA | 0 | -0.032 | -0.004 | 21.210 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 558 | PHE | 0 | -0.061 | -0.029 | 15.637 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | A | 559 | ARG | 1 | 0.812 | 0.890 | 19.182 | 0.260 | 0.260 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | A | 560 | PRO | 0 | 0.021 | 0.004 | 15.878 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
119 | A | 561 | GLU | -1 | -0.837 | -0.920 | 16.572 | -0.297 | -0.297 | 0.000 | 0.000 | 0.000 | 0.000 |
120 | A | 562 | GLU | -1 | -0.906 | -0.923 | 18.389 | -0.304 | -0.304 | 0.000 | 0.000 | 0.000 | 0.000 |
121 | A | 563 | LEU | 0 | -0.086 | -0.033 | 12.191 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
122 | A | 564 | THR | 0 | -0.087 | -0.057 | 12.316 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |