![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 6624Z
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 | 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 | 122 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -1042574.007098 |
---|---|
FMO2-HF: Nuclear repulsion | 992898.563375 |
FMO2-HF: Total energy | -49675.443723 |
FMO2-MP2: Total energy | -49820.249214 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F021757/ligand_interaction/ligand_F021757.png)
Ligand Interaction
![ligand interaction](./Kdata/F021757/ligand_interaction/ligand_interaction_F021757.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. |
-14.577 | -10.627 | 4.207 | -3.101 | -5.057 | 0.011 |
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 | 0.070 | 0.032 | 2.119 | 2.015 | 3.357 | 2.569 | -1.444 | -2.467 | 0.000 |
4 | A | 446 | ALA | 0 | -0.061 | -0.027 | 2.536 | -5.523 | -3.848 | 1.632 | -1.248 | -2.060 | 0.010 |
5 | A | 447 | ALA | 0 | -0.030 | -0.017 | 3.788 | -2.801 | -2.016 | 0.007 | -0.318 | -0.474 | 0.001 |
6 | A | 448 | ILE | 0 | -0.013 | -0.003 | 5.691 | -1.122 | -1.122 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 449 | ARG | 1 | 1.019 | 1.022 | 7.779 | -2.692 | -2.692 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 450 | HIS | 0 | 0.022 | 0.019 | 9.205 | -0.326 | -0.326 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 451 | ILE | 0 | -0.010 | -0.002 | 11.596 | -0.273 | -0.273 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 452 | THR | 0 | 0.031 | 0.006 | 9.654 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 453 | THR | 0 | -0.097 | -0.058 | 12.544 | -0.162 | -0.162 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 454 | GLY | 0 | 0.060 | 0.044 | 14.705 | -0.126 | -0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 455 | THR | 0 | -0.046 | -0.040 | 15.614 | -0.070 | -0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 456 | TYR | 0 | -0.001 | -0.010 | 15.146 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 457 | ILE | 0 | 0.018 | 0.020 | 19.049 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 458 | ALA | 0 | 0.045 | 0.032 | 21.012 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 459 | ARG | 1 | 0.837 | 0.885 | 22.181 | -0.578 | -0.578 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 460 | ILE | 0 | -0.037 | -0.017 | 22.754 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 461 | ARG | 1 | 0.776 | 0.839 | 23.614 | -0.433 | -0.433 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 462 | GLU | -1 | -0.939 | -0.964 | 25.333 | 0.454 | 0.454 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 463 | GLU | -1 | -0.821 | -0.876 | 27.142 | 0.434 | 0.434 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 464 | TYR | 0 | -0.027 | -0.016 | 24.391 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 465 | GLN | 0 | -0.039 | -0.044 | 29.346 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 466 | GLN | 0 | -0.068 | -0.033 | 31.371 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 467 | THR | 0 | -0.054 | -0.024 | 32.448 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 468 | GLU | -1 | -0.966 | -0.968 | 35.010 | 0.177 | 0.177 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 469 | VAL | 0 | -0.004 | 0.000 | 36.240 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 470 | LYS | 1 | 0.878 | 0.928 | 39.412 | -0.154 | -0.154 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 471 | PRO | 0 | 0.024 | -0.010 | 41.420 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 472 | GLU | -1 | -0.831 | -0.903 | 42.291 | 0.147 | 0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 473 | LEU | 0 | 0.012 | 0.006 | 36.068 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 474 | GLN | 0 | -0.026 | -0.024 | 37.277 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 475 | PRO | 0 | 0.020 | 0.010 | 37.276 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 476 | MET | 0 | -0.038 | -0.003 | 31.637 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 477 | LYS | 1 | 0.923 | 0.958 | 33.111 | -0.226 | -0.226 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 478 | GLU | -1 | -0.867 | -0.908 | 32.425 | 0.190 | 0.190 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 479 | ALA | 0 | -0.076 | -0.045 | 32.442 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 480 | LEU | 0 | 0.012 | 0.007 | 28.026 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 481 | ALA | 0 | 0.045 | 0.045 | 27.739 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 482 | ARG | 1 | 0.954 | 0.978 | 27.864 | -0.167 | -0.167 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 483 | MET | 0 | -0.038 | -0.007 | 25.637 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 484 | THR | 0 | 0.012 | -0.006 | 23.442 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 485 | ASP | -1 | -0.861 | -0.921 | 22.997 | 0.327 | 0.327 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 486 | ARG | 1 | 0.727 | 0.836 | 23.698 | -0.171 | -0.171 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 487 | ALA | 0 | 0.009 | -0.008 | 19.457 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 488 | GLU | -1 | -0.808 | -0.867 | 18.955 | 0.455 | 0.455 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 489 | ALA | 0 | 0.013 | 0.006 | 19.416 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 490 | LEU | 0 | -0.056 | -0.024 | 17.830 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 491 | ILE | 0 | 0.010 | 0.000 | 13.951 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 492 | ALA | 0 | 0.007 | 0.026 | 15.444 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 493 | PHE | 0 | -0.003 | -0.002 | 17.809 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 494 | VAL | 0 | -0.001 | 0.015 | 12.486 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 495 | THR | 0 | -0.046 | -0.049 | 11.660 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 496 | GLU | -1 | -0.945 | -0.972 | 13.896 | 0.229 | 0.229 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 497 | GLN | 0 | -0.073 | -0.049 | 15.626 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 498 | LYS | 1 | 0.851 | 0.931 | 13.462 | -0.194 | -0.194 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 499 | ASP | -1 | -0.804 | -0.897 | 12.486 | -0.455 | -0.455 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 500 | GLN | 0 | -0.060 | -0.063 | 5.044 | 0.614 | 0.614 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 501 | GLU | -1 | -0.885 | -0.943 | 7.816 | -1.669 | -1.669 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 502 | LEU | 0 | -0.013 | 0.007 | 9.697 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 503 | LEU | 0 | -0.043 | -0.027 | 7.596 | 0.106 | 0.106 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 504 | ASP | -1 | -0.808 | -0.915 | 4.126 | -2.598 | -2.450 | -0.001 | -0.091 | -0.056 | 0.000 |
63 | A | 505 | PHE | 0 | -0.057 | -0.017 | 7.053 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 506 | GLN | 0 | 0.031 | 0.010 | 10.568 | 0.114 | 0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 507 | ALA | 0 | 0.020 | 0.022 | 7.693 | 0.182 | 0.182 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 508 | ARG | 1 | 0.936 | 0.959 | 9.757 | 0.077 | 0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 509 | ARG | 1 | 0.973 | 0.990 | 11.512 | 0.174 | 0.174 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 510 | LEU | 0 | 0.044 | 0.031 | 11.632 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 511 | VAL | 0 | -0.010 | -0.001 | 10.770 | 0.063 | 0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 512 | GLU | -1 | -0.940 | -0.981 | 14.086 | 0.258 | 0.258 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 513 | MET | 0 | -0.033 | 0.011 | 16.903 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 514 | THR | 0 | 0.014 | 0.001 | 16.258 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 515 | ALA | 0 | -0.012 | -0.004 | 17.519 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 516 | HIS | 0 | 0.007 | 0.008 | 19.398 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 517 | ALA | 0 | 0.015 | 0.017 | 22.267 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 518 | VAL | 0 | 0.009 | 0.009 | 19.924 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 519 | PHE | 0 | -0.017 | -0.023 | 19.280 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 520 | GLY | 0 | 0.044 | 0.019 | 24.367 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 521 | HIS | 0 | 0.022 | -0.005 | 25.999 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 522 | LEU | 0 | -0.028 | -0.005 | 23.495 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 523 | LEU | 0 | -0.012 | -0.006 | 27.970 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 524 | MET | 0 | -0.009 | -0.001 | 30.497 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 525 | LEU | 0 | -0.014 | -0.013 | 29.164 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 526 | ALA | 0 | 0.030 | 0.019 | 32.095 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 527 | ALA | 0 | -0.040 | -0.025 | 33.841 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 528 | ASN | 0 | -0.022 | -0.024 | 35.942 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 529 | ASP | -1 | -0.961 | -0.963 | 35.252 | 0.238 | 0.238 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 530 | ASP | -1 | -0.883 | -0.920 | 38.177 | 0.153 | 0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 531 | ASP | -1 | -0.746 | -0.855 | 39.312 | 0.156 | 0.156 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 532 | SER | 0 | -0.067 | -0.052 | 41.329 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 533 | PHE | 0 | -0.072 | -0.035 | 36.176 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 534 | ARG | 1 | 0.789 | 0.873 | 36.827 | -0.143 | -0.143 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 535 | GLN | 0 | 0.013 | 0.006 | 37.462 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 536 | SER | 0 | 0.013 | -0.011 | 35.330 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 537 | ALA | 0 | 0.025 | 0.016 | 33.039 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 538 | GLU | -1 | -0.877 | -0.939 | 32.933 | 0.160 | 0.160 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 539 | VAL | 0 | -0.036 | -0.018 | 33.603 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 540 | TYR | 0 | -0.023 | -0.018 | 27.950 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 541 | LEU | 0 | 0.000 | 0.008 | 29.333 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 542 | ARG | 1 | 0.891 | 0.949 | 30.042 | -0.157 | -0.157 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 543 | TYR | 0 | -0.002 | 0.011 | 24.360 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 544 | GLY | 0 | 0.066 | 0.031 | 25.604 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 545 | GLN | 0 | 0.007 | -0.015 | 25.894 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 546 | ALA | 0 | 0.005 | 0.005 | 27.657 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 547 | GLU | -1 | -0.836 | -0.907 | 22.996 | 0.127 | 0.127 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 548 | GLN | 0 | -0.017 | -0.041 | 22.097 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 549 | GLU | -1 | -0.860 | -0.884 | 23.497 | 0.123 | 0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 550 | LYS | 1 | 0.797 | 0.878 | 24.016 | -0.131 | -0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 551 | ILE | 0 | -0.024 | -0.009 | 18.479 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 552 | ASP | -1 | -0.746 | -0.867 | 20.661 | 0.161 | 0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 553 | SER | 0 | -0.006 | -0.001 | 22.283 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 554 | TYR | 0 | -0.025 | -0.013 | 17.411 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 555 | VAL | 0 | -0.021 | -0.026 | 16.788 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 556 | ARG | 1 | 0.821 | 0.889 | 19.185 | -0.190 | -0.190 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 557 | ALA | 0 | -0.037 | -0.002 | 21.878 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 558 | PHE | 0 | -0.053 | -0.014 | 16.218 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | A | 559 | ARG | 1 | 0.863 | 0.920 | 20.284 | 0.197 | 0.197 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | A | 560 | PRO | 0 | 0.042 | 0.011 | 16.439 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
119 | A | 561 | GLU | -1 | -0.860 | -0.930 | 17.271 | -0.243 | -0.243 | 0.000 | 0.000 | 0.000 | 0.000 |
120 | A | 562 | GLU | -1 | -0.967 | -0.969 | 18.929 | -0.255 | -0.255 | 0.000 | 0.000 | 0.000 | 0.000 |
121 | A | 563 | LEU | 0 | -0.069 | -0.016 | 12.638 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
122 | A | 564 | THR | 0 | -0.021 | -0.008 | 13.603 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |