FMODB ID: 59L7Z
Calculation Name: 2NO2-A-Xray316
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2NO2
Chain ID: A
UniProt ID: O00291
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 | 103 |
LigandResidueName | |
LigandFragmentNumber | 0 |
LigandCharge | |
Software | ABINIT-MP - Open Ver.1 Rev. 15 / 20190524 |
Total energy (hartree)
FMO2-HF: Electronic energy | -484344.646777 |
---|---|
FMO2-HF: Nuclear repulsion | 443798.22634 |
FMO2-HF: Total energy | -40546.420437 |
FMO2-MP2: Total energy | -40665.901343 |
3D Structure
Ligand structure
Ligand Interaction
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:480:GLY )
Summations of interaction energy for
fragment #1(A:480:GLY )
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. |
-3.016 | -0.598 | 1.29 | -1.532 | -2.173 | 0.003 |
Interaction energy analysis for fragmet #1(A:480:GLY )
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 | 482 | HIS | 0 | 0.040 | 0.021 | 3.325 | 0.287 | 1.342 | 0.022 | -0.469 | -0.608 | 0.001 |
4 | A | 483 | ALA | 0 | 0.039 | 0.029 | 2.249 | -0.922 | -0.305 | 1.263 | -0.749 | -1.130 | 0.003 |
5 | A | 484 | ASP | -1 | -0.887 | -0.955 | 3.388 | -6.616 | -5.968 | 0.005 | -0.306 | -0.346 | -0.001 |
6 | A | 485 | LEU | 0 | -0.026 | -0.020 | 5.186 | 0.711 | 0.809 | 0.000 | -0.008 | -0.089 | 0.000 |
7 | A | 486 | LEU | 0 | 0.029 | 0.022 | 7.533 | 0.198 | 0.198 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 487 | ARG | 1 | 0.919 | 0.968 | 5.628 | 1.768 | 1.768 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 488 | LYS | 1 | 0.924 | 0.948 | 8.625 | 1.542 | 1.542 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 489 | ASN | 0 | 0.022 | -0.001 | 10.757 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 490 | ALA | 0 | -0.029 | -0.011 | 12.258 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 491 | GLU | -1 | -0.909 | -0.950 | 13.444 | -0.246 | -0.246 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 492 | VAL | 0 | 0.025 | 0.020 | 15.192 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 493 | THR | 0 | -0.025 | -0.008 | 17.002 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 494 | LYS | 1 | 0.961 | 0.975 | 18.215 | 0.104 | 0.104 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 495 | GLN | 0 | 0.041 | 0.008 | 18.069 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 496 | VAL | 0 | -0.007 | 0.013 | 21.214 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 497 | SER | 0 | -0.083 | -0.044 | 22.888 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 498 | MET | 0 | 0.009 | -0.005 | 23.098 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 499 | ALA | 0 | 0.012 | 0.017 | 25.393 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 500 | ARG | 1 | 0.955 | 0.974 | 25.518 | 0.079 | 0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 501 | GLN | 0 | -0.050 | -0.017 | 28.626 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 502 | ALA | 0 | 0.036 | 0.015 | 29.755 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 503 | GLN | 0 | -0.035 | 0.001 | 31.440 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 504 | VAL | 0 | 0.009 | 0.004 | 33.316 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 505 | ASP | -1 | -0.902 | -0.961 | 33.195 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 506 | LEU | 0 | 0.006 | -0.001 | 33.837 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 507 | GLU | -1 | -0.962 | -0.993 | 36.433 | -0.055 | -0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 508 | ARG | 1 | 0.895 | 0.960 | 38.733 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 509 | GLU | -1 | -0.919 | -0.969 | 38.846 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 510 | LYS | 1 | 0.917 | 0.949 | 41.298 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 511 | LYS | 1 | 0.958 | 0.989 | 43.126 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 512 | GLU | -1 | -0.917 | -0.954 | 44.157 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 513 | LEU | 0 | -0.021 | 0.002 | 43.554 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 514 | GLU | -1 | -0.868 | -0.941 | 46.871 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 515 | ASP | -1 | -0.892 | -0.940 | 49.109 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 516 | SER | 0 | -0.093 | -0.095 | 49.660 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 517 | LEU | 0 | -0.026 | -0.019 | 49.561 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 518 | GLU | -1 | -0.931 | -0.960 | 52.806 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 519 | ARG | 1 | 0.925 | 0.990 | 51.850 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 520 | ILE | 0 | -0.063 | -0.028 | 54.579 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 521 | SER | 0 | -0.020 | 0.005 | 57.020 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 522 | ASP | -1 | -0.824 | -0.897 | 58.709 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 523 | GLN | 0 | -0.081 | -0.070 | 60.289 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 524 | GLY | 0 | 0.036 | 0.014 | 61.202 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 525 | GLN | 0 | 0.004 | -0.001 | 62.702 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 526 | ARG | 1 | 0.868 | 0.930 | 63.124 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 527 | LYS | 1 | 0.970 | 0.987 | 64.363 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 528 | THR | 0 | -0.033 | -0.008 | 66.085 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 529 | GLN | 0 | -0.009 | -0.008 | 68.734 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 530 | GLU | -1 | -0.850 | -0.921 | 69.376 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 531 | GLN | 0 | 0.002 | 0.010 | 71.367 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 532 | LEU | 0 | -0.061 | -0.035 | 72.077 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 533 | GLU | -1 | -0.909 | -0.958 | 74.919 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 534 | VAL | 0 | -0.026 | -0.007 | 74.975 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 535 | LEU | 0 | -0.049 | -0.032 | 77.028 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 536 | GLU | -1 | -0.903 | -0.956 | 78.988 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 537 | SER | 0 | -0.012 | -0.008 | 80.853 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 538 | LEU | 0 | 0.003 | 0.015 | 80.332 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 539 | LYS | 1 | 0.897 | 0.956 | 81.075 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 540 | GLN | 0 | 0.007 | 0.005 | 85.248 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 541 | GLU | -1 | -0.919 | -0.970 | 83.998 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 542 | LEU | 0 | -0.019 | 0.000 | 87.427 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 543 | ALA | 0 | 0.002 | -0.013 | 89.234 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 544 | THR | 0 | -0.066 | -0.042 | 90.767 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 545 | SER | 0 | 0.072 | 0.043 | 91.732 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 546 | GLN | 0 | -0.037 | -0.014 | 92.844 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 547 | ARG | 1 | 0.909 | 0.968 | 91.959 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 548 | GLU | -1 | -0.889 | -0.961 | 94.760 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 549 | LEU | 0 | 0.002 | -0.009 | 96.014 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 550 | GLN | 0 | -0.039 | -0.011 | 99.142 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 551 | VAL | 0 | -0.012 | -0.003 | 101.304 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 552 | LEU | 0 | 0.001 | -0.004 | 101.042 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 553 | GLN | 0 | -0.006 | -0.005 | 102.526 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 554 | GLY | 0 | 0.028 | 0.029 | 105.126 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 555 | SER | 0 | -0.022 | -0.016 | 106.762 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 556 | LEU | 0 | -0.019 | -0.014 | 106.529 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 557 | GLU | -1 | -0.934 | -0.948 | 109.150 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 558 | THR | 0 | -0.017 | -0.013 | 111.258 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 559 | SER | 0 | -0.009 | -0.012 | 111.881 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 560 | ALA | 0 | 0.002 | 0.002 | 112.988 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 561 | GLN | 0 | 0.020 | 0.012 | 114.689 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 562 | SER | 0 | -0.091 | -0.053 | 116.693 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 563 | GLU | -1 | -0.949 | -0.983 | 114.967 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 564 | ALA | 0 | -0.023 | -0.005 | 118.895 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 565 | ASN | 0 | 0.005 | -0.009 | 121.051 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 566 | TRP | 0 | 0.017 | 0.027 | 120.034 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 567 | ALA | 0 | 0.016 | 0.025 | 123.190 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 568 | ALA | 0 | 0.000 | -0.006 | 124.909 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 569 | GLU | -1 | -0.942 | -0.982 | 126.250 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 570 | PHE | 0 | -0.089 | -0.051 | 126.942 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 571 | ALA | 0 | -0.027 | -0.013 | 128.878 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 572 | GLU | -1 | -0.922 | -0.960 | 130.841 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 573 | LEU | 0 | 0.020 | 0.009 | 131.979 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 574 | GLU | -1 | -0.985 | -0.978 | 131.736 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 575 | LYS | 1 | 0.984 | 0.994 | 134.297 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 576 | GLU | -1 | -0.959 | -0.979 | 136.940 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 577 | ARG | 1 | 0.862 | 0.925 | 134.039 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 578 | ASP | -1 | -0.889 | -0.971 | 136.966 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 579 | SER | 0 | -0.106 | -0.043 | 139.778 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 580 | LEU | 0 | -0.085 | -0.037 | 141.137 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 581 | VAL | 0 | -0.077 | -0.017 | 140.538 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 1 | NME | 0 | -0.009 | -0.004 | 143.462 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |