FMODB ID: Q16MY
Calculation Name: 2NO2-A-Xray372
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: 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 | OptH |
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 | 102 |
LigandResidueName | |
LigandFragmentNumber | 0 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -483643.687642 |
---|---|
FMO2-HF: Nuclear repulsion | 443116.407726 |
FMO2-HF: Total energy | -40527.279916 |
FMO2-MP2: Total energy | -40646.656253 |
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. |
-2.929 | -0.501 | 1.301 | -1.531 | -2.197 | 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 | 0.039 | 0.020 | 3.326 | 0.238 | 1.298 | 0.019 | -0.463 | -0.616 | 0.001 |
4 | A | 483 | ALA | 0 | 0.039 | 0.029 | 2.236 | -0.907 | -0.293 | 1.280 | -0.752 | -1.142 | 0.003 |
5 | A | 484 | ASP | -1 | -0.888 | -0.955 | 3.378 | -6.558 | -5.904 | 0.003 | -0.309 | -0.348 | -0.001 |
6 | A | 485 | LEU | 0 | -0.026 | -0.020 | 5.179 | 0.705 | 0.805 | -0.001 | -0.007 | -0.091 | 0.000 |
7 | A | 486 | LEU | 0 | 0.029 | 0.022 | 7.519 | 0.199 | 0.199 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 487 | ARG | 1 | 0.917 | 0.968 | 5.628 | 1.796 | 1.796 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 488 | LYS | 1 | 0.925 | 0.949 | 8.623 | 1.586 | 1.586 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 489 | ASN | 0 | 0.022 | -0.001 | 10.750 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 490 | ALA | 0 | -0.030 | -0.012 | 12.247 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 491 | GLU | -1 | -0.909 | -0.950 | 13.435 | -0.251 | -0.251 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 492 | VAL | 0 | 0.025 | 0.020 | 15.184 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 493 | THR | 0 | -0.022 | -0.007 | 16.992 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 494 | LYS | 1 | 0.956 | 0.974 | 18.207 | 0.109 | 0.109 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 495 | GLN | 0 | 0.043 | 0.009 | 18.064 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 496 | VAL | 0 | -0.005 | 0.013 | 21.206 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 497 | SER | 0 | -0.085 | -0.046 | 22.879 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 498 | MET | 0 | 0.010 | -0.004 | 23.093 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 499 | ALA | 0 | 0.012 | 0.018 | 25.386 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 500 | ARG | 1 | 0.955 | 0.973 | 25.507 | 0.083 | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 501 | GLN | 0 | -0.051 | -0.017 | 28.618 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 502 | ALA | 0 | 0.037 | 0.015 | 29.748 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 503 | GLN | 0 | -0.036 | 0.001 | 31.433 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 504 | VAL | 0 | 0.008 | 0.003 | 33.309 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 505 | ASP | -1 | -0.902 | -0.960 | 33.188 | -0.059 | -0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 506 | LEU | 0 | 0.006 | 0.000 | 33.832 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 507 | GLU | -1 | -0.960 | -0.993 | 36.425 | -0.058 | -0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 508 | ARG | 1 | 0.893 | 0.960 | 38.725 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 509 | GLU | -1 | -0.918 | -0.968 | 38.842 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 510 | LYS | 1 | 0.918 | 0.949 | 41.292 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 511 | LYS | 1 | 0.957 | 0.988 | 43.120 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 512 | GLU | -1 | -0.917 | -0.954 | 44.151 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 513 | LEU | 0 | -0.021 | 0.002 | 43.551 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 514 | GLU | -1 | -0.867 | -0.941 | 46.864 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 515 | ASP | -1 | -0.892 | -0.940 | 49.103 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 516 | SER | 0 | -0.094 | -0.094 | 49.655 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 517 | LEU | 0 | -0.025 | -0.019 | 49.557 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 518 | GLU | -1 | -0.930 | -0.961 | 52.801 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 519 | ARG | 1 | 0.924 | 0.990 | 51.844 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 520 | ILE | 0 | -0.062 | -0.028 | 54.575 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 521 | SER | 0 | -0.020 | 0.005 | 57.015 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 522 | ASP | -1 | -0.825 | -0.898 | 58.704 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 523 | GLN | 0 | -0.080 | -0.069 | 60.284 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 524 | GLY | 0 | 0.035 | 0.013 | 61.197 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 525 | GLN | 0 | 0.005 | 0.000 | 62.698 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 526 | ARG | 1 | 0.867 | 0.930 | 63.117 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 527 | LYS | 1 | 0.971 | 0.987 | 64.360 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 528 | THR | 0 | -0.033 | -0.008 | 66.078 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 529 | GLN | 0 | -0.009 | -0.008 | 68.731 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 530 | GLU | -1 | -0.850 | -0.921 | 69.371 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 531 | GLN | 0 | 0.003 | 0.009 | 71.364 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 532 | LEU | 0 | -0.063 | -0.036 | 72.073 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 533 | GLU | -1 | -0.911 | -0.959 | 74.914 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 534 | VAL | 0 | -0.023 | -0.006 | 74.972 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 535 | LEU | 0 | -0.049 | -0.031 | 77.026 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 536 | GLU | -1 | -0.903 | -0.956 | 78.985 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 537 | SER | 0 | -0.014 | -0.008 | 80.849 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 538 | LEU | 0 | 0.005 | 0.015 | 80.329 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 539 | LYS | 1 | 0.899 | 0.957 | 81.072 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 540 | GLN | 0 | 0.005 | 0.004 | 85.244 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 541 | GLU | -1 | -0.920 | -0.971 | 83.994 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 542 | LEU | 0 | -0.019 | 0.001 | 87.424 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 543 | ALA | 0 | 0.001 | -0.014 | 89.231 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 544 | THR | 0 | -0.065 | -0.042 | 90.763 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 545 | SER | 0 | 0.072 | 0.043 | 91.729 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 546 | GLN | 0 | -0.037 | -0.015 | 92.841 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 547 | ARG | 1 | 0.910 | 0.968 | 91.955 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 548 | GLU | -1 | -0.889 | -0.960 | 94.756 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 549 | LEU | 0 | 0.002 | -0.009 | 96.012 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 550 | GLN | 0 | -0.039 | -0.011 | 99.139 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 551 | VAL | 0 | -0.013 | -0.003 | 101.301 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 552 | LEU | 0 | 0.002 | -0.004 | 101.039 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 553 | GLN | 0 | -0.006 | -0.005 | 102.524 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 554 | GLY | 0 | 0.028 | 0.029 | 105.124 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 555 | SER | 0 | -0.023 | -0.016 | 106.760 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 556 | LEU | 0 | -0.017 | -0.013 | 106.526 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 557 | GLU | -1 | -0.935 | -0.949 | 109.147 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 558 | THR | 0 | -0.018 | -0.013 | 111.256 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 559 | SER | 0 | -0.008 | -0.011 | 111.879 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 560 | ALA | 0 | 0.003 | 0.002 | 112.986 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 561 | GLN | 0 | 0.019 | 0.011 | 114.687 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 562 | SER | 0 | -0.091 | -0.053 | 116.690 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 563 | GLU | -1 | -0.947 | -0.982 | 114.965 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 564 | ALA | 0 | -0.023 | -0.005 | 118.892 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 565 | ASN | 0 | 0.006 | -0.008 | 121.048 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 566 | TRP | 0 | 0.015 | 0.027 | 120.030 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 567 | ALA | 0 | 0.017 | 0.025 | 123.187 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 568 | ALA | 0 | 0.000 | -0.006 | 124.907 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 569 | GLU | -1 | -0.942 | -0.982 | 126.247 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 570 | PHE | 0 | -0.089 | -0.051 | 126.939 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 571 | ALA | 0 | -0.028 | -0.013 | 128.875 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 572 | GLU | -1 | -0.922 | -0.959 | 130.839 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 573 | LEU | 0 | 0.020 | 0.009 | 131.977 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 574 | GLU | -1 | -0.984 | -0.978 | 131.734 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 575 | LYS | 1 | 0.984 | 0.994 | 134.294 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 576 | GLU | -1 | -0.959 | -0.979 | 136.938 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 577 | ARG | 1 | 0.866 | 0.926 | 134.037 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 578 | ASP | -1 | -0.888 | -0.970 | 136.964 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 579 | SER | 0 | -0.113 | -0.047 | 139.776 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 580 | LEU | 0 | -0.084 | -0.037 | 141.134 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 581 | VAL | 0 | -0.081 | -0.018 | 140.534 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |