FMODB ID: K3583
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 | 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 | 102 |
LigandResidueName | |
LigandFragmentNumber | 0 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -483457.449513 |
---|---|
FMO2-HF: Nuclear repulsion | 442929.072331 |
FMO2-HF: Total energy | -40528.377183 |
FMO2-MP2: Total energy | -40647.676462 |
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. |
-3.343 | -0.853 | 1.157 | -1.412 | -2.234 | 0.006 |
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 | 0.044 | 0.022 | 3.336 | 0.228 | 1.285 | 0.019 | -0.459 | -0.617 | 0.001 |
4 | A | 483 | ALA | 0 | 0.040 | 0.027 | 2.436 | -1.445 | -0.705 | 1.139 | -0.759 | -1.120 | 0.005 |
5 | A | 484 | ASP | -1 | -0.833 | -0.913 | 3.583 | -5.146 | -4.605 | 0.001 | -0.185 | -0.356 | 0.000 |
6 | A | 485 | LEU | 0 | -0.025 | -0.014 | 5.326 | 0.445 | 0.545 | -0.001 | -0.007 | -0.092 | 0.000 |
7 | A | 486 | LEU | 0 | 0.014 | 0.016 | 7.739 | 0.107 | 0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 487 | ARG | 1 | 0.852 | 0.916 | 4.734 | 1.413 | 1.465 | -0.001 | -0.002 | -0.049 | 0.000 |
9 | A | 488 | LYS | 1 | 0.942 | 0.959 | 8.951 | 1.115 | 1.115 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 489 | ASN | 0 | 0.016 | -0.001 | 10.892 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 490 | ALA | 0 | -0.014 | -0.005 | 12.429 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 491 | GLU | -1 | -0.856 | -0.913 | 13.586 | -0.162 | -0.162 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 492 | VAL | 0 | 0.008 | 0.005 | 15.336 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 493 | THR | 0 | -0.023 | -0.009 | 17.145 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 494 | LYS | 1 | 0.953 | 0.974 | 18.358 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 495 | GLN | 0 | -0.011 | -0.021 | 18.160 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 496 | VAL | 0 | -0.005 | 0.009 | 21.357 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 497 | SER | 0 | -0.045 | -0.027 | 23.040 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 498 | MET | 0 | -0.021 | -0.017 | 23.103 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 499 | ALA | 0 | 0.019 | 0.021 | 25.522 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 500 | ARG | 1 | 0.957 | 0.971 | 25.699 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 501 | GLN | 0 | -0.053 | -0.030 | 28.765 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 502 | ALA | 0 | 0.026 | 0.011 | 29.879 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 503 | GLN | 0 | -0.073 | -0.030 | 31.569 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 504 | VAL | 0 | 0.010 | 0.001 | 33.455 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 505 | ASP | -1 | -0.823 | -0.901 | 34.005 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 506 | LEU | 0 | 0.018 | 0.005 | 34.089 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 507 | GLU | -1 | -0.915 | -0.955 | 37.092 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 508 | ARG | 1 | 0.822 | 0.914 | 37.881 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 509 | GLU | -1 | -0.950 | -0.978 | 38.898 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 510 | LYS | 1 | 0.813 | 0.877 | 41.420 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 511 | LYS | 1 | 0.864 | 0.920 | 43.237 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 512 | GLU | -1 | -0.904 | -0.955 | 43.918 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 513 | LEU | 0 | -0.015 | 0.011 | 43.620 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 514 | GLU | -1 | -0.779 | -0.876 | 46.562 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 515 | ASP | -1 | -0.848 | -0.896 | 49.220 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 516 | SER | 0 | -0.055 | -0.064 | 49.781 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 517 | LEU | 0 | -0.034 | -0.018 | 49.403 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 518 | GLU | -1 | -0.935 | -0.965 | 52.903 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 519 | ARG | 1 | 0.929 | 0.975 | 51.776 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 520 | ILE | 0 | -0.060 | -0.027 | 54.561 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 521 | SER | 0 | 0.022 | 0.021 | 57.068 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 522 | ASP | -1 | -0.870 | -0.912 | 58.804 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 523 | GLN | 0 | -0.065 | -0.055 | 60.527 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 524 | GLY | 0 | 0.028 | 0.013 | 61.286 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 525 | GLN | 0 | -0.007 | -0.003 | 62.789 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 526 | ARG | 1 | 0.872 | 0.925 | 63.029 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 527 | LYS | 1 | 0.983 | 0.996 | 64.855 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 528 | THR | 0 | -0.049 | -0.025 | 66.140 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 529 | GLN | 0 | -0.018 | -0.008 | 68.818 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 530 | GLU | -1 | -0.833 | -0.915 | 69.091 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 531 | GLN | 0 | -0.005 | 0.002 | 71.499 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 532 | LEU | 0 | -0.039 | -0.021 | 72.348 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 533 | GLU | -1 | -0.914 | -0.961 | 74.841 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 534 | VAL | 0 | -0.032 | -0.014 | 75.637 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 535 | LEU | 0 | -0.047 | -0.029 | 76.917 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 536 | GLU | -1 | -0.829 | -0.901 | 79.063 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 537 | SER | 0 | -0.028 | -0.031 | 80.937 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 538 | LEU | 0 | 0.029 | 0.025 | 80.769 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 539 | LYS | 1 | 0.827 | 0.906 | 81.089 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 540 | GLN | 0 | -0.035 | -0.025 | 84.868 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 541 | GLU | -1 | -0.888 | -0.926 | 83.930 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 542 | LEU | 0 | -0.007 | 0.003 | 87.500 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 543 | ALA | 0 | -0.002 | -0.012 | 89.305 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 544 | THR | 0 | -0.059 | -0.044 | 90.813 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 545 | SER | 0 | 0.059 | 0.047 | 91.804 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 546 | GLN | 0 | -0.036 | -0.018 | 92.950 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 547 | ARG | 1 | 0.906 | 0.959 | 92.453 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 548 | GLU | -1 | -0.891 | -0.960 | 94.669 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 549 | LEU | 0 | 0.000 | -0.009 | 95.703 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 550 | GLN | 0 | -0.026 | -0.008 | 99.210 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 551 | VAL | 0 | -0.007 | -0.004 | 101.377 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 552 | LEU | 0 | 0.004 | 0.002 | 100.578 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 553 | GLN | 0 | -0.016 | -0.006 | 102.144 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 554 | GLY | 0 | 0.039 | 0.032 | 105.191 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 555 | SER | 0 | -0.032 | -0.022 | 106.595 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 556 | LEU | 0 | -0.018 | -0.008 | 106.947 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 557 | GLU | -1 | -0.922 | -0.949 | 109.215 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 558 | THR | 0 | -0.040 | -0.027 | 111.322 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 559 | SER | 0 | -0.003 | -0.004 | 111.986 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 560 | ALA | 0 | 0.010 | 0.007 | 113.001 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 561 | GLN | 0 | -0.025 | -0.017 | 114.751 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 562 | SER | 0 | -0.045 | -0.032 | 116.761 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 563 | GLU | -1 | -0.979 | -0.994 | 114.770 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 564 | ALA | 0 | -0.017 | -0.003 | 118.958 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 565 | ASN | 0 | 0.015 | 0.003 | 121.111 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 566 | TRP | 0 | 0.019 | 0.025 | 119.908 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 567 | ALA | 0 | 0.023 | 0.029 | 123.223 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 568 | ALA | 0 | 0.001 | -0.004 | 124.969 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 569 | GLU | -1 | -0.952 | -0.987 | 126.447 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 570 | PHE | 0 | -0.085 | -0.047 | 127.039 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 571 | ALA | 0 | -0.028 | -0.013 | 128.941 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 572 | GLU | -1 | -0.791 | -0.882 | 130.900 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 573 | LEU | 0 | 0.029 | 0.022 | 132.179 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 574 | GLU | -1 | -0.867 | -0.916 | 131.590 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 575 | LYS | 1 | 0.828 | 0.892 | 134.356 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 576 | GLU | -1 | -0.954 | -0.967 | 136.998 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 577 | ARG | 1 | 0.713 | 0.817 | 133.714 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 578 | ASP | -1 | -0.849 | -0.926 | 136.984 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 579 | SER | 0 | -0.117 | -0.055 | 139.835 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 580 | LEU | 0 | -0.070 | -0.032 | 141.539 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 581 | VAL | 0 | -0.076 | -0.015 | 140.614 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |