FMODB ID: 3N24L
Calculation Name: 1NO1-A-Xray315
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1NO1
Chain ID: A
UniProt ID: Q38151
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 | 68 |
LigandResidueName | |
LigandFragmentNumber | 0 |
LigandCharge | |
Software | ABINIT-MP - Open Ver.1 Rev. 15 / 20190524 |
Total energy (hartree)
FMO2-HF: Electronic energy | -410394.969553 |
---|---|
FMO2-HF: Nuclear repulsion | 383311.92384 |
FMO2-HF: Total energy | -27083.045713 |
FMO2-MP2: Total energy | -27162.529889 |
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:1:HCS )
Summations of interaction energy for
fragment #1(A:1:HCS )
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. |
-31.275 | -21.426 | 20.286 | -11.639 | -18.499 | -0.085 |
Interaction energy analysis for fragmet #1(A:1:HCS )
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 | 3 | GLU | -1 | -0.787 | -0.905 | 3.597 | -0.606 | 1.183 | 0.012 | -1.010 | -0.792 | 0.004 |
4 | A | 4 | LYS | 1 | 0.902 | 0.968 | 6.074 | -0.895 | -0.895 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 5 | ASP | -1 | -0.843 | -0.946 | 2.231 | 0.845 | 2.006 | 1.894 | -1.049 | -2.006 | -0.004 |
6 | A | 6 | VAL | 0 | 0.003 | 0.006 | 3.231 | 0.359 | 1.608 | 0.420 | -0.378 | -1.291 | 0.002 |
7 | A | 7 | VAL | 0 | -0.059 | -0.038 | 4.724 | -1.292 | -1.228 | 0.008 | 0.024 | -0.096 | 0.000 |
8 | A | 8 | GLN | 0 | -0.049 | -0.023 | 6.718 | -0.715 | -0.715 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | ILE | 0 | 0.070 | 0.049 | 3.520 | -1.086 | -0.622 | 0.059 | -0.101 | -0.423 | 0.000 |
10 | A | 10 | LEU | 0 | -0.026 | -0.024 | 6.768 | -0.599 | -0.599 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | LYS | 1 | 0.923 | 0.966 | 9.359 | -0.765 | -0.765 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | ALA | 0 | 0.074 | 0.046 | 10.067 | -0.149 | -0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | VAL | 0 | -0.028 | -0.007 | 9.866 | -0.164 | -0.164 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | SER | 0 | -0.047 | -0.036 | 12.515 | -0.091 | -0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | GLU | -1 | -0.933 | -0.968 | 14.420 | 0.547 | 0.547 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | PHE | 0 | 0.008 | 0.004 | 13.592 | -0.064 | -0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | TYR | 0 | -0.097 | -0.043 | 15.376 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | PRO | 0 | 0.046 | 0.013 | 18.682 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | GLY | 0 | -0.031 | -0.018 | 21.054 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | ARG | 1 | 0.894 | 0.949 | 20.672 | -0.074 | -0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | PHE | 0 | 0.023 | 0.008 | 12.220 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | GLN | 0 | -0.043 | -0.022 | 17.658 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | PRO | 0 | -0.033 | -0.013 | 14.229 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | ASP | -1 | -0.882 | -0.930 | 17.276 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | ASP | -1 | -0.853 | -0.919 | 17.796 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | LEU | 0 | 0.018 | 0.004 | 12.628 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | LYS | 1 | 0.952 | 0.977 | 11.607 | -0.105 | -0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | GLY | 0 | 0.041 | 0.006 | 13.210 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | THR | 0 | -0.009 | -0.010 | 10.849 | -0.101 | -0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | VAL | 0 | -0.018 | -0.003 | 8.194 | -0.087 | -0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | LYS | 1 | 0.824 | 0.906 | 8.437 | 0.252 | 0.252 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | ALA | 0 | -0.031 | -0.024 | 9.739 | -0.220 | -0.220 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | TRP | 0 | 0.061 | 0.015 | 6.561 | -0.202 | -0.202 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | HIS | 0 | -0.026 | -0.011 | 3.642 | 0.013 | 0.352 | 0.001 | -0.067 | -0.273 | 0.000 |
35 | A | 35 | ARG | 1 | 0.915 | 0.962 | 5.866 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | VAL | 0 | 0.012 | 0.026 | 6.881 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | LEU | 0 | 0.003 | -0.036 | 2.075 | -0.765 | -0.284 | 2.314 | -0.799 | -1.995 | -0.006 |
38 | A | 38 | ALA | 0 | -0.032 | 0.015 | 2.229 | -8.599 | -7.331 | 3.281 | -1.895 | -2.654 | -0.017 |
39 | A | 39 | GLU | -1 | -0.921 | -0.962 | 2.771 | -1.931 | -0.885 | 0.590 | -0.431 | -1.206 | -0.008 |
40 | A | 40 | TYR | 0 | -0.043 | -0.019 | 3.420 | 1.397 | 2.417 | 0.019 | -0.303 | -0.736 | 0.000 |
41 | A | 41 | GLU | -1 | -0.851 | -0.919 | 1.854 | -15.859 | -16.789 | 10.815 | -5.167 | -4.718 | -0.053 |
42 | A | 42 | LEU | 0 | -0.017 | -0.022 | 2.934 | 0.418 | 2.281 | 0.839 | -0.804 | -1.899 | -0.003 |
43 | A | 43 | GLU | -1 | -0.976 | -0.998 | 3.974 | 0.299 | 0.020 | 0.021 | 0.396 | -0.138 | 0.000 |
44 | A | 44 | GLU | -1 | -0.913 | -0.952 | 6.998 | -0.490 | -0.490 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | ILE | 0 | -0.019 | -0.016 | 3.811 | -0.341 | -0.027 | 0.013 | -0.055 | -0.272 | 0.000 |
46 | A | 46 | MET | 0 | -0.003 | -0.008 | 6.463 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | ASN | 0 | 0.006 | 0.012 | 8.342 | -0.091 | -0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | ASN | 0 | 0.022 | 0.003 | 9.163 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | LEU | 0 | -0.052 | -0.025 | 9.386 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | THR | 0 | -0.008 | 0.000 | 11.164 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 51 | ASP | -1 | -0.855 | -0.932 | 14.154 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 52 | TYR | 0 | -0.025 | -0.007 | 13.645 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 53 | ALA | 0 | 0.029 | 0.014 | 15.461 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | LYS | 1 | 0.773 | 0.893 | 17.165 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | VAL | 0 | -0.046 | -0.021 | 19.544 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | ASN | 0 | -0.025 | 0.005 | 17.953 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | LYS | 1 | 0.946 | 0.966 | 20.249 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | PHE | 0 | -0.041 | -0.029 | 20.199 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | PRO | 0 | 0.049 | 0.024 | 15.856 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 60 | PRO | 0 | 0.005 | 0.036 | 11.984 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | THR | 0 | -0.036 | -0.032 | 12.808 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | VAL | 0 | 0.037 | 0.012 | 6.778 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 63 | SER | 0 | -0.008 | -0.011 | 9.162 | -0.137 | -0.137 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 64 | ASP | -1 | -0.873 | -0.946 | 11.610 | -0.289 | -0.289 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 65 | LEU | 0 | -0.007 | 0.000 | 7.619 | 0.074 | 0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 66 | LEU | 0 | -0.007 | 0.006 | 6.955 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 67 | LYS | 1 | 0.877 | 0.961 | 9.439 | 0.451 | 0.451 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 68 | NME | 0 | 0.026 | 0.019 | 12.661 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |