FMODB ID: 8548Y
Calculation Name: 5XFS-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 5XFS
Chain ID: A
UniProt ID: O53943
Base Structure: X-ray
Registration Date: 2023-06-26
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 | 78 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -339690.725426 |
---|---|
FMO2-HF: Nuclear repulsion | 312173.310815 |
FMO2-HF: Total energy | -27517.414611 |
FMO2-MP2: Total energy | -27596.405272 |
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:7:VAL)
Summations of interaction energy for
fragment #1(A:7:VAL)
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. |
-5.056 | 0.151 | 1.278 | -2.084 | -4.4 | -0.003 |
Interaction energy analysis for fragmet #1(A:7:VAL)
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 | 9 | GLU | -1 | -0.955 | -0.964 | 3.165 | -2.813 | -0.273 | 0.018 | -1.005 | -1.553 | 0.002 |
4 | A | 10 | GLU | -1 | -0.958 | -0.975 | 2.495 | -4.348 | -2.593 | 1.254 | -0.871 | -2.137 | -0.005 |
5 | A | 11 | LEU | 0 | -0.038 | -0.016 | 3.531 | 0.356 | 1.139 | 0.007 | -0.201 | -0.588 | 0.000 |
6 | A | 12 | THR | 0 | 0.016 | -0.013 | 5.337 | 0.370 | 0.499 | -0.001 | -0.007 | -0.122 | 0.000 |
7 | A | 13 | ALA | 0 | 0.020 | 0.026 | 7.198 | 0.280 | 0.280 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 14 | ALA | 0 | 0.019 | 0.007 | 7.650 | 0.286 | 0.286 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 15 | ALA | 0 | -0.016 | -0.007 | 9.339 | 0.200 | 0.200 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 16 | ALA | 0 | 0.028 | 0.011 | 11.465 | 0.104 | 0.104 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 17 | GLN | 0 | -0.042 | -0.025 | 11.983 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 18 | LEU | 0 | 0.017 | -0.005 | 12.226 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 19 | GLY | 0 | 0.031 | 0.021 | 15.068 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 20 | THR | 0 | -0.034 | -0.023 | 16.996 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 21 | ILE | 0 | -0.027 | -0.010 | 17.372 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 22 | GLY | 0 | 0.046 | 0.030 | 19.457 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 23 | ALA | 0 | 0.019 | 0.019 | 21.294 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 24 | ALA | 0 | 0.001 | -0.001 | 22.783 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 25 | MET | 0 | -0.044 | -0.007 | 23.399 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 26 | ALA | 0 | 0.048 | 0.002 | 25.184 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 27 | ALA | 0 | -0.058 | -0.021 | 26.945 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 28 | GLN | 0 | -0.007 | -0.012 | 28.425 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 29 | ASN | 0 | 0.046 | 0.028 | 28.094 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 30 | ALA | 0 | 0.033 | 0.025 | 31.258 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 31 | ALA | 0 | -0.042 | -0.007 | 33.065 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 32 | ALA | 0 | -0.001 | -0.010 | 34.301 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 33 | ALA | 0 | 0.050 | 0.045 | 36.157 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 34 | ALA | 0 | 0.037 | 0.036 | 37.663 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 35 | PRO | 0 | -0.031 | -0.019 | 39.098 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 36 | THR | 0 | -0.064 | -0.047 | 37.743 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 37 | THR | 0 | -0.029 | -0.039 | 40.137 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 38 | ALA | 0 | -0.038 | -0.005 | 42.912 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 39 | ILE | 0 | -0.016 | -0.006 | 43.935 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 40 | ALA | 0 | -0.011 | 0.000 | 47.647 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 41 | PRO | 0 | 0.004 | -0.014 | 51.395 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 42 | ALA | 0 | -0.005 | 0.009 | 53.036 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 43 | ALA | 0 | -0.011 | -0.009 | 54.551 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 44 | LEU | 0 | -0.022 | -0.024 | 57.608 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 45 | ASP | -1 | -0.791 | -0.855 | 58.811 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 46 | GLU | -1 | -0.867 | -0.951 | 58.441 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 47 | VAL | 0 | -0.037 | -0.019 | 55.103 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 48 | SER | 0 | -0.067 | -0.064 | 54.481 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 49 | ALA | 0 | -0.016 | 0.001 | 53.378 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 50 | LEU | 0 | -0.001 | 0.002 | 51.970 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 51 | GLN | 0 | 0.002 | -0.001 | 48.225 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 52 | ALA | 0 | 0.010 | 0.003 | 48.467 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 53 | ALA | 0 | 0.031 | 0.016 | 47.766 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 54 | LEU | 0 | -0.010 | 0.003 | 46.355 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 55 | PHE | 0 | 0.000 | -0.005 | 42.955 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 56 | THR | 0 | -0.004 | 0.013 | 42.713 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 57 | ALA | 0 | 0.016 | 0.016 | 42.952 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 58 | TYR | 0 | -0.041 | -0.021 | 36.653 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 59 | GLY | 0 | 0.045 | 0.024 | 38.408 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 60 | THR | 0 | -0.019 | -0.025 | 37.925 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 61 | PHE | 0 | -0.034 | -0.026 | 38.101 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 62 | TYR | 0 | -0.043 | -0.032 | 30.484 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 63 | GLN | 0 | -0.035 | -0.021 | 33.623 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 64 | GLN | 0 | -0.026 | -0.003 | 33.635 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 65 | VAL | 0 | 0.027 | 0.021 | 31.078 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 66 | SER | 0 | -0.019 | -0.017 | 29.239 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 67 | ALA | 0 | -0.013 | -0.001 | 28.289 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 68 | GLU | -1 | -0.961 | -0.986 | 28.458 | -0.048 | -0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 69 | ALA | 0 | -0.031 | -0.017 | 25.926 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 70 | GLN | 0 | -0.025 | -0.032 | 23.549 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 71 | ALA | 0 | 0.062 | 0.052 | 23.372 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 72 | MET | 0 | -0.006 | -0.007 | 21.863 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 73 | HIS | 0 | -0.038 | -0.017 | 17.757 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 74 | ASP | -1 | -0.876 | -0.952 | 18.693 | -0.145 | -0.145 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 75 | MET | 0 | -0.076 | -0.033 | 19.233 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 76 | PHE | 0 | -0.006 | 0.015 | 12.311 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 77 | VAL | 0 | 0.047 | 0.023 | 14.251 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 78 | ASN | 0 | -0.020 | -0.004 | 14.175 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 79 | THR | 0 | -0.045 | -0.042 | 13.821 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 80 | LEU | 0 | -0.063 | -0.026 | 8.286 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 81 | GLY | 0 | 0.001 | -0.013 | 9.756 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 82 | ILE | 0 | -0.069 | -0.026 | 11.090 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 83 | SER | 0 | -0.075 | -0.018 | 7.811 | 0.186 | 0.186 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 84 | ALA | 0 | -0.003 | 0.002 | 6.989 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |