FMODB ID: N1R5Q
Calculation Name: 2YX5-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2YX5
Chain ID: A
UniProt ID: Q58988
Base Structure: X-ray
Registration Date: 2023-06-21
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 | OptAll |
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 | 83 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -525488.461009 |
---|---|
FMO2-HF: Nuclear repulsion | 491022.618916 |
FMO2-HF: Total energy | -34465.842093 |
FMO2-MP2: Total energy | -34564.213036 |
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:MET)
Summations of interaction energy for
fragment #1(A:1:MET)
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. |
-12.944 | -5.094 | 11.506 | -6.423 | -12.929 | -0.04 |
Interaction energy analysis for fragmet #1(A:1:MET)
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 | LYS | 1 | 0.870 | 0.939 | 3.867 | 0.748 | 2.632 | -0.009 | -0.801 | -1.073 | 0.000 |
4 | A | 4 | ALA | 0 | 0.019 | 0.001 | 6.050 | -0.355 | -0.355 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 5 | THR | 0 | -0.037 | -0.026 | 9.599 | 0.096 | 0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | VAL | 0 | 0.012 | 0.007 | 12.530 | -0.081 | -0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 7 | ILE | 0 | -0.035 | -0.022 | 15.510 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | ILE | 0 | 0.009 | 0.004 | 18.831 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | LYS | 1 | 0.884 | 0.936 | 21.964 | -0.086 | -0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | LEU | 0 | 0.035 | 0.009 | 25.623 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | LYS | 1 | 0.830 | 0.912 | 28.761 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | LYS | 1 | 0.949 | 0.958 | 30.499 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | GLY | 0 | -0.016 | -0.004 | 31.999 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | VAL | 0 | -0.024 | 0.000 | 33.120 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | LEU | 0 | 0.001 | -0.009 | 34.074 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | ASN | 0 | 0.011 | -0.007 | 29.656 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | PRO | 0 | 0.013 | -0.006 | 33.577 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | GLU | -1 | -0.838 | -0.854 | 28.466 | 0.100 | 0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | GLY | 0 | 0.043 | 0.022 | 32.068 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | ARG | 1 | 0.962 | 0.976 | 32.837 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | THR | 0 | -0.007 | -0.003 | 35.521 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | ILE | 0 | 0.032 | 0.012 | 30.669 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | GLN | 0 | 0.003 | 0.009 | 34.947 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | ARG | 1 | 0.851 | 0.912 | 36.881 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | ALA | 0 | 0.029 | 0.020 | 37.146 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | LEU | 0 | 0.014 | 0.006 | 33.655 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | ASN | 0 | -0.059 | -0.043 | 38.292 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | PHE | 0 | -0.005 | 0.001 | 41.557 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | LEU | 0 | -0.023 | -0.011 | 38.343 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | GLY | 0 | 0.055 | 0.040 | 42.100 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | PHE | 0 | 0.003 | 0.013 | 38.298 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | ASN | 0 | -0.036 | -0.036 | 39.874 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | ASN | 0 | -0.017 | -0.002 | 39.433 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | VAL | 0 | -0.008 | 0.004 | 35.414 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | LYS | 1 | 0.894 | 0.941 | 37.515 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | GLU | -1 | -0.936 | -0.965 | 33.885 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | VAL | 0 | -0.025 | -0.013 | 31.030 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | GLN | 0 | 0.024 | 0.016 | 27.903 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | THR | 0 | -0.065 | -0.066 | 26.964 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | TYR | 0 | 0.019 | 0.004 | 22.570 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | LYS | 1 | 0.950 | 0.975 | 20.255 | -0.168 | -0.168 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | MET | 0 | 0.005 | 0.013 | 14.231 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | ILE | 0 | -0.020 | -0.021 | 13.449 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | ASP | -1 | -0.763 | -0.852 | 10.238 | 0.478 | 0.478 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | ILE | 0 | -0.036 | -0.012 | 8.167 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | ILE | 0 | -0.003 | -0.008 | 3.004 | -0.383 | -0.750 | 2.463 | -0.519 | -1.577 | 0.003 |
47 | A | 47 | MET | 0 | -0.039 | 0.005 | 3.880 | -1.213 | -0.296 | 0.166 | -0.311 | -0.772 | -0.001 |
48 | A | 48 | GLU | -1 | -0.878 | -0.956 | 2.349 | -8.643 | -5.029 | 6.251 | -3.747 | -6.117 | -0.039 |
49 | A | 49 | GLY | 0 | 0.012 | 0.014 | 3.586 | -0.406 | -0.402 | 0.005 | 0.049 | -0.059 | 0.000 |
50 | A | 50 | GLU | -1 | -0.835 | -0.912 | 5.975 | -0.415 | -0.415 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 51 | ASN | 0 | 0.006 | 0.008 | 6.219 | 0.132 | 0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 52 | GLU | -1 | -0.768 | -0.908 | 7.157 | -0.217 | -0.217 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 53 | GLU | -1 | -0.849 | -0.907 | 8.631 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | LYS | 1 | 0.830 | 0.900 | 9.448 | 0.264 | 0.264 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | VAL | 0 | 0.005 | 0.007 | 5.827 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | LYS | 1 | 0.816 | 0.896 | 9.205 | 0.153 | 0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | GLU | -1 | -0.910 | -0.963 | 12.598 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | GLU | -1 | -0.924 | -0.961 | 9.505 | -0.068 | -0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | VAL | 0 | 0.018 | -0.011 | 10.758 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 60 | GLU | -1 | -0.881 | -0.945 | 13.450 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | GLU | -1 | -0.846 | -0.903 | 16.184 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | MET | 0 | -0.032 | -0.011 | 10.777 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 63 | CYS | 0 | -0.068 | -0.038 | 16.621 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 64 | LYS | 1 | 0.856 | 0.926 | 19.092 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 65 | LYS | 1 | 0.776 | 0.882 | 19.556 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 66 | LEU | 0 | -0.025 | -0.001 | 17.255 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 67 | LEU | 0 | -0.010 | -0.010 | 14.841 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 68 | ALA | 0 | -0.004 | 0.001 | 19.520 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 69 | ASN | 0 | 0.054 | 0.029 | 22.722 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 70 | PRO | 0 | 0.040 | 0.013 | 25.423 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 71 | VAL | 0 | -0.009 | -0.008 | 27.491 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 72 | ILE | 0 | -0.028 | -0.021 | 28.888 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 73 | HIS | 0 | 0.012 | 0.016 | 25.302 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 74 | ASP | -1 | -0.816 | -0.890 | 25.968 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 75 | TYR | 0 | -0.013 | -0.018 | 19.136 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 76 | GLU | -1 | -0.873 | -0.917 | 19.495 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 77 | ILE | 0 | 0.024 | 0.000 | 13.816 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 78 | LYS | 1 | 0.851 | 0.936 | 14.130 | -0.152 | -0.152 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 79 | VAL | 0 | -0.008 | -0.013 | 8.396 | 0.063 | 0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 80 | GLU | -1 | -0.906 | -0.951 | 8.211 | 0.225 | 0.225 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 81 | LYS | 1 | 0.869 | 0.923 | 3.746 | -3.767 | -3.323 | 0.005 | -0.154 | -0.294 | 0.001 |
82 | A | 82 | ILE | 0 | -0.047 | -0.016 | 2.146 | -0.805 | 0.194 | 2.623 | -0.842 | -2.779 | -0.004 |
83 | A | 83 | GLU | -1 | -0.900 | -0.929 | 3.960 | 1.530 | 1.885 | 0.002 | -0.098 | -0.258 | 0.000 |