FMODB ID: 5381Z
Calculation Name: 2FI0-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2FI0
Chain ID: A
UniProt ID: Q8CZ42
Base Structure: X-ray
Registration Date: 2023-06-19
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 | 79 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -490540.409375 |
---|---|
FMO2-HF: Nuclear repulsion | 460398.844557 |
FMO2-HF: Total energy | -30141.564817 |
FMO2-MP2: Total energy | -30229.133309 |
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:3:VAL)
Summations of interaction energy for
fragment #1(A:3: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. |
-1.159 | -0.286 | 3.387 | -1.225 | -3.034 | -0.003 |
Interaction energy analysis for fragmet #1(A:3: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 | 5 | MET | 0 | -0.065 | -0.027 | 2.219 | -0.573 | 0.128 | 3.387 | -1.197 | -2.890 | -0.003 |
4 | A | 6 | ASP | -1 | -0.881 | -0.938 | 4.350 | -1.031 | -0.859 | 0.000 | -0.028 | -0.144 | 0.000 |
5 | A | 7 | ASN | 0 | -0.025 | -0.022 | 7.827 | 0.066 | 0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 8 | ILE | 0 | 0.051 | 0.038 | 6.873 | 0.141 | 0.141 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 9 | ILE | 0 | -0.029 | -0.018 | 10.969 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 10 | ASP | -1 | -0.779 | -0.868 | 14.705 | -0.189 | -0.189 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 11 | VAL | 0 | -0.042 | -0.036 | 16.617 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 12 | SER | 0 | -0.132 | -0.096 | 19.161 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 13 | ILE | 0 | 0.017 | 0.030 | 18.197 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 14 | PRO | 0 | -0.030 | -0.023 | 21.882 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 15 | VAL | 0 | 0.030 | -0.005 | 22.911 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 16 | ALA | 0 | -0.046 | -0.039 | 23.177 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 17 | GLU | -1 | -0.875 | -0.937 | 20.725 | -0.214 | -0.214 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 18 | VAL | 0 | -0.023 | -0.003 | 18.051 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 19 | VAL | 0 | -0.039 | -0.032 | 19.014 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 20 | ASP | -1 | -0.959 | -0.974 | 21.252 | -0.202 | -0.202 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 21 | LYS | 1 | 0.881 | 0.951 | 12.983 | 0.519 | 0.519 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 22 | HIS | 0 | -0.016 | -0.003 | 12.546 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 23 | PRO | 0 | 0.016 | 0.007 | 17.726 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 24 | GLU | -1 | -0.849 | -0.943 | 16.820 | -0.322 | -0.322 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 25 | VAL | 0 | 0.014 | 0.030 | 18.280 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 26 | LEU | 0 | -0.066 | -0.033 | 20.171 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 27 | GLU | -1 | -0.941 | -0.983 | 23.860 | -0.081 | -0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 28 | ILE | 0 | 0.047 | 0.033 | 19.486 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 29 | LEU | 0 | -0.007 | -0.010 | 21.511 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 30 | VAL | 0 | -0.079 | -0.045 | 24.790 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 31 | GLU | -1 | -0.912 | -0.950 | 26.558 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 32 | LEU | 0 | -0.075 | -0.034 | 22.542 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 33 | GLY | 0 | 0.004 | 0.014 | 27.097 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 34 | PHE | 0 | -0.005 | -0.002 | 25.684 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 35 | LYS | 1 | 1.022 | 1.011 | 29.317 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 36 | PRO | 0 | -0.036 | -0.023 | 31.443 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 37 | LEU | 0 | -0.032 | -0.017 | 27.791 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 38 | ALA | 0 | 0.089 | 0.055 | 29.290 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 39 | ASN | 0 | -0.001 | -0.010 | 30.475 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 40 | PRO | 0 | 0.056 | 0.013 | 30.484 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 41 | LEU | 0 | 0.021 | 0.029 | 31.534 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 42 | MET | 0 | 0.011 | 0.007 | 33.562 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 43 | ARG | 1 | 0.956 | 0.975 | 25.798 | 0.138 | 0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 44 | ASN | 0 | -0.012 | -0.014 | 28.475 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 45 | THR | 0 | -0.036 | -0.019 | 30.754 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 46 | VAL | 0 | -0.027 | -0.019 | 31.892 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 47 | GLY | 0 | 0.050 | 0.012 | 28.600 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 48 | ARG | 1 | 0.958 | 0.994 | 27.263 | 0.120 | 0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 49 | LYS | 1 | 0.889 | 0.954 | 28.869 | 0.071 | 0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 50 | VAL | 0 | -0.035 | 0.007 | 28.258 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 51 | SER | 0 | 0.084 | 0.055 | 23.650 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 52 | LEU | 0 | 0.075 | 0.024 | 20.138 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 53 | LYS | 1 | 0.848 | 0.914 | 21.500 | 0.079 | 0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 54 | GLN | 0 | -0.026 | -0.013 | 24.705 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 55 | GLY | 0 | 0.055 | 0.007 | 27.600 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 56 | SER | 0 | -0.047 | -0.008 | 25.700 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 57 | LYS | 1 | 0.926 | 0.962 | 27.442 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 58 | LEU | 0 | -0.054 | -0.024 | 30.545 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 59 | ALA | 0 | -0.028 | -0.012 | 30.235 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 60 | GLY | 0 | 0.000 | 0.016 | 31.965 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 61 | THR | 0 | -0.057 | -0.031 | 26.415 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 62 | PRO | 0 | -0.012 | -0.015 | 26.623 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 63 | MET | 0 | 0.047 | 0.023 | 21.345 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 64 | ASP | -1 | -0.836 | -0.919 | 21.486 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 65 | LYS | 1 | 0.902 | 0.955 | 21.470 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 66 | ILE | 0 | 0.012 | 0.011 | 20.340 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 67 | VAL | 0 | 0.047 | 0.015 | 16.142 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 68 | ARG | 1 | 0.976 | 0.992 | 17.130 | -0.117 | -0.117 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 69 | THR | 0 | -0.046 | -0.035 | 18.225 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 70 | LEU | 0 | -0.018 | -0.001 | 16.221 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 71 | GLU | -1 | -0.885 | -0.938 | 13.068 | 0.140 | 0.140 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 72 | ALA | 0 | -0.091 | -0.043 | 14.246 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 73 | ASN | 0 | -0.111 | -0.070 | 16.675 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 74 | GLY | 0 | 0.004 | 0.010 | 12.535 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 75 | TYR | 0 | -0.071 | -0.044 | 11.415 | -0.099 | -0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 76 | GLU | -1 | -0.883 | -0.932 | 7.672 | 0.201 | 0.201 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 77 | VAL | 0 | -0.019 | -0.011 | 10.634 | -0.085 | -0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 78 | ILE | 0 | 0.013 | 0.005 | 11.130 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 79 | GLY | 0 | 0.056 | 0.026 | 14.214 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 80 | LEU | 0 | 0.006 | -0.013 | 16.154 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 81 | ASP | -1 | -0.906 | -0.921 | 19.100 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |