FMODB ID: G5171
Calculation Name: 2RF4-F-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2RF4
Chain ID: F
UniProt ID: P50106
Base Structure: X-ray
Registration Date: 2023-09-24
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 | 60 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -284147.026456 |
---|---|
FMO2-HF: Nuclear repulsion | 260718.597778 |
FMO2-HF: Total energy | -23428.428677 |
FMO2-MP2: Total energy | -23498.347656 |
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(F:17:ASN)
Summations of interaction energy for
fragment #1(F:17:ASN)
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. |
0.945 | 2.7 | -0.015 | -0.795 | -0.944 | 0.003 |
Interaction energy analysis for fragmet #1(F:17:ASN)
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 | F | 19 | PRO | 0 | -0.010 | -0.001 | 3.880 | 0.358 | 2.113 | -0.015 | -0.795 | -0.944 | 0.003 |
4 | F | 20 | VAL | 0 | 0.017 | 0.011 | 6.064 | 0.228 | 0.228 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | F | 21 | VAL | 0 | -0.005 | -0.001 | 8.948 | 0.370 | 0.370 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | F | 22 | ILE | 0 | -0.003 | -0.009 | 11.961 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | F | 23 | HIS | 0 | 0.003 | -0.002 | 14.877 | 0.097 | 0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | F | 24 | ALA | 0 | 0.002 | 0.006 | 18.573 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | F | 25 | THR | 0 | 0.008 | 0.004 | 21.655 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | F | 26 | GLN | 0 | -0.028 | -0.018 | 23.991 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | F | 27 | LEU | 0 | 0.010 | 0.013 | 25.117 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | F | 28 | PRO | 0 | -0.013 | -0.030 | 23.931 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | F | 29 | GLN | 0 | -0.014 | 0.008 | 26.455 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | F | 30 | HIS | 0 | -0.012 | -0.002 | 28.609 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | F | 31 | VAL | 0 | 0.010 | 0.014 | 29.478 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | F | 32 | SER | 0 | -0.035 | -0.059 | 32.000 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | F | 33 | THR | 0 | 0.016 | -0.024 | 33.609 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | F | 34 | ASP | -1 | -0.916 | -0.950 | 35.261 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | F | 35 | GLU | -1 | -0.809 | -0.867 | 32.326 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | F | 36 | VAL | 0 | -0.007 | -0.001 | 28.439 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | F | 37 | LEU | 0 | 0.006 | 0.005 | 30.341 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | F | 38 | GLN | 0 | -0.003 | -0.006 | 32.656 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | F | 39 | PHE | 0 | -0.022 | -0.009 | 23.557 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | F | 40 | LEU | 0 | -0.016 | -0.013 | 26.670 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | F | 41 | GLU | -1 | -0.774 | -0.852 | 28.875 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | F | 42 | SER | 0 | 0.015 | 0.009 | 29.645 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | F | 43 | PHE | 0 | -0.036 | -0.016 | 20.429 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | F | 44 | ILE | 0 | -0.043 | -0.036 | 25.686 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | F | 45 | ASP | -1 | -0.930 | -0.959 | 27.559 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | F | 46 | GLU | -1 | -0.876 | -0.927 | 24.595 | -0.095 | -0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | F | 47 | LYS | 1 | 0.740 | 0.845 | 21.007 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | F | 48 | GLU | -1 | -0.810 | -0.867 | 24.424 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | F | 49 | ASN | 0 | 0.000 | 0.013 | 27.196 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | F | 50 | ILE | 0 | -0.029 | -0.016 | 27.308 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | F | 51 | ILE | 0 | -0.092 | -0.053 | 24.508 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | F | 52 | ASP | -1 | -0.828 | -0.908 | 23.894 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | F | 78 | ILE | 0 | -0.080 | -0.048 | 16.309 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | F | 79 | ASP | -1 | -0.814 | -0.887 | 20.027 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | F | 80 | THR | 0 | -0.036 | -0.042 | 14.455 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | F | 81 | ASN | 0 | -0.060 | -0.028 | 16.012 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | F | 82 | LEU | 0 | 0.064 | 0.051 | 18.025 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | F | 83 | SER | 0 | 0.082 | 0.033 | 19.634 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | F | 84 | SER | 0 | -0.034 | -0.019 | 20.753 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | F | 85 | SER | 0 | -0.010 | -0.017 | 19.387 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | F | 86 | ILE | 0 | 0.046 | 0.028 | 21.818 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | F | 87 | SER | 0 | -0.025 | -0.006 | 24.665 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | F | 88 | GLN | 0 | -0.047 | -0.029 | 22.769 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | F | 89 | LEU | 0 | 0.043 | 0.016 | 22.511 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | F | 90 | LYS | 1 | 0.821 | 0.887 | 26.389 | -0.084 | -0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | F | 91 | ARG | 1 | 0.867 | 0.938 | 28.786 | -0.195 | -0.195 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | F | 92 | ILE | 0 | 0.026 | 0.017 | 25.826 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | F | 93 | GLN | 0 | 0.036 | 0.006 | 29.994 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | F | 94 | ARG | 1 | 0.885 | 0.933 | 31.917 | -0.139 | -0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | F | 95 | ASP | -1 | -0.952 | -0.965 | 33.085 | 0.153 | 0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | F | 96 | PHE | 0 | 0.047 | 0.002 | 31.237 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | F | 97 | LYS | 1 | 0.746 | 0.860 | 34.982 | -0.072 | -0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | F | 98 | GLY | 0 | -0.042 | -0.012 | 37.619 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | F | 99 | LEU | 0 | -0.026 | 0.005 | 34.943 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | F | 100 | PRO | 0 | -0.033 | -0.011 | 39.423 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | F | 101 | PRO | 0 | -0.021 | -0.005 | 42.289 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |