FMODB ID: LZJJ9
Calculation Name: 2RF4-B-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2RF4
Chain ID: B
UniProt ID: P50106
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 | 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 | 61 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -291137.572142 |
---|---|
FMO2-HF: Nuclear repulsion | 267346.4903 |
FMO2-HF: Total energy | -23791.081843 |
FMO2-MP2: Total energy | -23862.209683 |
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(B:16:LEU)
Summations of interaction energy for
fragment #1(B:16:LEU)
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. |
-7.807 | -0.238 | 0.575 | -3.745 | -4.4 | -0.015 |
Interaction energy analysis for fragmet #1(B:16:LEU)
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 | B | 18 | THR | 0 | 0.029 | 0.050 | 2.345 | -4.917 | 1.135 | 0.430 | -3.098 | -3.385 | -0.009 |
4 | B | 19 | PRO | 0 | -0.023 | -0.003 | 3.132 | -2.370 | -0.960 | 0.146 | -0.642 | -0.914 | -0.006 |
5 | B | 20 | VAL | 0 | 0.044 | 0.017 | 4.778 | -0.299 | -0.192 | -0.001 | -0.005 | -0.101 | 0.000 |
6 | B | 21 | VAL | 0 | -0.031 | -0.018 | 6.317 | 0.230 | 0.230 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | B | 22 | ILE | 0 | 0.007 | -0.005 | 8.641 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | B | 23 | HIS | 0 | 0.004 | 0.003 | 11.879 | 0.058 | 0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | B | 24 | ALA | 0 | -0.006 | 0.010 | 15.666 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | B | 25 | THR | 0 | 0.001 | -0.008 | 18.344 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | B | 26 | GLN | 0 | -0.001 | -0.009 | 20.877 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | B | 27 | LEU | 0 | -0.014 | 0.008 | 21.878 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | B | 28 | PRO | 0 | -0.011 | -0.025 | 20.840 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | B | 29 | GLN | 0 | 0.014 | 0.021 | 23.311 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | B | 30 | HIS | 0 | -0.023 | -0.012 | 25.375 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | B | 31 | VAL | 0 | 0.011 | 0.009 | 25.430 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | B | 32 | SER | 0 | -0.030 | -0.051 | 28.072 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | B | 33 | THR | 0 | 0.041 | -0.009 | 30.045 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | B | 34 | ASP | -1 | -0.920 | -0.967 | 31.291 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | B | 35 | GLU | -1 | -0.828 | -0.865 | 28.394 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | B | 36 | VAL | 0 | -0.030 | -0.010 | 24.824 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | B | 37 | LEU | 0 | 0.003 | -0.007 | 26.867 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | B | 38 | GLN | 0 | 0.005 | 0.005 | 29.281 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | B | 39 | PHE | 0 | -0.028 | -0.016 | 19.693 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | B | 40 | LEU | 0 | -0.006 | -0.015 | 22.643 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | B | 41 | GLU | -1 | -0.817 | -0.862 | 24.945 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | B | 42 | SER | 0 | 0.036 | 0.007 | 25.526 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | B | 43 | PHE | 0 | -0.049 | -0.017 | 16.458 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | B | 44 | ILE | 0 | -0.046 | -0.049 | 21.626 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | B | 45 | ASP | -1 | -0.933 | -0.961 | 23.239 | -0.092 | -0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | B | 46 | GLU | -1 | -0.878 | -0.921 | 20.639 | -0.166 | -0.166 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | B | 47 | LYS | 1 | 0.786 | 0.872 | 17.116 | 0.181 | 0.181 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | B | 48 | GLU | -1 | -0.820 | -0.875 | 20.359 | -0.073 | -0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | B | 49 | ASN | 0 | -0.030 | -0.001 | 23.012 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | B | 50 | ILE | 0 | -0.008 | -0.011 | 22.666 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | B | 51 | ILE | 0 | -0.071 | -0.044 | 21.377 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | B | 52 | ASP | -1 | -0.849 | -0.914 | 19.923 | -0.167 | -0.167 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | B | 78 | ILE | 0 | -0.102 | -0.055 | 12.634 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | B | 79 | ASP | -1 | -0.810 | -0.890 | 16.602 | -0.173 | -0.173 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | B | 80 | THR | 0 | 0.018 | -0.009 | 10.609 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | B | 81 | ASN | 0 | -0.036 | -0.009 | 13.431 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | B | 82 | LEU | 0 | 0.038 | 0.030 | 13.772 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | B | 83 | SER | 0 | 0.035 | 0.013 | 15.820 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | B | 84 | SER | 0 | -0.049 | -0.034 | 17.568 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | B | 85 | SER | 0 | 0.012 | 0.000 | 15.443 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | B | 86 | ILE | 0 | 0.048 | 0.029 | 17.850 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | B | 87 | SER | 0 | -0.041 | -0.018 | 20.412 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | B | 88 | GLN | 0 | -0.024 | -0.021 | 19.398 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | B | 89 | LEU | 0 | 0.066 | 0.035 | 18.656 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | B | 90 | LYS | 1 | 0.806 | 0.888 | 22.544 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | B | 91 | ARG | 1 | 0.859 | 0.922 | 25.118 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | B | 92 | ILE | 0 | 0.001 | 0.004 | 22.062 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | B | 93 | GLN | 0 | 0.016 | -0.012 | 26.149 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | B | 94 | ARG | 1 | 0.903 | 0.951 | 28.001 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | B | 95 | ASP | -1 | -0.961 | -0.970 | 29.298 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | B | 96 | PHE | 0 | 0.060 | 0.001 | 27.286 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | B | 97 | LYS | 1 | 0.776 | 0.892 | 31.340 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | B | 98 | GLY | 0 | -0.034 | -0.007 | 33.810 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | B | 99 | LEU | 0 | -0.039 | -0.001 | 31.358 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | B | 100 | PRO | 0 | -0.027 | -0.011 | 35.697 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | B | 101 | PRO | 0 | -0.010 | 0.002 | 37.208 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |