![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: V24N1
Calculation Name: 4GI3-C-Xray313
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 4GI3
Chain ID: C
UniProt ID: P85064
Base Structure: X-ray
Registration Date: 2021-09-06
Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.
Modeling method
Optimization | MOE:Amber10:EHT |
---|---|
Restraint | OptH |
Protonation | MOE:Protonate 3D |
Complement | MOE:Structure Preparation |
Water | No |
Procedure | Auto-FMO protocol ver. 1.20200116 |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 55 |
LigandCharge | |
Software | ABINIT-MP - Open Ver.1 Rev. 15 / 20190524 |
Total energy (hartree)
FMO2-HF: Electronic energy | -303739.396215 |
---|---|
FMO2-HF: Nuclear repulsion | 279115.27496 |
FMO2-HF: Total energy | -24624.121255 |
FMO2-MP2: Total energy | -24688.437708 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F015758/ligand_interaction/ligand_F015758.png)
Ligand Interaction
![ligand interaction](./Kdata/F015758/ligand_interaction/ligand_interaction_F015758.png)
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(C:20:ACE )
Summations of interaction energy for
fragment #1(C:20:ACE )
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. |
0.284 | 1.006 | -0.006 | -0.296 | -0.421 | 0 |
Interaction energy analysis for fragmet #1(C:20:ACE )
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 | C | 22 | PRO | 0 | -0.030 | -0.009 | 3.841 | 1.215 | 1.937 | -0.006 | -0.296 | -0.421 | 0.000 |
4 | C | 23 | SER | 0 | 0.144 | 0.074 | 6.773 | 0.121 | 0.121 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | C | 24 | ILE | 0 | -0.093 | -0.036 | 8.877 | 0.098 | 0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | C | 48 | CYS | 0 | -0.130 | -0.048 | 12.031 | -0.138 | -0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | C | 26 | PRO | 0 | 0.005 | 0.007 | 14.706 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | C | 27 | LEU | 0 | 0.018 | 0.000 | 18.163 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | C | 28 | ILE | 0 | -0.019 | 0.007 | 20.561 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | C | 29 | TYR | 0 | 0.005 | 0.000 | 22.387 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | C | 30 | ALA | 0 | 0.001 | -0.015 | 23.365 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | C | 31 | PRO | 0 | -0.057 | -0.018 | 23.563 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | C | 32 | VAL | 0 | -0.005 | 0.004 | 20.736 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | C | 69 | CYS | 0 | -0.074 | 0.001 | 23.357 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | C | 34 | VAL | 0 | -0.012 | -0.005 | 19.864 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | C | 35 | GLU | -1 | -0.898 | -0.955 | 23.059 | -0.123 | -0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | C | 36 | ASP | -1 | -0.844 | -0.929 | 20.444 | -0.235 | -0.235 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | C | 37 | SER | 0 | 0.010 | -0.016 | 20.830 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | C | 38 | ASN | 0 | -0.130 | -0.061 | 21.880 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | C | 39 | GLN | 0 | -0.029 | -0.005 | 25.207 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | C | 40 | ASP | -1 | -0.902 | -0.926 | 24.927 | -0.116 | -0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | C | 41 | PHE | 0 | -0.004 | -0.025 | 25.016 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | C | 42 | TYR | 0 | -0.018 | -0.011 | 22.024 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | C | 43 | LEU | 0 | 0.008 | 0.001 | 23.481 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | C | 44 | PHE | 0 | 0.047 | 0.023 | 16.831 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | C | 45 | VAL | 0 | 0.010 | -0.018 | 19.881 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | C | 46 | ASN | 0 | -0.002 | -0.009 | 18.026 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | C | 47 | GLU | -1 | -0.858 | -0.941 | 17.875 | -0.274 | -0.274 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | C | 49 | GLU | -1 | -0.790 | -0.912 | 13.571 | -0.396 | -0.396 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | C | 50 | VAL | 0 | -0.013 | 0.015 | 14.467 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | C | 51 | ARG | 1 | 0.957 | 0.967 | 11.848 | 0.480 | 0.480 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | C | 52 | LYS | 1 | 0.834 | 0.930 | 9.688 | 0.242 | 0.242 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | C | 76 | CYS | 0 | -0.028 | -0.013 | 9.782 | -0.126 | -0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | C | 54 | GLY | 0 | 0.039 | 0.011 | 11.765 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | C | 56 | GLU | -1 | -0.947 | -0.986 | 6.305 | -0.946 | -0.946 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | C | 57 | ALA | 0 | -0.017 | -0.011 | 7.679 | 0.179 | 0.179 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | C | 58 | GLY | 0 | -0.014 | 0.014 | 10.530 | 0.096 | 0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | C | 59 | PHE | 0 | -0.027 | -0.010 | 11.980 | 0.088 | 0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | C | 60 | VAL | 0 | 0.010 | -0.004 | 14.630 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | C | 61 | TYR | 0 | -0.009 | -0.004 | 14.727 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | C | 62 | THR | 0 | 0.020 | 0.005 | 19.496 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | C | 63 | PHE | 0 | -0.005 | -0.004 | 19.135 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | C | 64 | VAL | 0 | 0.007 | 0.011 | 23.593 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | C | 65 | PRO | 0 | 0.009 | -0.003 | 27.263 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | C | 66 | ARG | 1 | 0.991 | 0.973 | 28.574 | 0.109 | 0.109 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | C | 67 | GLU | -1 | -0.931 | -0.971 | 30.016 | -0.094 | -0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | C | 68 | MET | 0 | -0.023 | 0.007 | 29.457 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | C | 70 | LYS | 1 | 0.978 | 0.993 | 29.478 | 0.101 | 0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | C | 71 | ALA | 0 | 0.012 | -0.011 | 29.869 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | C | 72 | THR | 0 | -0.051 | -0.022 | 29.130 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | C | 73 | THR | 0 | -0.013 | -0.011 | 23.783 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | C | 74 | SER | 0 | -0.040 | -0.013 | 22.949 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | C | 75 | LEU | 0 | -0.003 | -0.003 | 18.781 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | C | 77 | PRO | 0 | 0.001 | 0.019 | 17.047 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | C | 78 | NME | 0 | 0.008 | 0.010 | 15.509 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |