![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 43VGN
Calculation Name: 4GI3-C-Xray372
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: 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 | 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 | 53 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -300110.997026 |
---|---|
FMO2-HF: Nuclear repulsion | 275657.657674 |
FMO2-HF: Total energy | -24453.339352 |
FMO2-MP2: Total energy | -24517.13442 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F021372/ligand_interaction/ligand_F021372.png)
Ligand Interaction
![ligand interaction](./Kdata/F021372/ligand_interaction/ligand_interaction_F021372.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:21:CYS)
Summations of interaction energy for
fragment #1(C:21:CYS)
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. |
-34.716 | -27.419 | 8.53 | -2.748 | -13.078 | -0.02 |
Interaction energy analysis for fragmet #1(C:21:CYS)
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 | 23 | SER | 0 | 0.087 | 0.042 | 3.865 | -1.871 | -0.575 | -0.012 | -0.563 | -0.721 | 0.003 |
4 | C | 24 | ILE | 0 | -0.087 | -0.038 | 5.951 | 0.615 | 0.615 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | C | 25 | CYS | 0 | -0.123 | -0.046 | 8.191 | -1.008 | -1.008 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | C | 26 | PRO | 0 | 0.002 | 0.003 | 10.845 | 0.259 | 0.259 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | C | 27 | LEU | 0 | 0.012 | 0.000 | 14.379 | -0.192 | -0.192 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | C | 28 | ILE | 0 | -0.014 | 0.008 | 15.705 | 0.161 | 0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | C | 29 | TYR | 0 | 0.007 | 0.001 | 16.437 | -0.191 | -0.191 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | C | 30 | ALA | 0 | -0.002 | -0.015 | 16.450 | 0.175 | 0.175 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | C | 31 | PRO | 0 | -0.048 | -0.015 | 15.343 | -0.151 | -0.151 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | C | 32 | VAL | 0 | 0.000 | 0.007 | 11.492 | 0.186 | 0.186 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | C | 33 | CYS | 0 | -0.070 | 0.009 | 12.976 | -0.326 | -0.326 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | C | 34 | VAL | 0 | -0.013 | -0.010 | 8.258 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | C | 35 | GLU | -1 | -0.864 | -0.932 | 11.335 | -0.606 | -0.606 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | C | 36 | ASP | -1 | -0.805 | -0.910 | 8.872 | -1.318 | -1.318 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | C | 37 | SER | 0 | 0.002 | -0.005 | 9.666 | 0.369 | 0.369 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | C | 38 | ASN | 0 | -0.146 | -0.082 | 11.431 | 0.331 | 0.331 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | C | 39 | GLN | 0 | -0.070 | -0.031 | 13.685 | 0.093 | 0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | C | 40 | ASP | -1 | -0.862 | -0.898 | 13.384 | -0.848 | -0.848 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | C | 41 | PHE | 0 | -0.025 | -0.037 | 13.035 | -0.200 | -0.200 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | C | 42 | TYR | 0 | -0.059 | -0.036 | 10.697 | -0.067 | -0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | C | 43 | LEU | 0 | 0.013 | 0.004 | 12.259 | -0.174 | -0.174 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | C | 44 | PHE | 0 | 0.044 | 0.022 | 7.202 | -0.105 | -0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | C | 45 | VAL | 0 | 0.018 | -0.014 | 12.022 | 0.296 | 0.296 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | C | 46 | ASN | 0 | -0.010 | -0.018 | 11.561 | -0.072 | -0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | C | 47 | GLU | -1 | -0.845 | -0.932 | 10.206 | -2.586 | -2.586 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | C | 49 | GLU | -1 | -0.771 | -0.898 | 6.804 | -5.945 | -5.945 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | C | 50 | VAL | 0 | -0.026 | 0.013 | 5.593 | -1.445 | -1.445 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | C | 51 | ARG | 1 | 0.945 | 0.960 | 3.994 | -1.424 | -0.807 | 0.013 | -0.259 | -0.371 | -0.001 |
31 | C | 52 | LYS | 1 | 0.834 | 0.931 | 2.068 | -8.277 | -6.782 | 4.784 | -2.557 | -3.722 | -0.033 |
32 | C | 53 | CYS | 0 | -0.026 | -0.012 | 2.743 | -4.744 | -0.718 | 1.096 | -2.427 | -2.695 | -0.016 |
35 | C | 57 | ALA | 0 | -0.014 | -0.009 | 3.836 | 0.636 | 2.496 | 0.010 | -0.525 | -1.345 | 0.001 |
36 | C | 58 | GLY | 0 | -0.014 | 0.014 | 2.520 | -4.604 | -2.665 | 2.255 | -1.979 | -2.214 | 0.022 |
37 | C | 59 | PHE | 0 | -0.038 | -0.016 | 2.831 | -2.033 | -4.924 | 0.395 | 3.833 | -1.337 | 0.007 |
38 | C | 60 | VAL | 0 | 0.015 | 0.000 | 3.270 | -1.097 | -2.245 | -0.016 | 1.661 | -0.497 | -0.003 |
39 | C | 61 | TYR | 0 | -0.018 | -0.009 | 3.585 | -0.593 | -0.490 | 0.005 | 0.068 | -0.176 | 0.000 |
40 | C | 62 | THR | 0 | 0.028 | 0.012 | 7.609 | 0.390 | 0.390 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | C | 63 | PHE | 0 | -0.015 | -0.008 | 9.523 | -0.214 | -0.214 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | C | 64 | VAL | 0 | 0.014 | 0.013 | 12.547 | 0.273 | 0.273 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | C | 65 | PRO | 0 | 0.008 | -0.002 | 15.882 | -0.097 | -0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | C | 66 | ARG | 1 | 0.976 | 0.969 | 18.108 | 1.052 | 1.052 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | C | 67 | GLU | -1 | -0.915 | -0.969 | 19.110 | -0.795 | -0.795 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | C | 68 | MET | 0 | -0.028 | 0.001 | 17.675 | 0.077 | 0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | C | 70 | LYS | 1 | 0.979 | 0.992 | 18.274 | 1.036 | 1.036 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | C | 71 | ALA | 0 | 0.013 | -0.010 | 19.333 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | C | 72 | THR | 0 | -0.047 | -0.020 | 20.009 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | C | 73 | THR | 0 | 0.012 | 0.003 | 15.335 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | C | 74 | SER | 0 | -0.069 | -0.030 | 13.180 | 0.244 | 0.244 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | C | 75 | LEU | 0 | -0.009 | -0.006 | 11.783 | -0.264 | -0.264 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | C | 77 | PRO | 0 | 0.016 | 0.030 | 7.842 | 0.419 | 0.419 | 0.000 | 0.000 | 0.000 | 0.000 |