FMODB ID: 6614Z
Calculation Name: 3SWY-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3SWY
Chain ID: A
UniProt ID: Q16281
Base Structure: X-ray
Registration Date: 2023-06-20
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 | 46 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -173988.73626 |
---|---|
FMO2-HF: Nuclear repulsion | 155374.167129 |
FMO2-HF: Total energy | -18614.569131 |
FMO2-MP2: Total energy | -18667.864992 |
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:1:GLY)
Summations of interaction energy for
fragment #1(A:1:GLY)
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. |
-11.806 | -13.528 | 15.234 | -7.363 | -6.148 | -0.051 |
Interaction energy analysis for fragmet #1(A:1:GLY)
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 | 3 | LEU | 0 | -0.038 | -0.015 | 3.674 | -0.575 | 1.688 | -0.005 | -1.248 | -1.010 | 0.006 |
4 | A | 4 | GLU | -1 | -0.829 | -0.925 | 1.807 | -14.581 | -19.415 | 15.235 | -5.907 | -4.493 | -0.056 |
5 | A | 5 | GLU | -1 | -0.881 | -0.932 | 3.391 | -0.961 | -0.189 | 0.005 | -0.202 | -0.575 | -0.001 |
6 | A | 6 | LYS | 1 | 0.906 | 0.968 | 5.277 | 2.768 | 2.845 | -0.001 | -0.006 | -0.070 | 0.000 |
7 | A | 7 | VAL | 0 | -0.010 | -0.018 | 7.552 | 0.676 | 0.676 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | GLU | -1 | -0.862 | -0.914 | 7.483 | -0.772 | -0.772 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | GLN | 0 | -0.017 | -0.018 | 9.308 | 0.320 | 0.320 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | LEU | 0 | -0.070 | -0.028 | 11.387 | 0.278 | 0.278 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | GLY | 0 | 0.042 | 0.027 | 12.437 | 0.170 | 0.170 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | SER | 0 | 0.058 | 0.026 | 13.027 | 0.145 | 0.145 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | SER | 0 | -0.063 | -0.048 | 15.231 | 0.135 | 0.135 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | LEU | 0 | -0.026 | -0.015 | 17.066 | 0.091 | 0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | ASP | -1 | -0.850 | -0.914 | 17.771 | -0.424 | -0.424 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | THR | 0 | -0.074 | -0.047 | 19.348 | 0.074 | 0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | LEU | 0 | -0.046 | -0.032 | 21.437 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | GLN | 0 | 0.041 | 0.023 | 22.496 | 0.058 | 0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | THR | 0 | -0.030 | -0.006 | 23.980 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | ARG | 1 | 0.911 | 0.937 | 25.352 | 0.297 | 0.297 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | PHE | 0 | 0.008 | 0.015 | 27.334 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | ALA | 0 | 0.020 | 0.009 | 28.883 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | ARG | 1 | 0.926 | 0.965 | 27.695 | 0.220 | 0.220 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | LEU | 0 | 0.046 | 0.032 | 31.962 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | LEU | 0 | 0.006 | 0.009 | 33.340 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | ALA | 0 | -0.006 | -0.006 | 35.033 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | GLU | -1 | -0.903 | -0.956 | 35.136 | -0.142 | -0.142 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | TYR | 0 | -0.006 | 0.014 | 37.782 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | ASN | 0 | -0.002 | -0.022 | 38.551 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | ALA | 0 | 0.004 | 0.015 | 41.027 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | THR | 0 | -0.050 | -0.049 | 41.742 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | GLN | 0 | 0.010 | 0.007 | 43.725 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | MET | 0 | -0.047 | -0.020 | 45.462 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | LYS | 1 | 0.974 | 0.991 | 47.606 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | MET | 0 | 0.002 | -0.009 | 46.433 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | LYS | 1 | 0.982 | 0.995 | 47.509 | 0.095 | 0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | GLN | 0 | -0.012 | 0.001 | 51.533 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | ARG | 1 | 0.916 | 0.946 | 50.648 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | LEU | 0 | 0.022 | 0.015 | 51.661 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | SER | 0 | 0.049 | 0.026 | 55.470 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | GLN | 0 | -0.028 | -0.004 | 57.495 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | LEU | 0 | 0.007 | 0.012 | 56.863 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | GLU | -1 | -0.917 | -0.967 | 57.708 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | SER | 0 | -0.110 | -0.058 | 61.342 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | GLN | 0 | -0.056 | -0.027 | 62.275 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | VAL | 0 | -0.016 | 0.017 | 63.182 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |