FMODB ID: 22VMR
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 | OptH |
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 | -174141.292063 |
---|---|
FMO2-HF: Nuclear repulsion | 155526.89641 |
FMO2-HF: Total energy | -18614.395654 |
FMO2-MP2: Total energy | -18667.710528 |
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. |
-12.454 | -14.498 | 15.962 | -7.73 | -6.186 | -0.05 |
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 | -0.019 | 3.674 | -0.852 | 1.505 | -0.005 | -1.311 | -1.041 | 0.007 |
4 | A | 4 | GLU | -1 | -0.833 | -0.924 | 1.779 | -14.176 | -19.586 | 15.961 | -6.150 | -4.401 | -0.056 |
5 | A | 5 | GLU | -1 | -0.869 | -0.922 | 3.298 | -1.526 | -0.591 | 0.007 | -0.264 | -0.677 | -0.001 |
6 | A | 6 | LYS | 1 | 0.904 | 0.964 | 5.267 | 2.754 | 2.828 | -0.001 | -0.005 | -0.067 | 0.000 |
7 | A | 7 | VAL | 0 | -0.016 | -0.020 | 7.545 | 0.684 | 0.684 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | GLU | -1 | -0.864 | -0.917 | 7.442 | -0.889 | -0.889 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | GLN | 0 | -0.039 | -0.033 | 9.296 | 0.231 | 0.231 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | LEU | 0 | -0.077 | -0.040 | 11.376 | 0.273 | 0.273 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | GLY | 0 | 0.034 | 0.025 | 12.422 | 0.170 | 0.170 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | SER | 0 | 0.051 | 0.026 | 13.248 | 0.156 | 0.156 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | SER | 0 | -0.032 | -0.030 | 15.318 | 0.136 | 0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | LEU | 0 | -0.032 | -0.013 | 17.052 | 0.091 | 0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | ASP | -1 | -0.850 | -0.916 | 17.803 | -0.434 | -0.434 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | THR | 0 | -0.061 | -0.038 | 19.520 | 0.076 | 0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | LEU | 0 | -0.046 | -0.034 | 21.424 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | GLN | 0 | 0.037 | 0.023 | 22.288 | 0.062 | 0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | THR | 0 | -0.007 | 0.009 | 24.164 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | ARG | 1 | 0.894 | 0.926 | 25.294 | 0.295 | 0.295 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | PHE | 0 | 0.016 | 0.019 | 27.320 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | ALA | 0 | 0.019 | 0.009 | 28.870 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | ARG | 1 | 0.925 | 0.962 | 27.846 | 0.224 | 0.224 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | LEU | 0 | 0.046 | 0.031 | 31.949 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | LEU | 0 | 0.002 | 0.010 | 33.327 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | ALA | 0 | -0.006 | -0.007 | 35.021 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | GLU | -1 | -0.916 | -0.960 | 35.420 | -0.140 | -0.140 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | TYR | 0 | -0.018 | 0.004 | 37.770 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | ASN | 0 | 0.006 | -0.016 | 38.425 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | ALA | 0 | 0.004 | 0.012 | 41.013 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | THR | 0 | -0.053 | -0.045 | 41.806 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | GLN | 0 | 0.034 | 0.024 | 43.641 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | MET | 0 | -0.057 | -0.029 | 45.449 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | LYS | 1 | 0.960 | 0.988 | 47.595 | 0.079 | 0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | MET | 0 | 0.001 | -0.015 | 45.951 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | LYS | 1 | 0.987 | 0.996 | 47.951 | 0.095 | 0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | GLN | 0 | 0.021 | 0.025 | 51.520 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | ARG | 1 | 0.907 | 0.940 | 50.865 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | LEU | 0 | 0.035 | 0.022 | 51.691 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | SER | 0 | 0.036 | 0.017 | 55.458 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | GLN | 0 | -0.028 | -0.012 | 57.440 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | LEU | 0 | 0.000 | 0.011 | 56.855 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | GLU | -1 | -0.931 | -0.970 | 57.482 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | SER | 0 | -0.100 | -0.054 | 61.329 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | GLN | 0 | -0.052 | -0.026 | 62.441 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | VAL | 0 | -0.022 | 0.013 | 63.160 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |