FMODB ID: J31M9
Calculation Name: 4F3F-C-Xray372
Preferred Name: Mesothelin
Target Type: SINGLE PROTEIN
Ligand Name: pyroglutamic acid
ligand 3-letter code: PCA
PDB ID: 4F3F
Chain ID: C
ChEMBL ID: CHEMBL3712878
UniProt ID: Q13421
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 | 58 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -337990.670843 |
---|---|
FMO2-HF: Nuclear repulsion | 313526.309035 |
FMO2-HF: Total energy | -24464.361808 |
FMO2-MP2: Total energy | -24533.671831 |
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(C:6:MET)
Summations of interaction energy for
fragment #1(C:6:MET)
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. |
-3.087 | 1.676 | 1.791 | -2.357 | -4.197 | -0.017 |
Interaction energy analysis for fragmet #1(C:6:MET)
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 | 8 | PRO | 0 | 0.028 | 0.003 | 2.476 | -5.623 | -1.789 | 1.768 | -2.350 | -3.252 | -0.017 |
4 | C | 9 | SER | 0 | 0.020 | -0.004 | 3.213 | 1.077 | 1.263 | 0.007 | 0.189 | -0.383 | 0.000 |
5 | C | 10 | GLY | 0 | -0.012 | -0.006 | 5.014 | -0.010 | 0.028 | -0.001 | -0.003 | -0.034 | 0.000 |
6 | C | 11 | LYS | 1 | 0.854 | 0.924 | 6.990 | 1.453 | 1.453 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | C | 12 | LYS | 1 | 0.969 | 0.989 | 7.751 | 0.109 | 0.109 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | C | 13 | ALA | 0 | 0.007 | 0.010 | 9.171 | 0.084 | 0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | C | 14 | ARG | 1 | 0.886 | 0.930 | 12.580 | 0.370 | 0.370 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | C | 15 | GLU | -1 | -0.832 | -0.902 | 15.366 | -0.069 | -0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | C | 16 | ILE | 0 | -0.038 | -0.007 | 15.950 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | C | 17 | ASP | -1 | -0.757 | -0.864 | 18.451 | -0.242 | -0.242 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | C | 18 | GLU | -1 | -0.900 | -0.968 | 19.233 | -0.206 | -0.206 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | C | 19 | SER | 0 | -0.106 | -0.066 | 17.288 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | C | 20 | LEU | 0 | -0.006 | -0.025 | 13.800 | -0.077 | -0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | C | 21 | ILE | 0 | 0.027 | 0.025 | 15.889 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | C | 22 | PHE | 0 | -0.055 | -0.021 | 16.622 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | C | 23 | TYR | 0 | -0.077 | -0.047 | 10.489 | -0.123 | -0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | C | 24 | LYS | 1 | 0.942 | 0.958 | 10.670 | 0.747 | 0.747 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | C | 25 | LYS | 1 | 1.007 | 1.006 | 10.889 | 0.219 | 0.219 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | C | 26 | TRP | 0 | 0.012 | -0.003 | 3.628 | -0.023 | 0.269 | 0.000 | -0.061 | -0.230 | 0.000 |
22 | C | 27 | GLU | -1 | -0.788 | -0.876 | 6.709 | -1.298 | -1.298 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | C | 28 | LEU | 0 | 0.025 | 0.014 | 7.850 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | C | 29 | GLU | -1 | -0.845 | -0.916 | 7.086 | 0.800 | 0.800 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | C | 30 | ALA | 0 | -0.018 | -0.005 | 3.607 | -0.081 | 0.332 | 0.017 | -0.132 | -0.298 | 0.000 |
26 | C | 32 | VAL | 0 | 0.031 | 0.013 | 7.689 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | C | 33 | ASP | -1 | -0.866 | -0.929 | 10.755 | 0.326 | 0.326 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | C | 34 | ALA | 0 | 0.088 | 0.036 | 11.447 | -0.069 | -0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | C | 35 | ALA | 0 | 0.012 | 0.009 | 14.406 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | C | 36 | LEU | 0 | -0.034 | -0.008 | 14.284 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | C | 37 | LEU | 0 | -0.001 | 0.001 | 15.404 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | C | 38 | ALA | 0 | 0.019 | 0.004 | 17.387 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | C | 39 | THR | 0 | -0.137 | -0.070 | 19.817 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | C | 40 | GLN | 0 | 0.028 | 0.009 | 19.528 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | C | 41 | MET | 0 | 0.052 | 0.034 | 21.726 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | C | 42 | ASP | -1 | -0.913 | -0.955 | 22.585 | -0.055 | -0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | C | 43 | ARG | 1 | 0.826 | 0.899 | 22.293 | 0.071 | 0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | C | 44 | VAL | 0 | 0.009 | -0.002 | 20.083 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | C | 45 | ASN | 0 | -0.045 | -0.026 | 22.671 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | C | 46 | ALA | 0 | -0.020 | -0.003 | 25.379 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | C | 47 | ILE | 0 | -0.035 | 0.007 | 20.377 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | C | 48 | PRO | 0 | -0.032 | -0.006 | 23.401 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | C | 49 | PHE | 0 | 0.005 | -0.005 | 16.859 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | C | 50 | THR | 0 | -0.058 | -0.053 | 19.239 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | C | 51 | TYR | 0 | 0.062 | 0.017 | 20.298 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | C | 52 | GLU | -1 | -0.852 | -0.920 | 17.408 | -0.207 | -0.207 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | C | 53 | GLN | 0 | -0.075 | -0.038 | 15.394 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | C | 54 | LEU | 0 | 0.022 | 0.003 | 16.404 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | C | 55 | ASP | -1 | -0.928 | -0.948 | 17.629 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | C | 56 | VAL | 0 | -0.074 | -0.040 | 11.561 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | C | 57 | LEU | 0 | -0.007 | -0.007 | 14.368 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | C | 58 | LYS | 1 | 0.926 | 0.961 | 16.153 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | C | 59 | HIS | 0 | -0.052 | -0.019 | 13.343 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | C | 60 | LYS | 1 | 0.789 | 0.874 | 9.488 | -0.579 | -0.579 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | C | 61 | LEU | 0 | -0.065 | -0.037 | 14.859 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | C | 62 | ASP | -1 | -0.920 | -0.957 | 18.031 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | C | 63 | GLU | -1 | -0.879 | -0.920 | 12.530 | 0.456 | 0.456 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | C | 64 | LEU | 0 | -0.075 | -0.020 | 16.602 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |