FMODB ID: N143Q
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 | 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 | 58 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -338052.020851 |
---|---|
FMO2-HF: Nuclear repulsion | 313588.132013 |
FMO2-HF: Total energy | -24463.888837 |
FMO2-MP2: Total energy | -24533.233419 |
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. |
-3.048 | 1.253 | 2.626 | -2.385 | -4.541 | -0.021 |
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 | 0.025 | 0.001 | 2.421 | -5.658 | -2.041 | 2.600 | -2.668 | -3.548 | -0.021 |
4 | C | 9 | SER | 0 | 0.021 | -0.004 | 3.203 | 1.407 | 1.388 | 0.009 | 0.454 | -0.444 | 0.000 |
5 | C | 10 | GLY | 0 | -0.009 | -0.006 | 4.889 | -0.090 | -0.036 | -0.001 | -0.004 | -0.049 | 0.000 |
6 | C | 11 | LYS | 1 | 0.916 | 0.973 | 6.610 | 1.589 | 1.589 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | C | 12 | LYS | 1 | 0.980 | 0.996 | 7.774 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | C | 13 | ALA | 0 | 0.013 | 0.016 | 9.136 | 0.100 | 0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | C | 14 | ARG | 1 | 0.885 | 0.931 | 12.596 | 0.344 | 0.344 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | C | 15 | GLU | -1 | -0.853 | -0.913 | 15.261 | -0.085 | -0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | C | 16 | ILE | 0 | -0.043 | -0.014 | 16.213 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | C | 17 | ASP | -1 | -0.768 | -0.886 | 18.480 | -0.262 | -0.262 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | C | 18 | GLU | -1 | -0.904 | -0.972 | 19.100 | -0.237 | -0.237 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | C | 19 | SER | 0 | -0.096 | -0.048 | 17.068 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | C | 20 | LEU | 0 | 0.000 | -0.013 | 13.678 | -0.088 | -0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | C | 21 | ILE | 0 | 0.024 | 0.017 | 15.764 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | C | 22 | PHE | 0 | -0.058 | -0.021 | 16.556 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | C | 23 | TYR | 0 | -0.069 | -0.051 | 10.453 | -0.136 | -0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | C | 24 | LYS | 1 | 0.947 | 0.960 | 10.597 | 0.888 | 0.888 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | C | 25 | LYS | 1 | 1.001 | 1.006 | 10.782 | 0.317 | 0.317 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | C | 26 | TRP | 0 | 0.011 | -0.004 | 3.689 | 0.029 | 0.284 | 0.000 | -0.049 | -0.206 | 0.000 |
22 | C | 27 | GLU | -1 | -0.827 | -0.916 | 6.595 | -1.614 | -1.614 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | C | 28 | LEU | 0 | 0.011 | 0.011 | 7.734 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | C | 29 | GLU | -1 | -0.858 | -0.938 | 7.080 | 0.610 | 0.610 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | C | 30 | ALA | 0 | -0.024 | -0.002 | 3.488 | -0.065 | 0.329 | 0.018 | -0.118 | -0.294 | 0.000 |
26 | C | 32 | VAL | 0 | 0.036 | 0.014 | 7.716 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | C | 33 | ASP | -1 | -0.891 | -0.940 | 10.715 | 0.372 | 0.372 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | C | 34 | ALA | 0 | 0.107 | 0.044 | 11.479 | -0.076 | -0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | C | 35 | ALA | 0 | 0.032 | 0.018 | 14.444 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | C | 36 | LEU | 0 | -0.034 | -0.012 | 14.447 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | C | 37 | LEU | 0 | -0.008 | -0.007 | 15.676 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | C | 38 | ALA | 0 | 0.019 | 0.006 | 17.421 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | C | 39 | THR | 0 | -0.136 | -0.059 | 19.959 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | C | 40 | GLN | 0 | 0.032 | 0.016 | 19.867 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | C | 41 | MET | 0 | 0.044 | 0.028 | 21.763 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | C | 42 | ASP | -1 | -0.960 | -0.986 | 22.620 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | C | 43 | ARG | 1 | 0.874 | 0.928 | 22.383 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | C | 44 | VAL | 0 | 0.028 | 0.013 | 19.843 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | C | 45 | ASN | 0 | -0.058 | -0.038 | 22.528 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | C | 46 | ALA | 0 | -0.009 | 0.007 | 25.237 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | C | 47 | ILE | 0 | -0.042 | 0.005 | 20.279 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | C | 48 | PRO | 0 | -0.031 | -0.001 | 23.267 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | C | 49 | PHE | 0 | 0.003 | -0.008 | 16.786 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | C | 50 | THR | 0 | -0.019 | -0.018 | 18.947 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | C | 51 | TYR | 0 | 0.050 | 0.007 | 20.181 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | C | 52 | GLU | -1 | -0.866 | -0.943 | 17.196 | -0.282 | -0.282 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | C | 53 | GLN | 0 | -0.082 | -0.045 | 15.169 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | C | 54 | LEU | 0 | 0.019 | 0.005 | 16.279 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | C | 55 | ASP | -1 | -0.934 | -0.950 | 17.576 | -0.102 | -0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | C | 56 | VAL | 0 | -0.071 | -0.036 | 11.522 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | C | 57 | LEU | 0 | -0.010 | -0.012 | 14.211 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | C | 58 | LYS | 1 | 0.949 | 0.968 | 16.020 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | C | 59 | HIS | 0 | -0.007 | 0.008 | 13.042 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | C | 60 | LYS | 1 | 0.855 | 0.928 | 8.886 | -0.509 | -0.509 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | C | 61 | LEU | 0 | -0.059 | -0.037 | 14.859 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | C | 62 | ASP | -1 | -0.936 | -0.965 | 18.056 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | C | 63 | GLU | -1 | -0.978 | -0.982 | 11.946 | 0.461 | 0.461 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | C | 64 | LEU | 0 | -0.092 | -0.032 | 16.688 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |