FMO DATABASE

FMODB ID: 5392Z

Calculation Name: 4F3F-C-Xray321

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	59
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-339051.961281
FMO2-HF: Nuclear repulsion	314568.908077
FMO2-HF: Total energy	-24483.053204
FMO2-MP2: Total energy	-24552.508837

3D Structure

Snapshot

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.
-2.93	1.355	2.638	-2.405	-4.516	-0.022

Interaction energy analysis for fragmet #1(C:6:MET )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.020

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

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X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

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	0.002	2.421	-5.726	-2.107	2.606	-2.686	-3.539	-0.022
4	C	9	SER	0	0.026	-0.002	3.212	1.498	1.475	0.010	0.453	-0.439	0.000
5	C	10	GLY	0	-0.011	-0.006	4.899	-0.066	-0.024	0.000	-0.004	-0.038	0.000
6	C	11	LYS	1	0.915	0.973	6.609	1.624	1.624	0.000	0.000	0.000	0.000
7	C	12	LYS	1	0.979	0.995	7.775	0.020	0.020	0.000	0.000	0.000	0.000
8	C	13	ALA	0	0.013	0.017	9.136	0.109	0.109	0.000	0.000	0.000	0.000
9	C	14	ARG	1	0.885	0.932	12.596	0.359	0.359	0.000	0.000	0.000	0.000
10	C	15	GLU	-1	-0.852	-0.913	15.261	-0.087	-0.087	0.000	0.000	0.000	0.000
11	C	16	ILE	0	-0.047	-0.016	16.214	-0.053	-0.053	0.000	0.000	0.000	0.000
12	C	17	ASP	-1	-0.763	-0.885	18.481	-0.270	-0.270	0.000	0.000	0.000	0.000
13	C	18	GLU	-1	-0.906	-0.973	19.069	-0.246	-0.246	0.000	0.000	0.000	0.000
14	C	19	SER	0	-0.095	-0.047	17.067	-0.047	-0.047	0.000	0.000	0.000	0.000
15	C	20	LEU	0	0.000	-0.013	13.646	-0.092	-0.092	0.000	0.000	0.000	0.000
16	C	21	ILE	0	0.022	0.017	15.736	-0.035	-0.035	0.000	0.000	0.000	0.000
17	C	22	PHE	0	-0.055	-0.020	16.552	-0.014	-0.014	0.000	0.000	0.000	0.000
18	C	23	TYR	0	-0.068	-0.051	10.423	-0.143	-0.143	0.000	0.000	0.000	0.000
19	C	24	LYS	1	0.945	0.958	10.581	0.910	0.910	0.000	0.000	0.000	0.000
20	C	25	LYS	1	1.005	1.007	10.758	0.327	0.327	0.000	0.000	0.000	0.000
21	C	26	TRP	0	0.008	-0.005	3.678	0.038	0.293	0.001	-0.050	-0.206	0.000
22	C	27	GLU	-1	-0.826	-0.916	6.569	-1.680	-1.680	0.000	0.000	0.000	0.000
23	C	28	LEU	0	0.011	0.011	7.709	0.073	0.073	0.000	0.000	0.000	0.000
24	C	29	GLU	-1	-0.857	-0.937	7.052	0.615	0.615	0.000	0.000	0.000	0.000
25	C	30	ALA	0	-0.024	-0.002	3.453	-0.043	0.349	0.021	-0.118	-0.294	0.000
26	C	32	VAL	0	0.036	0.014	7.717	0.039	0.039	0.000	0.000	0.000	0.000
27	C	33	ASP	-1	-0.886	-0.939	10.715	0.389	0.389	0.000	0.000	0.000	0.000
28	C	34	ALA	0	0.106	0.043	11.480	-0.080	-0.080	0.000	0.000	0.000	0.000
29	C	35	ALA	0	0.034	0.019	14.444	-0.048	-0.048	0.000	0.000	0.000	0.000
30	C	36	LEU	0	-0.035	-0.012	14.445	-0.034	-0.034	0.000	0.000	0.000	0.000
31	C	37	LEU	0	-0.010	-0.007	15.676	-0.028	-0.028	0.000	0.000	0.000	0.000
32	C	38	ALA	0	0.018	0.006	17.422	-0.016	-0.016	0.000	0.000	0.000	0.000
33	C	39	THR	0	-0.134	-0.058	19.960	-0.015	-0.015	0.000	0.000	0.000	0.000
34	C	40	GLN	0	0.029	0.015	19.868	-0.030	-0.030	0.000	0.000	0.000	0.000
35	C	41	MET	0	0.046	0.029	21.763	-0.016	-0.016	0.000	0.000	0.000	0.000
36	C	42	ASP	-1	-0.960	-0.985	22.621	-0.064	-0.064	0.000	0.000	0.000	0.000
37	C	43	ARG	1	0.874	0.927	22.384	0.084	0.084	0.000	0.000	0.000	0.000
38	C	44	VAL	0	0.027	0.013	19.809	-0.016	-0.016	0.000	0.000	0.000	0.000
39	C	45	ASN	0	-0.057	-0.037	22.493	-0.017	-0.017	0.000	0.000	0.000	0.000
40	C	46	ALA	0	-0.008	0.007	25.204	0.002	0.002	0.000	0.000	0.000	0.000
41	C	47	ILE	0	-0.042	0.004	20.249	-0.009	-0.009	0.000	0.000	0.000	0.000
42	C	48	PRO	0	-0.030	0.000	23.236	0.006	0.006	0.000	0.000	0.000	0.000
43	C	49	PHE	0	-0.001	-0.009	16.756	-0.025	-0.025	0.000	0.000	0.000	0.000
44	C	50	THR	0	-0.018	-0.019	18.924	0.024	0.024	0.000	0.000	0.000	0.000
45	C	51	TYR	0	0.051	0.008	20.154	0.007	0.007	0.000	0.000	0.000	0.000
46	C	52	GLU	-1	-0.866	-0.943	17.170	-0.291	-0.291	0.000	0.000	0.000	0.000
47	C	53	GLN	0	-0.082	-0.045	15.143	0.043	0.043	0.000	0.000	0.000	0.000
48	C	54	LEU	0	0.021	0.006	16.249	0.024	0.024	0.000	0.000	0.000	0.000
49	C	55	ASP	-1	-0.935	-0.950	17.551	-0.105	-0.105	0.000	0.000	0.000	0.000
50	C	56	VAL	0	-0.068	-0.035	11.491	0.022	0.022	0.000	0.000	0.000	0.000
51	C	57	LEU	0	-0.013	-0.013	14.176	0.062	0.062	0.000	0.000	0.000	0.000
52	C	58	LYS	1	0.951	0.968	15.988	0.052	0.052	0.000	0.000	0.000	0.000
53	C	59	HIS	0	-0.009	0.008	13.015	-0.009	-0.009	0.000	0.000	0.000	0.000
54	C	60	LYS	1	0.855	0.928	8.886	-0.507	-0.507	0.000	0.000	0.000	0.000
55	C	61	LEU	0	-0.060	-0.038	14.859	0.028	0.028	0.000	0.000	0.000	0.000
56	C	62	ASP	-1	-0.935	-0.966	18.059	0.048	0.048	0.000	0.000	0.000	0.000
57	C	63	GLU	-1	-0.972	-0.981	11.946	0.474	0.474	0.000	0.000	0.000	0.000
58	C	64	LEU	0	-0.095	-0.038	16.688	0.012	0.012	0.000	0.000	0.000	0.000
59	C	1	NME	0	-0.007	0.006	19.084	-0.007	-0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:6:MET )