FMO DATABASE

FMODB ID: J31M9

Calculation Name: 4F3F-C-Xray372

Preferred Name: Mesothelin

Target Type: SINGLE PROTEIN

Ligand Name: pyroglutamic acid

Ligand 3-letter code: PCA

Ligand of Interest (LOI):

Structure Source: PDB

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.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	58
LigandResidueName
LigandFragmentNumber	0
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 Molmil

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.
-3.087	1.676	1.791	-2.357	-4.197	-0.017

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 : -0.026 / q_NPA : -0.021

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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Graph Options

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	0.028	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

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