FMO DATABASE

FMODB ID: N143Q

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	OptH
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	-338052.020851
FMO2-HF: Nuclear repulsion	313588.132013
FMO2-HF: Total energy	-24463.888837
FMO2-MP2: Total energy	-24533.233419

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.
-3.048	1.253	2.626	-2.385	-4.541	-0.021

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 : -0.013 / q_NPA : -0.019

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	0.025	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

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