FMO DATABASE

FMODB ID: 3Q6NL

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.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
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	-339160.126013
FMO2-HF: Nuclear repulsion	314695.424198
FMO2-HF: Total energy	-24464.701815
FMO2-MP2: Total energy	-24534.04211

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.
-2.43	2.04	0.932	-2.142	-3.26	-0.013

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 : -0.009 / q_NPA : -0.015

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	0.012	-0.004	2.633	-5.102	-1.666	0.891	-1.926	-2.401	-0.014
4	C	9	SER	0	0.031	0.008	3.835	0.909	1.104	-0.001	0.018	-0.212	0.000
5	C	10	GLY	0	-0.008	-0.004	5.700	0.036	0.036	0.000	0.000	0.000	0.000
6	C	11	LYS	1	0.805	0.904	7.347	1.432	1.432	0.000	0.000	0.000	0.000
7	C	12	LYS	1	0.969	0.986	7.871	0.084	0.084	0.000	0.000	0.000	0.000
8	C	13	ALA	0	0.014	0.018	9.206	0.074	0.074	0.000	0.000	0.000	0.000
9	C	14	ARG	1	0.880	0.919	12.467	0.376	0.376	0.000	0.000	0.000	0.000
10	C	15	GLU	-1	-0.822	-0.883	15.293	-0.049	-0.049	0.000	0.000	0.000	0.000
11	C	16	ILE	0	-0.017	-0.005	15.617	-0.039	-0.039	0.000	0.000	0.000	0.000
12	C	17	ASP	-1	-0.792	-0.874	18.050	-0.237	-0.237	0.000	0.000	0.000	0.000
13	C	18	GLU	-1	-0.887	-0.967	18.973	-0.185	-0.185	0.000	0.000	0.000	0.000
14	C	19	SER	0	-0.094	-0.067	17.138	-0.040	-0.040	0.000	0.000	0.000	0.000
15	C	20	LEU	0	0.014	-0.011	13.537	-0.068	-0.068	0.000	0.000	0.000	0.000
16	C	21	ILE	0	0.026	0.022	15.694	-0.025	-0.025	0.000	0.000	0.000	0.000
17	C	22	PHE	0	-0.053	-0.015	16.364	-0.007	-0.007	0.000	0.000	0.000	0.000
18	C	23	TYR	0	-0.100	-0.052	10.447	-0.123	-0.123	0.000	0.000	0.000	0.000
19	C	24	LYS	1	0.944	0.955	10.900	0.738	0.738	0.000	0.000	0.000	0.000
20	C	25	LYS	1	0.882	0.933	10.916	0.101	0.101	0.000	0.000	0.000	0.000
21	C	26	TRP	0	0.062	0.020	4.027	-0.042	0.235	-0.001	-0.054	-0.222	0.000
22	C	27	GLU	-1	-0.783	-0.867	6.433	-1.098	-1.098	0.000	0.000	0.000	0.000
23	C	28	LEU	0	0.006	-0.001	7.899	0.058	0.058	0.000	0.000	0.000	0.000
24	C	29	GLU	-1	-0.846	-0.908	6.680	1.083	1.083	0.000	0.000	0.000	0.000
25	C	30	ALA	0	-0.007	-0.002	3.506	-0.151	0.411	0.043	-0.180	-0.425	0.001
26	C	32	VAL	0	0.020	0.011	7.524	-0.091	-0.091	0.000	0.000	0.000	0.000
27	C	33	ASP	-1	-0.856	-0.929	10.573	0.414	0.414	0.000	0.000	0.000	0.000
28	C	34	ALA	0	0.093	0.051	11.286	-0.077	-0.077	0.000	0.000	0.000	0.000
29	C	35	ALA	0	-0.013	-0.003	14.145	-0.053	-0.053	0.000	0.000	0.000	0.000
30	C	36	LEU	0	-0.045	-0.025	13.861	-0.031	-0.031	0.000	0.000	0.000	0.000
31	C	37	LEU	0	0.003	0.002	15.092	-0.030	-0.030	0.000	0.000	0.000	0.000
32	C	38	ALA	0	0.016	0.005	17.014	-0.020	-0.020	0.000	0.000	0.000	0.000
33	C	39	THR	0	-0.135	-0.075	19.283	-0.019	-0.019	0.000	0.000	0.000	0.000
34	C	40	GLN	0	0.039	0.017	19.132	-0.027	-0.027	0.000	0.000	0.000	0.000
35	C	41	MET	0	0.038	0.027	21.415	-0.012	-0.012	0.000	0.000	0.000	0.000
36	C	42	ASP	-1	-0.891	-0.934	22.279	-0.034	-0.034	0.000	0.000	0.000	0.000
37	C	43	ARG	1	0.800	0.870	21.661	0.046	0.046	0.000	0.000	0.000	0.000
38	C	44	VAL	0	0.009	0.007	19.807	-0.014	-0.014	0.000	0.000	0.000	0.000
39	C	45	ASN	0	-0.064	-0.036	22.425	-0.005	-0.005	0.000	0.000	0.000	0.000
40	C	46	ALA	0	-0.020	-0.006	25.400	0.001	0.001	0.000	0.000	0.000	0.000
41	C	47	ILE	0	-0.015	0.017	20.554	-0.011	-0.011	0.000	0.000	0.000	0.000
42	C	48	PRO	0	-0.026	-0.001	23.399	0.008	0.008	0.000	0.000	0.000	0.000
43	C	49	PHE	0	-0.006	-0.017	16.745	-0.018	-0.018	0.000	0.000	0.000	0.000
44	C	50	THR	0	-0.041	-0.045	19.433	0.017	0.017	0.000	0.000	0.000	0.000
45	C	51	TYR	0	0.026	0.005	20.316	0.011	0.011	0.000	0.000	0.000	0.000
46	C	52	GLU	-1	-0.834	-0.903	17.864	-0.152	-0.152	0.000	0.000	0.000	0.000
47	C	53	GLN	0	-0.033	-0.025	15.429	0.045	0.045	0.000	0.000	0.000	0.000
48	C	54	LEU	0	0.036	0.015	16.240	0.034	0.034	0.000	0.000	0.000	0.000
49	C	55	ASP	-1	-0.879	-0.938	16.723	-0.022	-0.022	0.000	0.000	0.000	0.000
50	C	56	VAL	0	-0.072	-0.030	11.278	0.030	0.030	0.000	0.000	0.000	0.000
51	C	57	LEU	0	-0.001	0.001	14.398	0.063	0.063	0.000	0.000	0.000	0.000
52	C	58	LYS	1	0.826	0.897	16.205	-0.053	-0.053	0.000	0.000	0.000	0.000
53	C	59	HIS	0	-0.053	-0.034	13.240	-0.031	-0.031	0.000	0.000	0.000	0.000
54	C	60	LYS	1	0.798	0.862	9.240	-0.799	-0.799	0.000	0.000	0.000	0.000
55	C	61	LEU	0	-0.032	-0.014	14.464	0.004	0.004	0.000	0.000	0.000	0.000
56	C	62	ASP	-1	-0.847	-0.910	18.159	0.097	0.097	0.000	0.000	0.000	0.000
57	C	63	GLU	-1	-0.863	-0.903	12.171	0.572	0.572	0.000	0.000	0.000	0.000
58	C	64	LEU	0	-0.100	-0.027	16.452	0.002	0.002	0.000	0.000	0.000	0.000

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