FMO DATABASE

FMODB ID: N7V8Q

Calculation Name: 2J4W-D-Xray549

Preferred Name:

Target Type:

Ligand Name: pyroglutamic acid

Ligand 3-letter code: PCA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2J4W

Chain ID: D

ChEMBL ID:

UniProt ID: Q9TY14

Base Structure: X-ray

Registration Date: 2025-10-12

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	32
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-132646.911714
FMO2-HF: Nuclear repulsion	117651.66596
FMO2-HF: Total energy	-14995.245755
FMO2-MP2: Total energy	-15034.530284

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(D:421:ILE)

Summations of interaction energy for fragment #1(D:421:ILE)

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.
-97.172	-89.965	2.309	-3.446	-6.071	-0.03

Interaction energy analysis for fragmet #1(D:421:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.855 / q_NPA : 0.918

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

Sort

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	D	423	ILE	0	0.036	0.028	3.441	2.280	4.179	0.068	-0.753	-1.214	-0.002
4	D	424	SER	0	-0.009	-0.014	2.923	-7.226	-5.476	0.582	-0.882	-1.450	-0.009
5	D	425	ASN	0	0.021	0.007	4.746	1.665	1.688	-0.001	-0.010	-0.012	0.000
9	D	429	SER	0	-0.044	-0.054	2.925	-2.847	-2.397	0.073	-0.090	-0.433	0.000
10	D	430	ILE	0	-0.081	-0.041	2.583	-16.444	-13.521	1.588	-1.708	-2.804	-0.019
11	D	431	LYS	1	0.830	0.905	3.728	29.124	29.286	-0.001	-0.003	-0.158	0.000
6	D	426	ASP	-1	-0.848	-0.887	6.372	-27.289	-27.289	0.000	0.000	0.000	0.000
7	D	427	LYS	1	0.849	0.904	6.303	17.271	17.271	0.000	0.000	0.000	0.000
8	D	428	GLU	-1	-0.924	-0.949	8.155	-26.462	-26.462	0.000	0.000	0.000	0.000
12	D	432	CYS	0	-0.060	0.001	6.612	5.033	5.033	0.000	0.000	0.000	0.000
13	D	433	PRO	0	0.018	0.009	8.275	2.570	2.570	0.000	0.000	0.000	0.000
14	D	434	CYS	0	-0.096	-0.046	10.381	4.429	4.429	0.000	0.000	0.000	0.000
15	D	435	GLU	-1	-0.818	-0.901	12.048	-21.612	-21.612	0.000	0.000	0.000	0.000
16	D	436	PRO	0	-0.045	-0.026	8.753	0.050	0.050	0.000	0.000	0.000	0.000
17	D	437	GLU	-1	-0.866	-0.910	10.733	-19.519	-19.519	0.000	0.000	0.000	0.000
18	D	438	ARG	1	0.877	0.932	10.387	15.309	15.309	0.000	0.000	0.000	0.000
19	D	439	ILE	0	0.026	0.027	11.209	1.397	1.397	0.000	0.000	0.000	0.000
20	D	440	SER	0	-0.022	-0.034	13.252	-0.737	-0.737	0.000	0.000	0.000	0.000
21	D	441	GLU	-1	-0.873	-0.921	15.392	-16.750	-16.750	0.000	0.000	0.000	0.000
22	D	442	SER	0	-0.048	-0.018	18.310	0.685	0.685	0.000	0.000	0.000	0.000
23	D	443	THR	0	-0.034	-0.032	19.204	0.632	0.632	0.000	0.000	0.000	0.000
24	D	444	CYS	0	-0.049	-0.012	14.831	0.004	0.004	0.000	0.000	0.000	0.000
25	D	445	ASN	0	0.008	-0.007	12.626	0.818	0.818	0.000	0.000	0.000	0.000
26	D	446	PHE	0	0.017	0.002	8.618	-0.939	-0.939	0.000	0.000	0.000	0.000
27	D	447	TYR	0	0.000	-0.002	7.138	2.521	2.521	0.000	0.000	0.000	0.000
28	D	448	VAL	0	0.046	0.004	6.014	-4.796	-4.796	0.000	0.000	0.000	0.000
29	D	450	ASN	0	-0.001	-0.013	8.230	-2.176	-2.176	0.000	0.000	0.000	0.000
30	D	452	VAL	0	0.028	0.000	8.627	-2.228	-2.228	0.000	0.000	0.000	0.000
31	D	453	GLU	-1	-0.857	-0.910	8.456	-27.230	-27.230	0.000	0.000	0.000	0.000
32	D	454	LYS	0	0.000	0.007	9.290	-4.705	-4.705	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(D:421:ILE)