FMO DATABASE

FMODB ID: YMZN2

Calculation Name: 3E1R-A-Xray549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3E1R

Chain ID: A

ChEMBL ID:

UniProt ID: Q53EZ4

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	46
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-192509.531695
FMO2-HF: Nuclear repulsion	173052.236049
FMO2-HF: Total energy	-19457.295646
FMO2-MP2: Total energy	-19514.574392

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(A:165:ASN)

Summations of interaction energy for fragment #1(A:165:ASN)

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.
-47.773	-40.857	6.333	-4.687	-8.562	-0.027

Interaction energy analysis for fragmet #1(A:165:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.861 / q_NPA : 0.914

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	A	167	ILE	0	0.057	0.032	2.495	-1.240	2.088	1.979	-1.724	-3.583	0.012
4	A	168	HIS	0	0.028	-0.001	2.409	-13.322	-10.082	4.355	-2.896	-4.700	-0.039
5	A	169	GLU	-1	-0.878	-0.918	4.168	-39.194	-38.846	-0.001	-0.067	-0.279	0.000
6	A	170	MET	0	-0.008	-0.023	5.859	6.533	6.533	0.000	0.000	0.000	0.000
7	A	171	GLU	-1	-0.878	-0.915	7.407	-24.330	-24.330	0.000	0.000	0.000	0.000
8	A	172	ILE	0	-0.005	-0.010	6.640	3.052	3.052	0.000	0.000	0.000	0.000
9	A	173	GLN	0	0.018	0.017	9.821	2.093	2.093	0.000	0.000	0.000	0.000
10	A	174	LEU	0	-0.023	-0.010	11.621	2.299	2.299	0.000	0.000	0.000	0.000
11	A	175	LYS	1	0.850	0.901	11.850	24.575	24.575	0.000	0.000	0.000	0.000
12	A	176	ASP	-1	-0.817	-0.886	14.053	-17.245	-17.245	0.000	0.000	0.000	0.000
13	A	177	ALA	0	0.024	0.008	15.890	1.372	1.372	0.000	0.000	0.000	0.000
14	A	178	LEU	0	-0.053	-0.031	16.581	1.222	1.222	0.000	0.000	0.000	0.000
15	A	179	GLU	-1	-0.915	-0.951	18.540	-14.946	-14.946	0.000	0.000	0.000	0.000
16	A	180	LYS	1	0.883	0.925	18.247	17.651	17.651	0.000	0.000	0.000	0.000
17	A	181	ASN	0	-0.015	-0.005	21.427	1.032	1.032	0.000	0.000	0.000	0.000
18	A	182	GLN	0	0.025	0.021	23.287	0.611	0.611	0.000	0.000	0.000	0.000
19	A	183	GLN	0	-0.059	-0.038	22.341	0.641	0.641	0.000	0.000	0.000	0.000
20	A	184	TRP	0	0.000	-0.003	25.180	0.817	0.817	0.000	0.000	0.000	0.000
21	A	185	LEU	0	-0.009	0.010	27.764	0.521	0.521	0.000	0.000	0.000	0.000
22	A	186	VAL	0	-0.010	-0.009	29.033	0.449	0.449	0.000	0.000	0.000	0.000
23	A	187	TYR	0	-0.003	-0.001	30.542	0.429	0.429	0.000	0.000	0.000	0.000
24	A	188	ASP	-1	-0.837	-0.907	32.112	-8.904	-8.904	0.000	0.000	0.000	0.000
25	A	189	GLN	0	0.002	-0.003	32.559	0.321	0.321	0.000	0.000	0.000	0.000
26	A	190	GLN	0	-0.028	-0.012	33.711	0.306	0.306	0.000	0.000	0.000	0.000
27	A	191	ARG	1	0.866	0.921	33.644	9.453	9.453	0.000	0.000	0.000	0.000
28	A	192	GLU	-1	-0.854	-0.948	38.029	-7.633	-7.633	0.000	0.000	0.000	0.000
29	A	193	VAL	0	-0.058	-0.017	39.916	0.268	0.268	0.000	0.000	0.000	0.000
30	A	194	TYR	0	-0.004	-0.005	41.262	0.221	0.221	0.000	0.000	0.000	0.000
31	A	195	VAL	0	0.034	0.007	41.687	0.223	0.223	0.000	0.000	0.000	0.000
32	A	196	LYS	1	0.880	0.950	42.104	7.771	7.771	0.000	0.000	0.000	0.000
33	A	197	GLY	0	0.014	0.015	46.075	0.181	0.181	0.000	0.000	0.000	0.000
34	A	198	LEU	0	-0.028	-0.015	45.093	0.180	0.180	0.000	0.000	0.000	0.000
35	A	199	LEU	0	0.015	0.006	46.973	0.158	0.158	0.000	0.000	0.000	0.000
36	A	200	ALA	0	-0.006	0.004	50.221	0.155	0.155	0.000	0.000	0.000	0.000
37	A	201	LYS	1	0.827	0.902	51.761	5.998	5.998	0.000	0.000	0.000	0.000
38	A	202	ILE	0	0.010	0.005	50.395	0.110	0.110	0.000	0.000	0.000	0.000
39	A	203	PHE	0	0.088	0.046	54.287	0.141	0.141	0.000	0.000	0.000	0.000
40	A	204	GLU	-1	-0.949	-0.966	56.293	-5.513	-5.513	0.000	0.000	0.000	0.000
41	A	205	LEU	0	-0.019	-0.029	55.622	0.119	0.119	0.000	0.000	0.000	0.000
42	A	206	GLU	-1	-0.875	-0.927	56.686	-5.683	-5.683	0.000	0.000	0.000	0.000
43	A	207	LYS	1	0.922	0.964	59.579	5.512	5.512	0.000	0.000	0.000	0.000
44	A	208	LYS	1	0.832	0.929	60.109	5.451	5.451	0.000	0.000	0.000	0.000
45	A	209	THR	0	-0.120	-0.086	61.854	0.043	0.043	0.000	0.000	0.000	0.000
46	A	210	GLU	-2	-1.902	-1.913	64.345	-9.671	-9.671	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:165:ASN)