FMO DATABASE

FMODB ID: 3ZK3L

Calculation Name: 3QRF-F-Xray547

Preferred Name:

Target Type:

Ligand Name: magnesium ion

Ligand 3-letter code: MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3QRF

Chain ID: F

ChEMBL ID:

UniProt ID: Q9BZS1

Base Structure: X-ray

Registration Date: 2025-10-04

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	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	82
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-538986.851056
FMO2-HF: Nuclear repulsion	504050.74548
FMO2-HF: Total energy	-34936.105575
FMO2-MP2: Total energy	-35038.702884

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:336:MET)

Summations of interaction energy for fragment #1(A:336: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.
94.149	97.354	0.187	-1.4	-1.991	-0.005

Interaction energy analysis for fragmet #1(A:336:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.888 / q_NPA : 0.927

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	338	PRO	0	0.049	0.048	2.693	2.474	5.665	0.188	-1.396	-1.983	-0.005
4	A	339	PRO	0	0.053	0.030	5.291	0.713	0.727	-0.001	-0.004	-0.008	0.000
5	A	340	PHE	0	-0.003	-0.009	9.132	-0.267	-0.267	0.000	0.000	0.000	0.000
6	A	341	THR	0	0.068	0.042	10.235	1.738	1.738	0.000	0.000	0.000	0.000
7	A	342	TYR	0	0.080	0.029	12.982	-0.114	-0.114	0.000	0.000	0.000	0.000
8	A	343	ALA	0	0.032	0.019	14.068	0.314	0.314	0.000	0.000	0.000	0.000
9	A	344	THR	0	-0.053	-0.032	10.746	-0.307	-0.307	0.000	0.000	0.000	0.000
10	A	345	LEU	0	0.000	-0.001	13.702	0.236	0.236	0.000	0.000	0.000	0.000
11	A	346	ILE	0	0.018	0.010	16.327	0.635	0.635	0.000	0.000	0.000	0.000
12	A	347	ARG	1	0.978	0.996	12.131	21.979	21.979	0.000	0.000	0.000	0.000
13	A	348	TRP	0	0.003	-0.001	12.435	-0.309	-0.309	0.000	0.000	0.000	0.000
14	A	349	ALA	0	-0.013	-0.011	17.088	0.632	0.632	0.000	0.000	0.000	0.000
15	A	350	ILE	0	-0.018	-0.005	20.594	0.689	0.689	0.000	0.000	0.000	0.000
16	A	351	LEU	0	0.017	0.001	16.614	0.436	0.436	0.000	0.000	0.000	0.000
17	A	352	GLU	-1	-0.964	-0.970	18.337	-15.987	-15.987	0.000	0.000	0.000	0.000
18	A	353	ALA	0	-0.034	-0.016	21.290	0.588	0.588	0.000	0.000	0.000	0.000
19	A	354	PRO	0	-0.021	-0.013	24.681	-0.398	-0.398	0.000	0.000	0.000	0.000
20	A	355	GLU	-1	-0.862	-0.944	26.985	-10.836	-10.836	0.000	0.000	0.000	0.000
21	A	356	LYS	1	0.779	0.901	22.125	13.775	13.775	0.000	0.000	0.000	0.000
22	A	357	GLN	0	0.028	0.018	24.672	-0.211	-0.211	0.000	0.000	0.000	0.000
23	A	358	ARG	1	0.856	0.925	24.556	12.531	12.531	0.000	0.000	0.000	0.000
24	A	359	THR	0	0.002	0.002	27.605	0.029	0.029	0.000	0.000	0.000	0.000
25	A	360	LEU	0	0.031	0.010	26.794	-0.292	-0.292	0.000	0.000	0.000	0.000
26	A	361	ASN	0	0.070	0.022	28.135	-0.408	-0.408	0.000	0.000	0.000	0.000
27	A	362	GLU	-1	-0.785	-0.880	28.525	-10.703	-10.703	0.000	0.000	0.000	0.000
28	A	363	ILE	0	-0.007	0.010	22.955	-0.466	-0.466	0.000	0.000	0.000	0.000
29	A	364	TYR	0	0.034	0.007	24.964	-0.534	-0.534	0.000	0.000	0.000	0.000
30	A	365	HIS	0	-0.007	0.003	27.017	0.026	0.026	0.000	0.000	0.000	0.000
31	A	366	TRP	0	0.005	0.008	17.352	-0.063	-0.063	0.000	0.000	0.000	0.000
32	A	367	PHE	0	0.031	-0.003	19.176	-0.458	-0.458	0.000	0.000	0.000	0.000
33	A	368	THR	0	-0.036	-0.017	23.463	-0.065	-0.065	0.000	0.000	0.000	0.000
34	A	369	ARG	1	0.951	0.963	25.363	11.797	11.797	0.000	0.000	0.000	0.000
35	A	370	MET	0	0.005	0.018	17.351	0.013	0.013	0.000	0.000	0.000	0.000
36	A	371	PHE	0	-0.002	-0.012	22.397	-0.230	-0.230	0.000	0.000	0.000	0.000
37	A	372	ALA	0	-0.069	-0.031	24.302	0.156	0.156	0.000	0.000	0.000	0.000
38	A	373	PHE	0	0.018	0.023	20.106	0.251	0.251	0.000	0.000	0.000	0.000
39	A	374	PHE	0	-0.027	-0.045	17.637	-0.089	-0.089	0.000	0.000	0.000	0.000
40	A	375	ARG	1	0.928	0.970	22.130	11.059	11.059	0.000	0.000	0.000	0.000
41	A	376	ASN	0	-0.016	-0.004	25.327	0.358	0.358	0.000	0.000	0.000	0.000
42	A	377	HIS	0	-0.034	0.007	22.698	0.109	0.109	0.000	0.000	0.000	0.000
43	A	378	PRO	0	0.064	0.041	24.827	0.178	0.178	0.000	0.000	0.000	0.000
44	A	379	ALA	0	0.052	0.006	24.543	-0.651	-0.651	0.000	0.000	0.000	0.000
45	A	380	THR	0	0.014	0.002	24.782	-0.366	-0.366	0.000	0.000	0.000	0.000
46	A	381	TRP	0	0.051	0.020	15.787	-0.429	-0.429	0.000	0.000	0.000	0.000
47	A	382	LYS	1	0.970	0.977	16.711	17.888	17.888	0.000	0.000	0.000	0.000
48	A	383	ASN	0	-0.001	0.000	20.514	-0.348	-0.348	0.000	0.000	0.000	0.000
49	A	384	ALA	0	0.049	0.035	23.462	0.139	0.139	0.000	0.000	0.000	0.000
50	A	385	ILE	0	0.012	0.013	16.910	0.092	0.092	0.000	0.000	0.000	0.000
51	A	386	ARG	1	0.939	0.968	20.262	13.726	13.726	0.000	0.000	0.000	0.000
52	A	387	HIS	0	0.038	0.033	21.716	0.104	0.104	0.000	0.000	0.000	0.000
53	A	388	ASN	0	-0.028	-0.035	22.614	0.469	0.469	0.000	0.000	0.000	0.000
54	A	389	LEU	0	-0.016	-0.014	17.281	0.095	0.095	0.000	0.000	0.000	0.000
55	A	390	SER	0	-0.020	-0.006	21.654	0.187	0.187	0.000	0.000	0.000	0.000
56	A	391	LEU	0	-0.035	0.000	24.767	0.359	0.359	0.000	0.000	0.000	0.000
57	A	392	HIS	0	-0.031	-0.026	24.864	0.599	0.599	0.000	0.000	0.000	0.000
58	A	393	LYS	1	1.013	0.995	25.230	9.543	9.543	0.000	0.000	0.000	0.000
59	A	394	CYS	0	-0.001	0.034	23.031	0.047	0.047	0.000	0.000	0.000	0.000
60	A	395	PHE	0	-0.052	-0.018	19.526	-0.681	-0.681	0.000	0.000	0.000	0.000
61	A	396	VAL	0	0.070	0.035	20.637	0.513	0.513	0.000	0.000	0.000	0.000
62	A	397	ARG	1	0.927	0.967	18.811	13.832	13.832	0.000	0.000	0.000	0.000
63	A	398	VAL	0	0.030	0.015	17.552	0.798	0.798	0.000	0.000	0.000	0.000
64	A	399	GLU	-1	-0.952	-0.988	17.960	-15.046	-15.046	0.000	0.000	0.000	0.000
65	A	400	SER	0	0.003	-0.007	15.816	0.294	0.294	0.000	0.000	0.000	0.000
66	A	401	GLU	-1	-0.895	-0.946	12.887	-21.315	-21.315	0.000	0.000	0.000	0.000
67	A	402	LYS	1	0.905	0.950	7.693	34.242	34.242	0.000	0.000	0.000	0.000
68	A	403	GLY	0	0.037	0.020	13.965	0.668	0.668	0.000	0.000	0.000	0.000
69	A	404	ALA	0	-0.054	-0.017	14.757	-0.771	-0.771	0.000	0.000	0.000	0.000
70	A	405	VAL	0	-0.011	0.012	12.045	-1.197	-1.197	0.000	0.000	0.000	0.000
71	A	406	TRP	0	-0.035	-0.025	14.277	1.506	1.506	0.000	0.000	0.000	0.000
72	A	407	THR	0	-0.034	-0.013	14.729	-1.195	-1.195	0.000	0.000	0.000	0.000
73	A	408	VAL	0	0.021	-0.003	17.140	0.553	0.553	0.000	0.000	0.000	0.000
74	A	409	ASP	-1	-0.822	-0.887	19.798	-12.166	-12.166	0.000	0.000	0.000	0.000
75	A	410	GLU	-1	-0.887	-0.962	21.809	-13.707	-13.707	0.000	0.000	0.000	0.000
76	A	411	LEU	0	-0.009	-0.014	23.687	0.391	0.391	0.000	0.000	0.000	0.000
77	A	412	GLU	-1	-0.854	-0.924	26.515	-10.048	-10.048	0.000	0.000	0.000	0.000
78	A	413	PHE	0	-0.058	-0.049	22.997	0.174	0.174	0.000	0.000	0.000	0.000
79	A	414	ARG	1	0.891	0.936	25.637	11.837	11.837	0.000	0.000	0.000	0.000
80	A	415	LYS	1	0.856	0.906	27.960	10.540	10.540	0.000	0.000	0.000	0.000
81	A	416	LYS	1	0.817	0.928	25.865	12.136	12.136	0.000	0.000	0.000	0.000
82	A	417	ARG	0	0.037	0.048	24.681	2.358	2.358	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:336:MET)