FMO DATABASE

FMODB ID: 9R682

Calculation Name: 5X4Z-J-Xray547

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5X4Z

Chain ID: J

ChEMBL ID:

UniProt ID: F2QPE6

Base Structure: X-ray

Registration Date: 2025-10-06

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	64
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-373975.23058
FMO2-HF: Nuclear repulsion	346520.598321
FMO2-HF: Total energy	-27454.632259
FMO2-MP2: Total energy	-27531.097631

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:1:MET)

Summations of interaction energy for fragment #1(A:1: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.
-5.316	3.3770000000001	14.072	-9.425	-13.342	-0.072

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.786 / q_NPA : 0.907

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	3	ILE	0	-0.002	0.030	3.141	-11.593	-9.533	0.033	-1.356	-0.737	-0.006
52	A	52	HIS	0	-0.092	-0.034	2.179	-2.519	-2.580	1.846	-0.697	-1.089	-0.005
53	A	53	VAL	0	0.049	0.029	4.599	2.466	2.587	-0.001	-0.024	-0.096	0.000
54	A	54	ASP	-1	-0.823	-0.940	2.281	-99.590	-95.949	1.598	-2.867	-2.372	-0.029
55	A	55	LEU	0	-0.056	-0.049	2.022	4.306	5.837	4.971	-2.440	-4.062	-0.018
56	A	56	ILE	0	0.010	0.023	2.918	4.000	5.928	0.165	-0.719	-1.375	-0.008
57	A	57	GLU	-1	-0.873	-0.928	4.046	-24.511	-24.347	0.004	-0.066	-0.102	0.000
59	A	59	PHE	0	-0.013	-0.025	2.592	-0.645	-1.336	5.456	-1.256	-3.509	-0.006
4	A	4	PRO	0	-0.006	-0.016	5.037	4.687	4.687	0.000	0.000	0.000	0.000
5	A	5	VAL	0	0.036	0.014	7.617	3.646	3.646	0.000	0.000	0.000	0.000
6	A	6	ARG	1	0.869	0.927	10.996	19.015	19.015	0.000	0.000	0.000	0.000
7	A	7	CYS	0	-0.038	0.053	11.955	-1.383	-1.383	0.000	0.000	0.000	0.000
8	A	8	PHE	0	0.110	0.030	7.704	2.285	2.285	0.000	0.000	0.000	0.000
9	A	9	SER	0	-0.010	-0.018	13.943	0.905	0.905	0.000	0.000	0.000	0.000
10	A	10	CYS	0	-0.108	-0.066	17.097	1.018	1.018	0.000	0.000	0.000	0.000
11	A	11	GLY	0	0.092	0.062	17.177	0.788	0.788	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.894	0.942	17.929	15.789	15.789	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.067	0.020	15.312	-1.219	-1.219	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.018	-0.017	11.235	1.104	1.104	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.054	0.040	10.290	-0.759	-0.759	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.789	-0.887	11.233	-20.686	-20.686	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.776	0.868	13.397	19.280	19.280	0.000	0.000	0.000	0.000
18	A	18	TRP	0	0.033	0.023	7.022	0.453	0.453	0.000	0.000	0.000	0.000
19	A	19	ASP	-1	-0.774	-0.862	10.793	-21.290	-21.290	0.000	0.000	0.000	0.000
20	A	20	ALA	0	0.058	0.022	12.609	0.857	0.857	0.000	0.000	0.000	0.000
21	A	21	TYR	0	-0.011	-0.022	11.313	0.729	0.729	0.000	0.000	0.000	0.000
22	A	22	LEU	0	0.010	0.003	9.339	0.782	0.782	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.862	0.911	12.840	20.971	20.971	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.038	-0.033	16.634	1.010	1.010	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.071	-0.015	13.516	0.559	0.559	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.803	-0.906	16.899	-14.280	-14.280	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.919	-0.954	18.520	-13.432	-13.432	0.000	0.000	0.000	0.000
28	A	28	GLY	0	-0.062	-0.029	20.886	0.683	0.683	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.800	0.891	21.731	14.268	14.268	0.000	0.000	0.000	0.000
30	A	30	GLN	0	-0.044	-0.026	17.908	-0.149	-0.149	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.825	-0.886	21.260	-11.758	-11.758	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.023	0.015	21.741	-0.713	-0.713	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.840	-0.907	20.479	-14.967	-14.967	0.000	0.000	0.000	0.000
34	A	34	ALA	0	0.118	0.066	17.843	-1.036	-1.036	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.035	-0.031	14.357	-0.097	-0.097	0.000	0.000	0.000	0.000
36	A	36	ASP	0	-0.067	-0.038	18.227	0.425	0.425	0.000	0.000	0.000	0.000
37	A	37	GLU	0	0.036	0.015	21.499	0.380	0.380	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.037	0.028	15.496	0.397	0.397	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.827	0.917	19.006	12.871	12.871	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.027	-0.017	14.599	-0.088	-0.088	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.998	0.996	18.638	11.623	11.623	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.985	0.974	19.930	14.723	14.723	0.000	0.000	0.000	0.000
43	A	43	TYR	0	0.143	0.048	18.580	-1.022	-1.022	0.000	0.000	0.000	0.000
44	A	44	CYS	0	-0.005	0.004	16.762	-1.116	-1.116	0.000	0.000	0.000	0.000
45	A	45	CYS	0	0.005	-0.021	14.751	-0.660	-0.660	0.000	0.000	0.000	0.000
46	A	46	ARG	1	0.824	0.903	13.895	14.311	14.311	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.953	0.980	11.892	21.648	21.648	0.000	0.000	0.000	0.000
48	A	48	MET	0	-0.057	0.001	9.312	-1.551	-1.551	0.000	0.000	0.000	0.000
49	A	49	VAL	0	0.025	0.017	8.544	-3.368	-3.368	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.010	-0.010	9.631	-1.783	-1.783	0.000	0.000	0.000	0.000
51	A	51	THR	0	-0.018	-0.019	9.301	1.878	1.878	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.888	0.937	6.521	38.581	38.581	0.000	0.000	0.000	0.000
60	A	60	LEU	0	0.028	0.004	7.130	2.614	2.614	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.922	0.980	9.634	23.008	23.008	0.000	0.000	0.000	0.000
62	A	62	TYR	0	-0.060	-0.025	8.859	1.084	1.084	0.000	0.000	0.000	0.000
63	A	63	ASN	0	-0.032	-0.015	12.114	0.258	0.258	0.000	0.000	0.000	0.000
64	A	64	PRO	-1	-0.925	-0.947	13.031	-18.503	-18.503	0.000	0.000	0.000	0.000

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