FMO DATABASE

FMODB ID: 7YR2K

Calculation Name: 2ENT-A-Other547

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2ENT

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UIH9

Base Structure: SolutionNMR

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	48
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-179006.649725
FMO2-HF: Nuclear repulsion	161038.791263
FMO2-HF: Total energy	-17967.858462
FMO2-MP2: Total energy	-18019.098277

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:339:GLY)

Summations of interaction energy for fragment #1(A:339:GLY)

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.
54.909	56.312	-0.006	-0.69	-0.707	-0.004

Interaction energy analysis for fragmet #1(A:339:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.854 / q_NPA : 0.913

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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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	341	SER	0	0.017	0.022	3.684	7.287	8.298	-0.007	-0.413	-0.591	-0.002
4	A	342	GLY	0	0.022	0.008	3.577	-15.079	-14.687	0.001	-0.277	-0.116	-0.002
5	A	343	SER	0	-0.052	-0.017	5.885	2.707	2.707	0.000	0.000	0.000	0.000
6	A	344	SER	0	-0.013	-0.016	8.933	1.365	1.365	0.000	0.000	0.000	0.000
7	A	345	GLY	0	0.052	0.031	12.308	1.274	1.274	0.000	0.000	0.000	0.000
8	A	346	THR	0	-0.006	-0.003	13.160	0.690	0.690	0.000	0.000	0.000	0.000
9	A	347	GLY	0	0.029	0.002	12.506	-2.159	-2.159	0.000	0.000	0.000	0.000
10	A	348	GLU	-1	-0.924	-0.936	14.059	-15.190	-15.190	0.000	0.000	0.000	0.000
11	A	349	LYS	1	0.902	0.946	13.411	21.638	21.638	0.000	0.000	0.000	0.000
12	A	350	PRO	0	0.044	0.029	18.750	-0.015	-0.015	0.000	0.000	0.000	0.000
13	A	351	PHE	0	0.037	0.023	22.135	0.545	0.545	0.000	0.000	0.000	0.000
14	A	352	ALA	0	0.018	-0.002	22.043	-0.695	-0.695	0.000	0.000	0.000	0.000
15	A	353	CYS	0	-0.067	-0.035	22.556	0.907	0.907	0.000	0.000	0.000	0.000
16	A	354	THR	0	0.030	0.009	24.426	-0.046	-0.046	0.000	0.000	0.000	0.000
17	A	355	TRP	0	-0.012	-0.003	26.213	0.376	0.376	0.000	0.000	0.000	0.000
18	A	356	PRO	0	0.067	0.028	26.313	-0.487	-0.487	0.000	0.000	0.000	0.000
19	A	357	GLY	0	0.040	0.014	24.718	-0.038	-0.038	0.000	0.000	0.000	0.000
20	A	358	CYS	0	-0.107	-0.032	22.226	-0.774	-0.774	0.000	0.000	0.000	0.000
21	A	359	GLY	0	0.069	0.036	18.966	0.230	0.230	0.000	0.000	0.000	0.000
22	A	360	TRP	0	-0.027	-0.012	14.702	-0.939	-0.939	0.000	0.000	0.000	0.000
23	A	361	ARG	1	0.954	0.977	17.770	16.843	16.843	0.000	0.000	0.000	0.000
24	A	362	PHE	0	-0.008	-0.005	17.575	-1.105	-1.105	0.000	0.000	0.000	0.000
25	A	363	SER	0	0.016	-0.020	17.591	0.070	0.070	0.000	0.000	0.000	0.000
26	A	364	ARG	1	0.952	0.974	18.383	16.162	16.162	0.000	0.000	0.000	0.000
27	A	365	SER	0	0.057	0.014	23.240	-0.348	-0.348	0.000	0.000	0.000	0.000
28	A	366	ASP	-1	-0.839	-0.905	25.767	-11.569	-11.569	0.000	0.000	0.000	0.000
29	A	367	GLU	-1	-0.895	-0.951	19.876	-15.574	-15.574	0.000	0.000	0.000	0.000
30	A	368	LEU	0	-0.024	0.005	22.490	-0.184	-0.184	0.000	0.000	0.000	0.000
31	A	369	SER	0	-0.023	-0.017	24.003	0.183	0.183	0.000	0.000	0.000	0.000
32	A	370	ARG	1	0.902	0.935	21.129	14.623	14.623	0.000	0.000	0.000	0.000
33	A	371	HIS	0	0.093	0.060	21.034	0.362	0.362	0.000	0.000	0.000	0.000
34	A	372	ARG	1	0.932	0.959	23.786	11.288	11.288	0.000	0.000	0.000	0.000
35	A	373	ARG	1	0.952	0.980	27.050	10.676	10.676	0.000	0.000	0.000	0.000
36	A	374	SER	0	-0.048	-0.017	24.295	0.137	0.137	0.000	0.000	0.000	0.000
37	A	375	HIS	1	0.796	0.898	24.120	12.398	12.398	0.000	0.000	0.000	0.000
38	A	376	SER	0	0.040	0.028	28.967	0.127	0.127	0.000	0.000	0.000	0.000
39	A	377	GLY	0	0.026	0.003	32.781	0.042	0.042	0.000	0.000	0.000	0.000
40	A	378	VAL	0	-0.009	-0.008	34.170	0.062	0.062	0.000	0.000	0.000	0.000
41	A	379	LYS	1	0.932	0.987	34.945	8.208	8.208	0.000	0.000	0.000	0.000
42	A	380	PRO	0	0.005	0.002	35.042	0.224	0.224	0.000	0.000	0.000	0.000
43	A	381	SER	0	0.010	0.008	36.606	0.122	0.122	0.000	0.000	0.000	0.000
44	A	382	GLY	0	-0.002	-0.025	39.321	-0.014	-0.014	0.000	0.000	0.000	0.000
45	A	383	PRO	0	0.014	0.025	41.837	-0.096	-0.096	0.000	0.000	0.000	0.000
46	A	384	SER	0	-0.009	-0.013	41.663	0.107	0.107	0.000	0.000	0.000	0.000
47	A	385	SER	0	-0.069	-0.061	35.557	-0.063	-0.063	0.000	0.000	0.000	0.000
48	A	386	GLY	-1	-0.848	-0.891	34.106	-9.369	-9.369	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:339:GLY)