FMO DATABASE

FMODB ID: ZZJYN

Calculation Name: 4ZDT-D-Xray547

Preferred Name:

Target Type:

Ligand Name: sulfate ion | glycerol | zinc ion

Ligand 3-letter code: SO4 | GOL | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4ZDT

Chain ID: D

ChEMBL ID:

UniProt ID: Q9P7M3

Base Structure: X-ray

Registration Date: 2025-10-05

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	69
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-428594.519089
FMO2-HF: Nuclear repulsion	400771.849802
FMO2-HF: Total energy	-27822.669287
FMO2-MP2: Total energy	-27903.401333

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:349:GLY)

Summations of interaction energy for fragment #1(A:349: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.
80.536	81.69	-0.015	-0.47	-0.669	-0.002

Interaction energy analysis for fragmet #1(A:349:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.889 / q_NPA : 0.934

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	351	MET	0	0.096	0.046	3.848	2.798	3.863	-0.014	-0.458	-0.593	-0.002
5	A	353	VAL	0	0.029	0.035	4.451	3.080	3.169	-0.001	-0.012	-0.076	0.000
4	A	352	ILE	0	0.100	0.063	7.079	1.664	1.664	0.000	0.000	0.000	0.000
6	A	354	THR	0	-0.036	-0.025	5.242	4.429	4.429	0.000	0.000	0.000	0.000
7	A	355	GLN	0	-0.033	-0.032	7.638	2.300	2.300	0.000	0.000	0.000	0.000
8	A	356	THR	0	0.032	0.005	10.222	2.591	2.591	0.000	0.000	0.000	0.000
9	A	357	HIS	0	-0.010	-0.017	7.562	0.998	0.998	0.000	0.000	0.000	0.000
10	A	358	ARG	1	0.909	0.970	10.727	25.355	25.355	0.000	0.000	0.000	0.000
11	A	359	ALA	0	0.059	0.029	13.321	1.414	1.414	0.000	0.000	0.000	0.000
12	A	360	ILE	0	0.021	0.011	12.946	1.261	1.261	0.000	0.000	0.000	0.000
13	A	361	SER	0	0.011	0.003	14.356	1.131	1.131	0.000	0.000	0.000	0.000
14	A	362	GLN	0	-0.039	-0.017	16.879	0.235	0.235	0.000	0.000	0.000	0.000
15	A	363	VAL	0	0.018	0.009	19.124	0.848	0.848	0.000	0.000	0.000	0.000
16	A	364	VAL	0	-0.022	-0.021	19.283	0.759	0.759	0.000	0.000	0.000	0.000
17	A	365	LYS	1	0.914	0.963	18.988	15.720	15.720	0.000	0.000	0.000	0.000
18	A	366	GLN	0	-0.032	-0.009	21.967	0.033	0.033	0.000	0.000	0.000	0.000
19	A	367	ALA	0	-0.037	0.000	24.803	0.457	0.457	0.000	0.000	0.000	0.000
20	A	368	LYS	1	0.972	0.970	26.600	10.069	10.069	0.000	0.000	0.000	0.000
21	A	369	ASP	-1	-0.778	-0.835	29.116	-10.378	-10.378	0.000	0.000	0.000	0.000
22	A	370	ASN	0	0.070	0.025	27.313	-0.324	-0.324	0.000	0.000	0.000	0.000
23	A	371	SER	0	0.002	-0.023	27.561	-0.324	-0.324	0.000	0.000	0.000	0.000
24	A	372	VAL	0	0.019	0.007	22.076	-0.026	-0.026	0.000	0.000	0.000	0.000
25	A	373	TRP	0	0.025	0.009	23.034	-0.279	-0.279	0.000	0.000	0.000	0.000
26	A	374	ILE	0	0.020	0.009	24.660	-0.077	-0.077	0.000	0.000	0.000	0.000
27	A	375	LYS	1	0.970	0.997	25.664	11.210	11.210	0.000	0.000	0.000	0.000
28	A	376	ILE	0	0.004	0.003	20.058	-0.063	-0.063	0.000	0.000	0.000	0.000
29	A	377	LEU	0	-0.055	-0.031	23.673	-0.099	-0.099	0.000	0.000	0.000	0.000
30	A	378	THR	0	-0.048	-0.035	25.975	0.318	0.318	0.000	0.000	0.000	0.000
31	A	379	TYR	0	-0.020	-0.006	23.318	0.362	0.362	0.000	0.000	0.000	0.000
32	A	380	SER	0	-0.026	0.003	25.975	0.079	0.079	0.000	0.000	0.000	0.000
33	A	381	ALA	0	0.021	0.003	24.198	-0.354	-0.354	0.000	0.000	0.000	0.000
34	A	382	ILE	0	-0.036	-0.020	20.352	0.370	0.370	0.000	0.000	0.000	0.000
35	A	383	ASP	-1	-0.771	-0.871	22.121	-12.454	-12.454	0.000	0.000	0.000	0.000
36	A	384	VAL	0	0.018	-0.009	17.735	-0.166	-0.166	0.000	0.000	0.000	0.000
37	A	385	GLU	-1	-0.885	-0.941	20.526	-12.973	-12.973	0.000	0.000	0.000	0.000
38	A	386	GLU	-1	-0.953	-0.978	23.010	-10.906	-10.906	0.000	0.000	0.000	0.000
39	A	387	PHE	0	-0.029	-0.019	17.541	0.145	0.145	0.000	0.000	0.000	0.000
40	A	388	GLN	0	0.008	-0.014	18.853	0.179	0.179	0.000	0.000	0.000	0.000
41	A	389	LEU	0	0.019	0.004	20.995	0.124	0.124	0.000	0.000	0.000	0.000
42	A	390	TRP	0	-0.087	-0.046	21.850	0.197	0.197	0.000	0.000	0.000	0.000
43	A	391	LEU	0	0.002	-0.006	17.606	0.207	0.207	0.000	0.000	0.000	0.000
44	A	392	LYS	1	0.979	1.002	21.725	12.137	12.137	0.000	0.000	0.000	0.000
45	A	393	ARG	1	0.894	0.940	23.338	11.213	11.213	0.000	0.000	0.000	0.000
46	A	394	LYS	1	0.771	0.899	23.303	11.498	11.498	0.000	0.000	0.000	0.000
47	A	395	ASN	0	-0.022	-0.007	23.656	-0.180	-0.180	0.000	0.000	0.000	0.000
48	A	396	LEU	0	-0.001	0.008	16.210	-0.435	-0.435	0.000	0.000	0.000	0.000
49	A	397	ASN	0	-0.017	-0.013	19.459	0.333	0.333	0.000	0.000	0.000	0.000
50	A	398	VAL	0	0.032	0.015	14.672	-0.959	-0.959	0.000	0.000	0.000	0.000
51	A	399	SER	0	0.044	0.023	13.145	0.864	0.864	0.000	0.000	0.000	0.000
52	A	400	LEU	0	0.086	0.033	14.958	-0.859	-0.859	0.000	0.000	0.000	0.000
53	A	401	ASP	-1	-0.832	-0.910	12.099	-20.365	-20.365	0.000	0.000	0.000	0.000
54	A	402	LEU	0	-0.057	-0.021	8.833	-1.665	-1.665	0.000	0.000	0.000	0.000
55	A	403	ILE	0	0.017	0.016	11.435	-0.802	-0.802	0.000	0.000	0.000	0.000
56	A	404	LYS	1	0.972	0.983	13.419	17.988	17.988	0.000	0.000	0.000	0.000
57	A	405	SER	0	-0.007	-0.006	8.125	-1.312	-1.312	0.000	0.000	0.000	0.000
58	A	406	TRP	0	-0.049	-0.044	9.824	-1.293	-1.293	0.000	0.000	0.000	0.000
59	A	407	CYS	0	-0.029	-0.029	11.657	0.727	0.727	0.000	0.000	0.000	0.000
60	A	408	ASP	-1	-0.847	-0.919	11.901	-20.541	-20.541	0.000	0.000	0.000	0.000
61	A	409	LYS	1	0.818	0.916	6.124	32.894	32.894	0.000	0.000	0.000	0.000
62	A	410	TYR	0	-0.064	-0.047	9.272	-1.081	-1.081	0.000	0.000	0.000	0.000
63	A	411	GLY	0	0.021	0.028	14.320	1.131	1.131	0.000	0.000	0.000	0.000
64	A	412	VAL	0	-0.049	-0.018	16.680	1.128	1.128	0.000	0.000	0.000	0.000
65	A	413	LEU	0	0.025	0.019	18.334	-0.501	-0.501	0.000	0.000	0.000	0.000
66	A	414	MET	0	-0.008	0.004	15.729	0.264	0.264	0.000	0.000	0.000	0.000
67	A	415	LYS	1	0.822	0.894	20.719	11.643	11.643	0.000	0.000	0.000	0.000
68	A	416	GLY	0	0.008	-0.002	22.884	-0.577	-0.577	0.000	0.000	0.000	0.000
69	A	417	SER	-1	-0.951	-0.957	25.005	-10.624	-10.624	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:349:GLY)