FMO DATABASE

FMODB ID: QL5RY

Calculation Name: 3B0Z-B-Xray547

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3B0Z

Chain ID: B

ChEMBL ID:

UniProt ID: P40727

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	84
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-530230.243508
FMO2-HF: Nuclear repulsion	498103.884287
FMO2-HF: Total energy	-32126.359222
FMO2-MP2: Total energy	-32222.403592

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:270:PRO)

Summations of interaction energy for fragment #1(A:270:PRO)

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.
53.903	56.219	2.173	-1.578	-2.912	-0.009

Interaction energy analysis for fragmet #1(A:270:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.876 / q_NPA : 0.929

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	272	HIS	0	0.029	0.025	3.522	-2.418	-0.494	0.002	-0.889	-1.037	-0.002
26	A	295	GLY	0	-0.011	0.007	4.074	2.218	2.308	-0.001	-0.016	-0.074	0.000
27	A	296	LEU	0	0.020	-0.009	4.117	-3.423	-3.095	0.001	-0.080	-0.249	0.000
28	A	297	ILE	0	0.056	0.030	5.106	1.631	1.646	-0.001	-0.002	-0.011	0.000
30	A	299	LEU	0	-0.013	0.003	2.483	-0.527	-0.568	2.172	-0.591	-1.541	-0.007
4	A	273	TYR	0	0.027	0.002	5.812	1.243	1.243	0.000	0.000	0.000	0.000
5	A	274	SER	0	-0.014	-0.022	8.578	-1.044	-1.044	0.000	0.000	0.000	0.000
6	A	275	VAL	0	-0.023	-0.018	10.592	0.296	0.296	0.000	0.000	0.000	0.000
7	A	276	ALA	0	0.011	0.026	14.264	0.127	0.127	0.000	0.000	0.000	0.000
8	A	277	LEU	0	0.024	-0.002	16.746	0.415	0.415	0.000	0.000	0.000	0.000
9	A	278	GLN	0	0.014	0.008	20.341	-0.235	-0.235	0.000	0.000	0.000	0.000
10	A	279	TYR	0	-0.030	-0.041	23.291	0.008	0.008	0.000	0.000	0.000	0.000
11	A	280	ASP	-1	-0.818	-0.909	26.672	-9.629	-9.629	0.000	0.000	0.000	0.000
12	A	281	GLU	-1	-0.914	-0.946	29.669	-9.695	-9.695	0.000	0.000	0.000	0.000
13	A	282	ASN	0	-0.097	-0.058	32.248	0.464	0.464	0.000	0.000	0.000	0.000
14	A	283	LYS	1	0.983	0.964	32.882	7.966	7.966	0.000	0.000	0.000	0.000
15	A	284	MET	0	-0.049	-0.015	33.846	-0.053	-0.053	0.000	0.000	0.000	0.000
16	A	285	SER	0	0.002	0.029	32.474	0.145	0.145	0.000	0.000	0.000	0.000
17	A	286	ALA	0	-0.010	0.000	28.304	-0.231	-0.231	0.000	0.000	0.000	0.000
18	A	287	PRO	0	0.024	0.007	24.077	0.030	0.030	0.000	0.000	0.000	0.000
19	A	288	LYS	1	0.981	1.006	24.391	11.362	11.362	0.000	0.000	0.000	0.000
20	A	289	VAL	0	-0.026	-0.011	18.066	-0.481	-0.481	0.000	0.000	0.000	0.000
21	A	290	VAL	0	-0.023	-0.010	18.939	0.428	0.428	0.000	0.000	0.000	0.000
22	A	291	ALA	0	0.026	0.012	15.125	-0.112	-0.112	0.000	0.000	0.000	0.000
23	A	292	LYS	1	0.849	0.917	13.602	16.109	16.109	0.000	0.000	0.000	0.000
24	A	293	GLY	0	0.026	0.006	10.472	0.587	0.587	0.000	0.000	0.000	0.000
25	A	294	ALA	0	0.024	0.008	6.965	-0.980	-0.980	0.000	0.000	0.000	0.000
29	A	298	ALA	0	-0.001	0.016	5.614	1.892	1.892	0.000	0.000	0.000	0.000
31	A	300	ARG	1	0.921	0.951	6.200	23.616	23.616	0.000	0.000	0.000	0.000
32	A	301	ILE	0	0.013	0.005	9.380	1.862	1.862	0.000	0.000	0.000	0.000
33	A	302	ARG	1	0.897	0.946	6.706	35.394	35.394	0.000	0.000	0.000	0.000
34	A	303	GLU	-1	-0.865	-0.907	10.053	-23.279	-23.279	0.000	0.000	0.000	0.000
35	A	304	ILE	0	0.016	0.011	11.752	1.450	1.450	0.000	0.000	0.000	0.000
36	A	305	GLY	0	0.022	0.003	13.955	1.251	1.251	0.000	0.000	0.000	0.000
37	A	306	ALA	0	-0.003	-0.003	13.861	1.123	1.123	0.000	0.000	0.000	0.000
38	A	307	GLU	-1	-0.911	-0.944	15.573	-15.872	-15.872	0.000	0.000	0.000	0.000
39	A	308	HIS	0	-0.071	-0.045	17.418	1.482	1.482	0.000	0.000	0.000	0.000
40	A	309	ARG	1	0.859	0.931	19.062	14.116	14.116	0.000	0.000	0.000	0.000
41	A	310	VAL	0	0.007	0.010	17.808	0.633	0.633	0.000	0.000	0.000	0.000
42	A	311	PRO	0	-0.019	-0.012	18.245	-0.804	-0.804	0.000	0.000	0.000	0.000
43	A	312	THR	0	-0.029	-0.013	13.281	-0.610	-0.610	0.000	0.000	0.000	0.000
44	A	313	LEU	0	0.018	0.011	16.157	0.058	0.058	0.000	0.000	0.000	0.000
45	A	314	GLU	-1	-0.970	-0.977	11.435	-26.746	-26.746	0.000	0.000	0.000	0.000
46	A	315	ALA	0	0.072	0.031	14.639	1.086	1.086	0.000	0.000	0.000	0.000
47	A	316	PRO	0	0.024	0.005	12.806	0.139	0.139	0.000	0.000	0.000	0.000
48	A	317	PRO	0	-0.027	-0.032	14.456	-0.528	-0.528	0.000	0.000	0.000	0.000
49	A	318	LEU	0	0.063	0.039	17.130	0.080	0.080	0.000	0.000	0.000	0.000
50	A	319	ALA	0	0.017	0.016	12.548	0.153	0.153	0.000	0.000	0.000	0.000
51	A	320	ARG	1	0.952	0.975	12.467	20.309	20.309	0.000	0.000	0.000	0.000
52	A	321	ALA	0	-0.024	-0.001	14.662	0.455	0.455	0.000	0.000	0.000	0.000
53	A	322	LEU	0	0.053	0.016	16.763	0.583	0.583	0.000	0.000	0.000	0.000
54	A	323	TYR	0	0.016	0.011	11.694	-0.072	-0.072	0.000	0.000	0.000	0.000
55	A	324	ARG	1	0.850	0.923	15.201	15.870	15.870	0.000	0.000	0.000	0.000
56	A	325	HIS	0	0.017	0.007	17.575	0.081	0.081	0.000	0.000	0.000	0.000
57	A	326	ALA	0	0.023	0.026	19.606	0.664	0.664	0.000	0.000	0.000	0.000
58	A	327	GLU	-1	-0.887	-0.934	19.805	-12.499	-12.499	0.000	0.000	0.000	0.000
59	A	328	ILE	0	-0.020	-0.025	17.064	-0.071	-0.071	0.000	0.000	0.000	0.000
60	A	329	GLY	0	-0.006	0.003	21.111	0.368	0.368	0.000	0.000	0.000	0.000
61	A	330	GLN	0	-0.018	0.004	23.913	0.524	0.524	0.000	0.000	0.000	0.000
62	A	331	GLN	0	0.003	-0.008	24.393	-0.418	-0.418	0.000	0.000	0.000	0.000
63	A	332	ILE	0	-0.047	-0.019	22.132	-0.257	-0.257	0.000	0.000	0.000	0.000
64	A	333	PRO	0	0.047	0.019	23.281	0.471	0.471	0.000	0.000	0.000	0.000
65	A	334	GLY	0	0.065	0.017	26.321	-0.181	-0.181	0.000	0.000	0.000	0.000
66	A	335	GLN	0	-0.043	-0.025	24.060	0.070	0.070	0.000	0.000	0.000	0.000
67	A	336	LEU	0	-0.039	-0.026	20.963	-0.339	-0.339	0.000	0.000	0.000	0.000
68	A	337	TYR	0	0.018	0.016	25.011	-0.135	-0.135	0.000	0.000	0.000	0.000
69	A	338	ALA	0	0.038	0.021	27.395	-0.066	-0.066	0.000	0.000	0.000	0.000
70	A	339	ALA	0	0.056	0.029	22.891	-0.061	-0.061	0.000	0.000	0.000	0.000
71	A	340	VAL	0	0.008	-0.004	21.689	-0.350	-0.350	0.000	0.000	0.000	0.000
72	A	341	ALA	0	0.018	0.017	24.046	0.028	0.028	0.000	0.000	0.000	0.000
73	A	342	GLU	-1	-0.939	-0.963	25.025	-12.222	-12.222	0.000	0.000	0.000	0.000
74	A	343	VAL	0	-0.012	-0.016	20.467	-0.136	-0.136	0.000	0.000	0.000	0.000
75	A	344	LEU	0	-0.020	-0.002	23.385	-0.048	-0.048	0.000	0.000	0.000	0.000
76	A	345	ALA	0	0.047	0.018	26.197	0.205	0.205	0.000	0.000	0.000	0.000
77	A	346	TRP	0	0.010	0.007	19.474	0.057	0.057	0.000	0.000	0.000	0.000
78	A	347	VAL	0	-0.023	-0.015	23.139	0.048	0.048	0.000	0.000	0.000	0.000
79	A	348	TRP	0	-0.040	-0.038	25.462	0.286	0.286	0.000	0.000	0.000	0.000
80	A	349	GLN	0	-0.063	-0.027	26.765	0.178	0.178	0.000	0.000	0.000	0.000
81	A	350	LEU	0	0.040	0.020	21.939	0.168	0.168	0.000	0.000	0.000	0.000
82	A	351	LYS	1	0.865	0.935	26.007	10.951	10.951	0.000	0.000	0.000	0.000
83	A	352	ARG	1	0.871	0.939	28.904	10.156	10.156	0.000	0.000	0.000	0.000
84	A	353	TRP	-1	-0.884	-0.916	26.586	-11.411	-11.411	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:270:PRO)