FMO DATABASE

FMODB ID: JY9Z9

Calculation Name: 5X4Z-F-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: F

ChEMBL ID:

UniProt ID: F2QPE6

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

Total energy (hartree)

FMO2-HF: Electronic energy	-551862.903991
FMO2-HF: Nuclear repulsion	517986.32122
FMO2-HF: Total energy	-33876.582771
FMO2-MP2: Total energy	-33975.018819

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:72:LEU)

Summations of interaction energy for fragment #1(A:72:LEU)

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.
-37.265	-32.484	7.387	-3.744	-8.427	-0.038

Interaction energy analysis for fragmet #1(A:72:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.850 / q_NPA : 0.920

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	74	ILE	0	0.100	0.054	2.813	-2.347	0.922	0.712	-1.811	-2.171	-0.013
69	A	140	ASP	-1	-0.829	-0.887	4.300	-36.298	-36.101	-0.001	-0.041	-0.156	0.000
70	A	141	GLY	0	-0.010	0.002	4.129	-1.748	-1.533	0.001	-0.067	-0.149	0.000
71	A	142	SER	0	-0.085	-0.066	2.187	-9.626	-8.273	5.811	-3.336	-3.829	-0.019
72	A	143	TYR	0	-0.018	-0.037	2.333	9.141	8.860	0.865	1.513	-2.097	-0.006
73	A	144	GLU	-1	-0.690	-0.798	5.184	-24.327	-24.299	-0.001	-0.002	-0.025	0.000
4	A	75	LEU	0	0.005	0.024	5.782	0.386	0.386	0.000	0.000	0.000	0.000
5	A	76	LYS	1	0.951	0.958	9.487	22.966	22.966	0.000	0.000	0.000	0.000
6	A	77	GLU	-1	-0.879	-0.933	12.473	-17.662	-17.662	0.000	0.000	0.000	0.000
7	A	78	GLU	-1	-0.935	-0.974	8.972	-27.586	-27.586	0.000	0.000	0.000	0.000
8	A	79	ARG	1	0.735	0.865	9.992	21.165	21.165	0.000	0.000	0.000	0.000
9	A	80	THR	0	-0.008	-0.010	10.906	1.584	1.584	0.000	0.000	0.000	0.000
10	A	81	THR	0	-0.094	-0.060	11.304	1.455	1.455	0.000	0.000	0.000	0.000
11	A	82	THR	0	0.027	0.008	13.902	0.239	0.239	0.000	0.000	0.000	0.000
12	A	83	PRO	0	0.024	0.017	17.267	-0.333	-0.333	0.000	0.000	0.000	0.000
13	A	84	TYR	0	0.014	0.019	18.959	0.278	0.278	0.000	0.000	0.000	0.000
14	A	85	LEU	0	-0.023	-0.002	19.340	-0.733	-0.733	0.000	0.000	0.000	0.000
15	A	86	THR	0	0.003	-0.016	18.479	0.728	0.728	0.000	0.000	0.000	0.000
16	A	87	LYS	1	1.020	1.000	21.208	10.902	10.902	0.000	0.000	0.000	0.000
17	A	88	TYR	0	0.009	-0.006	20.026	0.300	0.300	0.000	0.000	0.000	0.000
18	A	89	GLU	-1	-0.760	-0.832	16.059	-16.596	-16.596	0.000	0.000	0.000	0.000
19	A	90	ARG	1	1.011	1.012	19.871	10.513	10.513	0.000	0.000	0.000	0.000
20	A	91	ALA	0	0.010	0.009	23.459	0.207	0.207	0.000	0.000	0.000	0.000
21	A	92	ARG	1	0.976	0.988	15.979	16.372	16.372	0.000	0.000	0.000	0.000
22	A	93	ILE	0	-0.003	0.011	19.885	-0.044	-0.044	0.000	0.000	0.000	0.000
23	A	94	LEU	0	0.009	0.013	22.484	0.185	0.185	0.000	0.000	0.000	0.000
24	A	95	GLY	0	0.038	0.021	25.538	0.282	0.282	0.000	0.000	0.000	0.000
25	A	96	THR	0	-0.069	-0.057	21.134	0.030	0.030	0.000	0.000	0.000	0.000
26	A	97	ARG	1	0.757	0.837	24.123	11.725	11.725	0.000	0.000	0.000	0.000
27	A	98	ALA	0	0.051	0.033	26.001	0.255	0.255	0.000	0.000	0.000	0.000
28	A	99	LEU	0	-0.006	0.002	25.225	0.244	0.244	0.000	0.000	0.000	0.000
29	A	100	GLN	0	-0.018	-0.011	22.183	0.262	0.262	0.000	0.000	0.000	0.000
30	A	101	ILE	0	0.016	0.008	27.706	0.193	0.193	0.000	0.000	0.000	0.000
31	A	102	SER	0	-0.060	-0.043	30.965	0.307	0.307	0.000	0.000	0.000	0.000
32	A	103	MET	0	-0.053	-0.022	27.239	0.240	0.240	0.000	0.000	0.000	0.000
33	A	104	ASN	0	-0.041	-0.018	31.427	0.235	0.235	0.000	0.000	0.000	0.000
34	A	105	ALA	0	-0.021	0.011	28.182	-0.066	-0.066	0.000	0.000	0.000	0.000
35	A	106	PRO	0	0.005	-0.002	28.314	0.262	0.262	0.000	0.000	0.000	0.000
36	A	107	VAL	0	0.004	0.012	29.455	-0.381	-0.381	0.000	0.000	0.000	0.000
37	A	108	LEU	0	-0.063	-0.031	26.493	0.087	0.087	0.000	0.000	0.000	0.000
38	A	109	VAL	0	-0.044	-0.032	30.880	-0.061	-0.061	0.000	0.000	0.000	0.000
39	A	110	ASP	-1	-0.863	-0.924	33.864	-8.345	-8.345	0.000	0.000	0.000	0.000
40	A	111	ILE	0	0.000	-0.005	36.429	-0.036	-0.036	0.000	0.000	0.000	0.000
41	A	112	GLU	-1	-0.886	-0.931	38.695	-7.668	-7.668	0.000	0.000	0.000	0.000
42	A	113	GLY	0	-0.025	-0.015	41.646	0.106	0.106	0.000	0.000	0.000	0.000
43	A	114	GLU	-1	-0.880	-0.933	38.227	-7.968	-7.968	0.000	0.000	0.000	0.000
44	A	115	THR	0	-0.002	-0.020	39.428	-0.043	-0.043	0.000	0.000	0.000	0.000
45	A	116	ASP	-1	-0.819	-0.900	36.094	-8.796	-8.796	0.000	0.000	0.000	0.000
46	A	117	PRO	0	0.017	0.005	32.436	-0.132	-0.132	0.000	0.000	0.000	0.000
47	A	118	LEU	0	-0.014	-0.012	30.271	-0.402	-0.402	0.000	0.000	0.000	0.000
48	A	119	GLN	0	-0.012	-0.019	32.272	-0.407	-0.407	0.000	0.000	0.000	0.000
49	A	120	ILE	0	-0.022	-0.002	32.002	-0.085	-0.085	0.000	0.000	0.000	0.000
50	A	121	ALA	0	0.004	0.002	28.401	-0.218	-0.218	0.000	0.000	0.000	0.000
51	A	122	MET	0	-0.038	-0.033	29.323	-0.386	-0.386	0.000	0.000	0.000	0.000
52	A	123	LYS	1	0.868	0.943	31.339	8.200	8.200	0.000	0.000	0.000	0.000
53	A	124	GLU	-1	-0.742	-0.861	28.299	-11.094	-11.094	0.000	0.000	0.000	0.000
54	A	125	LEU	0	-0.038	-0.027	25.130	-0.343	-0.343	0.000	0.000	0.000	0.000
55	A	126	SER	0	-0.023	-0.009	27.986	-0.077	-0.077	0.000	0.000	0.000	0.000
56	A	127	GLN	0	0.004	0.006	30.870	-0.031	-0.031	0.000	0.000	0.000	0.000
57	A	128	ARG	1	0.882	0.937	22.940	12.461	12.461	0.000	0.000	0.000	0.000
58	A	129	LYS	1	0.870	0.955	25.468	9.462	9.462	0.000	0.000	0.000	0.000
59	A	130	ILE	0	0.056	0.020	22.834	0.058	0.058	0.000	0.000	0.000	0.000
60	A	131	PRO	0	-0.036	-0.004	21.944	-0.567	-0.567	0.000	0.000	0.000	0.000
61	A	132	LEU	0	-0.016	-0.018	18.760	-0.470	-0.470	0.000	0.000	0.000	0.000
62	A	133	VAL	0	-0.025	-0.023	13.217	0.191	0.191	0.000	0.000	0.000	0.000
63	A	134	ILE	0	-0.021	-0.003	13.253	-0.208	-0.208	0.000	0.000	0.000	0.000
64	A	135	ARG	1	0.831	0.890	6.466	33.579	33.579	0.000	0.000	0.000	0.000
65	A	136	ARG	1	0.784	0.839	10.110	18.437	18.437	0.000	0.000	0.000	0.000
66	A	137	TYR	0	0.005	-0.007	5.431	-0.853	-0.853	0.000	0.000	0.000	0.000
67	A	138	LEU	0	0.026	0.026	6.542	3.054	3.054	0.000	0.000	0.000	0.000
68	A	139	PRO	0	-0.027	-0.026	7.098	-1.465	-1.465	0.000	0.000	0.000	0.000
74	A	145	ASP	-1	-0.809	-0.869	7.984	-29.681	-29.681	0.000	0.000	0.000	0.000
75	A	146	TRP	0	-0.050	-0.035	10.416	1.720	1.720	0.000	0.000	0.000	0.000
76	A	147	GLY	0	0.011	0.011	14.060	0.117	0.117	0.000	0.000	0.000	0.000
77	A	148	CYS	0	0.047	0.016	17.238	0.520	0.520	0.000	0.000	0.000	0.000
78	A	149	ASP	0	-0.033	-0.007	20.488	0.727	0.727	0.000	0.000	0.000	0.000
79	A	150	GLU	0	-0.040	-0.019	15.011	0.015	0.015	0.000	0.000	0.000	0.000
80	A	151	LEU	0	-0.025	-0.001	16.336	0.505	0.505	0.000	0.000	0.000	0.000
81	A	152	ILE	0	0.008	0.006	20.088	0.436	0.436	0.000	0.000	0.000	0.000
82	A	153	VAL	0	-0.030	-0.031	23.351	-0.291	-0.291	0.000	0.000	0.000	0.000
83	A	154	ASP	-1	-0.885	-0.938	25.547	-9.876	-9.876	0.000	0.000	0.000	0.000
84	A	155	ASN	-1	-0.982	-0.986	26.805	-10.146	-10.146	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:72:LEU)