FMO DATABASE

FMODB ID: N8GMQ

Calculation Name: 5X4Z-H-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: H

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	131
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1108567.861546
FMO2-HF: Nuclear repulsion	1056811.034315
FMO2-HF: Total energy	-51756.827232
FMO2-MP2: Total energy	-51907.515176

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:2:SER)

Summations of interaction energy for fragment #1(A:2:SER)

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.
-151.593	-142.229	3.18	-6.635	-5.91	-0.058

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.817 / q_NPA : 0.906

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	4	ALA	0	0.058	0.036	3.874	-1.252	0.349	-0.019	-0.809	-0.774	0.000
60	A	61	ASN	0	0.017	0.000	2.506	-16.180	-13.292	0.475	-1.860	-1.503	-0.026
61	A	62	SER	0	-0.073	-0.050	2.262	-36.083	-31.397	2.705	-3.798	-3.593	-0.031
62	A	63	LEU	-1	-0.854	-0.903	3.575	-30.665	-30.476	0.019	-0.168	-0.040	-0.001
4	A	5	LEU	0	-0.045	-0.026	5.062	0.336	0.336	0.000	0.000	0.000	0.000
5	A	6	PHE	0	-0.040	-0.037	8.351	3.132	3.132	0.000	0.000	0.000	0.000
6	A	7	ASP	-1	-0.897	-0.946	11.926	-22.403	-22.403	0.000	0.000	0.000	0.000
7	A	8	ASP	-1	-0.819	-0.866	14.471	-14.890	-14.890	0.000	0.000	0.000	0.000
8	A	9	ILE	0	0.013	0.010	18.277	-0.228	-0.228	0.000	0.000	0.000	0.000
9	A	10	PHE	0	-0.016	0.002	18.688	0.439	0.439	0.000	0.000	0.000	0.000
10	A	11	THR	0	0.038	0.034	23.583	0.158	0.158	0.000	0.000	0.000	0.000
11	A	12	VAL	0	-0.066	-0.016	26.305	-0.014	-0.014	0.000	0.000	0.000	0.000
12	A	13	GLN	0	0.007	-0.002	28.283	0.230	0.230	0.000	0.000	0.000	0.000
13	A	14	THR	0	-0.032	-0.032	30.409	0.476	0.476	0.000	0.000	0.000	0.000
14	A	15	VAL	0	0.038	0.029	29.603	-0.471	-0.471	0.000	0.000	0.000	0.000
15	A	16	ASP	-1	-0.855	-0.918	31.180	-9.030	-9.030	0.000	0.000	0.000	0.000
16	A	17	ASN	0	-0.005	-0.013	31.531	-0.391	-0.391	0.000	0.000	0.000	0.000
17	A	18	GLY	0	0.015	0.014	33.619	0.298	0.298	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.860	0.929	35.261	7.644	7.644	0.000	0.000	0.000	0.000
19	A	20	TYR	0	-0.015	-0.001	29.709	0.146	0.146	0.000	0.000	0.000	0.000
20	A	21	ASN	0	-0.003	-0.018	33.717	-0.016	-0.016	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.826	0.900	30.352	9.823	9.823	0.000	0.000	0.000	0.000
22	A	23	VAL	0	-0.030	-0.006	26.790	-0.334	-0.334	0.000	0.000	0.000	0.000
23	A	24	SER	0	0.044	0.019	27.949	0.474	0.474	0.000	0.000	0.000	0.000
24	A	25	ARG	1	0.813	0.891	26.962	10.911	10.911	0.000	0.000	0.000	0.000
25	A	26	ILE	0	0.005	0.006	25.650	0.445	0.445	0.000	0.000	0.000	0.000
26	A	27	ILE	0	-0.025	-0.013	26.071	-0.414	-0.414	0.000	0.000	0.000	0.000
27	A	28	GLY	0	0.062	0.024	26.006	0.366	0.366	0.000	0.000	0.000	0.000
28	A	29	ILE	0	-0.042	-0.003	25.288	-0.332	-0.332	0.000	0.000	0.000	0.000
29	A	30	SER	0	-0.008	-0.030	22.022	0.073	0.073	0.000	0.000	0.000	0.000
30	A	31	THR	0	-0.002	-0.029	23.911	0.730	0.730	0.000	0.000	0.000	0.000
31	A	32	THR	0	-0.051	-0.041	23.463	0.166	0.166	0.000	0.000	0.000	0.000
32	A	33	ASN	0	-0.037	-0.006	20.573	0.697	0.697	0.000	0.000	0.000	0.000
33	A	34	SER	0	0.017	0.003	23.860	-0.217	-0.217	0.000	0.000	0.000	0.000
34	A	35	ALA	0	0.015	0.011	25.680	0.334	0.334	0.000	0.000	0.000	0.000
35	A	36	ILE	0	-0.093	-0.034	20.243	-0.042	-0.042	0.000	0.000	0.000	0.000
36	A	37	LYS	1	0.862	0.925	23.140	11.613	11.613	0.000	0.000	0.000	0.000
37	A	38	LEU	0	0.012	0.008	19.052	-0.676	-0.676	0.000	0.000	0.000	0.000
38	A	39	THR	0	-0.015	-0.013	22.781	0.890	0.890	0.000	0.000	0.000	0.000
39	A	40	LEU	0	-0.004	-0.005	19.704	-0.732	-0.732	0.000	0.000	0.000	0.000
40	A	41	ASP	-1	-0.774	-0.838	23.127	-11.541	-11.541	0.000	0.000	0.000	0.000
41	A	42	ILE	0	0.045	0.011	21.542	-0.713	-0.713	0.000	0.000	0.000	0.000
42	A	43	ASN	0	-0.008	-0.014	23.644	1.009	1.009	0.000	0.000	0.000	0.000
43	A	44	ASN	0	0.032	-0.002	25.534	-0.148	-0.148	0.000	0.000	0.000	0.000
44	A	45	GLU	-1	-0.834	-0.899	28.300	-9.843	-9.843	0.000	0.000	0.000	0.000
45	A	46	MET	0	-0.088	-0.043	20.751	0.090	0.090	0.000	0.000	0.000	0.000
46	A	47	PHE	0	0.007	-0.005	23.168	-0.254	-0.254	0.000	0.000	0.000	0.000
47	A	48	PRO	0	0.006	0.011	25.674	-0.028	-0.028	0.000	0.000	0.000	0.000
48	A	49	VAL	0	-0.027	-0.001	25.167	-0.247	-0.247	0.000	0.000	0.000	0.000
49	A	50	SER	0	-0.041	-0.018	28.580	0.447	0.447	0.000	0.000	0.000	0.000
50	A	51	GLN	0	-0.105	-0.082	30.081	-0.126	-0.126	0.000	0.000	0.000	0.000
51	A	52	ASP	-1	-0.926	-0.978	31.327	-9.524	-9.524	0.000	0.000	0.000	0.000
52	A	53	ASP	-1	-0.814	-0.885	27.010	-10.929	-10.929	0.000	0.000	0.000	0.000
53	A	54	SER	0	-0.025	-0.027	25.788	-0.072	-0.072	0.000	0.000	0.000	0.000
54	A	55	LEU	0	0.031	0.031	21.595	-0.470	-0.470	0.000	0.000	0.000	0.000
55	A	56	THR	0	-0.055	-0.031	16.951	-0.137	-0.137	0.000	0.000	0.000	0.000
56	A	57	VAL	0	0.000	0.004	16.016	-0.412	-0.412	0.000	0.000	0.000	0.000
57	A	58	THR	0	0.000	0.005	10.358	-0.208	-0.208	0.000	0.000	0.000	0.000
58	A	59	LEU	0	0.021	0.017	10.463	0.440	0.440	0.000	0.000	0.000	0.000
59	A	60	ALA	0	0.030	0.006	5.229	-2.236	-2.236	0.000	0.000	0.000	0.000
63	A	77	SER	0	0.008	-0.001	16.220	0.550	0.550	0.000	0.000	0.000	0.000
64	A	78	TRP	0	0.020	0.009	14.553	-0.425	-0.425	0.000	0.000	0.000	0.000
65	A	79	ARG	1	0.918	0.950	15.583	18.394	18.394	0.000	0.000	0.000	0.000
66	A	80	PRO	0	0.056	0.027	17.616	-0.210	-0.210	0.000	0.000	0.000	0.000
67	A	81	PRO	0	0.071	0.034	18.580	-0.680	-0.680	0.000	0.000	0.000	0.000
68	A	82	LYS	1	0.916	0.939	19.249	13.475	13.475	0.000	0.000	0.000	0.000
69	A	83	PRO	0	-0.016	-0.010	14.656	0.071	0.071	0.000	0.000	0.000	0.000
70	A	84	THR	0	0.007	-0.002	16.058	-0.476	-0.476	0.000	0.000	0.000	0.000
71	A	85	ASP	-1	-0.874	-0.914	17.913	-14.366	-14.366	0.000	0.000	0.000	0.000
72	A	86	LYS	1	0.828	0.914	12.876	18.340	18.340	0.000	0.000	0.000	0.000
73	A	87	SER	0	0.005	0.007	9.007	0.033	0.033	0.000	0.000	0.000	0.000
74	A	88	LEU	0	-0.011	-0.006	11.010	0.230	0.230	0.000	0.000	0.000	0.000
75	A	89	ALA	0	-0.005	0.019	8.523	0.332	0.332	0.000	0.000	0.000	0.000
76	A	90	ASP	-1	-0.898	-0.963	10.616	-20.196	-20.196	0.000	0.000	0.000	0.000
77	A	91	ASP	-1	-0.905	-0.925	13.373	-19.734	-19.734	0.000	0.000	0.000	0.000
78	A	92	TYR	0	-0.152	-0.141	12.336	-0.112	-0.112	0.000	0.000	0.000	0.000
79	A	93	ASP	-1	-0.803	-0.896	16.842	-14.558	-14.558	0.000	0.000	0.000	0.000
80	A	94	TYR	0	-0.030	-0.022	17.923	0.882	0.882	0.000	0.000	0.000	0.000
81	A	95	VAL	0	0.011	0.000	12.556	-0.978	-0.978	0.000	0.000	0.000	0.000
82	A	96	MET	0	-0.050	0.007	14.636	1.237	1.237	0.000	0.000	0.000	0.000
83	A	97	PHE	0	0.009	0.006	10.243	-1.473	-1.473	0.000	0.000	0.000	0.000
84	A	98	GLY	0	-0.013	-0.021	13.239	1.935	1.935	0.000	0.000	0.000	0.000
85	A	99	THR	0	-0.048	-0.016	13.468	-1.258	-1.258	0.000	0.000	0.000	0.000
86	A	100	VAL	0	-0.004	0.004	13.162	1.301	1.301	0.000	0.000	0.000	0.000
87	A	101	TYR	0	-0.014	-0.008	15.941	0.129	0.129	0.000	0.000	0.000	0.000
88	A	102	LYS	1	0.908	0.954	19.231	12.285	12.285	0.000	0.000	0.000	0.000
89	A	103	PHE	0	0.025	0.010	13.928	-0.380	-0.380	0.000	0.000	0.000	0.000
90	A	104	GLU	-1	-0.909	-0.956	20.083	-11.400	-11.400	0.000	0.000	0.000	0.000
91	A	105	GLU	-1	-0.895	-0.945	22.512	-13.195	-13.195	0.000	0.000	0.000	0.000
92	A	106	GLY	0	-0.053	-0.021	24.940	0.461	0.461	0.000	0.000	0.000	0.000
93	A	107	ASP	-1	-0.817	-0.927	27.066	-9.866	-9.866	0.000	0.000	0.000	0.000
94	A	108	GLU	-1	-0.916	-0.924	27.934	-11.081	-11.081	0.000	0.000	0.000	0.000
95	A	109	ASP	-1	-0.925	-0.951	24.734	-11.888	-11.888	0.000	0.000	0.000	0.000
96	A	110	LYS	1	0.720	0.845	23.667	10.317	10.317	0.000	0.000	0.000	0.000
97	A	111	ILE	0	-0.029	-0.022	18.647	-0.018	-0.018	0.000	0.000	0.000	0.000
98	A	112	LYS	1	0.831	0.909	20.752	12.276	12.276	0.000	0.000	0.000	0.000
99	A	113	VAL	0	-0.044	-0.013	15.505	-0.177	-0.177	0.000	0.000	0.000	0.000
100	A	114	TYR	0	-0.048	-0.041	18.614	0.359	0.359	0.000	0.000	0.000	0.000
101	A	115	VAL	0	0.016	0.006	15.392	-0.636	-0.636	0.000	0.000	0.000	0.000
102	A	116	SER	0	-0.026	-0.019	18.106	1.031	1.031	0.000	0.000	0.000	0.000
103	A	117	PHE	0	0.063	0.007	14.272	-0.805	-0.805	0.000	0.000	0.000	0.000
104	A	118	GLY	0	-0.005	-0.006	18.624	0.648	0.648	0.000	0.000	0.000	0.000
105	A	119	GLY	0	-0.027	-0.010	20.960	0.669	0.669	0.000	0.000	0.000	0.000
106	A	120	LEU	0	-0.042	-0.004	21.411	0.564	0.564	0.000	0.000	0.000	0.000
107	A	121	LEU	0	-0.020	-0.014	21.278	-0.753	-0.753	0.000	0.000	0.000	0.000
108	A	122	MET	0	0.014	0.012	17.623	-0.336	-0.336	0.000	0.000	0.000	0.000
109	A	123	CYS	0	-0.094	-0.031	20.991	0.014	0.014	0.000	0.000	0.000	0.000
110	A	124	LEU	0	0.050	0.036	16.154	0.112	0.112	0.000	0.000	0.000	0.000
111	A	125	GLU	-1	-0.783	-0.889	20.072	-11.992	-11.992	0.000	0.000	0.000	0.000
112	A	126	GLY	0	0.048	-0.008	20.583	-0.186	-0.186	0.000	0.000	0.000	0.000
113	A	127	GLY	0	0.065	0.040	19.932	0.497	0.497	0.000	0.000	0.000	0.000
114	A	128	TYR	0	0.006	0.016	16.631	-0.233	-0.233	0.000	0.000	0.000	0.000
115	A	129	LYS	1	0.864	0.915	11.808	22.870	22.870	0.000	0.000	0.000	0.000
116	A	130	SER	0	0.048	0.023	13.847	-1.522	-1.522	0.000	0.000	0.000	0.000
117	A	131	LEU	0	-0.043	-0.013	13.039	0.223	0.223	0.000	0.000	0.000	0.000
118	A	132	ALA	0	-0.026	-0.007	9.465	-1.808	-1.808	0.000	0.000	0.000	0.000
119	A	133	SER	0	0.031	0.014	9.064	-2.886	-2.886	0.000	0.000	0.000	0.000
120	A	134	LEU	0	-0.013	-0.011	6.438	2.033	2.033	0.000	0.000	0.000	0.000
121	A	135	LYS	1	0.934	0.962	10.350	18.712	18.712	0.000	0.000	0.000	0.000
122	A	136	GLN	0	-0.047	-0.017	7.639	-1.251	-1.251	0.000	0.000	0.000	0.000
123	A	137	ASP	-1	-0.764	-0.886	11.132	-26.551	-26.551	0.000	0.000	0.000	0.000
124	A	138	ASN	0	-0.111	-0.059	7.831	-2.031	-2.031	0.000	0.000	0.000	0.000
125	A	139	LEU	0	0.001	0.004	9.624	-1.222	-1.222	0.000	0.000	0.000	0.000
126	A	140	TYR	0	0.016	0.018	7.891	2.518	2.518	0.000	0.000	0.000	0.000
127	A	141	ILE	0	-0.011	-0.007	10.261	-1.109	-1.109	0.000	0.000	0.000	0.000
128	A	142	LEU	0	-0.020	-0.007	9.547	0.256	0.256	0.000	0.000	0.000	0.000
129	A	143	ILE	0	0.007	-0.008	13.924	0.193	0.193	0.000	0.000	0.000	0.000
130	A	144	ARG	1	0.875	0.950	15.243	19.216	19.216	0.000	0.000	0.000	0.000
131	A	145	ARG	0	0.083	0.059	19.748	1.927	1.927	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)