FMO DATABASE

FMODB ID: 7YZRK

Calculation Name: 1J6X-A-Xray547

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1J6X

Chain ID: A

ChEMBL ID:

UniProt ID: Q9ZMW8

Base Structure: X-ray

Registration Date: 2025-10-03

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	151
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1490619.524355
FMO2-HF: Nuclear repulsion	1428960.580799
FMO2-HF: Total energy	-61658.943556
FMO2-MP2: Total energy	-61835.923526

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:1:MET)

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

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.
-36.254	-33.246	1.981	-1.565	-3.424	-0.008

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.862 / q_NPA : 0.921

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	3	MET	0	0.024	0.007	3.416	-0.533	2.397	1.982	-1.561	-3.351	-0.008
4	A	4	ASN	0	0.038	0.006	5.082	1.672	1.750	-0.001	-0.004	-0.073	0.000
5	A	5	VAL	0	-0.014	0.010	7.986	2.557	2.557	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.763	-0.871	9.189	-25.548	-25.548	0.000	0.000	0.000	0.000
7	A	7	SER	0	0.065	0.034	10.308	-2.912	-2.912	0.000	0.000	0.000	0.000
8	A	8	PHE	0	-0.031	-0.033	6.811	0.073	0.073	0.000	0.000	0.000	0.000
9	A	9	ASN	0	-0.057	-0.022	6.054	-13.762	-13.762	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.000	0.023	7.355	0.546	0.546	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.777	-0.864	9.831	-27.738	-27.738	0.000	0.000	0.000	0.000
12	A	12	HIS	0	0.003	-0.015	10.583	3.953	3.953	0.000	0.000	0.000	0.000
13	A	13	THR	0	-0.111	-0.071	12.367	1.790	1.790	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.828	0.906	11.386	26.326	26.326	0.000	0.000	0.000	0.000
15	A	15	VAL	0	0.030	0.036	15.095	0.187	0.187	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.967	0.994	17.665	12.359	12.359	0.000	0.000	0.000	0.000
17	A	17	ALA	0	-0.033	0.016	21.378	0.143	0.143	0.000	0.000	0.000	0.000
18	A	18	PRO	0	-0.042	-0.026	23.306	0.333	0.333	0.000	0.000	0.000	0.000
19	A	19	TYR	0	-0.008	-0.035	17.509	-0.189	-0.189	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.002	-0.004	23.473	-0.109	-0.109	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.774	0.864	14.581	20.345	20.345	0.000	0.000	0.000	0.000
22	A	22	ILE	0	0.013	-0.002	20.593	0.029	0.029	0.000	0.000	0.000	0.000
23	A	23	ALA	0	-0.042	-0.018	17.072	-0.798	-0.798	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.822	-0.915	16.187	-20.591	-20.591	0.000	0.000	0.000	0.000
25	A	25	ARG	1	0.841	0.901	17.719	14.922	14.922	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.829	0.912	14.902	17.924	17.924	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.895	0.946	20.412	12.565	12.565	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.029	0.029	22.988	-0.312	-0.312	0.000	0.000	0.000	0.000
29	A	29	VAL	0	-0.004	-0.018	25.498	0.058	0.058	0.000	0.000	0.000	0.000
30	A	30	ASN	0	0.003	0.001	27.065	0.227	0.227	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.025	0.022	28.390	0.284	0.284	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.847	-0.901	28.262	-10.368	-10.368	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.077	-0.043	24.140	-0.541	-0.541	0.000	0.000	0.000	0.000
34	A	34	ILE	0	0.018	0.012	22.654	0.313	0.313	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.003	0.003	22.358	-0.751	-0.751	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.869	0.943	16.936	17.760	17.760	0.000	0.000	0.000	0.000
37	A	37	TYR	0	0.064	0.020	21.020	-0.602	-0.602	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.762	-0.832	17.201	-17.801	-17.801	0.000	0.000	0.000	0.000
39	A	39	VAL	0	0.035	0.024	20.233	0.135	0.135	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.775	0.870	15.667	17.969	17.969	0.000	0.000	0.000	0.000
41	A	41	PHE	0	0.090	0.010	22.534	0.366	0.366	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.796	0.915	23.462	11.601	11.601	0.000	0.000	0.000	0.000
43	A	43	GLN	0	0.044	0.010	19.311	-0.127	-0.127	0.000	0.000	0.000	0.000
44	A	44	PRO	0	0.037	0.002	16.475	0.152	0.152	0.000	0.000	0.000	0.000
45	A	45	ASN	0	-0.055	-0.034	14.987	0.195	0.195	0.000	0.000	0.000	0.000
46	A	46	ARG	1	0.898	0.953	19.169	14.821	14.821	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.799	-0.884	22.633	-10.886	-10.886	0.000	0.000	0.000	0.000
48	A	48	HIS	0	-0.067	-0.049	23.046	-0.654	-0.654	0.000	0.000	0.000	0.000
49	A	49	MET	0	0.000	0.019	24.833	0.665	0.665	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.798	-0.860	27.151	-10.149	-10.149	0.000	0.000	0.000	0.000
51	A	51	MET	0	0.046	0.008	26.822	-0.124	-0.124	0.000	0.000	0.000	0.000
52	A	52	PRO	0	-0.006	0.004	29.741	-0.019	-0.019	0.000	0.000	0.000	0.000
53	A	53	SER	0	0.031	-0.011	32.097	0.195	0.195	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.031	-0.009	25.133	0.007	0.007	0.000	0.000	0.000	0.000
55	A	55	HIS	1	0.821	0.880	29.751	9.672	9.672	0.000	0.000	0.000	0.000
56	A	56	SER	0	0.056	0.002	31.332	0.225	0.225	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.011	-0.003	30.034	0.156	0.156	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.891	-0.935	28.550	-10.790	-10.790	0.000	0.000	0.000	0.000
59	A	59	HIS	1	0.754	0.829	30.751	8.998	8.998	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.019	-0.004	34.262	0.145	0.145	0.000	0.000	0.000	0.000
61	A	61	VAL	0	0.016	0.008	30.759	0.181	0.181	0.000	0.000	0.000	0.000
62	A	62	ALA	0	-0.001	0.000	31.298	0.021	0.021	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.935	-0.951	32.781	-8.025	-8.025	0.000	0.000	0.000	0.000
64	A	64	ILE	0	-0.015	-0.013	36.551	0.099	0.099	0.000	0.000	0.000	0.000
65	A	65	ILE	0	0.004	-0.003	30.950	0.085	0.085	0.000	0.000	0.000	0.000
66	A	66	ARG	1	0.782	0.877	30.310	9.920	9.920	0.000	0.000	0.000	0.000
67	A	67	ASN	0	-0.001	0.012	36.315	0.273	0.273	0.000	0.000	0.000	0.000
68	A	68	HIS	0	-0.062	-0.036	37.068	0.169	0.169	0.000	0.000	0.000	0.000
69	A	69	ALA	0	-0.040	-0.012	34.577	-0.049	-0.049	0.000	0.000	0.000	0.000
70	A	70	ASN	0	-0.002	-0.010	36.337	-0.107	-0.107	0.000	0.000	0.000	0.000
71	A	71	TYR	0	0.049	0.028	31.169	-0.097	-0.097	0.000	0.000	0.000	0.000
72	A	72	VAL	0	-0.008	-0.006	29.357	-0.450	-0.450	0.000	0.000	0.000	0.000
73	A	73	VAL	0	-0.026	-0.006	26.255	0.206	0.206	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.868	-0.930	25.130	-11.878	-11.878	0.000	0.000	0.000	0.000
75	A	75	TRP	0	0.013	0.007	26.663	-0.283	-0.283	0.000	0.000	0.000	0.000
76	A	76	SER	0	0.030	0.005	23.341	0.327	0.327	0.000	0.000	0.000	0.000
77	A	77	PRO	0	0.004	0.002	23.842	-0.485	-0.485	0.000	0.000	0.000	0.000
78	A	78	MET	0	-0.074	-0.030	18.560	-0.815	-0.815	0.000	0.000	0.000	0.000
79	A	79	GLY	0	0.027	0.008	19.604	0.416	0.416	0.000	0.000	0.000	0.000
80	A	80	CYS	0	-0.051	-0.011	16.799	0.307	0.307	0.000	0.000	0.000	0.000
81	A	81	GLN	0	-0.009	-0.018	19.310	-0.022	-0.022	0.000	0.000	0.000	0.000
82	A	82	THR	0	0.035	0.008	19.290	0.215	0.215	0.000	0.000	0.000	0.000
83	A	83	GLY	0	0.025	0.001	21.917	0.211	0.211	0.000	0.000	0.000	0.000
84	A	84	PHE	0	0.010	0.020	22.919	0.061	0.061	0.000	0.000	0.000	0.000
85	A	85	TYR	0	-0.013	-0.005	15.971	-1.067	-1.067	0.000	0.000	0.000	0.000
86	A	86	LEU	0	0.037	0.032	22.475	0.532	0.532	0.000	0.000	0.000	0.000
87	A	87	THR	0	-0.042	-0.031	22.944	-0.823	-0.823	0.000	0.000	0.000	0.000
88	A	88	VAL	0	0.003	0.005	24.802	0.526	0.526	0.000	0.000	0.000	0.000
89	A	89	LEU	0	0.008	-0.004	26.237	-0.515	-0.515	0.000	0.000	0.000	0.000
90	A	90	ASN	0	-0.063	-0.058	28.577	0.032	0.032	0.000	0.000	0.000	0.000
91	A	91	HIS	0	-0.011	-0.010	29.045	-0.015	-0.015	0.000	0.000	0.000	0.000
92	A	92	ASP	-1	-0.821	-0.903	26.487	-12.961	-12.961	0.000	0.000	0.000	0.000
93	A	93	ASN	0	-0.034	-0.013	28.841	-0.124	-0.124	0.000	0.000	0.000	0.000
94	A	94	TYR	0	0.035	-0.011	24.700	0.201	0.201	0.000	0.000	0.000	0.000
95	A	95	THR	0	0.057	0.019	28.368	-0.110	-0.110	0.000	0.000	0.000	0.000
96	A	96	GLU	-1	-0.822	-0.893	31.591	-9.199	-9.199	0.000	0.000	0.000	0.000
97	A	97	ILE	0	-0.034	-0.006	27.266	0.136	0.136	0.000	0.000	0.000	0.000
98	A	98	LEU	0	-0.011	0.005	27.601	0.024	0.024	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.793	-0.906	31.066	-9.074	-9.074	0.000	0.000	0.000	0.000
100	A	100	VAL	0	-0.062	-0.026	33.145	0.270	0.270	0.000	0.000	0.000	0.000
101	A	101	LEU	0	-0.005	0.005	27.912	0.102	0.102	0.000	0.000	0.000	0.000
102	A	102	GLU	-1	-0.846	-0.906	32.535	-8.705	-8.705	0.000	0.000	0.000	0.000
103	A	103	LYS	1	0.943	0.971	35.177	8.481	8.481	0.000	0.000	0.000	0.000
104	A	104	THR	0	0.009	-0.011	34.010	0.195	0.195	0.000	0.000	0.000	0.000
105	A	105	MET	0	-0.027	-0.008	30.495	0.163	0.163	0.000	0.000	0.000	0.000
106	A	106	GLN	0	-0.006	-0.009	35.683	0.309	0.309	0.000	0.000	0.000	0.000
107	A	107	ASP	-1	-0.827	-0.902	39.213	-7.509	-7.509	0.000	0.000	0.000	0.000
108	A	108	VAL	0	-0.004	0.000	35.276	0.146	0.146	0.000	0.000	0.000	0.000
109	A	109	LEU	0	-0.066	-0.029	37.762	0.163	0.163	0.000	0.000	0.000	0.000
110	A	110	LYS	1	0.827	0.919	40.795	7.622	7.622	0.000	0.000	0.000	0.000
111	A	111	ALA	0	-0.019	0.009	41.080	0.186	0.186	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.949	0.955	43.036	6.542	6.542	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.903	-0.948	43.322	-7.107	-7.107	0.000	0.000	0.000	0.000
114	A	114	VAL	0	-0.008	0.000	37.203	-0.141	-0.141	0.000	0.000	0.000	0.000
115	A	115	PRO	0	0.076	0.074	38.287	0.099	0.099	0.000	0.000	0.000	0.000
116	A	116	ALA	0	0.044	0.013	38.556	-0.248	-0.248	0.000	0.000	0.000	0.000
117	A	117	SER	0	-0.042	-0.025	38.818	-0.091	-0.091	0.000	0.000	0.000	0.000
118	A	118	ASN	0	0.011	-0.021	39.850	0.136	0.136	0.000	0.000	0.000	0.000
119	A	119	GLU	-1	-0.880	-0.963	40.337	-7.507	-7.507	0.000	0.000	0.000	0.000
120	A	120	LYS	1	0.883	0.948	40.965	6.830	6.830	0.000	0.000	0.000	0.000
121	A	121	GLN	0	-0.030	-0.004	38.830	0.062	0.062	0.000	0.000	0.000	0.000
122	A	122	CYS	-1	-0.866	-0.794	35.558	-9.286	-9.286	0.000	0.000	0.000	0.000
123	A	123	GLY	0	-0.004	0.008	33.811	0.152	0.152	0.000	0.000	0.000	0.000
124	A	124	TRP	0	-0.012	-0.042	30.885	-0.111	-0.111	0.000	0.000	0.000	0.000
125	A	125	ALA	0	0.032	0.020	35.450	-0.053	-0.053	0.000	0.000	0.000	0.000
126	A	126	ALA	0	0.033	0.017	38.538	0.074	0.074	0.000	0.000	0.000	0.000
127	A	127	ASN	0	-0.053	-0.011	32.426	0.122	0.122	0.000	0.000	0.000	0.000
128	A	128	HIS	0	0.035	-0.031	34.579	-0.385	-0.385	0.000	0.000	0.000	0.000
129	A	129	THR	0	-0.010	-0.008	35.996	0.245	0.245	0.000	0.000	0.000	0.000
130	A	130	LEU	0	0.028	0.020	37.229	-0.218	-0.218	0.000	0.000	0.000	0.000
131	A	131	GLU	-1	-0.872	-0.928	38.789	-7.856	-7.856	0.000	0.000	0.000	0.000
132	A	132	GLY	0	0.035	0.019	36.210	-0.111	-0.111	0.000	0.000	0.000	0.000
133	A	133	ALA	0	-0.001	-0.009	34.027	-0.268	-0.268	0.000	0.000	0.000	0.000
134	A	134	GLN	0	-0.035	-0.029	34.819	-0.115	-0.115	0.000	0.000	0.000	0.000
135	A	135	ASN	0	-0.069	-0.040	36.137	0.063	0.063	0.000	0.000	0.000	0.000
136	A	136	LEU	0	-0.029	-0.015	29.602	-0.178	-0.178	0.000	0.000	0.000	0.000
137	A	137	ALA	0	0.022	0.001	32.156	-0.210	-0.210	0.000	0.000	0.000	0.000
138	A	138	ARG	1	0.926	0.980	33.863	8.037	8.037	0.000	0.000	0.000	0.000
139	A	139	ALA	0	0.041	0.029	32.298	-0.048	-0.048	0.000	0.000	0.000	0.000
140	A	140	PHE	0	-0.041	-0.023	26.464	-0.179	-0.179	0.000	0.000	0.000	0.000
141	A	141	LEU	0	-0.011	-0.010	31.200	-0.123	-0.123	0.000	0.000	0.000	0.000
142	A	142	ASP	-1	-0.894	-0.951	34.252	-8.649	-8.649	0.000	0.000	0.000	0.000
143	A	143	LYS	1	0.783	0.869	27.893	11.084	11.084	0.000	0.000	0.000	0.000
144	A	144	ARG	1	0.835	0.904	30.629	9.270	9.270	0.000	0.000	0.000	0.000
145	A	145	ALA	0	-0.042	-0.028	31.576	-0.145	-0.145	0.000	0.000	0.000	0.000
146	A	146	GLU	-1	-0.768	-0.867	27.108	-11.298	-11.298	0.000	0.000	0.000	0.000
147	A	147	TRP	0	-0.059	-0.018	26.417	-0.502	-0.502	0.000	0.000	0.000	0.000
148	A	148	SER	0	0.028	0.010	25.401	-0.313	-0.313	0.000	0.000	0.000	0.000
149	A	149	GLU	-1	-1.020	-1.006	24.420	-11.759	-11.759	0.000	0.000	0.000	0.000
150	A	150	VAL	0	-0.041	-0.034	18.319	-0.240	-0.240	0.000	0.000	0.000	0.000
151	A	151	GLY	-1	-0.918	-0.942	19.213	-15.459	-15.459	0.000	0.000	0.000	0.000

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