FMO DATABASE

FMODB ID: 7N6RK

Calculation Name: 3L7X-A-Xray547

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

PDB ID: 3L7X

Chain ID: A

ChEMBL ID:

UniProt ID: Q8DVQ8

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	159
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1401477.600367
FMO2-HF: Nuclear repulsion	1338918.358709
FMO2-HF: Total energy	-62559.241658
FMO2-MP2: Total energy	-62739.250717

3D Structure

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:-20:LEU)

Summations of interaction energy for fragment #1(A:-20: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.
-109.417	-106.601	1.045	-1.445	-2.416	-0.016

Interaction energy analysis for fragmet #1(A:-20:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.859 / q_NPA : 0.926

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	-18	PRO	0	0.003	0.008	2.559	-5.994	-3.532	1.045	-1.408	-2.100	-0.016
4	A	-17	ARG	1	0.899	0.941	3.764	35.662	36.016	0.000	-0.037	-0.316	0.000
5	A	-16	GLY	0	0.039	0.010	6.873	0.631	0.631	0.000	0.000	0.000	0.000
6	A	-15	SER	0	0.004	0.000	10.680	0.713	0.713	0.000	0.000	0.000	0.000
7	A	-14	HIS	0	0.020	0.013	13.682	-0.566	-0.566	0.000	0.000	0.000	0.000
8	A	-13	MET	0	-0.030	-0.008	15.876	0.991	0.991	0.000	0.000	0.000	0.000
9	A	-12	ALA	0	-0.013	-0.004	10.685	-0.456	-0.456	0.000	0.000	0.000	0.000
10	A	-11	SER	0	0.005	0.016	10.284	1.491	1.491	0.000	0.000	0.000	0.000
11	A	-10	MET	0	-0.012	-0.003	9.405	-2.059	-2.059	0.000	0.000	0.000	0.000
12	A	-9	THR	0	-0.014	-0.042	8.331	-1.315	-1.315	0.000	0.000	0.000	0.000
13	A	-8	GLY	0	0.009	0.018	6.397	-2.223	-2.223	0.000	0.000	0.000	0.000
14	A	-7	GLY	0	0.029	0.028	7.184	2.367	2.367	0.000	0.000	0.000	0.000
15	A	-6	GLN	0	-0.065	-0.042	9.442	1.037	1.037	0.000	0.000	0.000	0.000
16	A	-5	GLN	0	0.064	0.034	12.960	-0.184	-0.184	0.000	0.000	0.000	0.000
17	A	-4	MET	0	0.056	0.043	15.760	-0.093	-0.093	0.000	0.000	0.000	0.000
18	A	-3	GLY	0	0.073	0.034	19.082	0.754	0.754	0.000	0.000	0.000	0.000
19	A	-2	ARG	1	0.766	0.862	21.239	12.187	12.187	0.000	0.000	0.000	0.000
20	A	-1	GLY	0	0.042	0.039	22.632	0.413	0.413	0.000	0.000	0.000	0.000
21	A	0	SER	0	0.019	0.012	22.187	-0.247	-0.247	0.000	0.000	0.000	0.000
22	A	1	MET	0	-0.001	-0.026	16.068	-0.021	-0.021	0.000	0.000	0.000	0.000
23	A	2	ASN	0	-0.001	-0.014	20.977	0.550	0.550	0.000	0.000	0.000	0.000
24	A	3	ASP	-1	-0.933	-0.972	20.752	-13.373	-13.373	0.000	0.000	0.000	0.000
25	A	4	CYS	0	-0.046	0.022	19.540	-0.131	-0.131	0.000	0.000	0.000	0.000
26	A	5	LEU	0	0.013	0.000	21.772	0.515	0.515	0.000	0.000	0.000	0.000
27	A	6	PHE	0	0.060	0.005	20.315	0.513	0.513	0.000	0.000	0.000	0.000
28	A	7	CYS	0	0.016	0.016	21.403	0.225	0.225	0.000	0.000	0.000	0.000
29	A	8	LYS	1	0.976	0.998	24.199	11.852	11.852	0.000	0.000	0.000	0.000
30	A	9	ILE	0	-0.037	-0.014	26.399	0.347	0.347	0.000	0.000	0.000	0.000
31	A	10	VAL	0	-0.069	-0.028	24.730	0.331	0.331	0.000	0.000	0.000	0.000
32	A	11	ALA	0	-0.039	-0.013	27.791	0.265	0.265	0.000	0.000	0.000	0.000
33	A	12	GLY	0	-0.010	0.004	29.959	0.333	0.333	0.000	0.000	0.000	0.000
34	A	13	ASP	-1	-0.931	-0.963	30.283	-9.550	-9.550	0.000	0.000	0.000	0.000
35	A	14	ILE	0	-0.072	-0.038	28.465	0.078	0.078	0.000	0.000	0.000	0.000
36	A	15	PRO	0	0.004	0.010	31.476	-0.089	-0.089	0.000	0.000	0.000	0.000
37	A	16	SER	0	0.027	0.001	29.618	-0.135	-0.135	0.000	0.000	0.000	0.000
38	A	17	SER	0	0.021	0.012	31.881	0.279	0.279	0.000	0.000	0.000	0.000
39	A	18	LYS	1	0.846	0.910	31.269	9.036	9.036	0.000	0.000	0.000	0.000
40	A	19	VAL	0	-0.020	-0.009	30.814	0.257	0.257	0.000	0.000	0.000	0.000
41	A	20	TYR	0	-0.080	-0.074	29.446	0.402	0.402	0.000	0.000	0.000	0.000
42	A	21	GLU	-1	-0.782	-0.875	30.194	-9.515	-9.515	0.000	0.000	0.000	0.000
43	A	22	ASP	-1	-0.774	-0.832	28.943	-9.537	-9.537	0.000	0.000	0.000	0.000
44	A	23	GLU	-1	-0.829	-0.923	29.558	-9.307	-9.307	0.000	0.000	0.000	0.000
45	A	24	ASP	-1	-0.821	-0.875	24.554	-10.897	-10.897	0.000	0.000	0.000	0.000
46	A	25	VAL	0	-0.063	-0.024	23.717	-0.532	-0.532	0.000	0.000	0.000	0.000
47	A	26	LEU	0	-0.008	0.006	25.555	0.486	0.486	0.000	0.000	0.000	0.000
48	A	27	ALA	0	0.000	0.001	25.857	-0.429	-0.429	0.000	0.000	0.000	0.000
49	A	28	PHE	0	0.013	-0.007	24.943	0.433	0.433	0.000	0.000	0.000	0.000
50	A	29	LEU	0	-0.012	0.005	28.435	-0.263	-0.263	0.000	0.000	0.000	0.000
51	A	30	ASP	-1	-0.822	-0.892	25.195	-11.516	-11.516	0.000	0.000	0.000	0.000
52	A	31	ILE	0	-0.012	-0.016	28.412	0.302	0.302	0.000	0.000	0.000	0.000
53	A	32	SER	0	-0.075	-0.059	27.049	0.215	0.215	0.000	0.000	0.000	0.000
54	A	33	GLN	0	-0.092	-0.058	29.460	0.421	0.421	0.000	0.000	0.000	0.000
55	A	34	ALA	0	0.045	0.029	27.172	0.191	0.191	0.000	0.000	0.000	0.000
56	A	35	THR	0	-0.011	-0.021	29.227	0.068	0.068	0.000	0.000	0.000	0.000
57	A	36	LYS	1	0.943	0.979	31.713	7.715	7.715	0.000	0.000	0.000	0.000
58	A	37	GLY	0	0.026	-0.002	33.178	0.028	0.028	0.000	0.000	0.000	0.000
59	A	38	HIS	0	-0.041	0.002	24.562	0.216	0.216	0.000	0.000	0.000	0.000
60	A	39	THR	0	-0.022	-0.022	27.398	0.246	0.246	0.000	0.000	0.000	0.000
61	A	40	LEU	0	-0.011	0.012	22.446	-0.424	-0.424	0.000	0.000	0.000	0.000
62	A	41	VAL	0	-0.024	-0.019	23.380	0.508	0.508	0.000	0.000	0.000	0.000
63	A	42	ILE	0	0.008	0.001	21.145	-0.673	-0.673	0.000	0.000	0.000	0.000
64	A	43	PRO	0	0.015	0.018	18.521	0.570	0.570	0.000	0.000	0.000	0.000
65	A	44	LYS	1	0.795	0.868	21.834	9.539	9.539	0.000	0.000	0.000	0.000
66	A	45	GLU	-1	-0.885	-0.922	19.422	-13.840	-13.840	0.000	0.000	0.000	0.000
67	A	46	HIS	0	-0.047	-0.054	16.185	-0.938	-0.938	0.000	0.000	0.000	0.000
68	A	47	VAL	0	0.040	0.011	12.847	-0.285	-0.285	0.000	0.000	0.000	0.000
69	A	48	ARG	1	0.863	0.920	9.045	27.009	27.009	0.000	0.000	0.000	0.000
70	A	49	ASN	0	-0.076	-0.072	8.994	0.470	0.470	0.000	0.000	0.000	0.000
71	A	50	ALA	0	0.065	0.018	11.818	0.085	0.085	0.000	0.000	0.000	0.000
72	A	51	LEU	0	-0.022	-0.007	5.749	0.068	0.068	0.000	0.000	0.000	0.000
73	A	52	GLU	-1	-0.875	-0.942	6.997	-29.886	-29.886	0.000	0.000	0.000	0.000
74	A	53	MET	0	-0.083	0.002	9.032	1.550	1.550	0.000	0.000	0.000	0.000
75	A	54	THR	0	0.008	0.000	12.171	-0.118	-0.118	0.000	0.000	0.000	0.000
76	A	55	GLN	0	0.034	-0.003	14.616	0.867	0.867	0.000	0.000	0.000	0.000
77	A	56	THR	0	0.026	0.009	16.966	0.328	0.328	0.000	0.000	0.000	0.000
78	A	57	GLN	0	0.015	0.015	15.494	-0.241	-0.241	0.000	0.000	0.000	0.000
79	A	58	ALA	0	0.052	0.023	15.751	0.390	0.390	0.000	0.000	0.000	0.000
80	A	59	ALA	0	-0.014	-0.005	17.783	0.486	0.486	0.000	0.000	0.000	0.000
81	A	60	ASN	0	0.006	-0.003	21.250	0.539	0.539	0.000	0.000	0.000	0.000
82	A	61	LEU	0	0.020	0.017	18.298	0.476	0.476	0.000	0.000	0.000	0.000
83	A	62	PHE	0	0.032	-0.006	17.295	0.447	0.447	0.000	0.000	0.000	0.000
84	A	63	ALA	0	-0.009	0.004	22.417	0.422	0.422	0.000	0.000	0.000	0.000
85	A	64	ARG	1	0.697	0.805	25.487	10.899	10.899	0.000	0.000	0.000	0.000
86	A	65	ILE	0	0.025	0.023	22.373	0.412	0.412	0.000	0.000	0.000	0.000
87	A	66	PRO	0	0.005	-0.003	26.237	0.331	0.331	0.000	0.000	0.000	0.000
88	A	67	LYS	1	0.857	0.934	29.228	9.014	9.014	0.000	0.000	0.000	0.000
89	A	68	ILE	0	0.027	0.016	27.317	0.291	0.291	0.000	0.000	0.000	0.000
90	A	69	ALA	0	0.060	0.030	28.452	0.218	0.218	0.000	0.000	0.000	0.000
91	A	70	ARG	1	1.016	1.007	30.488	9.026	9.026	0.000	0.000	0.000	0.000
92	A	71	ALA	0	-0.077	-0.022	33.746	0.327	0.327	0.000	0.000	0.000	0.000
93	A	72	LEU	0	0.045	0.027	30.320	0.272	0.272	0.000	0.000	0.000	0.000
94	A	73	GLN	0	0.000	0.018	33.890	0.096	0.096	0.000	0.000	0.000	0.000
95	A	74	LYS	1	0.839	0.904	35.344	8.023	8.023	0.000	0.000	0.000	0.000
96	A	75	ALA	0	-0.026	-0.006	37.169	0.190	0.190	0.000	0.000	0.000	0.000
97	A	76	THR	0	-0.073	-0.060	34.637	0.139	0.139	0.000	0.000	0.000	0.000
98	A	77	LYS	1	0.910	0.947	37.905	6.958	6.958	0.000	0.000	0.000	0.000
99	A	78	ALA	0	0.039	0.047	34.494	0.072	0.072	0.000	0.000	0.000	0.000
100	A	79	ASP	-1	-0.835	-0.913	36.164	-7.890	-7.890	0.000	0.000	0.000	0.000
101	A	80	GLY	0	-0.034	-0.022	32.807	-0.006	-0.006	0.000	0.000	0.000	0.000
102	A	81	LEU	0	-0.055	-0.033	27.159	0.043	0.043	0.000	0.000	0.000	0.000
103	A	82	ASN	0	0.011	0.016	24.596	0.033	0.033	0.000	0.000	0.000	0.000
104	A	83	ILE	0	0.011	-0.002	21.402	0.124	0.124	0.000	0.000	0.000	0.000
105	A	84	ILE	0	0.027	0.017	18.335	-0.291	-0.291	0.000	0.000	0.000	0.000
106	A	85	ASN	0	-0.022	-0.017	14.184	-0.437	-0.437	0.000	0.000	0.000	0.000
107	A	86	ASN	0	0.012	0.020	14.694	-0.496	-0.496	0.000	0.000	0.000	0.000
108	A	87	ASN	0	-0.026	-0.031	9.450	-0.486	-0.486	0.000	0.000	0.000	0.000
109	A	88	GLU	-1	-0.736	-0.840	6.428	-30.544	-30.544	0.000	0.000	0.000	0.000
110	A	89	GLU	-1	-0.920	-0.955	9.921	-20.158	-20.158	0.000	0.000	0.000	0.000
111	A	90	THR	0	-0.044	-0.022	9.362	1.408	1.408	0.000	0.000	0.000	0.000
112	A	91	ALA	0	-0.010	0.006	11.932	1.030	1.030	0.000	0.000	0.000	0.000
113	A	92	GLY	0	0.028	0.013	13.466	1.225	1.225	0.000	0.000	0.000	0.000
114	A	93	GLN	0	-0.056	-0.033	12.201	-0.376	-0.376	0.000	0.000	0.000	0.000
115	A	94	THR	0	0.033	0.010	14.467	-0.754	-0.754	0.000	0.000	0.000	0.000
116	A	95	VAL	0	0.007	0.011	17.046	-0.056	-0.056	0.000	0.000	0.000	0.000
117	A	96	PHE	0	-0.002	-0.007	11.553	-0.264	-0.264	0.000	0.000	0.000	0.000
118	A	97	HIS	0	0.023	0.003	15.279	-0.417	-0.417	0.000	0.000	0.000	0.000
119	A	98	ALA	0	-0.002	0.015	14.963	0.264	0.264	0.000	0.000	0.000	0.000
120	A	99	HIS	0	-0.034	-0.030	16.327	0.980	0.980	0.000	0.000	0.000	0.000
121	A	100	VAL	0	-0.036	-0.007	18.247	-0.644	-0.644	0.000	0.000	0.000	0.000
122	A	101	HIS	0	0.071	0.039	19.751	1.099	1.099	0.000	0.000	0.000	0.000
123	A	102	LEU	0	-0.037	-0.027	22.769	-0.036	-0.036	0.000	0.000	0.000	0.000
124	A	103	VAL	0	0.059	0.019	24.910	0.218	0.218	0.000	0.000	0.000	0.000
125	A	104	PRO	0	-0.026	-0.010	27.685	-0.008	-0.008	0.000	0.000	0.000	0.000
126	A	105	ARG	1	0.814	0.914	28.516	9.842	9.842	0.000	0.000	0.000	0.000
127	A	106	PHE	0	0.020	-0.022	33.033	0.249	0.249	0.000	0.000	0.000	0.000
128	A	107	ALA	0	0.061	0.044	35.789	0.038	0.038	0.000	0.000	0.000	0.000
129	A	108	ASP	-1	-0.946	-0.971	36.587	-7.696	-7.696	0.000	0.000	0.000	0.000
130	A	109	SER	0	-0.119	-0.069	37.764	0.156	0.156	0.000	0.000	0.000	0.000
131	A	110	ASP	-1	-0.831	-0.886	32.300	-9.241	-9.241	0.000	0.000	0.000	0.000
132	A	111	GLU	-1	-0.888	-0.943	32.635	-8.921	-8.921	0.000	0.000	0.000	0.000
133	A	112	PHE	0	-0.087	-0.036	24.243	-0.358	-0.358	0.000	0.000	0.000	0.000
134	A	113	ASP	-1	-0.856	-0.943	27.500	-10.716	-10.716	0.000	0.000	0.000	0.000
135	A	114	ILE	0	-0.068	-0.034	21.944	-0.515	-0.515	0.000	0.000	0.000	0.000
136	A	115	ARG	1	0.992	1.009	23.705	11.647	11.647	0.000	0.000	0.000	0.000
137	A	116	PHE	0	-0.001	-0.018	20.655	-0.556	-0.556	0.000	0.000	0.000	0.000
138	A	117	VAL	0	-0.065	-0.023	21.479	0.573	0.573	0.000	0.000	0.000	0.000
139	A	118	GLN	0	-0.018	-0.013	23.053	-0.167	-0.167	0.000	0.000	0.000	0.000
140	A	119	HIS	0	-0.001	-0.010	21.376	0.366	0.366	0.000	0.000	0.000	0.000
141	A	120	GLU	-1	-0.897	-0.947	25.262	-10.417	-10.417	0.000	0.000	0.000	0.000
142	A	121	PRO	0	-0.051	-0.011	23.885	-0.439	-0.439	0.000	0.000	0.000	0.000
143	A	122	ASP	-1	-0.818	-0.902	23.401	-12.121	-12.121	0.000	0.000	0.000	0.000
144	A	123	PHE	0	0.019	-0.022	23.344	-0.564	-0.564	0.000	0.000	0.000	0.000
145	A	124	THR	0	-0.002	0.017	24.205	-0.046	-0.046	0.000	0.000	0.000	0.000
146	A	125	ARG	1	0.792	0.889	15.097	17.887	17.887	0.000	0.000	0.000	0.000
147	A	126	LEU	0	0.000	0.000	19.044	-0.868	-0.868	0.000	0.000	0.000	0.000
148	A	127	GLY	0	0.018	0.008	19.510	-0.425	-0.425	0.000	0.000	0.000	0.000
149	A	128	GLN	0	-0.039	-0.033	17.352	0.580	0.580	0.000	0.000	0.000	0.000
150	A	129	LEU	0	-0.048	-0.021	13.252	-0.800	-0.800	0.000	0.000	0.000	0.000
151	A	130	ALA	0	-0.009	-0.005	15.044	-0.951	-0.951	0.000	0.000	0.000	0.000
152	A	131	GLU	-1	-0.866	-0.925	16.336	-15.516	-15.516	0.000	0.000	0.000	0.000
153	A	132	ASP	-1	-0.825	-0.913	12.885	-19.943	-19.943	0.000	0.000	0.000	0.000
154	A	133	ILE	0	-0.048	-0.027	11.361	-1.452	-1.452	0.000	0.000	0.000	0.000
155	A	134	GLN	0	-0.052	-0.031	12.634	-0.111	-0.111	0.000	0.000	0.000	0.000
156	A	135	LYS	1	0.863	0.923	9.625	23.846	23.846	0.000	0.000	0.000	0.000
157	A	136	GLU	-1	-0.916	-0.952	8.151	-29.403	-29.403	0.000	0.000	0.000	0.000
158	A	137	ILE	0	-0.136	-0.061	9.964	-0.612	-0.612	0.000	0.000	0.000	0.000
159	A	138	GLU	-2	-1.948	-1.951	12.650	-33.059	-33.059	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-20:LEU)