FMO DATABASE

FMODB ID: 8KJMY

Calculation Name: 4LKI-B-Xray547

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose

Ligand 3-letter code: NAG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4LKI

Chain ID: B

ChEMBL ID:

UniProt ID: V5IRV5

Base Structure: X-ray

Registration Date: 2025-10-06

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	167
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1432511.674447
FMO2-HF: Nuclear repulsion	1363330.613186
FMO2-HF: Total energy	-69181.061261
FMO2-MP2: Total energy	-69379.708295

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(B:323:LEU)

Summations of interaction energy for fragment #1(B:323: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.
-346.512	-340.212	19.599	-12.763	-13.132	-0.142

Interaction energy analysis for fragmet #1(B:323:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.722 / q_NPA : 0.850

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	B	325	GLY	0	0.023	0.011	2.505	5.113	7.771	1.891	-1.854	-2.694	-0.007
4	B	326	ALA	0	0.036	0.033	3.245	6.430	5.673	0.096	0.915	-0.254	-0.001
6	B	328	ALA	0	-0.046	-0.018	4.193	-4.611	-4.381	-0.001	-0.034	-0.195	0.000
7	B	329	GLY	0	-0.035	-0.008	4.544	-1.564	-1.464	-0.001	-0.010	-0.088	0.000
8	B	330	PHE	0	-0.040	-0.020	5.144	2.355	2.389	-0.001	-0.002	-0.031	0.000
104	B	426	GLN	0	-0.004	0.007	4.390	3.121	3.227	-0.001	-0.005	-0.100	0.000
107	B	429	ILE	0	-0.001	0.009	3.292	0.848	1.121	0.016	-0.051	-0.237	0.000
108	B	430	ASP	-1	-0.819	-0.908	1.718	-125.275	-124.877	16.488	-9.661	-7.225	-0.111
109	B	431	LEU	0	-0.051	-0.023	3.811	-0.753	-0.627	-0.001	-0.038	-0.087	0.000
111	B	433	ASP	-1	-0.700	-0.849	2.585	-61.370	-58.238	1.113	-2.023	-2.221	-0.023
5	B	327	ILE	0	-0.008	-0.021	5.374	3.670	3.670	0.000	0.000	0.000	0.000
9	B	331	ILE	0	-0.013	0.002	7.749	2.167	2.167	0.000	0.000	0.000	0.000
10	B	332	GLU	-1	-0.956	-0.977	8.768	-17.796	-17.796	0.000	0.000	0.000	0.000
11	B	333	ASN	0	-0.068	-0.042	10.921	0.117	0.117	0.000	0.000	0.000	0.000
12	B	334	GLY	0	0.043	0.032	12.088	-0.235	-0.235	0.000	0.000	0.000	0.000
13	B	335	TRP	0	-0.001	-0.022	13.204	1.125	1.125	0.000	0.000	0.000	0.000
14	B	336	GLU	-1	-0.892	-0.952	17.000	-14.052	-14.052	0.000	0.000	0.000	0.000
15	B	337	GLY	0	-0.038	-0.013	18.698	0.467	0.467	0.000	0.000	0.000	0.000
16	B	338	LEU	0	-0.079	-0.031	16.679	0.526	0.526	0.000	0.000	0.000	0.000
17	B	339	ILE	0	0.007	-0.009	19.510	-0.351	-0.351	0.000	0.000	0.000	0.000
18	B	340	ASP	-1	-0.946	-0.966	22.061	-11.823	-11.823	0.000	0.000	0.000	0.000
19	B	341	GLY	0	-0.059	-0.042	19.383	0.094	0.094	0.000	0.000	0.000	0.000
20	B	342	TRP	0	-0.009	-0.013	12.570	-0.305	-0.305	0.000	0.000	0.000	0.000
21	B	343	TYR	0	0.003	-0.010	9.803	-0.142	-0.142	0.000	0.000	0.000	0.000
22	B	344	GLY	0	-0.002	-0.009	15.208	1.091	1.091	0.000	0.000	0.000	0.000
23	B	345	PHE	0	-0.023	-0.008	17.218	-0.617	-0.617	0.000	0.000	0.000	0.000
24	B	346	ARG	1	0.925	0.958	19.480	13.970	13.970	0.000	0.000	0.000	0.000
25	B	347	HIS	0	-0.016	0.009	20.705	-0.606	-0.606	0.000	0.000	0.000	0.000
26	B	348	GLN	0	0.026	-0.008	23.412	-0.174	-0.174	0.000	0.000	0.000	0.000
27	B	349	ASN	0	-0.062	-0.045	25.885	0.141	0.141	0.000	0.000	0.000	0.000
28	B	350	ALA	0	-0.037	-0.033	29.344	0.097	0.097	0.000	0.000	0.000	0.000
29	B	351	GLN	0	-0.013	0.006	32.310	0.264	0.264	0.000	0.000	0.000	0.000
30	B	352	GLY	0	-0.011	-0.005	32.276	0.249	0.249	0.000	0.000	0.000	0.000
31	B	353	GLU	-1	-0.840	-0.901	26.518	-10.968	-10.968	0.000	0.000	0.000	0.000
32	B	354	GLY	0	-0.024	-0.011	26.948	0.245	0.245	0.000	0.000	0.000	0.000
33	B	355	THR	0	-0.053	-0.037	21.384	-0.542	-0.542	0.000	0.000	0.000	0.000
34	B	356	ALA	0	-0.004	0.010	22.528	0.460	0.460	0.000	0.000	0.000	0.000
35	B	357	ALA	0	0.056	0.033	19.974	-0.602	-0.602	0.000	0.000	0.000	0.000
36	B	358	ASP	-1	-0.827	-0.887	17.931	-15.663	-15.663	0.000	0.000	0.000	0.000
37	B	359	TYR	0	-0.002	0.009	19.105	-0.479	-0.479	0.000	0.000	0.000	0.000
38	B	360	LYS	1	0.947	0.958	19.501	12.916	12.916	0.000	0.000	0.000	0.000
39	B	361	SER	0	0.019	-0.015	14.172	-0.365	-0.365	0.000	0.000	0.000	0.000
40	B	362	THR	0	0.005	0.001	14.879	-1.215	-1.215	0.000	0.000	0.000	0.000
41	B	363	GLN	0	-0.061	-0.039	16.668	-0.188	-0.188	0.000	0.000	0.000	0.000
42	B	364	SER	0	0.000	0.004	14.256	0.220	0.220	0.000	0.000	0.000	0.000
43	B	365	ALA	0	0.018	0.016	12.457	-0.611	-0.611	0.000	0.000	0.000	0.000
44	B	366	ILE	0	-0.002	0.007	13.816	-0.060	-0.060	0.000	0.000	0.000	0.000
45	B	367	ASP	-1	-0.830	-0.922	17.087	-14.688	-14.688	0.000	0.000	0.000	0.000
46	B	368	GLN	0	-0.040	-0.023	12.873	-0.631	-0.631	0.000	0.000	0.000	0.000
47	B	369	ILE	0	0.002	0.001	11.615	-0.174	-0.174	0.000	0.000	0.000	0.000
48	B	370	THR	0	-0.036	-0.018	15.481	0.895	0.895	0.000	0.000	0.000	0.000
49	B	371	GLY	0	-0.029	-0.017	18.295	0.692	0.692	0.000	0.000	0.000	0.000
50	B	372	LYS	1	0.801	0.890	10.653	26.942	26.942	0.000	0.000	0.000	0.000
51	B	373	LEU	0	0.028	0.010	17.568	0.735	0.735	0.000	0.000	0.000	0.000
52	B	374	ASN	0	-0.049	-0.035	20.385	0.750	0.750	0.000	0.000	0.000	0.000
53	B	375	ARG	1	0.921	0.967	19.465	15.107	15.107	0.000	0.000	0.000	0.000
54	B	376	LEU	0	-0.004	0.004	17.345	0.083	0.083	0.000	0.000	0.000	0.000
55	B	377	ILE	0	-0.066	-0.014	21.900	0.509	0.509	0.000	0.000	0.000	0.000
56	B	378	GLU	-1	-0.869	-0.934	25.363	-11.562	-11.562	0.000	0.000	0.000	0.000
57	B	379	LYS	1	0.879	0.929	27.616	10.064	10.064	0.000	0.000	0.000	0.000
58	B	380	THR	0	0.037	0.023	29.659	0.028	0.028	0.000	0.000	0.000	0.000
59	B	381	ASN	0	-0.046	-0.022	32.200	0.129	0.129	0.000	0.000	0.000	0.000
60	B	382	GLN	0	-0.029	-0.012	34.300	0.223	0.223	0.000	0.000	0.000	0.000
61	B	383	GLN	0	-0.078	-0.053	36.221	-0.153	-0.153	0.000	0.000	0.000	0.000
62	B	384	PHE	0	-0.008	-0.016	34.553	-0.038	-0.038	0.000	0.000	0.000	0.000
63	B	385	GLU	-1	-0.855	-0.906	39.655	-7.297	-7.297	0.000	0.000	0.000	0.000
64	B	386	LEU	0	-0.039	-0.014	42.469	-0.125	-0.125	0.000	0.000	0.000	0.000
65	B	387	ILE	0	-0.010	-0.010	42.092	0.119	0.119	0.000	0.000	0.000	0.000
66	B	388	ASP	-1	-0.791	-0.878	43.652	-7.204	-7.204	0.000	0.000	0.000	0.000
67	B	389	ASN	0	-0.041	-0.048	46.377	-0.004	-0.004	0.000	0.000	0.000	0.000
68	B	390	GLU	-1	-0.900	-0.941	45.548	-6.900	-6.900	0.000	0.000	0.000	0.000
69	B	391	PHE	0	-0.030	-0.018	48.527	0.097	0.097	0.000	0.000	0.000	0.000
70	B	392	ASN	0	-0.103	-0.065	51.936	0.220	0.220	0.000	0.000	0.000	0.000
71	B	393	GLU	-1	-0.889	-0.928	49.239	-6.461	-6.461	0.000	0.000	0.000	0.000
72	B	394	VAL	0	0.012	0.015	48.070	0.126	0.126	0.000	0.000	0.000	0.000
73	B	395	GLU	-1	-0.902	-0.956	51.216	-5.828	-5.828	0.000	0.000	0.000	0.000
74	B	396	LYS	1	0.948	0.964	50.172	5.978	5.978	0.000	0.000	0.000	0.000
75	B	397	GLN	0	-0.032	-0.003	48.918	-0.056	-0.056	0.000	0.000	0.000	0.000
76	B	398	ILE	0	0.021	0.004	46.952	-0.132	-0.132	0.000	0.000	0.000	0.000
77	B	399	GLY	0	0.085	0.039	46.071	-0.163	-0.163	0.000	0.000	0.000	0.000
78	B	400	ASN	0	-0.031	-0.021	44.454	-0.274	-0.274	0.000	0.000	0.000	0.000
79	B	401	VAL	0	-0.008	0.009	42.899	-0.187	-0.187	0.000	0.000	0.000	0.000
80	B	402	ILE	0	0.003	0.017	41.559	-0.241	-0.241	0.000	0.000	0.000	0.000
81	B	403	ASN	0	0.011	0.002	40.231	-0.287	-0.287	0.000	0.000	0.000	0.000
82	B	404	TRP	0	0.033	0.026	38.040	-0.194	-0.194	0.000	0.000	0.000	0.000
83	B	405	THR	0	-0.039	-0.024	37.072	-0.278	-0.278	0.000	0.000	0.000	0.000
84	B	406	ARG	1	0.850	0.906	35.700	7.686	7.686	0.000	0.000	0.000	0.000
85	B	407	ASP	-1	-0.891	-0.935	34.395	-8.921	-8.921	0.000	0.000	0.000	0.000
86	B	408	SER	0	-0.029	-0.030	32.685	-0.379	-0.379	0.000	0.000	0.000	0.000
87	B	409	ILE	0	-0.045	-0.030	31.106	-0.380	-0.380	0.000	0.000	0.000	0.000
88	B	410	THR	0	-0.017	-0.017	29.922	-0.368	-0.368	0.000	0.000	0.000	0.000
89	B	411	GLU	-1	-0.922	-0.946	28.464	-11.200	-11.200	0.000	0.000	0.000	0.000
90	B	412	VAL	0	-0.041	-0.017	26.366	-0.570	-0.570	0.000	0.000	0.000	0.000
91	B	413	TRP	0	-0.006	-0.012	24.568	-0.759	-0.759	0.000	0.000	0.000	0.000
92	B	414	SER	0	-0.002	-0.001	24.464	-0.481	-0.481	0.000	0.000	0.000	0.000
93	B	415	TYR	0	-0.021	-0.007	19.694	-0.745	-0.745	0.000	0.000	0.000	0.000
94	B	416	ASN	0	-0.036	-0.033	20.566	-1.057	-1.057	0.000	0.000	0.000	0.000
95	B	417	ALA	0	-0.009	-0.001	19.832	-0.793	-0.793	0.000	0.000	0.000	0.000
96	B	418	GLU	-1	-0.929	-0.958	17.981	-16.524	-16.524	0.000	0.000	0.000	0.000
97	B	419	LEU	0	-0.021	-0.011	14.924	-1.305	-1.305	0.000	0.000	0.000	0.000
98	B	420	LEU	0	-0.009	-0.002	14.887	-1.540	-1.540	0.000	0.000	0.000	0.000
99	B	421	VAL	0	0.020	0.005	14.744	-1.328	-1.328	0.000	0.000	0.000	0.000
100	B	422	ALA	0	0.002	0.008	12.558	-1.500	-1.500	0.000	0.000	0.000	0.000
101	B	423	MET	0	-0.033	-0.019	10.534	-2.452	-2.452	0.000	0.000	0.000	0.000
102	B	424	GLU	-1	-0.840	-0.921	9.883	-25.338	-25.338	0.000	0.000	0.000	0.000
103	B	425	ASN	0	-0.022	-0.016	10.175	-1.456	-1.456	0.000	0.000	0.000	0.000
105	B	427	HIS	0	0.019	0.015	5.801	-5.122	-5.122	0.000	0.000	0.000	0.000
106	B	428	THR	0	0.008	-0.004	7.299	-1.628	-1.628	0.000	0.000	0.000	0.000
110	B	432	ALA	0	0.031	0.012	6.898	2.494	2.494	0.000	0.000	0.000	0.000
112	B	434	SER	0	0.007	0.012	5.259	3.124	3.124	0.000	0.000	0.000	0.000
113	B	435	GLU	-1	-0.830	-0.906	6.498	-22.348	-22.348	0.000	0.000	0.000	0.000
114	B	436	MET	0	-0.017	0.013	7.947	3.222	3.222	0.000	0.000	0.000	0.000
115	B	437	ASP	-1	-0.912	-0.953	7.444	-29.844	-29.844	0.000	0.000	0.000	0.000
116	B	438	LYS	1	0.800	0.868	9.483	28.594	28.594	0.000	0.000	0.000	0.000
117	B	439	LEU	0	-0.068	-0.023	11.910	2.309	2.309	0.000	0.000	0.000	0.000
118	B	440	TYR	0	-0.020	-0.028	11.878	1.460	1.460	0.000	0.000	0.000	0.000
119	B	441	GLU	-1	-0.733	-0.867	11.684	-19.331	-19.331	0.000	0.000	0.000	0.000
120	B	442	ARG	1	0.864	0.949	14.429	17.706	17.706	0.000	0.000	0.000	0.000
121	B	443	VAL	0	-0.031	-0.027	17.273	1.178	1.178	0.000	0.000	0.000	0.000
122	B	444	LYS	1	0.937	0.974	15.222	19.364	19.364	0.000	0.000	0.000	0.000
123	B	445	ARG	1	0.759	0.865	15.256	19.784	19.784	0.000	0.000	0.000	0.000
124	B	446	GLN	0	-0.042	-0.015	20.852	1.113	1.113	0.000	0.000	0.000	0.000
125	B	447	LEU	0	0.004	-0.004	21.790	0.695	0.695	0.000	0.000	0.000	0.000
126	B	448	ARG	1	0.882	0.929	24.032	11.614	11.614	0.000	0.000	0.000	0.000
127	B	449	GLU	-1	-0.887	-0.937	24.557	-11.699	-11.699	0.000	0.000	0.000	0.000
128	B	450	ASN	0	-0.036	-0.018	26.090	0.324	0.324	0.000	0.000	0.000	0.000
129	B	451	ALA	0	-0.004	-0.017	23.383	0.286	0.286	0.000	0.000	0.000	0.000
130	B	452	GLU	-1	-0.920	-0.940	21.635	-12.135	-12.135	0.000	0.000	0.000	0.000
131	B	453	GLU	-1	-0.886	-0.944	14.960	-18.617	-18.617	0.000	0.000	0.000	0.000
132	B	454	ASP	-1	-0.792	-0.873	16.778	-15.543	-15.543	0.000	0.000	0.000	0.000
133	B	455	GLY	0	-0.032	-0.006	14.280	0.116	0.116	0.000	0.000	0.000	0.000
134	B	456	THR	0	-0.057	-0.062	12.703	-1.239	-1.239	0.000	0.000	0.000	0.000
135	B	457	GLY	0	-0.012	-0.010	12.945	-0.669	-0.669	0.000	0.000	0.000	0.000
136	B	458	CYS	0	-0.072	-0.020	13.525	0.474	0.474	0.000	0.000	0.000	0.000
137	B	459	PHE	0	-0.043	-0.035	16.024	-0.147	-0.147	0.000	0.000	0.000	0.000
138	B	460	GLU	-1	-0.938	-0.954	20.053	-11.453	-11.453	0.000	0.000	0.000	0.000
139	B	461	ILE	0	-0.028	-0.024	23.411	0.058	0.058	0.000	0.000	0.000	0.000
140	B	462	PHE	0	0.014	0.016	25.515	0.335	0.335	0.000	0.000	0.000	0.000
141	B	463	HIS	0	0.052	0.040	29.504	0.002	0.002	0.000	0.000	0.000	0.000
142	B	464	LYS	1	0.890	0.938	30.680	9.194	9.194	0.000	0.000	0.000	0.000
143	B	465	CYS	0	-0.021	0.029	28.345	-0.165	-0.165	0.000	0.000	0.000	0.000
144	B	466	ASP	-1	-0.726	-0.856	30.253	-9.290	-9.290	0.000	0.000	0.000	0.000
145	B	467	ASP	-1	-0.841	-0.941	30.546	-9.933	-9.933	0.000	0.000	0.000	0.000
146	B	468	ASP	-1	-0.983	-0.990	31.038	-9.310	-9.310	0.000	0.000	0.000	0.000
147	B	470	MET	0	0.004	0.011	25.772	-0.592	-0.592	0.000	0.000	0.000	0.000
148	B	471	ALA	0	-0.061	-0.025	26.676	-0.490	-0.490	0.000	0.000	0.000	0.000
149	B	472	SER	0	-0.046	-0.041	27.918	-0.327	-0.327	0.000	0.000	0.000	0.000
150	B	473	ILE	0	0.035	0.018	23.003	-0.327	-0.327	0.000	0.000	0.000	0.000
151	B	474	ARG	1	0.919	0.969	23.060	11.099	11.099	0.000	0.000	0.000	0.000
152	B	475	ASN	0	-0.065	-0.024	23.873	-0.356	-0.356	0.000	0.000	0.000	0.000
153	B	476	ASN	0	-0.082	-0.040	23.178	0.168	0.168	0.000	0.000	0.000	0.000
154	B	477	THR	0	-0.021	-0.028	25.613	0.255	0.255	0.000	0.000	0.000	0.000
155	B	478	TYR	0	-0.033	-0.010	27.050	0.258	0.258	0.000	0.000	0.000	0.000
156	B	479	ASP	-1	-0.774	-0.869	28.849	-9.566	-9.566	0.000	0.000	0.000	0.000
157	B	480	HIS	0	0.004	-0.006	27.056	0.247	0.247	0.000	0.000	0.000	0.000
158	B	481	SER	0	-0.147	-0.090	29.525	0.115	0.115	0.000	0.000	0.000	0.000
159	B	482	LYS	1	0.830	0.899	32.933	8.849	8.849	0.000	0.000	0.000	0.000
160	B	483	TYR	0	0.061	0.025	31.364	0.092	0.092	0.000	0.000	0.000	0.000
161	B	484	ARG	1	0.849	0.916	30.234	9.860	9.860	0.000	0.000	0.000	0.000
162	B	485	GLU	-1	-0.892	-0.951	32.917	-8.808	-8.808	0.000	0.000	0.000	0.000
163	B	486	GLU	-1	-0.966	-0.980	34.530	-8.571	-8.571	0.000	0.000	0.000	0.000
164	B	487	ALA	0	0.004	0.003	29.708	-0.014	-0.014	0.000	0.000	0.000	0.000
165	B	488	MET	0	0.071	0.054	30.574	-0.162	-0.162	0.000	0.000	0.000	0.000
166	B	489	GLN	0	-0.141	-0.064	32.179	0.233	0.233	0.000	0.000	0.000	0.000
167	B	490	ASN	-1	-0.970	-0.963	31.465	-9.177	-9.177	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(B:323:LEU)