FMO DATABASE

FMODB ID: MZ6ZZ

Calculation Name: 6XGC-F-Other547

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: 6XGC

Chain ID: F

ChEMBL ID:

UniProt ID:

Base Structure: ElectronMicroscopy

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	163
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1376916.10233
FMO2-HF: Nuclear repulsion	1309613.839796
FMO2-HF: Total energy	-67302.262535
FMO2-MP2: Total energy	-67496.897608

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(F:10:ILE)

Summations of interaction energy for fragment #1(F:10:ILE)

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.
-92.783	-89.814	13.35	-6.437	-9.881	-0.06

Interaction energy analysis for fragmet #1(F:10:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.738 / q_NPA : 0.843

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	F	12	GLY	0	0.024	0.020	3.825	11.080	12.878	-0.016	-0.803	-0.980	-0.002
4	F	13	GLY	0	0.007	0.005	4.295	-5.492	-5.331	-0.001	-0.023	-0.137	0.000
106	F	115	VAL	0	0.000	0.002	2.308	-1.034	-0.692	1.535	-0.335	-1.541	-0.002
107	F	116	LYS	1	0.869	0.923	4.515	28.682	28.907	-0.001	-0.018	-0.206	0.000
110	F	119	TYR	0	-0.063	-0.042	3.153	-1.539	-0.440	0.161	-0.354	-0.905	-0.004
111	F	120	GLU	-1	-0.782	-0.876	5.121	-24.331	-24.329	-0.001	-0.001	0.000	0.000
126	F	135	ASN	0	0.039	0.009	3.276	-2.853	-1.963	0.045	-0.385	-0.550	-0.002
127	F	136	GLY	0	-0.015	-0.018	2.012	-31.623	-32.493	11.610	-5.568	-5.172	-0.049
128	F	137	CYS	0	-0.050	-0.003	3.206	9.589	8.911	0.018	1.050	-0.390	-0.001
5	F	14	TRP	0	-0.033	-0.031	5.469	2.116	2.116	0.000	0.000	0.000	0.000
6	F	15	THR	0	0.035	0.005	8.501	0.879	0.879	0.000	0.000	0.000	0.000
7	F	16	GLY	0	-0.014	0.003	11.759	1.520	1.520	0.000	0.000	0.000	0.000
8	F	17	MET	0	-0.044	-0.004	7.884	0.414	0.414	0.000	0.000	0.000	0.000
9	F	18	VAL	0	-0.003	-0.009	12.255	-0.361	-0.361	0.000	0.000	0.000	0.000
10	F	19	ASP	-1	-0.854	-0.922	14.309	-17.612	-17.612	0.000	0.000	0.000	0.000
11	F	20	GLY	0	0.012	-0.017	13.401	0.761	0.761	0.000	0.000	0.000	0.000
12	F	21	TRP	0	-0.017	-0.005	10.297	-0.725	-0.725	0.000	0.000	0.000	0.000
13	F	22	TYR	0	0.013	-0.004	6.949	-1.839	-1.839	0.000	0.000	0.000	0.000
14	F	23	GLY	0	0.020	0.009	7.516	2.624	2.624	0.000	0.000	0.000	0.000
15	F	24	TYR	0	-0.075	-0.057	7.399	-3.547	-3.547	0.000	0.000	0.000	0.000
16	F	25	HIS	0	0.004	0.004	8.917	1.531	1.531	0.000	0.000	0.000	0.000
17	F	26	HIS	0	-0.041	-0.021	10.605	-0.503	-0.503	0.000	0.000	0.000	0.000
18	F	27	GLN	0	0.009	-0.016	13.487	1.267	1.267	0.000	0.000	0.000	0.000
19	F	28	ASN	0	-0.002	-0.003	15.835	-0.647	-0.647	0.000	0.000	0.000	0.000
20	F	29	GLU	-1	-0.810	-0.899	18.968	-12.011	-12.011	0.000	0.000	0.000	0.000
21	F	30	GLN	0	-0.029	-0.007	21.981	0.142	0.142	0.000	0.000	0.000	0.000
22	F	31	GLY	0	0.014	0.017	21.164	0.337	0.337	0.000	0.000	0.000	0.000
23	F	32	SER	0	-0.055	-0.027	16.303	-0.784	-0.784	0.000	0.000	0.000	0.000
24	F	33	GLY	0	0.052	0.029	15.554	0.991	0.991	0.000	0.000	0.000	0.000
25	F	34	TYR	0	-0.030	-0.014	9.246	-0.709	-0.709	0.000	0.000	0.000	0.000
26	F	35	ALA	0	0.007	0.004	12.215	1.530	1.530	0.000	0.000	0.000	0.000
27	F	36	ALA	0	0.027	0.028	11.762	-1.692	-1.692	0.000	0.000	0.000	0.000
28	F	37	ASP	-1	-0.848	-0.922	10.819	-18.475	-18.475	0.000	0.000	0.000	0.000
29	F	38	LEU	0	0.036	0.008	12.662	0.112	0.112	0.000	0.000	0.000	0.000
30	F	39	LYS	1	0.883	0.946	15.280	15.503	15.503	0.000	0.000	0.000	0.000
31	F	40	SER	0	-0.011	-0.008	10.278	0.644	0.644	0.000	0.000	0.000	0.000
32	F	41	THR	0	0.036	0.016	12.871	-0.301	-0.301	0.000	0.000	0.000	0.000
33	F	42	GLN	0	-0.036	-0.021	14.122	0.151	0.151	0.000	0.000	0.000	0.000
34	F	43	ASN	0	-0.002	-0.010	15.700	0.849	0.849	0.000	0.000	0.000	0.000
35	F	44	ALA	0	-0.041	-0.014	13.446	0.329	0.329	0.000	0.000	0.000	0.000
36	F	45	ILE	0	0.040	0.025	15.488	0.409	0.409	0.000	0.000	0.000	0.000
37	F	46	ASP	-1	-0.808	-0.884	17.845	-12.122	-12.122	0.000	0.000	0.000	0.000
38	F	47	LYS	1	0.872	0.931	16.514	15.622	15.622	0.000	0.000	0.000	0.000
39	F	48	ILE	0	-0.005	0.004	15.900	0.329	0.329	0.000	0.000	0.000	0.000
40	F	49	THR	0	-0.006	-0.008	19.208	0.520	0.520	0.000	0.000	0.000	0.000
41	F	50	ASN	0	-0.028	-0.019	22.468	0.694	0.694	0.000	0.000	0.000	0.000
42	F	51	LYS	1	0.835	0.933	18.519	14.005	14.005	0.000	0.000	0.000	0.000
43	F	52	VAL	0	0.018	0.009	21.817	0.349	0.349	0.000	0.000	0.000	0.000
44	F	53	ASN	0	-0.002	-0.008	24.416	0.388	0.388	0.000	0.000	0.000	0.000
45	F	54	SER	0	-0.039	-0.035	25.910	0.343	0.343	0.000	0.000	0.000	0.000
46	F	55	VAL	0	-0.002	-0.010	24.906	0.348	0.348	0.000	0.000	0.000	0.000
47	F	56	ILE	0	-0.028	-0.004	27.735	0.268	0.268	0.000	0.000	0.000	0.000
48	F	57	GLU	-1	-0.876	-0.928	30.346	-8.518	-8.518	0.000	0.000	0.000	0.000
49	F	58	LYS	1	0.795	0.882	31.335	9.148	9.148	0.000	0.000	0.000	0.000
50	F	59	MET	0	0.002	0.028	33.635	0.250	0.250	0.000	0.000	0.000	0.000
51	F	60	ASN	0	-0.015	-0.023	35.278	0.033	0.033	0.000	0.000	0.000	0.000
52	F	61	THR	0	0.022	0.026	38.613	0.094	0.094	0.000	0.000	0.000	0.000
53	F	62	GLN	0	-0.048	-0.035	41.035	0.108	0.108	0.000	0.000	0.000	0.000
54	F	63	PHE	0	-0.013	-0.002	44.874	-0.034	-0.034	0.000	0.000	0.000	0.000
55	F	64	THR	0	-0.003	-0.011	45.836	0.151	0.151	0.000	0.000	0.000	0.000
56	F	65	ALA	0	0.014	0.011	48.408	-0.033	-0.033	0.000	0.000	0.000	0.000
57	F	66	VAL	0	0.036	0.012	45.385	0.114	0.114	0.000	0.000	0.000	0.000
58	F	67	GLY	0	0.045	0.037	48.732	0.020	0.020	0.000	0.000	0.000	0.000
59	F	68	LYS	1	0.825	0.899	51.126	5.874	5.874	0.000	0.000	0.000	0.000
60	F	69	GLU	-1	-0.908	-0.935	54.913	-5.350	-5.350	0.000	0.000	0.000	0.000
61	F	70	PHE	0	0.015	-0.008	55.355	0.025	0.025	0.000	0.000	0.000	0.000
62	F	71	ASN	0	0.053	0.035	60.399	0.008	0.008	0.000	0.000	0.000	0.000
63	F	72	HIS	0	0.003	-0.015	62.965	-0.006	-0.006	0.000	0.000	0.000	0.000
64	F	73	LEU	0	-0.007	-0.006	64.215	-0.033	-0.033	0.000	0.000	0.000	0.000
65	F	74	GLU	-1	-0.945	-0.970	62.034	-4.930	-4.930	0.000	0.000	0.000	0.000
66	F	75	LYS	1	0.888	0.928	58.894	5.188	5.188	0.000	0.000	0.000	0.000
67	F	76	ARG	1	0.940	0.958	58.793	4.787	4.787	0.000	0.000	0.000	0.000
68	F	77	ILE	0	-0.002	0.005	57.665	-0.075	-0.075	0.000	0.000	0.000	0.000
69	F	78	GLU	-1	-0.780	-0.860	55.760	-5.511	-5.511	0.000	0.000	0.000	0.000
70	F	79	ASN	0	0.005	-0.013	54.364	-0.166	-0.166	0.000	0.000	0.000	0.000
71	F	80	LEU	0	-0.049	-0.014	53.318	-0.109	-0.109	0.000	0.000	0.000	0.000
72	F	81	ASN	0	-0.005	-0.014	50.812	-0.089	-0.089	0.000	0.000	0.000	0.000
73	F	82	LYS	1	0.939	0.968	49.817	6.074	6.074	0.000	0.000	0.000	0.000
74	F	83	LYS	1	0.948	0.986	48.605	5.826	5.826	0.000	0.000	0.000	0.000
75	F	84	VAL	0	-0.063	-0.024	47.658	-0.102	-0.102	0.000	0.000	0.000	0.000
76	F	85	ASP	-1	-0.921	-0.955	45.289	-6.883	-6.883	0.000	0.000	0.000	0.000
77	F	86	ASP	-1	-0.857	-0.930	44.119	-6.710	-6.710	0.000	0.000	0.000	0.000
78	F	87	GLY	0	0.027	0.013	42.964	-0.169	-0.169	0.000	0.000	0.000	0.000
79	F	88	PHE	0	-0.035	-0.037	41.844	-0.142	-0.142	0.000	0.000	0.000	0.000
80	F	89	LEU	0	0.026	0.022	38.705	-0.222	-0.222	0.000	0.000	0.000	0.000
81	F	90	ASP	-1	-0.892	-0.929	38.211	-7.794	-7.794	0.000	0.000	0.000	0.000
82	F	91	ILE	0	-0.063	-0.036	37.103	-0.264	-0.264	0.000	0.000	0.000	0.000
83	F	92	TRP	0	-0.006	-0.018	34.702	-0.329	-0.329	0.000	0.000	0.000	0.000
84	F	93	THR	0	-0.016	-0.013	33.769	-0.304	-0.304	0.000	0.000	0.000	0.000
85	F	94	TYR	0	-0.014	-0.009	32.362	-0.301	-0.301	0.000	0.000	0.000	0.000
86	F	95	ASN	0	-0.024	-0.016	31.488	-0.483	-0.483	0.000	0.000	0.000	0.000
87	F	96	ALA	0	0.000	0.007	30.008	-0.323	-0.323	0.000	0.000	0.000	0.000
88	F	97	GLU	-1	-0.916	-0.958	27.836	-10.936	-10.936	0.000	0.000	0.000	0.000
89	F	98	LEU	0	-0.030	-0.014	26.454	-0.501	-0.501	0.000	0.000	0.000	0.000
90	F	99	LEU	0	0.003	0.006	25.714	-0.452	-0.452	0.000	0.000	0.000	0.000
91	F	100	VAL	0	0.015	0.000	23.302	-0.531	-0.531	0.000	0.000	0.000	0.000
92	F	101	LEU	0	-0.027	-0.011	22.001	-0.735	-0.735	0.000	0.000	0.000	0.000
93	F	102	LEU	0	0.023	0.013	20.761	-0.693	-0.693	0.000	0.000	0.000	0.000
94	F	103	GLU	-1	-0.852	-0.918	20.219	-13.394	-13.394	0.000	0.000	0.000	0.000
95	F	104	ASN	0	-0.028	0.001	18.012	-0.919	-0.919	0.000	0.000	0.000	0.000
96	F	105	GLU	-1	-0.940	-0.964	16.253	-15.861	-15.861	0.000	0.000	0.000	0.000
97	F	106	ARG	1	0.957	0.961	15.355	12.994	12.994	0.000	0.000	0.000	0.000
98	F	107	THR	0	-0.054	-0.039	14.520	-0.368	-0.368	0.000	0.000	0.000	0.000
99	F	108	LEU	0	-0.027	-0.008	11.285	-1.018	-1.018	0.000	0.000	0.000	0.000
100	F	109	ASP	-1	-0.877	-0.931	10.551	-21.244	-21.244	0.000	0.000	0.000	0.000
101	F	110	TYR	0	-0.031	-0.005	11.274	-0.567	-0.567	0.000	0.000	0.000	0.000
102	F	111	HIS	0	0.001	0.004	8.718	-0.937	-0.937	0.000	0.000	0.000	0.000
103	F	112	ASP	-1	-0.854	-0.924	6.296	-32.343	-32.343	0.000	0.000	0.000	0.000
104	F	113	SER	0	-0.027	-0.013	6.613	-2.214	-2.214	0.000	0.000	0.000	0.000
105	F	114	ASN	0	-0.034	-0.037	8.599	0.529	0.529	0.000	0.000	0.000	0.000
108	F	117	ASN	0	0.009	-0.006	5.550	0.312	0.312	0.000	0.000	0.000	0.000
109	F	118	LEU	0	-0.049	-0.018	6.006	1.838	1.838	0.000	0.000	0.000	0.000
112	F	121	LYS	1	0.879	0.960	8.468	21.899	21.899	0.000	0.000	0.000	0.000
113	F	122	VAL	0	0.008	0.005	7.661	1.559	1.559	0.000	0.000	0.000	0.000
114	F	123	ARG	1	0.873	0.911	8.159	28.168	28.168	0.000	0.000	0.000	0.000
115	F	124	ASN	0	-0.023	-0.025	9.990	1.957	1.957	0.000	0.000	0.000	0.000
116	F	125	GLN	0	-0.031	-0.028	12.689	1.222	1.222	0.000	0.000	0.000	0.000
117	F	126	LEU	0	-0.017	0.012	11.337	0.903	0.903	0.000	0.000	0.000	0.000
118	F	127	LYS	1	0.882	0.959	13.476	16.728	16.728	0.000	0.000	0.000	0.000
119	F	128	ASN	0	-0.070	-0.051	15.026	-0.471	-0.471	0.000	0.000	0.000	0.000
120	F	129	ASN	0	0.035	0.009	15.930	0.316	0.316	0.000	0.000	0.000	0.000
121	F	130	ALA	0	-0.012	-0.002	11.675	0.087	0.087	0.000	0.000	0.000	0.000
122	F	131	LYS	1	0.881	0.947	12.733	20.785	20.785	0.000	0.000	0.000	0.000
123	F	132	GLU	-1	-0.810	-0.880	7.369	-34.886	-34.886	0.000	0.000	0.000	0.000
124	F	133	ILE	0	-0.012	-0.010	7.261	1.998	1.998	0.000	0.000	0.000	0.000
125	F	134	GLY	0	0.001	0.011	6.690	0.456	0.456	0.000	0.000	0.000	0.000
129	F	138	PHE	0	0.000	-0.015	6.015	1.487	1.487	0.000	0.000	0.000	0.000
130	F	139	GLU	-1	-0.848	-0.909	9.480	-20.009	-20.009	0.000	0.000	0.000	0.000
131	F	140	PHE	0	-0.037	-0.036	11.978	0.436	0.436	0.000	0.000	0.000	0.000
132	F	141	TYR	0	0.025	0.021	15.705	0.178	0.178	0.000	0.000	0.000	0.000
133	F	142	HIS	0	0.026	0.027	18.443	0.048	0.048	0.000	0.000	0.000	0.000
134	F	143	LYS	1	0.853	0.915	19.824	11.525	11.525	0.000	0.000	0.000	0.000
135	F	144	CYS	0	-0.090	-0.029	17.631	-0.331	-0.331	0.000	0.000	0.000	0.000
136	F	145	ASP	-1	-0.775	-0.869	19.902	-13.128	-13.128	0.000	0.000	0.000	0.000
137	F	146	ASN	0	0.064	0.014	19.887	-1.090	-1.090	0.000	0.000	0.000	0.000
138	F	147	THR	0	-0.040	-0.031	20.327	-0.246	-0.246	0.000	0.000	0.000	0.000
139	F	149	MET	0	0.037	0.013	14.576	-0.919	-0.919	0.000	0.000	0.000	0.000
140	F	150	GLU	-1	-0.836	-0.908	15.916	-16.355	-16.355	0.000	0.000	0.000	0.000
141	F	151	SER	0	-0.010	0.010	17.580	-0.257	-0.257	0.000	0.000	0.000	0.000
142	F	152	VAL	0	0.000	-0.004	12.152	-0.090	-0.090	0.000	0.000	0.000	0.000
143	F	153	LYS	1	0.822	0.910	12.507	16.695	16.695	0.000	0.000	0.000	0.000
144	F	154	ASN	0	-0.007	-0.005	13.885	-0.297	-0.297	0.000	0.000	0.000	0.000
145	F	155	GLY	0	-0.001	0.005	15.520	0.206	0.206	0.000	0.000	0.000	0.000
146	F	156	THR	0	-0.088	-0.050	16.269	0.525	0.525	0.000	0.000	0.000	0.000
147	F	157	TYR	0	-0.055	-0.040	16.903	0.524	0.524	0.000	0.000	0.000	0.000
148	F	158	ASP	-1	-0.837	-0.928	18.867	-11.635	-11.635	0.000	0.000	0.000	0.000
149	F	159	TYR	0	0.023	0.012	18.770	0.127	0.127	0.000	0.000	0.000	0.000
150	F	160	PRO	0	-0.017	-0.004	21.080	-0.087	-0.087	0.000	0.000	0.000	0.000
151	F	161	LYS	1	0.898	0.964	24.015	11.689	11.689	0.000	0.000	0.000	0.000
152	F	162	TYR	0	0.043	0.015	20.888	0.282	0.282	0.000	0.000	0.000	0.000
153	F	163	SER	0	0.013	-0.004	21.795	-0.326	-0.326	0.000	0.000	0.000	0.000
154	F	164	GLU	-1	-0.860	-0.917	22.770	-10.597	-10.597	0.000	0.000	0.000	0.000
155	F	165	GLU	-1	-0.900	-0.957	23.735	-12.079	-12.079	0.000	0.000	0.000	0.000
156	F	166	ALA	0	-0.004	-0.006	19.674	-0.172	-0.172	0.000	0.000	0.000	0.000
157	F	167	LYS	1	0.795	0.908	21.591	10.351	10.351	0.000	0.000	0.000	0.000
158	F	168	LEU	0	0.021	0.008	23.826	-0.001	-0.001	0.000	0.000	0.000	0.000
159	F	169	ASN	0	-0.044	-0.039	22.364	0.193	0.193	0.000	0.000	0.000	0.000
160	F	170	ARG	1	0.909	0.964	18.617	14.473	14.473	0.000	0.000	0.000	0.000
161	F	171	GLU	-1	-0.946	-0.980	22.432	-11.334	-11.334	0.000	0.000	0.000	0.000
162	F	172	LYS	1	0.880	0.950	24.965	11.261	11.261	0.000	0.000	0.000	0.000
163	F	173	ILE	-1	-0.957	-0.964	22.142	-12.457	-12.457	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:10:ILE)