FMO DATABASE

FMODB ID: 4GR8N

Calculation Name: 1JSM-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: 1JSM

Chain ID: B

ChEMBL ID:

UniProt ID: A5Z226

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	159
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1325791.227712
FMO2-HF: Nuclear repulsion	1260298.849173
FMO2-HF: Total energy	-65492.378538
FMO2-MP2: Total energy	-65679.539213

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:1:GLY)

Summations of interaction energy for fragment #1(B:1:GLY)

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.
-262.937	-257.607	10.662	-8.2	-7.786	-0.1

Interaction energy analysis for fragmet #1(B:1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.799 / q_NPA : 0.891

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	3	PHE	0	-0.030	-0.016	3.456	12.638	13.932	0.000	-0.584	-0.709	-0.002
4	B	4	GLY	0	-0.009	-0.001	2.447	11.259	12.097	0.184	-0.443	-0.579	-0.002
5	B	5	ALA	0	0.012	0.014	3.570	10.686	10.875	0.000	0.019	-0.207	0.000
6	B	6	ILE	0	-0.005	-0.018	3.862	5.077	5.298	0.000	-0.058	-0.162	0.000
7	B	7	ALA	0	-0.049	-0.026	2.616	-25.348	-23.469	0.507	-1.233	-1.153	-0.015
8	B	8	GLY	0	-0.023	-0.008	4.598	-6.190	-6.125	-0.001	-0.015	-0.049	0.000
9	B	9	PHE	0	-0.085	-0.029	5.357	5.883	5.920	-0.001	-0.001	-0.034	0.000
109	B	109	ASP	-1	-0.793	-0.906	2.889	-71.079	-69.451	0.281	-0.999	-0.909	-0.009
110	B	110	PHE	0	-0.039	0.000	4.749	1.346	1.307	-0.001	-0.004	0.044	0.000
112	B	112	ASP	-1	-0.739	-0.862	1.905	-115.711	-116.475	9.694	-4.880	-4.050	-0.072
113	B	113	SER	0	-0.029	-0.007	5.165	4.518	4.500	-0.001	-0.002	0.022	0.000
10	B	10	ILE	0	0.009	0.006	7.292	4.593	4.593	0.000	0.000	0.000	0.000
11	B	11	GLU	-1	-0.888	-0.949	7.676	-29.095	-29.095	0.000	0.000	0.000	0.000
12	B	12	GLY	0	-0.033	-0.024	9.380	-0.661	-0.661	0.000	0.000	0.000	0.000
13	B	13	GLY	0	-0.013	0.008	10.351	0.302	0.302	0.000	0.000	0.000	0.000
14	B	14	TRP	0	0.013	-0.012	11.857	1.478	1.478	0.000	0.000	0.000	0.000
15	B	15	GLN	0	0.028	0.001	15.638	0.430	0.430	0.000	0.000	0.000	0.000
16	B	16	GLY	0	-0.003	0.008	18.075	0.665	0.665	0.000	0.000	0.000	0.000
17	B	17	MET	0	-0.062	-0.007	14.555	0.848	0.848	0.000	0.000	0.000	0.000
18	B	18	VAL	0	-0.010	-0.015	18.239	-0.595	-0.595	0.000	0.000	0.000	0.000
19	B	19	ASP	-1	-0.903	-0.946	20.777	-13.522	-13.522	0.000	0.000	0.000	0.000
20	B	20	GLY	0	-0.003	-0.015	18.545	0.358	0.358	0.000	0.000	0.000	0.000
21	B	21	TRP	0	-0.021	-0.009	13.107	-0.577	-0.577	0.000	0.000	0.000	0.000
22	B	22	TYR	0	-0.004	-0.036	10.691	-1.488	-1.488	0.000	0.000	0.000	0.000
23	B	23	GLY	0	0.019	0.003	14.019	1.564	1.564	0.000	0.000	0.000	0.000
24	B	24	TYR	0	-0.017	-0.024	15.586	-1.094	-1.094	0.000	0.000	0.000	0.000
25	B	25	HIS	0	-0.050	-0.030	18.099	0.621	0.621	0.000	0.000	0.000	0.000
26	B	26	HIS	0	0.054	0.032	19.643	-0.612	-0.612	0.000	0.000	0.000	0.000
27	B	27	SER	0	0.003	-0.021	22.822	0.375	0.375	0.000	0.000	0.000	0.000
28	B	28	ASN	0	0.017	0.004	25.513	0.102	0.102	0.000	0.000	0.000	0.000
29	B	29	GLU	-1	-0.836	-0.912	28.997	-9.007	-9.007	0.000	0.000	0.000	0.000
30	B	30	GLN	0	-0.039	0.000	32.023	0.044	0.044	0.000	0.000	0.000	0.000
31	B	31	GLY	0	-0.005	0.008	30.335	0.160	0.160	0.000	0.000	0.000	0.000
32	B	32	SER	0	-0.023	-0.010	24.957	-0.336	-0.336	0.000	0.000	0.000	0.000
33	B	33	GLY	0	0.001	0.003	24.421	0.435	0.435	0.000	0.000	0.000	0.000
34	B	34	TYR	0	-0.006	0.004	18.403	-0.316	-0.316	0.000	0.000	0.000	0.000
35	B	35	ALA	0	0.008	0.003	20.646	0.747	0.747	0.000	0.000	0.000	0.000
36	B	36	ALA	0	0.011	0.023	18.596	-0.885	-0.885	0.000	0.000	0.000	0.000
37	B	37	ASP	-1	-0.761	-0.839	16.959	-16.170	-16.170	0.000	0.000	0.000	0.000
38	B	38	LYS	1	0.983	0.974	18.415	12.117	12.117	0.000	0.000	0.000	0.000
39	B	39	GLU	-1	-0.874	-0.910	19.314	-15.859	-15.859	0.000	0.000	0.000	0.000
40	B	40	SER	0	-0.037	-0.072	14.844	-0.667	-0.667	0.000	0.000	0.000	0.000
41	B	41	THR	0	0.017	-0.007	16.022	-1.197	-1.197	0.000	0.000	0.000	0.000
42	B	42	GLN	0	-0.086	-0.048	17.093	-0.045	-0.045	0.000	0.000	0.000	0.000
43	B	43	LYS	1	0.948	0.987	14.706	20.002	20.002	0.000	0.000	0.000	0.000
44	B	44	ALA	0	0.002	0.008	13.674	-0.240	-0.240	0.000	0.000	0.000	0.000
45	B	45	ILE	0	0.016	0.021	15.550	-0.246	-0.246	0.000	0.000	0.000	0.000
46	B	46	ASP	-1	-0.832	-0.897	18.149	-13.936	-13.936	0.000	0.000	0.000	0.000
47	B	47	GLY	0	-0.011	-0.009	16.809	0.375	0.375	0.000	0.000	0.000	0.000
48	B	48	THR	0	-0.036	-0.036	14.784	-0.520	-0.520	0.000	0.000	0.000	0.000
49	B	49	THR	0	-0.034	-0.026	16.620	0.464	0.464	0.000	0.000	0.000	0.000
50	B	50	ASN	0	-0.006	-0.009	19.988	0.838	0.838	0.000	0.000	0.000	0.000
51	B	51	LYS	1	0.831	0.925	12.157	22.843	22.843	0.000	0.000	0.000	0.000
52	B	52	VAL	0	0.010	-0.001	17.974	0.326	0.326	0.000	0.000	0.000	0.000
53	B	53	ASN	0	0.013	0.004	20.055	0.378	0.378	0.000	0.000	0.000	0.000
54	B	54	SER	0	0.001	-0.008	20.819	0.517	0.517	0.000	0.000	0.000	0.000
55	B	55	ILE	0	-0.035	-0.020	17.217	0.319	0.319	0.000	0.000	0.000	0.000
56	B	56	ILE	0	-0.008	0.001	21.877	0.424	0.424	0.000	0.000	0.000	0.000
57	B	57	ASP	-1	-0.889	-0.950	25.116	-10.847	-10.847	0.000	0.000	0.000	0.000
58	B	58	LYS	1	0.779	0.882	23.945	11.743	11.743	0.000	0.000	0.000	0.000
59	B	59	MET	0	-0.005	0.034	23.387	0.357	0.357	0.000	0.000	0.000	0.000
60	B	60	ASN	0	0.012	0.000	27.497	0.152	0.152	0.000	0.000	0.000	0.000
61	B	61	THR	0	-0.053	-0.022	30.767	0.299	0.299	0.000	0.000	0.000	0.000
62	B	62	GLN	0	-0.016	-0.020	27.422	0.269	0.269	0.000	0.000	0.000	0.000
63	B	63	PHE	0	-0.011	-0.011	32.191	0.285	0.285	0.000	0.000	0.000	0.000
64	B	64	GLU	-1	-0.921	-0.951	35.191	-8.304	-8.304	0.000	0.000	0.000	0.000
65	B	65	ALA	0	-0.035	-0.016	37.942	0.171	0.171	0.000	0.000	0.000	0.000
66	B	66	VAL	0	-0.032	-0.019	40.212	0.102	0.102	0.000	0.000	0.000	0.000
67	B	67	GLY	0	0.016	0.014	43.979	0.079	0.079	0.000	0.000	0.000	0.000
68	B	68	LYS	1	0.827	0.898	45.423	7.012	7.012	0.000	0.000	0.000	0.000
69	B	69	GLU	-1	-0.936	-0.957	49.239	-6.052	-6.052	0.000	0.000	0.000	0.000
70	B	70	PHE	0	0.023	0.001	48.369	0.040	0.040	0.000	0.000	0.000	0.000
71	B	71	ASN	0	0.042	0.020	53.646	0.043	0.043	0.000	0.000	0.000	0.000
72	B	72	ASN	0	-0.010	-0.019	55.659	-0.079	-0.079	0.000	0.000	0.000	0.000
73	B	73	LEU	0	-0.047	-0.027	57.232	-0.011	-0.011	0.000	0.000	0.000	0.000
74	B	74	GLU	-1	-0.876	-0.932	54.152	-5.693	-5.693	0.000	0.000	0.000	0.000
75	B	75	ARG	1	0.908	0.938	51.875	5.868	5.868	0.000	0.000	0.000	0.000
76	B	76	ARG	1	0.936	0.968	50.292	5.647	5.647	0.000	0.000	0.000	0.000
77	B	77	ILE	0	0.026	0.009	49.168	-0.132	-0.132	0.000	0.000	0.000	0.000
78	B	78	GLU	-1	-0.835	-0.885	48.416	-6.387	-6.387	0.000	0.000	0.000	0.000
79	B	79	ASN	0	-0.017	-0.020	44.905	-0.247	-0.247	0.000	0.000	0.000	0.000
80	B	80	LEU	0	-0.028	-0.003	44.437	-0.163	-0.163	0.000	0.000	0.000	0.000
81	B	81	ASN	0	0.035	0.013	43.766	-0.115	-0.115	0.000	0.000	0.000	0.000
82	B	82	LYS	1	0.850	0.911	40.243	7.580	7.580	0.000	0.000	0.000	0.000
83	B	83	LYS	1	0.841	0.904	38.335	7.814	7.814	0.000	0.000	0.000	0.000
84	B	84	MET	0	-0.029	0.008	39.043	-0.137	-0.137	0.000	0.000	0.000	0.000
85	B	85	GLU	-1	-0.845	-0.926	38.302	-7.634	-7.634	0.000	0.000	0.000	0.000
86	B	86	ASP	-1	-0.767	-0.869	36.701	-8.245	-8.245	0.000	0.000	0.000	0.000
87	B	87	GLY	0	0.036	0.025	34.836	-0.264	-0.264	0.000	0.000	0.000	0.000
88	B	88	PHE	0	-0.005	-0.018	33.494	-0.275	-0.275	0.000	0.000	0.000	0.000
89	B	89	LEU	0	0.017	0.022	32.048	-0.265	-0.265	0.000	0.000	0.000	0.000
90	B	90	ASP	-1	-0.902	-0.941	30.492	-9.905	-9.905	0.000	0.000	0.000	0.000
91	B	91	VAL	0	-0.052	-0.028	28.781	-0.452	-0.452	0.000	0.000	0.000	0.000
92	B	92	TRP	0	0.007	-0.002	27.374	-0.558	-0.558	0.000	0.000	0.000	0.000
93	B	93	THR	0	-0.009	0.001	26.179	-0.330	-0.330	0.000	0.000	0.000	0.000
94	B	94	TYR	0	-0.001	0.001	22.969	-0.716	-0.716	0.000	0.000	0.000	0.000
95	B	95	ASN	0	-0.039	-0.034	23.000	-0.801	-0.801	0.000	0.000	0.000	0.000
96	B	96	ALA	0	-0.006	-0.002	22.459	-0.528	-0.528	0.000	0.000	0.000	0.000
97	B	97	GLU	-1	-0.928	-0.969	20.665	-13.684	-13.684	0.000	0.000	0.000	0.000
98	B	98	LEU	0	0.006	-0.001	17.441	-1.032	-1.032	0.000	0.000	0.000	0.000
99	B	99	LEU	0	-0.013	-0.001	17.222	-1.061	-1.061	0.000	0.000	0.000	0.000
100	B	100	VAL	0	0.014	0.003	16.514	-1.064	-1.064	0.000	0.000	0.000	0.000
101	B	101	LEU	0	-0.012	-0.010	14.349	-1.379	-1.379	0.000	0.000	0.000	0.000
102	B	102	MET	0	-0.009	-0.001	12.583	-1.727	-1.727	0.000	0.000	0.000	0.000
103	B	103	GLU	-1	-0.823	-0.920	11.824	-22.407	-22.407	0.000	0.000	0.000	0.000
104	B	104	ASN	0	-0.006	0.021	11.651	-1.017	-1.017	0.000	0.000	0.000	0.000
105	B	105	GLU	-1	-0.944	-0.959	7.403	-31.314	-31.314	0.000	0.000	0.000	0.000
106	B	106	ARG	1	0.942	0.957	7.012	18.933	18.933	0.000	0.000	0.000	0.000
107	B	107	THR	0	-0.046	-0.038	9.004	0.625	0.625	0.000	0.000	0.000	0.000
108	B	108	LEU	0	-0.034	-0.006	5.086	-0.573	-0.573	0.000	0.000	0.000	0.000
111	B	111	HIS	0	0.043	0.048	7.178	1.297	1.297	0.000	0.000	0.000	0.000
114	B	114	ASN	0	-0.029	-0.023	7.856	4.194	4.194	0.000	0.000	0.000	0.000
115	B	115	VAL	0	0.002	0.008	7.441	2.585	2.585	0.000	0.000	0.000	0.000
116	B	116	LYS	1	0.850	0.923	6.545	33.955	33.955	0.000	0.000	0.000	0.000
117	B	117	ASN	0	-0.014	-0.022	8.582	2.297	2.297	0.000	0.000	0.000	0.000
118	B	118	LEU	0	-0.032	-0.002	11.904	1.963	1.963	0.000	0.000	0.000	0.000
119	B	119	TYR	0	-0.036	-0.051	11.111	1.267	1.267	0.000	0.000	0.000	0.000
120	B	120	ASP	-1	-0.763	-0.870	12.072	-23.380	-23.380	0.000	0.000	0.000	0.000
121	B	121	LYS	1	0.838	0.922	14.396	17.614	17.614	0.000	0.000	0.000	0.000
122	B	122	VAL	0	0.031	0.018	16.598	1.065	1.065	0.000	0.000	0.000	0.000
123	B	123	ARG	1	0.832	0.907	14.653	20.640	20.640	0.000	0.000	0.000	0.000
124	B	124	LEU	0	-0.075	-0.032	18.027	0.836	0.836	0.000	0.000	0.000	0.000
125	B	125	GLN	0	-0.016	-0.007	20.442	0.123	0.123	0.000	0.000	0.000	0.000
126	B	126	LEU	0	-0.031	-0.012	20.241	0.732	0.732	0.000	0.000	0.000	0.000
127	B	127	ARG	1	0.942	0.961	23.040	11.763	11.763	0.000	0.000	0.000	0.000
128	B	128	ASP	-1	-0.895	-0.945	23.918	-11.783	-11.783	0.000	0.000	0.000	0.000
129	B	129	ASN	0	-0.040	-0.017	25.565	0.378	0.378	0.000	0.000	0.000	0.000
130	B	130	ALA	0	-0.013	-0.014	22.577	0.264	0.264	0.000	0.000	0.000	0.000
131	B	131	LYS	1	0.850	0.933	22.221	13.035	13.035	0.000	0.000	0.000	0.000
132	B	132	GLU	-1	-0.821	-0.897	15.199	-20.206	-20.206	0.000	0.000	0.000	0.000
133	B	133	LEU	0	-0.060	-0.036	17.701	0.464	0.464	0.000	0.000	0.000	0.000
134	B	134	GLY	0	-0.030	-0.005	14.052	-0.025	-0.025	0.000	0.000	0.000	0.000
135	B	135	ASN	0	0.035	0.011	12.537	-1.239	-1.239	0.000	0.000	0.000	0.000
136	B	136	GLY	0	0.020	0.006	12.341	-0.195	-0.195	0.000	0.000	0.000	0.000
137	B	137	CYS	0	-0.083	-0.026	12.810	1.170	1.170	0.000	0.000	0.000	0.000
138	B	138	PHE	0	0.042	0.006	15.903	-0.040	-0.040	0.000	0.000	0.000	0.000
139	B	139	GLU	-1	-0.885	-0.918	19.695	-12.511	-12.511	0.000	0.000	0.000	0.000
140	B	140	PHE	0	0.033	-0.002	23.309	0.051	0.051	0.000	0.000	0.000	0.000
141	B	141	TYR	0	-0.064	-0.015	26.246	0.142	0.142	0.000	0.000	0.000	0.000
142	B	142	HIS	0	-0.014	-0.006	29.018	0.475	0.475	0.000	0.000	0.000	0.000
143	B	143	LYS	1	0.815	0.882	30.162	8.762	8.762	0.000	0.000	0.000	0.000
144	B	144	CYS	0	0.006	0.043	27.629	-0.211	-0.211	0.000	0.000	0.000	0.000
145	B	145	ASP	-1	-0.736	-0.879	29.311	-10.001	-10.001	0.000	0.000	0.000	0.000
146	B	146	ASN	0	-0.020	-0.032	29.364	-0.635	-0.635	0.000	0.000	0.000	0.000
147	B	147	GLU	-1	-0.945	-0.959	29.768	-9.331	-9.331	0.000	0.000	0.000	0.000
148	B	149	MET	0	-0.013	-0.025	23.632	-0.340	-0.340	0.000	0.000	0.000	0.000
149	B	150	GLU	-1	-0.915	-0.950	25.294	-12.210	-12.210	0.000	0.000	0.000	0.000
150	B	151	SER	0	0.000	-0.017	26.476	-0.222	-0.222	0.000	0.000	0.000	0.000
151	B	152	VAL	0	-0.037	-0.015	21.513	-0.211	-0.211	0.000	0.000	0.000	0.000
152	B	153	LYS	1	0.873	0.939	21.867	12.870	12.870	0.000	0.000	0.000	0.000
153	B	154	ASN	0	-0.082	-0.027	23.159	-0.076	-0.076	0.000	0.000	0.000	0.000
154	B	155	GLY	0	-0.039	-0.011	23.748	0.190	0.190	0.000	0.000	0.000	0.000
155	B	156	THR	0	-0.056	-0.051	24.674	0.023	0.023	0.000	0.000	0.000	0.000
156	B	157	TYR	0	-0.044	-0.019	25.393	0.282	0.282	0.000	0.000	0.000	0.000
157	B	158	ASP	-1	-0.862	-0.938	26.563	-11.191	-11.191	0.000	0.000	0.000	0.000
158	B	159	TYR	0	-0.124	-0.060	29.219	0.299	0.299	0.000	0.000	0.000	0.000
159	B	160	PRO	-1	-0.969	-0.963	32.141	-8.823	-8.823	0.000	0.000	0.000	0.000

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