FMO DATABASE

FMODB ID: 4GR7N

Calculation Name: 4JUN-B-Xray547

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose | 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid

Ligand 3-letter code: NAG | EPE

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4JUN

Chain ID: B

ChEMBL ID:

UniProt ID: Q2F4V6

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	169
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1496244.591653
FMO2-HF: Nuclear repulsion	1426111.518624
FMO2-HF: Total energy	-70133.07303
FMO2-MP2: Total energy	-70334.138126

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.
-246.863	-241.229	8.077	-7.014	-6.695	-0.085

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 : 0.802 / q_NPA : 0.892

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	-0.035	-0.020	3.503	12.328	13.685	-0.006	-0.629	-0.723	-0.002
4	B	4	GLY	0	-0.011	-0.003	2.634	11.172	11.813	0.056	-0.281	-0.416	-0.001
5	B	5	ALA	0	0.009	0.010	3.820	10.025	10.188	-0.001	-0.009	-0.153	0.000
6	B	6	ILE	0	-0.004	-0.018	3.928	5.127	5.309	-0.001	-0.037	-0.144	0.000
7	B	7	ALA	0	-0.051	-0.021	2.789	-25.080	-23.323	0.328	-1.081	-1.003	-0.011
8	B	8	GLY	0	-0.029	-0.006	5.027	-3.635	-3.598	-0.001	-0.005	-0.030	0.000
108	B	108	LEU	0	-0.029	-0.010	4.794	-0.400	-0.360	-0.001	-0.010	-0.029	0.000
109	B	109	ASP	-1	-0.810	-0.915	3.237	-66.374	-65.346	0.063	-0.576	-0.515	-0.004
110	B	110	PHE	0	-0.066	-0.010	4.957	1.107	1.071	-0.001	-0.002	0.040	0.000
112	B	112	ASP	-1	-0.740	-0.865	1.956	-114.348	-113.880	7.642	-4.383	-3.727	-0.067
113	B	113	SER	0	-0.019	-0.004	5.340	3.954	3.951	-0.001	-0.001	0.005	0.000
9	B	9	PHE	0	-0.061	-0.022	5.629	5.530	5.530	0.000	0.000	0.000	0.000
10	B	10	ILE	0	-0.020	-0.012	7.495	4.650	4.650	0.000	0.000	0.000	0.000
11	B	11	GLU	-1	-0.935	-0.968	7.793	-27.354	-27.354	0.000	0.000	0.000	0.000
12	B	12	GLY	0	0.000	-0.011	8.665	-1.745	-1.745	0.000	0.000	0.000	0.000
13	B	13	GLY	0	-0.011	0.005	9.985	0.506	0.506	0.000	0.000	0.000	0.000
14	B	14	TRP	0	0.006	-0.013	11.757	1.165	1.165	0.000	0.000	0.000	0.000
15	B	15	GLN	0	0.028	-0.003	15.583	0.360	0.360	0.000	0.000	0.000	0.000
16	B	16	GLY	0	-0.015	0.004	17.925	0.671	0.671	0.000	0.000	0.000	0.000
17	B	17	MET	0	-0.067	-0.011	16.851	0.294	0.294	0.000	0.000	0.000	0.000
18	B	18	VAL	0	0.003	-0.006	18.368	-0.540	-0.540	0.000	0.000	0.000	0.000
19	B	19	ASP	-1	-0.939	-0.962	21.074	-13.473	-13.473	0.000	0.000	0.000	0.000
20	B	20	GLY	0	-0.036	-0.029	18.694	0.365	0.365	0.000	0.000	0.000	0.000
21	B	21	TRP	0	-0.012	-0.007	13.192	-0.606	-0.606	0.000	0.000	0.000	0.000
22	B	22	TYR	0	-0.001	-0.029	10.665	-1.320	-1.320	0.000	0.000	0.000	0.000
23	B	23	GLY	0	0.009	0.003	14.200	1.555	1.555	0.000	0.000	0.000	0.000
24	B	24	TYR	0	-0.039	-0.045	15.681	-1.067	-1.067	0.000	0.000	0.000	0.000
25	B	25	HIS	0	-0.031	-0.024	18.316	0.531	0.531	0.000	0.000	0.000	0.000
26	B	26	HIS	0	0.018	0.007	19.961	-0.548	-0.548	0.000	0.000	0.000	0.000
27	B	27	SER	0	0.010	-0.023	23.181	0.331	0.331	0.000	0.000	0.000	0.000
28	B	28	ASN	0	0.002	-0.003	25.790	0.067	0.067	0.000	0.000	0.000	0.000
29	B	29	GLU	-1	-0.876	-0.933	29.188	-9.143	-9.143	0.000	0.000	0.000	0.000
30	B	30	GLN	0	-0.032	-0.014	31.997	0.201	0.201	0.000	0.000	0.000	0.000
31	B	31	GLY	0	0.006	0.018	30.548	0.176	0.176	0.000	0.000	0.000	0.000
32	B	32	SER	0	-0.030	-0.014	25.053	-0.112	-0.112	0.000	0.000	0.000	0.000
33	B	33	GLY	0	0.005	0.004	24.809	0.400	0.400	0.000	0.000	0.000	0.000
34	B	34	TYR	0	-0.018	0.004	18.617	-0.403	-0.403	0.000	0.000	0.000	0.000
35	B	35	ALA	0	0.056	0.029	20.858	0.685	0.685	0.000	0.000	0.000	0.000
36	B	36	ALA	0	0.046	0.028	18.740	-0.827	-0.827	0.000	0.000	0.000	0.000
37	B	37	ASP	-1	-0.765	-0.838	17.147	-15.914	-15.914	0.000	0.000	0.000	0.000
38	B	38	LYS	1	0.982	0.986	18.700	11.397	11.397	0.000	0.000	0.000	0.000
39	B	39	GLU	-1	-0.900	-0.947	20.986	-13.584	-13.584	0.000	0.000	0.000	0.000
40	B	40	SER	0	-0.030	-0.044	15.242	-0.451	-0.451	0.000	0.000	0.000	0.000
41	B	41	THR	0	-0.019	-0.019	16.253	-1.178	-1.178	0.000	0.000	0.000	0.000
42	B	42	GLN	0	-0.048	-0.025	17.335	-0.126	-0.126	0.000	0.000	0.000	0.000
43	B	43	LYS	1	0.974	0.983	17.248	16.370	16.370	0.000	0.000	0.000	0.000
44	B	44	ALA	0	0.006	0.004	13.719	-0.206	-0.206	0.000	0.000	0.000	0.000
45	B	45	ILE	0	0.026	0.012	15.520	-0.196	-0.196	0.000	0.000	0.000	0.000
46	B	46	ASP	-1	-0.839	-0.899	18.109	-13.615	-13.615	0.000	0.000	0.000	0.000
47	B	47	GLY	0	-0.022	-0.006	16.311	0.393	0.393	0.000	0.000	0.000	0.000
48	B	48	VAL	0	-0.023	-0.020	13.789	-0.046	-0.046	0.000	0.000	0.000	0.000
49	B	49	THR	0	-0.015	-0.018	16.440	0.545	0.545	0.000	0.000	0.000	0.000
50	B	50	ASN	0	-0.035	-0.034	20.169	0.970	0.970	0.000	0.000	0.000	0.000
51	B	51	LYS	1	0.825	0.931	12.239	22.568	22.568	0.000	0.000	0.000	0.000
52	B	52	VAL	0	0.013	0.002	18.012	0.359	0.359	0.000	0.000	0.000	0.000
53	B	53	ASN	0	0.014	0.003	20.130	0.411	0.411	0.000	0.000	0.000	0.000
54	B	54	SER	0	-0.010	-0.016	21.022	0.564	0.564	0.000	0.000	0.000	0.000
55	B	55	ILE	0	-0.026	-0.012	17.484	0.339	0.339	0.000	0.000	0.000	0.000
56	B	56	ILE	0	0.016	0.014	22.150	0.452	0.452	0.000	0.000	0.000	0.000
57	B	57	ASP	-1	-0.902	-0.960	25.276	-10.584	-10.584	0.000	0.000	0.000	0.000
58	B	58	LYS	1	0.779	0.878	24.380	11.884	11.884	0.000	0.000	0.000	0.000
59	B	59	MET	0	0.010	0.016	23.705	0.299	0.299	0.000	0.000	0.000	0.000
60	B	60	ASN	0	-0.056	-0.016	27.967	0.444	0.444	0.000	0.000	0.000	0.000
61	B	61	THR	0	-0.002	-0.002	30.536	0.380	0.380	0.000	0.000	0.000	0.000
62	B	62	GLN	0	-0.043	-0.006	29.630	-0.196	-0.196	0.000	0.000	0.000	0.000
63	B	63	PHE	0	-0.032	-0.020	32.153	0.291	0.291	0.000	0.000	0.000	0.000
64	B	64	GLU	-1	-0.928	-0.962	34.449	-8.544	-8.544	0.000	0.000	0.000	0.000
65	B	65	ALA	0	-0.028	-0.012	37.225	0.169	0.169	0.000	0.000	0.000	0.000
66	B	66	VAL	0	-0.039	-0.033	39.474	0.098	0.098	0.000	0.000	0.000	0.000
67	B	67	GLY	0	-0.026	-0.002	43.273	0.050	0.050	0.000	0.000	0.000	0.000
68	B	68	ARG	1	0.796	0.865	42.995	7.236	7.236	0.000	0.000	0.000	0.000
69	B	69	GLU	-1	-0.948	-0.962	48.682	-6.142	-6.142	0.000	0.000	0.000	0.000
70	B	70	PHE	0	0.015	-0.004	48.249	0.045	0.045	0.000	0.000	0.000	0.000
71	B	71	ASN	0	0.043	0.019	53.419	0.063	0.063	0.000	0.000	0.000	0.000
72	B	72	ASN	0	-0.025	-0.032	55.590	-0.061	-0.061	0.000	0.000	0.000	0.000
73	B	73	LEU	0	-0.005	0.004	57.327	-0.006	-0.006	0.000	0.000	0.000	0.000
74	B	74	GLU	-1	-0.893	-0.945	54.049	-5.724	-5.724	0.000	0.000	0.000	0.000
75	B	75	ARG	1	0.883	0.920	52.017	5.829	5.829	0.000	0.000	0.000	0.000
76	B	76	ARG	1	0.940	0.967	50.324	5.641	5.641	0.000	0.000	0.000	0.000
77	B	77	ILE	0	0.024	0.009	49.117	-0.131	-0.131	0.000	0.000	0.000	0.000
78	B	78	GLU	-1	-0.807	-0.868	48.266	-6.349	-6.349	0.000	0.000	0.000	0.000
79	B	79	ASN	0	-0.068	-0.037	45.428	-0.252	-0.252	0.000	0.000	0.000	0.000
80	B	80	LEU	0	0.029	0.015	43.894	-0.161	-0.161	0.000	0.000	0.000	0.000
81	B	81	ASN	0	0.061	0.043	43.530	-0.152	-0.152	0.000	0.000	0.000	0.000
82	B	82	LYS	1	0.840	0.904	40.108	7.631	7.631	0.000	0.000	0.000	0.000
83	B	83	LYS	1	0.924	0.955	39.929	7.538	7.538	0.000	0.000	0.000	0.000
84	B	84	MET	0	-0.024	0.004	38.857	-0.154	-0.154	0.000	0.000	0.000	0.000
85	B	85	GLU	-1	-0.770	-0.874	38.205	-7.800	-7.800	0.000	0.000	0.000	0.000
86	B	86	ASP	-1	-0.810	-0.896	36.388	-8.311	-8.311	0.000	0.000	0.000	0.000
87	B	87	GLY	0	0.039	0.027	34.573	-0.274	-0.274	0.000	0.000	0.000	0.000
88	B	88	PHE	0	-0.015	-0.019	33.357	-0.274	-0.274	0.000	0.000	0.000	0.000
89	B	89	LEU	0	0.002	0.004	32.370	-0.282	-0.282	0.000	0.000	0.000	0.000
90	B	90	ASP	-1	-0.899	-0.931	30.203	-10.044	-10.044	0.000	0.000	0.000	0.000
91	B	91	VAL	0	-0.054	-0.028	28.584	-0.456	-0.456	0.000	0.000	0.000	0.000
92	B	92	TRP	0	0.006	-0.009	27.717	-0.518	-0.518	0.000	0.000	0.000	0.000
93	B	93	THR	0	-0.001	0.004	25.929	-0.350	-0.350	0.000	0.000	0.000	0.000
94	B	94	TYR	0	-0.005	-0.002	22.953	-0.732	-0.732	0.000	0.000	0.000	0.000
95	B	95	ASN	0	-0.040	-0.030	22.896	-0.811	-0.811	0.000	0.000	0.000	0.000
96	B	96	ALA	0	0.000	0.001	22.366	-0.562	-0.562	0.000	0.000	0.000	0.000
97	B	97	GLU	-1	-0.931	-0.970	20.490	-13.864	-13.864	0.000	0.000	0.000	0.000
98	B	98	LEU	0	0.006	0.000	17.582	-1.072	-1.072	0.000	0.000	0.000	0.000
99	B	99	LEU	0	-0.012	-0.002	17.191	-1.081	-1.081	0.000	0.000	0.000	0.000
100	B	100	VAL	0	0.015	0.003	16.479	-1.050	-1.050	0.000	0.000	0.000	0.000
101	B	101	LEU	0	-0.013	-0.010	14.249	-1.426	-1.426	0.000	0.000	0.000	0.000
102	B	102	MET	0	-0.015	-0.004	12.514	-1.758	-1.758	0.000	0.000	0.000	0.000
103	B	103	GLU	-1	-0.845	-0.924	11.865	-22.176	-22.176	0.000	0.000	0.000	0.000
104	B	104	ASN	0	-0.001	0.015	11.421	-0.892	-0.892	0.000	0.000	0.000	0.000
105	B	105	GLU	-1	-0.944	-0.957	7.230	-31.899	-31.899	0.000	0.000	0.000	0.000
106	B	106	ARG	1	0.977	0.973	7.023	18.902	18.902	0.000	0.000	0.000	0.000
107	B	107	THR	0	-0.056	-0.039	8.958	0.297	0.297	0.000	0.000	0.000	0.000
111	B	111	HIS	0	0.044	0.050	7.075	1.402	1.402	0.000	0.000	0.000	0.000
114	B	114	ASN	0	-0.045	-0.036	8.211	3.066	3.066	0.000	0.000	0.000	0.000
115	B	115	VAL	0	0.004	0.008	7.615	2.615	2.615	0.000	0.000	0.000	0.000
116	B	116	LYS	1	0.905	0.952	7.390	31.594	31.594	0.000	0.000	0.000	0.000
117	B	117	ASN	0	-0.034	-0.027	9.282	2.381	2.381	0.000	0.000	0.000	0.000
118	B	118	LEU	0	-0.030	0.001	12.421	1.908	1.908	0.000	0.000	0.000	0.000
119	B	119	TYR	0	-0.021	-0.029	11.820	1.414	1.414	0.000	0.000	0.000	0.000
120	B	120	ASP	-1	-0.810	-0.903	12.904	-21.971	-21.971	0.000	0.000	0.000	0.000
121	B	121	ARG	1	0.821	0.908	15.152	17.148	17.148	0.000	0.000	0.000	0.000
122	B	122	VAL	0	-0.013	0.002	17.208	1.187	1.187	0.000	0.000	0.000	0.000
123	B	123	ARG	1	0.912	0.943	15.633	19.548	19.548	0.000	0.000	0.000	0.000
124	B	124	LEU	0	-0.063	-0.039	18.743	0.885	0.885	0.000	0.000	0.000	0.000
125	B	125	GLN	0	-0.022	0.013	21.198	1.235	1.235	0.000	0.000	0.000	0.000
126	B	126	LEU	0	0.010	0.004	21.214	0.670	0.670	0.000	0.000	0.000	0.000
127	B	127	ARG	1	0.872	0.940	22.932	12.194	12.194	0.000	0.000	0.000	0.000
128	B	128	ASP	-1	-0.809	-0.877	23.801	-11.318	-11.318	0.000	0.000	0.000	0.000
129	B	129	ASN	0	-0.001	-0.012	26.479	0.522	0.522	0.000	0.000	0.000	0.000
130	B	130	ALA	0	-0.019	-0.012	23.385	0.241	0.241	0.000	0.000	0.000	0.000
131	B	131	LYS	1	0.941	0.991	22.095	13.769	13.769	0.000	0.000	0.000	0.000
132	B	132	GLU	-1	-0.832	-0.910	15.912	-19.276	-19.276	0.000	0.000	0.000	0.000
133	B	133	LEU	0	-0.034	-0.030	18.270	0.296	0.296	0.000	0.000	0.000	0.000
134	B	134	GLY	0	-0.016	0.003	14.906	0.093	0.093	0.000	0.000	0.000	0.000
135	B	135	ASN	0	0.033	0.009	13.006	-1.549	-1.549	0.000	0.000	0.000	0.000
136	B	136	GLY	0	0.030	0.009	12.743	-0.255	-0.255	0.000	0.000	0.000	0.000
137	B	137	CYS	0	-0.072	-0.016	13.284	0.993	0.993	0.000	0.000	0.000	0.000
138	B	138	PHE	0	0.004	-0.015	16.561	-0.026	-0.026	0.000	0.000	0.000	0.000
139	B	139	GLU	-1	-0.940	-0.960	20.254	-12.226	-12.226	0.000	0.000	0.000	0.000
140	B	140	PHE	0	-0.004	-0.011	23.851	-0.003	-0.003	0.000	0.000	0.000	0.000
141	B	141	TYR	0	-0.012	-0.009	26.650	0.144	0.144	0.000	0.000	0.000	0.000
142	B	142	HIS	0	-0.019	0.014	29.047	0.046	0.046	0.000	0.000	0.000	0.000
143	B	143	LYS	1	0.860	0.905	30.381	9.210	9.210	0.000	0.000	0.000	0.000
144	B	144	CYS	0	-0.040	0.006	28.096	-0.430	-0.430	0.000	0.000	0.000	0.000
145	B	145	ASP	-1	-0.819	-0.898	29.936	-9.819	-9.819	0.000	0.000	0.000	0.000
146	B	146	ASN	0	0.032	-0.017	29.673	-0.629	-0.629	0.000	0.000	0.000	0.000
147	B	147	GLU	-1	-0.926	-0.939	29.846	-9.743	-9.743	0.000	0.000	0.000	0.000
148	B	149	MET	0	-0.016	-0.008	23.754	-0.554	-0.554	0.000	0.000	0.000	0.000
149	B	150	GLU	-1	-0.818	-0.891	25.360	-12.626	-12.626	0.000	0.000	0.000	0.000
150	B	151	SER	0	-0.057	-0.029	26.252	-0.385	-0.385	0.000	0.000	0.000	0.000
151	B	152	VAL	0	-0.008	-0.009	21.737	-0.283	-0.283	0.000	0.000	0.000	0.000
152	B	153	ARG	1	0.811	0.898	21.618	12.130	12.130	0.000	0.000	0.000	0.000
153	B	154	ASN	0	-0.010	-0.002	22.435	-0.602	-0.602	0.000	0.000	0.000	0.000
154	B	155	GLY	0	-0.033	-0.007	23.489	0.248	0.248	0.000	0.000	0.000	0.000
155	B	156	THR	0	-0.038	-0.026	24.257	0.378	0.378	0.000	0.000	0.000	0.000
156	B	157	TYR	0	-0.009	-0.019	25.703	0.384	0.384	0.000	0.000	0.000	0.000
157	B	158	ASP	-1	-0.818	-0.905	27.635	-9.663	-9.663	0.000	0.000	0.000	0.000
158	B	159	TYR	0	-0.062	-0.066	27.644	0.483	0.483	0.000	0.000	0.000	0.000
159	B	160	PRO	0	-0.024	-0.030	30.149	0.113	0.113	0.000	0.000	0.000	0.000
160	B	161	GLN	0	-0.091	-0.043	33.629	0.250	0.250	0.000	0.000	0.000	0.000
161	B	162	TYR	0	0.055	0.023	30.857	0.169	0.169	0.000	0.000	0.000	0.000
162	B	163	SER	0	-0.006	0.002	32.360	0.024	0.024	0.000	0.000	0.000	0.000
163	B	164	GLU	-1	-0.993	-1.003	33.663	-8.026	-8.026	0.000	0.000	0.000	0.000
164	B	165	GLU	-1	-0.813	-0.909	34.679	-9.192	-9.192	0.000	0.000	0.000	0.000
165	B	166	ALA	0	0.025	0.005	30.573	-0.013	-0.013	0.000	0.000	0.000	0.000
166	B	167	ARG	1	0.892	0.955	32.574	8.382	8.382	0.000	0.000	0.000	0.000
167	B	168	LEU	0	-0.058	-0.030	34.487	0.149	0.149	0.000	0.000	0.000	0.000
168	B	169	LYS	1	0.857	0.942	32.541	9.544	9.544	0.000	0.000	0.000	0.000
169	B	170	ARG	0	-0.067	-0.011	29.446	0.925	0.925	0.000	0.000	0.000	0.000

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