FMO DATABASE

FMODB ID: N6JGQ

Calculation Name: 2IBX-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: 2IBX

Chain ID: B

ChEMBL ID:

UniProt ID: Q45ZQ3

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	-1333210.058169
FMO2-HF: Nuclear repulsion	1267535.954232
FMO2-HF: Total energy	-65674.103937
FMO2-MP2: Total energy	-65861.785352

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.
-264.745	-258.818	8.427	-7.49	-6.862	-0.093

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 : 0.805 / q_NPA : 0.897

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	-0.029	-0.013	3.519	11.616	12.788	-0.003	-0.510	-0.658	-0.002
4	B	4	GLY	0	0.002	0.007	2.761	11.191	11.750	0.025	-0.239	-0.345	-0.001
5	B	5	ALA	0	0.016	0.016	4.022	9.140	9.290	-0.001	-0.011	-0.138	0.000
6	B	6	ILE	0	-0.010	-0.020	4.220	4.688	4.809	-0.001	-0.017	-0.102	0.000
7	B	7	ALA	0	-0.050	-0.019	3.217	-19.565	-18.602	0.057	-0.511	-0.508	-0.004
8	B	8	GLY	0	-0.028	-0.007	4.965	-5.245	-5.203	-0.001	-0.006	-0.034	0.000
109	B	109	ASP	-1	-0.794	-0.902	2.561	-76.324	-74.195	1.073	-1.675	-1.527	-0.018
110	B	110	PHE	0	-0.051	0.001	4.520	2.029	1.991	-0.001	-0.008	0.046	0.000
112	B	112	ASP	-1	-0.758	-0.877	1.932	-111.628	-110.788	7.280	-4.512	-3.609	-0.068
113	B	113	SER	0	-0.016	-0.005	5.296	4.324	4.313	-0.001	-0.001	0.013	0.000
9	B	9	PHE	0	-0.069	-0.023	5.663	5.540	5.540	0.000	0.000	0.000	0.000
10	B	10	ILE	0	-0.018	-0.013	7.609	4.550	4.550	0.000	0.000	0.000	0.000
11	B	11	GLU	-1	-0.932	-0.967	8.074	-27.346	-27.346	0.000	0.000	0.000	0.000
12	B	12	GLY	0	-0.010	-0.010	9.324	-0.967	-0.967	0.000	0.000	0.000	0.000
13	B	13	GLY	0	-0.011	0.004	10.792	0.318	0.318	0.000	0.000	0.000	0.000
14	B	14	TRP	0	0.008	-0.018	12.359	1.348	1.348	0.000	0.000	0.000	0.000
15	B	15	GLN	0	0.043	0.008	16.128	0.431	0.431	0.000	0.000	0.000	0.000
16	B	16	GLY	0	-0.005	0.006	18.575	0.651	0.651	0.000	0.000	0.000	0.000
17	B	17	MET	0	-0.062	-0.014	14.846	0.873	0.873	0.000	0.000	0.000	0.000
18	B	18	VAL	0	-0.024	-0.019	18.738	-0.585	-0.585	0.000	0.000	0.000	0.000
19	B	19	ASP	-1	-0.926	-0.958	21.048	-12.962	-12.962	0.000	0.000	0.000	0.000
20	B	20	GLY	0	-0.001	-0.010	18.861	0.337	0.337	0.000	0.000	0.000	0.000
21	B	21	TRP	0	-0.022	-0.008	13.403	-0.607	-0.607	0.000	0.000	0.000	0.000
22	B	22	TYR	0	0.003	-0.029	10.820	-1.386	-1.386	0.000	0.000	0.000	0.000
23	B	23	GLY	0	0.019	0.005	14.431	1.493	1.493	0.000	0.000	0.000	0.000
24	B	24	TYR	0	-0.011	-0.012	16.031	-1.015	-1.015	0.000	0.000	0.000	0.000
25	B	25	HIS	0	-0.003	0.002	18.140	0.921	0.921	0.000	0.000	0.000	0.000
26	B	26	HIS	0	0.039	0.023	19.931	-0.629	-0.629	0.000	0.000	0.000	0.000
27	B	27	SER	0	0.008	-0.012	23.115	0.395	0.395	0.000	0.000	0.000	0.000
28	B	28	ASN	0	-0.007	-0.012	25.609	0.035	0.035	0.000	0.000	0.000	0.000
29	B	29	GLU	-1	-0.826	-0.902	29.011	-9.074	-9.074	0.000	0.000	0.000	0.000
30	B	30	GLN	0	-0.034	-0.010	31.925	0.142	0.142	0.000	0.000	0.000	0.000
31	B	31	GLY	0	0.000	0.016	30.477	0.079	0.079	0.000	0.000	0.000	0.000
32	B	32	SER	0	-0.015	-0.012	25.111	-0.136	-0.136	0.000	0.000	0.000	0.000
33	B	33	GLY	0	0.000	0.003	24.700	0.390	0.390	0.000	0.000	0.000	0.000
34	B	34	TYR	0	-0.029	-0.018	18.718	-0.255	-0.255	0.000	0.000	0.000	0.000
35	B	35	ALA	0	0.033	0.019	21.080	0.670	0.670	0.000	0.000	0.000	0.000
36	B	36	ALA	0	0.029	0.029	19.077	-0.798	-0.798	0.000	0.000	0.000	0.000
37	B	37	ASP	-1	-0.782	-0.860	17.258	-15.978	-15.978	0.000	0.000	0.000	0.000
38	B	38	LYS	1	0.983	0.979	18.767	11.675	11.675	0.000	0.000	0.000	0.000
39	B	39	GLU	-1	-0.922	-0.951	20.248	-14.362	-14.362	0.000	0.000	0.000	0.000
40	B	40	SER	0	-0.052	-0.068	14.991	-0.517	-0.517	0.000	0.000	0.000	0.000
41	B	41	THR	0	0.013	-0.003	16.159	-1.084	-1.084	0.000	0.000	0.000	0.000
42	B	42	GLN	0	-0.062	-0.034	17.512	-0.056	-0.056	0.000	0.000	0.000	0.000
43	B	43	LYS	1	0.980	0.983	17.295	15.861	15.861	0.000	0.000	0.000	0.000
44	B	44	ALA	0	0.010	0.014	13.760	-0.284	-0.284	0.000	0.000	0.000	0.000
45	B	45	ILE	0	0.021	0.009	15.380	-0.198	-0.198	0.000	0.000	0.000	0.000
46	B	46	ASP	-1	-0.846	-0.901	18.148	-13.923	-13.923	0.000	0.000	0.000	0.000
47	B	47	GLY	0	-0.022	-0.013	16.120	0.331	0.331	0.000	0.000	0.000	0.000
48	B	48	VAL	0	-0.015	-0.015	13.577	-0.083	-0.083	0.000	0.000	0.000	0.000
49	B	49	THR	0	-0.025	-0.023	16.200	0.515	0.515	0.000	0.000	0.000	0.000
50	B	50	ASN	0	-0.007	-0.011	19.638	0.921	0.921	0.000	0.000	0.000	0.000
51	B	51	LYS	1	0.831	0.931	11.826	23.347	23.347	0.000	0.000	0.000	0.000
52	B	52	VAL	0	0.013	0.001	17.632	0.385	0.385	0.000	0.000	0.000	0.000
53	B	53	ASN	0	0.012	0.001	19.718	0.536	0.536	0.000	0.000	0.000	0.000
54	B	54	SER	0	-0.024	-0.024	20.408	0.599	0.599	0.000	0.000	0.000	0.000
55	B	55	ILE	0	-0.045	-0.025	16.626	0.302	0.302	0.000	0.000	0.000	0.000
56	B	56	ILE	0	-0.006	0.002	21.292	0.384	0.384	0.000	0.000	0.000	0.000
57	B	57	ASP	-1	-0.927	-0.971	24.611	-10.484	-10.484	0.000	0.000	0.000	0.000
58	B	58	LYS	1	0.879	0.931	23.861	12.076	12.076	0.000	0.000	0.000	0.000
59	B	59	MET	0	-0.046	0.007	22.570	0.280	0.280	0.000	0.000	0.000	0.000
60	B	60	ASN	0	-0.013	-0.005	26.720	0.383	0.383	0.000	0.000	0.000	0.000
61	B	61	THR	0	-0.024	-0.015	30.101	0.238	0.238	0.000	0.000	0.000	0.000
62	B	62	GLN	0	-0.021	-0.015	26.998	0.398	0.398	0.000	0.000	0.000	0.000
63	B	63	PHE	0	-0.007	-0.013	31.934	0.299	0.299	0.000	0.000	0.000	0.000
64	B	64	GLU	-1	-0.913	-0.944	34.841	-8.312	-8.312	0.000	0.000	0.000	0.000
65	B	65	ALA	0	-0.029	-0.012	37.440	0.181	0.181	0.000	0.000	0.000	0.000
66	B	66	VAL	0	-0.027	-0.013	39.303	0.120	0.120	0.000	0.000	0.000	0.000
67	B	67	GLY	0	0.002	0.010	43.129	0.067	0.067	0.000	0.000	0.000	0.000
68	B	68	ARG	1	0.846	0.912	42.830	7.268	7.268	0.000	0.000	0.000	0.000
69	B	69	GLU	-1	-0.943	-0.960	48.265	-6.175	-6.175	0.000	0.000	0.000	0.000
70	B	70	PHE	0	0.018	-0.004	47.603	0.053	0.053	0.000	0.000	0.000	0.000
71	B	71	ASN	0	0.022	0.003	52.884	0.057	0.057	0.000	0.000	0.000	0.000
72	B	72	ASN	0	-0.029	-0.027	54.988	-0.082	-0.082	0.000	0.000	0.000	0.000
73	B	73	LEU	0	-0.025	-0.018	56.426	-0.027	-0.027	0.000	0.000	0.000	0.000
74	B	74	GLU	-1	-0.849	-0.913	53.417	-5.769	-5.769	0.000	0.000	0.000	0.000
75	B	75	ARG	1	0.879	0.920	51.051	5.970	5.970	0.000	0.000	0.000	0.000
76	B	76	ARG	1	0.942	0.969	49.521	5.736	5.736	0.000	0.000	0.000	0.000
77	B	77	ILE	0	0.011	0.005	48.430	-0.137	-0.137	0.000	0.000	0.000	0.000
78	B	78	GLU	-1	-0.804	-0.862	47.566	-6.512	-6.512	0.000	0.000	0.000	0.000
79	B	79	ASN	0	-0.016	-0.018	44.373	-0.258	-0.258	0.000	0.000	0.000	0.000
80	B	80	LEU	0	-0.042	-0.009	43.684	-0.174	-0.174	0.000	0.000	0.000	0.000
81	B	81	ASN	0	0.004	-0.008	42.889	-0.152	-0.152	0.000	0.000	0.000	0.000
82	B	82	LYS	1	0.875	0.927	39.658	7.708	7.708	0.000	0.000	0.000	0.000
83	B	83	LYS	1	0.949	0.964	38.338	7.855	7.855	0.000	0.000	0.000	0.000
84	B	84	MET	0	-0.036	0.003	38.136	-0.154	-0.154	0.000	0.000	0.000	0.000
85	B	85	GLU	-1	-0.811	-0.912	37.543	-7.797	-7.797	0.000	0.000	0.000	0.000
86	B	86	ASP	-1	-0.847	-0.921	35.697	-8.576	-8.576	0.000	0.000	0.000	0.000
87	B	87	GLY	0	0.019	0.017	33.925	-0.283	-0.283	0.000	0.000	0.000	0.000
88	B	88	PHE	0	-0.020	-0.022	32.709	-0.277	-0.277	0.000	0.000	0.000	0.000
89	B	89	LEU	0	0.015	0.015	31.753	-0.305	-0.305	0.000	0.000	0.000	0.000
90	B	90	ASP	-1	-0.904	-0.934	29.670	-10.212	-10.212	0.000	0.000	0.000	0.000
91	B	91	VAL	0	-0.054	-0.030	27.965	-0.491	-0.491	0.000	0.000	0.000	0.000
92	B	92	TRP	0	-0.002	-0.011	26.897	-0.543	-0.543	0.000	0.000	0.000	0.000
93	B	93	THR	0	0.002	0.000	25.567	-0.403	-0.403	0.000	0.000	0.000	0.000
94	B	94	TYR	0	-0.016	-0.005	22.027	-0.759	-0.759	0.000	0.000	0.000	0.000
95	B	95	ASN	0	-0.025	-0.022	22.210	-0.914	-0.914	0.000	0.000	0.000	0.000
96	B	96	ALA	0	0.002	-0.001	21.584	-0.635	-0.635	0.000	0.000	0.000	0.000
97	B	97	GLU	-1	-0.925	-0.968	20.136	-14.077	-14.077	0.000	0.000	0.000	0.000
98	B	98	LEU	0	-0.004	-0.002	17.498	-1.124	-1.124	0.000	0.000	0.000	0.000
99	B	99	LEU	0	-0.012	-0.001	16.680	-1.155	-1.155	0.000	0.000	0.000	0.000
100	B	100	VAL	0	0.005	0.001	15.941	-1.160	-1.160	0.000	0.000	0.000	0.000
101	B	101	LEU	0	-0.016	-0.013	13.844	-1.513	-1.513	0.000	0.000	0.000	0.000
102	B	102	MET	0	-0.017	-0.004	12.097	-1.867	-1.867	0.000	0.000	0.000	0.000
103	B	103	GLU	-1	-0.849	-0.933	11.316	-22.923	-22.923	0.000	0.000	0.000	0.000
104	B	104	ASN	0	-0.002	0.016	11.200	-0.855	-0.855	0.000	0.000	0.000	0.000
105	B	105	GLU	-1	-0.937	-0.954	6.756	-32.976	-32.976	0.000	0.000	0.000	0.000
106	B	106	ARG	1	0.961	0.964	6.593	20.102	20.102	0.000	0.000	0.000	0.000
107	B	107	THR	0	-0.051	-0.038	8.710	1.179	1.179	0.000	0.000	0.000	0.000
108	B	108	LEU	0	-0.033	-0.012	5.175	-0.294	-0.294	0.000	0.000	0.000	0.000
111	B	111	HIS	0	0.046	0.047	7.253	1.547	1.547	0.000	0.000	0.000	0.000
114	B	114	ASN	0	-0.051	-0.035	7.991	3.255	3.255	0.000	0.000	0.000	0.000
115	B	115	VAL	0	0.008	0.005	7.839	2.647	2.647	0.000	0.000	0.000	0.000
116	B	116	LYS	1	0.853	0.915	7.136	32.075	32.075	0.000	0.000	0.000	0.000
117	B	117	ASN	0	0.005	-0.009	9.191	2.329	2.329	0.000	0.000	0.000	0.000
118	B	118	LEU	0	-0.054	-0.013	12.408	1.882	1.882	0.000	0.000	0.000	0.000
119	B	119	TYR	0	-0.041	-0.050	11.562	1.059	1.059	0.000	0.000	0.000	0.000
120	B	120	ASP	-1	-0.768	-0.860	12.571	-22.749	-22.749	0.000	0.000	0.000	0.000
121	B	121	LYS	1	0.915	0.967	14.966	17.214	17.214	0.000	0.000	0.000	0.000
122	B	122	VAL	0	0.019	0.013	17.099	1.028	1.028	0.000	0.000	0.000	0.000
123	B	123	ARG	1	0.855	0.918	15.032	20.174	20.174	0.000	0.000	0.000	0.000
124	B	124	LEU	0	-0.072	-0.035	18.354	0.789	0.789	0.000	0.000	0.000	0.000
125	B	125	GLN	0	-0.020	-0.016	20.742	0.254	0.254	0.000	0.000	0.000	0.000
126	B	126	LEU	0	-0.031	-0.012	20.546	0.678	0.678	0.000	0.000	0.000	0.000
127	B	127	ARG	1	0.821	0.910	23.312	11.906	11.906	0.000	0.000	0.000	0.000
128	B	128	ASP	-1	-0.889	-0.933	23.777	-12.250	-12.250	0.000	0.000	0.000	0.000
129	B	129	ASN	0	-0.040	-0.033	26.007	0.737	0.737	0.000	0.000	0.000	0.000
130	B	130	ALA	0	-0.009	-0.007	22.935	0.245	0.245	0.000	0.000	0.000	0.000
131	B	131	LYS	1	0.908	0.972	23.054	11.694	11.694	0.000	0.000	0.000	0.000
132	B	132	GLU	-1	-0.793	-0.887	15.886	-19.646	-19.646	0.000	0.000	0.000	0.000
133	B	133	LEU	0	-0.043	-0.026	18.277	0.130	0.130	0.000	0.000	0.000	0.000
134	B	134	GLY	0	-0.026	-0.001	14.510	-0.149	-0.149	0.000	0.000	0.000	0.000
135	B	135	ASN	0	0.033	0.010	12.985	-1.601	-1.601	0.000	0.000	0.000	0.000
136	B	136	GLY	0	0.017	0.002	12.649	-0.312	-0.312	0.000	0.000	0.000	0.000
137	B	137	CYS	0	-0.083	-0.029	13.205	0.980	0.980	0.000	0.000	0.000	0.000
138	B	138	PHE	0	0.030	0.000	15.896	-0.067	-0.067	0.000	0.000	0.000	0.000
139	B	139	GLU	-1	-0.951	-0.965	20.080	-12.381	-12.381	0.000	0.000	0.000	0.000
140	B	140	PHE	0	0.020	-0.001	23.655	0.110	0.110	0.000	0.000	0.000	0.000
141	B	141	TYR	0	-0.046	-0.018	25.849	0.274	0.274	0.000	0.000	0.000	0.000
142	B	142	HIS	0	-0.016	-0.001	29.579	0.486	0.486	0.000	0.000	0.000	0.000
143	B	143	LYS	1	0.830	0.886	30.221	8.604	8.604	0.000	0.000	0.000	0.000
144	B	144	CYS	0	0.010	0.019	27.999	-0.288	-0.288	0.000	0.000	0.000	0.000
145	B	145	ASP	-1	-0.794	-0.896	29.466	-9.886	-9.886	0.000	0.000	0.000	0.000
146	B	146	ASN	0	0.005	-0.025	29.919	-0.581	-0.581	0.000	0.000	0.000	0.000
147	B	147	GLU	-1	-0.912	-0.933	30.247	-9.155	-9.155	0.000	0.000	0.000	0.000
148	B	149	MET	0	-0.038	-0.027	25.070	-0.585	-0.585	0.000	0.000	0.000	0.000
149	B	150	GLU	-1	-0.996	-1.003	25.652	-11.092	-11.092	0.000	0.000	0.000	0.000
150	B	151	SER	0	0.002	0.007	27.095	-0.342	-0.342	0.000	0.000	0.000	0.000
151	B	152	VAL	0	0.006	-0.011	21.862	-0.237	-0.237	0.000	0.000	0.000	0.000
152	B	153	ARG	1	0.809	0.901	22.116	12.984	12.984	0.000	0.000	0.000	0.000
153	B	154	ASN	0	-0.074	-0.011	23.666	-0.067	-0.067	0.000	0.000	0.000	0.000
154	B	155	GLY	0	0.005	0.017	23.767	0.083	0.083	0.000	0.000	0.000	0.000
155	B	156	THR	0	-0.051	-0.034	24.634	0.065	0.065	0.000	0.000	0.000	0.000
156	B	157	TYR	0	-0.021	0.002	25.487	0.389	0.389	0.000	0.000	0.000	0.000
157	B	158	ASP	-1	-0.853	-0.949	26.807	-12.012	-12.012	0.000	0.000	0.000	0.000
158	B	159	TYR	0	-0.062	-0.029	29.584	0.304	0.304	0.000	0.000	0.000	0.000
159	B	160	PRO	-1	-0.956	-0.950	32.247	-8.872	-8.872	0.000	0.000	0.000	0.000

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