FMO DATABASE

FMODB ID: L6JG9

Calculation Name: 4ZJF-D-Xray549

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: 4ZJF

Chain ID: D

ChEMBL ID:

UniProt ID: P08669

Base Structure: X-ray

Registration Date: 2025-10-12

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	154
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1563129.743383
FMO2-HF: Nuclear repulsion	1498786.508008
FMO2-HF: Total energy	-64343.235375
FMO2-MP2: Total energy	-64522.408005

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(D:81:THR)

Summations of interaction energy for fragment #1(D:81:THR)

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.
21.928	25.678	1.147	-1.95	-2.946	-0.018

Interaction energy analysis for fragmet #1(D:81:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.834 / q_NPA : 0.904

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	D	83	PRO	0	0.047	0.025	2.822	-4.881	-1.896	0.309	-1.475	-1.819	-0.014
149	D	232	GLN	0	-0.085	-0.042	2.516	0.821	1.281	0.831	-0.398	-0.893	-0.004
152	D	235	ARG	1	0.921	0.955	3.198	48.868	49.173	0.007	-0.077	-0.234	0.000
4	D	84	LEU	0	0.039	0.020	5.541	0.582	0.582	0.000	0.000	0.000	0.000
5	D	85	SER	0	-0.025	-0.014	7.578	1.514	1.514	0.000	0.000	0.000	0.000
6	D	86	CYS	0	0.017	0.007	10.755	1.987	1.987	0.000	0.000	0.000	0.000
7	D	87	THR	0	0.004	0.000	10.689	-0.852	-0.852	0.000	0.000	0.000	0.000
8	D	88	LYS	1	0.971	0.967	12.956	17.566	17.566	0.000	0.000	0.000	0.000
9	D	89	ASN	0	-0.001	0.006	15.114	0.252	0.252	0.000	0.000	0.000	0.000
10	D	90	ASN	0	-0.025	0.017	11.817	0.732	0.732	0.000	0.000	0.000	0.000
11	D	91	SER	0	0.010	0.015	16.160	0.793	0.793	0.000	0.000	0.000	0.000
12	D	92	HIS	0	-0.030	-0.020	15.642	-0.148	-0.148	0.000	0.000	0.000	0.000
13	D	93	HIS	1	0.895	0.948	17.583	13.801	13.801	0.000	0.000	0.000	0.000
14	D	94	TYR	0	0.026	0.008	16.969	0.158	0.158	0.000	0.000	0.000	0.000
15	D	95	ILE	0	-0.058	-0.026	19.276	0.747	0.747	0.000	0.000	0.000	0.000
16	D	96	MET	0	0.028	0.012	21.435	-0.366	-0.366	0.000	0.000	0.000	0.000
17	D	97	VAL	0	-0.032	-0.015	23.149	0.436	0.436	0.000	0.000	0.000	0.000
18	D	98	GLY	0	-0.004	-0.002	23.969	0.525	0.525	0.000	0.000	0.000	0.000
19	D	99	ASN	0	-0.046	-0.039	24.886	0.048	0.048	0.000	0.000	0.000	0.000
20	D	100	GLU	-1	-0.903	-0.939	21.347	-12.548	-12.548	0.000	0.000	0.000	0.000
21	D	101	THR	0	-0.048	-0.030	19.791	-0.631	-0.631	0.000	0.000	0.000	0.000
22	D	102	GLY	0	0.067	0.033	19.378	0.776	0.776	0.000	0.000	0.000	0.000
23	D	103	LEU	0	-0.054	-0.015	18.256	-0.738	-0.738	0.000	0.000	0.000	0.000
24	D	104	GLU	-1	-0.745	-0.852	13.352	-17.911	-17.911	0.000	0.000	0.000	0.000
25	D	105	LEU	0	-0.040	-0.017	16.413	-0.331	-0.331	0.000	0.000	0.000	0.000
26	D	106	THR	0	-0.023	-0.033	13.084	0.107	0.107	0.000	0.000	0.000	0.000
27	D	107	LEU	0	-0.010	0.013	16.212	-0.216	-0.216	0.000	0.000	0.000	0.000
28	D	108	THR	0	-0.010	-0.034	13.584	-0.853	-0.853	0.000	0.000	0.000	0.000
29	D	109	ASN	0	0.040	0.014	15.883	1.000	1.000	0.000	0.000	0.000	0.000
30	D	110	THR	0	-0.026	-0.010	10.021	-0.752	-0.752	0.000	0.000	0.000	0.000
31	D	111	SER	0	-0.002	0.006	13.150	1.098	1.098	0.000	0.000	0.000	0.000
32	D	112	ILE	0	-0.033	-0.018	9.377	-2.687	-2.687	0.000	0.000	0.000	0.000
33	D	113	ILE	0	-0.021	-0.004	10.706	-1.424	-1.424	0.000	0.000	0.000	0.000
34	D	114	ASN	0	0.010	-0.003	12.196	1.066	1.066	0.000	0.000	0.000	0.000
35	D	115	HIS	0	-0.042	-0.016	14.117	1.968	1.968	0.000	0.000	0.000	0.000
36	D	116	LYS	1	0.933	0.964	17.178	15.656	15.656	0.000	0.000	0.000	0.000
37	D	117	PHE	0	0.051	0.038	19.573	0.816	0.816	0.000	0.000	0.000	0.000
38	D	118	CYS	0	0.002	-0.011	18.555	-0.756	-0.756	0.000	0.000	0.000	0.000
39	D	119	ASN	0	0.050	0.033	21.589	1.010	1.010	0.000	0.000	0.000	0.000
40	D	120	LEU	0	-0.003	-0.004	23.381	-0.173	-0.173	0.000	0.000	0.000	0.000
41	D	121	SER	0	-0.041	-0.043	25.334	0.274	0.274	0.000	0.000	0.000	0.000
42	D	122	ASP	-1	-0.832	-0.925	26.483	-10.983	-10.983	0.000	0.000	0.000	0.000
43	D	123	ALA	0	-0.005	-0.001	28.227	-0.141	-0.141	0.000	0.000	0.000	0.000
44	D	124	HIS	0	0.053	0.037	24.600	0.218	0.218	0.000	0.000	0.000	0.000
45	D	125	LYS	1	0.912	0.956	21.773	13.611	13.611	0.000	0.000	0.000	0.000
46	D	126	LYS	1	0.925	0.972	24.865	10.035	10.035	0.000	0.000	0.000	0.000
47	D	127	ASN	0	0.048	0.022	27.621	0.099	0.099	0.000	0.000	0.000	0.000
48	D	128	LEU	0	-0.019	-0.004	22.229	-0.043	-0.043	0.000	0.000	0.000	0.000
49	D	129	TYR	0	0.000	-0.015	23.108	-0.175	-0.175	0.000	0.000	0.000	0.000
50	D	130	ASP	-1	-0.913	-0.958	24.927	-10.307	-10.307	0.000	0.000	0.000	0.000
51	D	131	HIS	0	0.061	0.033	25.233	0.222	0.222	0.000	0.000	0.000	0.000
52	D	132	ALA	0	-0.007	0.012	22.391	-0.056	-0.056	0.000	0.000	0.000	0.000
53	D	133	LEU	0	-0.014	-0.017	24.360	-0.066	-0.066	0.000	0.000	0.000	0.000
54	D	134	MET	0	0.040	0.019	26.579	0.230	0.230	0.000	0.000	0.000	0.000
55	D	135	SER	0	0.000	0.003	25.088	0.277	0.277	0.000	0.000	0.000	0.000
56	D	136	ILE	0	-0.032	-0.003	22.290	0.124	0.124	0.000	0.000	0.000	0.000
57	D	137	ILE	0	-0.035	-0.023	26.343	0.232	0.232	0.000	0.000	0.000	0.000
58	D	138	SER	0	-0.006	-0.016	30.048	0.418	0.418	0.000	0.000	0.000	0.000
59	D	139	THR	0	-0.056	-0.034	26.318	0.203	0.203	0.000	0.000	0.000	0.000
60	D	140	PHE	0	-0.040	-0.048	23.740	-0.010	-0.010	0.000	0.000	0.000	0.000
61	D	141	HIS	0	0.009	0.022	29.924	0.335	0.335	0.000	0.000	0.000	0.000
62	D	142	LEU	0	-0.044	-0.003	28.332	0.190	0.190	0.000	0.000	0.000	0.000
63	D	143	SER	0	0.024	0.008	32.983	0.067	0.067	0.000	0.000	0.000	0.000
64	D	144	ILE	0	-0.003	-0.004	30.948	0.149	0.149	0.000	0.000	0.000	0.000
65	D	145	PRO	0	-0.047	-0.006	35.061	0.245	0.245	0.000	0.000	0.000	0.000
66	D	146	ASN	0	0.014	0.002	36.884	-0.370	-0.370	0.000	0.000	0.000	0.000
67	D	147	PHE	0	-0.002	-0.024	37.025	0.235	0.235	0.000	0.000	0.000	0.000
68	D	148	ASN	0	-0.037	-0.012	37.242	-0.097	-0.097	0.000	0.000	0.000	0.000
69	D	149	GLN	0	0.032	0.028	33.860	-0.188	-0.188	0.000	0.000	0.000	0.000
70	D	150	TYR	0	0.033	0.011	29.618	-0.173	-0.173	0.000	0.000	0.000	0.000
71	D	151	GLU	-1	-0.769	-0.864	25.573	-11.677	-11.677	0.000	0.000	0.000	0.000
72	D	152	ALA	0	0.001	0.006	24.130	0.061	0.061	0.000	0.000	0.000	0.000
73	D	153	MET	0	-0.044	-0.019	22.161	-0.622	-0.622	0.000	0.000	0.000	0.000
74	D	154	SER	0	-0.003	-0.002	18.260	0.636	0.636	0.000	0.000	0.000	0.000
75	D	156	ASP	-1	-0.827	-0.905	14.721	-19.657	-19.657	0.000	0.000	0.000	0.000
76	D	157	PHE	0	-0.028	-0.032	16.735	0.554	0.554	0.000	0.000	0.000	0.000
77	D	158	ASN	0	0.023	0.031	10.979	1.144	1.144	0.000	0.000	0.000	0.000
78	D	159	GLY	0	0.042	0.013	14.680	0.414	0.414	0.000	0.000	0.000	0.000
79	D	160	GLY	0	-0.046	-0.025	17.215	0.532	0.532	0.000	0.000	0.000	0.000
80	D	161	LYS	1	0.911	0.964	15.205	18.032	18.032	0.000	0.000	0.000	0.000
81	D	162	ILE	0	0.003	0.010	16.300	-0.821	-0.821	0.000	0.000	0.000	0.000
82	D	163	SER	0	0.018	0.012	13.847	-1.167	-1.167	0.000	0.000	0.000	0.000
83	D	164	VAL	0	0.004	-0.013	16.163	0.518	0.518	0.000	0.000	0.000	0.000
84	D	165	GLN	0	0.015	0.002	14.882	-2.086	-2.086	0.000	0.000	0.000	0.000
85	D	166	TYR	0	0.021	0.003	18.480	0.814	0.814	0.000	0.000	0.000	0.000
86	D	167	ASN	0	0.021	-0.004	19.321	-1.183	-1.183	0.000	0.000	0.000	0.000
87	D	168	LEU	0	-0.035	-0.010	21.670	0.755	0.755	0.000	0.000	0.000	0.000
88	D	169	SER	0	-0.016	-0.006	24.262	0.068	0.068	0.000	0.000	0.000	0.000
89	D	170	HIS	1	0.785	0.862	26.787	11.613	11.613	0.000	0.000	0.000	0.000
90	D	171	SER	0	0.023	0.013	26.545	0.051	0.051	0.000	0.000	0.000	0.000
91	D	172	TYR	0	0.018	0.013	28.964	0.351	0.351	0.000	0.000	0.000	0.000
92	D	173	ALA	0	0.075	0.017	32.773	-0.071	-0.071	0.000	0.000	0.000	0.000
93	D	174	GLY	0	0.006	0.005	35.628	0.072	0.072	0.000	0.000	0.000	0.000
94	D	175	ASP	-1	-0.878	-0.947	30.409	-10.511	-10.511	0.000	0.000	0.000	0.000
95	D	176	ALA	0	-0.026	-0.009	31.762	-0.120	-0.120	0.000	0.000	0.000	0.000
96	D	177	ALA	0	0.029	0.008	32.732	-0.012	-0.012	0.000	0.000	0.000	0.000
97	D	178	ASN	0	-0.018	-0.013	34.742	0.286	0.286	0.000	0.000	0.000	0.000
98	D	179	HIS	1	0.787	0.902	30.222	10.437	10.437	0.000	0.000	0.000	0.000
99	D	180	CYS	0	-0.007	0.006	31.148	-0.517	-0.517	0.000	0.000	0.000	0.000
100	D	181	GLY	0	-0.010	-0.004	33.266	-0.035	-0.035	0.000	0.000	0.000	0.000
101	D	182	THR	0	-0.043	-0.031	28.905	-0.120	-0.120	0.000	0.000	0.000	0.000
102	D	183	VAL	0	0.070	0.018	26.065	0.056	0.056	0.000	0.000	0.000	0.000
103	D	184	ALA	0	-0.002	0.002	24.667	-0.116	-0.116	0.000	0.000	0.000	0.000
104	D	185	ASN	0	0.004	-0.002	25.868	-0.214	-0.214	0.000	0.000	0.000	0.000
105	D	186	GLY	0	0.053	0.021	28.866	0.146	0.146	0.000	0.000	0.000	0.000
106	D	187	VAL	0	0.000	0.006	22.517	0.065	0.065	0.000	0.000	0.000	0.000
107	D	188	LEU	0	-0.007	-0.004	23.942	-0.060	-0.060	0.000	0.000	0.000	0.000
108	D	189	GLN	0	0.056	0.025	26.458	0.315	0.315	0.000	0.000	0.000	0.000
109	D	190	THR	0	-0.025	-0.022	26.907	0.341	0.341	0.000	0.000	0.000	0.000
110	D	191	PHE	0	-0.060	-0.038	19.934	0.043	0.043	0.000	0.000	0.000	0.000
111	D	192	MET	0	-0.031	-0.003	25.752	0.065	0.065	0.000	0.000	0.000	0.000
112	D	193	ARG	1	0.764	0.853	28.759	9.134	9.134	0.000	0.000	0.000	0.000
113	D	194	MET	0	-0.036	-0.012	27.462	0.316	0.316	0.000	0.000	0.000	0.000
114	D	195	ALA	0	-0.003	0.014	27.663	-0.146	-0.146	0.000	0.000	0.000	0.000
115	D	196	TRP	0	-0.041	-0.021	22.487	-0.323	-0.323	0.000	0.000	0.000	0.000
116	D	197	GLY	0	0.038	0.022	21.825	-0.712	-0.712	0.000	0.000	0.000	0.000
117	D	198	GLY	0	0.043	0.033	23.057	0.001	0.001	0.000	0.000	0.000	0.000
118	D	199	SER	0	-0.042	-0.019	23.777	0.422	0.422	0.000	0.000	0.000	0.000
119	D	200	TYR	0	-0.036	-0.051	23.635	-0.341	-0.341	0.000	0.000	0.000	0.000
120	D	201	ILE	0	-0.001	0.001	29.319	0.278	0.278	0.000	0.000	0.000	0.000
121	D	202	ALA	0	0.034	0.020	32.889	-0.186	-0.186	0.000	0.000	0.000	0.000
122	D	203	LEU	0	-0.045	-0.019	34.762	0.206	0.206	0.000	0.000	0.000	0.000
123	D	204	ASP	-1	-0.839	-0.915	37.370	-7.668	-7.668	0.000	0.000	0.000	0.000
124	D	205	SER	0	-0.036	-0.040	38.250	-0.009	-0.009	0.000	0.000	0.000	0.000
125	D	206	GLY	0	-0.012	-0.002	40.288	0.168	0.168	0.000	0.000	0.000	0.000
126	D	207	ARG	1	0.870	0.930	38.838	8.186	8.186	0.000	0.000	0.000	0.000
127	D	208	GLY	0	0.035	0.017	41.042	-0.164	-0.164	0.000	0.000	0.000	0.000
128	D	209	ASN	0	0.039	0.022	38.386	-0.132	-0.132	0.000	0.000	0.000	0.000
129	D	210	TRP	0	-0.029	0.007	31.699	-0.254	-0.254	0.000	0.000	0.000	0.000
130	D	211	ASP	-1	-0.774	-0.852	34.458	-8.498	-8.498	0.000	0.000	0.000	0.000
131	D	213	ILE	0	0.004	0.007	28.630	0.098	0.098	0.000	0.000	0.000	0.000
132	D	214	MET	0	-0.018	0.018	30.258	-0.214	-0.214	0.000	0.000	0.000	0.000
133	D	215	THR	0	0.010	-0.017	24.674	-0.255	-0.255	0.000	0.000	0.000	0.000
134	D	216	SER	0	0.022	0.014	24.682	0.056	0.056	0.000	0.000	0.000	0.000
135	D	217	TYR	0	-0.044	-0.013	18.373	-0.238	-0.238	0.000	0.000	0.000	0.000
136	D	218	GLN	0	0.029	0.004	19.044	0.286	0.286	0.000	0.000	0.000	0.000
137	D	219	TYR	0	-0.041	-0.016	16.542	0.038	0.038	0.000	0.000	0.000	0.000
138	D	220	LEU	0	0.005	0.014	18.826	0.088	0.088	0.000	0.000	0.000	0.000
139	D	221	ILE	0	-0.041	-0.013	12.696	0.058	0.058	0.000	0.000	0.000	0.000
140	D	222	ILE	0	0.027	0.013	16.549	0.574	0.574	0.000	0.000	0.000	0.000
141	D	223	GLN	0	-0.026	-0.036	10.898	-1.302	-1.302	0.000	0.000	0.000	0.000
142	D	224	ASN	0	-0.009	0.000	15.621	0.238	0.238	0.000	0.000	0.000	0.000
143	D	225	THR	0	0.012	0.002	12.341	-0.730	-0.730	0.000	0.000	0.000	0.000
144	D	226	THR	0	0.064	0.050	14.352	1.117	1.117	0.000	0.000	0.000	0.000
145	D	227	TRP	0	0.037	0.016	15.668	-0.691	-0.691	0.000	0.000	0.000	0.000
146	D	228	GLU	-1	-0.881	-0.938	14.645	-16.037	-16.037	0.000	0.000	0.000	0.000
147	D	229	ASP	-1	-0.867	-0.927	10.560	-22.964	-22.964	0.000	0.000	0.000	0.000
148	D	230	HIS	1	0.775	0.880	10.433	16.221	16.221	0.000	0.000	0.000	0.000
150	D	233	PHE	0	0.017	0.005	6.902	1.986	1.986	0.000	0.000	0.000	0.000
151	D	234	SER	0	0.038	0.012	6.737	-3.620	-3.620	0.000	0.000	0.000	0.000
153	D	236	PRO	0	-0.023	-0.017	8.500	1.989	1.989	0.000	0.000	0.000	0.000
154	D	237	SER	-1	-0.889	-0.926	10.788	-25.043	-25.043	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:81:THR)