FMO DATABASE

FMODB ID: 4GZGN

Calculation Name: 1JSD-B-Xray549

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose | phosphate ion

Ligand 3-letter code: NAG | PO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1JSD

Chain ID: B

ChEMBL ID:

UniProt ID: Q91CD4

Base Structure: X-ray

Registration Date: 2025-10-11

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1295308.499654
FMO2-HF: Nuclear repulsion	1230757.553732
FMO2-HF: Total energy	-64550.945923
FMO2-MP2: Total energy	-64735.265706

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.
-219.936	-214.279	9.77	-7.86	-7.567	-0.101

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 : 0.809 / q_NPA : 0.899

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	-0.028	-0.024	3.457	12.281	13.389	-0.004	-0.500	-0.603	-0.002
4	B	4	GLY	0	0.001	0.008	2.907	8.246	9.031	0.068	-0.355	-0.498	-0.002
5	B	5	ALA	0	0.011	0.019	3.707	7.686	7.956	-0.001	-0.036	-0.234	0.000
6	B	6	ILE	0	0.003	-0.012	3.774	5.060	5.315	0.000	-0.072	-0.182	0.000
7	B	7	ALA	0	-0.037	-0.020	2.379	-29.831	-27.793	1.301	-1.695	-1.644	-0.022
8	B	8	GLY	0	-0.030	-0.007	4.081	-7.567	-7.365	0.000	-0.073	-0.130	0.000
9	B	9	PHE	0	-0.038	-0.017	4.746	7.369	7.418	-0.001	-0.005	-0.043	0.000
109	B	109	ASP	-1	-0.797	-0.898	3.219	-65.538	-64.613	0.058	-0.487	-0.497	-0.004
110	B	110	GLU	-1	-0.881	-0.931	5.375	-22.090	-22.118	-0.001	0.000	0.029	0.000
112	B	112	ASP	-1	-0.764	-0.883	1.910	-115.990	-115.948	8.351	-4.637	-3.755	-0.071
113	B	113	ALA	0	-0.003	0.002	5.293	2.798	2.809	-0.001	0.000	-0.010	0.000
10	B	10	ILE	0	-0.031	-0.010	7.034	5.008	5.008	0.000	0.000	0.000	0.000
11	B	11	GLU	-1	-0.932	-0.969	7.466	-28.031	-28.031	0.000	0.000	0.000	0.000
12	B	12	GLY	0	-0.006	-0.009	8.609	-1.166	-1.166	0.000	0.000	0.000	0.000
13	B	13	GLY	0	-0.018	0.002	10.171	0.444	0.444	0.000	0.000	0.000	0.000
14	B	14	TRP	0	0.019	-0.006	11.828	1.458	1.458	0.000	0.000	0.000	0.000
15	B	15	PRO	0	0.014	0.000	15.632	0.097	0.097	0.000	0.000	0.000	0.000
16	B	16	GLY	0	0.028	0.010	18.231	0.725	0.725	0.000	0.000	0.000	0.000
17	B	17	LEU	0	-0.030	-0.007	15.079	0.730	0.730	0.000	0.000	0.000	0.000
18	B	18	VAL	0	-0.021	-0.024	18.462	-0.438	-0.438	0.000	0.000	0.000	0.000
19	B	19	ALA	0	-0.027	-0.006	20.775	0.314	0.314	0.000	0.000	0.000	0.000
20	B	20	GLY	0	-0.001	-0.013	18.208	0.392	0.392	0.000	0.000	0.000	0.000
21	B	21	TRP	0	0.003	0.003	12.706	-0.443	-0.443	0.000	0.000	0.000	0.000
22	B	22	TYR	0	0.014	-0.021	10.649	-1.489	-1.489	0.000	0.000	0.000	0.000
23	B	23	GLY	0	0.002	-0.003	13.928	1.607	1.607	0.000	0.000	0.000	0.000
24	B	24	PHE	0	-0.010	0.010	15.573	-1.065	-1.065	0.000	0.000	0.000	0.000
25	B	25	GLN	0	0.031	0.012	18.277	0.645	0.645	0.000	0.000	0.000	0.000
26	B	26	HIS	0	-0.015	-0.006	19.824	-0.741	-0.741	0.000	0.000	0.000	0.000
27	B	27	SER	0	0.001	-0.026	22.931	-0.047	-0.047	0.000	0.000	0.000	0.000
28	B	28	ASN	0	-0.031	-0.023	25.465	0.099	0.099	0.000	0.000	0.000	0.000
29	B	29	ASP	-1	-0.835	-0.905	29.075	-9.681	-9.681	0.000	0.000	0.000	0.000
30	B	30	GLN	0	-0.042	-0.014	31.682	0.223	0.223	0.000	0.000	0.000	0.000
31	B	31	GLY	0	0.020	0.019	29.974	0.168	0.168	0.000	0.000	0.000	0.000
32	B	32	VAL	0	-0.001	-0.001	23.744	-0.237	-0.237	0.000	0.000	0.000	0.000
33	B	33	GLY	0	0.001	0.010	24.483	0.338	0.338	0.000	0.000	0.000	0.000
34	B	34	MET	0	-0.029	-0.007	18.849	-0.614	-0.614	0.000	0.000	0.000	0.000
35	B	35	ALA	0	0.003	0.008	20.594	0.599	0.599	0.000	0.000	0.000	0.000
36	B	36	ALA	0	0.022	0.019	18.376	-0.759	-0.759	0.000	0.000	0.000	0.000
37	B	37	ASP	-1	-0.815	-0.886	17.141	-15.885	-15.885	0.000	0.000	0.000	0.000
38	B	38	SER	0	0.010	-0.001	18.677	-0.332	-0.332	0.000	0.000	0.000	0.000
39	B	39	ASP	-1	-0.848	-0.910	20.202	-15.141	-15.141	0.000	0.000	0.000	0.000
40	B	40	SER	0	-0.043	-0.069	15.013	-0.499	-0.499	0.000	0.000	0.000	0.000
41	B	41	THR	0	0.010	-0.003	16.435	-1.039	-1.039	0.000	0.000	0.000	0.000
42	B	42	GLN	0	-0.047	-0.027	17.417	-0.170	-0.170	0.000	0.000	0.000	0.000
43	B	43	LYS	1	0.854	0.920	18.250	15.375	15.375	0.000	0.000	0.000	0.000
44	B	44	ALA	0	0.009	0.011	14.351	-0.100	-0.100	0.000	0.000	0.000	0.000
45	B	45	ILE	0	0.010	0.011	16.201	-0.131	-0.131	0.000	0.000	0.000	0.000
46	B	46	ASP	-1	-0.824	-0.894	18.811	-13.584	-13.584	0.000	0.000	0.000	0.000
47	B	47	LYS	1	0.846	0.927	15.533	19.336	19.336	0.000	0.000	0.000	0.000
48	B	48	ILE	0	0.000	0.005	14.424	0.197	0.197	0.000	0.000	0.000	0.000
49	B	49	THR	0	-0.008	-0.012	17.133	0.553	0.553	0.000	0.000	0.000	0.000
50	B	50	SER	0	-0.037	-0.032	20.631	0.764	0.764	0.000	0.000	0.000	0.000
51	B	51	LYS	1	0.831	0.919	13.049	21.777	21.777	0.000	0.000	0.000	0.000
52	B	52	VAL	0	0.017	0.008	18.294	0.392	0.392	0.000	0.000	0.000	0.000
53	B	53	ASN	0	0.018	0.003	20.550	0.498	0.498	0.000	0.000	0.000	0.000
54	B	54	ASN	0	-0.053	-0.039	22.237	0.870	0.870	0.000	0.000	0.000	0.000
55	B	55	ILE	0	-0.003	0.002	17.921	0.286	0.286	0.000	0.000	0.000	0.000
56	B	56	VAL	0	-0.008	-0.008	22.568	0.425	0.425	0.000	0.000	0.000	0.000
57	B	57	ASP	-1	-0.911	-0.957	25.527	-10.117	-10.117	0.000	0.000	0.000	0.000
58	B	58	LYS	1	0.831	0.904	25.022	11.352	11.352	0.000	0.000	0.000	0.000
59	B	59	MET	0	-0.035	-0.010	23.742	0.033	0.033	0.000	0.000	0.000	0.000
60	B	60	ASN	0	-0.032	0.000	27.072	0.345	0.345	0.000	0.000	0.000	0.000
61	B	61	LYS	1	0.940	0.978	29.897	9.139	9.139	0.000	0.000	0.000	0.000
62	B	62	GLN	0	0.017	0.014	32.390	-0.105	-0.105	0.000	0.000	0.000	0.000
63	B	63	TYR	0	0.022	0.007	31.729	0.033	0.033	0.000	0.000	0.000	0.000
64	B	64	GLY	0	-0.050	-0.029	36.183	0.040	0.040	0.000	0.000	0.000	0.000
65	B	65	ILE	0	0.006	0.005	37.250	-0.005	-0.005	0.000	0.000	0.000	0.000
66	B	66	ILE	0	-0.055	-0.034	41.101	0.027	0.027	0.000	0.000	0.000	0.000
67	B	67	ASP	-1	-0.914	-0.945	44.671	-6.814	-6.814	0.000	0.000	0.000	0.000
68	B	68	HIS	0	-0.037	-0.020	46.103	0.253	0.253	0.000	0.000	0.000	0.000
69	B	69	GLU	-1	-0.936	-0.959	49.067	-5.833	-5.833	0.000	0.000	0.000	0.000
70	B	70	PHE	0	-0.025	-0.021	48.013	0.038	0.038	0.000	0.000	0.000	0.000
71	B	71	SER	0	-0.026	-0.044	53.527	0.056	0.056	0.000	0.000	0.000	0.000
72	B	72	GLU	-1	-0.889	-0.963	55.824	-5.653	-5.653	0.000	0.000	0.000	0.000
73	B	73	ILE	0	-0.072	-0.032	57.431	-0.013	-0.013	0.000	0.000	0.000	0.000
74	B	74	GLU	-1	-0.873	-0.905	53.904	-5.737	-5.737	0.000	0.000	0.000	0.000
75	B	75	THR	0	0.033	0.020	52.208	-0.155	-0.155	0.000	0.000	0.000	0.000
76	B	76	ARG	1	0.945	0.962	50.533	5.636	5.636	0.000	0.000	0.000	0.000
77	B	77	LEU	0	0.002	0.009	49.463	-0.129	-0.129	0.000	0.000	0.000	0.000
78	B	78	ASN	0	0.052	0.041	47.961	-0.266	-0.266	0.000	0.000	0.000	0.000
79	B	79	MET	0	-0.001	-0.011	46.045	-0.158	-0.158	0.000	0.000	0.000	0.000
80	B	80	ILE	0	-0.101	-0.054	44.715	-0.181	-0.181	0.000	0.000	0.000	0.000
81	B	81	ASN	0	-0.003	-0.003	44.027	-0.092	-0.092	0.000	0.000	0.000	0.000
82	B	82	ASN	0	0.048	0.020	42.314	-0.174	-0.174	0.000	0.000	0.000	0.000
83	B	83	LYS	1	0.953	0.987	40.257	7.094	7.094	0.000	0.000	0.000	0.000
84	B	84	ILE	0	-0.061	-0.027	39.050	-0.201	-0.201	0.000	0.000	0.000	0.000
85	B	85	ASP	-1	-0.821	-0.920	38.042	-7.824	-7.824	0.000	0.000	0.000	0.000
86	B	86	ASP	-1	-0.899	-0.954	36.509	-8.370	-8.370	0.000	0.000	0.000	0.000
87	B	87	GLN	0	-0.085	-0.048	33.943	-0.426	-0.426	0.000	0.000	0.000	0.000
88	B	88	ILE	0	-0.036	-0.013	33.288	-0.311	-0.311	0.000	0.000	0.000	0.000
89	B	89	GLN	0	0.004	0.006	31.934	-0.130	-0.130	0.000	0.000	0.000	0.000
90	B	90	ASP	-1	-0.856	-0.913	30.166	-10.108	-10.108	0.000	0.000	0.000	0.000
91	B	91	ILE	0	-0.046	-0.024	28.542	-0.505	-0.505	0.000	0.000	0.000	0.000
92	B	92	TRP	0	-0.017	-0.017	27.629	-0.585	-0.585	0.000	0.000	0.000	0.000
93	B	93	THR	0	-0.026	-0.012	25.895	-0.370	-0.370	0.000	0.000	0.000	0.000
94	B	94	TYR	0	0.017	0.009	22.412	-0.668	-0.668	0.000	0.000	0.000	0.000
95	B	95	ASN	0	-0.045	-0.037	22.792	-0.850	-0.850	0.000	0.000	0.000	0.000
96	B	96	ALA	0	0.019	0.010	22.342	-0.592	-0.592	0.000	0.000	0.000	0.000
97	B	97	GLU	-1	-0.930	-0.966	20.476	-13.998	-13.998	0.000	0.000	0.000	0.000
98	B	98	LEU	0	-0.023	-0.015	18.038	-1.189	-1.189	0.000	0.000	0.000	0.000
99	B	99	LEU	0	-0.005	0.009	17.188	-1.101	-1.101	0.000	0.000	0.000	0.000
100	B	100	VAL	0	0.012	0.002	16.656	-1.108	-1.108	0.000	0.000	0.000	0.000
101	B	101	LEU	0	-0.012	-0.005	14.236	-1.559	-1.559	0.000	0.000	0.000	0.000
102	B	102	LEU	0	-0.015	-0.012	12.466	-2.083	-2.083	0.000	0.000	0.000	0.000
103	B	103	GLU	-1	-0.807	-0.899	12.030	-21.321	-21.321	0.000	0.000	0.000	0.000
104	B	104	ASN	0	0.003	0.025	11.406	-1.164	-1.164	0.000	0.000	0.000	0.000
105	B	105	GLN	0	-0.046	-0.026	4.901	0.815	0.815	0.000	0.000	0.000	0.000
106	B	106	LYS	1	0.902	0.931	7.187	16.389	16.389	0.000	0.000	0.000	0.000
107	B	107	THR	0	-0.013	-0.019	9.098	-0.171	-0.171	0.000	0.000	0.000	0.000
108	B	108	LEU	0	-0.032	-0.006	5.380	-0.614	-0.614	0.000	0.000	0.000	0.000
111	B	111	HIS	0	0.022	0.036	7.554	1.404	1.404	0.000	0.000	0.000	0.000
114	B	114	ASN	0	-0.038	-0.026	8.033	3.535	3.535	0.000	0.000	0.000	0.000
115	B	115	VAL	0	0.013	0.015	7.376	2.727	2.727	0.000	0.000	0.000	0.000
116	B	116	ASN	0	0.025	0.014	6.921	2.807	2.807	0.000	0.000	0.000	0.000
117	B	117	ASN	0	-0.035	-0.027	8.783	2.661	2.661	0.000	0.000	0.000	0.000
118	B	118	LEU	0	-0.019	0.002	12.190	2.110	2.110	0.000	0.000	0.000	0.000
119	B	119	TYR	0	0.011	-0.022	11.265	1.441	1.441	0.000	0.000	0.000	0.000
120	B	120	ASN	0	-0.008	-0.027	11.318	3.509	3.509	0.000	0.000	0.000	0.000
121	B	121	LYS	1	0.892	0.955	14.450	17.154	17.154	0.000	0.000	0.000	0.000
122	B	122	VAL	0	0.028	0.017	16.796	1.136	1.136	0.000	0.000	0.000	0.000
123	B	123	LYS	1	0.931	0.978	14.967	20.662	20.662	0.000	0.000	0.000	0.000
124	B	124	ARG	1	0.891	0.936	16.344	18.365	18.365	0.000	0.000	0.000	0.000
125	B	125	ALA	0	-0.017	-0.005	20.475	0.813	0.813	0.000	0.000	0.000	0.000
126	B	126	LEU	0	0.037	0.016	20.489	0.660	0.660	0.000	0.000	0.000	0.000
127	B	127	GLY	0	0.051	0.045	23.020	0.483	0.483	0.000	0.000	0.000	0.000
128	B	128	SER	0	-0.036	-0.029	23.584	-0.295	-0.295	0.000	0.000	0.000	0.000
129	B	129	ASN	0	-0.097	-0.066	25.422	0.684	0.684	0.000	0.000	0.000	0.000
130	B	130	ALA	0	0.029	0.023	22.003	0.252	0.252	0.000	0.000	0.000	0.000
131	B	131	MET	0	-0.018	0.015	21.813	-0.016	-0.016	0.000	0.000	0.000	0.000
132	B	132	GLU	-1	-0.834	-0.905	15.197	-20.431	-20.431	0.000	0.000	0.000	0.000
133	B	133	ASP	-1	-0.791	-0.901	16.088	-19.325	-19.325	0.000	0.000	0.000	0.000
134	B	134	GLY	0	-0.043	-0.018	14.167	0.112	0.112	0.000	0.000	0.000	0.000
135	B	135	LYS	1	0.859	0.922	12.159	17.385	17.385	0.000	0.000	0.000	0.000
136	B	136	GLY	0	0.012	0.011	12.539	-1.123	-1.123	0.000	0.000	0.000	0.000
137	B	137	CYS	0	-0.059	-0.020	13.061	1.000	1.000	0.000	0.000	0.000	0.000
138	B	138	PHE	0	-0.015	-0.019	15.590	-0.050	-0.050	0.000	0.000	0.000	0.000
139	B	139	GLU	-1	-0.886	-0.936	19.623	-13.223	-13.223	0.000	0.000	0.000	0.000
140	B	140	LEU	0	-0.012	-0.016	22.913	0.341	0.341	0.000	0.000	0.000	0.000
141	B	141	TYR	0	-0.026	-0.015	25.548	0.388	0.388	0.000	0.000	0.000	0.000
142	B	142	HIS	1	0.813	0.866	28.010	11.495	11.495	0.000	0.000	0.000	0.000
143	B	143	LYS	1	0.893	0.934	29.601	9.566	9.566	0.000	0.000	0.000	0.000
144	B	144	CYS	0	-0.051	-0.018	28.071	-0.281	-0.281	0.000	0.000	0.000	0.000
145	B	145	ASP	-1	-0.766	-0.869	29.596	-9.918	-9.918	0.000	0.000	0.000	0.000
146	B	146	ASP	-1	-0.792	-0.909	29.159	-11.043	-11.043	0.000	0.000	0.000	0.000
147	B	147	GLN	0	-0.019	-0.002	29.333	-0.429	-0.429	0.000	0.000	0.000	0.000
148	B	149	MET	0	-0.004	0.006	25.339	-0.556	-0.556	0.000	0.000	0.000	0.000
149	B	150	GLU	-1	-0.826	-0.896	25.222	-12.540	-12.540	0.000	0.000	0.000	0.000
150	B	151	THR	0	-0.082	-0.047	26.391	-0.242	-0.242	0.000	0.000	0.000	0.000
151	B	152	ILE	0	-0.034	-0.021	21.571	-0.251	-0.251	0.000	0.000	0.000	0.000
152	B	153	ARG	1	0.813	0.913	21.741	12.167	12.167	0.000	0.000	0.000	0.000
153	B	154	ASN	0	-0.018	-0.008	22.193	-0.409	-0.409	0.000	0.000	0.000	0.000
154	B	155	GLY	0	-0.028	-0.007	23.992	0.024	0.024	0.000	0.000	0.000	0.000
155	B	156	THR	0	-0.061	-0.047	24.566	0.295	0.295	0.000	0.000	0.000	0.000
156	B	157	TYR	0	-0.031	-0.013	25.913	0.460	0.460	0.000	0.000	0.000	0.000
157	B	158	ASN	0	-0.013	-0.009	27.860	-0.137	-0.137	0.000	0.000	0.000	0.000
158	B	159	ARG	1	0.885	0.947	29.148	10.754	10.754	0.000	0.000	0.000	0.000
159	B	160	ARG	0	0.054	0.064	23.276	1.221	1.221	0.000	0.000	0.000	0.000

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