FMO DATABASE

FMODB ID: 942Y2

Calculation Name: 4HG4-Z-Xray372

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose

ligand 3-letter code: NAG

PDB ID: 4HG4

Chain ID: Z

ChEMBL ID:

UniProt ID: P03451

Base Structure: X-ray

Registration Date: 2023-06-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	166
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1489788.166019
FMO2-HF: Nuclear repulsion	1427044.06586
FMO2-HF: Total energy	-62744.100159
FMO2-MP2: Total energy	-62927.934133

3D Structure

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(Z:1:GLU)

Summations of interaction energy for fragment #1(Z:1:GLU)

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.
-64.88	-66.004	23.525	-10.59	-11.809	0.125

Interaction energy analysis for fragmet #1(Z:1:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.865 / q_NPA : -0.937

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	Z	3	GLN	0	-0.070	-0.026	1.827	-34.933	-36.603	15.004	-5.951	-7.382	0.067
4	Z	4	LEU	0	-0.011	-0.017	4.205	-0.439	-0.350	0.001	-0.006	-0.084	0.000
5	Z	5	VAL	0	0.003	0.009	7.433	-0.904	-0.904	0.000	0.000	0.000	0.000
6	Z	6	GLU	-1	-0.770	-0.880	10.068	20.305	20.305	0.000	0.000	0.000	0.000
7	Z	7	SER	0	0.005	0.023	13.841	0.182	0.182	0.000	0.000	0.000	0.000
8	Z	8	GLY	0	0.022	0.030	17.160	-0.009	-0.009	0.000	0.000	0.000	0.000
9	Z	9	ALA	0	-0.003	-0.002	18.984	-0.403	-0.403	0.000	0.000	0.000	0.000
10	Z	10	GLU	-1	-0.817	-0.910	22.172	12.777	12.777	0.000	0.000	0.000	0.000
11	Z	11	VAL	0	-0.031	-0.018	25.093	-0.254	-0.254	0.000	0.000	0.000	0.000
12	Z	12	LYS	1	0.799	0.889	26.816	-11.652	-11.652	0.000	0.000	0.000	0.000
13	Z	13	LYS	1	0.968	0.990	31.117	-9.006	-9.006	0.000	0.000	0.000	0.000
14	Z	14	PRO	0	0.043	0.025	34.498	0.170	0.170	0.000	0.000	0.000	0.000
15	Z	15	GLY	0	-0.011	0.006	35.977	-0.175	-0.175	0.000	0.000	0.000	0.000
16	Z	16	SER	0	-0.082	-0.056	32.637	0.183	0.183	0.000	0.000	0.000	0.000
17	Z	17	SER	0	0.051	0.007	29.134	-0.072	-0.072	0.000	0.000	0.000	0.000
18	Z	18	VAL	0	-0.030	-0.002	23.969	-0.053	-0.053	0.000	0.000	0.000	0.000
19	Z	19	LYS	1	0.855	0.904	22.056	-12.617	-12.617	0.000	0.000	0.000	0.000
20	Z	20	VAL	0	0.016	0.023	18.042	0.420	0.420	0.000	0.000	0.000	0.000
21	Z	21	SER	0	-0.021	-0.022	16.079	0.540	0.540	0.000	0.000	0.000	0.000
22	Z	22	CYS	0	-0.051	-0.016	12.678	0.131	0.131	0.000	0.000	0.000	0.000
23	Z	23	LYS	1	0.845	0.928	8.553	-27.239	-27.239	0.000	0.000	0.000	0.000
24	Z	24	ALA	0	0.031	0.020	7.155	1.254	1.254	0.000	0.000	0.000	0.000
25	Z	25	SER	0	-0.035	-0.008	1.809	-23.975	-25.641	7.884	-3.451	-2.768	0.051
26	Z	26	GLY	0	0.058	0.028	2.696	1.924	3.669	0.580	-1.181	-1.143	0.004
27	Z	27	GLY	0	0.004	-0.004	3.477	-9.449	-9.071	0.056	-0.001	-0.432	0.003
28	Z	28	THR	0	-0.002	-0.002	6.932	0.090	0.090	0.000	0.000	0.000	0.000
29	Z	29	PHE	0	0.104	0.061	10.475	-0.113	-0.113	0.000	0.000	0.000	0.000
30	Z	30	ILE	0	0.056	0.009	12.257	-0.073	-0.073	0.000	0.000	0.000	0.000
31	Z	31	THR	0	-0.067	-0.041	10.083	-1.325	-1.325	0.000	0.000	0.000	0.000
32	Z	32	HIS	0	0.007	0.024	7.038	-1.240	-1.240	0.000	0.000	0.000	0.000
33	Z	33	VAL	0	-0.010	-0.002	12.031	-1.487	-1.487	0.000	0.000	0.000	0.000
34	Z	34	PHE	0	0.042	0.023	11.414	0.392	0.392	0.000	0.000	0.000	0.000
35	Z	35	THR	0	-0.028	-0.030	14.562	-1.704	-1.704	0.000	0.000	0.000	0.000
36	Z	36	TRP	0	0.030	0.007	16.161	0.773	0.773	0.000	0.000	0.000	0.000
37	Z	37	VAL	0	-0.012	-0.008	18.491	-0.948	-0.948	0.000	0.000	0.000	0.000
38	Z	38	ARG	1	0.758	0.838	20.409	-10.668	-10.668	0.000	0.000	0.000	0.000
39	Z	39	GLN	0	0.033	0.018	23.003	0.338	0.338	0.000	0.000	0.000	0.000
40	Z	40	ALA	0	0.048	0.037	25.013	0.121	0.121	0.000	0.000	0.000	0.000
41	Z	41	PRO	0	0.013	-0.015	28.176	0.065	0.065	0.000	0.000	0.000	0.000
42	Z	42	GLY	0	-0.003	0.004	28.594	-0.383	-0.383	0.000	0.000	0.000	0.000
43	Z	43	GLN	0	-0.046	-0.006	29.071	-0.406	-0.406	0.000	0.000	0.000	0.000
44	Z	44	GLY	0	0.018	0.006	26.960	0.350	0.350	0.000	0.000	0.000	0.000
45	Z	45	LEU	0	-0.024	-0.013	21.033	0.075	0.075	0.000	0.000	0.000	0.000
46	Z	46	GLU	-1	-0.807	-0.870	24.680	10.518	10.518	0.000	0.000	0.000	0.000
47	Z	47	TRP	0	-0.026	-0.012	20.358	-0.011	-0.011	0.000	0.000	0.000	0.000
48	Z	48	VAL	0	-0.002	-0.001	22.440	-0.519	-0.519	0.000	0.000	0.000	0.000
49	Z	49	GLY	0	0.030	-0.007	22.252	-0.546	-0.546	0.000	0.000	0.000	0.000
50	Z	50	GLY	0	-0.015	0.007	19.083	0.728	0.728	0.000	0.000	0.000	0.000
51	Z	51	PHE	0	-0.007	0.007	16.488	-0.686	-0.686	0.000	0.000	0.000	0.000
52	Z	52	ILE	0	-0.002	0.022	16.958	1.160	1.160	0.000	0.000	0.000	0.000
53	Z	52	ALA	0	0.016	0.014	14.887	-0.746	-0.746	0.000	0.000	0.000	0.000
54	Z	53	ILE	0	-0.038	-0.016	16.861	-0.444	-0.444	0.000	0.000	0.000	0.000
55	Z	54	PHE	0	-0.048	-0.033	18.628	-0.666	-0.666	0.000	0.000	0.000	0.000
56	Z	55	GLY	0	0.022	0.023	20.355	-0.568	-0.568	0.000	0.000	0.000	0.000
57	Z	56	THR	0	-0.028	-0.011	21.682	-0.378	-0.378	0.000	0.000	0.000	0.000
58	Z	57	SER	0	0.012	-0.010	21.802	0.770	0.770	0.000	0.000	0.000	0.000
59	Z	58	ASN	0	-0.040	-0.003	22.881	-0.193	-0.193	0.000	0.000	0.000	0.000
60	Z	59	TYR	0	0.091	0.035	23.835	0.483	0.483	0.000	0.000	0.000	0.000
61	Z	60	ALA	0	0.035	0.033	26.350	-0.321	-0.321	0.000	0.000	0.000	0.000
62	Z	61	GLN	0	-0.024	-0.007	27.937	-0.541	-0.541	0.000	0.000	0.000	0.000
63	Z	62	LYS	1	0.892	0.942	31.575	-8.990	-8.990	0.000	0.000	0.000	0.000
64	Z	63	PHE	0	0.059	0.019	27.858	-0.019	-0.019	0.000	0.000	0.000	0.000
65	Z	64	GLN	0	0.025	0.008	31.472	0.335	0.335	0.000	0.000	0.000	0.000
66	Z	65	GLY	0	-0.007	-0.005	32.761	-0.210	-0.210	0.000	0.000	0.000	0.000
67	Z	66	ARG	1	0.784	0.864	31.286	-9.733	-9.733	0.000	0.000	0.000	0.000
68	Z	67	VAL	0	0.002	0.003	25.655	0.213	0.213	0.000	0.000	0.000	0.000
69	Z	68	THR	0	-0.012	0.000	26.591	-0.379	-0.379	0.000	0.000	0.000	0.000
70	Z	69	ILE	0	-0.012	-0.005	20.260	0.290	0.290	0.000	0.000	0.000	0.000
71	Z	70	THR	0	-0.024	0.004	21.389	-0.344	-0.344	0.000	0.000	0.000	0.000
72	Z	71	ALA	0	0.006	-0.008	17.132	0.746	0.746	0.000	0.000	0.000	0.000
73	Z	72	ASP	-1	-0.779	-0.839	16.449	17.653	17.653	0.000	0.000	0.000	0.000
74	Z	73	GLU	-1	-0.922	-0.953	14.700	18.519	18.519	0.000	0.000	0.000	0.000
75	Z	74	SER	0	-0.089	-0.063	13.977	1.456	1.456	0.000	0.000	0.000	0.000
76	Z	75	THR	0	-0.057	-0.048	12.781	1.293	1.293	0.000	0.000	0.000	0.000
77	Z	76	SER	0	-0.024	-0.020	8.841	0.912	0.912	0.000	0.000	0.000	0.000
78	Z	77	THR	0	-0.003	-0.010	10.760	2.802	2.802	0.000	0.000	0.000	0.000
79	Z	78	ALA	0	0.016	0.014	13.464	-1.457	-1.457	0.000	0.000	0.000	0.000
80	Z	79	TYR	0	-0.012	-0.025	16.151	0.750	0.750	0.000	0.000	0.000	0.000
81	Z	80	MET	0	-0.015	0.012	18.938	-0.923	-0.923	0.000	0.000	0.000	0.000
82	Z	81	GLU	-1	-0.841	-0.903	21.498	11.903	11.903	0.000	0.000	0.000	0.000
83	Z	82	LEU	0	0.007	0.000	24.843	-0.232	-0.232	0.000	0.000	0.000	0.000
84	Z	82	THR	0	-0.015	-0.026	27.688	-0.152	-0.152	0.000	0.000	0.000	0.000
85	Z	82	SER	0	0.010	0.004	31.226	-0.190	-0.190	0.000	0.000	0.000	0.000
86	Z	82	LEU	0	-0.042	0.009	28.874	-0.100	-0.100	0.000	0.000	0.000	0.000
87	Z	83	THR	0	0.023	-0.008	33.045	-0.397	-0.397	0.000	0.000	0.000	0.000
88	Z	84	SER	0	0.062	0.014	33.219	0.212	0.212	0.000	0.000	0.000	0.000
89	Z	85	GLU	-1	-0.953	-0.960	33.378	8.844	8.844	0.000	0.000	0.000	0.000
90	Z	86	ASP	-1	-0.750	-0.811	29.323	10.331	10.331	0.000	0.000	0.000	0.000
91	Z	87	THR	0	-0.056	-0.027	28.402	0.490	0.490	0.000	0.000	0.000	0.000
92	Z	88	ALA	0	0.009	0.003	25.486	-0.153	-0.153	0.000	0.000	0.000	0.000
93	Z	89	VAL	0	0.005	0.020	20.175	0.199	0.199	0.000	0.000	0.000	0.000
94	Z	90	TYR	0	-0.027	-0.044	20.637	-0.287	-0.287	0.000	0.000	0.000	0.000
95	Z	91	TYR	0	-0.001	-0.004	16.466	0.771	0.771	0.000	0.000	0.000	0.000
96	Z	93	ALA	0	0.023	0.001	12.324	0.758	0.758	0.000	0.000	0.000	0.000
97	Z	94	ARG	1	0.869	0.931	7.934	-27.605	-27.605	0.000	0.000	0.000	0.000
98	Z	95	GLY	0	0.046	0.017	11.638	-0.235	-0.235	0.000	0.000	0.000	0.000
99	Z	96	ILE	0	-0.024	-0.007	13.317	0.909	0.909	0.000	0.000	0.000	0.000
100	Z	97	SER	0	-0.011	-0.012	15.558	-1.385	-1.385	0.000	0.000	0.000	0.000
101	Z	98	GLY	0	0.046	0.003	18.781	0.292	0.292	0.000	0.000	0.000	0.000
102	Z	99	SER	0	-0.045	-0.024	21.220	-0.547	-0.547	0.000	0.000	0.000	0.000
103	Z	100	TYR	0	-0.064	-0.044	18.259	-0.059	-0.059	0.000	0.000	0.000	0.000
104	Z	100	GLY	0	0.007	0.014	19.067	-0.051	-0.051	0.000	0.000	0.000	0.000
105	Z	100	TRP	0	0.020	0.003	13.065	-1.079	-1.079	0.000	0.000	0.000	0.000
106	Z	100	PHE	0	-0.031	-0.023	14.242	0.518	0.518	0.000	0.000	0.000	0.000
107	Z	101	ASP	-1	-0.898	-0.944	8.812	25.134	25.134	0.000	0.000	0.000	0.000
108	Z	102	PRO	0	-0.008	0.005	6.847	0.064	0.064	0.000	0.000	0.000	0.000
109	Z	103	TRP	0	-0.036	-0.036	9.032	-1.880	-1.880	0.000	0.000	0.000	0.000
110	Z	104	GLY	0	0.016	0.015	10.698	1.987	1.987	0.000	0.000	0.000	0.000
111	Z	105	GLN	0	-0.066	-0.048	12.424	-0.220	-0.220	0.000	0.000	0.000	0.000
112	Z	106	GLY	0	-0.009	-0.017	14.878	-1.272	-1.272	0.000	0.000	0.000	0.000
113	Z	107	THR	0	-0.034	-0.024	17.583	-0.177	-0.177	0.000	0.000	0.000	0.000
114	Z	108	LEU	0	-0.026	-0.003	19.544	-0.613	-0.613	0.000	0.000	0.000	0.000
115	Z	109	VAL	0	0.000	0.004	22.932	-0.013	-0.013	0.000	0.000	0.000	0.000
116	Z	110	THR	0	0.007	0.000	25.614	-0.408	-0.408	0.000	0.000	0.000	0.000
117	Z	111	VAL	0	-0.023	-0.018	29.130	-0.018	-0.018	0.000	0.000	0.000	0.000
118	Z	112	SER	0	0.021	0.010	32.104	-0.304	-0.304	0.000	0.000	0.000	0.000
119	Z	113	SER	0	0.022	-0.006	35.715	0.122	0.122	0.000	0.000	0.000	0.000
120	Z	114	ALA	0	-0.024	0.011	36.487	-0.141	-0.141	0.000	0.000	0.000	0.000
121	Z	115	SER	0	0.008	-0.011	34.718	0.277	0.277	0.000	0.000	0.000	0.000
122	Z	116	THR	0	0.025	0.010	30.670	-0.268	-0.268	0.000	0.000	0.000	0.000
123	Z	117	LYS	1	0.830	0.918	33.779	-8.897	-8.897	0.000	0.000	0.000	0.000
124	Z	118	GLY	0	0.095	0.065	34.945	0.212	0.212	0.000	0.000	0.000	0.000
125	Z	119	PRO	0	-0.006	0.001	34.655	-0.201	-0.201	0.000	0.000	0.000	0.000
126	Z	120	SER	0	-0.024	-0.005	37.497	-0.220	-0.220	0.000	0.000	0.000	0.000
127	Z	121	VAL	0	-0.012	-0.018	38.848	0.131	0.131	0.000	0.000	0.000	0.000
128	Z	122	PHE	0	-0.009	0.004	41.658	-0.179	-0.179	0.000	0.000	0.000	0.000
129	Z	123	PRO	0	0.016	0.017	42.553	-0.047	-0.047	0.000	0.000	0.000	0.000
130	Z	141	LEU	0	-0.033	-0.009	40.249	0.053	0.053	0.000	0.000	0.000	0.000
131	Z	142	VAL	0	0.008	-0.002	35.517	-0.056	-0.056	0.000	0.000	0.000	0.000
132	Z	143	LYS	1	0.836	0.932	38.470	-7.607	-7.607	0.000	0.000	0.000	0.000
133	Z	144	ASP	-1	-0.741	-0.890	38.887	7.921	7.921	0.000	0.000	0.000	0.000
134	Z	145	TYR	0	0.037	0.043	31.886	-0.117	-0.117	0.000	0.000	0.000	0.000
135	Z	146	PHE	0	-0.008	-0.009	32.963	0.025	0.025	0.000	0.000	0.000	0.000
136	Z	147	PRO	0	0.025	0.007	28.437	-0.051	-0.051	0.000	0.000	0.000	0.000
137	Z	148	GLU	-1	-0.812	-0.935	28.269	10.556	10.556	0.000	0.000	0.000	0.000
138	Z	149	PRO	0	-0.033	0.009	24.627	0.262	0.262	0.000	0.000	0.000	0.000
139	Z	150	VAL	0	-0.002	-0.011	27.025	-0.293	-0.293	0.000	0.000	0.000	0.000
140	Z	164	HIS	0	-0.011	-0.013	33.778	0.127	0.127	0.000	0.000	0.000	0.000
141	Z	165	THR	0	-0.010	-0.001	30.265	-0.238	-0.238	0.000	0.000	0.000	0.000
142	Z	166	PHE	0	-0.008	-0.009	33.092	-0.086	-0.086	0.000	0.000	0.000	0.000
143	Z	167	PRO	0	0.016	0.016	30.305	0.240	0.240	0.000	0.000	0.000	0.000
144	Z	168	ALA	0	-0.029	-0.016	31.433	-0.340	-0.340	0.000	0.000	0.000	0.000
145	Z	169	VAL	0	-0.017	-0.003	33.484	-0.028	-0.028	0.000	0.000	0.000	0.000
146	Z	170	LEU	0	-0.009	-0.006	34.346	0.001	0.001	0.000	0.000	0.000	0.000
147	Z	171	GLN	0	-0.033	-0.019	37.175	-0.332	-0.332	0.000	0.000	0.000	0.000
148	Z	172	SER	0	0.019	0.000	40.638	0.123	0.123	0.000	0.000	0.000	0.000
149	Z	173	SER	0	-0.037	-0.041	41.794	-0.020	-0.020	0.000	0.000	0.000	0.000
150	Z	174	GLY	0	0.004	0.006	39.034	0.036	0.036	0.000	0.000	0.000	0.000
151	Z	175	LEU	0	-0.073	-0.026	37.016	0.295	0.295	0.000	0.000	0.000	0.000
152	Z	176	TYR	0	0.032	0.014	31.001	-0.149	-0.149	0.000	0.000	0.000	0.000
153	Z	177	SER	0	-0.075	-0.044	35.948	-0.229	-0.229	0.000	0.000	0.000	0.000
154	Z	178	LEU	0	0.052	0.030	31.866	0.116	0.116	0.000	0.000	0.000	0.000
155	Z	179	SER	0	0.043	0.020	35.927	-0.164	-0.164	0.000	0.000	0.000	0.000
156	Z	195	ILE	0	0.007	-0.011	37.204	-0.044	-0.044	0.000	0.000	0.000	0.000
157	Z	196	CYS	0	0.012	0.006	36.313	0.263	0.263	0.000	0.000	0.000	0.000
158	Z	197	ASN	0	-0.035	-0.006	32.175	0.191	0.191	0.000	0.000	0.000	0.000
159	Z	198	VAL	0	0.045	0.014	32.465	0.174	0.174	0.000	0.000	0.000	0.000
160	Z	199	ASN	0	0.023	0.010	27.295	0.420	0.420	0.000	0.000	0.000	0.000
161	Z	200	HIS	0	0.066	0.032	28.610	0.345	0.345	0.000	0.000	0.000	0.000
162	Z	201	LYS	1	0.924	0.953	23.424	-13.363	-13.363	0.000	0.000	0.000	0.000
163	Z	202	PRO	0	-0.009	0.006	26.948	0.100	0.100	0.000	0.000	0.000	0.000
164	Z	203	SER	0	-0.019	-0.013	28.284	-0.159	-0.159	0.000	0.000	0.000	0.000
165	Z	204	ASN	0	-0.061	-0.027	29.090	-0.003	-0.003	0.000	0.000	0.000	0.000
166	Z	205	THR	0	-0.007	0.007	30.815	-0.190	-0.190	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(Z:1:GLU)