FMO DATABASE

FMODB ID: 17K2Z

Calculation Name: 4H32-F-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 4H32

Chain ID: F

ChEMBL ID:

UniProt ID: H6QM93

Base Structure: X-ray

Registration Date: 2023-09-19

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

DOI:

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	170
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1458383.277058
FMO2-HF: Nuclear repulsion	1388436.205522
FMO2-HF: Total energy	-69947.071536
FMO2-MP2: Total energy	-70148.668939

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(F:335:ALA)

Summations of interaction energy for fragment #1(F:335:ALA)

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.
-16.944	-13.521	9.44	-5.259	-7.605	0.015

Interaction energy analysis for fragmet #1(F:335:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.021

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	F	337	PHE	0	-0.072	-0.034	3.867	-2.474	-0.886	-0.006	-0.739	-0.843	-0.001
4	F	338	ILE	0	0.055	0.047	5.864	-0.199	-0.199	0.000	0.000	0.000	0.000
5	F	339	GLU	-1	-0.888	-0.945	9.011	0.009	0.009	0.000	0.000	0.000	0.000
6	F	340	GLY	0	-0.030	-0.031	8.052	-0.217	-0.217	0.000	0.000	0.000	0.000
7	F	341	GLY	0	-0.005	0.005	7.608	0.320	0.320	0.000	0.000	0.000	0.000
8	F	342	TRP	0	0.001	-0.013	2.561	1.246	2.067	1.649	-0.664	-1.806	0.001
9	F	343	GLN	0	0.000	-0.002	5.649	0.028	0.028	0.000	0.000	0.000	0.000
10	F	344	GLY	0	0.003	-0.006	7.000	-0.223	-0.223	0.000	0.000	0.000	0.000
11	F	345	MET	0	-0.072	-0.008	7.624	0.289	0.289	0.000	0.000	0.000	0.000
12	F	346	ILE	0	-0.008	-0.016	8.312	-0.151	-0.151	0.000	0.000	0.000	0.000
13	F	347	ASP	-1	-0.842	-0.921	12.061	0.613	0.613	0.000	0.000	0.000	0.000
14	F	348	GLY	0	-0.044	-0.023	14.078	-0.052	-0.052	0.000	0.000	0.000	0.000
15	F	349	TRP	0	-0.015	-0.005	13.957	0.029	0.029	0.000	0.000	0.000	0.000
16	F	350	TYR	0	0.029	-0.012	12.547	0.052	0.052	0.000	0.000	0.000	0.000
17	F	351	GLY	0	-0.014	-0.012	11.064	-0.099	-0.099	0.000	0.000	0.000	0.000
18	F	352	TYR	0	-0.020	-0.020	9.106	0.063	0.063	0.000	0.000	0.000	0.000
19	F	353	HIS	0	-0.036	-0.021	2.226	-9.281	-9.514	5.529	-2.324	-2.972	0.020
20	F	354	HIS	0	0.035	0.033	6.485	-0.275	-0.275	0.000	0.000	0.000	0.000
21	F	355	GLU	-1	-0.797	-0.890	4.780	-0.966	-0.812	-0.001	-0.010	-0.143	0.000
22	F	356	ASN	0	-0.028	-0.021	7.848	-0.098	-0.098	0.000	0.000	0.000	0.000
23	F	357	GLN	0	-0.018	-0.007	11.606	-0.074	-0.074	0.000	0.000	0.000	0.000
24	F	358	GLU	-1	-0.843	-0.927	14.132	0.156	0.156	0.000	0.000	0.000	0.000
25	F	359	GLY	0	-0.018	0.001	11.242	-0.018	-0.018	0.000	0.000	0.000	0.000
26	F	360	SER	0	-0.026	-0.036	5.837	-0.014	-0.014	0.000	0.000	0.000	0.000
27	F	361	GLY	0	-0.020	-0.008	7.238	-0.176	-0.176	0.000	0.000	0.000	0.000
28	F	362	TYR	0	0.010	0.000	2.201	-4.896	-3.803	2.269	-1.522	-1.841	-0.005
29	F	363	ALA	0	0.001	-0.007	7.872	-0.451	-0.451	0.000	0.000	0.000	0.000
30	F	364	ALA	0	0.017	0.019	11.349	0.091	0.091	0.000	0.000	0.000	0.000
31	F	365	ASP	-1	-0.768	-0.880	13.138	0.420	0.420	0.000	0.000	0.000	0.000
32	F	366	LYS	1	0.901	0.925	15.793	-0.578	-0.578	0.000	0.000	0.000	0.000
33	F	367	GLU	-1	-0.829	-0.890	18.662	0.277	0.277	0.000	0.000	0.000	0.000
34	F	368	ALA	0	0.014	0.008	17.575	-0.039	-0.039	0.000	0.000	0.000	0.000
35	F	369	THR	0	-0.024	-0.014	16.556	-0.006	-0.006	0.000	0.000	0.000	0.000
36	F	370	GLN	0	-0.064	-0.038	18.893	-0.016	-0.016	0.000	0.000	0.000	0.000
37	F	371	LYS	1	0.813	0.894	22.477	-0.322	-0.322	0.000	0.000	0.000	0.000
38	F	372	ALA	0	0.026	0.019	20.420	-0.027	-0.027	0.000	0.000	0.000	0.000
39	F	373	VAL	0	0.014	0.005	20.976	-0.024	-0.024	0.000	0.000	0.000	0.000
40	F	374	ASP	-1	-0.856	-0.906	23.450	0.195	0.195	0.000	0.000	0.000	0.000
41	F	375	ALA	0	-0.028	-0.012	25.357	-0.020	-0.020	0.000	0.000	0.000	0.000
42	F	376	ILE	0	0.001	-0.006	22.790	-0.018	-0.018	0.000	0.000	0.000	0.000
43	F	377	THR	0	-0.017	-0.016	26.088	-0.017	-0.017	0.000	0.000	0.000	0.000
44	F	378	ASN	0	-0.046	-0.023	28.476	-0.017	-0.017	0.000	0.000	0.000	0.000
45	F	379	LYS	1	0.843	0.925	26.614	-0.157	-0.157	0.000	0.000	0.000	0.000
46	F	380	VAL	0	0.017	0.002	27.908	-0.012	-0.012	0.000	0.000	0.000	0.000
47	F	381	ASN	0	-0.040	-0.045	30.847	-0.001	-0.001	0.000	0.000	0.000	0.000
48	F	382	SER	0	-0.088	-0.052	33.601	-0.011	-0.011	0.000	0.000	0.000	0.000
49	F	383	ILE	0	-0.047	-0.021	31.218	-0.007	-0.007	0.000	0.000	0.000	0.000
50	F	384	ILE	0	-0.018	0.004	33.101	-0.007	-0.007	0.000	0.000	0.000	0.000
51	F	385	ASP	-1	-0.858	-0.923	36.897	0.092	0.092	0.000	0.000	0.000	0.000
52	F	386	LYS	1	0.878	0.938	38.604	-0.087	-0.087	0.000	0.000	0.000	0.000
53	F	387	MET	0	0.016	0.031	40.773	-0.005	-0.005	0.000	0.000	0.000	0.000
54	F	388	ASN	0	-0.036	-0.018	42.480	0.000	0.000	0.000	0.000	0.000	0.000
55	F	389	SER	0	-0.039	-0.022	45.612	-0.002	-0.002	0.000	0.000	0.000	0.000
56	F	390	GLN	0	-0.004	-0.012	47.565	0.001	0.001	0.000	0.000	0.000	0.000
57	F	391	PHE	0	-0.018	-0.003	51.173	0.000	0.000	0.000	0.000	0.000	0.000
58	F	392	GLU	-1	-0.891	-0.933	51.815	0.034	0.034	0.000	0.000	0.000	0.000
59	F	393	SER	0	-0.049	-0.038	54.332	0.000	0.000	0.000	0.000	0.000	0.000
60	F	394	ASN	0	-0.014	-0.007	53.158	-0.001	-0.001	0.000	0.000	0.000	0.000
61	F	395	ILE	0	-0.023	-0.012	56.363	0.000	0.000	0.000	0.000	0.000	0.000
62	F	396	LYS	1	0.798	0.881	55.588	-0.021	-0.021	0.000	0.000	0.000	0.000
63	F	397	GLU	-1	-1.012	-0.979	59.924	0.017	0.017	0.000	0.000	0.000	0.000
64	F	398	PHE	0	0.070	0.011	62.642	0.000	0.000	0.000	0.000	0.000	0.000
65	F	399	ASN	0	-0.054	-0.021	65.972	-0.001	-0.001	0.000	0.000	0.000	0.000
66	F	400	ARG	1	0.930	0.944	68.241	-0.011	-0.011	0.000	0.000	0.000	0.000
67	F	401	LEU	0	0.000	0.005	70.138	0.000	0.000	0.000	0.000	0.000	0.000
68	F	402	GLU	-1	-0.771	-0.870	67.646	0.015	0.015	0.000	0.000	0.000	0.000
69	F	403	LEU	0	0.024	0.008	66.873	0.001	0.001	0.000	0.000	0.000	0.000
70	F	404	ARG	1	0.890	0.946	65.188	-0.015	-0.015	0.000	0.000	0.000	0.000
71	F	405	ILE	0	0.002	-0.001	64.661	0.000	0.000	0.000	0.000	0.000	0.000
72	F	406	GLN	0	0.021	0.006	62.556	0.001	0.001	0.000	0.000	0.000	0.000
73	F	407	HIS	0	-0.004	-0.001	60.932	0.000	0.000	0.000	0.000	0.000	0.000
74	F	408	LEU	0	-0.060	-0.032	60.462	0.000	0.000	0.000	0.000	0.000	0.000
75	F	409	SER	0	0.067	0.032	58.418	0.001	0.001	0.000	0.000	0.000	0.000
76	F	410	ASP	-1	-0.794	-0.884	56.910	0.020	0.020	0.000	0.000	0.000	0.000
77	F	411	ARG	1	0.877	0.940	55.707	-0.019	-0.019	0.000	0.000	0.000	0.000
78	F	412	VAL	0	-0.059	-0.032	55.144	0.000	0.000	0.000	0.000	0.000	0.000
79	F	413	ASP	-1	-0.786	-0.890	52.941	0.026	0.026	0.000	0.000	0.000	0.000
80	F	414	ASP	-1	-0.895	-0.948	51.162	0.022	0.022	0.000	0.000	0.000	0.000
81	F	415	ALA	0	-0.050	-0.022	50.137	0.001	0.001	0.000	0.000	0.000	0.000
82	F	416	LEU	0	0.003	-0.012	49.375	0.001	0.001	0.000	0.000	0.000	0.000
83	F	417	LEU	0	0.009	0.019	45.561	0.002	0.002	0.000	0.000	0.000	0.000
84	F	418	ASP	-1	-0.876	-0.926	45.406	0.026	0.026	0.000	0.000	0.000	0.000
85	F	419	ILE	0	-0.069	-0.036	44.715	0.002	0.002	0.000	0.000	0.000	0.000
86	F	420	TRP	0	0.015	0.001	42.274	0.004	0.004	0.000	0.000	0.000	0.000
87	F	421	SER	0	-0.021	-0.008	41.138	0.004	0.004	0.000	0.000	0.000	0.000
88	F	422	TYR	0	-0.016	-0.007	39.857	0.002	0.002	0.000	0.000	0.000	0.000
89	F	423	ASN	0	-0.033	-0.032	39.343	0.002	0.002	0.000	0.000	0.000	0.000
90	F	424	THR	0	-0.027	-0.019	36.433	0.005	0.005	0.000	0.000	0.000	0.000
91	F	425	GLU	-1	-0.926	-0.963	35.023	0.049	0.049	0.000	0.000	0.000	0.000
92	F	426	LEU	0	-0.016	-0.006	34.090	0.003	0.003	0.000	0.000	0.000	0.000
93	F	427	LEU	0	-0.011	0.002	33.858	0.004	0.004	0.000	0.000	0.000	0.000
94	F	428	VAL	0	0.009	0.001	30.400	0.008	0.008	0.000	0.000	0.000	0.000
95	F	429	LEU	0	-0.006	0.002	29.706	0.007	0.007	0.000	0.000	0.000	0.000
96	F	430	LEU	0	0.028	0.022	28.870	0.006	0.006	0.000	0.000	0.000	0.000
97	F	431	GLU	-1	-0.775	-0.877	28.970	0.120	0.120	0.000	0.000	0.000	0.000
98	F	432	ASN	0	-0.066	-0.016	25.431	0.025	0.025	0.000	0.000	0.000	0.000
99	F	433	GLU	-1	-0.903	-0.944	24.325	0.084	0.084	0.000	0.000	0.000	0.000
100	F	434	ARG	1	0.856	0.900	24.367	-0.093	-0.093	0.000	0.000	0.000	0.000
101	F	435	THR	0	-0.089	-0.070	22.032	0.013	0.013	0.000	0.000	0.000	0.000
102	F	436	LEU	0	-0.022	-0.011	19.274	0.030	0.030	0.000	0.000	0.000	0.000
103	F	437	ASP	-1	-0.834	-0.910	19.489	0.155	0.155	0.000	0.000	0.000	0.000
104	F	438	PHE	0	-0.082	-0.033	21.106	0.018	0.018	0.000	0.000	0.000	0.000
105	F	439	HIS	0	0.020	0.028	16.472	0.060	0.060	0.000	0.000	0.000	0.000
106	F	440	ASP	-1	-0.850	-0.921	16.078	0.317	0.317	0.000	0.000	0.000	0.000
107	F	441	ALA	0	-0.027	-0.016	17.101	0.021	0.021	0.000	0.000	0.000	0.000
108	F	442	ASN	0	-0.050	-0.028	18.107	-0.006	-0.006	0.000	0.000	0.000	0.000
109	F	443	VAL	0	0.006	-0.001	12.593	0.046	0.046	0.000	0.000	0.000	0.000
110	F	444	LYS	1	0.903	0.952	14.612	-0.148	-0.148	0.000	0.000	0.000	0.000
111	F	445	ASN	0	-0.015	-0.023	16.580	-0.024	-0.024	0.000	0.000	0.000	0.000
112	F	446	LEU	0	-0.062	-0.020	12.670	-0.031	-0.031	0.000	0.000	0.000	0.000
113	F	447	PHE	0	0.005	0.017	12.673	0.020	0.020	0.000	0.000	0.000	0.000
114	F	448	GLU	-1	-0.814	-0.921	14.831	0.152	0.152	0.000	0.000	0.000	0.000
115	F	449	LYS	1	0.886	0.951	17.884	-0.486	-0.486	0.000	0.000	0.000	0.000
116	F	450	VAL	0	-0.015	0.007	13.313	-0.029	-0.029	0.000	0.000	0.000	0.000
117	F	451	LYS	1	0.884	0.949	16.571	-0.169	-0.169	0.000	0.000	0.000	0.000
118	F	452	ALA	0	-0.020	-0.006	17.928	-0.039	-0.039	0.000	0.000	0.000	0.000
119	F	453	GLN	0	-0.039	-0.020	18.213	-0.045	-0.045	0.000	0.000	0.000	0.000
120	F	454	LEU	0	0.019	0.012	14.363	-0.033	-0.033	0.000	0.000	0.000	0.000
121	F	455	LYS	1	0.810	0.895	19.029	-0.166	-0.166	0.000	0.000	0.000	0.000
122	F	456	ASP	-1	-0.768	-0.851	19.556	0.039	0.039	0.000	0.000	0.000	0.000
123	F	457	ASN	0	0.006	-0.009	19.767	-0.034	-0.034	0.000	0.000	0.000	0.000
124	F	458	ALA	0	-0.009	-0.001	14.879	0.003	0.003	0.000	0.000	0.000	0.000
125	F	459	ILE	0	-0.026	-0.003	15.395	0.004	0.004	0.000	0.000	0.000	0.000
126	F	460	ASP	-1	-0.833	-0.920	14.104	0.052	0.052	0.000	0.000	0.000	0.000
127	F	461	GLU	-1	-0.902	-0.966	9.390	-0.499	-0.499	0.000	0.000	0.000	0.000
128	F	462	GLY	0	-0.033	0.001	12.370	-0.099	-0.099	0.000	0.000	0.000	0.000
129	F	463	ASN	0	-0.011	-0.025	6.572	0.350	0.350	0.000	0.000	0.000	0.000
130	F	464	GLY	0	0.021	0.005	8.482	0.106	0.106	0.000	0.000	0.000	0.000
131	F	465	CYS	0	-0.111	-0.031	6.881	0.324	0.324	0.000	0.000	0.000	0.000
132	F	466	PHE	0	0.029	-0.006	9.440	-0.073	-0.073	0.000	0.000	0.000	0.000
133	F	467	LEU	0	0.049	0.042	11.346	0.041	0.041	0.000	0.000	0.000	0.000
134	F	468	LEU	0	-0.002	-0.017	12.450	0.026	0.026	0.000	0.000	0.000	0.000
135	F	469	LEU	0	-0.068	-0.020	14.719	-0.039	-0.039	0.000	0.000	0.000	0.000
136	F	470	HIS	0	0.029	0.019	17.162	0.014	0.014	0.000	0.000	0.000	0.000
137	F	471	LYS	1	0.865	0.917	16.687	0.056	0.056	0.000	0.000	0.000	0.000
138	F	472	CYS	0	-0.022	0.012	14.540	0.036	0.036	0.000	0.000	0.000	0.000
139	F	473	ASN	0	0.032	0.020	14.598	0.039	0.039	0.000	0.000	0.000	0.000
140	F	474	ASN	0	0.024	-0.007	13.681	0.096	0.096	0.000	0.000	0.000	0.000
141	F	475	SER	0	0.017	0.014	15.708	0.029	0.029	0.000	0.000	0.000	0.000
142	F	477	MET	0	-0.018	-0.007	10.821	0.061	0.061	0.000	0.000	0.000	0.000
143	F	478	ASP	-1	-0.867	-0.933	14.535	0.591	0.591	0.000	0.000	0.000	0.000
144	F	479	ASP	-1	-0.865	-0.910	16.697	0.231	0.231	0.000	0.000	0.000	0.000
145	F	480	ILE	0	-0.023	-0.009	14.303	-0.006	-0.006	0.000	0.000	0.000	0.000
146	F	481	LYS	1	0.755	0.880	11.667	-0.788	-0.788	0.000	0.000	0.000	0.000
147	F	482	ASN	0	-0.078	-0.044	16.257	-0.005	-0.005	0.000	0.000	0.000	0.000
148	F	483	GLY	0	-0.030	0.002	19.429	-0.026	-0.026	0.000	0.000	0.000	0.000
149	F	484	THR	0	-0.090	-0.069	21.113	-0.028	-0.028	0.000	0.000	0.000	0.000
150	F	485	TYR	0	-0.011	-0.004	18.708	-0.030	-0.030	0.000	0.000	0.000	0.000
151	F	486	LYS	1	0.842	0.918	21.176	-0.131	-0.131	0.000	0.000	0.000	0.000
152	F	487	TYR	0	-0.048	-0.054	22.848	-0.004	-0.004	0.000	0.000	0.000	0.000
153	F	488	MET	0	-0.001	-0.005	24.085	-0.012	-0.012	0.000	0.000	0.000	0.000
154	F	489	ASP	-1	-0.839	-0.918	24.980	0.094	0.094	0.000	0.000	0.000	0.000
155	F	490	TYR	0	0.059	0.035	21.097	-0.001	-0.001	0.000	0.000	0.000	0.000
156	F	491	ARG	1	0.777	0.886	23.217	-0.055	-0.055	0.000	0.000	0.000	0.000
157	F	492	GLU	-1	-0.921	-0.971	25.414	0.015	0.015	0.000	0.000	0.000	0.000
158	F	493	GLU	-1	-0.868	-0.928	21.137	0.021	0.021	0.000	0.000	0.000	0.000
159	F	494	SER	0	0.019	0.000	21.227	-0.011	-0.011	0.000	0.000	0.000	0.000
160	F	495	HIS	0	-0.065	-0.025	22.366	-0.011	-0.011	0.000	0.000	0.000	0.000
161	F	496	ILE	0	-0.009	-0.007	25.516	-0.011	-0.011	0.000	0.000	0.000	0.000
162	F	497	GLU	-1	-0.783	-0.870	19.432	-0.104	-0.104	0.000	0.000	0.000	0.000
163	F	498	LYS	1	0.841	0.902	22.207	0.034	0.034	0.000	0.000	0.000	0.000
164	F	499	GLN	0	-0.005	-0.008	23.078	-0.006	-0.006	0.000	0.000	0.000	0.000
165	F	500	LYS	1	0.758	0.860	21.145	0.091	0.091	0.000	0.000	0.000	0.000
166	F	501	ILE	0	-0.047	-0.015	19.031	-0.012	-0.012	0.000	0.000	0.000	0.000
167	F	502	ASP	-1	-0.857	-0.914	23.170	-0.072	-0.072	0.000	0.000	0.000	0.000
168	F	503	GLY	0	-0.010	0.011	26.082	-0.001	-0.001	0.000	0.000	0.000	0.000
169	F	504	VAL	0	-0.040	-0.030	28.213	0.009	0.009	0.000	0.000	0.000	0.000
170	F	505	GLU	-1	-1.017	-0.995	30.872	-0.079	-0.079	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:335:ALA)