FMO DATABASE

FMODB ID: V5L81

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	OptHSide
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	-1453069.554877
FMO2-HF: Nuclear repulsion	1383123.015081
FMO2-HF: Total energy	-69946.539796
FMO2-MP2: Total energy	-70148.132809

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.
-16.691	-12.666	6.609	-4.445	-6.188	0.011

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 : -0.004 / q_NPA : -0.016

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	-0.064	-0.048	3.792	-2.610	-0.876	-0.026	-0.782	-0.925	-0.002
4	F	338	ILE	0	0.035	0.057	5.739	-0.274	-0.274	0.000	0.000	0.000	0.000
5	F	339	GLU	-1	-0.930	-0.962	8.768	0.028	0.028	0.000	0.000	0.000	0.000
6	F	340	GLY	0	-0.006	-0.018	7.932	-0.216	-0.216	0.000	0.000	0.000	0.000
7	F	341	GLY	0	-0.021	-0.004	7.987	0.262	0.262	0.000	0.000	0.000	0.000
8	F	342	TRP	0	-0.005	-0.021	2.565	-0.774	0.445	0.633	-0.633	-1.218	0.003
9	F	343	GLN	0	0.003	0.002	6.290	-0.014	-0.014	0.000	0.000	0.000	0.000
10	F	344	GLY	0	-0.014	-0.013	7.211	-0.136	-0.136	0.000	0.000	0.000	0.000
11	F	345	MET	0	-0.056	0.009	8.148	0.293	0.293	0.000	0.000	0.000	0.000
12	F	346	ILE	0	-0.005	-0.018	9.016	-0.100	-0.100	0.000	0.000	0.000	0.000
13	F	347	ASP	-1	-0.903	-0.951	12.705	0.498	0.498	0.000	0.000	0.000	0.000
14	F	348	GLY	0	-0.059	-0.044	14.353	-0.038	-0.038	0.000	0.000	0.000	0.000
15	F	349	TRP	0	-0.031	-0.006	13.747	0.039	0.039	0.000	0.000	0.000	0.000
16	F	350	TYR	0	0.036	-0.008	12.665	0.071	0.071	0.000	0.000	0.000	0.000
17	F	351	GLY	0	0.013	-0.002	10.993	-0.118	-0.118	0.000	0.000	0.000	0.000
18	F	352	TYR	0	-0.072	-0.054	9.144	0.077	0.077	0.000	0.000	0.000	0.000
19	F	353	HIS	0	-0.013	-0.014	2.239	-9.099	-9.776	5.631	-2.185	-2.769	0.017
20	F	354	HIS	0	0.016	0.021	6.611	-0.079	-0.079	0.000	0.000	0.000	0.000
21	F	355	GLU	-1	-0.883	-0.953	3.995	-1.578	-1.200	0.000	-0.124	-0.254	-0.001
22	F	356	ASN	0	-0.048	-0.034	7.826	-0.089	-0.089	0.000	0.000	0.000	0.000
23	F	357	GLN	0	-0.023	-0.011	11.457	-0.060	-0.060	0.000	0.000	0.000	0.000
24	F	358	GLU	-1	-0.837	-0.920	14.328	0.123	0.123	0.000	0.000	0.000	0.000
25	F	359	GLY	0	-0.010	0.007	11.215	-0.023	-0.023	0.000	0.000	0.000	0.000
26	F	360	SER	0	0.012	0.011	6.045	-0.009	-0.009	0.000	0.000	0.000	0.000
27	F	361	GLY	0	-0.017	-0.011	7.266	-0.177	-0.177	0.000	0.000	0.000	0.000
28	F	362	TYR	0	0.030	0.013	2.654	-2.370	-0.999	0.371	-0.721	-1.022	-0.006
29	F	363	ALA	0	-0.005	-0.009	8.164	-0.367	-0.367	0.000	0.000	0.000	0.000
30	F	364	ALA	0	0.044	0.034	11.551	0.122	0.122	0.000	0.000	0.000	0.000
31	F	365	ASP	-1	-0.807	-0.901	13.417	0.392	0.392	0.000	0.000	0.000	0.000
32	F	366	LYS	1	0.980	0.967	16.039	-0.429	-0.429	0.000	0.000	0.000	0.000
33	F	367	GLU	-1	-0.821	-0.897	18.912	0.254	0.254	0.000	0.000	0.000	0.000
34	F	368	ALA	0	0.030	0.023	18.103	-0.035	-0.035	0.000	0.000	0.000	0.000
35	F	369	THR	0	-0.012	-0.008	16.835	0.000	0.000	0.000	0.000	0.000	0.000
36	F	370	GLN	0	-0.056	-0.041	19.163	-0.015	-0.015	0.000	0.000	0.000	0.000
37	F	371	LYS	1	0.818	0.909	22.600	-0.285	-0.285	0.000	0.000	0.000	0.000
38	F	372	ALA	0	0.025	0.018	20.522	-0.023	-0.023	0.000	0.000	0.000	0.000
39	F	373	VAL	0	0.011	0.003	21.027	-0.022	-0.022	0.000	0.000	0.000	0.000
40	F	374	ASP	-1	-0.872	-0.907	23.538	0.165	0.165	0.000	0.000	0.000	0.000
41	F	375	ALA	0	-0.035	-0.019	25.529	-0.017	-0.017	0.000	0.000	0.000	0.000
42	F	376	ILE	0	-0.010	-0.012	22.915	-0.016	-0.016	0.000	0.000	0.000	0.000
43	F	377	THR	0	-0.008	-0.017	26.224	-0.016	-0.016	0.000	0.000	0.000	0.000
44	F	378	ASN	0	-0.040	-0.018	28.480	-0.015	-0.015	0.000	0.000	0.000	0.000
45	F	379	LYS	1	0.858	0.928	26.873	-0.141	-0.141	0.000	0.000	0.000	0.000
46	F	380	VAL	0	0.006	-0.004	27.963	-0.010	-0.010	0.000	0.000	0.000	0.000
47	F	381	ASN	0	-0.036	-0.037	30.961	-0.002	-0.002	0.000	0.000	0.000	0.000
48	F	382	SER	0	-0.074	-0.022	33.764	-0.009	-0.009	0.000	0.000	0.000	0.000
49	F	383	ILE	0	-0.044	-0.032	31.667	-0.006	-0.006	0.000	0.000	0.000	0.000
50	F	384	ILE	0	-0.025	-0.003	33.120	-0.006	-0.006	0.000	0.000	0.000	0.000
51	F	385	ASP	-1	-0.849	-0.927	36.847	0.078	0.078	0.000	0.000	0.000	0.000
52	F	386	LYS	1	0.838	0.923	39.012	-0.075	-0.075	0.000	0.000	0.000	0.000
53	F	387	MET	0	-0.015	0.018	41.006	-0.004	-0.004	0.000	0.000	0.000	0.000
54	F	388	ASN	0	-0.019	-0.025	42.749	0.001	0.001	0.000	0.000	0.000	0.000
55	F	389	SER	0	-0.011	-0.004	45.963	-0.001	-0.001	0.000	0.000	0.000	0.000
56	F	390	GLN	0	0.004	0.003	48.172	0.001	0.001	0.000	0.000	0.000	0.000
57	F	391	PHE	0	-0.022	-0.003	51.565	0.000	0.000	0.000	0.000	0.000	0.000
58	F	392	GLU	-1	-0.889	-0.937	51.974	0.030	0.030	0.000	0.000	0.000	0.000
59	F	393	SER	0	-0.050	-0.023	54.508	0.000	0.000	0.000	0.000	0.000	0.000
60	F	394	ASN	0	-0.021	-0.025	53.711	0.000	0.000	0.000	0.000	0.000	0.000
61	F	395	ILE	0	-0.014	-0.011	56.765	0.000	0.000	0.000	0.000	0.000	0.000
62	F	396	LYS	1	0.842	0.911	55.845	-0.019	-0.019	0.000	0.000	0.000	0.000
63	F	397	GLU	-1	-1.023	-0.995	60.144	0.015	0.015	0.000	0.000	0.000	0.000
64	F	398	PHE	0	0.052	0.015	62.753	0.000	0.000	0.000	0.000	0.000	0.000
65	F	399	ASN	0	-0.101	-0.055	65.918	-0.001	-0.001	0.000	0.000	0.000	0.000
66	F	400	ARG	1	0.980	0.990	68.022	-0.009	-0.009	0.000	0.000	0.000	0.000
67	F	401	LEU	0	0.033	0.011	70.160	0.000	0.000	0.000	0.000	0.000	0.000
68	F	402	GLU	-1	-0.748	-0.864	68.070	0.013	0.013	0.000	0.000	0.000	0.000
69	F	403	LEU	0	-0.037	-0.027	67.291	0.000	0.000	0.000	0.000	0.000	0.000
70	F	404	ARG	1	0.899	0.963	65.186	-0.014	-0.014	0.000	0.000	0.000	0.000
71	F	405	ILE	0	0.016	-0.018	64.928	0.000	0.000	0.000	0.000	0.000	0.000
72	F	406	GLN	0	0.043	0.024	62.274	0.001	0.001	0.000	0.000	0.000	0.000
73	F	407	HIS	0	-0.013	0.009	61.185	0.000	0.000	0.000	0.000	0.000	0.000
74	F	408	LEU	0	-0.064	-0.040	60.751	0.000	0.000	0.000	0.000	0.000	0.000
75	F	409	SER	0	0.050	0.018	59.069	0.001	0.001	0.000	0.000	0.000	0.000
76	F	410	ASP	-1	-0.814	-0.889	57.392	0.018	0.018	0.000	0.000	0.000	0.000
77	F	411	ARG	1	0.931	0.963	56.134	-0.018	-0.018	0.000	0.000	0.000	0.000
78	F	412	VAL	0	-0.044	-0.029	55.337	0.001	0.001	0.000	0.000	0.000	0.000
79	F	413	ASP	-1	-0.815	-0.898	53.355	0.023	0.023	0.000	0.000	0.000	0.000
80	F	414	ASP	-1	-0.895	-0.951	51.542	0.020	0.020	0.000	0.000	0.000	0.000
81	F	415	ALA	0	-0.070	-0.033	50.604	0.001	0.001	0.000	0.000	0.000	0.000
82	F	416	LEU	0	-0.010	-0.022	49.844	0.001	0.001	0.000	0.000	0.000	0.000
83	F	417	LEU	0	0.000	0.013	45.946	0.002	0.002	0.000	0.000	0.000	0.000
84	F	418	ASP	-1	-0.879	-0.930	45.796	0.024	0.024	0.000	0.000	0.000	0.000
85	F	419	ILE	0	-0.079	-0.039	45.140	0.002	0.002	0.000	0.000	0.000	0.000
86	F	420	TRP	0	0.005	-0.005	42.362	0.003	0.003	0.000	0.000	0.000	0.000
87	F	421	SER	0	-0.020	-0.006	41.505	0.003	0.003	0.000	0.000	0.000	0.000
88	F	422	TYR	0	-0.013	0.001	40.136	0.001	0.001	0.000	0.000	0.000	0.000
89	F	423	ASN	0	-0.001	-0.017	39.610	0.001	0.001	0.000	0.000	0.000	0.000
90	F	424	THR	0	-0.026	-0.025	36.666	0.005	0.005	0.000	0.000	0.000	0.000
91	F	425	GLU	-1	-0.935	-0.960	35.326	0.044	0.044	0.000	0.000	0.000	0.000
92	F	426	LEU	0	-0.008	-0.005	34.408	0.004	0.004	0.000	0.000	0.000	0.000
93	F	427	LEU	0	-0.023	0.000	34.134	0.004	0.004	0.000	0.000	0.000	0.000
94	F	428	VAL	0	-0.005	-0.010	30.498	0.007	0.007	0.000	0.000	0.000	0.000
95	F	429	LEU	0	-0.027	-0.016	29.943	0.006	0.006	0.000	0.000	0.000	0.000
96	F	430	LEU	0	0.024	0.022	29.292	0.005	0.005	0.000	0.000	0.000	0.000
97	F	431	GLU	-1	-0.770	-0.882	29.169	0.111	0.111	0.000	0.000	0.000	0.000
98	F	432	ASN	0	-0.029	0.003	25.751	0.022	0.022	0.000	0.000	0.000	0.000
99	F	433	GLU	-1	-0.934	-0.954	24.489	0.082	0.082	0.000	0.000	0.000	0.000
100	F	434	ARG	1	0.907	0.930	24.598	-0.091	-0.091	0.000	0.000	0.000	0.000
101	F	435	THR	0	-0.059	-0.045	22.441	0.016	0.016	0.000	0.000	0.000	0.000
102	F	436	LEU	0	-0.034	-0.021	19.633	0.026	0.026	0.000	0.000	0.000	0.000
103	F	437	ASP	-1	-0.840	-0.905	19.815	0.146	0.146	0.000	0.000	0.000	0.000
104	F	438	PHE	0	-0.121	-0.059	21.570	0.017	0.017	0.000	0.000	0.000	0.000
105	F	439	HIS	0	-0.001	0.013	17.075	0.048	0.048	0.000	0.000	0.000	0.000
106	F	440	ASP	-1	-0.854	-0.918	16.607	0.302	0.302	0.000	0.000	0.000	0.000
107	F	441	ALA	0	-0.030	-0.021	17.434	0.027	0.027	0.000	0.000	0.000	0.000
108	F	442	ASN	0	-0.047	-0.031	18.382	-0.007	-0.007	0.000	0.000	0.000	0.000
109	F	443	VAL	0	0.006	0.002	12.942	0.041	0.041	0.000	0.000	0.000	0.000
110	F	444	LYS	1	0.913	0.963	14.761	-0.161	-0.161	0.000	0.000	0.000	0.000
111	F	445	ASN	0	-0.008	-0.019	16.923	-0.026	-0.026	0.000	0.000	0.000	0.000
112	F	446	LEU	0	-0.060	-0.017	13.336	-0.031	-0.031	0.000	0.000	0.000	0.000
113	F	447	PHE	0	0.025	0.017	12.763	0.012	0.012	0.000	0.000	0.000	0.000
114	F	448	GLU	-1	-0.820	-0.923	15.291	0.173	0.173	0.000	0.000	0.000	0.000
115	F	449	LYS	1	0.907	0.961	18.562	-0.403	-0.403	0.000	0.000	0.000	0.000
116	F	450	VAL	0	-0.027	-0.008	13.990	-0.033	-0.033	0.000	0.000	0.000	0.000
117	F	451	LYS	1	0.922	0.969	17.202	-0.178	-0.178	0.000	0.000	0.000	0.000
118	F	452	ALA	0	-0.029	-0.008	18.409	-0.036	-0.036	0.000	0.000	0.000	0.000
119	F	453	GLN	0	-0.037	-0.010	18.759	-0.044	-0.044	0.000	0.000	0.000	0.000
120	F	454	LEU	0	0.032	0.023	14.939	-0.030	-0.030	0.000	0.000	0.000	0.000
121	F	455	LYS	1	0.801	0.887	19.522	-0.167	-0.167	0.000	0.000	0.000	0.000
122	F	456	ASP	-1	-0.783	-0.862	20.140	0.051	0.051	0.000	0.000	0.000	0.000
123	F	457	ASN	0	-0.006	-0.003	20.271	-0.034	-0.034	0.000	0.000	0.000	0.000
124	F	458	ALA	0	0.006	-0.001	15.302	0.004	0.004	0.000	0.000	0.000	0.000
125	F	459	ILE	0	-0.016	-0.010	15.475	0.000	0.000	0.000	0.000	0.000	0.000
126	F	460	ASP	-1	-0.846	-0.915	14.004	0.110	0.110	0.000	0.000	0.000	0.000
127	F	461	GLU	-1	-0.925	-0.969	9.274	-0.439	-0.439	0.000	0.000	0.000	0.000
128	F	462	GLY	0	-0.056	-0.019	12.673	-0.073	-0.073	0.000	0.000	0.000	0.000
129	F	463	ASN	0	0.009	-0.012	6.946	0.186	0.186	0.000	0.000	0.000	0.000
130	F	464	GLY	0	0.048	0.021	8.764	0.101	0.101	0.000	0.000	0.000	0.000
131	F	465	CYS	0	-0.098	-0.012	6.825	0.377	0.377	0.000	0.000	0.000	0.000
132	F	466	PHE	0	-0.002	-0.020	9.429	-0.135	-0.135	0.000	0.000	0.000	0.000
133	F	467	LEU	0	0.059	0.039	11.169	0.041	0.041	0.000	0.000	0.000	0.000
134	F	468	LEU	0	-0.002	-0.007	12.350	0.017	0.017	0.000	0.000	0.000	0.000
135	F	469	LEU	0	-0.053	-0.021	14.797	-0.040	-0.040	0.000	0.000	0.000	0.000
136	F	470	HIS	0	0.039	0.019	17.185	0.011	0.011	0.000	0.000	0.000	0.000
137	F	471	LYS	1	0.866	0.933	16.446	0.040	0.040	0.000	0.000	0.000	0.000
138	F	472	CYS	0	-0.023	0.009	14.448	0.035	0.035	0.000	0.000	0.000	0.000
139	F	473	ASN	0	0.047	0.026	14.807	0.036	0.036	0.000	0.000	0.000	0.000
140	F	474	ASN	0	0.051	-0.006	14.076	0.071	0.071	0.000	0.000	0.000	0.000
141	F	475	SER	0	-0.016	0.000	16.281	0.024	0.024	0.000	0.000	0.000	0.000
142	F	477	MET	0	-0.011	-0.005	11.090	0.061	0.061	0.000	0.000	0.000	0.000
143	F	478	ASP	-1	-0.861	-0.935	15.157	0.484	0.484	0.000	0.000	0.000	0.000
144	F	479	ASP	-1	-0.852	-0.901	17.553	0.203	0.203	0.000	0.000	0.000	0.000
145	F	480	ILE	0	-0.035	-0.009	14.989	-0.009	-0.009	0.000	0.000	0.000	0.000
146	F	481	LYS	1	0.791	0.896	12.159	-0.666	-0.666	0.000	0.000	0.000	0.000
147	F	482	ASN	0	-0.060	-0.024	16.590	-0.001	-0.001	0.000	0.000	0.000	0.000
148	F	483	GLY	0	-0.054	-0.019	19.650	-0.031	-0.031	0.000	0.000	0.000	0.000
149	F	484	THR	0	-0.083	-0.070	21.460	-0.024	-0.024	0.000	0.000	0.000	0.000
150	F	485	TYR	0	-0.016	0.000	19.123	-0.027	-0.027	0.000	0.000	0.000	0.000
151	F	486	LYS	1	0.909	0.965	21.771	-0.123	-0.123	0.000	0.000	0.000	0.000
152	F	487	TYR	0	-0.045	-0.059	23.358	-0.005	-0.005	0.000	0.000	0.000	0.000
153	F	488	MET	0	0.009	-0.017	24.685	-0.008	-0.008	0.000	0.000	0.000	0.000
154	F	489	ASP	-1	-0.916	-0.954	25.092	0.091	0.091	0.000	0.000	0.000	0.000
155	F	490	TYR	0	0.049	0.025	21.334	0.000	0.000	0.000	0.000	0.000	0.000
156	F	491	ARG	1	0.784	0.901	23.568	-0.060	-0.060	0.000	0.000	0.000	0.000
157	F	492	GLU	-1	-0.917	-0.967	25.654	0.018	0.018	0.000	0.000	0.000	0.000
158	F	493	GLU	-1	-0.868	-0.943	21.336	0.030	0.030	0.000	0.000	0.000	0.000
159	F	494	SER	0	0.016	0.003	21.520	-0.007	-0.007	0.000	0.000	0.000	0.000
160	F	495	HIS	0	-0.092	-0.044	22.686	-0.010	-0.010	0.000	0.000	0.000	0.000
161	F	496	ILE	0	-0.017	-0.012	25.735	-0.010	-0.010	0.000	0.000	0.000	0.000
162	F	497	GLU	-1	-0.772	-0.870	19.544	-0.082	-0.082	0.000	0.000	0.000	0.000
163	F	498	LYS	1	0.836	0.900	22.200	0.019	0.019	0.000	0.000	0.000	0.000
164	F	499	GLN	0	0.007	0.000	23.205	-0.004	-0.004	0.000	0.000	0.000	0.000
165	F	500	LYS	1	0.771	0.875	21.461	0.070	0.070	0.000	0.000	0.000	0.000
166	F	501	ILE	0	-0.035	-0.013	19.070	-0.010	-0.010	0.000	0.000	0.000	0.000
167	F	502	ASP	-1	-0.889	-0.922	23.108	-0.055	-0.055	0.000	0.000	0.000	0.000
168	F	503	GLY	0	-0.014	0.010	26.206	0.003	0.003	0.000	0.000	0.000	0.000
169	F	504	VAL	0	-0.016	-0.017	28.153	0.007	0.007	0.000	0.000	0.000	0.000
170	F	505	GLU	-1	-1.022	-1.001	30.652	-0.064	-0.064	0.000	0.000	0.000	0.000

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