FMO DATABASE

FMODB ID: 4J7YN

Calculation Name: 4BQ6-D-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 4BQ6

Chain ID: D

ChEMBL ID:

UniProt ID: P97798

Base Structure: X-ray

Registration Date: 2023-09-24

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	OptH
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	152
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1428456.928152
FMO2-HF: Nuclear repulsion	1368220.780176
FMO2-HF: Total energy	-60236.147975
FMO2-MP2: Total energy	-60409.335822

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(D:169:PRO)

Summations of interaction energy for fragment #1(D:169:PRO)

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.
-10.391	-8.366	29.059	-15.035	-16.045	-0.064

Interaction energy analysis for fragmet #1(D:169:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : 0.020

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	171	LEU	0	0.000	0.003	3.292	-3.085	0.478	0.035	-1.831	-1.766	0.006
4	D	172	ARG	1	0.845	0.916	5.704	0.490	0.490	0.000	0.000	0.000	0.000
5	D	173	THR	0	-0.014	-0.022	9.165	0.046	0.046	0.000	0.000	0.000	0.000
6	D	174	PHE	0	0.016	-0.004	11.578	0.070	0.070	0.000	0.000	0.000	0.000
7	D	175	LYS	1	0.928	0.970	14.613	0.419	0.419	0.000	0.000	0.000	0.000
8	D	176	ASP	-1	-0.859	-0.908	14.070	-0.253	-0.253	0.000	0.000	0.000	0.000
9	D	177	ASN	0	-0.025	0.007	12.333	-0.023	-0.023	0.000	0.000	0.000	0.000
10	D	178	PHE	0	0.016	-0.001	9.679	-0.074	-0.074	0.000	0.000	0.000	0.000
11	D	179	GLN	0	-0.003	-0.008	7.409	-0.030	-0.030	0.000	0.000	0.000	0.000
12	D	180	THR	0	0.001	0.009	3.965	-0.438	-0.233	0.001	-0.068	-0.139	0.000
13	D	181	CYS	0	-0.063	-0.025	2.958	0.230	1.822	0.056	-0.660	-0.987	0.001
14	D	182	LYS	1	0.989	1.036	1.658	-2.923	-14.669	23.021	-8.201	-3.074	-0.045
15	D	183	VAL	0	-0.010	0.010	2.568	-1.643	-0.480	0.825	-0.525	-1.462	-0.003
16	D	184	GLU	-1	-0.878	-0.940	4.273	-0.237	-0.043	-0.001	-0.031	-0.162	0.000
17	D	185	GLY	0	0.019	0.018	6.080	-0.011	-0.011	0.000	0.000	0.000	0.000
18	D	186	ALA	0	-0.044	-0.033	7.074	-0.160	-0.160	0.000	0.000	0.000	0.000
19	D	187	TRP	0	0.028	-0.002	6.681	-0.120	-0.120	0.000	0.000	0.000	0.000
20	D	188	PRO	0	0.040	0.035	8.765	0.000	0.000	0.000	0.000	0.000	0.000
21	D	189	LEU	0	-0.044	-0.032	5.448	-0.112	-0.112	0.000	0.000	0.000	0.000
22	D	190	ILE	0	-0.023	-0.032	9.475	0.025	0.025	0.000	0.000	0.000	0.000
23	D	191	ASP	-1	-0.875	-0.942	13.170	-0.290	-0.290	0.000	0.000	0.000	0.000
24	D	192	ASN	0	0.071	0.046	16.136	0.027	0.027	0.000	0.000	0.000	0.000
25	D	193	ASN	0	-0.021	-0.032	19.268	0.015	0.015	0.000	0.000	0.000	0.000
26	D	194	TYR	0	-0.004	0.005	21.229	0.022	0.022	0.000	0.000	0.000	0.000
27	D	195	LEU	0	-0.045	-0.026	15.785	0.016	0.016	0.000	0.000	0.000	0.000
28	D	196	SER	0	0.009	0.013	15.647	-0.014	-0.014	0.000	0.000	0.000	0.000
29	D	197	VAL	0	-0.017	-0.005	9.748	0.040	0.040	0.000	0.000	0.000	0.000
30	D	198	GLN	0	0.034	0.013	10.311	-0.106	-0.106	0.000	0.000	0.000	0.000
31	D	199	VAL	0	0.021	0.009	4.732	0.049	0.105	-0.001	-0.001	-0.053	0.000
32	D	200	THR	0	-0.049	-0.022	7.480	-0.074	-0.074	0.000	0.000	0.000	0.000
33	D	201	ASN	0	0.000	0.005	2.961	-1.234	0.681	0.627	-0.770	-1.772	-0.006
34	D	202	VAL	0	0.002	0.000	4.749	-0.155	-0.110	-0.001	-0.006	-0.038	0.000
35	D	203	PRO	0	0.023	0.012	6.127	0.766	0.766	0.000	0.000	0.000	0.000
36	D	204	VAL	0	-0.028	-0.017	7.100	-0.241	-0.241	0.000	0.000	0.000	0.000
37	D	205	VAL	0	-0.008	-0.001	8.944	-0.246	-0.246	0.000	0.000	0.000	0.000
38	D	206	PRO	0	0.024	-0.007	11.788	0.057	0.057	0.000	0.000	0.000	0.000
39	D	207	GLY	0	0.017	0.011	12.896	-0.014	-0.014	0.000	0.000	0.000	0.000
40	D	208	SER	0	-0.035	0.002	9.224	-0.062	-0.062	0.000	0.000	0.000	0.000
41	D	209	SER	0	0.010	-0.006	7.779	0.082	0.082	0.000	0.000	0.000	0.000
42	D	210	ALA	0	0.012	0.015	5.088	-0.015	-0.015	0.000	0.000	0.000	0.000
43	D	211	THR	0	-0.035	-0.058	2.533	-0.394	0.960	2.018	-1.201	-2.171	-0.006
44	D	212	ALA	0	0.010	0.008	2.429	2.653	5.426	2.307	-1.724	-3.355	-0.009
45	D	213	THR	0	0.002	-0.003	3.037	-1.820	-0.958	0.172	-0.003	-1.031	-0.002
46	D	214	ASN	0	0.021	0.000	4.449	-0.027	0.022	0.000	-0.014	-0.035	0.000
47	D	215	LYS	1	0.942	0.981	7.665	-0.026	-0.026	0.000	0.000	0.000	0.000
48	D	216	ILE	0	0.010	0.010	7.647	-0.110	-0.110	0.000	0.000	0.000	0.000
49	D	217	THR	0	-0.006	0.005	10.215	0.058	0.058	0.000	0.000	0.000	0.000
50	D	218	ILE	0	-0.012	0.002	12.672	-0.056	-0.056	0.000	0.000	0.000	0.000
51	D	219	ILE	0	0.003	-0.004	15.023	0.029	0.029	0.000	0.000	0.000	0.000
52	D	220	PHE	0	0.030	0.010	18.022	-0.019	-0.019	0.000	0.000	0.000	0.000
53	D	221	LYS	1	0.925	0.954	19.891	0.209	0.209	0.000	0.000	0.000	0.000
54	D	222	ALA	0	-0.004	0.000	23.165	0.006	0.006	0.000	0.000	0.000	0.000
55	D	223	HIS	0	0.012	0.012	26.714	-0.010	-0.010	0.000	0.000	0.000	0.000
56	D	224	HIS	0	0.046	-0.001	28.529	0.005	0.005	0.000	0.000	0.000	0.000
57	D	225	GLY	0	0.005	0.007	32.307	-0.001	-0.001	0.000	0.000	0.000	0.000
58	D	226	CYS	0	-0.104	-0.030	29.565	0.002	0.002	0.000	0.000	0.000	0.000
59	D	227	THR	0	0.008	-0.034	25.489	0.007	0.007	0.000	0.000	0.000	0.000
60	D	228	ASP	-1	-0.781	-0.867	28.710	-0.051	-0.051	0.000	0.000	0.000	0.000
61	D	229	GLN	0	-0.011	-0.004	23.252	-0.008	-0.008	0.000	0.000	0.000	0.000
62	D	230	LYS	1	0.819	0.938	22.819	0.044	0.044	0.000	0.000	0.000	0.000
63	D	231	VAL	0	0.011	-0.005	18.086	-0.016	-0.016	0.000	0.000	0.000	0.000
64	D	232	TYR	0	-0.007	-0.005	14.535	0.019	0.019	0.000	0.000	0.000	0.000
65	D	233	GLN	0	-0.045	-0.055	14.237	-0.006	-0.006	0.000	0.000	0.000	0.000
66	D	234	ALA	0	0.031	0.048	12.925	0.017	0.017	0.000	0.000	0.000	0.000
67	D	235	VAL	0	-0.011	-0.029	11.891	-0.026	-0.026	0.000	0.000	0.000	0.000
68	D	236	THR	0	-0.037	-0.024	10.314	0.010	0.010	0.000	0.000	0.000	0.000
69	D	237	ASP	-1	-0.807	-0.870	12.594	0.314	0.314	0.000	0.000	0.000	0.000
70	D	238	ASP	-1	-0.925	-0.955	15.452	0.077	0.077	0.000	0.000	0.000	0.000
71	D	239	LEU	0	-0.030	-0.016	13.165	0.000	0.000	0.000	0.000	0.000	0.000
72	D	240	PRO	0	0.072	0.059	17.054	-0.003	-0.003	0.000	0.000	0.000	0.000
73	D	241	ALA	0	0.009	-0.004	19.422	-0.004	-0.004	0.000	0.000	0.000	0.000
74	D	242	ALA	0	-0.009	-0.035	21.414	-0.007	-0.007	0.000	0.000	0.000	0.000
75	D	243	PHE	0	-0.013	-0.011	20.276	0.000	0.000	0.000	0.000	0.000	0.000
76	D	244	VAL	0	0.001	-0.018	19.873	0.008	0.008	0.000	0.000	0.000	0.000
77	D	245	ASP	-1	-0.834	-0.890	22.476	-0.020	-0.020	0.000	0.000	0.000	0.000
78	D	246	GLY	0	-0.013	-0.005	25.173	0.002	0.002	0.000	0.000	0.000	0.000
79	D	247	THR	0	-0.073	-0.040	26.450	0.002	0.002	0.000	0.000	0.000	0.000
80	D	248	THR	0	0.033	-0.006	25.182	-0.001	-0.001	0.000	0.000	0.000	0.000
81	D	249	SER	0	-0.029	-0.036	26.030	0.000	0.000	0.000	0.000	0.000	0.000
82	D	250	GLY	0	-0.014	0.007	27.252	0.000	0.000	0.000	0.000	0.000	0.000
83	D	251	GLY	0	-0.001	-0.011	27.774	0.002	0.002	0.000	0.000	0.000	0.000
84	D	252	ASP	-1	-0.919	-0.958	31.173	-0.027	-0.027	0.000	0.000	0.000	0.000
85	D	253	SER	0	0.007	0.004	32.870	0.000	0.000	0.000	0.000	0.000	0.000
86	D	254	ASP	-1	-0.943	-0.985	34.478	-0.015	-0.015	0.000	0.000	0.000	0.000
87	D	255	ALA	0	-0.037	0.001	31.798	-0.001	-0.001	0.000	0.000	0.000	0.000
88	D	256	LYS	1	0.954	0.970	29.902	0.016	0.016	0.000	0.000	0.000	0.000
89	D	257	SER	0	-0.051	-0.023	28.516	0.001	0.001	0.000	0.000	0.000	0.000
90	D	258	LEU	0	-0.009	-0.003	21.717	-0.007	-0.007	0.000	0.000	0.000	0.000
91	D	259	ARG	1	0.793	0.880	24.377	0.016	0.016	0.000	0.000	0.000	0.000
92	D	260	ILE	0	0.004	0.030	20.285	-0.006	-0.006	0.000	0.000	0.000	0.000
93	D	261	VAL	0	-0.049	-0.013	22.092	0.004	0.004	0.000	0.000	0.000	0.000
94	D	262	GLU	-1	-0.799	-0.895	21.372	0.088	0.088	0.000	0.000	0.000	0.000
95	D	263	ARG	1	0.759	0.855	22.069	-0.098	-0.098	0.000	0.000	0.000	0.000
96	D	264	GLU	-1	-0.757	-0.832	24.179	0.000	0.000	0.000	0.000	0.000	0.000
97	D	265	SER	0	0.021	-0.014	20.154	0.000	0.000	0.000	0.000	0.000	0.000
98	D	266	GLY	0	-0.052	-0.007	21.950	0.011	0.011	0.000	0.000	0.000	0.000
99	D	267	HIS	0	-0.047	-0.037	15.047	0.001	0.001	0.000	0.000	0.000	0.000
100	D	268	TYR	0	0.013	-0.018	12.960	0.005	0.005	0.000	0.000	0.000	0.000
101	D	269	VAL	0	0.006	0.034	16.414	-0.010	-0.010	0.000	0.000	0.000	0.000
102	D	270	GLU	-1	-0.859	-0.926	16.840	0.008	0.008	0.000	0.000	0.000	0.000
103	D	271	MET	0	-0.016	0.006	15.374	-0.007	-0.007	0.000	0.000	0.000	0.000
104	D	272	HIS	0	-0.015	-0.019	19.618	-0.024	-0.024	0.000	0.000	0.000	0.000
105	D	273	ALA	0	0.045	0.028	21.357	0.006	0.006	0.000	0.000	0.000	0.000
106	D	274	ARG	1	0.891	0.935	23.055	0.030	0.030	0.000	0.000	0.000	0.000
107	D	275	TYR	0	0.020	0.000	23.463	0.000	0.000	0.000	0.000	0.000	0.000
108	D	276	ILE	0	0.021	0.031	20.783	-0.001	-0.001	0.000	0.000	0.000	0.000
109	D	277	GLY	0	0.009	0.011	22.990	-0.012	-0.012	0.000	0.000	0.000	0.000
110	D	278	THR	0	-0.037	-0.033	17.924	-0.014	-0.014	0.000	0.000	0.000	0.000
111	D	279	THR	0	-0.082	-0.030	18.482	0.016	0.016	0.000	0.000	0.000	0.000
112	D	280	VAL	0	0.041	0.018	13.220	-0.028	-0.028	0.000	0.000	0.000	0.000
113	D	281	PHE	0	-0.004	-0.001	13.865	0.022	0.022	0.000	0.000	0.000	0.000
114	D	282	VAL	0	0.035	0.014	11.366	-0.008	-0.008	0.000	0.000	0.000	0.000
115	D	283	ARG	1	0.946	0.972	11.408	-0.293	-0.293	0.000	0.000	0.000	0.000
116	D	284	GLN	0	0.032	0.025	10.720	0.013	0.013	0.000	0.000	0.000	0.000
117	D	285	VAL	0	-0.052	-0.027	9.103	-0.078	-0.078	0.000	0.000	0.000	0.000
118	D	286	GLY	0	0.026	0.010	9.556	0.149	0.149	0.000	0.000	0.000	0.000
119	D	287	ARG	1	0.758	0.836	10.478	-0.541	-0.541	0.000	0.000	0.000	0.000
120	D	288	TYR	0	0.031	0.012	5.947	0.105	0.105	0.000	0.000	0.000	0.000
121	D	289	LEU	0	0.006	0.014	7.152	-0.106	-0.106	0.000	0.000	0.000	0.000
122	D	290	THR	0	-0.070	-0.035	6.099	0.169	0.169	0.000	0.000	0.000	0.000
123	D	291	LEU	0	0.039	0.005	7.258	-0.077	-0.077	0.000	0.000	0.000	0.000
124	D	292	ALA	0	-0.019	0.008	8.521	-0.058	-0.058	0.000	0.000	0.000	0.000
125	D	293	ILE	0	0.020	0.003	10.374	0.017	0.017	0.000	0.000	0.000	0.000
126	D	294	ARG	1	0.949	0.985	13.807	0.068	0.068	0.000	0.000	0.000	0.000
127	D	295	MET	0	-0.005	-0.006	17.190	-0.001	-0.001	0.000	0.000	0.000	0.000
128	D	296	PRO	0	0.000	0.014	19.041	-0.006	-0.006	0.000	0.000	0.000	0.000
129	D	297	GLU	-1	-0.914	-0.959	21.300	-0.183	-0.183	0.000	0.000	0.000	0.000
130	D	298	ASP	-1	-0.888	-0.952	22.288	-0.146	-0.146	0.000	0.000	0.000	0.000
131	D	299	LEU	0	-0.018	-0.008	22.072	-0.003	-0.003	0.000	0.000	0.000	0.000
132	D	300	ALA	0	-0.041	-0.029	17.856	-0.012	-0.012	0.000	0.000	0.000	0.000
133	D	301	MET	0	-0.071	-0.043	18.105	-0.044	-0.044	0.000	0.000	0.000	0.000
134	D	302	SER	0	-0.004	0.021	21.165	0.012	0.012	0.000	0.000	0.000	0.000
135	D	303	TYR	0	-0.034	-0.040	19.123	-0.015	-0.015	0.000	0.000	0.000	0.000
136	D	304	GLU	-1	-0.835	-0.916	22.150	-0.157	-0.157	0.000	0.000	0.000	0.000
137	D	305	GLU	-1	-0.974	-0.991	21.979	-0.190	-0.190	0.000	0.000	0.000	0.000
138	D	306	SER	0	0.019	0.007	21.847	-0.009	-0.009	0.000	0.000	0.000	0.000
139	D	307	GLN	0	-0.088	-0.013	18.501	-0.001	-0.001	0.000	0.000	0.000	0.000
140	D	308	ASP	-1	-0.904	-0.951	17.534	-0.360	-0.360	0.000	0.000	0.000	0.000
141	D	309	LEU	0	-0.037	-0.009	10.757	-0.064	-0.064	0.000	0.000	0.000	0.000
142	D	310	GLN	0	0.009	-0.014	12.074	0.008	0.008	0.000	0.000	0.000	0.000
143	D	311	LEU	0	-0.001	-0.001	5.075	-0.017	-0.017	0.000	0.000	0.000	0.000
144	D	312	CYS	0	-0.028	-0.013	9.136	-0.054	-0.054	0.000	0.000	0.000	0.000
145	D	313	VAL	0	0.032	0.035	11.103	0.064	0.064	0.000	0.000	0.000	0.000
146	D	314	ASN	0	-0.056	-0.038	13.173	0.054	0.054	0.000	0.000	0.000	0.000
147	D	315	GLY	0	0.018	0.022	9.337	0.007	0.007	0.000	0.000	0.000	0.000
148	D	317	PRO	0	0.101	0.056	8.534	0.151	0.151	0.000	0.000	0.000	0.000
149	D	318	LEU	0	0.018	-0.002	10.244	-0.121	-0.121	0.000	0.000	0.000	0.000
150	D	319	SER	0	-0.004	-0.011	11.537	-0.013	-0.013	0.000	0.000	0.000	0.000
151	D	320	GLU	-1	-0.892	-0.939	6.935	-0.892	-0.892	0.000	0.000	0.000	0.000
152	D	321	ARG	1	0.830	0.925	6.424	0.614	0.614	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(D:169:PRO)