FMO DATABASE

FMODB ID: 3QN3L

Calculation Name: 4BQ6-D-Xray321

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	153
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1428065.869404
FMO2-HF: Nuclear repulsion	1367810.092424
FMO2-HF: Total energy	-60255.77698
FMO2-MP2: Total energy	-60429.058634

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.
-140.576	-131.901	25.522	-16.518	-17.678	-0.16

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 : 1 / q_Mulliken : 0.797 / q_NPA : 0.894

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	-0.001	0.007	3.291	-1.916	-0.050	0.035	-0.861	-1.040	-0.003
4	D	172	ARG	1	0.860	0.925	5.703	23.886	23.886	0.000	0.000	0.000	0.000
5	D	173	THR	0	-0.022	-0.024	9.163	0.451	0.451	0.000	0.000	0.000	0.000
6	D	174	PHE	0	0.026	0.000	11.566	0.870	0.870	0.000	0.000	0.000	0.000
7	D	175	LYS	1	0.932	0.973	14.603	18.370	18.370	0.000	0.000	0.000	0.000
8	D	176	ASP	-1	-0.858	-0.906	14.068	-17.804	-17.804	0.000	0.000	0.000	0.000
9	D	177	ASN	0	-0.021	0.009	12.326	-0.507	-0.507	0.000	0.000	0.000	0.000
10	D	178	PHE	0	0.019	0.001	9.679	-1.838	-1.838	0.000	0.000	0.000	0.000
11	D	179	GLN	0	0.003	-0.004	7.376	-0.223	-0.223	0.000	0.000	0.000	0.000
12	D	180	THR	0	0.002	0.008	3.963	-5.733	-5.535	0.002	-0.067	-0.134	0.000
13	D	316	CYS	0	-0.055	-0.021	2.976	9.531	11.042	0.046	-0.592	-0.964	-0.001
14	D	182	LYS	1	0.975	1.024	1.668	-7.261	-13.909	18.146	-7.652	-3.846	-0.071
15	D	183	VAL	0	-0.006	0.013	2.552	-13.668	-12.262	0.757	-0.687	-1.476	-0.007
16	D	184	GLU	-1	-0.885	-0.943	4.262	-34.643	-34.457	0.000	-0.038	-0.148	0.000
17	D	185	GLY	0	0.031	0.024	6.074	4.100	4.100	0.000	0.000	0.000	0.000
18	D	186	ALA	0	-0.041	-0.030	7.071	-3.233	-3.233	0.000	0.000	0.000	0.000
19	D	187	TRP	0	0.025	-0.005	6.668	0.731	0.731	0.000	0.000	0.000	0.000
20	D	188	PRO	0	0.047	0.038	8.767	-0.882	-0.882	0.000	0.000	0.000	0.000
21	D	189	LEU	0	-0.051	-0.036	5.447	-1.518	-1.518	0.000	0.000	0.000	0.000
22	D	190	ILE	0	-0.022	-0.031	9.473	0.949	0.949	0.000	0.000	0.000	0.000
23	D	191	ASP	-1	-0.876	-0.942	13.168	-16.996	-16.996	0.000	0.000	0.000	0.000
24	D	192	ASN	0	0.075	0.047	16.135	0.941	0.941	0.000	0.000	0.000	0.000
25	D	193	ASN	0	-0.022	-0.031	19.266	0.324	0.324	0.000	0.000	0.000	0.000
26	D	194	TYR	0	-0.002	0.006	21.227	0.578	0.578	0.000	0.000	0.000	0.000
27	D	195	LEU	0	-0.046	-0.028	15.783	0.075	0.075	0.000	0.000	0.000	0.000
28	D	196	SER	0	0.011	0.013	15.646	0.040	0.040	0.000	0.000	0.000	0.000
29	D	197	VAL	0	-0.019	-0.005	9.748	0.175	0.175	0.000	0.000	0.000	0.000
30	D	198	GLN	0	0.039	0.015	10.313	-1.217	-1.217	0.000	0.000	0.000	0.000
31	D	199	VAL	0	0.016	0.006	4.733	0.311	0.367	0.000	-0.002	-0.054	0.000
32	D	200	THR	0	-0.039	-0.017	7.464	1.610	1.610	0.000	0.000	0.000	0.000
33	D	201	ASN	0	-0.022	-0.008	2.979	-5.787	-3.644	0.559	-0.932	-1.770	-0.009
34	D	202	VAL	0	0.019	0.008	4.743	4.857	4.904	0.000	-0.006	-0.041	0.000
35	D	203	PRO	0	0.018	0.008	6.110	-6.039	-6.039	0.000	0.000	0.000	0.000
36	D	204	VAL	0	-0.036	-0.019	6.922	3.273	3.273	0.000	0.000	0.000	0.000
37	D	205	VAL	0	0.009	0.008	8.440	3.236	3.236	0.000	0.000	0.000	0.000
38	D	206	PRO	0	0.027	-0.006	10.797	-1.932	-1.932	0.000	0.000	0.000	0.000
39	D	207	GLY	0	0.022	0.014	12.345	0.892	0.892	0.000	0.000	0.000	0.000
40	D	208	SER	0	-0.030	0.006	8.783	-0.390	-0.390	0.000	0.000	0.000	0.000
41	D	209	SER	0	0.020	-0.001	7.739	-1.707	-1.707	0.000	0.000	0.000	0.000
42	D	210	ALA	0	0.011	0.016	4.699	-7.857	-7.809	0.000	-0.005	-0.043	0.000
43	D	211	THR	0	-0.030	-0.055	2.331	-11.879	-9.190	2.645	-2.233	-3.101	-0.028
44	D	212	ALA	0	-0.018	-0.014	2.313	-23.014	-18.881	3.184	-3.302	-4.014	-0.038
45	D	213	THR	0	0.007	-0.001	3.066	2.036	3.033	0.148	-0.128	-1.017	-0.003
46	D	214	ASN	0	0.031	0.007	4.433	3.064	3.107	0.000	-0.013	-0.030	0.000
47	D	215	LYS	1	0.950	0.987	7.646	23.942	23.942	0.000	0.000	0.000	0.000
48	D	216	ILE	0	0.009	0.007	7.648	-2.889	-2.889	0.000	0.000	0.000	0.000
49	D	217	THR	0	-0.007	0.006	10.219	2.419	2.419	0.000	0.000	0.000	0.000
50	D	218	ILE	0	-0.012	0.001	12.674	-0.993	-0.993	0.000	0.000	0.000	0.000
51	D	219	ILE	0	0.005	-0.003	15.024	0.902	0.902	0.000	0.000	0.000	0.000
52	D	220	PHE	0	0.029	0.009	18.022	-0.278	-0.278	0.000	0.000	0.000	0.000
53	D	221	LYS	1	0.923	0.954	19.891	14.911	14.911	0.000	0.000	0.000	0.000
54	D	222	ALA	0	-0.006	0.000	23.165	0.192	0.192	0.000	0.000	0.000	0.000
55	D	223	HIS	0	0.012	0.011	26.713	-0.219	-0.219	0.000	0.000	0.000	0.000
56	D	224	HIS	0	0.050	0.001	28.528	0.032	0.032	0.000	0.000	0.000	0.000
57	D	225	GLY	0	0.008	0.009	32.307	0.052	0.052	0.000	0.000	0.000	0.000
58	D	226	CYS	0	-0.107	-0.032	29.564	0.051	0.051	0.000	0.000	0.000	0.000
59	D	227	THR	0	0.002	-0.038	25.489	-0.064	-0.064	0.000	0.000	0.000	0.000
60	D	228	ASP	-1	-0.775	-0.865	28.711	-10.479	-10.479	0.000	0.000	0.000	0.000
61	D	229	GLN	0	-0.011	-0.003	23.252	-0.237	-0.237	0.000	0.000	0.000	0.000
62	D	230	LYS	1	0.819	0.938	22.821	11.051	11.051	0.000	0.000	0.000	0.000
63	D	231	VAL	0	0.011	-0.006	18.089	-0.578	-0.578	0.000	0.000	0.000	0.000
64	D	232	TYR	0	-0.011	-0.006	14.537	-0.034	-0.034	0.000	0.000	0.000	0.000
65	D	233	GLN	0	-0.046	-0.055	14.241	-0.632	-0.632	0.000	0.000	0.000	0.000
66	D	234	ALA	0	0.041	0.053	12.928	0.770	0.770	0.000	0.000	0.000	0.000
67	D	235	VAL	0	-0.017	-0.034	11.873	-1.874	-1.874	0.000	0.000	0.000	0.000
68	D	236	THR	0	-0.045	-0.027	10.305	-0.124	-0.124	0.000	0.000	0.000	0.000
69	D	237	ASP	-1	-0.799	-0.866	12.581	-17.293	-17.293	0.000	0.000	0.000	0.000
70	D	238	ASP	-1	-0.922	-0.954	15.436	-14.054	-14.054	0.000	0.000	0.000	0.000
71	D	239	LEU	0	-0.023	-0.015	13.145	-1.155	-1.155	0.000	0.000	0.000	0.000
72	D	240	PRO	0	0.076	0.063	17.034	0.675	0.675	0.000	0.000	0.000	0.000
73	D	241	ALA	0	0.019	0.003	19.424	-0.569	-0.569	0.000	0.000	0.000	0.000
74	D	242	ALA	0	-0.015	-0.041	21.419	0.567	0.567	0.000	0.000	0.000	0.000
75	D	243	PHE	0	-0.023	-0.017	20.277	-0.867	-0.867	0.000	0.000	0.000	0.000
76	D	244	VAL	0	0.004	-0.016	19.877	0.315	0.315	0.000	0.000	0.000	0.000
77	D	245	ASP	-1	-0.832	-0.888	22.480	-11.092	-11.092	0.000	0.000	0.000	0.000
78	D	246	GLY	0	-0.010	-0.003	25.177	0.479	0.479	0.000	0.000	0.000	0.000
79	D	247	THR	0	-0.071	-0.039	26.452	0.198	0.198	0.000	0.000	0.000	0.000
80	D	248	THR	0	0.040	-0.003	25.184	-0.421	-0.421	0.000	0.000	0.000	0.000
81	D	249	SER	0	-0.041	-0.043	26.031	-0.151	-0.151	0.000	0.000	0.000	0.000
82	D	250	GLY	0	-0.011	0.008	27.252	0.004	0.004	0.000	0.000	0.000	0.000
83	D	251	GLY	0	0.000	-0.011	27.774	0.257	0.257	0.000	0.000	0.000	0.000
84	D	252	ASP	-1	-0.916	-0.956	31.174	-8.567	-8.567	0.000	0.000	0.000	0.000
85	D	253	SER	0	0.010	0.006	32.871	-0.154	-0.154	0.000	0.000	0.000	0.000
86	D	254	ASP	-1	-0.941	-0.983	34.478	-8.005	-8.005	0.000	0.000	0.000	0.000
87	D	255	ALA	0	-0.036	0.003	31.798	-0.023	-0.023	0.000	0.000	0.000	0.000
88	D	256	LYS	1	0.947	0.967	29.902	8.512	8.512	0.000	0.000	0.000	0.000
89	D	257	SER	0	-0.052	-0.025	28.515	-0.160	-0.160	0.000	0.000	0.000	0.000
90	D	258	LEU	0	0.001	0.003	21.717	-0.387	-0.387	0.000	0.000	0.000	0.000
91	D	259	ARG	1	0.936	0.979	24.374	11.513	11.513	0.000	0.000	0.000	0.000
92	D	260	ILE	0	0.014	0.036	20.286	-0.531	-0.531	0.000	0.000	0.000	0.000
93	D	261	VAL	0	-0.079	-0.038	22.081	0.644	0.644	0.000	0.000	0.000	0.000
94	D	262	GLU	-1	-0.862	-0.931	21.367	-13.634	-13.634	0.000	0.000	0.000	0.000
95	D	263	ARG	1	0.722	0.843	20.244	13.100	13.100	0.000	0.000	0.000	0.000
96	D	264	GLU	-1	-0.752	-0.826	23.171	-12.268	-12.268	0.000	0.000	0.000	0.000
97	D	265	SER	0	-0.033	-0.044	21.678	0.244	0.244	0.000	0.000	0.000	0.000
98	D	266	GLY	0	-0.001	-0.008	21.034	-0.492	-0.492	0.000	0.000	0.000	0.000
99	D	267	HIS	0	-0.003	-0.010	15.389	-1.274	-1.274	0.000	0.000	0.000	0.000
100	D	268	TYR	0	-0.022	-0.032	12.954	-1.541	-1.541	0.000	0.000	0.000	0.000
101	D	269	VAL	0	0.049	0.060	16.410	0.957	0.957	0.000	0.000	0.000	0.000
102	D	270	GLU	-1	-0.879	-0.941	16.837	-14.501	-14.501	0.000	0.000	0.000	0.000
103	D	271	MET	0	-0.012	0.010	15.374	0.719	0.719	0.000	0.000	0.000	0.000
104	D	272	HIS	0	-0.050	-0.040	19.617	0.023	0.023	0.000	0.000	0.000	0.000
105	D	273	ALA	0	0.060	0.035	21.355	0.517	0.517	0.000	0.000	0.000	0.000
106	D	274	ARG	1	0.884	0.934	23.053	11.272	11.272	0.000	0.000	0.000	0.000
107	D	275	TYR	0	0.026	0.003	23.462	0.051	0.051	0.000	0.000	0.000	0.000
108	D	276	ILE	0	0.027	0.034	20.781	0.194	0.194	0.000	0.000	0.000	0.000
109	D	277	GLY	0	0.012	0.013	22.987	-0.455	-0.455	0.000	0.000	0.000	0.000
110	D	278	THR	0	-0.036	-0.032	17.922	-0.557	-0.557	0.000	0.000	0.000	0.000
111	D	279	THR	0	-0.092	-0.037	18.477	0.600	0.600	0.000	0.000	0.000	0.000
112	D	280	VAL	0	0.047	0.020	13.219	-0.934	-0.934	0.000	0.000	0.000	0.000
113	D	281	PHE	0	-0.021	-0.009	13.862	0.806	0.806	0.000	0.000	0.000	0.000
114	D	282	VAL	0	0.037	0.012	11.367	-1.919	-1.919	0.000	0.000	0.000	0.000
115	D	283	ARG	1	0.916	0.955	11.406	21.325	21.325	0.000	0.000	0.000	0.000
116	D	284	GLN	0	0.036	0.024	10.706	-1.891	-1.891	0.000	0.000	0.000	0.000
117	D	285	VAL	0	-0.046	-0.019	9.090	1.772	1.772	0.000	0.000	0.000	0.000
118	D	286	GLY	0	0.019	0.006	9.546	-1.800	-1.800	0.000	0.000	0.000	0.000
119	D	287	ARG	1	0.759	0.836	10.476	20.503	20.503	0.000	0.000	0.000	0.000
120	D	288	TYR	0	0.018	0.003	5.942	-1.049	-1.049	0.000	0.000	0.000	0.000
121	D	289	LEU	0	0.014	0.020	7.147	2.130	2.130	0.000	0.000	0.000	0.000
122	D	290	THR	0	-0.078	-0.040	6.087	-4.036	-4.036	0.000	0.000	0.000	0.000
123	D	291	LEU	0	0.041	0.007	7.256	2.266	2.266	0.000	0.000	0.000	0.000
124	D	292	ALA	0	-0.024	0.005	8.518	-1.423	-1.423	0.000	0.000	0.000	0.000
125	D	293	ILE	0	0.020	0.002	10.371	0.994	0.994	0.000	0.000	0.000	0.000
126	D	294	ARG	1	0.946	0.984	13.804	13.508	13.508	0.000	0.000	0.000	0.000
127	D	295	MET	0	0.000	-0.005	17.186	-0.060	-0.060	0.000	0.000	0.000	0.000
128	D	296	PRO	0	-0.003	0.013	19.037	-0.086	-0.086	0.000	0.000	0.000	0.000
129	D	297	GLU	-1	-0.914	-0.959	21.295	-13.131	-13.131	0.000	0.000	0.000	0.000
130	D	298	ASP	-1	-0.883	-0.948	22.283	-11.864	-11.864	0.000	0.000	0.000	0.000
131	D	299	LEU	0	-0.018	-0.009	22.069	-0.020	-0.020	0.000	0.000	0.000	0.000
132	D	300	ALA	0	-0.046	-0.031	17.851	-0.381	-0.381	0.000	0.000	0.000	0.000
133	D	301	MET	0	-0.069	-0.043	18.098	-1.028	-1.028	0.000	0.000	0.000	0.000
134	D	302	SER	0	-0.003	0.022	21.160	0.580	0.580	0.000	0.000	0.000	0.000
135	D	303	TYR	0	-0.031	-0.039	19.125	-0.601	-0.601	0.000	0.000	0.000	0.000
136	D	304	GLU	-1	-0.835	-0.917	22.151	-11.404	-11.404	0.000	0.000	0.000	0.000
137	D	305	GLU	-1	-0.970	-0.989	21.984	-12.038	-12.038	0.000	0.000	0.000	0.000
138	D	306	SER	0	0.021	0.008	21.855	-0.250	-0.250	0.000	0.000	0.000	0.000
139	D	307	GLN	0	-0.086	-0.013	18.505	-0.038	-0.038	0.000	0.000	0.000	0.000
140	D	308	ASP	-1	-0.905	-0.950	17.541	-16.926	-16.926	0.000	0.000	0.000	0.000
141	D	309	LEU	0	-0.037	-0.010	10.771	-1.361	-1.361	0.000	0.000	0.000	0.000
142	D	310	GLN	0	0.011	-0.013	12.077	-0.490	-0.490	0.000	0.000	0.000	0.000
143	D	311	LEU	0	-0.013	-0.007	5.080	-0.373	-0.373	0.000	0.000	0.000	0.000
144	D	312	CYS	0	-0.026	-0.013	9.137	-1.153	-1.153	0.000	0.000	0.000	0.000
145	D	313	VAL	0	0.038	0.038	11.096	1.114	1.114	0.000	0.000	0.000	0.000
146	D	314	ASN	0	-0.053	-0.035	13.174	1.099	1.099	0.000	0.000	0.000	0.000
147	D	315	GLY	0	0.018	0.020	9.335	-0.024	-0.024	0.000	0.000	0.000	0.000
148	D	317	PRO	0	0.113	0.061	8.544	2.223	2.223	0.000	0.000	0.000	0.000
149	D	318	LEU	0	0.018	-0.002	10.259	-2.269	-2.269	0.000	0.000	0.000	0.000
150	D	319	SER	0	0.006	-0.006	11.534	-0.455	-0.455	0.000	0.000	0.000	0.000
151	D	320	GLU	-1	-0.888	-0.939	6.933	-35.899	-35.899	0.000	0.000	0.000	0.000
152	D	321	ARG	1	0.829	0.915	6.429	20.786	20.786	0.000	0.000	0.000	0.000
153	D	1	NME	0	0.001	0.011	8.292	0.354	0.354	0.000	0.000	0.000	0.000

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