FMO DATABASE

FMODB ID: 5JM5Z

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	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	152
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1429196.853866
FMO2-HF: Nuclear repulsion	1368960.129681
FMO2-HF: Total energy	-60236.724186
FMO2-MP2: Total energy	-60409.95781

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.
-10.206	-8.782	28.415	-13.963	-15.878	-0.066

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 : 0.019 / q_NPA : 0.015

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	0.001	3.322	-2.710	0.532	0.029	-1.648	-1.623	0.005
4	D	172	ARG	1	0.821	0.885	5.713	0.556	0.556	0.000	0.000	0.000	0.000
5	D	173	THR	0	-0.017	-0.013	9.186	0.040	0.040	0.000	0.000	0.000	0.000
6	D	174	PHE	0	0.025	-0.002	11.475	0.071	0.071	0.000	0.000	0.000	0.000
7	D	175	LYS	1	0.880	0.945	14.545	0.481	0.481	0.000	0.000	0.000	0.000
8	D	176	ASP	-1	-0.828	-0.879	14.073	-0.281	-0.281	0.000	0.000	0.000	0.000
9	D	177	ASN	0	-0.026	0.000	12.381	-0.009	-0.009	0.000	0.000	0.000	0.000
10	D	178	PHE	0	0.013	-0.001	9.783	-0.089	-0.089	0.000	0.000	0.000	0.000
11	D	179	GLN	0	-0.001	-0.007	7.509	-0.024	-0.024	0.000	0.000	0.000	0.000
12	D	180	THR	0	0.024	0.017	4.150	-0.503	-0.345	0.000	-0.053	-0.105	0.000
13	D	181	CYS	0	-0.080	-0.037	2.911	0.569	2.023	0.036	-0.588	-0.902	0.001
14	D	182	LYS	1	0.930	0.998	1.671	-3.077	-14.272	22.168	-7.860	-3.114	-0.047
15	D	183	VAL	0	-0.012	-0.002	2.400	-1.165	-0.238	0.946	-0.468	-1.405	-0.002
16	D	184	GLU	-1	-0.840	-0.917	4.325	-0.063	0.120	-0.001	-0.026	-0.157	0.000
17	D	185	GLY	0	0.016	0.020	6.183	-0.054	-0.054	0.000	0.000	0.000	0.000
18	D	186	ALA	0	-0.028	-0.024	7.111	-0.168	-0.168	0.000	0.000	0.000	0.000
19	D	187	TRP	0	0.017	-0.013	6.654	-0.121	-0.121	0.000	0.000	0.000	0.000
20	D	188	PRO	0	0.026	0.030	8.781	-0.017	-0.017	0.000	0.000	0.000	0.000
21	D	189	LEU	0	-0.029	-0.029	5.774	-0.111	-0.111	0.000	0.000	0.000	0.000
22	D	190	ILE	0	-0.020	-0.030	9.787	0.025	0.025	0.000	0.000	0.000	0.000
23	D	191	ASP	-1	-0.818	-0.904	13.487	-0.278	-0.278	0.000	0.000	0.000	0.000
24	D	192	ASN	0	0.070	0.043	16.405	0.026	0.026	0.000	0.000	0.000	0.000
25	D	193	ASN	0	0.001	-0.006	19.552	0.010	0.010	0.000	0.000	0.000	0.000
26	D	194	TYR	0	-0.021	-0.007	21.481	0.022	0.022	0.000	0.000	0.000	0.000
27	D	195	LEU	0	-0.046	-0.025	15.948	0.015	0.015	0.000	0.000	0.000	0.000
28	D	196	SER	0	-0.017	-0.005	15.801	-0.010	-0.010	0.000	0.000	0.000	0.000
29	D	197	VAL	0	-0.029	-0.006	9.904	0.036	0.036	0.000	0.000	0.000	0.000
30	D	198	GLN	0	0.031	0.012	10.403	-0.093	-0.093	0.000	0.000	0.000	0.000
31	D	199	VAL	0	0.018	0.008	4.683	0.043	0.100	-0.001	-0.002	-0.055	0.000
32	D	200	THR	0	-0.042	-0.016	7.345	-0.044	-0.044	0.000	0.000	0.000	0.000
33	D	201	ASN	0	-0.003	-0.001	2.916	-1.710	0.249	0.627	-0.779	-1.807	-0.006
34	D	202	VAL	0	0.002	-0.002	4.773	-0.136	-0.093	-0.001	-0.006	-0.036	0.000
35	D	203	PRO	0	0.014	0.008	5.762	0.755	0.755	0.000	0.000	0.000	0.000
36	D	204	VAL	0	-0.021	-0.011	7.192	-0.264	-0.264	0.000	0.000	0.000	0.000
37	D	205	VAL	0	-0.017	-0.005	8.718	-0.266	-0.266	0.000	0.000	0.000	0.000
38	D	206	PRO	0	0.026	-0.008	11.635	0.071	0.071	0.000	0.000	0.000	0.000
39	D	207	GLY	0	0.016	0.011	13.047	-0.018	-0.018	0.000	0.000	0.000	0.000
40	D	208	SER	0	-0.032	0.003	9.247	-0.058	-0.058	0.000	0.000	0.000	0.000
41	D	209	SER	0	0.018	0.000	7.859	0.106	0.106	0.000	0.000	0.000	0.000
42	D	210	ALA	0	0.003	0.009	5.056	0.119	0.119	0.000	0.000	0.000	0.000
43	D	211	THR	0	-0.034	-0.046	2.645	-1.855	0.067	1.063	-1.119	-1.865	-0.004
44	D	212	ALA	0	0.010	0.005	2.287	2.518	4.953	3.320	-2.097	-3.658	-0.010
45	D	213	THR	0	0.014	0.008	2.843	-1.095	-0.901	0.229	0.698	-1.121	-0.003
46	D	214	ASN	0	0.020	-0.002	4.506	-0.020	0.025	0.000	-0.015	-0.030	0.000
47	D	215	LYS	1	0.882	0.948	7.756	-0.003	-0.003	0.000	0.000	0.000	0.000
48	D	216	ILE	0	0.005	0.009	7.761	-0.134	-0.134	0.000	0.000	0.000	0.000
49	D	217	THR	0	-0.026	-0.015	10.002	0.075	0.075	0.000	0.000	0.000	0.000
50	D	218	ILE	0	-0.013	-0.002	12.654	-0.062	-0.062	0.000	0.000	0.000	0.000
51	D	219	ILE	0	0.005	0.000	15.012	0.034	0.034	0.000	0.000	0.000	0.000
52	D	220	PHE	0	0.029	0.009	17.860	-0.020	-0.020	0.000	0.000	0.000	0.000
53	D	221	LYS	1	0.906	0.943	19.365	0.240	0.240	0.000	0.000	0.000	0.000
54	D	222	ALA	0	-0.006	-0.003	23.277	0.006	0.006	0.000	0.000	0.000	0.000
55	D	223	HIS	0	0.021	0.020	26.848	-0.011	-0.011	0.000	0.000	0.000	0.000
56	D	224	HIS	0	0.038	-0.002	28.671	0.005	0.005	0.000	0.000	0.000	0.000
57	D	225	GLY	0	0.013	0.008	32.441	-0.001	-0.001	0.000	0.000	0.000	0.000
58	D	226	CYS	0	-0.092	-0.025	29.599	0.002	0.002	0.000	0.000	0.000	0.000
59	D	227	THR	0	0.016	-0.023	25.538	0.006	0.006	0.000	0.000	0.000	0.000
60	D	228	ASP	-1	-0.769	-0.849	28.530	-0.062	-0.062	0.000	0.000	0.000	0.000
61	D	229	GLN	0	-0.013	-0.013	23.308	-0.011	-0.011	0.000	0.000	0.000	0.000
62	D	230	LYS	1	0.799	0.908	22.753	0.057	0.057	0.000	0.000	0.000	0.000
63	D	231	VAL	0	0.010	-0.004	18.010	-0.018	-0.018	0.000	0.000	0.000	0.000
64	D	232	TYR	0	-0.004	-0.015	14.528	0.017	0.017	0.000	0.000	0.000	0.000
65	D	233	GLN	0	0.017	-0.005	13.989	-0.007	-0.007	0.000	0.000	0.000	0.000
66	D	234	ALA	0	0.033	0.048	12.696	0.020	0.020	0.000	0.000	0.000	0.000
67	D	235	VAL	0	-0.005	-0.030	11.941	-0.034	-0.034	0.000	0.000	0.000	0.000
68	D	236	THR	0	-0.029	-0.021	10.311	0.007	0.007	0.000	0.000	0.000	0.000
69	D	237	ASP	-1	-0.831	-0.878	12.570	0.313	0.313	0.000	0.000	0.000	0.000
70	D	238	ASP	-1	-0.910	-0.950	15.491	0.063	0.063	0.000	0.000	0.000	0.000
71	D	239	LEU	0	-0.031	-0.013	12.906	-0.006	-0.006	0.000	0.000	0.000	0.000
72	D	240	PRO	0	0.061	0.054	16.826	-0.002	-0.002	0.000	0.000	0.000	0.000
73	D	241	ALA	0	-0.001	0.000	19.150	-0.006	-0.006	0.000	0.000	0.000	0.000
74	D	242	ALA	0	0.001	-0.019	21.168	-0.006	-0.006	0.000	0.000	0.000	0.000
75	D	243	PHE	0	0.000	-0.012	20.210	-0.003	-0.003	0.000	0.000	0.000	0.000
76	D	244	VAL	0	-0.005	-0.020	19.724	0.009	0.009	0.000	0.000	0.000	0.000
77	D	245	ASP	-1	-0.828	-0.871	22.246	-0.030	-0.030	0.000	0.000	0.000	0.000
78	D	246	GLY	0	-0.008	-0.003	24.940	0.003	0.003	0.000	0.000	0.000	0.000
79	D	247	THR	0	-0.073	-0.047	26.235	0.002	0.002	0.000	0.000	0.000	0.000
80	D	248	THR	0	0.058	0.008	25.004	0.000	0.000	0.000	0.000	0.000	0.000
81	D	249	SER	0	-0.054	-0.044	25.923	0.000	0.000	0.000	0.000	0.000	0.000
82	D	250	GLY	0	-0.027	0.001	27.208	0.000	0.000	0.000	0.000	0.000	0.000
83	D	251	GLY	0	-0.005	-0.012	27.748	0.002	0.002	0.000	0.000	0.000	0.000
84	D	252	ASP	-1	-0.927	-0.961	31.155	-0.035	-0.035	0.000	0.000	0.000	0.000
85	D	253	SER	0	0.021	0.011	32.817	0.000	0.000	0.000	0.000	0.000	0.000
86	D	254	ASP	-1	-0.888	-0.967	34.417	-0.022	-0.022	0.000	0.000	0.000	0.000
87	D	255	ALA	0	-0.024	0.007	31.884	-0.001	-0.001	0.000	0.000	0.000	0.000
88	D	256	LYS	1	0.880	0.939	29.911	0.027	0.027	0.000	0.000	0.000	0.000
89	D	257	SER	0	-0.064	-0.027	28.519	0.000	0.000	0.000	0.000	0.000	0.000
90	D	258	LEU	0	-0.014	-0.009	21.851	-0.009	-0.009	0.000	0.000	0.000	0.000
91	D	259	ARG	1	0.793	0.872	24.384	0.031	0.031	0.000	0.000	0.000	0.000
92	D	260	ILE	0	-0.005	0.011	20.370	-0.008	-0.008	0.000	0.000	0.000	0.000
93	D	261	VAL	0	-0.055	-0.016	21.985	0.006	0.006	0.000	0.000	0.000	0.000
94	D	262	GLU	-1	-0.791	-0.889	21.229	0.070	0.070	0.000	0.000	0.000	0.000
95	D	263	ARG	1	0.794	0.863	21.868	-0.087	-0.087	0.000	0.000	0.000	0.000
96	D	264	GLU	-1	-0.753	-0.825	24.449	-0.008	-0.008	0.000	0.000	0.000	0.000
97	D	265	SER	0	0.029	0.002	20.469	-0.002	-0.002	0.000	0.000	0.000	0.000
98	D	266	GLY	0	-0.052	-0.005	21.919	0.013	0.013	0.000	0.000	0.000	0.000
99	D	267	HIS	0	-0.075	-0.057	15.032	0.000	0.000	0.000	0.000	0.000	0.000
100	D	268	TYR	0	0.032	-0.004	12.674	0.014	0.014	0.000	0.000	0.000	0.000
101	D	269	VAL	0	0.007	0.034	15.878	-0.007	-0.007	0.000	0.000	0.000	0.000
102	D	270	GLU	-1	-0.844	-0.901	16.758	-0.018	-0.018	0.000	0.000	0.000	0.000
103	D	271	MET	0	-0.012	0.007	15.158	-0.003	-0.003	0.000	0.000	0.000	0.000
104	D	272	HIS	0	-0.038	-0.041	19.669	-0.022	-0.022	0.000	0.000	0.000	0.000
105	D	273	ALA	0	0.046	0.027	21.438	0.008	0.008	0.000	0.000	0.000	0.000
106	D	274	ARG	1	0.867	0.914	23.165	0.048	0.048	0.000	0.000	0.000	0.000
107	D	275	TYR	0	0.016	-0.004	23.647	-0.001	-0.001	0.000	0.000	0.000	0.000
108	D	276	ILE	0	0.030	0.035	21.169	0.000	0.000	0.000	0.000	0.000	0.000
109	D	277	GLY	0	0.010	0.010	23.248	-0.013	-0.013	0.000	0.000	0.000	0.000
110	D	278	THR	0	-0.042	-0.033	18.184	-0.015	-0.015	0.000	0.000	0.000	0.000
111	D	279	THR	0	-0.090	-0.035	18.630	0.018	0.018	0.000	0.000	0.000	0.000
112	D	280	VAL	0	0.036	0.014	13.300	-0.031	-0.031	0.000	0.000	0.000	0.000
113	D	281	PHE	0	0.000	0.005	13.929	0.025	0.025	0.000	0.000	0.000	0.000
114	D	282	VAL	0	0.037	0.015	11.314	-0.019	-0.019	0.000	0.000	0.000	0.000
115	D	283	ARG	1	0.940	0.970	11.424	-0.230	-0.230	0.000	0.000	0.000	0.000
116	D	284	GLN	0	0.035	0.022	10.679	0.005	0.005	0.000	0.000	0.000	0.000
117	D	285	VAL	0	-0.052	-0.022	8.942	-0.067	-0.067	0.000	0.000	0.000	0.000
118	D	286	GLY	0	0.027	0.008	9.457	0.147	0.147	0.000	0.000	0.000	0.000
119	D	287	ARG	1	0.776	0.841	10.421	-0.526	-0.526	0.000	0.000	0.000	0.000
120	D	288	TYR	0	0.034	0.016	5.910	0.125	0.125	0.000	0.000	0.000	0.000
121	D	289	LEU	0	0.009	0.015	7.173	-0.100	-0.100	0.000	0.000	0.000	0.000
122	D	290	THR	0	-0.063	-0.033	6.093	0.130	0.130	0.000	0.000	0.000	0.000
123	D	291	LEU	0	0.031	-0.001	7.274	-0.064	-0.064	0.000	0.000	0.000	0.000
124	D	292	ALA	0	-0.019	0.003	8.540	-0.061	-0.061	0.000	0.000	0.000	0.000
125	D	293	ILE	0	0.026	0.007	10.886	0.024	0.024	0.000	0.000	0.000	0.000
126	D	294	ARG	1	0.953	0.988	13.852	0.093	0.093	0.000	0.000	0.000	0.000
127	D	295	MET	0	-0.016	-0.006	17.199	-0.001	-0.001	0.000	0.000	0.000	0.000
128	D	296	PRO	0	0.002	0.017	19.275	-0.006	-0.006	0.000	0.000	0.000	0.000
129	D	297	GLU	-1	-0.908	-0.957	21.477	-0.198	-0.198	0.000	0.000	0.000	0.000
130	D	298	ASP	-1	-0.878	-0.950	22.385	-0.162	-0.162	0.000	0.000	0.000	0.000
131	D	299	LEU	0	-0.025	-0.011	22.451	-0.002	-0.002	0.000	0.000	0.000	0.000
132	D	300	ALA	0	-0.038	-0.031	18.091	-0.013	-0.013	0.000	0.000	0.000	0.000
133	D	301	MET	0	-0.062	-0.036	18.029	-0.044	-0.044	0.000	0.000	0.000	0.000
134	D	302	SER	0	-0.032	0.002	21.122	0.014	0.014	0.000	0.000	0.000	0.000
135	D	303	TYR	0	-0.025	-0.034	19.119	-0.022	-0.022	0.000	0.000	0.000	0.000
136	D	304	GLU	-1	-0.828	-0.901	22.162	-0.167	-0.167	0.000	0.000	0.000	0.000
137	D	305	GLU	-1	-0.974	-0.992	22.059	-0.192	-0.192	0.000	0.000	0.000	0.000
138	D	306	SER	0	0.015	0.007	21.977	-0.010	-0.010	0.000	0.000	0.000	0.000
139	D	307	GLN	0	-0.105	-0.046	18.561	-0.002	-0.002	0.000	0.000	0.000	0.000
140	D	308	ASP	-1	-0.897	-0.946	17.620	-0.374	-0.374	0.000	0.000	0.000	0.000
141	D	309	LEU	0	-0.034	-0.008	11.112	-0.063	-0.063	0.000	0.000	0.000	0.000
142	D	310	GLN	0	0.023	-0.008	12.101	0.006	0.006	0.000	0.000	0.000	0.000
143	D	311	LEU	0	-0.006	0.001	5.260	-0.021	-0.021	0.000	0.000	0.000	0.000
144	D	312	CYS	0	-0.027	-0.011	9.183	-0.066	-0.066	0.000	0.000	0.000	0.000
145	D	313	VAL	0	0.061	0.044	11.038	0.060	0.060	0.000	0.000	0.000	0.000
146	D	314	ASN	0	-0.050	-0.033	13.216	0.050	0.050	0.000	0.000	0.000	0.000
147	D	315	GLY	0	0.025	0.029	9.387	0.013	0.013	0.000	0.000	0.000	0.000
148	D	317	PRO	0	0.103	0.059	8.734	0.146	0.146	0.000	0.000	0.000	0.000
149	D	318	LEU	0	0.012	-0.005	10.239	-0.117	-0.117	0.000	0.000	0.000	0.000
150	D	319	SER	0	0.002	-0.003	11.521	-0.013	-0.013	0.000	0.000	0.000	0.000
151	D	320	GLU	-1	-0.877	-0.931	6.880	-0.817	-0.817	0.000	0.000	0.000	0.000
152	D	321	ARG	1	0.822	0.920	6.424	0.691	0.691	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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