FMO DATABASE

FMODB ID: YVL12

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1430137.963854
FMO2-HF: Nuclear repulsion	1369900.889594
FMO2-HF: Total energy	-60237.07426
FMO2-MP2: Total energy	-60410.268614

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.
-14.904	-5.653	16.604	-9.959	-15.894	-0.057

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 : 0.040 / q_NPA : 0.028

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	0.004	0.001	2.998	-3.142	0.179	0.167	-1.805	-1.683	0.000
4	D	172	ARG	1	0.812	0.877	5.596	0.577	0.577	0.000	0.000	0.000	0.000
5	D	173	THR	0	-0.006	0.007	9.303	0.046	0.046	0.000	0.000	0.000	0.000
6	D	174	PHE	0	-0.010	-0.024	11.824	0.060	0.060	0.000	0.000	0.000	0.000
7	D	175	LYS	1	0.886	0.943	14.838	0.465	0.465	0.000	0.000	0.000	0.000
8	D	176	ASP	-1	-0.822	-0.878	14.131	-0.300	-0.300	0.000	0.000	0.000	0.000
9	D	177	ASN	0	-0.014	0.004	12.545	-0.007	-0.007	0.000	0.000	0.000	0.000
10	D	178	PHE	0	0.030	0.008	10.051	-0.124	-0.124	0.000	0.000	0.000	0.000
11	D	179	GLN	0	-0.002	-0.002	7.692	-0.095	-0.095	0.000	0.000	0.000	0.000
12	D	180	THR	0	-0.010	-0.009	4.048	-0.105	0.148	0.001	-0.079	-0.175	0.000
13	D	181	CYS	0	-0.062	-0.020	2.893	1.054	2.140	0.025	-0.374	-0.737	0.001
14	D	182	LYS	1	0.896	0.975	1.883	-6.065	-8.650	8.654	-3.523	-2.546	-0.035
15	D	183	VAL	0	-0.022	-0.011	2.209	-0.868	-0.691	3.051	-0.917	-2.311	-0.005
16	D	184	GLU	-1	-0.822	-0.901	4.100	0.004	0.255	0.000	-0.055	-0.196	0.000
17	D	185	GLY	0	0.012	0.027	5.849	-0.091	-0.091	0.000	0.000	0.000	0.000
18	D	186	ALA	0	-0.016	-0.025	7.085	-0.105	-0.105	0.000	0.000	0.000	0.000
19	D	187	TRP	0	0.001	-0.014	6.506	-0.135	-0.135	0.000	0.000	0.000	0.000
20	D	188	PRO	0	0.036	0.036	8.735	0.005	0.005	0.000	0.000	0.000	0.000
21	D	189	LEU	0	-0.011	-0.019	5.683	-0.113	-0.113	0.000	0.000	0.000	0.000
22	D	190	ILE	0	-0.018	-0.021	9.718	0.021	0.021	0.000	0.000	0.000	0.000
23	D	191	ASP	-1	-0.806	-0.874	13.498	-0.244	-0.244	0.000	0.000	0.000	0.000
24	D	192	ASN	0	0.057	0.037	16.527	0.017	0.017	0.000	0.000	0.000	0.000
25	D	193	ASN	0	0.001	-0.001	19.713	0.011	0.011	0.000	0.000	0.000	0.000
26	D	194	TYR	0	-0.024	-0.006	21.627	0.022	0.022	0.000	0.000	0.000	0.000
27	D	195	LEU	0	-0.047	-0.020	16.117	0.015	0.015	0.000	0.000	0.000	0.000
28	D	196	SER	0	-0.006	-0.017	15.606	-0.008	-0.008	0.000	0.000	0.000	0.000
29	D	197	VAL	0	-0.044	-0.024	10.000	0.041	0.041	0.000	0.000	0.000	0.000
30	D	198	GLN	0	0.035	0.029	10.261	-0.101	-0.101	0.000	0.000	0.000	0.000
31	D	199	VAL	0	0.008	-0.001	4.550	0.036	0.098	-0.001	-0.002	-0.057	0.000
32	D	200	THR	0	-0.044	-0.033	7.046	-0.021	-0.021	0.000	0.000	0.000	0.000
33	D	201	ASN	0	0.029	0.024	2.801	-1.390	0.380	0.566	-0.682	-1.653	-0.005
34	D	202	VAL	0	0.000	0.005	4.796	-0.276	-0.234	-0.001	-0.005	-0.036	0.000
35	D	203	PRO	0	0.005	-0.001	5.813	0.855	0.855	0.000	0.000	0.000	0.000
36	D	204	VAL	0	-0.024	-0.003	7.007	-0.273	-0.273	0.000	0.000	0.000	0.000
37	D	205	VAL	0	-0.002	0.001	8.713	-0.314	-0.314	0.000	0.000	0.000	0.000
38	D	206	PRO	0	0.025	-0.010	11.502	0.066	0.066	0.000	0.000	0.000	0.000
39	D	207	GLY	0	0.017	0.013	12.578	-0.026	-0.026	0.000	0.000	0.000	0.000
40	D	208	SER	0	-0.076	-0.028	7.996	-0.229	-0.229	0.000	0.000	0.000	0.000
41	D	209	SER	0	0.023	-0.001	7.663	0.133	0.133	0.000	0.000	0.000	0.000
42	D	210	ALA	0	0.024	0.024	4.584	-0.274	-0.210	-0.001	-0.007	-0.056	0.000
43	D	211	THR	0	-0.026	-0.030	2.377	-3.177	-1.049	1.454	-1.385	-2.197	-0.003
44	D	212	ALA	0	0.032	0.014	2.273	2.213	4.617	2.439	-1.802	-3.041	-0.007
45	D	213	THR	0	0.012	0.000	2.843	-1.353	-1.133	0.250	0.693	-1.164	-0.003
46	D	214	ASN	0	-0.007	-0.018	4.322	-0.050	0.008	0.000	-0.016	-0.042	0.000
47	D	215	LYS	1	0.884	0.944	7.758	-0.087	-0.087	0.000	0.000	0.000	0.000
48	D	216	ILE	0	0.003	0.011	7.842	-0.113	-0.113	0.000	0.000	0.000	0.000
49	D	217	THR	0	-0.021	-0.018	9.926	0.070	0.070	0.000	0.000	0.000	0.000
50	D	218	ILE	0	-0.024	-0.002	12.623	-0.060	-0.060	0.000	0.000	0.000	0.000
51	D	219	ILE	0	0.014	0.004	15.061	0.033	0.033	0.000	0.000	0.000	0.000
52	D	220	PHE	0	0.035	0.009	17.797	-0.020	-0.020	0.000	0.000	0.000	0.000
53	D	221	LYS	1	0.862	0.924	19.314	0.226	0.226	0.000	0.000	0.000	0.000
54	D	222	ALA	0	-0.001	-0.003	23.228	0.005	0.005	0.000	0.000	0.000	0.000
55	D	223	HIS	0	0.021	0.016	26.931	-0.011	-0.011	0.000	0.000	0.000	0.000
56	D	224	HIS	0	0.044	0.012	29.038	0.005	0.005	0.000	0.000	0.000	0.000
57	D	225	GLY	0	0.012	0.007	32.782	-0.001	-0.001	0.000	0.000	0.000	0.000
58	D	226	CYS	0	-0.090	-0.035	29.848	0.001	0.001	0.000	0.000	0.000	0.000
59	D	227	THR	0	0.017	-0.007	25.770	0.006	0.006	0.000	0.000	0.000	0.000
60	D	228	ASP	-1	-0.754	-0.852	28.662	-0.051	-0.051	0.000	0.000	0.000	0.000
61	D	229	GLN	0	-0.006	-0.003	23.284	-0.012	-0.012	0.000	0.000	0.000	0.000
62	D	230	LYS	1	0.788	0.910	22.972	0.043	0.043	0.000	0.000	0.000	0.000
63	D	231	VAL	0	0.013	-0.003	18.268	-0.016	-0.016	0.000	0.000	0.000	0.000
64	D	232	TYR	0	-0.004	-0.016	14.708	0.016	0.016	0.000	0.000	0.000	0.000
65	D	233	GLN	0	0.010	-0.008	14.080	-0.003	-0.003	0.000	0.000	0.000	0.000
66	D	234	ALA	0	0.039	0.040	12.990	0.015	0.015	0.000	0.000	0.000	0.000
67	D	235	VAL	0	-0.020	-0.033	11.760	-0.025	-0.025	0.000	0.000	0.000	0.000
68	D	236	THR	0	-0.040	-0.035	10.323	0.013	0.013	0.000	0.000	0.000	0.000
69	D	237	ASP	-1	-0.803	-0.860	12.439	0.353	0.353	0.000	0.000	0.000	0.000
70	D	238	ASP	-1	-0.920	-0.950	15.378	0.088	0.088	0.000	0.000	0.000	0.000
71	D	239	LEU	0	-0.026	-0.014	13.478	0.004	0.004	0.000	0.000	0.000	0.000
72	D	240	PRO	0	0.064	0.058	16.933	-0.004	-0.004	0.000	0.000	0.000	0.000
73	D	241	ALA	0	0.003	0.000	19.481	-0.009	-0.009	0.000	0.000	0.000	0.000
74	D	242	ALA	0	-0.011	-0.017	21.464	-0.009	-0.009	0.000	0.000	0.000	0.000
75	D	243	PHE	0	0.009	-0.012	20.302	0.000	0.000	0.000	0.000	0.000	0.000
76	D	244	VAL	0	-0.019	-0.020	19.630	0.009	0.009	0.000	0.000	0.000	0.000
77	D	245	ASP	-1	-0.810	-0.861	22.262	-0.017	-0.017	0.000	0.000	0.000	0.000
78	D	246	GLY	0	-0.006	0.002	24.986	0.003	0.003	0.000	0.000	0.000	0.000
79	D	247	THR	0	-0.072	-0.055	26.328	0.001	0.001	0.000	0.000	0.000	0.000
80	D	248	THR	0	0.052	0.010	25.095	0.000	0.000	0.000	0.000	0.000	0.000
81	D	249	SER	0	-0.056	-0.034	26.107	-0.001	-0.001	0.000	0.000	0.000	0.000
82	D	250	GLY	0	0.007	0.012	27.149	0.001	0.001	0.000	0.000	0.000	0.000
83	D	251	GLY	0	-0.017	-0.016	27.845	-0.001	-0.001	0.000	0.000	0.000	0.000
84	D	252	ASP	-1	-0.916	-0.955	31.367	-0.028	-0.028	0.000	0.000	0.000	0.000
85	D	253	SER	0	0.018	0.004	33.332	0.000	0.000	0.000	0.000	0.000	0.000
86	D	254	ASP	-1	-0.874	-0.938	34.948	-0.015	-0.015	0.000	0.000	0.000	0.000
87	D	255	ALA	0	-0.031	0.009	31.896	-0.002	-0.002	0.000	0.000	0.000	0.000
88	D	256	LYS	1	0.827	0.889	29.989	0.023	0.023	0.000	0.000	0.000	0.000
89	D	257	SER	0	-0.039	-0.035	29.007	0.001	0.001	0.000	0.000	0.000	0.000
90	D	258	LEU	0	-0.006	0.002	22.010	-0.010	-0.010	0.000	0.000	0.000	0.000
91	D	259	ARG	1	0.794	0.865	24.532	0.021	0.021	0.000	0.000	0.000	0.000
92	D	260	ILE	0	-0.013	0.007	20.589	-0.010	-0.010	0.000	0.000	0.000	0.000
93	D	261	VAL	0	-0.048	-0.014	22.085	0.004	0.004	0.000	0.000	0.000	0.000
94	D	262	GLU	-1	-0.768	-0.883	21.194	0.087	0.087	0.000	0.000	0.000	0.000
95	D	263	ARG	1	0.762	0.854	22.023	-0.101	-0.101	0.000	0.000	0.000	0.000
96	D	264	GLU	-1	-0.775	-0.842	24.754	0.002	0.002	0.000	0.000	0.000	0.000
97	D	265	SER	0	0.026	0.001	20.737	-0.005	-0.005	0.000	0.000	0.000	0.000
98	D	266	GLY	0	-0.047	-0.003	22.055	0.012	0.012	0.000	0.000	0.000	0.000
99	D	267	HIS	0	-0.081	-0.058	15.326	0.003	0.003	0.000	0.000	0.000	0.000
100	D	268	TYR	0	0.026	-0.010	12.791	0.009	0.009	0.000	0.000	0.000	0.000
101	D	269	VAL	0	0.023	0.032	16.152	-0.005	-0.005	0.000	0.000	0.000	0.000
102	D	270	GLU	-1	-0.817	-0.879	16.705	-0.004	-0.004	0.000	0.000	0.000	0.000
103	D	271	MET	0	-0.007	0.006	15.121	-0.003	-0.003	0.000	0.000	0.000	0.000
104	D	272	HIS	0	-0.039	-0.043	19.899	-0.023	-0.023	0.000	0.000	0.000	0.000
105	D	273	ALA	0	0.035	0.025	21.545	0.007	0.007	0.000	0.000	0.000	0.000
106	D	274	ARG	1	0.888	0.925	23.269	0.042	0.042	0.000	0.000	0.000	0.000
107	D	275	TYR	0	-0.013	-0.015	23.723	-0.002	-0.002	0.000	0.000	0.000	0.000
108	D	276	ILE	0	0.035	0.036	21.505	-0.002	-0.002	0.000	0.000	0.000	0.000
109	D	277	GLY	0	0.018	0.017	23.730	-0.013	-0.013	0.000	0.000	0.000	0.000
110	D	278	THR	0	-0.024	-0.024	18.703	-0.009	-0.009	0.000	0.000	0.000	0.000
111	D	279	THR	0	-0.129	-0.066	19.100	0.021	0.021	0.000	0.000	0.000	0.000
112	D	280	VAL	0	0.015	0.014	13.484	-0.028	-0.028	0.000	0.000	0.000	0.000
113	D	281	PHE	0	0.009	0.013	14.223	0.023	0.023	0.000	0.000	0.000	0.000
114	D	282	VAL	0	0.031	0.006	11.308	-0.019	-0.019	0.000	0.000	0.000	0.000
115	D	283	ARG	1	0.942	0.974	11.597	-0.238	-0.238	0.000	0.000	0.000	0.000
116	D	284	GLN	0	0.019	0.017	10.634	0.028	0.028	0.000	0.000	0.000	0.000
117	D	285	VAL	0	-0.026	-0.018	8.977	-0.077	-0.077	0.000	0.000	0.000	0.000
118	D	286	GLY	0	0.023	0.006	9.812	0.146	0.146	0.000	0.000	0.000	0.000
119	D	287	ARG	1	0.756	0.837	10.529	-0.593	-0.593	0.000	0.000	0.000	0.000
120	D	288	TYR	0	0.056	0.041	5.991	0.102	0.102	0.000	0.000	0.000	0.000
121	D	289	LEU	0	-0.005	0.007	7.285	-0.124	-0.124	0.000	0.000	0.000	0.000
122	D	290	THR	0	-0.065	-0.038	6.004	0.202	0.202	0.000	0.000	0.000	0.000
123	D	291	LEU	0	0.030	0.001	7.541	-0.064	-0.064	0.000	0.000	0.000	0.000
124	D	292	ALA	0	-0.018	0.002	8.809	-0.052	-0.052	0.000	0.000	0.000	0.000
125	D	293	ILE	0	0.029	0.002	10.901	0.025	0.025	0.000	0.000	0.000	0.000
126	D	294	ARG	1	0.918	0.964	13.931	0.092	0.092	0.000	0.000	0.000	0.000
127	D	295	MET	0	-0.027	0.004	17.341	0.008	0.008	0.000	0.000	0.000	0.000
128	D	296	PRO	0	0.003	0.010	19.436	-0.009	-0.009	0.000	0.000	0.000	0.000
129	D	297	GLU	-1	-0.906	-0.948	21.299	-0.201	-0.201	0.000	0.000	0.000	0.000
130	D	298	ASP	-1	-0.841	-0.932	22.334	-0.163	-0.163	0.000	0.000	0.000	0.000
131	D	299	LEU	0	-0.027	-0.025	22.936	-0.006	-0.006	0.000	0.000	0.000	0.000
132	D	300	ALA	0	-0.059	-0.037	18.308	-0.010	-0.010	0.000	0.000	0.000	0.000
133	D	301	MET	0	-0.025	-0.029	18.130	-0.040	-0.040	0.000	0.000	0.000	0.000
134	D	302	SER	0	-0.039	-0.015	21.230	0.010	0.010	0.000	0.000	0.000	0.000
135	D	303	TYR	0	-0.017	-0.018	19.357	-0.022	-0.022	0.000	0.000	0.000	0.000
136	D	304	GLU	-1	-0.819	-0.895	22.295	-0.165	-0.165	0.000	0.000	0.000	0.000
137	D	305	GLU	-1	-0.972	-0.994	22.172	-0.190	-0.190	0.000	0.000	0.000	0.000
138	D	306	SER	0	-0.032	-0.011	22.039	-0.008	-0.008	0.000	0.000	0.000	0.000
139	D	307	GLN	0	-0.064	-0.033	18.496	0.000	0.000	0.000	0.000	0.000	0.000
140	D	308	ASP	-1	-0.834	-0.904	17.662	-0.384	-0.384	0.000	0.000	0.000	0.000
141	D	309	LEU	0	-0.057	-0.032	11.029	-0.070	-0.070	0.000	0.000	0.000	0.000
142	D	310	GLN	0	0.030	0.014	12.340	-0.002	-0.002	0.000	0.000	0.000	0.000
143	D	311	LEU	0	0.008	-0.001	5.458	-0.037	-0.037	0.000	0.000	0.000	0.000
144	D	312	CYS	0	-0.041	-0.027	9.431	-0.079	-0.079	0.000	0.000	0.000	0.000
145	D	313	VAL	0	0.021	0.027	11.255	0.056	0.056	0.000	0.000	0.000	0.000
146	D	314	ASN	0	-0.040	-0.033	12.845	0.067	0.067	0.000	0.000	0.000	0.000
147	D	315	GLY	0	0.003	0.016	9.259	0.003	0.003	0.000	0.000	0.000	0.000
148	D	317	PRO	0	0.085	0.043	8.331	0.148	0.148	0.000	0.000	0.000	0.000
149	D	318	LEU	0	0.009	-0.001	10.238	-0.129	-0.129	0.000	0.000	0.000	0.000
150	D	319	SER	0	0.008	-0.002	11.572	-0.015	-0.015	0.000	0.000	0.000	0.000
151	D	320	GLU	-1	-0.881	-0.925	6.867	-0.959	-0.959	0.000	0.000	0.000	0.000
152	D	321	ARG	1	0.845	0.922	6.461	0.663	0.663	0.000	0.000	0.000	0.000

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