FMO DATABASE

FMODB ID: 17V7Z

Calculation Name: 1QFW-I-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 1QFW

Chain ID: I

ChEMBL ID:

UniProt ID: P0DN86

Base Structure: X-ray

Registration Date: 2023-06-26

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	119
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-983790.853888
FMO2-HF: Nuclear repulsion	937072.118477
FMO2-HF: Total energy	-46718.735411
FMO2-MP2: Total energy	-46854.761385

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(I:201:GLN)

Summations of interaction energy for fragment #1(I:201:GLN)

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.
-0.524	2.993	0.078	-1.413	-2.182	0.002

Interaction energy analysis for fragmet #1(I:201:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.068 / q_NPA : 0.021

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	I	203	GLN	0	-0.023	-0.017	3.074	-0.509	2.492	0.076	-1.273	-1.804	0.002
4	I	204	LEU	0	0.013	-0.009	5.171	-1.082	-1.023	-0.001	-0.007	-0.052	0.000
5	I	205	GLN	0	-0.004	0.010	8.985	0.526	0.526	0.000	0.000	0.000	0.000
6	I	206	GLU	-1	-0.745	-0.872	11.484	0.398	0.398	0.000	0.000	0.000	0.000
7	I	207	SER	0	0.010	0.001	15.281	-0.023	-0.023	0.000	0.000	0.000	0.000
8	I	208	GLY	0	-0.007	0.009	18.073	-0.009	-0.009	0.000	0.000	0.000	0.000
9	I	209	GLY	0	0.028	-0.010	21.858	0.014	0.014	0.000	0.000	0.000	0.000
10	I	210	HIS	0	-0.032	-0.026	23.775	-0.012	-0.012	0.000	0.000	0.000	0.000
11	I	211	LEU	0	0.007	0.011	26.906	0.003	0.003	0.000	0.000	0.000	0.000
12	I	212	VAL	0	-0.017	0.004	29.954	-0.021	-0.021	0.000	0.000	0.000	0.000
13	I	213	LYS	1	0.909	0.942	32.444	-0.002	-0.002	0.000	0.000	0.000	0.000
14	I	214	PRO	0	0.063	0.008	35.449	-0.002	-0.002	0.000	0.000	0.000	0.000
15	I	215	GLY	0	0.032	0.026	36.771	-0.008	-0.008	0.000	0.000	0.000	0.000
16	I	216	GLY	0	-0.045	-0.005	34.623	-0.012	-0.012	0.000	0.000	0.000	0.000
17	I	217	SER	0	-0.052	-0.047	31.863	0.004	0.004	0.000	0.000	0.000	0.000
18	I	218	LEU	0	0.002	0.002	25.506	-0.007	-0.007	0.000	0.000	0.000	0.000
19	I	219	LYS	1	0.848	0.934	23.024	0.152	0.152	0.000	0.000	0.000	0.000
20	I	220	LEU	0	0.034	0.047	20.944	-0.017	-0.017	0.000	0.000	0.000	0.000
21	I	221	SER	0	-0.041	-0.042	18.211	-0.040	-0.040	0.000	0.000	0.000	0.000
22	I	222	CYS	0	-0.027	-0.002	14.167	0.008	0.008	0.000	0.000	0.000	0.000
23	I	223	ALA	0	-0.011	0.011	11.634	-0.088	-0.088	0.000	0.000	0.000	0.000
24	I	224	ALA	0	0.031	0.016	9.200	0.204	0.204	0.000	0.000	0.000	0.000
25	I	225	SER	0	-0.030	-0.010	4.895	-1.099	-0.940	-0.001	-0.010	-0.148	0.000
26	I	226	GLY	0	0.054	0.017	3.649	0.129	0.245	0.005	-0.109	-0.011	0.000
27	I	227	PHE	0	0.035	0.015	4.453	0.744	0.926	-0.001	-0.014	-0.167	0.000
28	I	228	ALA	0	0.049	0.037	7.604	-0.163	-0.163	0.000	0.000	0.000	0.000
29	I	229	PHE	0	0.038	0.017	10.915	0.196	0.196	0.000	0.000	0.000	0.000
30	I	230	SER	0	-0.027	-0.024	12.652	0.133	0.133	0.000	0.000	0.000	0.000
31	I	231	SER	0	-0.025	-0.024	14.279	0.072	0.072	0.000	0.000	0.000	0.000
32	I	232	PHE	0	0.036	0.025	12.919	0.075	0.075	0.000	0.000	0.000	0.000
33	I	233	ASP	-1	-0.792	-0.868	16.529	-0.026	-0.026	0.000	0.000	0.000	0.000
34	I	234	MET	0	-0.044	-0.008	13.381	0.057	0.057	0.000	0.000	0.000	0.000
35	I	235	SER	0	-0.029	-0.029	17.709	-0.023	-0.023	0.000	0.000	0.000	0.000
36	I	236	TRP	0	0.004	0.000	18.236	0.048	0.048	0.000	0.000	0.000	0.000
37	I	237	ILE	0	-0.010	-0.011	19.479	-0.028	-0.028	0.000	0.000	0.000	0.000
38	I	238	ARG	1	0.798	0.892	21.170	-0.172	-0.172	0.000	0.000	0.000	0.000
39	I	239	GLN	0	-0.032	-0.031	22.495	0.044	0.044	0.000	0.000	0.000	0.000
40	I	240	THR	0	-0.025	-0.028	24.514	-0.004	-0.004	0.000	0.000	0.000	0.000
41	I	241	PRO	0	0.043	0.009	27.943	0.024	0.024	0.000	0.000	0.000	0.000
42	I	242	GLU	-1	-0.814	-0.873	29.907	0.238	0.238	0.000	0.000	0.000	0.000
43	I	243	LYS	1	0.931	0.964	26.635	-0.332	-0.332	0.000	0.000	0.000	0.000
44	I	244	ARG	1	0.801	0.895	26.623	-0.197	-0.197	0.000	0.000	0.000	0.000
45	I	245	LEU	0	0.023	0.007	21.760	-0.005	-0.005	0.000	0.000	0.000	0.000
46	I	246	GLU	-1	-0.802	-0.882	25.318	0.174	0.174	0.000	0.000	0.000	0.000
47	I	247	TRP	0	0.008	0.009	22.997	0.002	0.002	0.000	0.000	0.000	0.000
48	I	248	VAL	0	-0.026	-0.023	24.004	-0.024	-0.024	0.000	0.000	0.000	0.000
49	I	249	ALA	0	0.019	-0.002	23.723	-0.032	-0.032	0.000	0.000	0.000	0.000
50	I	250	SER	0	-0.060	-0.025	22.215	0.026	0.026	0.000	0.000	0.000	0.000
51	I	251	ILE	0	0.016	0.009	20.609	-0.021	-0.021	0.000	0.000	0.000	0.000
52	I	252	THR	0	0.038	0.000	21.094	0.003	0.003	0.000	0.000	0.000	0.000
53	I	253	ASN	0	-0.060	-0.032	19.067	-0.031	-0.031	0.000	0.000	0.000	0.000
54	I	254	VAL	0	-0.042	-0.025	20.624	-0.011	-0.011	0.000	0.000	0.000	0.000
55	I	255	GLY	0	-0.015	0.003	22.524	0.006	0.006	0.000	0.000	0.000	0.000
56	I	256	THR	0	0.032	0.000	25.131	0.006	0.006	0.000	0.000	0.000	0.000
57	I	257	TYR	0	-0.013	0.012	27.515	0.011	0.011	0.000	0.000	0.000	0.000
58	I	258	THR	0	-0.019	-0.021	26.116	-0.003	-0.003	0.000	0.000	0.000	0.000
59	I	259	TYR	0	-0.020	-0.005	25.808	0.005	0.005	0.000	0.000	0.000	0.000
60	I	260	TYR	0	0.057	0.023	27.085	0.008	0.008	0.000	0.000	0.000	0.000
61	I	261	PRO	0	0.030	0.028	28.305	-0.008	-0.008	0.000	0.000	0.000	0.000
62	I	262	GLY	0	0.016	-0.014	31.358	-0.011	-0.011	0.000	0.000	0.000	0.000
63	I	263	SER	0	0.015	0.013	32.501	-0.010	-0.010	0.000	0.000	0.000	0.000
64	I	264	VAL	0	0.002	0.007	28.595	-0.001	-0.001	0.000	0.000	0.000	0.000
65	I	265	LYS	1	0.948	0.974	32.037	-0.075	-0.075	0.000	0.000	0.000	0.000
66	I	266	GLY	0	0.019	0.017	33.788	0.002	0.002	0.000	0.000	0.000	0.000
67	I	267	ARG	1	0.706	0.836	32.488	-0.088	-0.088	0.000	0.000	0.000	0.000
68	I	268	PHE	0	0.011	-0.007	27.348	-0.005	-0.005	0.000	0.000	0.000	0.000
69	I	269	SER	0	-0.035	-0.017	28.315	-0.005	-0.005	0.000	0.000	0.000	0.000
70	I	270	ILE	0	0.002	0.012	20.956	-0.007	-0.007	0.000	0.000	0.000	0.000
71	I	271	SER	0	-0.048	-0.029	22.850	-0.018	-0.018	0.000	0.000	0.000	0.000
72	I	272	ARG	1	0.811	0.895	16.750	0.184	0.184	0.000	0.000	0.000	0.000
73	I	273	ASP	-1	-0.836	-0.900	17.563	-0.537	-0.537	0.000	0.000	0.000	0.000
74	I	274	ASN	0	0.021	-0.004	16.345	-0.044	-0.044	0.000	0.000	0.000	0.000
75	I	275	ALA	0	-0.011	0.011	16.253	-0.055	-0.055	0.000	0.000	0.000	0.000
76	I	276	ARG	1	0.905	0.943	14.706	0.476	0.476	0.000	0.000	0.000	0.000
77	I	277	ASN	0	-0.023	-0.001	11.280	0.008	0.008	0.000	0.000	0.000	0.000
78	I	278	THR	0	0.002	0.001	12.540	0.023	0.023	0.000	0.000	0.000	0.000
79	I	279	LEU	0	0.028	0.013	15.257	0.021	0.021	0.000	0.000	0.000	0.000
80	I	280	ASN	0	-0.030	-0.025	17.633	0.043	0.043	0.000	0.000	0.000	0.000
81	I	281	LEU	0	0.030	0.010	20.629	0.004	0.004	0.000	0.000	0.000	0.000
82	I	282	GLN	0	0.011	0.010	23.813	-0.011	-0.011	0.000	0.000	0.000	0.000
83	I	283	MET	0	-0.013	-0.001	26.106	0.014	0.014	0.000	0.000	0.000	0.000
84	I	284	SER	0	0.013	0.008	28.856	-0.004	-0.004	0.000	0.000	0.000	0.000
85	I	285	SER	0	0.052	0.030	32.462	-0.004	-0.004	0.000	0.000	0.000	0.000
86	I	286	LEU	0	-0.044	-0.004	29.591	0.010	0.010	0.000	0.000	0.000	0.000
87	I	287	ARG	1	0.899	0.926	33.310	-0.094	-0.094	0.000	0.000	0.000	0.000
88	I	288	SER	0	0.051	0.008	33.697	0.004	0.004	0.000	0.000	0.000	0.000
89	I	289	GLU	-1	-0.820	-0.901	33.847	0.114	0.114	0.000	0.000	0.000	0.000
90	I	290	ASP	-1	-0.765	-0.830	29.945	0.121	0.121	0.000	0.000	0.000	0.000
91	I	291	THR	0	-0.046	0.002	28.757	0.004	0.004	0.000	0.000	0.000	0.000
92	I	292	ALA	0	0.024	0.010	25.772	0.010	0.010	0.000	0.000	0.000	0.000
93	I	293	LEU	0	0.006	0.017	19.883	-0.020	-0.020	0.000	0.000	0.000	0.000
94	I	294	TYR	0	-0.046	-0.048	21.148	-0.014	-0.014	0.000	0.000	0.000	0.000
95	I	295	PHE	0	0.040	0.011	15.950	-0.006	-0.006	0.000	0.000	0.000	0.000
96	I	297	ALA	0	0.054	0.021	14.145	0.146	0.146	0.000	0.000	0.000	0.000
97	I	298	ARG	1	0.841	0.910	7.548	-1.224	-1.224	0.000	0.000	0.000	0.000
98	I	299	GLN	0	0.006	0.012	14.988	0.063	0.063	0.000	0.000	0.000	0.000
99	I	300	GLY	0	-0.026	-0.011	16.992	-0.039	-0.039	0.000	0.000	0.000	0.000
100	I	301	THR	0	0.007	-0.007	16.168	0.041	0.041	0.000	0.000	0.000	0.000
101	I	302	ALA	0	0.014	0.006	16.397	-0.023	-0.023	0.000	0.000	0.000	0.000
102	I	303	ALA	0	0.006	0.012	18.151	-0.033	-0.033	0.000	0.000	0.000	0.000
103	I	304	GLN	0	-0.015	-0.006	20.671	0.007	0.007	0.000	0.000	0.000	0.000
104	I	305	PRO	0	0.046	0.039	20.106	0.051	0.051	0.000	0.000	0.000	0.000
105	I	306	TYR	0	0.009	-0.004	21.173	0.010	0.010	0.000	0.000	0.000	0.000
106	I	307	TRP	0	-0.039	-0.011	20.053	0.016	0.016	0.000	0.000	0.000	0.000
107	I	308	TYR	0	0.021	0.008	14.616	-0.014	-0.014	0.000	0.000	0.000	0.000
108	I	309	PHE	0	0.017	-0.005	17.283	-0.052	-0.052	0.000	0.000	0.000	0.000
109	I	310	ASP	-1	-0.816	-0.893	11.285	1.348	1.348	0.000	0.000	0.000	0.000
110	I	311	VAL	0	-0.062	-0.046	7.631	-0.093	-0.093	0.000	0.000	0.000	0.000
111	I	312	TRP	0	-0.016	-0.011	10.612	-0.300	-0.300	0.000	0.000	0.000	0.000
112	I	313	GLY	0	0.016	0.020	11.223	0.291	0.291	0.000	0.000	0.000	0.000
113	I	314	ALA	0	-0.032	-0.021	11.847	0.104	0.104	0.000	0.000	0.000	0.000
114	I	315	GLY	0	-0.002	-0.006	13.515	-0.047	-0.047	0.000	0.000	0.000	0.000
115	I	316	THR	0	-0.048	-0.034	16.972	-0.070	-0.070	0.000	0.000	0.000	0.000
116	I	317	THR	0	-0.007	0.006	19.648	0.002	0.002	0.000	0.000	0.000	0.000
117	I	318	VAL	0	-0.012	-0.006	23.290	-0.034	-0.034	0.000	0.000	0.000	0.000
118	I	319	THR	0	0.023	0.001	26.411	0.011	0.011	0.000	0.000	0.000	0.000
119	I	320	VAL	0	0.024	0.025	29.943	-0.013	-0.013	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(I:201:GLN)