FMO DATABASE

FMODB ID: V5Z51

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:

Apendix: None

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	119
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-984754.341307
FMO2-HF: Nuclear repulsion	938037.006687
FMO2-HF: Total energy	-46717.33462
FMO2-MP2: Total energy	-46853.390978

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.
-0.542	3.027	0.143	-1.476	-2.237	0.004

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 : 0.065 / q_NPA : 0.016

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	-0.030	-0.028	2.875	-0.401	2.671	0.141	-1.337	-1.876	0.004
4	I	204	LEU	0	0.031	-0.003	5.039	-1.040	-0.994	-0.001	-0.009	-0.037	0.000
5	I	205	GLN	0	-0.004	0.019	8.791	0.443	0.443	0.000	0.000	0.000	0.000
6	I	206	GLU	-1	-0.719	-0.855	11.020	0.547	0.547	0.000	0.000	0.000	0.000
7	I	207	SER	0	-0.002	0.000	14.776	0.008	0.008	0.000	0.000	0.000	0.000
8	I	208	GLY	0	0.011	0.011	17.430	-0.041	-0.041	0.000	0.000	0.000	0.000
9	I	209	GLY	0	0.021	-0.015	21.176	0.019	0.019	0.000	0.000	0.000	0.000
10	I	210	HIS	0	-0.038	-0.012	23.343	-0.008	-0.008	0.000	0.000	0.000	0.000
11	I	211	LEU	0	-0.001	-0.006	26.682	-0.004	-0.004	0.000	0.000	0.000	0.000
12	I	212	VAL	0	-0.005	0.024	29.557	-0.020	-0.020	0.000	0.000	0.000	0.000
13	I	213	LYS	1	0.963	0.990	31.900	-0.044	-0.044	0.000	0.000	0.000	0.000
14	I	214	PRO	0	0.064	0.008	35.163	-0.003	-0.003	0.000	0.000	0.000	0.000
15	I	215	GLY	0	0.033	0.030	36.002	-0.008	-0.008	0.000	0.000	0.000	0.000
16	I	216	GLY	0	-0.134	-0.073	34.197	-0.012	-0.012	0.000	0.000	0.000	0.000
17	I	217	SER	0	-0.015	-0.004	31.264	0.005	0.005	0.000	0.000	0.000	0.000
18	I	218	LEU	0	0.016	0.006	25.042	-0.007	-0.007	0.000	0.000	0.000	0.000
19	I	219	LYS	1	0.875	0.940	23.019	0.068	0.068	0.000	0.000	0.000	0.000
20	I	220	LEU	0	-0.011	0.031	20.136	-0.016	-0.016	0.000	0.000	0.000	0.000
21	I	221	SER	0	-0.024	-0.031	17.794	-0.040	-0.040	0.000	0.000	0.000	0.000
22	I	222	CYS	0	-0.063	-0.019	14.108	-0.004	-0.004	0.000	0.000	0.000	0.000
23	I	223	ALA	0	-0.012	0.002	11.715	-0.098	-0.098	0.000	0.000	0.000	0.000
24	I	224	ALA	0	0.025	0.006	9.313	0.204	0.204	0.000	0.000	0.000	0.000
25	I	225	SER	0	-0.020	-0.012	4.819	-1.016	-0.857	-0.001	-0.012	-0.146	0.000
26	I	226	GLY	0	0.057	0.027	3.670	0.069	0.180	0.005	-0.107	-0.009	0.000
27	I	227	PHE	0	0.036	0.018	4.359	0.409	0.590	-0.001	-0.011	-0.169	0.000
28	I	228	ALA	0	0.044	0.027	7.500	-0.081	-0.081	0.000	0.000	0.000	0.000
29	I	229	PHE	0	0.057	0.020	10.996	0.200	0.200	0.000	0.000	0.000	0.000
30	I	230	SER	0	-0.036	-0.034	12.615	0.114	0.114	0.000	0.000	0.000	0.000
31	I	231	SER	0	-0.049	-0.026	14.000	0.058	0.058	0.000	0.000	0.000	0.000
32	I	232	PHE	0	0.032	0.014	12.204	0.070	0.070	0.000	0.000	0.000	0.000
33	I	233	ASP	-1	-0.795	-0.867	16.181	-0.002	-0.002	0.000	0.000	0.000	0.000
34	I	234	MET	0	-0.062	-0.022	13.143	0.040	0.040	0.000	0.000	0.000	0.000
35	I	235	SER	0	-0.015	-0.016	17.605	-0.021	-0.021	0.000	0.000	0.000	0.000
36	I	236	TRP	0	0.004	-0.006	17.886	0.064	0.064	0.000	0.000	0.000	0.000
37	I	237	ILE	0	-0.025	-0.009	19.494	-0.038	-0.038	0.000	0.000	0.000	0.000
38	I	238	ARG	1	0.815	0.906	20.707	-0.203	-0.203	0.000	0.000	0.000	0.000
39	I	239	GLN	0	-0.004	-0.016	22.025	0.031	0.031	0.000	0.000	0.000	0.000
40	I	240	THR	0	-0.029	-0.031	24.236	0.002	0.002	0.000	0.000	0.000	0.000
41	I	241	PRO	0	0.056	0.020	27.301	0.028	0.028	0.000	0.000	0.000	0.000
42	I	242	GLU	-1	-0.855	-0.902	29.288	0.270	0.270	0.000	0.000	0.000	0.000
43	I	243	LYS	1	0.904	0.949	26.469	-0.358	-0.358	0.000	0.000	0.000	0.000
44	I	244	ARG	1	0.845	0.922	26.966	-0.245	-0.245	0.000	0.000	0.000	0.000
45	I	245	LEU	0	-0.005	-0.007	21.292	-0.002	-0.002	0.000	0.000	0.000	0.000
46	I	246	GLU	-1	-0.796	-0.883	24.889	0.213	0.213	0.000	0.000	0.000	0.000
47	I	247	TRP	0	0.013	0.000	22.841	0.007	0.007	0.000	0.000	0.000	0.000
48	I	248	VAL	0	-0.023	-0.037	23.957	-0.029	-0.029	0.000	0.000	0.000	0.000
49	I	249	ALA	0	-0.003	-0.010	22.799	-0.030	-0.030	0.000	0.000	0.000	0.000
50	I	250	SER	0	-0.027	0.003	22.225	0.027	0.027	0.000	0.000	0.000	0.000
51	I	251	ILE	0	0.011	0.017	20.174	-0.025	-0.025	0.000	0.000	0.000	0.000
52	I	252	THR	0	-0.057	-0.078	20.978	0.018	0.018	0.000	0.000	0.000	0.000
53	I	253	ASN	0	0.122	0.146	18.565	-0.001	-0.001	0.000	0.000	0.000	0.000
54	I	254	VAL	0	-0.054	-0.049	20.271	-0.008	-0.008	0.000	0.000	0.000	0.000
55	I	255	GLY	0	-0.121	-0.068	22.418	0.011	0.011	0.000	0.000	0.000	0.000
56	I	256	THR	0	0.110	0.044	24.357	0.009	0.009	0.000	0.000	0.000	0.000
57	I	257	TYR	0	-0.012	-0.014	27.030	0.008	0.008	0.000	0.000	0.000	0.000
58	I	258	THR	0	-0.038	-0.026	25.804	0.005	0.005	0.000	0.000	0.000	0.000
59	I	259	TYR	0	-0.008	0.003	25.899	0.002	0.002	0.000	0.000	0.000	0.000
60	I	260	TYR	0	0.033	0.019	27.001	0.015	0.015	0.000	0.000	0.000	0.000
61	I	261	PRO	0	0.038	0.033	27.871	-0.010	-0.010	0.000	0.000	0.000	0.000
62	I	262	GLY	0	0.018	-0.024	30.739	-0.006	-0.006	0.000	0.000	0.000	0.000
63	I	263	SER	0	-0.021	0.010	33.026	-0.010	-0.010	0.000	0.000	0.000	0.000
64	I	264	VAL	0	0.011	0.002	28.497	0.004	0.004	0.000	0.000	0.000	0.000
65	I	265	LYS	1	0.935	0.970	31.962	-0.097	-0.097	0.000	0.000	0.000	0.000
66	I	266	GLY	0	0.028	0.020	33.371	0.001	0.001	0.000	0.000	0.000	0.000
67	I	267	ARG	1	0.717	0.846	32.082	-0.126	-0.126	0.000	0.000	0.000	0.000
68	I	268	PHE	0	0.022	-0.001	26.906	-0.007	-0.007	0.000	0.000	0.000	0.000
69	I	269	SER	0	-0.015	0.000	28.081	-0.006	-0.006	0.000	0.000	0.000	0.000
70	I	270	ILE	0	-0.010	-0.002	20.646	-0.002	-0.002	0.000	0.000	0.000	0.000
71	I	271	SER	0	-0.032	-0.015	22.792	-0.022	-0.022	0.000	0.000	0.000	0.000
72	I	272	ARG	1	0.823	0.889	15.961	0.155	0.155	0.000	0.000	0.000	0.000
73	I	273	ASP	-1	-0.803	-0.885	17.745	-0.434	-0.434	0.000	0.000	0.000	0.000
74	I	274	ASN	0	0.003	-0.022	16.300	-0.031	-0.031	0.000	0.000	0.000	0.000
75	I	275	ALA	0	-0.002	0.012	15.883	-0.077	-0.077	0.000	0.000	0.000	0.000
76	I	276	ARG	1	0.908	0.960	14.864	0.363	0.363	0.000	0.000	0.000	0.000
77	I	277	ASN	0	-0.025	0.001	11.017	0.023	0.023	0.000	0.000	0.000	0.000
78	I	278	THR	0	-0.007	-0.002	12.419	0.043	0.043	0.000	0.000	0.000	0.000
79	I	279	LEU	0	0.013	0.009	15.027	-0.007	-0.007	0.000	0.000	0.000	0.000
80	I	280	ASN	0	0.001	-0.014	17.618	0.038	0.038	0.000	0.000	0.000	0.000
81	I	281	LEU	0	0.028	0.020	20.436	-0.009	-0.009	0.000	0.000	0.000	0.000
82	I	282	GLN	0	0.006	0.005	23.450	-0.008	-0.008	0.000	0.000	0.000	0.000
83	I	283	MET	0	-0.021	0.006	25.601	0.006	0.006	0.000	0.000	0.000	0.000
84	I	284	SER	0	0.056	0.010	28.392	-0.007	-0.007	0.000	0.000	0.000	0.000
85	I	285	SER	0	0.028	0.020	32.046	0.001	0.001	0.000	0.000	0.000	0.000
86	I	286	LEU	0	-0.073	-0.039	29.192	0.007	0.007	0.000	0.000	0.000	0.000
87	I	287	ARG	1	0.919	0.942	33.043	-0.125	-0.125	0.000	0.000	0.000	0.000
88	I	288	SER	0	0.048	-0.003	33.444	0.005	0.005	0.000	0.000	0.000	0.000
89	I	289	GLU	-1	-0.850	-0.906	33.479	0.149	0.149	0.000	0.000	0.000	0.000
90	I	290	ASP	-1	-0.756	-0.841	29.363	0.165	0.165	0.000	0.000	0.000	0.000
91	I	291	THR	0	-0.033	0.005	28.233	0.013	0.013	0.000	0.000	0.000	0.000
92	I	292	ALA	0	0.025	0.018	25.701	0.005	0.005	0.000	0.000	0.000	0.000
93	I	293	LEU	0	-0.009	0.008	19.605	-0.015	-0.015	0.000	0.000	0.000	0.000
94	I	294	TYR	0	-0.035	-0.038	20.578	-0.019	-0.019	0.000	0.000	0.000	0.000
95	I	295	PHE	0	0.039	0.024	15.703	0.000	0.000	0.000	0.000	0.000	0.000
96	I	297	ALA	0	0.062	0.035	13.905	0.122	0.122	0.000	0.000	0.000	0.000
97	I	298	ARG	1	0.859	0.926	7.692	-0.939	-0.939	0.000	0.000	0.000	0.000
98	I	299	GLN	0	-0.031	-0.027	14.754	0.030	0.030	0.000	0.000	0.000	0.000
99	I	300	GLY	0	-0.038	-0.023	16.276	-0.027	-0.027	0.000	0.000	0.000	0.000
100	I	301	THR	0	0.030	0.011	16.717	0.033	0.033	0.000	0.000	0.000	0.000
101	I	302	ALA	0	0.016	0.003	16.041	-0.020	-0.020	0.000	0.000	0.000	0.000
102	I	303	ALA	0	-0.029	0.002	17.987	-0.024	-0.024	0.000	0.000	0.000	0.000
103	I	304	GLN	0	0.023	0.023	21.217	-0.002	-0.002	0.000	0.000	0.000	0.000
104	I	305	PRO	0	0.040	0.023	20.115	0.048	0.048	0.000	0.000	0.000	0.000
105	I	306	TYR	0	0.026	0.005	21.151	0.016	0.016	0.000	0.000	0.000	0.000
106	I	307	TRP	0	-0.056	-0.015	20.157	0.025	0.025	0.000	0.000	0.000	0.000
107	I	308	TYR	0	-0.002	-0.002	13.948	-0.032	-0.032	0.000	0.000	0.000	0.000
108	I	309	PHE	0	0.025	0.002	17.226	-0.039	-0.039	0.000	0.000	0.000	0.000
109	I	310	ASP	-1	-0.841	-0.923	11.383	1.213	1.213	0.000	0.000	0.000	0.000
110	I	311	VAL	0	-0.059	-0.044	7.475	-0.012	-0.012	0.000	0.000	0.000	0.000
111	I	312	TRP	0	-0.010	-0.002	10.602	-0.282	-0.282	0.000	0.000	0.000	0.000
112	I	313	GLY	0	0.052	0.031	11.200	0.178	0.178	0.000	0.000	0.000	0.000
113	I	314	ALA	0	-0.072	-0.051	11.833	0.208	0.208	0.000	0.000	0.000	0.000
114	I	315	GLY	0	-0.035	-0.022	13.665	-0.064	-0.064	0.000	0.000	0.000	0.000
115	I	316	THR	0	-0.026	-0.014	17.029	-0.033	-0.033	0.000	0.000	0.000	0.000
116	I	317	THR	0	0.009	-0.003	19.350	-0.016	-0.016	0.000	0.000	0.000	0.000
117	I	318	VAL	0	-0.007	0.001	22.867	-0.036	-0.036	0.000	0.000	0.000	0.000
118	I	319	THR	0	0.019	0.003	25.854	0.005	0.005	0.000	0.000	0.000	0.000
119	I	320	VAL	0	0.014	0.015	29.316	-0.013	-0.013	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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