FMO DATABASE

FMODB ID: YZ7Z2

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	OptH
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	-985311.109654
FMO2-HF: Nuclear repulsion	938594.663885
FMO2-HF: Total energy	-46716.44577
FMO2-MP2: Total energy	-46852.596357

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.
-0.39	3.157	0.057	-1.528	-2.076	0.003

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 : 0.076 / q_NPA : 0.019

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	-0.019	-0.016	3.231	-0.718	2.500	0.049	-1.401	-1.866	0.003
4	I	204	LEU	0	0.029	-0.007	5.037	-1.016	-0.978	-0.001	-0.008	-0.029	0.000
5	I	205	GLN	0	0.003	0.021	8.788	0.403	0.403	0.000	0.000	0.000	0.000
6	I	206	GLU	-1	-0.750	-0.864	11.019	0.628	0.628	0.000	0.000	0.000	0.000
7	I	207	SER	0	0.001	0.004	14.774	0.016	0.016	0.000	0.000	0.000	0.000
8	I	208	GLY	0	0.017	0.012	17.426	-0.037	-0.037	0.000	0.000	0.000	0.000
9	I	209	GLY	0	0.017	-0.015	21.171	0.021	0.021	0.000	0.000	0.000	0.000
10	I	210	HIS	0	-0.018	-0.006	23.343	-0.013	-0.013	0.000	0.000	0.000	0.000
11	I	211	LEU	0	0.004	-0.007	26.682	-0.004	-0.004	0.000	0.000	0.000	0.000
12	I	212	VAL	0	-0.017	0.026	29.392	-0.021	-0.021	0.000	0.000	0.000	0.000
13	I	213	LYS	1	0.982	0.988	31.899	-0.060	-0.060	0.000	0.000	0.000	0.000
14	I	214	PRO	0	0.039	0.001	35.162	-0.001	-0.001	0.000	0.000	0.000	0.000
15	I	215	GLY	0	0.035	0.031	36.001	-0.008	-0.008	0.000	0.000	0.000	0.000
16	I	216	GLY	0	-0.134	-0.077	34.192	-0.011	-0.011	0.000	0.000	0.000	0.000
17	I	217	SER	0	-0.015	0.002	31.293	0.005	0.005	0.000	0.000	0.000	0.000
18	I	218	LEU	0	-0.002	0.000	25.483	-0.007	-0.007	0.000	0.000	0.000	0.000
19	I	219	LYS	1	0.910	0.953	23.147	0.039	0.039	0.000	0.000	0.000	0.000
20	I	220	LEU	0	-0.016	0.025	20.107	-0.016	-0.016	0.000	0.000	0.000	0.000
21	I	221	SER	0	-0.013	-0.025	17.783	-0.039	-0.039	0.000	0.000	0.000	0.000
22	I	222	CYS	0	-0.079	-0.019	14.028	-0.005	-0.005	0.000	0.000	0.000	0.000
23	I	223	ALA	0	-0.012	-0.002	11.845	-0.095	-0.095	0.000	0.000	0.000	0.000
24	I	224	ALA	0	0.017	0.003	9.282	0.203	0.203	0.000	0.000	0.000	0.000
25	I	225	SER	0	-0.043	-0.025	5.313	-0.673	-0.673	0.000	0.000	0.000	0.000
26	I	226	GLY	0	0.066	0.031	3.516	0.131	0.256	0.010	-0.112	-0.023	0.000
27	I	227	PHE	0	0.017	0.009	4.199	0.383	0.549	-0.001	-0.007	-0.158	0.000
28	I	228	ALA	0	0.056	0.029	7.403	-0.112	-0.112	0.000	0.000	0.000	0.000
29	I	229	PHE	0	0.027	0.003	10.841	0.177	0.177	0.000	0.000	0.000	0.000
30	I	230	SER	0	-0.023	-0.036	12.475	0.105	0.105	0.000	0.000	0.000	0.000
31	I	231	SER	0	-0.006	-0.009	14.053	0.007	0.007	0.000	0.000	0.000	0.000
32	I	232	PHE	0	0.000	-0.001	11.637	0.070	0.070	0.000	0.000	0.000	0.000
33	I	233	ASP	-1	-0.818	-0.903	16.095	0.086	0.086	0.000	0.000	0.000	0.000
34	I	234	MET	0	-0.057	-0.018	12.608	0.075	0.075	0.000	0.000	0.000	0.000
35	I	235	SER	0	-0.062	-0.050	17.603	-0.037	-0.037	0.000	0.000	0.000	0.000
36	I	236	TRP	0	0.009	0.003	18.191	0.071	0.071	0.000	0.000	0.000	0.000
37	I	237	ILE	0	-0.021	-0.006	19.028	-0.043	-0.043	0.000	0.000	0.000	0.000
38	I	238	ARG	1	0.845	0.918	20.715	-0.226	-0.226	0.000	0.000	0.000	0.000
39	I	239	GLN	0	0.000	-0.017	22.280	0.023	0.023	0.000	0.000	0.000	0.000
40	I	240	THR	0	0.011	0.002	24.236	0.002	0.002	0.000	0.000	0.000	0.000
41	I	241	PRO	0	0.043	0.008	27.301	0.028	0.028	0.000	0.000	0.000	0.000
42	I	242	GLU	-1	-0.942	-0.962	29.304	0.276	0.276	0.000	0.000	0.000	0.000
43	I	243	LYS	1	0.905	0.953	26.446	-0.364	-0.364	0.000	0.000	0.000	0.000
44	I	244	ARG	1	0.981	1.005	26.966	-0.269	-0.269	0.000	0.000	0.000	0.000
45	I	245	LEU	0	-0.021	-0.012	20.977	0.000	0.000	0.000	0.000	0.000	0.000
46	I	246	GLU	-1	-0.883	-0.935	24.900	0.239	0.239	0.000	0.000	0.000	0.000
47	I	247	TRP	0	0.031	-0.001	22.710	0.005	0.005	0.000	0.000	0.000	0.000
48	I	248	VAL	0	-0.029	-0.029	23.888	-0.032	-0.032	0.000	0.000	0.000	0.000
49	I	249	ALA	0	-0.006	-0.013	22.879	-0.032	-0.032	0.000	0.000	0.000	0.000
50	I	250	SER	0	0.014	0.055	22.229	0.030	0.030	0.000	0.000	0.000	0.000
51	I	251	ILE	0	0.016	0.021	20.005	-0.029	-0.029	0.000	0.000	0.000	0.000
52	I	252	THR	0	-0.023	-0.045	20.974	0.022	0.022	0.000	0.000	0.000	0.000
53	I	253	ASN	0	0.147	0.158	18.263	0.011	0.011	0.000	0.000	0.000	0.000
54	I	254	VAL	0	-0.059	-0.051	20.145	-0.011	-0.011	0.000	0.000	0.000	0.000
55	I	255	GLY	0	-0.115	-0.069	22.277	0.005	0.005	0.000	0.000	0.000	0.000
56	I	256	THR	0	0.111	0.036	24.219	0.011	0.011	0.000	0.000	0.000	0.000
57	I	257	TYR	0	-0.014	-0.007	26.886	0.004	0.004	0.000	0.000	0.000	0.000
58	I	258	THR	0	-0.036	-0.020	25.924	0.009	0.009	0.000	0.000	0.000	0.000
59	I	259	TYR	0	-0.009	0.004	25.969	-0.005	-0.005	0.000	0.000	0.000	0.000
60	I	260	TYR	0	0.031	0.023	27.001	0.017	0.017	0.000	0.000	0.000	0.000
61	I	261	PRO	0	0.021	0.023	27.845	-0.012	-0.012	0.000	0.000	0.000	0.000
62	I	262	GLY	0	0.031	-0.026	30.739	-0.007	-0.007	0.000	0.000	0.000	0.000
63	I	263	SER	0	-0.010	0.012	33.264	-0.011	-0.011	0.000	0.000	0.000	0.000
64	I	264	VAL	0	0.005	0.005	28.537	0.004	0.004	0.000	0.000	0.000	0.000
65	I	265	LYS	1	0.939	0.968	31.962	-0.127	-0.127	0.000	0.000	0.000	0.000
66	I	266	GLY	0	0.021	0.020	33.371	-0.001	-0.001	0.000	0.000	0.000	0.000
67	I	267	ARG	1	0.723	0.853	32.397	-0.146	-0.146	0.000	0.000	0.000	0.000
68	I	268	PHE	0	0.010	0.001	26.899	-0.006	-0.006	0.000	0.000	0.000	0.000
69	I	269	SER	0	0.018	0.001	28.072	-0.006	-0.006	0.000	0.000	0.000	0.000
70	I	270	ILE	0	-0.031	-0.005	21.137	-0.002	-0.002	0.000	0.000	0.000	0.000
71	I	271	SER	0	-0.015	-0.016	22.796	-0.024	-0.024	0.000	0.000	0.000	0.000
72	I	272	ARG	1	0.803	0.875	15.860	0.070	0.070	0.000	0.000	0.000	0.000
73	I	273	ASP	-1	-0.824	-0.899	17.759	-0.333	-0.333	0.000	0.000	0.000	0.000
74	I	274	ASN	0	-0.020	-0.018	16.359	-0.022	-0.022	0.000	0.000	0.000	0.000
75	I	275	ALA	0	0.003	0.019	16.048	-0.069	-0.069	0.000	0.000	0.000	0.000
76	I	276	ARG	1	0.933	0.972	15.053	0.296	0.296	0.000	0.000	0.000	0.000
77	I	277	ASN	0	-0.016	0.008	9.853	0.050	0.050	0.000	0.000	0.000	0.000
78	I	278	THR	0	-0.013	-0.002	12.608	0.048	0.048	0.000	0.000	0.000	0.000
79	I	279	LEU	0	0.046	0.013	15.212	-0.013	-0.013	0.000	0.000	0.000	0.000
80	I	280	ASN	0	-0.032	-0.026	17.604	0.023	0.023	0.000	0.000	0.000	0.000
81	I	281	LEU	0	0.020	0.020	20.424	-0.008	-0.008	0.000	0.000	0.000	0.000
82	I	282	GLN	0	0.025	0.012	23.441	-0.005	-0.005	0.000	0.000	0.000	0.000
83	I	283	MET	0	-0.032	0.003	25.779	0.007	0.007	0.000	0.000	0.000	0.000
84	I	284	SER	0	0.054	0.010	28.386	-0.009	-0.009	0.000	0.000	0.000	0.000
85	I	285	SER	0	0.032	0.014	32.040	0.000	0.000	0.000	0.000	0.000	0.000
86	I	286	LEU	0	-0.067	-0.015	29.372	0.006	0.006	0.000	0.000	0.000	0.000
87	I	287	ARG	1	0.931	0.956	33.043	-0.149	-0.149	0.000	0.000	0.000	0.000
88	I	288	SER	0	0.043	-0.001	33.448	0.005	0.005	0.000	0.000	0.000	0.000
89	I	289	GLU	-1	-0.873	-0.930	33.487	0.172	0.172	0.000	0.000	0.000	0.000
90	I	290	ASP	-1	-0.758	-0.867	29.319	0.192	0.192	0.000	0.000	0.000	0.000
91	I	291	THR	0	-0.066	-0.033	28.240	0.016	0.016	0.000	0.000	0.000	0.000
92	I	292	ALA	0	0.037	0.031	25.655	0.004	0.004	0.000	0.000	0.000	0.000
93	I	293	LEU	0	-0.013	0.019	19.547	-0.016	-0.016	0.000	0.000	0.000	0.000
94	I	294	TYR	0	-0.034	-0.024	20.585	-0.015	-0.015	0.000	0.000	0.000	0.000
95	I	295	PHE	0	0.036	0.028	15.708	0.001	0.001	0.000	0.000	0.000	0.000
96	I	297	ALA	0	0.059	0.037	13.909	0.132	0.132	0.000	0.000	0.000	0.000
97	I	298	ARG	1	0.936	0.971	8.862	-0.924	-0.924	0.000	0.000	0.000	0.000
98	I	299	GLN	0	-0.065	-0.058	14.767	0.024	0.024	0.000	0.000	0.000	0.000
99	I	300	GLY	0	-0.059	-0.031	16.384	-0.019	-0.019	0.000	0.000	0.000	0.000
100	I	301	THR	0	0.025	0.010	16.818	0.039	0.039	0.000	0.000	0.000	0.000
101	I	302	ALA	0	0.026	0.002	16.095	-0.027	-0.027	0.000	0.000	0.000	0.000
102	I	303	ALA	0	-0.035	0.006	17.956	-0.031	-0.031	0.000	0.000	0.000	0.000
103	I	304	GLN	0	0.028	0.017	21.285	-0.002	-0.002	0.000	0.000	0.000	0.000
104	I	305	PRO	0	0.044	0.037	20.197	0.052	0.052	0.000	0.000	0.000	0.000
105	I	306	TYR	0	0.013	0.001	21.258	0.017	0.017	0.000	0.000	0.000	0.000
106	I	307	TRP	0	-0.052	-0.008	20.287	0.023	0.023	0.000	0.000	0.000	0.000
107	I	308	TYR	0	-0.004	-0.003	14.380	-0.047	-0.047	0.000	0.000	0.000	0.000
108	I	309	PHE	0	0.017	0.000	17.352	-0.035	-0.035	0.000	0.000	0.000	0.000
109	I	310	ASP	-1	-0.872	-0.946	11.876	1.378	1.378	0.000	0.000	0.000	0.000
110	I	311	VAL	0	-0.063	-0.043	7.442	-0.039	-0.039	0.000	0.000	0.000	0.000
111	I	312	TRP	0	-0.013	-0.008	10.602	-0.293	-0.293	0.000	0.000	0.000	0.000
112	I	313	GLY	0	0.065	0.018	11.200	0.190	0.190	0.000	0.000	0.000	0.000
113	I	314	ALA	0	-0.070	-0.044	11.917	0.210	0.210	0.000	0.000	0.000	0.000
114	I	315	GLY	0	-0.040	-0.035	13.679	-0.070	-0.070	0.000	0.000	0.000	0.000
115	I	316	THR	0	-0.018	-0.005	17.038	-0.035	-0.035	0.000	0.000	0.000	0.000
116	I	317	THR	0	0.015	-0.011	19.356	-0.018	-0.018	0.000	0.000	0.000	0.000
117	I	318	VAL	0	0.001	0.013	22.875	-0.037	-0.037	0.000	0.000	0.000	0.000
118	I	319	THR	0	0.024	0.002	25.859	0.005	0.005	0.000	0.000	0.000	0.000
119	I	320	VAL	0	0.015	0.013	29.323	-0.014	-0.014	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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