FMO DATABASE

FMODB ID: QYG8Y

Calculation Name: 1EGJ-A-Xray372

Preferred Name:

Target Type:

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

Ligand 3-letter code: NAG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1EGJ

Chain ID: A

ChEMBL ID:

UniProt ID: P01865

Base Structure: X-ray

Registration Date: 2023-09-19

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	101
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-802029.237342
FMO2-HF: Nuclear repulsion	759629.824307
FMO2-HF: Total energy	-42399.413034
FMO2-MP2: Total energy	-42522.267292

3D Structure Molmil

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(A:338:ILE)

Summations of interaction energy for fragment #1(A:338:ILE)

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.
-0.562	1.864	-0.029	-1.045	-1.352	0

Interaction energy analysis for fragmet #1(A:338:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / 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].
3	A	340	MET	0	-0.047	-0.014	3.811	-1.341	0.808	-0.027	-1.022	-1.100
4	A	341	ALA	0	0.038	0.017	6.110	0.214	0.214	0.000	0.000	0.000
5	A	342	PRO	0	0.002	0.016	8.850	-0.043	-0.043	0.000	0.000	0.000
6	A	343	PRO	0	-0.029	-0.009	12.285	-0.008	-0.008	0.000	0.000	0.000
7	A	344	SER	0	-0.001	-0.011	14.266	0.045	0.045	0.000	0.000	0.000
8	A	345	LEU	0	-0.027	0.003	17.561	-0.007	-0.007	0.000	0.000	0.000
9	A	346	ASN	0	-0.064	-0.026	20.834	0.014	0.014	0.000	0.000	0.000
10	A	347	VAL	0	0.022	0.000	24.344	-0.005	-0.005	0.000	0.000	0.000
11	A	348	THR	0	0.000	0.009	27.574	0.005	0.005	0.000	0.000	0.000
12	A	349	LYS	1	0.785	0.860	30.053	0.031	0.031	0.000	0.000	0.000
13	A	350	ASP	-1	-0.895	-0.936	33.586	-0.049	-0.049	0.000	0.000	0.000
14	A	351	GLY	0	0.047	0.027	36.039	0.001	0.001	0.000	0.000	0.000
15	A	352	ASP	-1	-0.817	-0.911	37.986	-0.026	-0.026	0.000	0.000	0.000
16	A	353	SER	0	-0.059	-0.003	34.745	0.001	0.001	0.000	0.000	0.000
17	A	354	TYR	0	-0.011	-0.028	31.365	-0.002	-0.002	0.000	0.000	0.000
18	A	355	SER	0	-0.008	-0.015	27.973	-0.005	-0.005	0.000	0.000	0.000
19	A	356	LEU	0	-0.024	0.008	23.707	0.001	0.001	0.000	0.000	0.000
20	A	357	ARG	1	0.884	0.927	21.564	0.119	0.119	0.000	0.000	0.000
21	A	358	TRP	0	0.011	-0.009	16.566	0.015	0.015	0.000	0.000	0.000
22	A	359	GLU	-1	-0.804	-0.892	16.294	-0.160	-0.160	0.000	0.000	0.000
23	A	360	THR	0	-0.031	-0.020	10.661	0.008	0.008	0.000	0.000	0.000
24	A	361	MET	0	0.012	0.009	8.994	0.025	0.025	0.000	0.000	0.000
25	A	362	LYS	1	0.956	0.986	6.947	0.544	0.544	0.000	0.000	0.000
26	A	363	MET	0	0.014	0.007	9.952	-0.017	-0.017	0.000	0.000	0.000
27	A	364	ARG	1	0.867	0.936	9.735	0.296	0.296	0.000	0.000	0.000
28	A	365	TYR	0	0.001	-0.013	5.900	0.061	0.061	0.000	0.000	0.000
29	A	366	GLU	-1	-0.862	-0.932	10.670	-0.237	-0.237	0.000	0.000	0.000
30	A	367	HIS	0	-0.022	-0.007	9.630	0.056	0.056	0.000	0.000	0.000
31	A	368	ILE	0	-0.012	-0.016	7.120	-0.035	-0.035	0.000	0.000	0.000
32	A	369	ASP	-1	-0.844	-0.875	11.285	-0.275	-0.275	0.000	0.000	0.000
33	A	370	HIS	0	0.004	-0.007	8.027	-0.080	-0.080	0.000	0.000	0.000
34	A	371	THR	0	-0.015	-0.009	11.942	0.077	0.077	0.000	0.000	0.000
35	A	372	PHE	0	0.032	-0.004	13.166	-0.036	-0.036	0.000	0.000	0.000
36	A	373	GLU	-1	-0.828	-0.893	15.640	-0.033	-0.033	0.000	0.000	0.000
37	A	374	ILE	0	0.000	-0.004	17.851	0.001	0.001	0.000	0.000	0.000
38	A	375	GLN	0	0.025	0.027	20.798	0.017	0.017	0.000	0.000	0.000
39	A	376	TYR	0	-0.006	-0.018	23.606	0.001	0.001	0.000	0.000	0.000
40	A	377	ARG	1	0.879	0.967	26.586	-0.009	-0.009	0.000	0.000	0.000
41	A	378	LYS	1	0.852	0.901	29.750	0.002	0.002	0.000	0.000	0.000
42	A	379	ASP	-1	-0.872	-0.936	32.160	0.009	0.009	0.000	0.000	0.000
43	A	380	THR	0	-0.008	0.003	33.171	0.002	0.002	0.000	0.000	0.000
44	A	381	ALA	0	-0.005	0.023	32.321	0.003	0.003	0.000	0.000	0.000
45	A	382	THR	0	0.051	0.012	28.454	0.001	0.001	0.000	0.000	0.000
46	A	383	TRP	0	-0.021	-0.019	23.974	-0.004	-0.004	0.000	0.000	0.000
47	A	384	LYS	1	0.962	0.967	25.060	-0.071	-0.071	0.000	0.000	0.000
48	A	385	ASP	-1	-0.902	-0.949	26.450	0.032	0.032	0.000	0.000	0.000
49	A	386	SER	0	-0.037	-0.016	26.958	-0.007	-0.007	0.000	0.000	0.000
50	A	387	LYS	1	0.803	0.903	26.305	0.035	0.035	0.000	0.000	0.000
51	A	388	THR	0	-0.014	-0.034	21.448	0.000	0.000	0.000	0.000	0.000
52	A	389	GLU	-1	-0.775	-0.858	22.724	-0.043	-0.043	0.000	0.000	0.000
53	A	390	THR	0	-0.032	-0.038	17.710	-0.005	-0.005	0.000	0.000	0.000
54	A	391	LEU	0	-0.005	0.002	18.667	0.005	0.005	0.000	0.000	0.000
55	A	392	GLN	0	-0.037	-0.029	15.676	-0.012	-0.012	0.000	0.000	0.000
56	A	393	ASN	0	-0.063	-0.043	14.843	-0.027	-0.027	0.000	0.000	0.000
57	A	394	ALA	0	0.033	0.024	16.857	0.020	0.020	0.000	0.000	0.000
58	A	395	HIS	0	-0.007	-0.011	14.926	-0.002	-0.002	0.000	0.000	0.000
59	A	396	SER	0	0.010	-0.004	19.736	0.010	0.010	0.000	0.000	0.000
60	A	397	MET	0	-0.048	-0.018	23.003	-0.006	-0.006	0.000	0.000	0.000
61	A	398	ALA	0	0.034	0.030	25.248	0.005	0.005	0.000	0.000	0.000
62	A	399	LEU	0	-0.014	-0.012	27.447	0.000	0.000	0.000	0.000	0.000
63	A	400	PRO	0	-0.026	-0.008	30.388	0.001	0.001	0.000	0.000	0.000
64	A	401	ALA	0	0.041	0.024	33.560	0.000	0.000	0.000	0.000	0.000
65	A	402	LEU	0	-0.010	-0.012	32.468	0.001	0.001	0.000	0.000	0.000
66	A	403	GLU	-1	-0.862	-0.910	36.755	-0.008	-0.008	0.000	0.000	0.000
67	A	404	PRO	0	0.052	0.017	39.070	0.000	0.000	0.000	0.000	0.000
68	A	405	SER	0	-0.044	-0.008	40.845	0.001	0.001	0.000	0.000	0.000
69	A	406	THR	0	0.007	0.001	36.160	0.003	0.003	0.000	0.000	0.000
70	A	407	ARG	1	0.882	0.966	30.923	0.002	0.002	0.000	0.000	0.000
71	A	408	TYR	0	0.001	0.000	30.615	0.003	0.003	0.000	0.000	0.000
72	A	409	TRP	0	-0.028	-0.037	26.377	0.001	0.001	0.000	0.000	0.000
73	A	410	ALA	0	0.029	0.008	24.193	-0.002	-0.002	0.000	0.000	0.000
74	A	411	ARG	1	0.874	0.942	19.775	-0.019	-0.019	0.000	0.000	0.000
75	A	412	VAL	0	0.030	0.009	16.162	-0.002	-0.002	0.000	0.000	0.000
76	A	413	ARG	1	0.870	0.941	13.050	0.019	0.019	0.000	0.000	0.000
77	A	414	VAL	0	0.032	0.018	10.405	0.003	0.003	0.000	0.000	0.000
78	A	415	ARG	1	0.923	0.979	8.537	0.057	0.057	0.000	0.000	0.000
79	A	416	THR	0	0.041	0.016	4.482	-0.026	0.070	-0.001	-0.006	-0.089
80	A	417	SER	0	-0.014	-0.004	7.952	-0.002	-0.002	0.000	0.000	0.000
81	A	418	ARG	1	0.958	0.964	10.844	0.354	0.354	0.000	0.000	0.000
82	A	419	THR	0	-0.003	-0.006	12.836	0.003	0.003	0.000	0.000	0.000
83	A	420	GLY	0	0.035	0.026	15.409	0.026	0.026	0.000	0.000	0.000
84	A	421	TYR	0	-0.003	0.019	10.749	0.051	0.051	0.000	0.000	0.000
85	A	422	ASN	0	-0.034	-0.044	10.246	-0.101	-0.101	0.000	0.000	0.000
86	A	423	GLY	0	0.057	0.041	6.387	0.019	0.019	0.000	0.000	0.000
87	A	424	ILE	0	-0.037	-0.033	4.617	-0.012	0.169	-0.001	-0.017	-0.163
88	A	425	TRP	0	-0.049	-0.022	7.095	-0.334	-0.334	0.000	0.000	0.000
89	A	426	SER	0	0.015	0.011	8.979	0.097	0.097	0.000	0.000	0.000
90	A	427	GLU	-1	-0.898	-0.945	9.902	0.260	0.260	0.000	0.000	0.000
91	A	428	TRP	0	-0.029	-0.048	12.296	-0.073	-0.073	0.000	0.000	0.000
92	A	429	SER	0	0.012	0.024	15.757	0.004	0.004	0.000	0.000	0.000
93	A	430	GLU	-1	-0.874	-0.918	16.826	-0.006	-0.006	0.000	0.000	0.000
94	A	431	ALA	0	-0.060	-0.034	19.544	-0.010	-0.010	0.000	0.000	0.000
95	A	432	ARG	1	0.827	0.906	21.363	0.051	0.051	0.000	0.000	0.000
96	A	433	SER	0	0.017	-0.005	24.924	0.002	0.002	0.000	0.000	0.000
97	A	434	TRP	0	-0.036	-0.025	27.649	-0.004	-0.004	0.000	0.000	0.000
98	A	435	ASP	-1	-0.839	-0.946	31.802	-0.009	-0.009	0.000	0.000	0.000
99	A	436	THR	0	-0.058	-0.021	35.485	-0.002	-0.002	0.000	0.000	0.000
100	A	437	GLU	-1	-0.848	-0.907	37.175	-0.022	-0.022	0.000	0.000	0.000
101	A	438	SER	0	-0.025	-0.008	40.265	0.001	0.001	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:338:ILE)