FMO DATABASE

FMODB ID: R9G18

Calculation Name: 1EGJ-A-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

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:

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	101
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-802560.882143
FMO2-HF: Nuclear repulsion	760162.590966
FMO2-HF: Total energy	-42398.291176
FMO2-MP2: Total energy	-42521.293873

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(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.
-0.066	2.299	-0.028	-1.021	-1.316	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 : -0.005 / q_NPA : -0.011

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	-0.045	0.000	3.811	-1.141	0.946	-0.026	-0.999	-1.062
4	A	341	ALA	0	0.045	0.019	6.006	0.231	0.231	0.000	0.000	0.000
5	A	342	PRO	0	-0.024	0.013	8.807	-0.057	-0.057	0.000	0.000	0.000
6	A	343	PRO	0	0.001	-0.009	12.229	0.005	0.005	0.000	0.000	0.000
7	A	344	SER	0	0.007	-0.006	14.172	0.053	0.053	0.000	0.000	0.000
8	A	345	LEU	0	-0.010	0.009	17.485	-0.006	-0.006	0.000	0.000	0.000
9	A	346	ASN	0	-0.072	-0.027	20.745	0.018	0.018	0.000	0.000	0.000
10	A	347	VAL	0	0.026	0.006	24.328	-0.007	-0.007	0.000	0.000	0.000
11	A	348	THR	0	-0.012	0.005	27.580	0.007	0.007	0.000	0.000	0.000
12	A	349	LYS	1	0.973	0.971	30.265	0.046	0.046	0.000	0.000	0.000
13	A	350	ASP	-1	-0.937	-0.940	33.783	-0.062	-0.062	0.000	0.000	0.000
14	A	351	GLY	0	0.031	0.008	36.214	0.001	0.001	0.000	0.000	0.000
15	A	352	ASP	-1	-0.895	-0.956	38.274	-0.037	-0.037	0.000	0.000	0.000
16	A	353	SER	0	-0.104	-0.035	35.014	-0.001	-0.001	0.000	0.000	0.000
17	A	354	TYR	0	0.053	0.010	31.356	-0.002	-0.002	0.000	0.000	0.000
18	A	355	SER	0	-0.023	-0.024	28.178	-0.006	-0.006	0.000	0.000	0.000
19	A	356	LEU	0	-0.016	0.008	23.892	0.002	0.002	0.000	0.000	0.000
20	A	357	ARG	1	0.973	0.989	22.497	0.131	0.131	0.000	0.000	0.000
21	A	358	TRP	0	0.013	-0.008	16.764	0.017	0.017	0.000	0.000	0.000
22	A	359	GLU	-1	-0.868	-0.934	16.457	-0.200	-0.200	0.000	0.000	0.000
23	A	360	THR	0	-0.048	-0.032	10.776	0.017	0.017	0.000	0.000	0.000
24	A	361	MET	0	0.022	0.013	9.354	0.033	0.033	0.000	0.000	0.000
25	A	362	LYS	1	0.966	0.990	7.049	0.581	0.581	0.000	0.000	0.000
26	A	363	MET	0	0.036	0.015	10.138	-0.027	-0.027	0.000	0.000	0.000
27	A	364	ARG	1	0.869	0.940	9.957	0.348	0.348	0.000	0.000	0.000
28	A	365	TYR	0	-0.012	-0.011	6.262	0.059	0.059	0.000	0.000	0.000
29	A	366	GLU	-1	-0.872	-0.938	10.782	-0.287	-0.287	0.000	0.000	0.000
30	A	367	HIS	0	-0.034	-0.013	9.346	0.061	0.061	0.000	0.000	0.000
31	A	368	ILE	0	-0.036	-0.035	7.307	-0.054	-0.054	0.000	0.000	0.000
32	A	369	ASP	-1	-0.840	-0.867	11.195	-0.340	-0.340	0.000	0.000	0.000
33	A	370	HIS	0	-0.020	-0.023	8.300	-0.133	-0.133	0.000	0.000	0.000
34	A	371	THR	0	-0.028	-0.017	11.951	0.102	0.102	0.000	0.000	0.000
35	A	372	PHE	0	0.025	-0.013	13.194	-0.054	-0.054	0.000	0.000	0.000
36	A	373	GLU	-1	-0.831	-0.929	15.689	-0.109	-0.109	0.000	0.000	0.000
37	A	374	ILE	0	0.005	-0.002	17.886	0.002	0.002	0.000	0.000	0.000
38	A	375	GLN	0	0.047	0.033	20.860	0.014	0.014	0.000	0.000	0.000
39	A	376	TYR	0	0.018	-0.009	23.667	-0.002	-0.002	0.000	0.000	0.000
40	A	377	ARG	1	0.904	0.976	26.562	0.011	0.011	0.000	0.000	0.000
41	A	378	LYS	1	0.892	0.927	29.824	0.017	0.017	0.000	0.000	0.000
42	A	379	ASP	-1	-0.949	-0.987	32.171	0.000	0.000	0.000	0.000	0.000
43	A	380	THR	0	0.032	0.014	33.164	0.002	0.002	0.000	0.000	0.000
44	A	381	ALA	0	-0.008	0.021	32.228	0.003	0.003	0.000	0.000	0.000
45	A	382	THR	0	0.059	0.021	28.266	0.000	0.000	0.000	0.000	0.000
46	A	383	TRP	0	-0.038	-0.024	23.808	-0.006	-0.006	0.000	0.000	0.000
47	A	384	LYS	1	0.964	0.966	24.518	-0.053	-0.053	0.000	0.000	0.000
48	A	385	ASP	-1	-0.909	-0.953	26.460	0.008	0.008	0.000	0.000	0.000
49	A	386	SER	0	-0.040	-0.013	27.226	-0.006	-0.006	0.000	0.000	0.000
50	A	387	LYS	1	0.873	0.956	26.318	0.063	0.063	0.000	0.000	0.000
51	A	388	THR	0	0.009	-0.031	21.467	0.000	0.000	0.000	0.000	0.000
52	A	389	GLU	-1	-0.885	-0.926	22.724	-0.083	-0.083	0.000	0.000	0.000
53	A	390	THR	0	-0.018	-0.015	17.678	-0.003	-0.003	0.000	0.000	0.000
54	A	391	LEU	0	-0.015	-0.004	18.693	0.010	0.010	0.000	0.000	0.000
55	A	392	GLN	0	-0.022	-0.018	15.726	-0.028	-0.028	0.000	0.000	0.000
56	A	393	ASN	0	-0.074	-0.059	14.928	-0.032	-0.032	0.000	0.000	0.000
57	A	394	ALA	0	0.033	0.026	16.919	0.027	0.027	0.000	0.000	0.000
58	A	395	HIS	0	-0.010	-0.008	15.290	-0.004	-0.004	0.000	0.000	0.000
59	A	396	SER	0	-0.026	-0.022	19.831	0.017	0.017	0.000	0.000	0.000
60	A	397	MET	0	-0.022	-0.008	23.122	-0.010	-0.010	0.000	0.000	0.000
61	A	398	ALA	0	0.032	0.030	25.345	0.007	0.007	0.000	0.000	0.000
62	A	399	LEU	0	-0.014	-0.014	27.777	-0.002	-0.002	0.000	0.000	0.000
63	A	400	PRO	0	-0.045	-0.012	30.372	0.003	0.003	0.000	0.000	0.000
64	A	401	ALA	0	0.064	0.036	33.636	0.000	0.000	0.000	0.000	0.000
65	A	402	LEU	0	-0.043	-0.036	32.544	0.000	0.000	0.000	0.000	0.000
66	A	403	GLU	-1	-0.889	-0.928	36.848	-0.020	-0.020	0.000	0.000	0.000
67	A	404	PRO	0	0.050	0.007	39.142	0.000	0.000	0.000	0.000	0.000
68	A	405	SER	0	-0.025	-0.003	40.758	0.001	0.001	0.000	0.000	0.000
69	A	406	THR	0	0.000	0.007	36.502	0.003	0.003	0.000	0.000	0.000
70	A	407	ARG	1	0.939	0.993	31.785	0.011	0.011	0.000	0.000	0.000
71	A	408	TYR	0	-0.011	-0.005	30.553	0.004	0.004	0.000	0.000	0.000
72	A	409	TRP	0	-0.031	-0.024	26.169	0.001	0.001	0.000	0.000	0.000
73	A	410	ALA	0	0.015	-0.008	24.283	-0.003	-0.003	0.000	0.000	0.000
74	A	411	ARG	1	0.854	0.936	19.809	0.025	0.025	0.000	0.000	0.000
75	A	412	VAL	0	0.037	0.008	16.127	-0.003	-0.003	0.000	0.000	0.000
76	A	413	ARG	1	0.940	0.981	12.929	0.100	0.100	0.000	0.000	0.000
77	A	414	VAL	0	0.001	0.007	10.610	0.003	0.003	0.000	0.000	0.000
78	A	415	ARG	1	0.886	0.966	8.556	0.241	0.241	0.000	0.000	0.000
79	A	416	THR	0	0.065	0.018	4.553	0.005	0.092	-0.001	-0.005	-0.081
80	A	417	SER	0	0.001	0.010	7.925	-0.050	-0.050	0.000	0.000	0.000
81	A	418	ARG	1	0.985	0.993	10.760	0.456	0.456	0.000	0.000	0.000
82	A	419	THR	0	-0.009	-0.038	12.644	0.003	0.003	0.000	0.000	0.000
83	A	420	GLY	0	0.041	0.051	15.281	0.033	0.033	0.000	0.000	0.000
84	A	421	TYR	0	-0.010	0.019	10.699	0.050	0.050	0.000	0.000	0.000
85	A	422	ASN	0	-0.011	-0.032	10.169	-0.130	-0.130	0.000	0.000	0.000
86	A	423	GLY	0	0.041	0.027	6.270	-0.015	-0.015	0.000	0.000	0.000
87	A	424	ILE	0	-0.030	-0.027	4.468	0.121	0.312	-0.001	-0.017	-0.173
88	A	425	TRP	0	-0.040	-0.024	6.942	-0.334	-0.334	0.000	0.000	0.000
89	A	426	SER	0	0.025	0.004	8.974	0.105	0.105	0.000	0.000	0.000
90	A	427	GLU	-1	-0.911	-0.941	9.902	0.257	0.257	0.000	0.000	0.000
91	A	428	TRP	0	-0.054	-0.049	12.290	-0.076	-0.076	0.000	0.000	0.000
92	A	429	SER	0	0.000	0.019	15.749	0.008	0.008	0.000	0.000	0.000
93	A	430	GLU	-1	-0.906	-0.956	16.767	-0.010	-0.010	0.000	0.000	0.000
94	A	431	ALA	0	-0.067	-0.035	19.512	-0.012	-0.012	0.000	0.000	0.000
95	A	432	ARG	1	0.866	0.946	21.098	0.073	0.073	0.000	0.000	0.000
96	A	433	SER	0	0.014	-0.016	24.866	0.000	0.000	0.000	0.000	0.000
97	A	434	TRP	0	-0.048	-0.018	27.413	-0.004	-0.004	0.000	0.000	0.000
98	A	435	ASP	-1	-0.835	-0.938	31.732	-0.020	-0.020	0.000	0.000	0.000
99	A	436	THR	0	-0.081	-0.021	35.414	-0.003	-0.003	0.000	0.000	0.000
100	A	437	GLU	-1	-0.921	-0.957	37.086	-0.031	-0.031	0.000	0.000	0.000
101	A	438	SER	0	-0.010	-0.002	40.174	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)