FMO DATABASE

FMODB ID: K9LR3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-801022.962314
FMO2-HF: Nuclear repulsion	758622.946967
FMO2-HF: Total energy	-42400.015347
FMO2-MP2: Total energy	-42522.842134

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.
-0.735	1.486	-0.001	-0.881	-1.34	0.001

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 : -0.010 / 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

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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	A	340	MET	0	-0.050	-0.013	3.661	-1.222	0.596	0.000	-0.829	-0.990	0.001
4	A	341	ALA	0	0.045	0.010	5.887	0.239	0.239	0.000	0.000	0.000	0.000
5	A	342	PRO	0	0.018	0.023	8.687	-0.032	-0.032	0.000	0.000	0.000	0.000
6	A	343	PRO	0	-0.050	-0.014	12.140	-0.004	-0.004	0.000	0.000	0.000	0.000
7	A	344	SER	0	0.009	-0.016	14.333	0.045	0.045	0.000	0.000	0.000	0.000
8	A	345	LEU	0	-0.052	-0.012	17.354	0.005	0.005	0.000	0.000	0.000	0.000
9	A	346	ASN	0	-0.076	-0.031	20.271	0.020	0.020	0.000	0.000	0.000	0.000
10	A	347	VAL	0	0.041	0.004	23.653	-0.004	-0.004	0.000	0.000	0.000	0.000
11	A	348	THR	0	-0.017	-0.003	27.000	0.005	0.005	0.000	0.000	0.000	0.000
12	A	349	LYS	1	0.783	0.873	29.942	0.040	0.040	0.000	0.000	0.000	0.000
13	A	350	ASP	-1	-0.871	-0.925	33.378	-0.054	-0.054	0.000	0.000	0.000	0.000
14	A	351	GLY	0	0.033	0.029	35.929	0.001	0.001	0.000	0.000	0.000	0.000
15	A	352	ASP	-1	-0.821	-0.898	37.509	-0.037	-0.037	0.000	0.000	0.000	0.000
16	A	353	SER	0	-0.031	-0.015	34.593	0.001	0.001	0.000	0.000	0.000	0.000
17	A	354	TYR	0	-0.001	-0.018	31.320	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	355	SER	0	-0.055	-0.029	27.995	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	356	LEU	0	0.013	0.010	23.553	0.000	0.000	0.000	0.000	0.000	0.000
20	A	357	ARG	1	0.865	0.914	21.260	0.138	0.138	0.000	0.000	0.000	0.000
21	A	358	TRP	0	0.004	0.003	16.314	0.013	0.013	0.000	0.000	0.000	0.000
22	A	359	GLU	-1	-0.749	-0.856	16.370	-0.178	-0.178	0.000	0.000	0.000	0.000
23	A	360	THR	0	-0.021	-0.027	10.756	0.000	0.000	0.000	0.000	0.000	0.000
24	A	361	MET	0	0.010	0.002	9.078	0.022	0.022	0.000	0.000	0.000	0.000
25	A	362	LYS	1	0.932	0.978	7.204	0.497	0.497	0.000	0.000	0.000	0.000
26	A	363	MET	0	0.022	0.023	10.221	-0.016	-0.016	0.000	0.000	0.000	0.000
27	A	364	ARG	1	0.835	0.911	9.581	0.258	0.258	0.000	0.000	0.000	0.000
28	A	365	TYR	0	0.021	-0.006	5.536	0.061	0.061	0.000	0.000	0.000	0.000
29	A	366	GLU	-1	-0.893	-0.945	10.740	-0.210	-0.210	0.000	0.000	0.000	0.000
30	A	367	HIS	0	0.015	0.015	9.720	0.043	0.043	0.000	0.000	0.000	0.000
31	A	368	ILE	0	-0.045	-0.019	6.911	-0.007	-0.007	0.000	0.000	0.000	0.000
32	A	369	ASP	-1	-0.805	-0.868	10.785	-0.268	-0.268	0.000	0.000	0.000	0.000
33	A	370	HIS	0	0.017	0.009	7.698	-0.067	-0.067	0.000	0.000	0.000	0.000
34	A	371	THR	0	0.001	0.004	11.453	0.090	0.090	0.000	0.000	0.000	0.000
35	A	372	PHE	0	0.010	-0.008	12.509	-0.054	-0.054	0.000	0.000	0.000	0.000
36	A	373	GLU	-1	-0.816	-0.879	14.988	-0.038	-0.038	0.000	0.000	0.000	0.000
37	A	374	ILE	0	0.000	0.004	17.406	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	375	GLN	0	-0.005	0.000	20.346	0.015	0.015	0.000	0.000	0.000	0.000
39	A	376	TYR	0	-0.030	-0.046	23.272	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	377	ARG	1	0.818	0.933	26.440	0.021	0.021	0.000	0.000	0.000	0.000
41	A	378	LYS	1	0.876	0.922	29.571	0.014	0.014	0.000	0.000	0.000	0.000
42	A	379	ASP	-1	-0.792	-0.915	31.650	-0.013	-0.013	0.000	0.000	0.000	0.000
43	A	380	THR	0	-0.041	-0.012	33.235	0.002	0.002	0.000	0.000	0.000	0.000
44	A	381	ALA	0	-0.009	0.011	32.241	0.003	0.003	0.000	0.000	0.000	0.000
45	A	382	THR	0	0.041	0.020	28.079	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	383	TRP	0	0.049	0.018	23.578	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	384	LYS	1	0.934	0.977	25.212	-0.048	-0.048	0.000	0.000	0.000	0.000
48	A	385	ASP	-1	-0.893	-0.946	26.305	0.020	0.020	0.000	0.000	0.000	0.000
49	A	386	SER	0	-0.064	-0.033	26.438	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	387	LYS	1	0.838	0.905	25.621	0.042	0.042	0.000	0.000	0.000	0.000
51	A	388	THR	0	-0.003	-0.023	21.126	0.000	0.000	0.000	0.000	0.000	0.000
52	A	389	GLU	-1	-0.749	-0.832	22.377	-0.055	-0.055	0.000	0.000	0.000	0.000
53	A	390	THR	0	-0.012	-0.024	17.322	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	391	LEU	0	-0.023	-0.009	18.130	0.008	0.008	0.000	0.000	0.000	0.000
55	A	392	GLN	0	-0.037	-0.038	15.010	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	393	ASN	0	-0.057	-0.052	14.477	-0.019	-0.019	0.000	0.000	0.000	0.000
57	A	394	ALA	0	0.032	0.028	16.467	0.017	0.017	0.000	0.000	0.000	0.000
58	A	395	HIS	0	0.004	-0.004	14.449	0.001	0.001	0.000	0.000	0.000	0.000
59	A	396	SER	0	-0.003	-0.004	19.234	0.009	0.009	0.000	0.000	0.000	0.000
60	A	397	MET	0	-0.050	-0.016	22.634	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	398	ALA	0	0.033	0.023	24.994	0.003	0.003	0.000	0.000	0.000	0.000
62	A	399	LEU	0	-0.038	-0.019	27.215	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	400	PRO	0	-0.006	-0.010	30.156	0.002	0.002	0.000	0.000	0.000	0.000
64	A	401	ALA	0	0.021	0.018	33.351	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	402	LEU	0	-0.019	-0.005	32.233	0.001	0.001	0.000	0.000	0.000	0.000
66	A	403	GLU	-1	-0.788	-0.878	36.382	-0.019	-0.019	0.000	0.000	0.000	0.000
67	A	404	PRO	0	0.055	0.009	38.557	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	405	SER	0	-0.037	-0.003	40.850	0.002	0.002	0.000	0.000	0.000	0.000
69	A	406	THR	0	-0.012	-0.002	36.252	0.003	0.003	0.000	0.000	0.000	0.000
70	A	407	ARG	1	0.820	0.913	31.042	0.024	0.024	0.000	0.000	0.000	0.000
71	A	408	TYR	0	-0.040	-0.027	30.733	0.003	0.003	0.000	0.000	0.000	0.000
72	A	409	TRP	0	-0.040	-0.038	25.984	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	410	ALA	0	0.002	0.002	23.770	0.001	0.001	0.000	0.000	0.000	0.000
74	A	411	ARG	1	0.880	0.934	19.269	0.024	0.024	0.000	0.000	0.000	0.000
75	A	412	VAL	0	0.035	0.017	15.839	0.004	0.004	0.000	0.000	0.000	0.000
76	A	413	ARG	1	0.799	0.905	12.780	0.076	0.076	0.000	0.000	0.000	0.000
77	A	414	VAL	0	0.029	0.001	10.218	0.022	0.022	0.000	0.000	0.000	0.000
78	A	415	ARG	1	0.881	0.951	7.905	0.054	0.054	0.000	0.000	0.000	0.000
79	A	416	THR	0	0.050	0.034	4.191	-0.005	0.126	-0.001	-0.010	-0.120	0.000
80	A	417	SER	0	-0.014	-0.017	7.567	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	418	ARG	1	0.957	0.961	10.283	0.261	0.261	0.000	0.000	0.000	0.000
82	A	419	THR	0	-0.004	-0.006	12.673	0.017	0.017	0.000	0.000	0.000	0.000
83	A	420	GLY	0	0.048	0.037	15.513	0.024	0.024	0.000	0.000	0.000	0.000
84	A	421	TYR	0	0.011	0.020	10.469	0.041	0.041	0.000	0.000	0.000	0.000
85	A	422	ASN	0	-0.028	-0.049	10.040	-0.120	-0.120	0.000	0.000	0.000	0.000
86	A	423	GLY	0	0.030	0.033	6.062	0.131	0.131	0.000	0.000	0.000	0.000
87	A	424	ILE	0	-0.016	-0.016	4.178	-0.176	0.096	0.000	-0.042	-0.230	0.000
88	A	425	TRP	0	-0.040	-0.007	6.741	-0.484	-0.484	0.000	0.000	0.000	0.000
89	A	426	SER	0	0.003	-0.006	8.664	0.077	0.077	0.000	0.000	0.000	0.000
90	A	427	GLU	-1	-0.845	-0.929	9.571	0.157	0.157	0.000	0.000	0.000	0.000
91	A	428	TRP	0	-0.020	-0.023	12.019	-0.081	-0.081	0.000	0.000	0.000	0.000
92	A	429	SER	0	-0.006	0.004	15.388	0.000	0.000	0.000	0.000	0.000	0.000
93	A	430	GLU	-1	-0.842	-0.896	16.855	-0.051	-0.051	0.000	0.000	0.000	0.000
94	A	431	ALA	0	-0.044	-0.017	19.660	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	432	ARG	1	0.821	0.886	21.403	0.093	0.093	0.000	0.000	0.000	0.000
96	A	433	SER	0	-0.003	0.000	24.784	0.003	0.003	0.000	0.000	0.000	0.000
97	A	434	TRP	0	-0.005	-0.021	27.049	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	435	ASP	-1	-0.796	-0.892	31.480	-0.025	-0.025	0.000	0.000	0.000	0.000
99	A	436	THR	0	-0.071	-0.026	35.212	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	437	GLU	-1	-0.824	-0.897	37.098	-0.032	-0.032	0.000	0.000	0.000	0.000
101	A	438	SER	0	-0.043	-0.023	40.163	0.002	0.002	0.000	0.000	0.000	0.000

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