FMO DATABASE

FMODB ID: Q1LNY

Calculation Name: 3CZU-A-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 3CZU

Chain ID: A

ChEMBL ID:

UniProt ID: P20827

Base Structure: X-ray

Registration Date: 2023-03-14

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	173
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1870504.126003
FMO2-HF: Nuclear repulsion	1799125.725534
FMO2-HF: Total energy	-71378.400469
FMO2-MP2: Total energy	-71582.515934

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:27:LYS)

Summations of interaction energy for fragment #1(A:27:LYS)

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.
-53.443	-55.72	20.638	-8.003	-10.358	-0.071

Interaction energy analysis for fragmet #1(A:27:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.891 / q_NPA : 0.908

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	A	29	VAL	0	-0.016	0.006	3.718	0.717	2.605	-0.013	-0.759	-1.116	-0.001
4	A	30	VAL	0	0.003	-0.008	5.900	1.799	1.799	0.000	0.000	0.000	0.000
5	A	31	LEU	0	-0.044	-0.028	9.419	0.631	0.631	0.000	0.000	0.000	0.000
6	A	32	LEU	0	-0.019	-0.014	12.425	1.636	1.636	0.000	0.000	0.000	0.000
7	A	33	ASP	-1	-0.855	-0.939	13.605	-19.633	-19.633	0.000	0.000	0.000	0.000
8	A	34	PHE	0	-0.046	-0.022	15.664	0.523	0.523	0.000	0.000	0.000	0.000
9	A	35	ALA	0	0.021	0.012	18.120	0.533	0.533	0.000	0.000	0.000	0.000
10	A	36	ALA	0	-0.022	-0.002	15.859	0.453	0.453	0.000	0.000	0.000	0.000
11	A	37	ALA	0	-0.025	-0.015	17.968	0.243	0.243	0.000	0.000	0.000	0.000
12	A	38	GLY	0	0.032	0.022	20.498	0.470	0.470	0.000	0.000	0.000	0.000
13	A	39	GLY	0	-0.014	-0.015	23.482	0.427	0.427	0.000	0.000	0.000	0.000
14	A	40	GLU	-1	-0.951	-0.966	24.127	-11.275	-11.275	0.000	0.000	0.000	0.000
15	A	41	LEU	0	-0.063	-0.027	20.244	-0.017	-0.017	0.000	0.000	0.000	0.000
16	A	42	GLY	0	-0.013	0.005	24.605	0.010	0.010	0.000	0.000	0.000	0.000
17	A	43	TRP	0	0.009	-0.004	20.702	-0.024	-0.024	0.000	0.000	0.000	0.000
18	A	44	LEU	0	-0.007	0.018	27.428	0.384	0.384	0.000	0.000	0.000	0.000
19	A	45	THR	0	0.010	-0.005	29.969	-0.192	-0.192	0.000	0.000	0.000	0.000
20	A	46	HIS	0	-0.024	0.010	32.555	0.208	0.208	0.000	0.000	0.000	0.000
21	A	47	PRO	0	0.018	-0.006	34.980	-0.150	-0.150	0.000	0.000	0.000	0.000
22	A	48	TYR	0	0.003	-0.018	37.565	-0.127	-0.127	0.000	0.000	0.000	0.000
23	A	49	GLY	0	0.020	0.022	37.351	0.201	0.201	0.000	0.000	0.000	0.000
24	A	50	LYS	1	0.833	0.903	38.002	8.112	8.112	0.000	0.000	0.000	0.000
25	A	51	GLY	0	-0.021	-0.012	35.475	0.064	0.064	0.000	0.000	0.000	0.000
26	A	52	TRP	0	-0.027	-0.028	28.393	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	53	ASP	-1	-0.841	-0.918	32.842	-8.523	-8.523	0.000	0.000	0.000	0.000
28	A	54	LEU	0	-0.080	-0.038	27.419	-0.295	-0.295	0.000	0.000	0.000	0.000
29	A	55	MET	0	-0.015	0.001	30.538	0.341	0.341	0.000	0.000	0.000	0.000
30	A	56	GLN	0	0.020	-0.006	29.933	-0.508	-0.508	0.000	0.000	0.000	0.000
31	A	57	ASN	0	-0.028	-0.026	29.972	0.401	0.401	0.000	0.000	0.000	0.000
32	A	58	ILE	0	0.016	0.031	29.595	-0.263	-0.263	0.000	0.000	0.000	0.000
33	A	59	MET	0	-0.018	-0.007	23.877	0.224	0.224	0.000	0.000	0.000	0.000
34	A	60	ASN	0	-0.015	-0.012	24.094	0.022	0.022	0.000	0.000	0.000	0.000
35	A	61	ASP	-1	-0.913	-0.954	27.304	-9.562	-9.562	0.000	0.000	0.000	0.000
36	A	62	MET	0	-0.023	-0.009	24.226	-0.058	-0.058	0.000	0.000	0.000	0.000
37	A	63	PRO	0	-0.021	-0.005	26.428	0.157	0.157	0.000	0.000	0.000	0.000
38	A	64	ILE	0	-0.014	-0.010	24.084	-0.472	-0.472	0.000	0.000	0.000	0.000
39	A	65	TYR	0	0.036	0.005	25.074	0.351	0.351	0.000	0.000	0.000	0.000
40	A	66	MET	0	-0.025	-0.013	25.368	-0.340	-0.340	0.000	0.000	0.000	0.000
41	A	67	TYR	0	0.036	0.036	25.804	0.263	0.263	0.000	0.000	0.000	0.000
42	A	68	SER	0	-0.022	-0.012	28.322	-0.164	-0.164	0.000	0.000	0.000	0.000
43	A	69	VAL	0	-0.006	-0.003	31.034	0.197	0.197	0.000	0.000	0.000	0.000
44	A	70	CYS	0	-0.042	-0.021	33.889	0.024	0.024	0.000	0.000	0.000	0.000
45	A	71	ASN	0	0.008	0.014	36.640	0.232	0.232	0.000	0.000	0.000	0.000
46	A	72	VAL	0	0.038	0.007	38.208	0.052	0.052	0.000	0.000	0.000	0.000
47	A	73	MET	0	-0.053	-0.017	40.555	0.134	0.134	0.000	0.000	0.000	0.000
48	A	74	SER	0	-0.033	-0.015	42.800	0.115	0.115	0.000	0.000	0.000	0.000
49	A	75	GLY	0	0.009	0.016	44.144	0.048	0.048	0.000	0.000	0.000	0.000
50	A	76	ASP	-1	-0.924	-0.972	41.614	-7.450	-7.450	0.000	0.000	0.000	0.000
51	A	77	GLN	0	0.024	0.031	37.722	-0.072	-0.072	0.000	0.000	0.000	0.000
52	A	78	ASP	-1	-0.769	-0.862	35.698	-8.877	-8.877	0.000	0.000	0.000	0.000
53	A	79	ASN	0	-0.040	-0.002	34.244	0.184	0.184	0.000	0.000	0.000	0.000
54	A	80	TRP	0	-0.041	-0.043	29.034	-0.386	-0.386	0.000	0.000	0.000	0.000
55	A	81	LEU	0	0.000	0.027	26.321	0.200	0.200	0.000	0.000	0.000	0.000
56	A	82	ARG	1	0.847	0.919	25.847	10.873	10.873	0.000	0.000	0.000	0.000
57	A	83	THR	0	0.030	0.016	21.033	0.092	0.092	0.000	0.000	0.000	0.000
58	A	84	ASN	0	0.001	-0.016	22.417	0.576	0.576	0.000	0.000	0.000	0.000
59	A	85	TRP	0	-0.023	-0.015	21.197	-0.751	-0.751	0.000	0.000	0.000	0.000
60	A	86	VAL	0	0.000	0.010	15.640	-0.233	-0.233	0.000	0.000	0.000	0.000
61	A	87	TYR	0	-0.026	-0.019	15.304	0.354	0.354	0.000	0.000	0.000	0.000
62	A	88	ARG	1	0.882	0.925	14.685	17.913	17.913	0.000	0.000	0.000	0.000
63	A	89	GLY	0	-0.003	-0.005	13.018	-1.756	-1.756	0.000	0.000	0.000	0.000
64	A	90	GLU	-1	-0.823	-0.869	6.825	-36.345	-36.345	0.000	0.000	0.000	0.000
65	A	91	ALA	0	-0.019	0.011	10.586	-1.430	-1.430	0.000	0.000	0.000	0.000
66	A	92	GLU	-1	-0.898	-0.935	11.238	-21.161	-21.161	0.000	0.000	0.000	0.000
67	A	93	ARG	1	0.901	0.945	11.115	21.873	21.873	0.000	0.000	0.000	0.000
68	A	94	ILE	0	-0.035	-0.003	10.407	-2.638	-2.638	0.000	0.000	0.000	0.000
69	A	95	PHE	0	-0.027	-0.037	8.548	0.963	0.963	0.000	0.000	0.000	0.000
70	A	96	ILE	0	-0.008	-0.015	11.978	-0.419	-0.419	0.000	0.000	0.000	0.000
71	A	97	GLU	-1	-0.766	-0.866	12.648	-19.376	-19.376	0.000	0.000	0.000	0.000
72	A	98	LEU	0	-0.007	-0.014	15.263	0.362	0.362	0.000	0.000	0.000	0.000
73	A	99	LYS	1	0.886	0.928	15.455	16.843	16.843	0.000	0.000	0.000	0.000
74	A	100	PHE	0	-0.014	-0.014	20.579	0.269	0.269	0.000	0.000	0.000	0.000
75	A	101	THR	0	0.028	0.020	24.377	-0.020	-0.020	0.000	0.000	0.000	0.000
76	A	102	VAL	0	0.031	0.007	27.814	0.012	0.012	0.000	0.000	0.000	0.000
77	A	103	ARG	1	0.834	0.908	30.660	7.922	7.922	0.000	0.000	0.000	0.000
78	A	104	ASP	-1	-0.786	-0.878	34.303	-7.812	-7.812	0.000	0.000	0.000	0.000
79	A	105	CYS	0	-0.028	0.003	36.746	-0.039	-0.039	0.000	0.000	0.000	0.000
80	A	106	ASN	0	-0.051	-0.033	39.148	0.356	0.356	0.000	0.000	0.000	0.000
81	A	107	SER	0	-0.083	-0.031	39.091	0.168	0.168	0.000	0.000	0.000	0.000
82	A	108	PHE	0	-0.003	-0.028	37.721	0.026	0.026	0.000	0.000	0.000	0.000
83	A	109	PRO	0	-0.017	-0.009	43.367	0.088	0.088	0.000	0.000	0.000	0.000
84	A	110	GLY	0	-0.020	0.001	46.728	0.115	0.115	0.000	0.000	0.000	0.000
85	A	111	GLY	0	0.070	0.022	43.901	0.010	0.010	0.000	0.000	0.000	0.000
86	A	112	ALA	0	0.028	0.034	44.847	0.101	0.101	0.000	0.000	0.000	0.000
87	A	113	SER	0	0.005	0.000	43.721	-0.107	-0.107	0.000	0.000	0.000	0.000
88	A	114	SER	0	-0.029	-0.027	42.380	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	116	LYS	1	0.792	0.889	35.270	8.069	8.069	0.000	0.000	0.000	0.000
90	A	117	GLU	-1	-0.778	-0.904	33.131	-8.609	-8.609	0.000	0.000	0.000	0.000
91	A	118	THR	0	-0.030	-0.013	30.002	-0.211	-0.211	0.000	0.000	0.000	0.000
92	A	119	PHE	0	-0.013	0.002	24.104	0.262	0.262	0.000	0.000	0.000	0.000
93	A	120	ASN	0	-0.018	-0.003	27.383	-0.363	-0.363	0.000	0.000	0.000	0.000
94	A	121	LEU	0	0.060	0.047	19.755	0.022	0.022	0.000	0.000	0.000	0.000
95	A	122	TYR	0	-0.039	-0.038	24.477	0.112	0.112	0.000	0.000	0.000	0.000
96	A	123	TYR	0	0.027	0.005	20.558	-0.376	-0.376	0.000	0.000	0.000	0.000
97	A	124	ALA	0	0.032	0.023	23.102	0.575	0.575	0.000	0.000	0.000	0.000
98	A	125	GLU	-1	-0.772	-0.879	20.830	-15.705	-15.705	0.000	0.000	0.000	0.000
99	A	126	SER	0	-0.060	-0.056	22.844	0.780	0.780	0.000	0.000	0.000	0.000
100	A	127	ASP	-1	-0.795	-0.888	23.062	-13.299	-13.299	0.000	0.000	0.000	0.000
101	A	128	LEU	0	-0.033	-0.024	24.567	-0.207	-0.207	0.000	0.000	0.000	0.000
102	A	129	ASP	-1	-0.784	-0.853	25.083	-11.854	-11.854	0.000	0.000	0.000	0.000
103	A	130	TYR	0	-0.005	-0.006	26.532	0.495	0.495	0.000	0.000	0.000	0.000
104	A	131	GLY	0	0.047	0.027	28.612	0.455	0.455	0.000	0.000	0.000	0.000
105	A	132	THR	0	0.008	-0.012	30.153	-0.227	-0.227	0.000	0.000	0.000	0.000
106	A	133	ASN	0	-0.062	-0.017	32.688	0.410	0.410	0.000	0.000	0.000	0.000
107	A	134	PHE	0	0.011	-0.001	29.482	-0.377	-0.377	0.000	0.000	0.000	0.000
108	A	135	GLN	0	0.048	0.033	32.379	0.226	0.226	0.000	0.000	0.000	0.000
109	A	136	LYS	1	0.923	0.936	31.828	8.473	8.473	0.000	0.000	0.000	0.000
110	A	137	ARG	1	0.852	0.915	31.505	9.124	9.124	0.000	0.000	0.000	0.000
111	A	138	LEU	0	0.011	0.018	29.912	0.027	0.027	0.000	0.000	0.000	0.000
112	A	139	PHE	0	-0.047	-0.022	25.378	-0.377	-0.377	0.000	0.000	0.000	0.000
113	A	140	THR	0	-0.017	0.001	25.238	0.472	0.472	0.000	0.000	0.000	0.000
114	A	141	LYS	1	0.808	0.881	25.333	10.251	10.251	0.000	0.000	0.000	0.000
115	A	142	ILE	0	-0.037	-0.019	19.368	-0.104	-0.104	0.000	0.000	0.000	0.000
116	A	143	ASP	-1	-0.767	-0.868	22.799	-12.405	-12.405	0.000	0.000	0.000	0.000
117	A	144	THR	0	-0.074	-0.044	24.599	0.267	0.267	0.000	0.000	0.000	0.000
118	A	145	ILE	0	-0.024	0.002	22.157	-0.336	-0.336	0.000	0.000	0.000	0.000
119	A	146	ALA	0	0.027	-0.008	25.602	0.489	0.489	0.000	0.000	0.000	0.000
120	A	147	PRO	0	-0.042	-0.007	25.863	-0.424	-0.424	0.000	0.000	0.000	0.000
121	A	148	ASP	-1	-0.881	-0.926	23.920	-11.759	-11.759	0.000	0.000	0.000	0.000
122	A	149	GLU	-1	-0.953	-0.994	27.107	-9.970	-9.970	0.000	0.000	0.000	0.000
123	A	150	ILE	0	-0.036	-0.007	28.933	-0.120	-0.120	0.000	0.000	0.000	0.000
124	A	151	THR	0	-0.026	-0.018	31.337	0.028	0.028	0.000	0.000	0.000	0.000
125	A	152	VAL	0	0.027	-0.010	33.247	0.193	0.193	0.000	0.000	0.000	0.000
126	A	153	SER	0	0.021	-0.002	36.910	-0.063	-0.063	0.000	0.000	0.000	0.000
127	A	154	SER	0	0.026	0.004	38.238	0.050	0.050	0.000	0.000	0.000	0.000
128	A	155	ASP	-1	-0.776	-0.864	34.165	-8.740	-8.740	0.000	0.000	0.000	0.000
129	A	156	PHE	0	-0.055	-0.029	35.721	-0.144	-0.144	0.000	0.000	0.000	0.000
130	A	157	GLU	-1	-1.002	-0.996	37.919	-7.210	-7.210	0.000	0.000	0.000	0.000
131	A	158	ALA	0	0.043	0.028	36.860	0.038	0.038	0.000	0.000	0.000	0.000
132	A	159	ARG	1	0.859	0.929	34.073	8.324	8.324	0.000	0.000	0.000	0.000
133	A	160	HIS	0	0.019	0.025	29.366	-0.227	-0.227	0.000	0.000	0.000	0.000
134	A	161	VAL	0	-0.017	-0.018	26.933	0.043	0.043	0.000	0.000	0.000	0.000
135	A	162	LYS	1	0.848	0.924	27.602	8.892	8.892	0.000	0.000	0.000	0.000
136	A	163	LEU	0	-0.050	-0.026	21.435	-0.038	-0.038	0.000	0.000	0.000	0.000
137	A	164	ASN	0	0.022	0.023	22.954	-0.339	-0.339	0.000	0.000	0.000	0.000
138	A	165	VAL	0	0.012	-0.014	16.522	-0.361	-0.361	0.000	0.000	0.000	0.000
139	A	166	GLU	-1	-0.764	-0.842	19.033	-13.520	-13.520	0.000	0.000	0.000	0.000
140	A	167	GLU	-1	-0.851	-0.900	11.867	-24.034	-24.034	0.000	0.000	0.000	0.000
141	A	168	ARG	1	0.700	0.811	16.158	14.820	14.820	0.000	0.000	0.000	0.000
142	A	169	SER	0	0.021	0.013	13.140	-1.126	-1.126	0.000	0.000	0.000	0.000
143	A	170	VAL	0	-0.009	0.008	14.996	1.043	1.043	0.000	0.000	0.000	0.000
144	A	171	GLY	0	0.006	0.009	15.124	-1.510	-1.510	0.000	0.000	0.000	0.000
145	A	172	PRO	0	-0.069	-0.025	16.006	0.633	0.633	0.000	0.000	0.000	0.000
146	A	173	LEU	0	-0.008	-0.023	15.426	0.949	0.949	0.000	0.000	0.000	0.000
147	A	174	THR	0	-0.011	-0.030	17.335	-0.375	-0.375	0.000	0.000	0.000	0.000
148	A	175	ARG	1	0.816	0.910	19.904	12.621	12.621	0.000	0.000	0.000	0.000
149	A	176	LYS	1	0.929	0.982	19.421	12.524	12.524	0.000	0.000	0.000	0.000
150	A	177	GLY	0	0.039	0.009	18.849	-0.774	-0.774	0.000	0.000	0.000	0.000
151	A	178	PHE	0	-0.007	0.003	15.222	0.445	0.445	0.000	0.000	0.000	0.000
152	A	179	TYR	0	-0.054	-0.031	20.505	0.005	0.005	0.000	0.000	0.000	0.000
153	A	180	LEU	0	0.026	0.006	17.798	-0.163	-0.163	0.000	0.000	0.000	0.000
154	A	181	ALA	0	-0.017	-0.016	22.238	0.429	0.429	0.000	0.000	0.000	0.000
155	A	182	PHE	0	0.021	0.015	21.248	-0.264	-0.264	0.000	0.000	0.000	0.000
156	A	183	GLN	0	0.019	0.009	26.845	0.115	0.115	0.000	0.000	0.000	0.000
157	A	184	ASP	-1	-0.725	-0.858	30.245	-9.095	-9.095	0.000	0.000	0.000	0.000
158	A	185	ILE	0	-0.020	-0.013	32.423	0.186	0.186	0.000	0.000	0.000	0.000
159	A	186	GLY	0	-0.021	-0.015	35.380	0.295	0.295	0.000	0.000	0.000	0.000
160	A	187	ALA	0	0.008	0.017	32.892	0.169	0.169	0.000	0.000	0.000	0.000
161	A	189	VAL	0	0.017	0.012	28.028	-0.106	-0.106	0.000	0.000	0.000	0.000
162	A	190	ALA	0	0.028	0.013	28.713	0.173	0.173	0.000	0.000	0.000	0.000
163	A	191	LEU	0	-0.012	-0.010	22.057	-0.279	-0.279	0.000	0.000	0.000	0.000
164	A	192	LEU	0	0.010	-0.002	22.868	0.087	0.087	0.000	0.000	0.000	0.000
165	A	193	SER	0	0.022	0.012	17.314	-0.477	-0.477	0.000	0.000	0.000	0.000
166	A	194	VAL	0	-0.008	-0.004	17.941	0.180	0.180	0.000	0.000	0.000	0.000
167	A	195	ARG	1	0.872	0.932	7.671	26.176	26.176	0.000	0.000	0.000	0.000
168	A	196	VAL	0	-0.022	-0.008	13.333	-0.126	-0.126	0.000	0.000	0.000	0.000
169	A	197	TYR	0	-0.059	-0.059	6.910	-2.064	-2.064	0.000	0.000	0.000	0.000
170	A	198	TYR	0	0.014	-0.020	6.479	1.866	1.866	0.000	0.000	0.000	0.000
171	A	199	LYS	1	0.859	0.950	3.741	28.385	28.704	0.001	-0.084	-0.235	0.000
172	A	200	LYS	1	0.894	0.935	2.071	45.107	46.792	2.122	-1.158	-2.650	-0.005
173	A	201	CYS	0	0.021	0.031	1.829	-37.756	-43.925	18.528	-6.002	-6.357	-0.065

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Interactive mode: IFIE and PIEDA for fragment #1(A:27:LYS)