FMO DATABASE

FMODB ID: N8Q8Q

Calculation Name: 5YXA-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5YXA

Chain ID: A

ChEMBL ID:

UniProt ID: Q1X881

Base Structure: X-ray

Registration Date: 2025-10-04

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

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. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1824438.596384
FMO2-HF: Nuclear repulsion	1752995.508323
FMO2-HF: Total energy	-71443.088061
FMO2-MP2: Total energy	-71640.483298

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:5:SER)

Summations of interaction energy for fragment #1(A:5:SER)

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.
-187.696	-187.54	14.776	-8.863	-6.07	-0.108

Interaction energy analysis for fragmet #1(A:5:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.765 / q_NPA : 0.862

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	7	ASP	-1	-0.858	-0.907	3.870	-43.318	-41.996	-0.015	-0.576	-0.731	-0.002
49	A	54	GLU	-1	-0.743	-0.854	1.716	-114.784	-116.006	14.792	-8.285	-5.285	-0.106
69	A	74	ARG	1	0.896	0.941	4.407	48.235	48.291	-0.001	-0.002	-0.054	0.000
4	A	8	CYS	0	-0.129	-0.063	5.106	-1.661	-1.661	0.000	0.000	0.000	0.000
5	A	9	ASP	-1	-0.810	-0.920	9.413	-20.093	-20.093	0.000	0.000	0.000	0.000
6	A	10	GLY	0	0.034	0.011	12.796	1.486	1.486	0.000	0.000	0.000	0.000
7	A	11	ALA	0	-0.067	-0.022	14.588	1.376	1.376	0.000	0.000	0.000	0.000
8	A	12	ILE	0	-0.047	-0.022	15.789	1.313	1.313	0.000	0.000	0.000	0.000
9	A	13	LEU	0	-0.050	-0.017	12.336	0.280	0.280	0.000	0.000	0.000	0.000
10	A	14	GLY	0	-0.004	-0.001	17.072	0.643	0.643	0.000	0.000	0.000	0.000
11	A	15	ALA	0	0.002	-0.013	18.284	-0.574	-0.574	0.000	0.000	0.000	0.000
12	A	16	ALA	0	-0.027	-0.003	20.372	0.513	0.513	0.000	0.000	0.000	0.000
13	A	17	VAL	0	0.033	-0.004	23.597	-0.184	-0.184	0.000	0.000	0.000	0.000
14	A	18	ASN	0	-0.023	-0.012	25.939	0.329	0.329	0.000	0.000	0.000	0.000
15	A	19	GLY	0	0.029	0.024	29.734	0.117	0.117	0.000	0.000	0.000	0.000
16	A	20	LYS	1	0.841	0.910	29.856	9.175	9.175	0.000	0.000	0.000	0.000
17	A	21	LYS	1	0.942	0.969	28.130	10.125	10.125	0.000	0.000	0.000	0.000
18	A	22	SER	0	0.001	-0.030	23.174	0.083	0.083	0.000	0.000	0.000	0.000
19	A	23	ALA	0	0.001	0.009	22.235	0.280	0.280	0.000	0.000	0.000	0.000
20	A	24	HIS	0	0.021	0.027	16.443	-0.540	-0.540	0.000	0.000	0.000	0.000
21	A	25	GLY	0	0.013	0.004	18.415	0.410	0.410	0.000	0.000	0.000	0.000
22	A	26	SER	0	0.049	0.031	16.366	-0.735	-0.735	0.000	0.000	0.000	0.000
23	A	27	PRO	0	0.018	0.003	18.499	0.468	0.468	0.000	0.000	0.000	0.000
24	A	28	THR	0	-0.015	0.003	16.519	-0.016	-0.016	0.000	0.000	0.000	0.000
25	A	29	PHE	0	-0.006	-0.014	15.789	-0.390	-0.390	0.000	0.000	0.000	0.000
26	A	30	TRP	0	0.031	0.027	18.270	0.068	0.068	0.000	0.000	0.000	0.000
27	A	31	MET	0	0.018	0.023	15.863	-0.165	-0.165	0.000	0.000	0.000	0.000
28	A	32	GLY	0	0.005	0.018	20.153	-0.018	-0.018	0.000	0.000	0.000	0.000
29	A	33	SER	0	0.020	-0.020	21.367	0.065	0.065	0.000	0.000	0.000	0.000
30	A	34	HIS	0	-0.048	-0.041	24.272	0.371	0.371	0.000	0.000	0.000	0.000
31	A	35	GLU	-1	-0.832	-0.896	27.006	-10.188	-10.188	0.000	0.000	0.000	0.000
32	A	36	VAL	0	-0.025	-0.026	29.157	0.395	0.395	0.000	0.000	0.000	0.000
33	A	37	ASN	0	-0.014	-0.013	31.163	-0.051	-0.051	0.000	0.000	0.000	0.000
34	A	38	GLY	0	0.030	0.022	31.493	0.008	0.008	0.000	0.000	0.000	0.000
35	A	39	THR	0	-0.041	-0.016	26.653	-0.388	-0.388	0.000	0.000	0.000	0.000
36	A	40	TRP	0	-0.004	-0.003	23.975	0.126	0.126	0.000	0.000	0.000	0.000
37	A	41	MET	0	-0.046	-0.023	23.700	-0.044	-0.044	0.000	0.000	0.000	0.000
38	A	42	ILE	0	0.015	0.014	18.920	0.224	0.224	0.000	0.000	0.000	0.000
39	A	43	HIS	0	-0.128	-0.044	23.400	0.521	0.521	0.000	0.000	0.000	0.000
40	A	44	THR	0	0.019	0.008	24.366	0.356	0.356	0.000	0.000	0.000	0.000
41	A	45	LEU	0	-0.026	-0.028	17.533	-0.546	-0.546	0.000	0.000	0.000	0.000
42	A	46	GLU	-1	-0.909	-0.949	20.689	-12.263	-12.263	0.000	0.000	0.000	0.000
43	A	47	THR	0	-0.005	-0.012	16.095	-0.894	-0.894	0.000	0.000	0.000	0.000
44	A	48	LEU	0	-0.004	-0.018	18.830	0.484	0.484	0.000	0.000	0.000	0.000
45	A	49	ASP	-1	-0.833	-0.910	15.401	-19.896	-19.896	0.000	0.000	0.000	0.000
46	A	50	TYR	0	-0.091	-0.055	11.026	0.059	0.059	0.000	0.000	0.000	0.000
47	A	51	LYS	1	0.845	0.899	10.388	22.452	22.452	0.000	0.000	0.000	0.000
48	A	52	GLU	-1	-0.851	-0.906	6.088	-32.603	-32.603	0.000	0.000	0.000	0.000
50	A	55	TRP	0	-0.027	-0.035	5.816	3.053	3.053	0.000	0.000	0.000	0.000
51	A	56	PRO	0	0.038	0.039	9.364	-0.478	-0.478	0.000	0.000	0.000	0.000
52	A	57	LEU	0	0.013	-0.007	9.692	2.799	2.799	0.000	0.000	0.000	0.000
53	A	58	THR	0	-0.041	-0.041	12.128	1.215	1.215	0.000	0.000	0.000	0.000
54	A	59	HIS	0	0.015	0.033	14.120	0.674	0.674	0.000	0.000	0.000	0.000
55	A	60	THR	0	-0.037	-0.007	13.075	-0.168	-0.168	0.000	0.000	0.000	0.000
56	A	61	ILE	0	-0.008	-0.002	15.483	0.800	0.800	0.000	0.000	0.000	0.000
57	A	62	GLY	0	-0.003	0.017	18.604	-0.145	-0.145	0.000	0.000	0.000	0.000
58	A	63	THR	0	-0.025	-0.006	14.321	-0.142	-0.142	0.000	0.000	0.000	0.000
59	A	64	SER	0	-0.045	-0.060	16.439	0.801	0.801	0.000	0.000	0.000	0.000
60	A	65	VAL	0	-0.073	-0.014	15.030	0.503	0.503	0.000	0.000	0.000	0.000
61	A	66	GLU	-1	-0.829	-0.900	15.458	-19.086	-19.086	0.000	0.000	0.000	0.000
62	A	67	GLU	-1	-0.862	-0.965	9.602	-30.333	-30.333	0.000	0.000	0.000	0.000
63	A	68	SER	0	-0.049	-0.027	14.043	0.321	0.321	0.000	0.000	0.000	0.000
64	A	69	ASP	-1	-0.930	-0.981	16.766	-13.751	-13.751	0.000	0.000	0.000	0.000
65	A	70	MET	0	-0.068	-0.003	11.039	0.376	0.376	0.000	0.000	0.000	0.000
66	A	71	PHE	0	-0.028	-0.012	16.311	0.442	0.442	0.000	0.000	0.000	0.000
67	A	72	MET	0	0.000	-0.004	12.564	0.483	0.483	0.000	0.000	0.000	0.000
68	A	73	PRO	0	0.039	0.014	10.572	-0.451	-0.451	0.000	0.000	0.000	0.000
70	A	75	SER	0	-0.053	-0.065	5.071	-1.862	-1.862	0.000	0.000	0.000	0.000
71	A	76	ILE	0	-0.007	-0.001	6.114	-2.770	-2.770	0.000	0.000	0.000	0.000
72	A	77	GLY	0	0.054	0.033	8.059	3.367	3.367	0.000	0.000	0.000	0.000
73	A	78	GLY	0	-0.019	-0.003	9.868	2.363	2.363	0.000	0.000	0.000	0.000
74	A	79	PRO	0	-0.005	-0.013	10.705	-1.599	-1.599	0.000	0.000	0.000	0.000
75	A	80	VAL	0	0.077	0.042	9.833	1.029	1.029	0.000	0.000	0.000	0.000
76	A	81	SER	0	0.014	-0.024	12.818	1.301	1.301	0.000	0.000	0.000	0.000
77	A	82	SER	0	-0.001	0.000	16.640	0.152	0.152	0.000	0.000	0.000	0.000
78	A	83	HIS	0	0.038	0.029	19.426	0.521	0.521	0.000	0.000	0.000	0.000
79	A	84	ASN	0	0.016	0.003	13.892	1.512	1.512	0.000	0.000	0.000	0.000
80	A	85	ARG	1	0.986	1.001	17.636	12.893	12.893	0.000	0.000	0.000	0.000
81	A	86	ILE	0	0.033	0.021	20.382	0.637	0.637	0.000	0.000	0.000	0.000
82	A	87	PRO	0	0.011	0.000	23.508	-0.073	-0.073	0.000	0.000	0.000	0.000
83	A	88	GLY	0	-0.006	0.012	26.030	0.337	0.337	0.000	0.000	0.000	0.000
84	A	89	TYR	0	-0.060	-0.044	22.527	0.206	0.206	0.000	0.000	0.000	0.000
85	A	90	LYS	1	0.963	0.990	19.731	13.451	13.451	0.000	0.000	0.000	0.000
86	A	91	VAL	0	0.074	0.055	13.241	0.314	0.314	0.000	0.000	0.000	0.000
87	A	92	GLN	0	-0.056	-0.042	16.229	0.763	0.763	0.000	0.000	0.000	0.000
88	A	93	THR	0	0.039	0.023	13.131	0.250	0.250	0.000	0.000	0.000	0.000
89	A	94	ASN	0	-0.062	-0.062	14.510	-0.068	-0.068	0.000	0.000	0.000	0.000
90	A	95	GLY	0	0.080	0.033	16.736	1.202	1.202	0.000	0.000	0.000	0.000
91	A	96	PRO	0	-0.030	-0.002	17.780	-0.668	-0.668	0.000	0.000	0.000	0.000
92	A	97	TRP	0	0.006	-0.019	15.031	0.506	0.506	0.000	0.000	0.000	0.000
93	A	98	MET	0	0.053	0.025	15.928	-0.548	-0.548	0.000	0.000	0.000	0.000
94	A	99	GLN	0	-0.083	-0.028	17.854	-0.189	-0.189	0.000	0.000	0.000	0.000
95	A	100	VAL	0	-0.014	0.018	17.881	0.602	0.602	0.000	0.000	0.000	0.000
96	A	101	PRO	0	-0.009	-0.020	21.144	0.310	0.310	0.000	0.000	0.000	0.000
97	A	102	LEU	0	-0.041	-0.020	18.909	0.426	0.426	0.000	0.000	0.000	0.000
98	A	103	GLU	-1	-0.844	-0.919	22.466	-11.268	-11.268	0.000	0.000	0.000	0.000
99	A	104	VAL	0	-0.056	-0.028	21.238	0.069	0.069	0.000	0.000	0.000	0.000
100	A	105	LYS	1	0.867	0.952	24.465	10.695	10.695	0.000	0.000	0.000	0.000
101	A	106	ARG	1	0.811	0.888	27.190	10.711	10.711	0.000	0.000	0.000	0.000
102	A	107	GLU	-1	-0.876	-0.941	30.042	-9.270	-9.270	0.000	0.000	0.000	0.000
103	A	108	VAL	0	-0.021	0.011	31.231	-0.305	-0.305	0.000	0.000	0.000	0.000
104	A	109	CYS	0	0.002	0.023	27.750	-0.412	-0.412	0.000	0.000	0.000	0.000
105	A	110	PRO	0	0.063	0.021	32.906	0.272	0.272	0.000	0.000	0.000	0.000
106	A	111	GLY	0	-0.004	0.002	36.172	-0.043	-0.043	0.000	0.000	0.000	0.000
107	A	112	THR	0	-0.079	-0.025	33.804	-0.011	-0.011	0.000	0.000	0.000	0.000
108	A	113	SER	0	-0.022	-0.024	36.635	0.154	0.154	0.000	0.000	0.000	0.000
109	A	114	VAL	0	0.008	-0.012	31.725	-0.170	-0.170	0.000	0.000	0.000	0.000
110	A	115	VAL	0	-0.014	0.001	34.992	0.161	0.161	0.000	0.000	0.000	0.000
111	A	116	VAL	0	-0.003	-0.013	33.350	-0.274	-0.274	0.000	0.000	0.000	0.000
112	A	117	ASP	-1	-0.810	-0.899	34.729	-7.998	-7.998	0.000	0.000	0.000	0.000
113	A	118	SER	0	0.012	-0.001	34.433	-0.237	-0.237	0.000	0.000	0.000	0.000
114	A	119	ASN	0	-0.111	-0.070	34.846	-0.141	-0.141	0.000	0.000	0.000	0.000
115	A	120	CYS	0	-0.043	0.016	32.414	0.127	0.127	0.000	0.000	0.000	0.000
116	A	121	ASP	-1	-0.843	-0.915	29.953	-9.937	-9.937	0.000	0.000	0.000	0.000
117	A	122	GLY	0	-0.050	-0.036	27.448	-0.060	-0.060	0.000	0.000	0.000	0.000
118	A	123	ARG	1	0.784	0.861	18.456	15.534	15.534	0.000	0.000	0.000	0.000
119	A	124	GLY	0	0.015	0.009	23.140	0.033	0.033	0.000	0.000	0.000	0.000
120	A	125	LYS	1	0.963	0.979	19.996	14.310	14.310	0.000	0.000	0.000	0.000
121	A	126	SER	0	0.009	-0.004	21.027	0.508	0.508	0.000	0.000	0.000	0.000
122	A	127	THR	0	-0.070	-0.044	22.845	0.055	0.055	0.000	0.000	0.000	0.000
123	A	128	ARG	1	0.818	0.905	26.150	10.752	10.752	0.000	0.000	0.000	0.000
124	A	129	SER	0	-0.012	-0.039	28.165	0.378	0.378	0.000	0.000	0.000	0.000
125	A	130	THR	0	-0.003	-0.003	31.329	0.274	0.274	0.000	0.000	0.000	0.000
126	A	131	THR	0	0.029	0.018	31.585	-0.304	-0.304	0.000	0.000	0.000	0.000
127	A	132	ASP	-1	-0.830	-0.915	32.152	-9.279	-9.279	0.000	0.000	0.000	0.000
128	A	133	SER	0	-0.084	-0.042	33.219	0.169	0.169	0.000	0.000	0.000	0.000
129	A	134	GLY	0	-0.015	-0.008	35.168	0.261	0.261	0.000	0.000	0.000	0.000
130	A	135	LYS	1	0.904	0.959	36.186	7.871	7.871	0.000	0.000	0.000	0.000
131	A	136	ILE	0	0.037	0.019	36.053	-0.230	-0.230	0.000	0.000	0.000	0.000
132	A	137	ILE	0	0.001	0.013	32.556	0.225	0.225	0.000	0.000	0.000	0.000
133	A	138	PRO	0	0.017	0.003	36.044	-0.152	-0.152	0.000	0.000	0.000	0.000
134	A	139	GLU	-1	-0.812	-0.886	37.571	-7.710	-7.710	0.000	0.000	0.000	0.000
135	A	140	TRP	0	0.024	0.004	28.852	-0.323	-0.323	0.000	0.000	0.000	0.000
136	A	142	CYS	0	-0.021	0.025	27.645	-0.414	-0.414	0.000	0.000	0.000	0.000
137	A	143	ARG	1	0.871	0.927	29.669	10.526	10.526	0.000	0.000	0.000	0.000
138	A	144	SER	0	-0.017	-0.015	29.517	0.205	0.205	0.000	0.000	0.000	0.000
139	A	146	THR	0	0.019	-0.012	28.506	0.382	0.382	0.000	0.000	0.000	0.000
140	A	147	MET	0	0.017	0.026	30.393	-0.156	-0.156	0.000	0.000	0.000	0.000
141	A	148	PRO	0	0.036	0.007	32.804	0.100	0.100	0.000	0.000	0.000	0.000
142	A	149	PRO	0	0.009	0.011	30.024	-0.267	-0.267	0.000	0.000	0.000	0.000
143	A	150	VAL	0	-0.028	-0.008	23.562	0.021	0.021	0.000	0.000	0.000	0.000
144	A	151	SER	0	-0.009	-0.032	26.634	-0.050	-0.050	0.000	0.000	0.000	0.000
145	A	152	PHE	0	-0.011	-0.008	19.324	-0.176	-0.176	0.000	0.000	0.000	0.000
146	A	153	HIS	0	-0.017	-0.019	24.720	0.483	0.483	0.000	0.000	0.000	0.000
147	A	154	GLY	0	0.064	0.026	24.523	-0.393	-0.393	0.000	0.000	0.000	0.000
148	A	155	SER	0	-0.025	-0.005	24.519	0.370	0.370	0.000	0.000	0.000	0.000
149	A	156	ASP	-1	-0.813	-0.879	25.867	-11.750	-11.750	0.000	0.000	0.000	0.000
150	A	157	GLY	0	0.010	0.014	28.359	0.344	0.344	0.000	0.000	0.000	0.000
151	A	159	TRP	0	-0.012	-0.009	23.864	0.046	0.046	0.000	0.000	0.000	0.000
152	A	160	TYR	0	0.045	0.012	26.169	-0.099	-0.099	0.000	0.000	0.000	0.000
153	A	161	PRO	0	0.016	0.031	22.512	-0.439	-0.439	0.000	0.000	0.000	0.000
154	A	162	MET	0	-0.007	0.034	18.732	0.101	0.101	0.000	0.000	0.000	0.000
155	A	163	GLU	-1	-0.764	-0.871	22.397	-13.648	-13.648	0.000	0.000	0.000	0.000
156	A	164	ILE	0	-0.042	-0.007	25.511	0.487	0.487	0.000	0.000	0.000	0.000
157	A	165	ARG	1	0.849	0.928	24.971	11.716	11.716	0.000	0.000	0.000	0.000
158	A	166	PRO	0	0.020	0.022	29.612	0.310	0.310	0.000	0.000	0.000	0.000
159	A	167	MET	0	0.013	0.002	32.619	0.036	0.036	0.000	0.000	0.000	0.000
160	A	168	LYS	1	0.781	0.881	36.167	7.749	7.749	0.000	0.000	0.000	0.000
161	A	169	THR	0	0.023	0.012	35.107	0.212	0.212	0.000	0.000	0.000	0.000
162	A	170	SER	0	-0.032	-0.012	36.003	-0.195	-0.195	0.000	0.000	0.000	0.000
163	A	171	ASP	-1	-0.781	-0.878	30.734	-10.609	-10.609	0.000	0.000	0.000	0.000
164	A	172	SER	0	-0.034	-0.032	32.005	-0.137	-0.137	0.000	0.000	0.000	0.000
165	A	173	HIS	0	0.064	0.051	33.297	-0.177	-0.177	0.000	0.000	0.000	0.000
166	A	174	LEU	0	-0.029	-0.010	29.576	-0.067	-0.067	0.000	0.000	0.000	0.000
167	A	175	VAL	0	-0.004	0.011	26.441	-0.258	-0.258	0.000	0.000	0.000	0.000
168	A	176	ARG	1	0.819	0.869	23.914	11.208	11.208	0.000	0.000	0.000	0.000
169	A	177	SER	0	-0.012	-0.023	18.385	-0.167	-0.167	0.000	0.000	0.000	0.000
170	A	178	TRP	0	-0.023	-0.025	18.316	0.210	0.210	0.000	0.000	0.000	0.000
171	A	179	VAL	0	0.003	0.022	13.116	-0.602	-0.602	0.000	0.000	0.000	0.000
172	A	180	THR	0	-0.049	-0.033	12.433	1.910	1.910	0.000	0.000	0.000	0.000
173	A	181	ALA	-1	-0.809	-0.854	9.263	-30.832	-30.832	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:SER)