FMO DATABASE

FMODB ID: QV44Y

Calculation Name: 1YA9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YA9

Chain ID: A

ChEMBL ID:

UniProt ID: P08226

Base Structure: X-ray

Registration Date: 2023-09-23

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	174
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1745320.03087
FMO2-HF: Nuclear repulsion	1673923.961963
FMO2-HF: Total energy	-71396.068907
FMO2-MP2: Total energy	-71603.473125

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:4:PRO)

Summations of interaction energy for fragment #1(A:4:PRO)

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.
-1.406	1.635	0.016	-1.433	-1.625	0.001

Interaction energy analysis for fragmet #1(A:4:PRO)

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 : -0.001

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	6	VAL	0	-0.024	-0.011	3.172	-0.919	1.699	0.011	-1.301	-1.329	0.002
4	A	7	THR	0	-0.004	0.004	3.866	-0.671	-0.248	0.005	-0.132	-0.296	-0.001
5	A	8	ASP	-1	-0.864	-0.920	5.876	0.842	0.842	0.000	0.000	0.000	0.000
6	A	9	GLN	0	-0.063	-0.042	8.015	-0.021	-0.021	0.000	0.000	0.000	0.000
7	A	10	LEU	0	0.005	0.019	11.523	0.005	0.005	0.000	0.000	0.000	0.000
8	A	11	GLU	-1	-0.822	-0.914	14.225	-0.067	-0.067	0.000	0.000	0.000	0.000
9	A	12	TRP	0	-0.048	-0.028	15.246	-0.033	-0.033	0.000	0.000	0.000	0.000
10	A	13	GLN	0	-0.053	-0.055	9.585	-0.030	-0.030	0.000	0.000	0.000	0.000
11	A	14	SER	0	0.036	0.035	11.845	-0.006	-0.006	0.000	0.000	0.000	0.000
12	A	15	ASN	0	-0.056	-0.041	12.763	-0.053	-0.053	0.000	0.000	0.000	0.000
13	A	16	GLN	0	0.006	-0.001	9.940	0.051	0.051	0.000	0.000	0.000	0.000
14	A	17	PRO	0	0.051	0.039	7.487	0.105	0.105	0.000	0.000	0.000	0.000
15	A	18	TRP	0	0.058	0.012	8.633	0.057	0.057	0.000	0.000	0.000	0.000
16	A	19	GLU	-1	-0.812	-0.884	11.674	0.113	0.113	0.000	0.000	0.000	0.000
17	A	20	GLN	0	-0.008	-0.002	6.417	0.197	0.197	0.000	0.000	0.000	0.000
18	A	21	ALA	0	0.006	0.021	9.400	0.061	0.061	0.000	0.000	0.000	0.000
19	A	22	LEU	0	-0.002	-0.002	10.134	0.028	0.028	0.000	0.000	0.000	0.000
20	A	23	ASN	0	-0.057	-0.045	12.053	0.007	0.007	0.000	0.000	0.000	0.000
21	A	24	ARG	1	0.862	0.920	5.987	0.057	0.057	0.000	0.000	0.000	0.000
22	A	25	PHE	0	0.026	0.005	11.178	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	26	TRP	0	-0.020	-0.037	14.237	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	27	ASP	-1	-0.798	-0.893	14.011	0.309	0.309	0.000	0.000	0.000	0.000
25	A	28	TYR	0	-0.007	-0.026	14.227	-0.010	-0.010	0.000	0.000	0.000	0.000
26	A	29	LEU	0	0.011	0.000	16.094	-0.017	-0.017	0.000	0.000	0.000	0.000
27	A	30	ARG	1	0.749	0.854	17.171	-0.274	-0.274	0.000	0.000	0.000	0.000
28	A	31	TRP	0	0.012	0.026	19.005	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	32	VAL	0	0.060	0.036	19.956	-0.015	-0.015	0.000	0.000	0.000	0.000
30	A	33	GLN	0	-0.080	-0.049	22.430	-0.013	-0.013	0.000	0.000	0.000	0.000
31	A	34	THR	0	-0.044	-0.032	24.164	-0.010	-0.010	0.000	0.000	0.000	0.000
32	A	35	LEU	0	-0.064	-0.024	26.186	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	36	SER	0	0.062	0.033	25.631	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	37	ASP	-1	-0.857	-0.945	27.836	0.071	0.071	0.000	0.000	0.000	0.000
35	A	38	GLN	0	-0.051	-0.028	21.471	0.000	0.000	0.000	0.000	0.000	0.000
36	A	39	VAL	0	-0.027	0.001	22.908	-0.007	-0.007	0.000	0.000	0.000	0.000
37	A	40	GLN	0	-0.067	-0.029	25.064	-0.016	-0.016	0.000	0.000	0.000	0.000
38	A	41	GLU	-1	-0.818	-0.893	27.471	0.034	0.034	0.000	0.000	0.000	0.000
39	A	42	GLU	-1	-0.821	-0.905	21.056	0.097	0.097	0.000	0.000	0.000	0.000
40	A	43	LEU	0	-0.044	-0.013	23.655	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	44	GLN	0	-0.082	-0.046	25.682	-0.018	-0.018	0.000	0.000	0.000	0.000
42	A	45	SER	0	0.067	0.032	24.035	-0.010	-0.010	0.000	0.000	0.000	0.000
43	A	46	SER	0	-0.062	-0.039	24.460	-0.014	-0.014	0.000	0.000	0.000	0.000
44	A	47	GLN	0	0.004	-0.001	18.417	-0.018	-0.018	0.000	0.000	0.000	0.000
45	A	48	VAL	0	0.053	0.033	19.320	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	49	THR	0	-0.070	-0.043	19.448	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	50	GLN	0	-0.046	-0.002	18.536	-0.022	-0.022	0.000	0.000	0.000	0.000
48	A	51	GLU	-1	-0.787	-0.866	14.924	0.066	0.066	0.000	0.000	0.000	0.000
49	A	52	LEU	0	-0.016	-0.007	14.692	-0.010	-0.010	0.000	0.000	0.000	0.000
50	A	53	THR	0	0.017	-0.020	16.398	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	54	ALA	0	0.033	0.024	12.646	-0.023	-0.023	0.000	0.000	0.000	0.000
52	A	55	LEU	0	0.016	0.007	10.408	-0.041	-0.041	0.000	0.000	0.000	0.000
53	A	56	MET	0	-0.060	-0.016	12.875	0.000	0.000	0.000	0.000	0.000	0.000
54	A	57	GLU	-1	-0.922	-0.963	14.524	-0.214	-0.214	0.000	0.000	0.000	0.000
55	A	58	ASP	-1	-0.809	-0.866	8.347	-0.379	-0.379	0.000	0.000	0.000	0.000
56	A	59	THR	0	-0.007	-0.019	11.158	-0.026	-0.026	0.000	0.000	0.000	0.000
57	A	60	MET	0	-0.051	-0.037	12.985	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	61	THR	0	-0.010	0.000	11.457	0.010	0.010	0.000	0.000	0.000	0.000
59	A	62	GLU	-1	-0.848	-0.928	7.194	-0.738	-0.738	0.000	0.000	0.000	0.000
60	A	63	VAL	0	-0.053	-0.027	11.579	0.026	0.026	0.000	0.000	0.000	0.000
61	A	64	LYS	1	0.779	0.877	15.163	0.228	0.228	0.000	0.000	0.000	0.000
62	A	65	ALA	0	0.040	0.028	11.957	0.016	0.016	0.000	0.000	0.000	0.000
63	A	66	TYR	0	0.066	0.032	13.418	0.043	0.043	0.000	0.000	0.000	0.000
64	A	67	LYS	1	0.801	0.879	14.823	0.197	0.197	0.000	0.000	0.000	0.000
65	A	68	LYS	1	0.762	0.852	17.044	0.264	0.264	0.000	0.000	0.000	0.000
66	A	69	GLU	-1	-0.811	-0.904	13.880	-0.225	-0.225	0.000	0.000	0.000	0.000
67	A	70	LEU	0	0.001	0.000	17.128	0.027	0.027	0.000	0.000	0.000	0.000
68	A	71	GLU	-1	-0.861	-0.913	19.914	-0.162	-0.162	0.000	0.000	0.000	0.000
69	A	72	GLU	-1	-0.917	-0.943	19.278	-0.263	-0.263	0.000	0.000	0.000	0.000
70	A	73	GLN	0	-0.038	-0.025	17.161	0.029	0.029	0.000	0.000	0.000	0.000
71	A	74	LEU	0	-0.072	-0.005	22.452	0.018	0.018	0.000	0.000	0.000	0.000
72	A	75	GLY	0	-0.008	-0.005	25.444	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	76	PRO	0	0.004	-0.008	28.739	0.001	0.001	0.000	0.000	0.000	0.000
74	A	77	VAL	0	-0.001	-0.011	29.769	0.007	0.007	0.000	0.000	0.000	0.000
75	A	78	ALA	0	0.014	0.010	32.625	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	79	GLU	-1	-0.767	-0.864	32.070	-0.091	-0.091	0.000	0.000	0.000	0.000
77	A	80	GLU	-1	-0.875	-0.934	33.021	-0.059	-0.059	0.000	0.000	0.000	0.000
78	A	81	THR	0	-0.007	-0.012	31.510	0.003	0.003	0.000	0.000	0.000	0.000
79	A	82	ARG	1	0.898	0.943	27.475	0.106	0.106	0.000	0.000	0.000	0.000
80	A	83	ALA	0	0.019	0.006	28.846	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	84	ARG	1	0.805	0.884	30.753	0.042	0.042	0.000	0.000	0.000	0.000
82	A	85	LEU	0	0.031	0.015	26.961	0.002	0.002	0.000	0.000	0.000	0.000
83	A	86	GLY	0	0.027	0.017	25.796	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	87	LYS	1	0.873	0.926	26.422	0.071	0.071	0.000	0.000	0.000	0.000
85	A	88	GLU	-1	-0.800	-0.870	27.888	-0.036	-0.036	0.000	0.000	0.000	0.000
86	A	89	VAL	0	0.056	0.027	21.390	0.005	0.005	0.000	0.000	0.000	0.000
87	A	90	GLN	0	0.008	0.017	23.489	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	91	ALA	0	-0.001	-0.002	25.007	0.001	0.001	0.000	0.000	0.000	0.000
89	A	92	ALA	0	-0.008	-0.001	24.130	0.005	0.005	0.000	0.000	0.000	0.000
90	A	93	GLN	0	0.057	0.035	19.314	-0.013	-0.013	0.000	0.000	0.000	0.000
91	A	94	ALA	0	0.002	0.000	22.334	0.000	0.000	0.000	0.000	0.000	0.000
92	A	95	ARG	1	0.770	0.858	25.163	0.022	0.022	0.000	0.000	0.000	0.000
93	A	96	LEU	0	0.024	0.018	18.109	0.007	0.007	0.000	0.000	0.000	0.000
94	A	97	GLY	0	0.055	0.018	21.312	0.004	0.004	0.000	0.000	0.000	0.000
95	A	98	ALA	0	0.006	0.001	22.286	0.004	0.004	0.000	0.000	0.000	0.000
96	A	99	ASH	0	-0.074	-0.077	23.362	0.008	0.008	0.000	0.000	0.000	0.000
97	A	100	MET	0	-0.024	0.003	16.100	0.001	0.001	0.000	0.000	0.000	0.000
98	A	101	GLU	-1	-0.799	-0.882	21.612	-0.067	-0.067	0.000	0.000	0.000	0.000
99	A	102	ASP	-1	-0.825	-0.903	24.244	0.005	0.005	0.000	0.000	0.000	0.000
100	A	103	LEU	0	-0.007	-0.023	21.515	0.007	0.007	0.000	0.000	0.000	0.000
101	A	104	ARG	1	0.866	0.921	20.988	0.076	0.076	0.000	0.000	0.000	0.000
102	A	105	ASN	0	-0.002	-0.010	23.319	0.000	0.000	0.000	0.000	0.000	0.000
103	A	106	ARG	1	0.766	0.876	26.914	-0.011	-0.011	0.000	0.000	0.000	0.000
104	A	107	LEU	0	0.014	0.003	22.634	0.004	0.004	0.000	0.000	0.000	0.000
105	A	108	GLY	0	0.022	0.011	26.457	0.001	0.001	0.000	0.000	0.000	0.000
106	A	109	GLN	0	-0.053	-0.032	27.686	0.004	0.004	0.000	0.000	0.000	0.000
107	A	110	TYR	0	0.025	0.008	29.100	0.002	0.002	0.000	0.000	0.000	0.000
108	A	111	ARG	1	0.878	0.950	25.109	0.008	0.008	0.000	0.000	0.000	0.000
109	A	112	ASN	0	-0.004	-0.006	30.354	0.000	0.000	0.000	0.000	0.000	0.000
110	A	113	GLU	-1	-0.757	-0.851	33.262	0.014	0.014	0.000	0.000	0.000	0.000
111	A	114	VAL	0	0.036	0.028	32.357	0.000	0.000	0.000	0.000	0.000	0.000
112	A	115	HIS	0	0.013	0.006	30.727	0.002	0.002	0.000	0.000	0.000	0.000
113	A	116	THR	0	-0.096	-0.058	35.550	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	117	MET	0	-0.054	-0.015	37.979	0.001	0.001	0.000	0.000	0.000	0.000
115	A	118	LEU	0	-0.020	-0.011	38.353	0.002	0.002	0.000	0.000	0.000	0.000
116	A	119	GLY	0	0.037	0.020	34.950	0.001	0.001	0.000	0.000	0.000	0.000
117	A	120	GLN	0	-0.058	-0.022	35.278	0.006	0.006	0.000	0.000	0.000	0.000
118	A	121	SER	0	0.048	0.003	34.016	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	122	THR	0	0.014	0.006	36.389	0.003	0.003	0.000	0.000	0.000	0.000
120	A	123	GLU	-1	-0.898	-0.947	36.790	0.045	0.045	0.000	0.000	0.000	0.000
121	A	124	GLU	-1	-0.780	-0.885	37.095	0.023	0.023	0.000	0.000	0.000	0.000
122	A	125	ILE	0	-0.007	-0.005	34.693	0.001	0.001	0.000	0.000	0.000	0.000
123	A	126	ARG	1	0.898	0.939	32.323	-0.046	-0.046	0.000	0.000	0.000	0.000
124	A	127	ALA	0	0.024	0.016	32.680	0.004	0.004	0.000	0.000	0.000	0.000
125	A	128	ARG	1	0.762	0.868	34.282	-0.015	-0.015	0.000	0.000	0.000	0.000
126	A	129	LEU	0	0.045	0.034	27.703	0.000	0.000	0.000	0.000	0.000	0.000
127	A	130	SER	0	0.056	0.035	29.320	0.002	0.002	0.000	0.000	0.000	0.000
128	A	131	THR	0	-0.047	-0.044	29.799	0.006	0.006	0.000	0.000	0.000	0.000
129	A	132	HIS	0	-0.032	-0.018	30.093	0.002	0.002	0.000	0.000	0.000	0.000
130	A	133	LEU	0	0.069	0.024	24.545	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	134	ARG	1	0.893	0.958	26.461	-0.063	-0.063	0.000	0.000	0.000	0.000
132	A	135	LYS	1	0.889	0.944	28.304	-0.021	-0.021	0.000	0.000	0.000	0.000
133	A	136	MET	0	-0.021	0.017	25.834	-0.002	-0.002	0.000	0.000	0.000	0.000
134	A	137	ARG	1	0.919	0.967	22.057	-0.105	-0.105	0.000	0.000	0.000	0.000
135	A	138	LYS	1	0.973	0.981	24.254	-0.065	-0.065	0.000	0.000	0.000	0.000
136	A	139	ARG	1	0.719	0.854	26.765	-0.005	-0.005	0.000	0.000	0.000	0.000
137	A	140	LEU	0	0.051	0.020	18.960	-0.002	-0.002	0.000	0.000	0.000	0.000
138	A	141	MET	0	-0.027	0.009	21.736	-0.005	-0.005	0.000	0.000	0.000	0.000
139	A	142	ARG	1	1.002	1.008	22.962	-0.030	-0.030	0.000	0.000	0.000	0.000
140	A	143	ASP	-1	-0.806	-0.869	24.489	-0.007	-0.007	0.000	0.000	0.000	0.000
141	A	144	ALA	0	0.033	0.022	19.456	-0.013	-0.013	0.000	0.000	0.000	0.000
142	A	145	GLU	-1	-0.867	-0.938	21.117	0.056	0.056	0.000	0.000	0.000	0.000
143	A	146	ASP	-1	-0.856	-0.903	23.036	-0.021	-0.021	0.000	0.000	0.000	0.000
144	A	147	LEU	0	-0.001	-0.004	18.908	-0.005	-0.005	0.000	0.000	0.000	0.000
145	A	148	GLN	0	-0.024	-0.017	17.743	-0.013	-0.013	0.000	0.000	0.000	0.000
146	A	149	LYS	1	0.899	0.946	20.721	-0.004	-0.004	0.000	0.000	0.000	0.000
147	A	150	ARG	1	0.734	0.839	23.858	0.023	0.023	0.000	0.000	0.000	0.000
148	A	151	LEU	0	0.025	0.004	17.687	-0.007	-0.007	0.000	0.000	0.000	0.000
149	A	152	ALA	0	0.000	0.005	21.471	-0.006	-0.006	0.000	0.000	0.000	0.000
150	A	153	VAL	0	-0.059	-0.031	22.697	-0.001	-0.001	0.000	0.000	0.000	0.000
151	A	154	TYR	0	-0.026	-0.022	22.591	-0.006	-0.006	0.000	0.000	0.000	0.000
152	A	155	LYS	1	0.830	0.931	17.415	0.075	0.075	0.000	0.000	0.000	0.000
153	A	156	ALA	0	0.034	0.012	22.932	0.013	0.013	0.000	0.000	0.000	0.000
154	A	157	GLY	0	-0.009	-0.008	26.225	-0.010	-0.010	0.000	0.000	0.000	0.000
155	A	158	ALA	0	-0.020	0.005	28.564	0.006	0.006	0.000	0.000	0.000	0.000
156	A	159	ARG	1	0.853	0.908	29.628	0.047	0.047	0.000	0.000	0.000	0.000
157	A	160	GLU	-1	-0.830	-0.889	31.668	-0.018	-0.018	0.000	0.000	0.000	0.000
158	A	161	GLY	0	0.001	-0.001	34.269	0.003	0.003	0.000	0.000	0.000	0.000
159	A	162	ALA	0	-0.013	-0.003	34.514	0.000	0.000	0.000	0.000	0.000	0.000
160	A	163	GLU	-1	-0.845	-0.907	34.052	-0.040	-0.040	0.000	0.000	0.000	0.000
161	A	164	ARG	1	0.817	0.866	28.316	0.023	0.023	0.000	0.000	0.000	0.000
162	A	165	GLY	0	0.027	0.013	27.393	0.005	0.005	0.000	0.000	0.000	0.000
163	A	166	VAL	0	0.020	0.003	28.424	-0.002	-0.002	0.000	0.000	0.000	0.000
164	A	167	SER	0	-0.039	-0.026	30.921	0.003	0.003	0.000	0.000	0.000	0.000
165	A	168	ALA	0	0.086	0.038	28.648	0.000	0.000	0.000	0.000	0.000	0.000
166	A	169	ILE	0	-0.025	-0.015	25.954	-0.004	-0.004	0.000	0.000	0.000	0.000
167	A	170	ARG	1	0.945	0.966	28.945	0.018	0.018	0.000	0.000	0.000	0.000
168	A	171	GLU	-1	-0.886	-0.921	32.206	-0.057	-0.057	0.000	0.000	0.000	0.000
169	A	172	ARG	1	0.908	0.963	23.741	0.109	0.109	0.000	0.000	0.000	0.000
170	A	173	LEU	0	-0.048	-0.024	27.525	-0.002	-0.002	0.000	0.000	0.000	0.000
171	A	174	GLY	0	-0.006	0.023	31.077	0.001	0.001	0.000	0.000	0.000	0.000
172	A	175	PRO	0	-0.030	-0.046	34.858	0.004	0.004	0.000	0.000	0.000	0.000
173	A	176	LEU	0	0.005	0.013	35.031	0.001	0.001	0.000	0.000	0.000	0.000
174	A	177	VAL	0	-0.013	0.007	38.285	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:PRO)