FMO DATABASE

FMODB ID: NZ7ZQ

Calculation Name: 1HA7-B-Xray547

Preferred Name:

Target Type:

Ligand Name: phycocyanobilin | n-methyl asparagine

Ligand 3-letter code: CYC | MEN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1HA7

Chain ID: B

ChEMBL ID:

UniProt ID: P72509

Base Structure: X-ray

Registration Date: 2025-10-03

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	172
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1514644.308379
FMO2-HF: Nuclear repulsion	1449493.357387
FMO2-HF: Total energy	-65150.950992
FMO2-MP2: Total energy	-65335.17521

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:1:MET)

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

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.
-154.863	-146.208	15.326	-9.392	-14.591	-0.114

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.748 / q_NPA : 0.866

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	3	ASP	-1	-0.729	-0.831	3.106	-35.360	-32.654	0.071	-1.283	-1.494	-0.009
99	A	101	ALA	0	-0.017	-0.007	4.795	0.336	0.425	-0.001	-0.008	-0.079	0.000
101	A	103	ASP	-1	-0.780	-0.868	4.927	-48.993	-48.924	-0.001	-0.004	-0.063	0.000
103	A	105	SER	0	-0.027	-0.030	2.383	-10.489	-8.720	2.445	-2.109	-2.106	-0.016
104	A	106	VAL	0	-0.020	-0.011	2.162	-7.903	-6.088	3.787	-1.724	-3.879	-0.007
105	A	107	LEU	0	-0.008	0.003	2.841	5.076	3.610	0.177	1.599	-0.311	-0.001
107	A	109	ASP	-1	-0.855	-0.940	1.884	-110.416	-107.622	6.737	-5.410	-4.121	-0.078
108	A	110	ARG	1	0.876	0.931	2.816	49.832	50.711	2.111	-0.453	-2.538	-0.003
4	A	4	ALA	0	0.041	0.005	5.594	-1.056	-1.056	0.000	0.000	0.000	0.000
5	A	5	PHE	0	0.002	0.000	8.983	1.532	1.532	0.000	0.000	0.000	0.000
6	A	6	THR	0	-0.048	-0.054	6.655	1.253	1.253	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.820	0.916	6.546	37.268	37.268	0.000	0.000	0.000	0.000
8	A	8	VAL	0	0.043	0.027	8.502	1.435	1.435	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.004	0.005	11.458	1.552	1.552	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.039	-0.021	8.281	0.474	0.474	0.000	0.000	0.000	0.000
11	A	11	GLN	0	-0.007	-0.012	10.259	1.322	1.322	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.036	-0.017	12.492	1.702	1.702	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.889	-0.939	12.765	-20.967	-20.967	0.000	0.000	0.000	0.000
14	A	14	THR	0	-0.048	-0.033	12.068	0.801	0.801	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.746	0.855	14.635	18.272	18.272	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.002	0.016	17.586	1.028	1.028	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.901	-0.925	18.481	-13.791	-13.791	0.000	0.000	0.000	0.000
18	A	18	MET	0	-0.019	-0.016	18.271	-0.876	-0.876	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.030	-0.015	15.549	0.051	0.051	0.000	0.000	0.000	0.000
20	A	20	SER	0	0.011	-0.005	19.582	0.882	0.882	0.000	0.000	0.000	0.000
21	A	21	THR	0	0.027	-0.009	21.801	-0.544	-0.544	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.070	0.045	22.795	-0.289	-0.289	0.000	0.000	0.000	0.000
23	A	23	GLN	0	0.015	0.020	17.241	0.205	0.205	0.000	0.000	0.000	0.000
24	A	24	ILE	0	0.010	0.010	18.084	-0.818	-0.818	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.875	-0.946	19.713	-12.868	-12.868	0.000	0.000	0.000	0.000
26	A	26	ALA	0	-0.034	-0.017	18.256	0.036	0.036	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.009	-0.005	13.144	-0.398	-0.398	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.014	-0.003	16.596	-0.091	-0.091	0.000	0.000	0.000	0.000
29	A	29	GLN	0	-0.005	-0.006	19.633	0.373	0.373	0.000	0.000	0.000	0.000
30	A	30	MET	0	-0.011	-0.006	12.216	-0.294	-0.294	0.000	0.000	0.000	0.000
31	A	31	VAL	0	0.003	-0.006	16.343	-0.186	-0.186	0.000	0.000	0.000	0.000
32	A	32	ALA	0	-0.026	0.009	17.792	0.319	0.319	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.823	-0.902	18.280	-12.989	-12.989	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.076	-0.044	15.991	-0.058	-0.058	0.000	0.000	0.000	0.000
35	A	35	ASN	0	0.032	0.005	16.997	-0.647	-0.647	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.855	0.910	19.263	12.858	12.858	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.765	0.843	11.545	20.840	20.840	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.013	-0.010	13.587	-0.521	-0.521	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.862	-0.936	16.106	-12.610	-12.610	0.000	0.000	0.000	0.000
40	A	40	ALA	0	-0.026	-0.009	16.761	0.256	0.256	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.003	0.000	12.295	-0.026	-0.026	0.000	0.000	0.000	0.000
42	A	42	ASN	0	0.011	0.016	15.227	0.061	0.061	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.839	0.917	17.995	11.869	11.869	0.000	0.000	0.000	0.000
44	A	44	ILE	0	0.022	0.012	15.955	0.385	0.385	0.000	0.000	0.000	0.000
45	A	45	THR	0	-0.044	-0.043	15.059	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	46	SER	0	-0.046	-0.024	17.149	0.415	0.415	0.000	0.000	0.000	0.000
47	A	47	ASN	0	-0.060	-0.028	20.289	0.994	0.994	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.035	0.030	17.405	0.180	0.180	0.000	0.000	0.000	0.000
49	A	49	SER	0	0.059	0.015	19.245	0.076	0.076	0.000	0.000	0.000	0.000
50	A	50	THR	0	-0.008	0.015	21.975	0.339	0.339	0.000	0.000	0.000	0.000
51	A	51	ILE	0	0.003	0.008	19.782	0.298	0.298	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.035	0.017	18.876	0.223	0.223	0.000	0.000	0.000	0.000
53	A	53	SER	0	-0.063	-0.048	21.711	0.434	0.434	0.000	0.000	0.000	0.000
54	A	54	ASN	0	0.011	0.007	25.325	0.629	0.629	0.000	0.000	0.000	0.000
55	A	55	ALA	0	0.023	0.025	23.127	0.319	0.319	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.022	0.010	24.141	0.172	0.172	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.894	0.939	25.840	9.949	9.949	0.000	0.000	0.000	0.000
58	A	58	SER	0	-0.004	0.004	28.380	0.248	0.248	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.031	0.012	24.845	0.224	0.224	0.000	0.000	0.000	0.000
60	A	60	PHE	0	-0.011	-0.041	26.157	0.164	0.164	0.000	0.000	0.000	0.000
61	A	61	ALA	0	-0.025	-0.005	30.932	0.284	0.284	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.869	-0.913	30.464	-9.669	-9.669	0.000	0.000	0.000	0.000
63	A	63	GLN	0	0.008	0.015	28.748	-0.046	-0.046	0.000	0.000	0.000	0.000
64	A	64	PRO	0	0.073	0.047	32.423	-0.146	-0.146	0.000	0.000	0.000	0.000
65	A	65	GLN	0	0.032	0.001	32.928	0.226	0.226	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.041	-0.013	27.926	-0.086	-0.086	0.000	0.000	0.000	0.000
67	A	67	ILE	0	-0.023	-0.022	30.958	-0.133	-0.133	0.000	0.000	0.000	0.000
68	A	68	ALA	0	0.015	0.021	33.169	0.202	0.202	0.000	0.000	0.000	0.000
69	A	69	PRO	0	0.000	-0.022	35.600	-0.218	-0.218	0.000	0.000	0.000	0.000
70	A	70	GLY	0	-0.005	0.005	35.740	0.110	0.110	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.050	0.046	33.281	-0.199	-0.199	0.000	0.000	0.000	0.000
72	A	72	ASN	0	0.011	0.010	26.523	-0.362	-0.362	0.000	0.000	0.000	0.000
73	A	75	ALA	0	0.054	0.023	27.551	-0.242	-0.242	0.000	0.000	0.000	0.000
74	A	76	TYR	0	0.030	0.034	28.719	0.110	0.110	0.000	0.000	0.000	0.000
75	A	77	THR	0	-0.052	-0.036	31.059	-0.202	-0.202	0.000	0.000	0.000	0.000
76	A	78	SER	0	0.063	0.012	30.023	-0.252	-0.252	0.000	0.000	0.000	0.000
77	A	79	ARG	1	0.979	0.996	25.990	10.484	10.484	0.000	0.000	0.000	0.000
78	A	80	ARG	1	0.848	0.921	25.687	9.457	9.457	0.000	0.000	0.000	0.000
79	A	81	MET	0	0.022	0.035	25.409	-0.484	-0.484	0.000	0.000	0.000	0.000
80	A	82	ALA	0	0.004	-0.006	24.374	-0.336	-0.336	0.000	0.000	0.000	0.000
81	A	83	ALA	0	-0.027	-0.010	21.445	-0.471	-0.471	0.000	0.000	0.000	0.000
82	A	84	CYS	0	0.020	0.017	20.574	-0.678	-0.678	0.000	0.000	0.000	0.000
83	A	85	LEU	0	0.011	-0.006	20.961	-0.423	-0.423	0.000	0.000	0.000	0.000
84	A	86	ARG	1	0.876	0.927	17.071	14.372	14.372	0.000	0.000	0.000	0.000
85	A	87	ASP	-1	-0.765	-0.855	16.468	-16.387	-16.387	0.000	0.000	0.000	0.000
86	A	88	MET	0	-0.034	-0.003	16.077	-0.975	-0.975	0.000	0.000	0.000	0.000
87	A	89	GLU	-1	-0.918	-0.965	15.599	-15.277	-15.277	0.000	0.000	0.000	0.000
88	A	90	ILE	0	-0.074	-0.036	11.334	-0.993	-0.993	0.000	0.000	0.000	0.000
89	A	91	ILE	0	0.041	0.015	11.560	-1.602	-1.602	0.000	0.000	0.000	0.000
90	A	92	LEU	0	0.005	0.007	12.504	-1.057	-1.057	0.000	0.000	0.000	0.000
91	A	93	ARG	1	0.941	0.972	8.803	20.581	20.581	0.000	0.000	0.000	0.000
92	A	94	TYR	0	0.021	0.001	4.855	-1.988	-1.988	0.000	0.000	0.000	0.000
93	A	95	VAL	0	0.024	0.017	8.181	-2.299	-2.299	0.000	0.000	0.000	0.000
94	A	96	THR	0	-0.064	-0.040	10.389	-0.316	-0.316	0.000	0.000	0.000	0.000
95	A	97	TYR	0	0.003	-0.001	5.583	-0.081	-0.081	0.000	0.000	0.000	0.000
96	A	98	ALA	0	0.016	0.016	6.598	-1.635	-1.635	0.000	0.000	0.000	0.000
97	A	99	VAL	0	0.002	0.005	7.500	0.112	0.112	0.000	0.000	0.000	0.000
98	A	100	PHE	0	-0.021	-0.004	7.293	0.906	0.906	0.000	0.000	0.000	0.000
100	A	102	GLY	0	0.025	0.013	6.837	-0.247	-0.247	0.000	0.000	0.000	0.000
102	A	104	ALA	0	0.023	0.012	5.926	-1.421	-1.421	0.000	0.000	0.000	0.000
106	A	108	GLU	-1	-0.805	-0.907	6.273	-27.259	-27.259	0.000	0.000	0.000	0.000
109	A	111	CYS	0	-0.067	-0.017	6.881	4.335	4.335	0.000	0.000	0.000	0.000
110	A	112	LEU	0	0.007	0.017	9.595	2.604	2.604	0.000	0.000	0.000	0.000
111	A	113	ASN	0	-0.023	-0.007	8.504	4.288	4.288	0.000	0.000	0.000	0.000
112	A	114	GLY	0	0.047	0.038	10.866	0.364	0.364	0.000	0.000	0.000	0.000
113	A	115	LEU	0	-0.022	0.008	14.068	1.554	1.554	0.000	0.000	0.000	0.000
114	A	116	ARG	1	0.844	0.895	15.880	17.491	17.491	0.000	0.000	0.000	0.000
115	A	117	GLU	-1	-0.889	-0.956	17.006	-16.744	-16.744	0.000	0.000	0.000	0.000
116	A	118	THR	0	-0.034	-0.024	16.940	0.884	0.884	0.000	0.000	0.000	0.000
117	A	119	TYR	0	-0.056	-0.072	18.160	0.695	0.695	0.000	0.000	0.000	0.000
118	A	120	LEU	0	-0.017	-0.003	21.949	0.801	0.801	0.000	0.000	0.000	0.000
119	A	121	ALA	0	-0.016	-0.009	22.688	0.644	0.644	0.000	0.000	0.000	0.000
120	A	122	LEU	0	-0.065	-0.027	21.152	0.494	0.494	0.000	0.000	0.000	0.000
121	A	123	GLY	0	-0.021	0.005	25.263	0.479	0.479	0.000	0.000	0.000	0.000
122	A	124	THR	0	-0.074	-0.051	22.983	0.361	0.361	0.000	0.000	0.000	0.000
123	A	125	PRO	0	-0.021	-0.012	25.193	-0.300	-0.300	0.000	0.000	0.000	0.000
124	A	126	GLY	0	0.081	0.031	22.401	-0.047	-0.047	0.000	0.000	0.000	0.000
125	A	127	SER	0	0.017	0.019	22.445	-0.117	-0.117	0.000	0.000	0.000	0.000
126	A	128	SER	0	-0.009	-0.036	24.824	0.063	0.063	0.000	0.000	0.000	0.000
127	A	129	VAL	0	-0.014	0.005	19.251	0.102	0.102	0.000	0.000	0.000	0.000
128	A	130	ALA	0	0.020	0.018	20.491	-0.314	-0.314	0.000	0.000	0.000	0.000
129	A	131	VAL	0	-0.003	0.004	21.526	0.031	0.031	0.000	0.000	0.000	0.000
130	A	132	GLY	0	0.010	-0.001	22.901	0.201	0.201	0.000	0.000	0.000	0.000
131	A	133	VAL	0	0.021	-0.010	16.956	0.011	0.011	0.000	0.000	0.000	0.000
132	A	134	GLY	0	0.032	0.014	19.769	-0.227	-0.227	0.000	0.000	0.000	0.000
133	A	135	LYS	1	0.824	0.897	22.093	10.762	10.762	0.000	0.000	0.000	0.000
134	A	136	MET	0	-0.062	-0.022	17.634	0.211	0.211	0.000	0.000	0.000	0.000
135	A	137	LYS	1	0.821	0.915	19.037	14.161	14.161	0.000	0.000	0.000	0.000
136	A	138	GLU	-1	-0.947	-0.967	20.255	-10.837	-10.837	0.000	0.000	0.000	0.000
137	A	139	ALA	0	0.007	-0.002	23.104	0.215	0.215	0.000	0.000	0.000	0.000
138	A	140	ALA	0	0.005	-0.001	18.687	0.164	0.164	0.000	0.000	0.000	0.000
139	A	141	LEU	0	-0.011	-0.007	19.488	0.013	0.013	0.000	0.000	0.000	0.000
140	A	142	ALA	0	-0.006	0.007	22.071	0.279	0.279	0.000	0.000	0.000	0.000
141	A	143	ILE	0	-0.024	-0.018	22.114	0.210	0.210	0.000	0.000	0.000	0.000
142	A	144	VAL	0	-0.033	-0.016	18.907	0.021	0.021	0.000	0.000	0.000	0.000
143	A	145	ASN	0	-0.059	-0.044	22.272	0.084	0.084	0.000	0.000	0.000	0.000
144	A	146	ASP	-1	-0.831	-0.891	25.308	-9.487	-9.487	0.000	0.000	0.000	0.000
145	A	147	PRO	0	-0.006	0.002	27.685	-0.198	-0.198	0.000	0.000	0.000	0.000
146	A	148	ALA	0	-0.024	-0.011	30.109	0.186	0.186	0.000	0.000	0.000	0.000
147	A	149	GLY	0	-0.046	-0.032	28.880	-0.286	-0.286	0.000	0.000	0.000	0.000
148	A	150	ILE	0	-0.009	0.005	23.621	-0.225	-0.225	0.000	0.000	0.000	0.000
149	A	151	THR	0	-0.008	-0.010	27.540	0.402	0.402	0.000	0.000	0.000	0.000
150	A	152	PRO	0	-0.022	-0.009	27.835	-0.293	-0.293	0.000	0.000	0.000	0.000
151	A	153	GLY	0	0.034	0.009	27.438	0.107	0.107	0.000	0.000	0.000	0.000
152	A	154	ASP	-1	-0.848	-0.915	25.259	-11.835	-11.835	0.000	0.000	0.000	0.000
153	A	155	CYS	0	0.033	0.018	21.909	-0.461	-0.461	0.000	0.000	0.000	0.000
154	A	156	SER	0	-0.002	0.010	21.588	-0.734	-0.734	0.000	0.000	0.000	0.000
155	A	157	ALA	0	0.033	0.013	19.767	-0.366	-0.366	0.000	0.000	0.000	0.000
156	A	158	LEU	0	0.035	0.024	15.362	-0.813	-0.813	0.000	0.000	0.000	0.000
157	A	159	ALA	0	0.009	-0.001	17.341	-0.756	-0.756	0.000	0.000	0.000	0.000
158	A	160	SER	0	-0.006	-0.012	19.286	-0.107	-0.107	0.000	0.000	0.000	0.000
159	A	161	GLU	-1	-0.777	-0.827	11.989	-22.351	-22.351	0.000	0.000	0.000	0.000
160	A	162	ILE	0	0.016	0.009	14.619	-1.105	-1.105	0.000	0.000	0.000	0.000
161	A	163	ALA	0	-0.006	-0.001	15.472	-0.449	-0.449	0.000	0.000	0.000	0.000
162	A	164	SER	0	-0.017	-0.019	14.413	-0.668	-0.668	0.000	0.000	0.000	0.000
163	A	165	TYR	0	-0.041	-0.043	9.629	-1.861	-1.861	0.000	0.000	0.000	0.000
164	A	166	PHE	0	0.041	0.009	12.892	-0.469	-0.469	0.000	0.000	0.000	0.000
165	A	167	ASP	-1	-0.804	-0.884	15.696	-14.831	-14.831	0.000	0.000	0.000	0.000
166	A	168	ARG	1	0.841	0.907	10.577	26.642	26.642	0.000	0.000	0.000	0.000
167	A	169	ALA	0	0.022	-0.002	13.262	0.048	0.048	0.000	0.000	0.000	0.000
168	A	170	CYS	0	-0.071	-0.031	14.683	0.815	0.815	0.000	0.000	0.000	0.000
169	A	171	ALA	0	0.019	0.002	16.924	0.523	0.523	0.000	0.000	0.000	0.000
170	A	172	ALA	0	-0.016	-0.003	14.307	0.240	0.240	0.000	0.000	0.000	0.000
171	A	173	VAL	0	-0.056	-0.031	16.345	0.067	0.067	0.000	0.000	0.000	0.000
172	A	174	SER	-1	-0.846	-0.883	19.210	-13.380	-13.380	0.000	0.000	0.000	0.000

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