FMO DATABASE

FMODB ID: 6Z49Z

Calculation Name: 1CPC-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: 1CPC

Chain ID: B

ChEMBL ID:

UniProt ID: P07122

Base Structure: X-ray

Registration Date: 2025-09-02

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	-1482334.199228
FMO2-HF: Nuclear repulsion	1418090.655864
FMO2-HF: Total energy	-64243.543364
FMO2-MP2: Total energy	-64426.093108

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.
-116.385	-106.802	10.65	-9.378	-10.852	-0.056

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 : 0.800 / q_NPA : 0.890

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	-0.780	-0.884	3.572	-34.933	-32.795	-0.002	-0.949	-1.186	-0.003
95	A	97	TYR	0	-0.010	-0.003	5.615	-0.412	-0.330	-0.001	-0.010	-0.070	0.000
99	A	101	ALA	0	-0.002	-0.004	5.583	0.274	0.333	-0.001	-0.007	-0.052	0.000
103	A	105	SER	0	-0.035	-0.028	1.846	-6.247	-7.388	6.424	-3.425	-1.858	-0.008
104	A	106	VAL	0	-0.013	-0.011	2.732	-3.784	-2.437	3.090	-1.171	-3.266	-0.002
105	A	107	LEU	0	0.000	0.011	3.650	3.089	3.100	0.046	0.047	-0.103	0.000
107	A	109	ASP	-1	-0.917	-0.974	2.503	-88.899	-83.185	0.690	-3.464	-2.939	-0.042
108	A	110	ARG	1	0.866	0.926	2.818	48.106	49.479	0.404	-0.399	-1.378	-0.001
4	A	4	ALA	0	0.022	0.001	6.137	-0.141	-0.141	0.000	0.000	0.000	0.000
5	A	5	PHE	0	-0.017	-0.007	9.417	1.997	1.997	0.000	0.000	0.000	0.000
6	A	6	ALA	0	-0.001	-0.008	6.686	0.807	0.807	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.857	0.943	7.075	33.988	33.988	0.000	0.000	0.000	0.000
8	A	8	VAL	0	0.025	0.009	8.686	1.611	1.611	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.002	0.002	11.578	1.377	1.377	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.032	-0.019	8.646	0.658	0.658	0.000	0.000	0.000	0.000
11	A	11	GLN	0	-0.036	-0.036	10.724	0.125	0.125	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.019	0.004	13.277	1.482	1.482	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.889	-0.945	13.148	-20.586	-20.586	0.000	0.000	0.000	0.000
14	A	14	ALA	0	-0.017	-0.007	13.421	1.081	1.081	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.817	0.914	15.317	18.328	18.328	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.009	0.010	18.157	0.980	0.980	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.946	-0.976	18.993	-14.337	-14.337	0.000	0.000	0.000	0.000
18	A	18	TYR	0	-0.011	-0.010	18.842	-0.792	-0.792	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.021	-0.012	15.835	0.097	0.097	0.000	0.000	0.000	0.000
20	A	20	SER	0	0.006	-0.009	19.984	0.862	0.862	0.000	0.000	0.000	0.000
21	A	21	GLY	0	0.042	0.004	22.127	-0.433	-0.433	0.000	0.000	0.000	0.000
22	A	22	SER	0	0.046	0.026	23.474	-0.297	-0.297	0.000	0.000	0.000	0.000
23	A	23	GLN	0	0.045	0.031	17.300	0.373	0.373	0.000	0.000	0.000	0.000
24	A	24	ILE	0	0.018	0.012	18.739	-0.790	-0.790	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.885	-0.926	20.293	-12.705	-12.705	0.000	0.000	0.000	0.000
26	A	26	ALA	0	-0.038	-0.020	19.099	-0.056	-0.056	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.004	-0.010	13.934	-0.417	-0.417	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.015	-0.023	17.285	-0.196	-0.196	0.000	0.000	0.000	0.000
29	A	29	ALA	0	-0.035	-0.020	19.984	0.247	0.247	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.014	-0.008	13.462	0.114	0.114	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.013	-0.003	15.905	-0.423	-0.423	0.000	0.000	0.000	0.000
32	A	32	ALA	0	-0.029	-0.003	17.717	0.323	0.323	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.842	-0.910	18.419	-13.436	-13.436	0.000	0.000	0.000	0.000
34	A	34	GLY	0	0.017	0.008	16.426	-0.373	-0.373	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.007	-0.016	17.029	-0.651	-0.651	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.861	0.915	19.126	12.766	12.766	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.787	0.857	12.115	20.520	20.520	0.000	0.000	0.000	0.000
38	A	38	MET	0	-0.029	-0.013	11.911	-0.574	-0.574	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.897	-0.948	16.032	-12.650	-12.650	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.013	-0.008	16.383	0.301	0.301	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.005	0.005	11.880	0.040	0.040	0.000	0.000	0.000	0.000
42	A	42	ASN	0	-0.012	0.007	15.026	0.046	0.046	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.825	0.904	17.344	11.776	11.776	0.000	0.000	0.000	0.000
44	A	44	ILE	0	0.021	0.015	16.405	0.389	0.389	0.000	0.000	0.000	0.000
45	A	45	THR	0	-0.028	-0.033	14.489	-0.026	-0.026	0.000	0.000	0.000	0.000
46	A	46	GLY	0	-0.013	0.002	16.667	0.280	0.280	0.000	0.000	0.000	0.000
47	A	47	ASN	0	-0.055	-0.032	20.089	0.966	0.966	0.000	0.000	0.000	0.000
48	A	48	SER	0	0.004	-0.002	17.336	0.322	0.322	0.000	0.000	0.000	0.000
49	A	49	SER	0	0.050	0.014	19.386	0.112	0.112	0.000	0.000	0.000	0.000
50	A	50	THR	0	-0.016	-0.009	21.996	0.292	0.292	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.008	0.009	20.225	0.324	0.324	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.029	0.015	19.600	0.205	0.205	0.000	0.000	0.000	0.000
53	A	53	ALA	0	-0.006	-0.002	22.538	0.311	0.311	0.000	0.000	0.000	0.000
54	A	54	ASN	0	-0.005	-0.009	26.033	0.565	0.565	0.000	0.000	0.000	0.000
55	A	55	ALA	0	0.028	0.033	24.007	0.312	0.312	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.020	0.003	25.436	0.206	0.206	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.873	0.928	27.053	9.720	9.720	0.000	0.000	0.000	0.000
58	A	58	SER	0	-0.012	0.011	29.462	0.238	0.238	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.047	0.018	25.877	0.240	0.240	0.000	0.000	0.000	0.000
60	A	60	PHE	0	-0.007	-0.039	27.528	0.179	0.179	0.000	0.000	0.000	0.000
61	A	61	ALA	0	-0.025	-0.001	32.149	0.288	0.288	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.844	-0.911	31.698	-9.372	-9.372	0.000	0.000	0.000	0.000
63	A	63	GLN	0	-0.049	-0.032	29.921	-0.029	-0.029	0.000	0.000	0.000	0.000
64	A	64	PRO	0	0.057	0.038	33.346	-0.144	-0.144	0.000	0.000	0.000	0.000
65	A	65	GLN	0	-0.010	-0.025	34.275	-0.171	-0.171	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.003	0.006	28.892	-0.072	-0.072	0.000	0.000	0.000	0.000
67	A	67	ILE	0	-0.015	-0.016	32.098	-0.144	-0.144	0.000	0.000	0.000	0.000
68	A	68	ALA	0	0.014	0.021	34.259	0.181	0.181	0.000	0.000	0.000	0.000
69	A	69	PRO	0	0.000	-0.024	36.695	-0.200	-0.200	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.003	0.010	36.714	0.117	0.117	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.043	0.042	34.193	-0.185	-0.185	0.000	0.000	0.000	0.000
72	A	72	ASN	0	0.018	0.014	27.285	-0.346	-0.346	0.000	0.000	0.000	0.000
73	A	75	ALA	0	0.050	0.022	28.638	-0.242	-0.242	0.000	0.000	0.000	0.000
74	A	76	TYR	0	0.022	0.029	29.908	0.099	0.099	0.000	0.000	0.000	0.000
75	A	77	THR	0	-0.050	-0.036	32.351	-0.207	-0.207	0.000	0.000	0.000	0.000
76	A	78	SER	0	0.062	0.012	31.322	-0.230	-0.230	0.000	0.000	0.000	0.000
77	A	79	ARG	1	0.973	0.992	27.484	10.321	10.321	0.000	0.000	0.000	0.000
78	A	80	ARG	1	0.852	0.925	27.014	9.262	9.262	0.000	0.000	0.000	0.000
79	A	81	MET	0	0.017	0.030	26.693	-0.462	-0.462	0.000	0.000	0.000	0.000
80	A	82	ALA	0	0.018	0.001	25.185	-0.315	-0.315	0.000	0.000	0.000	0.000
81	A	83	ALA	0	-0.031	-0.013	22.724	-0.471	-0.471	0.000	0.000	0.000	0.000
82	A	84	CYS	0	0.040	0.020	21.907	-0.511	-0.511	0.000	0.000	0.000	0.000
83	A	85	LEU	0	-0.005	-0.006	22.370	-0.340	-0.340	0.000	0.000	0.000	0.000
84	A	86	ARG	1	0.868	0.915	18.188	14.219	14.219	0.000	0.000	0.000	0.000
85	A	87	ASP	-1	-0.759	-0.843	17.725	-16.005	-16.005	0.000	0.000	0.000	0.000
86	A	88	MET	0	-0.040	-0.011	17.281	-0.601	-0.601	0.000	0.000	0.000	0.000
87	A	89	GLU	-1	-0.901	-0.957	16.146	-14.952	-14.952	0.000	0.000	0.000	0.000
88	A	90	ILE	0	-0.071	-0.036	12.830	-0.962	-0.962	0.000	0.000	0.000	0.000
89	A	91	ILE	0	0.038	0.010	12.821	-1.385	-1.385	0.000	0.000	0.000	0.000
90	A	92	LEU	0	0.000	0.006	13.392	-0.874	-0.874	0.000	0.000	0.000	0.000
91	A	93	ARG	1	0.949	0.978	9.315	20.426	20.426	0.000	0.000	0.000	0.000
92	A	94	TYR	0	-0.001	-0.013	6.564	-0.648	-0.648	0.000	0.000	0.000	0.000
93	A	95	VAL	0	0.029	0.021	8.888	-2.003	-2.003	0.000	0.000	0.000	0.000
94	A	96	THR	0	-0.058	-0.041	10.958	-0.289	-0.289	0.000	0.000	0.000	0.000
96	A	98	ALA	0	0.013	0.016	6.764	-1.825	-1.825	0.000	0.000	0.000	0.000
97	A	99	ILE	0	0.001	0.005	7.753	0.045	0.045	0.000	0.000	0.000	0.000
98	A	100	PHE	0	-0.025	-0.009	7.129	0.744	0.744	0.000	0.000	0.000	0.000
100	A	102	GLY	0	0.027	0.013	7.605	-0.399	-0.399	0.000	0.000	0.000	0.000
101	A	103	ASP	-1	-0.797	-0.880	5.608	-41.367	-41.367	0.000	0.000	0.000	0.000
102	A	104	ALA	0	0.005	0.003	5.971	-1.466	-1.466	0.000	0.000	0.000	0.000
106	A	108	ASP	-1	-0.779	-0.892	6.586	-27.106	-27.106	0.000	0.000	0.000	0.000
109	A	111	CYS	0	-0.057	-0.010	6.986	3.510	3.510	0.000	0.000	0.000	0.000
110	A	112	LEU	0	0.003	0.009	9.691	2.095	2.095	0.000	0.000	0.000	0.000
111	A	113	ASN	0	-0.030	-0.007	8.838	4.013	4.013	0.000	0.000	0.000	0.000
112	A	114	GLY	0	0.063	0.042	11.695	0.272	0.272	0.000	0.000	0.000	0.000
113	A	115	LEU	0	0.000	0.005	14.221	1.293	1.293	0.000	0.000	0.000	0.000
114	A	116	LYS	1	0.843	0.921	16.185	14.918	14.918	0.000	0.000	0.000	0.000
115	A	117	GLU	-1	-0.877	-0.952	18.128	-15.798	-15.798	0.000	0.000	0.000	0.000
116	A	118	THR	0	-0.049	-0.023	17.634	0.755	0.755	0.000	0.000	0.000	0.000
117	A	119	TYR	0	-0.058	-0.071	19.130	0.617	0.617	0.000	0.000	0.000	0.000
118	A	120	LEU	0	-0.010	-0.008	22.342	0.725	0.725	0.000	0.000	0.000	0.000
119	A	121	ALA	0	-0.030	-0.007	23.448	0.579	0.579	0.000	0.000	0.000	0.000
120	A	122	LEU	0	-0.065	-0.029	22.150	0.451	0.451	0.000	0.000	0.000	0.000
121	A	123	GLY	0	-0.010	0.009	25.920	0.437	0.437	0.000	0.000	0.000	0.000
122	A	124	THR	0	-0.076	-0.047	23.604	0.313	0.313	0.000	0.000	0.000	0.000
123	A	125	PRO	0	-0.012	-0.008	25.432	-0.266	-0.266	0.000	0.000	0.000	0.000
124	A	126	GLY	0	0.079	0.035	22.799	-0.041	-0.041	0.000	0.000	0.000	0.000
125	A	127	SER	0	0.040	0.016	22.945	-0.285	-0.285	0.000	0.000	0.000	0.000
126	A	128	SER	0	0.013	0.002	25.365	0.248	0.248	0.000	0.000	0.000	0.000
127	A	129	VAL	0	0.000	0.012	20.037	0.068	0.068	0.000	0.000	0.000	0.000
128	A	130	ALA	0	0.003	0.011	21.120	-0.296	-0.296	0.000	0.000	0.000	0.000
129	A	131	VAL	0	0.029	0.023	22.157	-0.090	-0.090	0.000	0.000	0.000	0.000
130	A	132	GLY	0	0.023	0.004	23.730	0.145	0.145	0.000	0.000	0.000	0.000
131	A	133	VAL	0	-0.008	-0.019	17.703	-0.080	-0.080	0.000	0.000	0.000	0.000
132	A	134	GLN	0	0.000	-0.006	20.617	0.169	0.169	0.000	0.000	0.000	0.000
133	A	135	LYS	1	0.840	0.910	22.747	10.365	10.365	0.000	0.000	0.000	0.000
134	A	136	MET	0	-0.071	-0.019	18.591	0.169	0.169	0.000	0.000	0.000	0.000
135	A	137	LYS	1	0.809	0.906	19.756	13.459	13.459	0.000	0.000	0.000	0.000
136	A	138	ASP	-1	-0.883	-0.940	20.888	-11.707	-11.707	0.000	0.000	0.000	0.000
137	A	139	ALA	0	-0.022	-0.011	23.866	0.228	0.228	0.000	0.000	0.000	0.000
138	A	140	ALA	0	0.000	-0.005	19.105	0.099	0.099	0.000	0.000	0.000	0.000
139	A	141	LEU	0	-0.013	-0.012	19.897	-0.097	-0.097	0.000	0.000	0.000	0.000
140	A	142	ALA	0	-0.015	-0.001	22.366	0.207	0.207	0.000	0.000	0.000	0.000
141	A	143	ILE	0	-0.040	-0.023	22.250	0.223	0.223	0.000	0.000	0.000	0.000
142	A	144	ALA	0	-0.016	-0.009	20.207	0.028	0.028	0.000	0.000	0.000	0.000
143	A	145	GLY	0	0.002	-0.003	22.084	0.023	0.023	0.000	0.000	0.000	0.000
144	A	146	ASP	-1	-0.826	-0.891	25.147	-9.445	-9.445	0.000	0.000	0.000	0.000
145	A	147	THR	0	-0.007	0.000	27.518	-0.183	-0.183	0.000	0.000	0.000	0.000
146	A	148	ASN	0	-0.078	-0.043	30.093	0.413	0.413	0.000	0.000	0.000	0.000
147	A	149	GLY	0	-0.016	-0.017	28.871	-0.278	-0.278	0.000	0.000	0.000	0.000
148	A	150	ILE	0	0.018	0.031	23.817	-0.154	-0.154	0.000	0.000	0.000	0.000
149	A	151	THR	0	-0.049	-0.037	27.302	0.554	0.554	0.000	0.000	0.000	0.000
150	A	152	ARG	1	0.943	0.971	27.930	8.925	8.925	0.000	0.000	0.000	0.000
151	A	153	GLY	0	0.035	0.006	27.771	0.042	0.042	0.000	0.000	0.000	0.000
152	A	154	ASP	-1	-0.851	-0.910	26.171	-11.494	-11.494	0.000	0.000	0.000	0.000
153	A	155	CYS	0	0.014	0.004	22.146	-0.414	-0.414	0.000	0.000	0.000	0.000
154	A	156	ALA	0	0.021	0.015	21.759	-0.549	-0.549	0.000	0.000	0.000	0.000
155	A	157	SER	0	0.023	0.001	19.539	-0.145	-0.145	0.000	0.000	0.000	0.000
156	A	158	LEU	0	0.037	0.028	15.674	-0.663	-0.663	0.000	0.000	0.000	0.000
157	A	159	MET	0	-0.025	-0.007	17.608	-0.660	-0.660	0.000	0.000	0.000	0.000
158	A	160	ALA	0	0.020	0.009	19.690	-0.080	-0.080	0.000	0.000	0.000	0.000
159	A	161	GLU	-1	-0.750	-0.819	12.196	-21.495	-21.495	0.000	0.000	0.000	0.000
160	A	162	VAL	0	0.022	0.009	14.797	-0.872	-0.872	0.000	0.000	0.000	0.000
161	A	163	ALA	0	-0.005	-0.003	15.984	-0.287	-0.287	0.000	0.000	0.000	0.000
162	A	164	SER	0	-0.023	-0.021	14.778	-0.375	-0.375	0.000	0.000	0.000	0.000
163	A	165	TYR	0	-0.020	-0.038	9.584	-1.256	-1.256	0.000	0.000	0.000	0.000
164	A	166	PHE	0	0.021	0.006	13.418	-0.370	-0.370	0.000	0.000	0.000	0.000
165	A	167	ASP	-1	-0.802	-0.881	16.385	-13.913	-13.913	0.000	0.000	0.000	0.000
166	A	168	LYS	1	0.812	0.913	10.230	26.066	26.066	0.000	0.000	0.000	0.000
167	A	169	ALA	0	0.016	-0.005	13.790	-0.280	-0.280	0.000	0.000	0.000	0.000
168	A	170	ALA	0	-0.024	-0.017	15.133	0.432	0.432	0.000	0.000	0.000	0.000
169	A	171	SER	0	-0.044	-0.050	17.841	0.757	0.757	0.000	0.000	0.000	0.000
170	A	172	ALA	0	-0.019	0.009	14.924	0.040	0.040	0.000	0.000	0.000	0.000
171	A	173	VAL	0	-0.054	-0.028	16.904	0.048	0.048	0.000	0.000	0.000	0.000
172	A	174	ALA	-1	-0.846	-0.897	19.392	-12.748	-12.748	0.000	0.000	0.000	0.000

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