FMO DATABASE

FMODB ID: 2ML5R

Calculation Name: 2C7J-B-Xray547

Preferred Name:

Target Type:

Ligand Name: biliverdine ix alpha | phycocyanobilin

Ligand 3-letter code: BLA | CYC

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2C7J

Chain ID: B

ChEMBL ID:

UniProt ID: P00309

Base Structure: X-ray

Registration Date: 2025-10-05

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	-1560409.313963
FMO2-HF: Nuclear repulsion	1494535.456474
FMO2-HF: Total energy	-65873.857488
FMO2-MP2: Total energy	-66062.573774

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.
-116.475	-108.208	11.563	-7.966	-11.863	-0.091

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 : 0.751 / q_NPA : 0.867

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	-0.805	-0.911	3.823	-32.605	-31.210	-0.017	-0.441	-0.936	0.000
103	A	103	SER	0	-0.038	-0.022	2.852	-8.478	-6.763	0.373	-0.999	-1.089	-0.009
104	A	104	VAL	0	-0.018	-0.011	2.092	-6.541	-6.441	4.677	-1.029	-3.749	-0.004
105	A	105	MET	0	-0.022	-0.005	3.482	3.952	4.045	0.005	0.121	-0.219	-0.001
107	A	107	ASP	-1	-0.827	-0.930	1.953	-107.983	-104.590	5.620	-5.128	-3.884	-0.074
108	A	108	ARG	1	0.867	0.930	2.940	55.336	56.907	0.905	-0.490	-1.986	-0.003
4	A	4	ALA	0	0.035	0.013	6.096	0.663	0.663	0.000	0.000	0.000	0.000
5	A	5	PHE	0	-0.025	-0.009	9.457	2.087	2.087	0.000	0.000	0.000	0.000
6	A	6	SER	0	0.018	-0.001	6.806	0.870	0.870	0.000	0.000	0.000	0.000
7	A	7	ARG	1	0.836	0.895	5.964	41.380	41.380	0.000	0.000	0.000	0.000
8	A	8	VAL	0	0.033	0.017	9.423	1.487	1.487	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.012	0.005	11.792	1.539	1.539	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.941	-0.959	7.343	-39.188	-39.188	0.000	0.000	0.000	0.000
11	A	11	GLN	0	-0.065	-0.052	11.261	1.995	1.995	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.006	0.003	13.730	1.514	1.514	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.897	-0.945	13.653	-20.284	-20.284	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.924	0.954	12.068	24.968	24.968	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.853	0.937	15.742	17.442	17.442	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.006	0.007	18.663	0.921	0.921	0.000	0.000	0.000	0.000
17	A	17	ALA	0	-0.047	-0.017	19.560	0.847	0.847	0.000	0.000	0.000	0.000
18	A	18	TYR	0	-0.002	-0.009	19.469	-0.673	-0.673	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.006	-0.006	16.129	0.056	0.056	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.040	-0.040	20.003	0.961	0.961	0.000	0.000	0.000	0.000
21	A	21	ASN	0	0.002	-0.020	22.008	-0.292	-0.292	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.849	-0.918	23.419	-12.521	-12.521	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.854	-0.896	18.325	-17.027	-17.027	0.000	0.000	0.000	0.000
24	A	24	ILE	0	0.007	0.002	18.778	-0.673	-0.673	0.000	0.000	0.000	0.000
25	A	25	ASN	0	-0.066	-0.039	20.338	0.263	0.263	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.005	0.004	19.013	0.089	0.089	0.000	0.000	0.000	0.000
27	A	27	LEU	0	0.006	-0.005	14.236	-0.377	-0.377	0.000	0.000	0.000	0.000
28	A	28	GLN	0	-0.007	0.000	17.346	-0.167	-0.167	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.008	0.010	20.308	0.371	0.371	0.000	0.000	0.000	0.000
30	A	30	ILE	0	-0.026	-0.009	13.731	0.085	0.085	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.004	-0.003	16.626	-0.195	-0.195	0.000	0.000	0.000	0.000
32	A	32	ALA	0	-0.024	0.009	18.161	0.333	0.333	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.853	-0.921	19.667	-12.861	-12.861	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.029	-0.025	16.595	-0.282	-0.282	0.000	0.000	0.000	0.000
35	A	35	ASN	0	0.015	-0.008	17.434	-0.701	-0.701	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.879	0.941	19.863	12.585	12.585	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.837	0.901	12.482	20.112	20.112	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.019	-0.008	14.184	-0.565	-0.565	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.870	-0.930	16.931	-12.649	-12.649	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.038	-0.020	16.730	0.212	0.212	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.021	0.009	12.641	0.014	0.014	0.000	0.000	0.000	0.000
42	A	42	ASN	0	-0.007	0.009	15.248	0.286	0.286	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.867	0.921	17.616	11.886	11.886	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.000	0.000	15.153	0.453	0.453	0.000	0.000	0.000	0.000
45	A	45	THR	0	-0.043	-0.038	14.386	-0.074	-0.074	0.000	0.000	0.000	0.000
46	A	46	SER	0	-0.031	-0.017	16.192	0.388	0.388	0.000	0.000	0.000	0.000
47	A	47	ASN	0	-0.061	-0.030	19.634	0.963	0.963	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.032	0.024	16.698	0.211	0.211	0.000	0.000	0.000	0.000
49	A	49	SER	0	0.019	-0.011	18.568	-0.119	-0.119	0.000	0.000	0.000	0.000
50	A	50	SER	0	0.006	0.001	21.176	0.272	0.272	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.007	0.006	19.514	0.305	0.305	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.023	0.009	18.004	0.189	0.189	0.000	0.000	0.000	0.000
53	A	53	ALA	0	-0.002	0.005	21.179	0.275	0.275	0.000	0.000	0.000	0.000
54	A	54	ASN	0	-0.007	-0.010	24.646	0.532	0.532	0.000	0.000	0.000	0.000
55	A	55	ALA	0	0.015	0.023	22.485	0.280	0.280	0.000	0.000	0.000	0.000
56	A	56	TYR	0	-0.005	-0.021	24.219	0.250	0.250	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.918	0.949	25.690	10.023	10.023	0.000	0.000	0.000	0.000
58	A	58	ALA	0	0.013	0.006	27.608	0.306	0.306	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.001	0.004	24.619	0.178	0.178	0.000	0.000	0.000	0.000
60	A	60	VAL	0	-0.043	-0.030	28.288	0.211	0.211	0.000	0.000	0.000	0.000
61	A	61	ALA	0	-0.019	-0.009	30.845	0.294	0.294	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.783	-0.833	29.547	-10.196	-10.196	0.000	0.000	0.000	0.000
63	A	63	ARG	1	0.798	0.874	28.706	10.772	10.772	0.000	0.000	0.000	0.000
64	A	64	PRO	0	0.066	0.036	32.194	-0.131	-0.131	0.000	0.000	0.000	0.000
65	A	65	GLN	0	0.037	0.006	34.430	-0.144	-0.144	0.000	0.000	0.000	0.000
66	A	66	VAL	0	0.012	0.009	28.366	0.008	0.008	0.000	0.000	0.000	0.000
67	A	67	PHE	0	-0.006	-0.012	26.806	-0.220	-0.220	0.000	0.000	0.000	0.000
68	A	68	ASN	0	-0.027	-0.014	31.917	0.289	0.289	0.000	0.000	0.000	0.000
69	A	69	PRO	0	0.004	-0.011	35.090	-0.183	-0.183	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.007	0.009	36.093	0.137	0.137	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.010	0.028	33.222	-0.102	-0.102	0.000	0.000	0.000	0.000
72	A	72	PRO	0	0.007	-0.011	28.451	-0.032	-0.032	0.000	0.000	0.000	0.000
73	A	73	CYS	0	-0.042	-0.008	26.780	-0.429	-0.429	0.000	0.000	0.000	0.000
74	A	74	PHE	0	-0.013	0.008	28.606	0.067	0.067	0.000	0.000	0.000	0.000
75	A	75	HIS	0	0.061	0.019	30.544	-0.127	-0.127	0.000	0.000	0.000	0.000
76	A	76	HIS	0	0.047	0.014	29.367	-0.546	-0.546	0.000	0.000	0.000	0.000
77	A	77	ARG	1	0.906	0.960	24.636	10.868	10.868	0.000	0.000	0.000	0.000
78	A	78	ASN	0	-0.009	-0.001	25.164	-0.720	-0.720	0.000	0.000	0.000	0.000
79	A	79	GLN	0	0.065	0.035	24.757	-0.671	-0.671	0.000	0.000	0.000	0.000
80	A	80	ALA	0	0.024	0.004	23.674	-0.301	-0.301	0.000	0.000	0.000	0.000
81	A	81	ALA	0	-0.029	-0.006	20.799	-0.498	-0.498	0.000	0.000	0.000	0.000
82	A	82	CYS	0	0.024	0.019	19.994	-0.724	-0.724	0.000	0.000	0.000	0.000
83	A	83	ILE	0	0.011	0.004	20.452	-0.511	-0.511	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.839	0.904	16.247	14.823	14.823	0.000	0.000	0.000	0.000
85	A	85	ASP	-1	-0.774	-0.838	15.910	-16.748	-16.748	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.004	0.000	15.645	-0.951	-0.951	0.000	0.000	0.000	0.000
87	A	87	GLY	0	0.039	0.011	15.824	-0.523	-0.523	0.000	0.000	0.000	0.000
88	A	88	PHE	0	-0.054	-0.042	11.921	-0.912	-0.912	0.000	0.000	0.000	0.000
89	A	89	ILE	0	0.037	0.016	11.372	-1.522	-1.522	0.000	0.000	0.000	0.000
90	A	90	LEU	0	0.043	0.019	12.196	-0.995	-0.995	0.000	0.000	0.000	0.000
91	A	91	ARG	1	0.916	0.970	7.358	22.563	22.563	0.000	0.000	0.000	0.000
92	A	92	TYR	0	0.028	-0.003	5.075	-0.189	-0.189	0.000	0.000	0.000	0.000
93	A	93	VAL	0	0.021	0.026	8.441	-2.115	-2.115	0.000	0.000	0.000	0.000
94	A	94	THR	0	-0.029	-0.022	10.908	-0.204	-0.204	0.000	0.000	0.000	0.000
95	A	95	TYR	0	-0.012	-0.010	5.704	0.045	0.045	0.000	0.000	0.000	0.000
96	A	96	SER	0	-0.018	-0.001	7.347	-2.593	-2.593	0.000	0.000	0.000	0.000
97	A	97	VAL	0	0.007	0.003	8.313	0.163	0.163	0.000	0.000	0.000	0.000
98	A	98	LEU	0	-0.042	-0.013	8.660	0.818	0.818	0.000	0.000	0.000	0.000
99	A	99	ALA	0	-0.008	-0.004	5.731	0.535	0.535	0.000	0.000	0.000	0.000
100	A	100	GLY	0	0.032	0.023	7.647	-0.099	-0.099	0.000	0.000	0.000	0.000
101	A	101	ASP	-1	-0.773	-0.846	5.547	-48.961	-48.961	0.000	0.000	0.000	0.000
102	A	102	THR	0	0.037	0.002	6.577	0.188	0.188	0.000	0.000	0.000	0.000
106	A	106	ASP	-1	-0.766	-0.859	6.304	-32.195	-32.195	0.000	0.000	0.000	0.000
109	A	109	CYS	0	-0.082	-0.020	6.335	4.710	4.710	0.000	0.000	0.000	0.000
110	A	110	LEU	0	0.042	0.000	9.399	2.182	2.182	0.000	0.000	0.000	0.000
111	A	111	ASN	0	-0.057	-0.013	8.497	-0.416	-0.416	0.000	0.000	0.000	0.000
112	A	112	GLY	0	0.088	0.055	10.566	0.828	0.828	0.000	0.000	0.000	0.000
113	A	113	LEU	0	-0.054	-0.002	13.585	1.568	1.568	0.000	0.000	0.000	0.000
114	A	114	ARG	1	0.880	0.932	15.845	17.231	17.231	0.000	0.000	0.000	0.000
115	A	115	GLU	-1	-0.878	-0.951	16.847	-17.135	-17.135	0.000	0.000	0.000	0.000
116	A	116	THR	0	-0.060	-0.039	16.944	0.802	0.802	0.000	0.000	0.000	0.000
117	A	117	TYR	0	-0.051	-0.068	17.824	0.574	0.574	0.000	0.000	0.000	0.000
118	A	118	GLN	0	0.008	0.012	21.646	0.784	0.784	0.000	0.000	0.000	0.000
119	A	119	ALA	0	-0.042	-0.022	22.811	0.681	0.681	0.000	0.000	0.000	0.000
120	A	120	LEU	0	-0.027	-0.010	21.813	0.198	0.198	0.000	0.000	0.000	0.000
121	A	121	GLY	0	-0.012	-0.001	25.126	0.245	0.245	0.000	0.000	0.000	0.000
122	A	122	THR	0	-0.061	-0.027	22.620	0.320	0.320	0.000	0.000	0.000	0.000
123	A	123	PRO	0	-0.017	-0.024	25.090	-0.296	-0.296	0.000	0.000	0.000	0.000
124	A	124	GLY	0	0.093	0.075	22.470	0.046	0.046	0.000	0.000	0.000	0.000
125	A	125	ASP	-1	-0.789	-0.904	22.983	-11.436	-11.436	0.000	0.000	0.000	0.000
126	A	126	ALA	0	-0.030	-0.021	25.345	-0.016	-0.016	0.000	0.000	0.000	0.000
127	A	127	VAL	0	0.019	0.017	19.138	0.069	0.069	0.000	0.000	0.000	0.000
128	A	128	ALA	0	0.028	0.014	20.978	-0.309	-0.309	0.000	0.000	0.000	0.000
129	A	129	SER	0	-0.074	-0.060	22.005	-0.062	-0.062	0.000	0.000	0.000	0.000
130	A	130	GLY	0	0.023	0.013	22.853	0.171	0.171	0.000	0.000	0.000	0.000
131	A	131	ILE	0	-0.004	-0.010	16.967	-0.021	-0.021	0.000	0.000	0.000	0.000
132	A	132	LYS	1	0.912	0.969	20.174	13.453	13.453	0.000	0.000	0.000	0.000
133	A	133	LYS	1	0.883	0.934	22.975	10.818	10.818	0.000	0.000	0.000	0.000
134	A	134	MET	0	-0.066	-0.018	16.630	0.296	0.296	0.000	0.000	0.000	0.000
135	A	135	LYS	1	0.814	0.910	20.045	13.951	13.951	0.000	0.000	0.000	0.000
136	A	136	GLU	-1	-0.948	-0.977	20.920	-10.966	-10.966	0.000	0.000	0.000	0.000
137	A	137	ALA	0	-0.017	-0.009	23.196	0.245	0.245	0.000	0.000	0.000	0.000
138	A	138	ALA	0	0.017	0.006	18.914	0.152	0.152	0.000	0.000	0.000	0.000
139	A	139	LEU	0	-0.001	-0.005	20.919	0.016	0.016	0.000	0.000	0.000	0.000
140	A	140	LYS	1	0.897	0.950	22.701	10.888	10.888	0.000	0.000	0.000	0.000
141	A	141	ILE	0	-0.012	0.000	22.374	0.297	0.297	0.000	0.000	0.000	0.000
142	A	142	ALA	0	0.005	0.004	20.230	0.128	0.128	0.000	0.000	0.000	0.000
143	A	143	ASN	0	0.029	-0.001	22.130	-0.160	-0.160	0.000	0.000	0.000	0.000
144	A	144	ASP	-1	-0.801	-0.878	25.180	-9.525	-9.525	0.000	0.000	0.000	0.000
145	A	145	PRO	0	-0.021	-0.011	27.889	-0.092	-0.092	0.000	0.000	0.000	0.000
146	A	146	ASN	0	-0.054	-0.029	30.384	0.429	0.429	0.000	0.000	0.000	0.000
147	A	147	GLY	0	0.001	-0.007	29.008	-0.280	-0.280	0.000	0.000	0.000	0.000
148	A	148	ILE	0	-0.009	0.014	24.193	-0.183	-0.183	0.000	0.000	0.000	0.000
149	A	149	THR	0	0.001	-0.004	28.128	0.420	0.420	0.000	0.000	0.000	0.000
150	A	150	LYS	1	0.862	0.929	28.688	8.910	8.910	0.000	0.000	0.000	0.000
151	A	151	GLY	0	0.040	0.011	28.615	0.121	0.121	0.000	0.000	0.000	0.000
152	A	152	ASP	-1	-0.863	-0.918	26.979	-11.338	-11.338	0.000	0.000	0.000	0.000
153	A	153	CYS	0	0.018	-0.005	22.281	-0.257	-0.257	0.000	0.000	0.000	0.000
154	A	154	SER	0	0.002	0.004	22.566	-0.658	-0.658	0.000	0.000	0.000	0.000
155	A	155	GLN	0	0.016	-0.005	20.629	-0.474	-0.474	0.000	0.000	0.000	0.000
156	A	156	LEU	0	0.042	0.026	16.702	-0.654	-0.654	0.000	0.000	0.000	0.000
157	A	157	MET	0	-0.031	-0.001	18.288	-0.761	-0.761	0.000	0.000	0.000	0.000
158	A	158	SER	0	-0.020	-0.006	20.344	-0.297	-0.297	0.000	0.000	0.000	0.000
159	A	159	GLU	-1	-0.758	-0.852	13.162	-21.209	-21.209	0.000	0.000	0.000	0.000
160	A	160	LEU	0	0.014	0.007	15.587	-0.898	-0.898	0.000	0.000	0.000	0.000
161	A	161	ALA	0	-0.025	-0.021	16.668	-0.364	-0.364	0.000	0.000	0.000	0.000
162	A	162	SER	0	-0.018	-0.016	15.492	-0.394	-0.394	0.000	0.000	0.000	0.000
163	A	163	TYR	0	0.002	-0.027	10.998	-1.071	-1.071	0.000	0.000	0.000	0.000
164	A	164	PHE	0	0.021	0.001	14.236	-0.395	-0.395	0.000	0.000	0.000	0.000
165	A	165	ASP	-1	-0.844	-0.913	16.666	-14.206	-14.206	0.000	0.000	0.000	0.000
166	A	166	ARG	1	0.808	0.880	9.756	28.482	28.482	0.000	0.000	0.000	0.000
167	A	167	ALA	0	0.026	0.006	13.742	-0.141	-0.141	0.000	0.000	0.000	0.000
168	A	168	ALA	0	-0.029	-0.026	15.199	0.511	0.511	0.000	0.000	0.000	0.000
169	A	169	ALA	0	-0.003	-0.002	17.963	0.614	0.614	0.000	0.000	0.000	0.000
170	A	170	ALA	0	-0.028	-0.008	14.713	0.245	0.245	0.000	0.000	0.000	0.000
171	A	171	VAL	0	-0.059	-0.033	16.737	-0.181	-0.181	0.000	0.000	0.000	0.000
172	A	172	ALA	-1	-0.864	-0.902	19.251	-13.528	-13.528	0.000	0.000	0.000	0.000

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