FMO DATABASE

FMODB ID: 5GM3Z

Calculation Name: 1V0A-A-Xray549

Preferred Name:

Target Type:

Ligand Name: calcium ion

Ligand 3-letter code: CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1V0A

Chain ID: A

ChEMBL ID:

UniProt ID: P16218

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

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	-1777407.320503
FMO2-HF: Nuclear repulsion	1710048.553886
FMO2-HF: Total energy	-67358.766617
FMO2-MP2: Total energy	-67555.564264

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:3:SER)

Summations of interaction energy for fragment #1(A:3: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.
-148.55	-140.729	7.235	-6.384	-8.669	-0.046

Interaction energy analysis for fragmet #1(A:3:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.809 / q_NPA : 0.896

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	5	VAL	0	0.025	0.014	3.329	-8.495	-6.548	0.067	-0.918	-1.095	-0.004
65	A	67	LYS	1	0.829	0.902	2.429	38.745	39.751	0.632	-0.671	-0.967	-0.003
66	A	68	TRP	0	0.020	0.012	2.416	-22.959	-19.846	2.757	-2.864	-3.005	-0.037
67	A	69	LEU	0	-0.057	-0.036	2.060	-7.196	-6.252	3.633	-1.622	-2.955	0.000
68	A	70	LYS	1	0.840	0.937	4.388	38.276	38.328	-0.001	-0.023	-0.029	0.000
167	A	169	GLY	0	0.044	0.021	3.499	-3.979	-3.848	0.007	-0.045	-0.092	0.000
168	A	170	ALA	0	-0.032	-0.031	2.809	3.525	4.120	0.140	-0.226	-0.508	-0.002
169	A	171	LEU	0	-0.010	-0.017	4.365	2.984	3.017	0.000	-0.015	-0.018	0.000
4	A	6	GLY	0	0.019	0.021	6.072	2.815	2.815	0.000	0.000	0.000	0.000
5	A	7	GLU	-1	-0.850	-0.925	7.467	-23.717	-23.717	0.000	0.000	0.000	0.000
6	A	8	LYS	1	0.951	0.978	9.223	24.942	24.942	0.000	0.000	0.000	0.000
7	A	9	MET	0	0.000	0.019	10.886	-0.299	-0.299	0.000	0.000	0.000	0.000
8	A	10	LEU	0	-0.077	-0.039	12.684	-0.307	-0.307	0.000	0.000	0.000	0.000
9	A	11	ASP	-1	-0.791	-0.908	15.778	-12.831	-12.831	0.000	0.000	0.000	0.000
10	A	12	ASP	-1	-0.849	-0.927	19.190	-14.383	-14.383	0.000	0.000	0.000	0.000
11	A	13	PHE	0	-0.042	-0.028	21.149	0.545	0.545	0.000	0.000	0.000	0.000
12	A	14	GLU	-1	-0.800	-0.868	23.975	-10.741	-10.741	0.000	0.000	0.000	0.000
13	A	15	GLY	0	-0.047	-0.009	24.283	0.299	0.299	0.000	0.000	0.000	0.000
14	A	16	VAL	0	-0.052	-0.032	24.692	0.457	0.457	0.000	0.000	0.000	0.000
15	A	17	LEU	0	-0.001	-0.007	25.019	-0.309	-0.309	0.000	0.000	0.000	0.000
16	A	18	ASN	0	-0.037	-0.028	22.196	0.312	0.312	0.000	0.000	0.000	0.000
17	A	19	TRP	0	-0.049	-0.034	19.623	-0.188	-0.188	0.000	0.000	0.000	0.000
18	A	20	GLY	0	0.011	0.017	25.527	0.495	0.495	0.000	0.000	0.000	0.000
19	A	21	SER	0	-0.015	-0.016	27.610	-0.303	-0.303	0.000	0.000	0.000	0.000
20	A	22	TYR	0	-0.045	-0.032	25.030	0.452	0.452	0.000	0.000	0.000	0.000
21	A	23	SER	0	-0.034	-0.033	31.242	-0.011	-0.011	0.000	0.000	0.000	0.000
22	A	24	GLY	0	0.023	0.014	33.568	0.115	0.115	0.000	0.000	0.000	0.000
23	A	25	GLU	-1	-0.879	-0.940	36.110	-7.932	-7.932	0.000	0.000	0.000	0.000
24	A	26	GLY	0	-0.013	0.003	38.500	0.063	0.063	0.000	0.000	0.000	0.000
25	A	27	ALA	0	-0.034	0.009	35.061	0.080	0.080	0.000	0.000	0.000	0.000
26	A	28	LYS	1	0.871	0.928	36.251	8.032	8.032	0.000	0.000	0.000	0.000
27	A	29	VAL	0	0.000	-0.004	30.305	-0.088	-0.088	0.000	0.000	0.000	0.000
28	A	30	SER	0	-0.051	-0.008	33.392	0.191	0.191	0.000	0.000	0.000	0.000
29	A	31	THR	0	0.038	0.005	28.420	-0.057	-0.057	0.000	0.000	0.000	0.000
30	A	32	LYS	1	0.829	0.923	31.179	8.960	8.960	0.000	0.000	0.000	0.000
31	A	33	ILE	0	0.031	0.025	27.866	-0.235	-0.235	0.000	0.000	0.000	0.000
32	A	34	VAL	0	-0.076	-0.033	30.191	0.448	0.448	0.000	0.000	0.000	0.000
33	A	35	SER	0	0.021	0.003	30.053	-0.130	-0.130	0.000	0.000	0.000	0.000
34	A	36	GLY	0	0.011	0.008	26.434	0.049	0.049	0.000	0.000	0.000	0.000
35	A	37	LYS	1	0.718	0.849	22.554	13.355	13.355	0.000	0.000	0.000	0.000
36	A	38	THR	0	-0.065	-0.055	23.776	0.156	0.156	0.000	0.000	0.000	0.000
37	A	39	GLY	0	0.032	0.043	25.564	-0.223	-0.223	0.000	0.000	0.000	0.000
38	A	40	ASN	0	-0.058	-0.053	27.181	0.688	0.688	0.000	0.000	0.000	0.000
39	A	41	GLY	0	0.072	0.029	25.477	-0.436	-0.436	0.000	0.000	0.000	0.000
40	A	42	MET	0	-0.043	0.007	24.212	0.589	0.589	0.000	0.000	0.000	0.000
41	A	43	GLU	-1	-0.836	-0.920	27.109	-9.104	-9.104	0.000	0.000	0.000	0.000
42	A	44	VAL	0	-0.005	-0.014	26.646	0.073	0.073	0.000	0.000	0.000	0.000
43	A	45	SER	0	-0.005	-0.009	29.989	0.173	0.173	0.000	0.000	0.000	0.000
44	A	46	TYR	0	0.010	0.008	30.480	0.113	0.113	0.000	0.000	0.000	0.000
45	A	47	THR	0	0.004	-0.016	34.083	0.176	0.176	0.000	0.000	0.000	0.000
46	A	48	GLY	0	0.007	0.012	35.253	-0.011	-0.011	0.000	0.000	0.000	0.000
47	A	49	THR	0	-0.003	-0.022	35.903	0.186	0.186	0.000	0.000	0.000	0.000
48	A	50	THR	0	-0.053	-0.055	36.626	-0.218	-0.218	0.000	0.000	0.000	0.000
49	A	51	ASP	-1	-0.870	-0.923	36.451	-7.986	-7.986	0.000	0.000	0.000	0.000
50	A	52	GLY	0	-0.042	-0.005	35.618	-0.111	-0.111	0.000	0.000	0.000	0.000
51	A	53	TYR	0	0.002	0.010	30.541	-0.187	-0.187	0.000	0.000	0.000	0.000
52	A	54	TRP	0	0.013	-0.019	27.927	0.179	0.179	0.000	0.000	0.000	0.000
53	A	55	GLY	0	0.021	0.003	27.086	-0.294	-0.294	0.000	0.000	0.000	0.000
54	A	56	THR	0	-0.032	-0.004	24.881	0.306	0.306	0.000	0.000	0.000	0.000
55	A	57	VAL	0	0.020	0.000	22.434	-0.444	-0.444	0.000	0.000	0.000	0.000
56	A	58	TYR	0	0.025	0.031	18.615	0.398	0.398	0.000	0.000	0.000	0.000
57	A	59	SER	0	0.002	-0.020	20.164	-0.468	-0.468	0.000	0.000	0.000	0.000
58	A	60	LEU	0	-0.028	-0.003	15.163	0.179	0.179	0.000	0.000	0.000	0.000
59	A	61	PRO	0	-0.022	-0.004	17.961	0.131	0.131	0.000	0.000	0.000	0.000
60	A	62	ASP	-1	-0.916	-0.975	12.511	-22.595	-22.595	0.000	0.000	0.000	0.000
61	A	63	GLY	0	0.008	0.004	14.122	-0.029	-0.029	0.000	0.000	0.000	0.000
62	A	64	ASP	-1	-0.839	-0.868	8.793	-31.785	-31.785	0.000	0.000	0.000	0.000
63	A	65	TRP	0	0.016	-0.014	8.253	-1.947	-1.947	0.000	0.000	0.000	0.000
64	A	66	SER	0	-0.022	-0.031	6.312	-6.665	-6.665	0.000	0.000	0.000	0.000
69	A	71	ILE	0	-0.001	0.028	8.203	-1.350	-1.350	0.000	0.000	0.000	0.000
70	A	72	SER	0	-0.027	-0.014	11.243	1.271	1.271	0.000	0.000	0.000	0.000
71	A	73	PHE	0	0.073	0.038	13.751	0.260	0.260	0.000	0.000	0.000	0.000
72	A	74	ASP	-1	-0.779	-0.847	17.403	-14.143	-14.143	0.000	0.000	0.000	0.000
73	A	75	ILE	0	-0.048	-0.035	20.855	0.243	0.243	0.000	0.000	0.000	0.000
74	A	76	LYS	1	0.905	0.967	23.700	10.217	10.217	0.000	0.000	0.000	0.000
75	A	77	SER	0	-0.008	-0.013	27.486	0.008	0.008	0.000	0.000	0.000	0.000
76	A	78	VAL	0	-0.027	-0.030	30.825	-0.050	-0.050	0.000	0.000	0.000	0.000
77	A	79	ASP	-1	-0.853	-0.909	33.664	-7.711	-7.711	0.000	0.000	0.000	0.000
78	A	80	GLY	0	0.039	0.016	35.366	0.059	0.059	0.000	0.000	0.000	0.000
79	A	81	SER	0	-0.019	-0.003	35.137	-0.125	-0.125	0.000	0.000	0.000	0.000
80	A	82	ALA	0	0.032	0.024	31.075	-0.161	-0.161	0.000	0.000	0.000	0.000
81	A	83	ASN	0	-0.062	-0.049	31.529	0.044	0.044	0.000	0.000	0.000	0.000
82	A	84	GLU	-1	-0.865	-0.921	26.408	-11.209	-11.209	0.000	0.000	0.000	0.000
83	A	85	ILE	0	-0.018	-0.006	24.388	0.305	0.305	0.000	0.000	0.000	0.000
84	A	86	ARG	1	0.801	0.856	22.413	11.211	11.211	0.000	0.000	0.000	0.000
85	A	87	PHE	0	0.024	0.023	15.115	0.116	0.116	0.000	0.000	0.000	0.000
86	A	88	MET	0	-0.072	-0.038	18.607	-0.267	-0.267	0.000	0.000	0.000	0.000
87	A	89	ILE	0	0.032	0.021	12.453	-0.178	-0.178	0.000	0.000	0.000	0.000
88	A	90	ALA	0	0.026	0.012	16.654	0.321	0.321	0.000	0.000	0.000	0.000
89	A	91	GLU	0	0.031	0.015	15.361	-0.984	-0.984	0.000	0.000	0.000	0.000
90	A	92	LYS	1	0.945	0.978	16.750	18.200	18.200	0.000	0.000	0.000	0.000
91	A	93	SER	0	-0.040	-0.007	20.158	-0.056	-0.056	0.000	0.000	0.000	0.000
92	A	94	ILE	0	0.008	0.001	22.685	-0.148	-0.148	0.000	0.000	0.000	0.000
93	A	95	ASN	0	-0.061	-0.025	24.389	0.094	0.094	0.000	0.000	0.000	0.000
94	A	96	GLY	0	-0.026	-0.007	24.299	0.353	0.353	0.000	0.000	0.000	0.000
95	A	97	VAL	0	-0.025	-0.020	24.904	-0.205	-0.205	0.000	0.000	0.000	0.000
96	A	98	GLY	0	-0.004	0.004	26.171	0.291	0.291	0.000	0.000	0.000	0.000
97	A	99	ASP	-1	-0.800	-0.899	22.888	-12.232	-12.232	0.000	0.000	0.000	0.000
98	A	100	GLY	0	0.038	0.010	21.002	0.474	0.474	0.000	0.000	0.000	0.000
99	A	101	GLU	-1	-0.797	-0.893	18.658	-14.399	-14.399	0.000	0.000	0.000	0.000
100	A	102	HIS	0	-0.015	-0.028	18.741	-0.585	-0.585	0.000	0.000	0.000	0.000
101	A	103	TRP	0	0.008	0.003	15.555	0.033	0.033	0.000	0.000	0.000	0.000
102	A	104	VAL	0	-0.016	-0.016	17.609	-0.095	-0.095	0.000	0.000	0.000	0.000
103	A	105	TYR	0	-0.018	-0.015	16.257	-0.532	-0.532	0.000	0.000	0.000	0.000
104	A	106	SER	0	-0.029	-0.032	18.914	0.077	0.077	0.000	0.000	0.000	0.000
105	A	107	ILE	0	-0.049	-0.024	20.064	-0.375	-0.375	0.000	0.000	0.000	0.000
106	A	108	THR	0	0.019	0.013	23.059	0.292	0.292	0.000	0.000	0.000	0.000
107	A	109	PRO	0	-0.020	0.001	25.809	-0.263	-0.263	0.000	0.000	0.000	0.000
108	A	110	ASP	-1	-0.820	-0.925	27.209	-10.520	-10.520	0.000	0.000	0.000	0.000
109	A	111	SER	0	-0.010	-0.011	29.703	-0.088	-0.088	0.000	0.000	0.000	0.000
110	A	112	SER	0	-0.026	-0.013	28.976	0.224	0.224	0.000	0.000	0.000	0.000
111	A	113	TRP	0	-0.017	0.003	24.414	-0.188	-0.188	0.000	0.000	0.000	0.000
112	A	114	LYS	1	0.918	0.983	22.507	12.235	12.235	0.000	0.000	0.000	0.000
113	A	115	THR	0	0.007	-0.027	17.132	0.070	0.070	0.000	0.000	0.000	0.000
114	A	116	ILE	0	-0.080	-0.038	16.903	0.242	0.242	0.000	0.000	0.000	0.000
115	A	117	GLU	-1	-0.828	-0.922	10.581	-26.029	-26.029	0.000	0.000	0.000	0.000
116	A	118	ILE	0	-0.018	-0.012	12.957	0.518	0.518	0.000	0.000	0.000	0.000
117	A	119	PRO	0	0.018	-0.010	8.807	-1.465	-1.465	0.000	0.000	0.000	0.000
118	A	120	PHE	0	0.071	0.025	6.166	2.362	2.362	0.000	0.000	0.000	0.000
119	A	121	SER	0	-0.005	-0.001	8.818	1.620	1.620	0.000	0.000	0.000	0.000
120	A	122	SER	0	-0.020	-0.006	10.499	1.758	1.758	0.000	0.000	0.000	0.000
121	A	123	PHE	0	0.012	0.010	12.303	1.599	1.599	0.000	0.000	0.000	0.000
122	A	124	ARG	1	0.831	0.912	14.971	15.463	15.463	0.000	0.000	0.000	0.000
123	A	125	ARG	1	0.862	0.940	18.162	13.227	13.227	0.000	0.000	0.000	0.000
124	A	126	ARG	1	0.768	0.863	19.517	12.059	12.059	0.000	0.000	0.000	0.000
125	A	127	LEU	0	0.004	-0.011	22.492	0.133	0.133	0.000	0.000	0.000	0.000
126	A	128	ASP	-1	-0.788	-0.838	25.992	-10.795	-10.795	0.000	0.000	0.000	0.000
127	A	129	TYR	0	-0.002	-0.009	26.160	0.515	0.515	0.000	0.000	0.000	0.000
128	A	130	GLN	0	-0.007	-0.004	21.330	-0.569	-0.569	0.000	0.000	0.000	0.000
129	A	131	PRO	0	0.004	0.039	24.160	0.537	0.537	0.000	0.000	0.000	0.000
130	A	132	PRO	0	-0.026	-0.035	26.732	-0.153	-0.153	0.000	0.000	0.000	0.000
131	A	133	GLY	0	0.038	0.028	25.882	0.115	0.115	0.000	0.000	0.000	0.000
132	A	134	GLN	0	-0.001	-0.002	22.760	-0.899	-0.899	0.000	0.000	0.000	0.000
133	A	135	ASP	-1	-0.783	-0.918	19.019	-14.721	-14.721	0.000	0.000	0.000	0.000
134	A	136	MET	0	-0.147	-0.064	22.211	0.606	0.606	0.000	0.000	0.000	0.000
135	A	137	SER	0	-0.002	0.004	17.129	0.410	0.410	0.000	0.000	0.000	0.000
136	A	138	GLY	0	-0.037	-0.016	18.871	0.095	0.095	0.000	0.000	0.000	0.000
137	A	139	THR	0	-0.104	-0.086	13.540	-0.143	-0.143	0.000	0.000	0.000	0.000
138	A	140	LEU	0	-0.022	0.005	11.028	0.252	0.252	0.000	0.000	0.000	0.000
139	A	141	ASP	-1	-0.780	-0.863	11.008	-21.270	-21.270	0.000	0.000	0.000	0.000
140	A	142	LEU	0	-0.028	-0.030	6.263	0.098	0.098	0.000	0.000	0.000	0.000
141	A	143	ASP	-1	-0.925	-0.959	9.963	-24.234	-24.234	0.000	0.000	0.000	0.000
142	A	144	ASN	0	-0.022	-0.008	11.333	1.487	1.487	0.000	0.000	0.000	0.000
143	A	145	ILE	0	-0.020	-0.005	11.847	1.281	1.281	0.000	0.000	0.000	0.000
144	A	146	ASP	-1	-0.882	-0.918	14.890	-13.862	-13.862	0.000	0.000	0.000	0.000
145	A	147	SER	0	-0.021	-0.043	18.276	0.289	0.289	0.000	0.000	0.000	0.000
146	A	148	ILE	0	-0.045	-0.011	15.328	-0.656	-0.656	0.000	0.000	0.000	0.000
147	A	149	HIS	0	0.055	0.020	18.522	1.174	1.174	0.000	0.000	0.000	0.000
148	A	150	PHE	0	-0.020	0.004	19.726	-0.357	-0.357	0.000	0.000	0.000	0.000
149	A	151	MET	0	-0.041	-0.027	23.329	0.315	0.315	0.000	0.000	0.000	0.000
150	A	152	TYR	0	0.044	0.021	25.913	-0.211	-0.211	0.000	0.000	0.000	0.000
151	A	153	ALA	0	0.015	0.017	26.710	-0.334	-0.334	0.000	0.000	0.000	0.000
152	A	154	ASN	0	0.006	0.009	28.262	0.432	0.432	0.000	0.000	0.000	0.000
153	A	155	ASN	0	0.055	0.041	32.053	-0.144	-0.144	0.000	0.000	0.000	0.000
154	A	156	LYS	1	0.870	0.943	34.332	8.624	8.624	0.000	0.000	0.000	0.000
155	A	157	SER	0	0.010	-0.001	34.897	-0.109	-0.109	0.000	0.000	0.000	0.000
156	A	158	GLY	0	-0.026	-0.010	33.597	0.040	0.040	0.000	0.000	0.000	0.000
157	A	159	LYS	1	0.843	0.920	32.475	8.209	8.209	0.000	0.000	0.000	0.000
158	A	160	PHE	0	-0.032	-0.010	25.030	0.038	0.038	0.000	0.000	0.000	0.000
159	A	161	VAL	0	-0.005	0.003	27.115	0.129	0.129	0.000	0.000	0.000	0.000
160	A	162	VAL	0	-0.019	-0.017	22.103	-0.242	-0.242	0.000	0.000	0.000	0.000
161	A	163	ASP	-1	-0.714	-0.859	22.003	-12.543	-12.543	0.000	0.000	0.000	0.000
162	A	164	ASN	0	-0.070	-0.041	18.038	-0.660	-0.660	0.000	0.000	0.000	0.000
163	A	165	ILE	0	0.000	0.012	15.909	-0.975	-0.975	0.000	0.000	0.000	0.000
164	A	166	LYS	1	0.878	0.913	12.348	19.883	19.883	0.000	0.000	0.000	0.000
165	A	167	LEU	0	0.008	0.015	7.881	-0.533	-0.533	0.000	0.000	0.000	0.000
166	A	168	ILE	0	-0.012	-0.005	7.587	0.147	0.147	0.000	0.000	0.000	0.000
170	A	172	GLU	-1	-0.926	-0.967	8.056	-28.359	-28.359	0.000	0.000	0.000	0.000
171	A	173	HIS	0	-0.031	-0.013	9.134	3.330	3.330	0.000	0.000	0.000	0.000
172	A	174	HIS	0	-0.013	-0.015	12.222	-0.174	-0.174	0.000	0.000	0.000	0.000
173	A	175	HIS	-1	-0.960	-0.960	15.229	-18.458	-18.458	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:SER)