FMO DATABASE

FMODB ID: LRLV9

Calculation Name: 4J2K-B-Xray547

Preferred Name:

Target Type:

Ligand Name: imidazole | glycerol

Ligand 3-letter code: IMD | GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4J2K

Chain ID: B

ChEMBL ID:

UniProt ID: P86451

Base Structure: X-ray

Registration Date: 2025-10-06

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	171
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1834354.650394
FMO2-HF: Nuclear repulsion	1766432.844218
FMO2-HF: Total energy	-67921.806176
FMO2-MP2: Total energy	-68121.409271

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(B:1:LYS)

Summations of interaction energy for fragment #1(B:1:LYS)

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.
-379.3	-375.468	12.233	-8.093	-7.972	-0.085

Interaction energy analysis for fragmet #1(B:1:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.722 / q_NPA : 1.842

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	B	3	LEU	0	0.012	0.018	3.416	-9.172	-7.219	0.007	-0.952	-1.009	-0.003
122	B	123	PRO	0	-0.032	-0.031	2.661	-1.546	-0.415	0.627	-0.360	-1.398	-0.003
123	B	124	TYR	0	-0.001	-0.010	4.876	4.291	4.390	-0.001	-0.004	-0.094	0.000
124	B	125	ARG	1	0.914	0.961	3.921	59.460	60.090	0.001	-0.336	-0.295	-0.001
125	B	126	ASP	-1	-0.935	-0.971	1.794	-152.867	-153.329	11.599	-6.420	-4.716	-0.078
126	B	127	ASP	-1	-0.888	-0.927	3.592	-58.211	-58.058	0.000	0.000	-0.153	0.000
127	B	128	TYR	0	-0.044	-0.036	3.865	-10.478	-10.150	0.000	-0.021	-0.307	0.000
4	B	4	LEU	0	-0.009	0.004	5.411	4.449	4.449	0.000	0.000	0.000	0.000
5	B	5	ASP	-1	-0.778	-0.894	7.779	-40.662	-40.662	0.000	0.000	0.000	0.000
6	B	6	SER	0	-0.050	-0.040	10.684	-1.950	-1.950	0.000	0.000	0.000	0.000
7	B	7	ASP	-1	-0.888	-0.916	12.957	-34.891	-34.891	0.000	0.000	0.000	0.000
8	B	8	GLY	0	-0.030	-0.007	10.081	0.589	0.589	0.000	0.000	0.000	0.000
9	B	9	ASP	-1	-0.867	-0.904	9.867	-40.751	-40.751	0.000	0.000	0.000	0.000
10	B	10	ILE	0	-0.018	-0.024	8.051	-1.662	-1.662	0.000	0.000	0.000	0.000
11	B	11	LEU	0	-0.022	-0.005	9.340	4.591	4.591	0.000	0.000	0.000	0.000
12	B	12	ARG	1	0.902	0.929	11.661	34.357	34.357	0.000	0.000	0.000	0.000
13	B	13	ASN	0	0.002	0.006	15.182	0.166	0.166	0.000	0.000	0.000	0.000
14	B	14	GLY	0	0.011	0.003	17.075	1.380	1.380	0.000	0.000	0.000	0.000
15	B	15	GLY	0	-0.034	-0.011	17.206	1.191	1.191	0.000	0.000	0.000	0.000
16	B	16	THR	0	-0.023	-0.017	18.223	0.259	0.259	0.000	0.000	0.000	0.000
17	B	17	TYR	0	0.023	0.009	14.310	-0.449	-0.449	0.000	0.000	0.000	0.000
18	B	18	TYR	0	-0.023	-0.009	17.774	1.205	1.205	0.000	0.000	0.000	0.000
19	B	19	ILE	0	0.024	0.018	14.612	-1.971	-1.971	0.000	0.000	0.000	0.000
20	B	20	LEU	0	-0.001	-0.003	15.346	2.592	2.592	0.000	0.000	0.000	0.000
21	B	21	PRO	0	0.021	0.023	14.373	-2.848	-2.848	0.000	0.000	0.000	0.000
22	B	22	ALA	0	0.020	0.014	10.017	0.390	0.390	0.000	0.000	0.000	0.000
23	B	23	LEU	0	-0.022	-0.010	11.779	1.473	1.473	0.000	0.000	0.000	0.000
24	B	24	ARG	1	0.839	0.877	14.146	37.371	37.371	0.000	0.000	0.000	0.000
25	B	25	GLY	0	0.037	0.012	17.612	0.496	0.496	0.000	0.000	0.000	0.000
26	B	26	LYS	1	0.891	0.946	19.041	27.257	27.257	0.000	0.000	0.000	0.000
27	B	27	GLY	0	0.061	0.047	19.654	-1.030	-1.030	0.000	0.000	0.000	0.000
28	B	28	GLY	0	-0.001	0.004	20.535	-0.835	-0.835	0.000	0.000	0.000	0.000
29	B	29	GLY	0	0.005	-0.013	19.271	-1.392	-1.392	0.000	0.000	0.000	0.000
30	B	30	LEU	0	-0.029	0.002	17.495	1.115	1.115	0.000	0.000	0.000	0.000
31	B	31	GLU	-1	-0.902	-0.974	21.187	-22.401	-22.401	0.000	0.000	0.000	0.000
32	B	32	LEU	0	-0.021	0.004	24.866	-0.342	-0.342	0.000	0.000	0.000	0.000
33	B	33	ALA	0	-0.009	-0.007	27.977	0.485	0.485	0.000	0.000	0.000	0.000
34	B	34	LYS	1	0.876	0.945	30.506	16.562	16.562	0.000	0.000	0.000	0.000
35	B	35	THR	0	0.013	-0.005	30.493	0.006	0.006	0.000	0.000	0.000	0.000
36	B	36	GLY	0	0.057	0.030	33.847	0.250	0.250	0.000	0.000	0.000	0.000
37	B	37	ASP	-1	-0.920	-0.961	36.944	-15.224	-15.224	0.000	0.000	0.000	0.000
38	B	38	GLU	-1	-0.880	-0.913	34.009	-18.192	-18.192	0.000	0.000	0.000	0.000
39	B	39	THR	0	-0.013	-0.026	37.754	-0.240	-0.240	0.000	0.000	0.000	0.000
40	B	40	CYS	0	-0.140	-0.056	36.207	0.041	0.041	0.000	0.000	0.000	0.000
41	B	41	PRO	0	-0.025	-0.025	31.744	-0.073	-0.073	0.000	0.000	0.000	0.000
42	B	42	LEU	0	0.060	0.024	31.105	-0.373	-0.373	0.000	0.000	0.000	0.000
43	B	43	ASN	0	0.004	0.006	28.004	0.087	0.087	0.000	0.000	0.000	0.000
44	B	44	VAL	0	-0.001	0.003	21.892	0.128	0.128	0.000	0.000	0.000	0.000
45	B	45	VAL	0	-0.011	-0.004	24.153	-0.060	-0.060	0.000	0.000	0.000	0.000
46	B	46	GLN	0	-0.009	-0.001	18.943	-0.352	-0.352	0.000	0.000	0.000	0.000
47	B	47	ALA	0	0.039	0.029	22.426	1.143	1.143	0.000	0.000	0.000	0.000
48	B	48	ARG	1	0.942	0.949	23.753	19.306	19.306	0.000	0.000	0.000	0.000
49	B	49	SER	0	-0.056	-0.018	25.717	0.065	0.065	0.000	0.000	0.000	0.000
50	B	50	GLU	-1	-0.774	-0.885	22.403	-23.219	-23.219	0.000	0.000	0.000	0.000
51	B	51	THR	0	-0.085	-0.047	23.055	-0.370	-0.370	0.000	0.000	0.000	0.000
52	B	52	LYS	1	0.885	0.947	24.900	21.386	21.386	0.000	0.000	0.000	0.000
53	B	53	ARG	1	0.990	0.985	20.496	26.531	26.531	0.000	0.000	0.000	0.000
54	B	54	GLY	0	0.030	0.038	21.768	-1.052	-1.052	0.000	0.000	0.000	0.000
55	B	55	ARG	1	0.802	0.875	23.758	22.050	22.050	0.000	0.000	0.000	0.000
56	B	56	PRO	0	-0.010	0.003	21.115	-0.977	-0.977	0.000	0.000	0.000	0.000
57	B	57	ALA	0	0.028	0.001	19.090	1.254	1.254	0.000	0.000	0.000	0.000
58	B	58	ILE	0	-0.031	-0.007	19.402	-1.094	-1.094	0.000	0.000	0.000	0.000
59	B	59	ILE	0	0.006	0.003	14.368	-0.083	-0.083	0.000	0.000	0.000	0.000
60	B	60	TRP	0	-0.062	-0.047	17.472	-0.503	-0.503	0.000	0.000	0.000	0.000
61	B	61	THR	0	0.010	-0.004	16.350	0.117	0.117	0.000	0.000	0.000	0.000
62	B	62	PRO	0	0.016	0.016	18.994	0.266	0.266	0.000	0.000	0.000	0.000
63	B	63	PRO	0	-0.010	0.002	18.747	1.035	1.035	0.000	0.000	0.000	0.000
64	B	64	ARG	1	0.951	0.984	20.173	22.089	22.089	0.000	0.000	0.000	0.000
65	B	65	ILE	0	-0.011	-0.007	14.709	0.294	0.294	0.000	0.000	0.000	0.000
66	B	66	ALA	0	0.022	0.001	17.145	-0.021	-0.021	0.000	0.000	0.000	0.000
67	B	67	ILE	0	-0.020	-0.003	10.601	0.762	0.762	0.000	0.000	0.000	0.000
68	B	68	LEU	0	0.019	0.018	11.523	1.389	1.389	0.000	0.000	0.000	0.000
69	B	69	THR	0	-0.002	-0.010	8.383	-4.748	-4.748	0.000	0.000	0.000	0.000
70	B	70	PRO	0	0.013	-0.010	5.242	2.704	2.704	0.000	0.000	0.000	0.000
71	B	71	ALA	0	0.004	0.023	8.485	2.146	2.146	0.000	0.000	0.000	0.000
72	B	72	PHE	0	-0.074	-0.035	11.146	2.814	2.814	0.000	0.000	0.000	0.000
73	B	73	TYR	-1	-0.748	-0.851	13.979	-33.485	-33.485	0.000	0.000	0.000	0.000
74	B	74	LEU	0	-0.046	-0.022	12.852	0.750	0.750	0.000	0.000	0.000	0.000
75	B	75	ASN	0	-0.019	-0.008	17.410	1.192	1.192	0.000	0.000	0.000	0.000
76	B	76	ILE	0	-0.008	-0.002	16.016	-1.461	-1.461	0.000	0.000	0.000	0.000
77	B	77	GLU	-1	-0.751	-0.827	19.845	-22.814	-22.814	0.000	0.000	0.000	0.000
78	B	78	PHE	0	-0.003	0.002	22.103	-0.601	-0.601	0.000	0.000	0.000	0.000
79	B	79	GLN	0	0.025	0.008	24.395	0.548	0.548	0.000	0.000	0.000	0.000
80	B	80	THR	0	0.008	0.005	26.089	0.164	0.164	0.000	0.000	0.000	0.000
81	B	81	ARG	1	0.892	0.954	29.385	20.628	20.628	0.000	0.000	0.000	0.000
82	B	82	ASP	-1	-0.879	-0.942	31.160	-19.585	-19.585	0.000	0.000	0.000	0.000
83	B	83	LEU	0	-0.013	0.016	30.742	-0.491	-0.491	0.000	0.000	0.000	0.000
84	B	84	PRO	0	0.020	0.017	34.093	0.451	0.451	0.000	0.000	0.000	0.000
85	B	85	ALA	0	0.103	0.035	37.081	-0.166	-0.166	0.000	0.000	0.000	0.000
86	B	87	LEU	0	0.021	-0.008	31.720	-0.212	-0.212	0.000	0.000	0.000	0.000
87	B	88	GLU	-1	-0.959	-0.987	35.008	-16.077	-16.077	0.000	0.000	0.000	0.000
88	B	89	GLU	-1	-0.911	-0.928	36.956	-15.607	-15.607	0.000	0.000	0.000	0.000
89	B	90	TYR	0	-0.079	-0.040	33.025	-0.172	-0.172	0.000	0.000	0.000	0.000
90	B	91	SER	0	-0.031	-0.020	32.595	-0.439	-0.439	0.000	0.000	0.000	0.000
91	B	92	ARG	1	0.819	0.874	25.206	21.987	21.987	0.000	0.000	0.000	0.000
92	B	93	LEU	0	0.027	0.006	27.508	0.577	0.577	0.000	0.000	0.000	0.000
93	B	94	PRO	0	0.004	-0.001	24.649	-0.981	-0.981	0.000	0.000	0.000	0.000
94	B	95	TRP	0	-0.021	-0.021	18.327	0.024	0.024	0.000	0.000	0.000	0.000
95	B	96	LYS	1	0.845	0.914	24.112	19.906	19.906	0.000	0.000	0.000	0.000
96	B	97	VAL	0	0.032	0.009	22.637	-0.589	-0.589	0.000	0.000	0.000	0.000
97	B	98	GLU	-1	-0.906	-0.952	25.495	-19.090	-19.090	0.000	0.000	0.000	0.000
98	B	99	GLY	0	0.009	0.009	28.749	-0.346	-0.346	0.000	0.000	0.000	0.000
99	B	100	GLU	-1	-0.997	-1.010	29.620	-17.506	-17.506	0.000	0.000	0.000	0.000
100	B	101	SER	0	0.005	0.009	30.161	-0.621	-0.621	0.000	0.000	0.000	0.000
101	B	102	GLN	0	-0.012	-0.004	24.748	-0.292	-0.292	0.000	0.000	0.000	0.000
102	B	103	GLU	-1	-0.847	-0.912	24.912	-22.117	-22.117	0.000	0.000	0.000	0.000
103	B	104	VAL	0	-0.027	-0.019	21.031	0.095	0.095	0.000	0.000	0.000	0.000
104	B	105	LYS	1	0.858	0.922	24.510	20.115	20.115	0.000	0.000	0.000	0.000
105	B	106	ILE	0	-0.035	-0.017	26.313	-0.619	-0.619	0.000	0.000	0.000	0.000
106	B	107	ALA	0	0.013	0.007	28.056	0.688	0.688	0.000	0.000	0.000	0.000
107	B	108	PRO	0	-0.005	0.003	29.935	-0.062	-0.062	0.000	0.000	0.000	0.000
108	B	109	LYS	1	0.891	0.934	32.165	16.711	16.711	0.000	0.000	0.000	0.000
109	B	110	GLU	-1	-0.904	-0.954	32.985	-17.777	-17.777	0.000	0.000	0.000	0.000
110	B	111	GLU	-1	-0.903	-0.954	33.354	-16.660	-16.660	0.000	0.000	0.000	0.000
111	B	112	GLU	-1	-0.860	-0.912	31.136	-19.164	-19.164	0.000	0.000	0.000	0.000
112	B	113	GLN	0	-0.087	-0.036	28.784	-1.010	-1.010	0.000	0.000	0.000	0.000
113	B	114	HIS	0	0.043	0.031	26.095	0.323	0.323	0.000	0.000	0.000	0.000
114	B	115	LEU	0	-0.038	-0.016	25.553	-0.486	-0.486	0.000	0.000	0.000	0.000
115	B	116	PHE	0	-0.001	-0.028	20.790	-0.715	-0.715	0.000	0.000	0.000	0.000
116	B	117	GLY	0	0.038	0.025	21.279	0.948	0.948	0.000	0.000	0.000	0.000
117	B	118	SER	0	0.023	0.011	20.277	-0.533	-0.533	0.000	0.000	0.000	0.000
118	B	119	PHE	0	-0.020	-0.004	16.719	-0.454	-0.454	0.000	0.000	0.000	0.000
119	B	120	LYS	0	0.003	0.012	11.980	-0.427	-0.427	0.000	0.000	0.000	0.000
120	B	121	ILE	0	-0.019	-0.005	8.291	0.289	0.289	0.000	0.000	0.000	0.000
121	B	122	LYS	0	0.022	-0.001	7.270	-3.313	-3.313	0.000	0.000	0.000	0.000
128	B	129	LYS	1	0.821	0.901	7.453	55.876	55.876	0.000	0.000	0.000	0.000
129	B	130	LEU	0	-0.002	0.001	10.535	-1.778	-1.778	0.000	0.000	0.000	0.000
130	B	131	VAL	0	-0.019	-0.015	12.030	-0.373	-0.373	0.000	0.000	0.000	0.000
131	B	132	TYR	0	-0.005	-0.037	14.754	0.214	0.214	0.000	0.000	0.000	0.000
132	B	133	CYS	0	-0.064	-0.021	14.701	-1.888	-1.888	0.000	0.000	0.000	0.000
133	B	134	GLU	-1	-0.791	-0.849	19.136	-23.599	-23.599	0.000	0.000	0.000	0.000
134	B	135	GLY	0	0.003	0.000	20.796	-0.644	-0.644	0.000	0.000	0.000	0.000
135	B	136	ASN	0	-0.044	-0.068	15.022	-2.024	-2.024	0.000	0.000	0.000	0.000
136	B	137	SER	0	-0.137	-0.087	17.998	-0.700	-0.700	0.000	0.000	0.000	0.000
137	B	138	ASP	-1	-0.874	-0.907	20.710	-24.919	-24.919	0.000	0.000	0.000	0.000
138	B	139	ASP	-1	-0.980	-0.999	20.791	-26.258	-26.258	0.000	0.000	0.000	0.000
139	B	140	ASP	-1	-0.840	-0.923	21.418	-27.838	-27.838	0.000	0.000	0.000	0.000
140	B	141	SER	0	-0.048	-0.021	18.079	-1.934	-1.934	0.000	0.000	0.000	0.000
141	B	143	LYS	1	0.808	0.908	16.465	29.122	29.122	0.000	0.000	0.000	0.000
142	B	144	ASP	-1	-0.835	-0.903	13.301	-45.823	-45.823	0.000	0.000	0.000	0.000
143	B	145	LEU	0	0.018	0.015	15.591	2.445	2.445	0.000	0.000	0.000	0.000
144	B	146	GLY	0	0.017	-0.002	15.854	-2.580	-2.580	0.000	0.000	0.000	0.000
145	B	147	ILE	0	-0.058	-0.020	17.913	1.269	1.269	0.000	0.000	0.000	0.000
146	B	148	SER	0	0.010	0.005	20.624	-0.048	-0.048	0.000	0.000	0.000	0.000
147	B	149	ILE	0	-0.105	-0.057	23.911	-0.009	-0.009	0.000	0.000	0.000	0.000
148	B	150	ASP	-1	-0.723	-0.842	26.517	-19.553	-19.553	0.000	0.000	0.000	0.000
149	B	151	ASP	-1	-0.903	-0.965	30.153	-17.745	-17.745	0.000	0.000	0.000	0.000
150	B	152	GLU	-1	-0.934	-0.955	33.184	-16.503	-16.503	0.000	0.000	0.000	0.000
151	B	153	ASN	0	-0.185	-0.102	29.745	-0.446	-0.446	0.000	0.000	0.000	0.000
152	B	154	ASN	0	-0.059	-0.040	28.704	-0.731	-0.731	0.000	0.000	0.000	0.000
153	B	155	ARG	1	0.810	0.895	20.674	26.025	26.025	0.000	0.000	0.000	0.000
154	B	156	LEU	0	0.091	0.047	23.988	-0.926	-0.926	0.000	0.000	0.000	0.000
155	B	157	LEU	0	-0.031	-0.004	18.205	-0.983	-0.983	0.000	0.000	0.000	0.000
156	B	158	VAL	0	0.041	0.020	21.461	0.831	0.831	0.000	0.000	0.000	0.000
157	B	159	VAL	0	0.022	0.006	20.315	-1.874	-1.874	0.000	0.000	0.000	0.000
158	B	160	LYS	1	0.754	0.878	18.750	30.060	30.060	0.000	0.000	0.000	0.000
159	B	161	ASP	-1	-0.778	-0.894	17.278	-35.609	-35.609	0.000	0.000	0.000	0.000
160	B	162	GLY	0	-0.017	-0.003	14.958	1.130	1.130	0.000	0.000	0.000	0.000
161	B	163	ASP	-1	-0.965	-0.968	15.119	-33.559	-33.559	0.000	0.000	0.000	0.000
162	B	164	PRO	0	-0.006	0.006	11.520	0.837	0.837	0.000	0.000	0.000	0.000
163	B	165	LEU	0	-0.044	-0.025	13.416	-0.307	-0.307	0.000	0.000	0.000	0.000
164	B	166	ALA	0	-0.028	-0.017	9.649	-2.092	-2.092	0.000	0.000	0.000	0.000
165	B	167	VAL	0	-0.019	-0.013	10.629	3.453	3.453	0.000	0.000	0.000	0.000
166	B	168	ARG	0	0.082	0.065	9.848	-2.883	-2.883	0.000	0.000	0.000	0.000
167	B	169	PHE	0	0.006	0.009	9.273	4.112	4.112	0.000	0.000	0.000	0.000
168	B	170	VAL	0	0.012	0.003	13.100	-0.886	-0.886	0.000	0.000	0.000	0.000
169	B	171	LYS	1	0.768	0.840	15.005	37.399	37.399	0.000	0.000	0.000	0.000
170	B	172	ALA	0	-0.060	-0.048	17.994	0.786	0.786	0.000	0.000	0.000	0.000
171	B	173	HIS	-1	-0.970	-0.967	21.241	-25.374	-25.374	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1:LYS)