FMO DATABASE

FMODB ID: L6JM9

Calculation Name: 2Y1B-A-Xray549

Preferred Name:

Target Type:

Ligand Name: 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid

Ligand 3-letter code: I3C

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2Y1B

Chain ID: A

ChEMBL ID:

UniProt ID: P69411

Base Structure: X-ray

Registration Date: 2025-10-12

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	84
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-511318.23256
FMO2-HF: Nuclear repulsion	478045.508058
FMO2-HF: Total energy	-33272.724502
FMO2-MP2: Total energy	-33365.723428

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:47:THR)

Summations of interaction energy for fragment #1(A:47:THR)

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.
28.934	35.728	13.898	-7.187	-13.503	-0.06

Interaction energy analysis for fragmet #1(A:47:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.823 / q_NPA : 0.913

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

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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	49	VAL	0	0.023	0.029	2.205	3.128	5.948	1.798	-1.789	-2.829	-0.010
4	A	50	ARG	1	0.970	0.992	4.355	22.927	23.098	-0.001	-0.033	-0.137	0.000
44	A	90	LYS	1	0.940	0.982	3.966	29.161	29.369	-0.001	-0.016	-0.190	0.000
45	A	91	ARG	1	0.854	0.930	3.895	16.533	16.870	0.001	-0.096	-0.242	0.000
47	A	93	GLN	0	0.011	-0.009	2.353	-9.703	-7.119	2.955	-2.335	-3.203	-0.021
48	A	94	ILE	0	-0.018	-0.034	2.197	-9.533	-8.620	5.959	-2.371	-4.502	-0.018
49	A	95	ASN	0	-0.027	-0.016	3.174	1.768	0.573	0.079	1.237	-0.121	-0.001
50	A	96	ALA	0	0.084	0.053	4.700	1.659	1.702	-0.001	-0.008	-0.033	0.000
51	A	97	SER	0	-0.015	-0.022	2.076	-9.756	-8.922	3.107	-1.718	-2.223	-0.010
52	A	98	LYS	1	0.846	0.925	4.120	31.851	31.930	0.002	-0.058	-0.023	0.000
5	A	51	ILE	0	-0.043	-0.017	5.405	1.579	1.579	0.000	0.000	0.000	0.000
6	A	52	TYR	0	0.004	0.000	8.033	1.360	1.360	0.000	0.000	0.000	0.000
7	A	53	THR	0	-0.075	-0.050	11.771	-0.393	-0.393	0.000	0.000	0.000	0.000
8	A	54	ASN	0	0.032	0.006	14.367	1.303	1.303	0.000	0.000	0.000	0.000
9	A	55	ALA	0	0.049	0.024	17.149	-0.550	-0.550	0.000	0.000	0.000	0.000
10	A	56	GLU	-1	-0.870	-0.935	19.113	-12.695	-12.695	0.000	0.000	0.000	0.000
11	A	57	GLU	-1	-0.886	-0.950	15.127	-19.467	-19.467	0.000	0.000	0.000	0.000
12	A	58	LEU	0	-0.048	-0.031	14.162	-0.896	-0.896	0.000	0.000	0.000	0.000
13	A	59	VAL	0	0.030	0.036	18.165	0.313	0.313	0.000	0.000	0.000	0.000
14	A	60	GLY	0	-0.010	-0.005	21.824	-0.029	-0.029	0.000	0.000	0.000	0.000
15	A	61	LYS	1	0.870	0.942	15.653	18.398	18.398	0.000	0.000	0.000	0.000
16	A	62	PRO	0	0.031	0.023	19.290	-0.098	-0.098	0.000	0.000	0.000	0.000
17	A	63	PHE	0	0.017	-0.015	15.147	-1.147	-1.147	0.000	0.000	0.000	0.000
18	A	64	ARG	1	0.933	0.976	15.639	17.936	17.936	0.000	0.000	0.000	0.000
19	A	65	ASP	-1	-0.805	-0.915	14.445	-20.181	-20.181	0.000	0.000	0.000	0.000
20	A	66	LEU	0	-0.103	-0.049	10.095	0.505	0.505	0.000	0.000	0.000	0.000
21	A	67	GLY	0	0.035	0.029	13.745	0.473	0.473	0.000	0.000	0.000	0.000
22	A	68	GLU	-1	-0.815	-0.884	12.455	-19.882	-19.882	0.000	0.000	0.000	0.000
23	A	69	VAL	0	-0.035	-0.014	7.972	-0.727	-0.727	0.000	0.000	0.000	0.000
24	A	70	SER	0	0.017	-0.013	10.747	1.440	1.440	0.000	0.000	0.000	0.000
25	A	71	GLY	0	-0.050	-0.027	9.058	-1.901	-1.901	0.000	0.000	0.000	0.000
26	A	72	ASP	-1	-0.809	-0.907	10.093	-18.414	-18.414	0.000	0.000	0.000	0.000
27	A	73	SER	0	-0.053	-0.032	11.876	-1.026	-1.026	0.000	0.000	0.000	0.000
28	A	74	CYS	0	-0.064	-0.036	14.449	0.403	0.403	0.000	0.000	0.000	0.000
29	A	75	GLN	0	0.012	0.008	17.968	-0.188	-0.188	0.000	0.000	0.000	0.000
30	A	76	ALA	0	0.043	0.009	21.065	0.314	0.314	0.000	0.000	0.000	0.000
31	A	77	SER	0	-0.003	-0.021	23.344	0.558	0.558	0.000	0.000	0.000	0.000
32	A	78	ASN	0	-0.038	-0.030	25.669	-0.364	-0.364	0.000	0.000	0.000	0.000
33	A	79	GLN	0	0.016	0.009	27.851	-0.216	-0.216	0.000	0.000	0.000	0.000
34	A	80	ASP	-1	-0.832	-0.888	22.392	-12.381	-12.381	0.000	0.000	0.000	0.000
35	A	81	SER	0	-0.007	-0.018	19.809	0.366	0.366	0.000	0.000	0.000	0.000
36	A	82	PRO	0	0.015	0.019	20.466	-0.173	-0.173	0.000	0.000	0.000	0.000
37	A	83	PRO	0	-0.011	0.001	17.429	-0.728	-0.728	0.000	0.000	0.000	0.000
38	A	84	SER	0	0.017	0.013	12.892	-0.798	-0.798	0.000	0.000	0.000	0.000
39	A	85	ILE	0	0.106	0.033	12.974	-1.417	-1.417	0.000	0.000	0.000	0.000
40	A	86	PRO	0	-0.008	-0.008	10.007	-1.564	-1.564	0.000	0.000	0.000	0.000
41	A	87	THR	0	-0.060	-0.032	8.399	-3.785	-3.785	0.000	0.000	0.000	0.000
42	A	88	ALA	0	0.019	0.030	8.554	-2.177	-2.177	0.000	0.000	0.000	0.000
43	A	89	ARG	1	1.029	1.004	7.947	27.284	27.284	0.000	0.000	0.000	0.000
46	A	92	MET	0	0.012	0.042	6.126	-0.592	-0.592	0.000	0.000	0.000	0.000
53	A	99	MET	0	-0.042	-0.006	7.279	3.129	3.129	0.000	0.000	0.000	0.000
54	A	100	LYS	1	0.906	0.955	7.578	26.904	26.904	0.000	0.000	0.000	0.000
55	A	101	ALA	0	-0.012	0.012	6.284	2.004	2.004	0.000	0.000	0.000	0.000
56	A	102	ASN	0	-0.041	-0.021	6.171	-4.952	-4.952	0.000	0.000	0.000	0.000
57	A	103	ALA	0	-0.021	-0.027	7.376	-2.990	-2.990	0.000	0.000	0.000	0.000
58	A	104	VAL	0	-0.012	-0.015	6.103	-0.558	-0.558	0.000	0.000	0.000	0.000
59	A	105	LEU	0	0.008	0.027	8.896	-0.145	-0.145	0.000	0.000	0.000	0.000
60	A	106	LEU	0	-0.051	-0.033	10.628	-0.051	-0.051	0.000	0.000	0.000	0.000
61	A	107	HIS	0	-0.022	-0.008	12.720	1.000	1.000	0.000	0.000	0.000	0.000
62	A	108	SER	0	0.002	-0.008	15.285	0.896	0.896	0.000	0.000	0.000	0.000
63	A	109	CYS	0	-0.123	-0.060	10.639	-1.641	-1.641	0.000	0.000	0.000	0.000
64	A	110	GLU	-1	-0.854	-0.899	15.872	-12.344	-12.344	0.000	0.000	0.000	0.000
65	A	111	VAL	0	-0.026	-0.029	17.764	-0.786	-0.786	0.000	0.000	0.000	0.000
66	A	112	THR	0	-0.002	0.002	20.229	0.451	0.451	0.000	0.000	0.000	0.000
67	A	113	SER	0	-0.027	-0.033	22.411	-0.233	-0.233	0.000	0.000	0.000	0.000
68	A	114	GLY	0	0.040	0.023	25.178	0.242	0.242	0.000	0.000	0.000	0.000
69	A	115	THR	0	-0.016	-0.007	20.120	-0.019	-0.019	0.000	0.000	0.000	0.000
70	A	116	PRO	0	0.001	-0.005	23.084	0.085	0.085	0.000	0.000	0.000	0.000
71	A	117	GLY	0	0.013	0.019	22.477	0.273	0.273	0.000	0.000	0.000	0.000
72	A	119	TYR	0	0.062	0.065	22.803	0.136	0.136	0.000	0.000	0.000	0.000
73	A	120	ARG	1	0.881	0.934	21.962	11.453	11.453	0.000	0.000	0.000	0.000
74	A	121	GLN	0	-0.001	-0.005	16.660	-0.048	-0.048	0.000	0.000	0.000	0.000
75	A	122	ALA	0	-0.015	0.004	15.575	0.333	0.333	0.000	0.000	0.000	0.000
76	A	123	VAL	0	0.003	-0.014	13.819	-1.101	-1.101	0.000	0.000	0.000	0.000
77	A	125	ILE	0	0.035	-0.003	11.726	-1.060	-1.060	0.000	0.000	0.000	0.000
78	A	126	GLY	0	0.079	0.017	11.728	0.139	0.139	0.000	0.000	0.000	0.000
79	A	127	SER	0	-0.001	0.006	11.840	-0.412	-0.412	0.000	0.000	0.000	0.000
80	A	128	ALA	0	-0.035	-0.026	8.610	-1.803	-1.803	0.000	0.000	0.000	0.000
81	A	129	LEU	0	0.019	0.015	9.731	1.472	1.472	0.000	0.000	0.000	0.000
82	A	130	ASN	0	-0.015	-0.029	10.088	-3.212	-3.212	0.000	0.000	0.000	0.000
83	A	131	ILE	0	-0.003	-0.011	11.893	1.603	1.603	0.000	0.000	0.000	0.000
84	A	132	THR	-1	-0.952	-0.953	13.433	-18.309	-18.309	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:47:THR)