FMO DATABASE

FMODB ID: 9L3J2

Calculation Name: 2AXY-A-Xray547

Preferred Name: Poly(rC)-binding protein 2

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2AXY

Chain ID: A

ChEMBL ID: CHEMBL4295826

UniProt ID: Q15366

Base Structure: X-ray

Registration Date: 2025-10-03

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	72
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-417321.177131
FMO2-HF: Nuclear repulsion	389237.461833
FMO2-HF: Total energy	-28083.715298
FMO2-MP2: Total energy	-28163.797933

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:10:LYS)

Summations of interaction energy for fragment #1(A:10: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.
75.106	78.297	1.557	-1.507	-3.241	-0.013

Interaction energy analysis for fragmet #1(A:10:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.841 / q_NPA : 1.906

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	12	VAL	0	0.008	0.015	2.448	-0.564	2.589	1.558	-1.495	-3.216	-0.013
4	A	13	THR	0	0.019	0.010	4.511	4.425	4.463	-0.001	-0.012	-0.025	0.000
5	A	14	LEU	0	0.018	0.005	5.750	-6.270	-6.270	0.000	0.000	0.000	0.000
6	A	15	THR	0	-0.027	-0.036	8.896	6.008	6.008	0.000	0.000	0.000	0.000
7	A	16	ILE	0	0.012	0.018	10.860	-1.657	-1.657	0.000	0.000	0.000	0.000
8	A	17	ARG	1	0.923	0.954	13.952	33.068	33.068	0.000	0.000	0.000	0.000
9	A	18	LEU	0	0.035	0.026	17.291	-0.696	-0.696	0.000	0.000	0.000	0.000
10	A	19	LEU	0	-0.028	-0.008	20.378	0.637	0.637	0.000	0.000	0.000	0.000
11	A	20	MET	0	0.030	0.018	23.402	0.138	0.138	0.000	0.000	0.000	0.000
12	A	21	HIS	1	0.898	0.934	26.565	21.390	21.390	0.000	0.000	0.000	0.000
13	A	22	GLY	0	0.009	-0.002	30.348	-0.159	-0.159	0.000	0.000	0.000	0.000
14	A	23	LYS	1	0.925	0.951	32.368	17.058	17.058	0.000	0.000	0.000	0.000
15	A	24	GLU	-1	-0.789	-0.880	28.883	-21.426	-21.426	0.000	0.000	0.000	0.000
16	A	25	VAL	0	0.014	0.000	27.328	-0.270	-0.270	0.000	0.000	0.000	0.000
17	A	26	GLY	0	-0.020	-0.008	29.658	0.008	0.008	0.000	0.000	0.000	0.000
18	A	27	SER	0	-0.006	0.003	31.307	0.294	0.294	0.000	0.000	0.000	0.000
19	A	28	ILE	0	0.053	0.021	25.485	-0.081	-0.081	0.000	0.000	0.000	0.000
20	A	29	ILE	0	-0.030	-0.011	28.874	-0.262	-0.262	0.000	0.000	0.000	0.000
21	A	30	GLY	0	0.087	0.045	30.483	0.090	0.090	0.000	0.000	0.000	0.000
22	A	31	LYS	1	0.956	0.957	33.724	15.724	15.724	0.000	0.000	0.000	0.000
23	A	32	LYS	1	0.931	0.950	35.726	15.466	15.466	0.000	0.000	0.000	0.000
24	A	33	GLY	0	0.043	0.041	32.127	-0.097	-0.097	0.000	0.000	0.000	0.000
25	A	34	GLU	-1	-0.845	-0.928	30.883	-19.242	-19.242	0.000	0.000	0.000	0.000
26	A	35	SER	0	-0.021	0.001	29.262	-0.378	-0.378	0.000	0.000	0.000	0.000
27	A	36	VAL	0	0.039	0.009	25.396	-0.755	-0.755	0.000	0.000	0.000	0.000
28	A	37	LYS	1	0.797	0.904	25.971	18.136	18.136	0.000	0.000	0.000	0.000
29	A	38	LYS	1	0.966	0.993	26.627	20.898	20.898	0.000	0.000	0.000	0.000
30	A	39	MET	0	-0.003	0.005	23.181	-1.072	-1.072	0.000	0.000	0.000	0.000
31	A	40	ARG	1	0.841	0.934	22.077	22.992	22.992	0.000	0.000	0.000	0.000
32	A	41	GLU	-1	-0.945	-0.973	22.151	-22.588	-22.588	0.000	0.000	0.000	0.000
33	A	42	GLU	-1	-0.848	-0.928	23.303	-23.704	-23.704	0.000	0.000	0.000	0.000
34	A	43	SER	0	-0.081	-0.076	18.423	-1.613	-1.613	0.000	0.000	0.000	0.000
35	A	44	GLY	0	0.004	0.004	17.805	-1.846	-1.846	0.000	0.000	0.000	0.000
36	A	45	ALA	0	-0.053	-0.018	16.477	-1.733	-1.733	0.000	0.000	0.000	0.000
37	A	46	ARG	1	0.947	0.968	15.480	36.834	36.834	0.000	0.000	0.000	0.000
38	A	47	ILE	0	0.012	0.015	18.307	-1.062	-1.062	0.000	0.000	0.000	0.000
39	A	48	ASN	0	-0.030	-0.025	20.736	1.078	1.078	0.000	0.000	0.000	0.000
40	A	49	ILE	0	0.032	0.012	22.294	-0.791	-0.791	0.000	0.000	0.000	0.000
41	A	50	SER	0	0.021	0.023	24.852	0.355	0.355	0.000	0.000	0.000	0.000
42	A	51	GLU	-1	-0.870	-0.942	26.220	-20.167	-20.167	0.000	0.000	0.000	0.000
43	A	52	GLY	0	0.022	0.023	29.701	0.100	0.100	0.000	0.000	0.000	0.000
44	A	53	ASN	0	-0.057	-0.035	32.053	-0.870	-0.870	0.000	0.000	0.000	0.000
45	A	54	CYS	0	-0.003	-0.001	31.083	0.654	0.654	0.000	0.000	0.000	0.000
46	A	55	PRO	0	0.036	0.002	32.535	-0.311	-0.311	0.000	0.000	0.000	0.000
47	A	56	GLU	-1	-0.827	-0.895	28.288	-21.227	-21.227	0.000	0.000	0.000	0.000
48	A	57	ARG	1	0.826	0.919	27.345	20.811	20.811	0.000	0.000	0.000	0.000
49	A	58	ILE	0	0.019	0.004	20.830	-0.823	-0.823	0.000	0.000	0.000	0.000
50	A	59	ILE	0	0.030	0.031	20.777	0.483	0.483	0.000	0.000	0.000	0.000
51	A	60	THR	0	-0.043	-0.032	16.700	-1.731	-1.731	0.000	0.000	0.000	0.000
52	A	61	LEU	0	0.040	0.029	15.922	0.927	0.927	0.000	0.000	0.000	0.000
53	A	62	ALA	0	-0.024	-0.025	13.420	-2.364	-2.364	0.000	0.000	0.000	0.000
54	A	63	GLY	0	0.056	0.037	12.117	3.106	3.106	0.000	0.000	0.000	0.000
55	A	64	PRO	0	0.027	0.016	8.900	-4.699	-4.699	0.000	0.000	0.000	0.000
56	A	65	THR	0	0.044	0.011	6.712	5.456	5.456	0.000	0.000	0.000	0.000
57	A	66	ASN	0	0.034	0.016	9.583	1.434	1.434	0.000	0.000	0.000	0.000
58	A	67	ALA	0	0.031	0.029	12.780	2.707	2.707	0.000	0.000	0.000	0.000
59	A	68	ILE	0	-0.026	-0.010	11.305	2.354	2.354	0.000	0.000	0.000	0.000
60	A	69	PHE	0	-0.001	-0.010	9.782	1.465	1.465	0.000	0.000	0.000	0.000
61	A	70	LYS	1	0.933	0.991	15.097	34.194	34.194	0.000	0.000	0.000	0.000
62	A	71	ALA	0	0.028	0.007	17.533	1.610	1.610	0.000	0.000	0.000	0.000
63	A	72	PHE	0	-0.035	-0.021	17.102	1.118	1.118	0.000	0.000	0.000	0.000
64	A	73	ALA	0	0.020	0.016	18.991	1.148	1.148	0.000	0.000	0.000	0.000
65	A	74	MET	0	0.019	0.017	20.701	0.807	0.807	0.000	0.000	0.000	0.000
66	A	75	ILE	0	-0.036	-0.030	21.080	1.135	1.135	0.000	0.000	0.000	0.000
67	A	76	ILE	0	-0.037	-0.027	21.264	0.771	0.771	0.000	0.000	0.000	0.000
68	A	77	ASP	-1	-0.860	-0.925	24.566	-24.455	-24.455	0.000	0.000	0.000	0.000
69	A	78	LYS	1	0.730	0.850	26.580	20.925	20.925	0.000	0.000	0.000	0.000
70	A	79	LEU	0	-0.116	-0.076	26.114	0.703	0.703	0.000	0.000	0.000	0.000
71	A	80	GLU	-1	-0.980	-0.975	28.307	-21.223	-21.223	0.000	0.000	0.000	0.000
72	A	81	GLU	-2	-1.834	-1.873	30.672	-37.265	-37.265	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:10:LYS)