FMO DATABASE

FMODB ID: RLQL8

Calculation Name: 2F9D-A-Xray547

Preferred Name: Splicing factor 3B subunit 1

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

PDB ID: 2F9D

Chain ID: A

ChEMBL ID: CHEMBL1229013

UniProt ID: O75533

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	114
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-950715.347742
FMO2-HF: Nuclear repulsion	903869.400124
FMO2-HF: Total energy	-46845.947618
FMO2-MP2: Total energy	-46982.727625

3D Structure

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:12:ARG)

Summations of interaction energy for fragment #1(A:12:ARG)

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.
2.2370000000001	4.621	8.968	-5.377	-5.974	-0.062

Interaction energy analysis for fragmet #1(A:12:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.806 / q_NPA : 1.889

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	14	PRO	0	0.053	0.032	1.930	-27.391	-26.140	8.563	-4.827	-4.986	-0.055
4	A	15	PRO	0	0.016	0.014	3.767	1.003	1.163	-0.001	0.006	-0.165	0.000
57	A	68	PHE	0	-0.068	-0.039	2.290	-12.963	-11.990	0.406	-0.556	-0.823	-0.007
5	A	16	GLU	-1	-0.876	-0.945	5.954	-57.181	-57.181	0.000	0.000	0.000	0.000
6	A	17	VAL	0	-0.046	-0.014	6.541	4.302	4.302	0.000	0.000	0.000	0.000
7	A	18	ASN	0	-0.017	-0.022	9.030	1.023	1.023	0.000	0.000	0.000	0.000
8	A	19	ARG	1	0.939	0.957	11.527	41.483	41.483	0.000	0.000	0.000	0.000
9	A	20	ILE	0	-0.036	0.000	13.568	2.384	2.384	0.000	0.000	0.000	0.000
10	A	21	LEU	0	0.043	0.015	13.955	-1.428	-1.428	0.000	0.000	0.000	0.000
11	A	22	TYR	0	-0.047	-0.036	17.690	1.902	1.902	0.000	0.000	0.000	0.000
12	A	23	ILE	0	0.015	0.008	20.199	-0.723	-0.723	0.000	0.000	0.000	0.000
13	A	24	ARG	1	0.955	0.965	22.766	26.160	26.160	0.000	0.000	0.000	0.000
14	A	25	ASN	0	-0.009	-0.010	25.656	0.280	0.280	0.000	0.000	0.000	0.000
15	A	26	LEU	0	0.038	0.030	26.202	0.159	0.159	0.000	0.000	0.000	0.000
16	A	27	PRO	0	0.007	-0.013	28.965	0.744	0.744	0.000	0.000	0.000	0.000
17	A	28	TYR	0	-0.023	-0.031	32.248	-0.142	-0.142	0.000	0.000	0.000	0.000
18	A	29	LYS	1	0.950	0.975	34.518	16.474	16.474	0.000	0.000	0.000	0.000
19	A	30	ILE	0	-0.029	0.016	28.227	0.270	0.270	0.000	0.000	0.000	0.000
20	A	31	THR	0	-0.005	-0.035	32.257	-0.009	-0.009	0.000	0.000	0.000	0.000
21	A	32	ALA	0	-0.002	-0.020	29.418	-0.632	-0.632	0.000	0.000	0.000	0.000
22	A	33	GLU	-1	-0.901	-0.940	28.312	-19.328	-19.328	0.000	0.000	0.000	0.000
23	A	34	GLU	-1	-0.769	-0.868	27.852	-19.634	-19.634	0.000	0.000	0.000	0.000
24	A	35	MET	0	-0.062	-0.023	24.365	-0.857	-0.857	0.000	0.000	0.000	0.000
25	A	36	TYR	0	0.012	-0.026	23.837	-1.181	-1.181	0.000	0.000	0.000	0.000
26	A	37	ASP	-1	-0.927	-0.938	23.328	-23.151	-23.151	0.000	0.000	0.000	0.000
27	A	38	ILE	0	-0.037	-0.020	22.235	-0.943	-0.943	0.000	0.000	0.000	0.000
28	A	39	PHE	0	-0.022	-0.022	18.774	-1.187	-1.187	0.000	0.000	0.000	0.000
29	A	40	GLY	0	0.052	0.030	18.531	-1.844	-1.844	0.000	0.000	0.000	0.000
30	A	41	LYS	1	0.913	0.971	18.739	28.249	28.249	0.000	0.000	0.000	0.000
31	A	42	TYR	0	-0.023	-0.019	14.376	-0.356	-0.356	0.000	0.000	0.000	0.000
32	A	43	GLY	0	0.063	0.044	14.029	-2.833	-2.833	0.000	0.000	0.000	0.000
33	A	44	PRO	0	-0.022	-0.016	15.425	1.637	1.637	0.000	0.000	0.000	0.000
34	A	45	ILE	0	-0.014	0.005	17.260	-1.363	-1.363	0.000	0.000	0.000	0.000
35	A	46	ARG	1	0.937	0.981	18.281	28.727	28.727	0.000	0.000	0.000	0.000
36	A	47	GLN	0	-0.015	-0.007	20.310	1.423	1.423	0.000	0.000	0.000	0.000
37	A	48	ILE	0	0.045	0.028	21.812	-1.212	-1.212	0.000	0.000	0.000	0.000
38	A	49	ARG	1	0.854	0.924	24.296	24.731	24.731	0.000	0.000	0.000	0.000
39	A	50	VAL	0	0.047	0.018	26.410	-0.765	-0.765	0.000	0.000	0.000	0.000
40	A	51	GLY	0	-0.020	-0.008	28.945	0.420	0.420	0.000	0.000	0.000	0.000
41	A	52	ASN	0	0.017	-0.002	30.903	0.098	0.098	0.000	0.000	0.000	0.000
42	A	53	THR	0	0.063	0.049	34.118	0.477	0.477	0.000	0.000	0.000	0.000
43	A	54	PRO	0	0.022	-0.012	35.160	-0.412	-0.412	0.000	0.000	0.000	0.000
44	A	55	GLU	-1	-0.848	-0.906	33.428	-17.738	-17.738	0.000	0.000	0.000	0.000
45	A	56	THR	0	-0.028	-0.020	30.136	-0.636	-0.636	0.000	0.000	0.000	0.000
46	A	57	ARG	1	0.946	1.014	30.628	16.101	16.101	0.000	0.000	0.000	0.000
47	A	58	GLY	0	0.025	0.008	31.248	0.172	0.172	0.000	0.000	0.000	0.000
48	A	59	THR	0	-0.132	-0.073	26.374	-0.835	-0.835	0.000	0.000	0.000	0.000
49	A	60	ALA	0	0.047	0.017	25.127	0.730	0.730	0.000	0.000	0.000	0.000
50	A	61	TYR	0	-0.028	-0.011	21.028	-1.206	-1.206	0.000	0.000	0.000	0.000
51	A	62	VAL	0	0.013	0.017	18.792	1.160	1.160	0.000	0.000	0.000	0.000
52	A	63	VAL	0	-0.051	-0.019	17.642	-1.623	-1.623	0.000	0.000	0.000	0.000
53	A	64	TYR	0	0.031	-0.001	14.006	1.033	1.033	0.000	0.000	0.000	0.000
54	A	65	GLU	-1	-0.858	-0.946	15.567	-31.388	-31.388	0.000	0.000	0.000	0.000
55	A	66	ASP	-1	-0.797	-0.893	9.293	-55.671	-55.671	0.000	0.000	0.000	0.000
56	A	67	ILE	0	-0.028	-0.032	6.534	1.579	1.579	0.000	0.000	0.000	0.000
58	A	69	ASP	-1	-0.818	-0.907	7.225	-41.357	-41.357	0.000	0.000	0.000	0.000
59	A	70	ALA	0	-0.020	-0.004	10.976	1.539	1.539	0.000	0.000	0.000	0.000
60	A	71	LYS	1	0.809	0.873	5.829	67.740	67.740	0.000	0.000	0.000	0.000
61	A	72	ASN	0	0.027	0.016	9.611	1.765	1.765	0.000	0.000	0.000	0.000
62	A	73	ALA	0	0.039	0.025	10.940	2.716	2.716	0.000	0.000	0.000	0.000
63	A	74	CYS	0	-0.102	-0.055	12.598	3.092	3.092	0.000	0.000	0.000	0.000
64	A	75	ASP	-1	-0.835	-0.901	9.970	-54.908	-54.908	0.000	0.000	0.000	0.000
65	A	76	HIS	0	-0.058	-0.025	12.782	3.008	3.008	0.000	0.000	0.000	0.000
66	A	77	LEU	0	-0.014	0.000	16.354	2.305	2.305	0.000	0.000	0.000	0.000
67	A	78	SER	0	-0.090	-0.033	17.854	1.906	1.906	0.000	0.000	0.000	0.000
68	A	79	GLY	0	0.036	0.013	19.758	-0.053	-0.053	0.000	0.000	0.000	0.000
69	A	80	PHE	0	0.009	0.010	21.642	0.994	0.994	0.000	0.000	0.000	0.000
70	A	81	ASN	0	-0.052	-0.032	23.505	0.757	0.757	0.000	0.000	0.000	0.000
71	A	82	VAL	0	0.053	0.025	27.266	0.011	0.011	0.000	0.000	0.000	0.000
72	A	83	CYS	0	0.000	-0.007	29.132	0.373	0.373	0.000	0.000	0.000	0.000
73	A	84	ASN	0	-0.018	-0.011	32.466	-0.261	-0.261	0.000	0.000	0.000	0.000
74	A	85	ARG	1	0.899	0.973	29.618	18.781	18.781	0.000	0.000	0.000	0.000
75	A	86	TYR	0	0.068	0.033	26.655	-0.145	-0.145	0.000	0.000	0.000	0.000
76	A	87	LEU	0	-0.018	0.005	23.334	0.215	0.215	0.000	0.000	0.000	0.000
77	A	88	VAL	0	-0.003	-0.006	21.831	-0.888	-0.888	0.000	0.000	0.000	0.000
78	A	89	VAL	0	-0.010	0.002	17.323	0.538	0.538	0.000	0.000	0.000	0.000
79	A	90	LEU	0	-0.002	-0.007	16.551	-0.792	-0.792	0.000	0.000	0.000	0.000
80	A	91	TYR	0	0.127	0.075	10.727	0.238	0.238	0.000	0.000	0.000	0.000
81	A	92	TYR	0	0.015	0.004	14.622	2.146	2.146	0.000	0.000	0.000	0.000
82	A	93	ASN	0	-0.013	-0.021	14.864	-0.183	-0.183	0.000	0.000	0.000	0.000
83	A	94	ALA	0	0.067	0.039	17.044	1.516	1.516	0.000	0.000	0.000	0.000
84	A	95	ASN	0	-0.011	-0.005	19.346	2.407	2.407	0.000	0.000	0.000	0.000
85	A	96	ARG	1	0.898	0.927	16.475	33.204	33.204	0.000	0.000	0.000	0.000
86	A	97	ALA	0	-0.023	-0.004	21.417	1.094	1.094	0.000	0.000	0.000	0.000
87	A	98	PHE	0	0.017	-0.008	22.914	1.005	1.005	0.000	0.000	0.000	0.000
88	A	99	GLN	0	-0.057	-0.034	24.533	0.606	0.606	0.000	0.000	0.000	0.000
89	A	100	LYS	1	0.864	0.917	26.987	19.550	19.550	0.000	0.000	0.000	0.000
90	A	101	MET	0	-0.047	0.007	29.407	0.464	0.464	0.000	0.000	0.000	0.000
91	A	102	ASP	-1	-0.795	-0.902	30.792	-17.807	-17.807	0.000	0.000	0.000	0.000
92	A	103	THR	0	0.008	-0.014	30.620	-0.637	-0.637	0.000	0.000	0.000	0.000
93	A	104	LYS	1	0.894	0.957	30.466	17.491	17.491	0.000	0.000	0.000	0.000
94	A	105	LYS	1	0.960	0.977	31.656	17.114	17.114	0.000	0.000	0.000	0.000
95	A	106	LYS	1	0.866	0.939	24.070	23.042	23.042	0.000	0.000	0.000	0.000
96	A	107	GLU	-1	-0.913	-0.958	26.811	-20.428	-20.428	0.000	0.000	0.000	0.000
97	A	108	GLU	-1	-0.857	-0.922	27.010	-18.534	-18.534	0.000	0.000	0.000	0.000
98	A	109	GLN	0	0.001	-0.002	25.772	0.090	0.090	0.000	0.000	0.000	0.000
99	A	110	LEU	0	-0.058	-0.030	21.590	-0.880	-0.880	0.000	0.000	0.000	0.000
100	A	111	LYS	1	0.858	0.925	22.785	20.085	20.085	0.000	0.000	0.000	0.000
101	A	112	LEU	0	0.015	0.003	24.096	-0.598	-0.598	0.000	0.000	0.000	0.000
102	A	113	LEU	0	-0.049	-0.023	21.489	-0.449	-0.449	0.000	0.000	0.000	0.000
103	A	114	LYS	1	0.950	0.986	17.861	27.944	27.944	0.000	0.000	0.000	0.000
104	A	115	GLU	-1	-0.829	-0.913	20.396	-22.821	-22.821	0.000	0.000	0.000	0.000
105	A	116	LYS	1	0.888	0.964	23.005	22.280	22.280	0.000	0.000	0.000	0.000
106	A	117	TYR	0	-0.026	-0.029	19.703	0.351	0.351	0.000	0.000	0.000	0.000
107	A	118	GLY	0	0.034	0.035	17.115	-1.608	-1.608	0.000	0.000	0.000	0.000
108	A	119	ILE	0	-0.070	-0.026	15.337	-2.025	-2.025	0.000	0.000	0.000	0.000
109	A	120	ASN	0	0.049	0.015	12.774	2.204	2.204	0.000	0.000	0.000	0.000
110	A	121	THR	0	0.023	-0.007	14.897	1.027	1.027	0.000	0.000	0.000	0.000
111	A	122	ASP	-1	-0.890	-0.922	15.844	-30.085	-30.085	0.000	0.000	0.000	0.000
112	A	123	PRO	0	-0.031	-0.028	17.449	-0.714	-0.714	0.000	0.000	0.000	0.000
113	A	124	PRO	0	-0.061	-0.035	15.775	-1.587	-1.587	0.000	0.000	0.000	0.000
114	A	125	LYS	0	0.062	0.054	11.733	1.310	1.310	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:12:ARG)