FMO DATABASE

FMODB ID: V5GY1

Calculation Name: 2PEH-B-Xray372

Preferred Name: Splicing factor 3B subunit 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2PEH

Chain ID: B

ChEMBL ID: CHEMBL1229013

UniProt ID: O75533

Base Structure: X-ray

Registration Date: 2023-09-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	104
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-812534.046471
FMO2-HF: Nuclear repulsion	771098.526581
FMO2-HF: Total energy	-41435.51989
FMO2-MP2: Total energy	-41553.784586

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(B:298:ALA)

Summations of interaction energy for fragment #1(B:298:ALA)

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.
-1.293	2.236	0.495	-1.548	-2.475	-0.003

Interaction energy analysis for fragmet #1(B:298:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.015

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	B	300	GLY	0	0.047	0.023	3.697	-0.971	0.459	-0.005	-0.645	-0.779	0.001
4	B	301	LYS	1	0.919	0.954	2.887	0.683	1.787	0.254	-0.343	-1.015	0.001
5	B	302	CYS	0	-0.022	-0.001	5.032	0.386	0.527	-0.001	-0.014	-0.126	0.000
6	B	303	PRO	0	-0.004	-0.004	7.038	0.186	0.186	0.000	0.000	0.000	0.000
7	B	304	THR	0	-0.032	-0.019	10.231	0.120	0.120	0.000	0.000	0.000	0.000
8	B	305	LYS	1	0.882	0.916	12.914	0.079	0.079	0.000	0.000	0.000	0.000
9	B	306	VAL	0	-0.026	0.008	13.367	0.026	0.026	0.000	0.000	0.000	0.000
10	B	307	VAL	0	-0.014	-0.001	12.528	-0.083	-0.083	0.000	0.000	0.000	0.000
11	B	308	LEU	0	-0.030	-0.013	9.788	0.056	0.056	0.000	0.000	0.000	0.000
12	B	309	LEU	0	0.014	0.008	12.162	-0.073	-0.073	0.000	0.000	0.000	0.000
13	B	310	ARG	1	0.833	0.866	8.025	0.309	0.309	0.000	0.000	0.000	0.000
14	B	311	ASN	0	-0.013	-0.017	14.831	-0.001	-0.001	0.000	0.000	0.000	0.000
15	B	312	MET	0	-0.006	0.012	17.474	-0.009	-0.009	0.000	0.000	0.000	0.000
16	B	313	VAL	0	0.022	0.004	19.677	0.004	0.004	0.000	0.000	0.000	0.000
17	B	314	GLY	0	-0.011	-0.009	20.532	-0.005	-0.005	0.000	0.000	0.000	0.000
18	B	315	ALA	0	-0.031	-0.032	22.363	0.002	0.002	0.000	0.000	0.000	0.000
19	B	316	GLY	0	-0.029	-0.017	23.360	0.000	0.000	0.000	0.000	0.000	0.000
20	B	317	GLU	-1	-0.864	-0.911	24.895	-0.037	-0.037	0.000	0.000	0.000	0.000
21	B	318	VAL	0	-0.031	-0.022	22.909	-0.006	-0.006	0.000	0.000	0.000	0.000
22	B	319	ASP	-1	-0.864	-0.926	25.846	-0.029	-0.029	0.000	0.000	0.000	0.000
23	B	320	GLU	-1	-0.949	-0.986	27.940	-0.012	-0.012	0.000	0.000	0.000	0.000
24	B	321	ASP	-1	-0.928	-0.957	29.665	-0.032	-0.032	0.000	0.000	0.000	0.000
25	B	322	LEU	0	-0.022	0.006	23.280	-0.007	-0.007	0.000	0.000	0.000	0.000
26	B	323	GLU	-1	-0.930	-0.975	23.844	-0.045	-0.045	0.000	0.000	0.000	0.000
27	B	324	VAL	0	0.016	0.010	25.416	-0.008	-0.008	0.000	0.000	0.000	0.000
28	B	325	GLU	-1	-0.903	-0.950	26.689	-0.066	-0.066	0.000	0.000	0.000	0.000
29	B	326	THR	0	-0.049	-0.037	20.591	-0.012	-0.012	0.000	0.000	0.000	0.000
30	B	327	LYS	1	0.858	0.925	23.119	0.047	0.047	0.000	0.000	0.000	0.000
31	B	328	GLU	-1	-0.949	-0.991	24.526	-0.056	-0.056	0.000	0.000	0.000	0.000
32	B	329	GLU	-1	-0.750	-0.829	23.079	-0.110	-0.110	0.000	0.000	0.000	0.000
33	B	330	CYS	0	-0.037	-0.035	20.812	-0.015	-0.015	0.000	0.000	0.000	0.000
34	B	331	GLU	-1	-0.773	-0.894	22.844	-0.082	-0.082	0.000	0.000	0.000	0.000
35	B	332	LYS	1	0.764	0.892	22.857	0.126	0.126	0.000	0.000	0.000	0.000
36	B	333	TYR	0	-0.099	-0.067	20.417	-0.005	-0.005	0.000	0.000	0.000	0.000
37	B	334	GLY	0	-0.062	-0.028	22.758	-0.007	-0.007	0.000	0.000	0.000	0.000
38	B	335	LYS	1	0.835	0.906	23.852	0.054	0.054	0.000	0.000	0.000	0.000
39	B	336	VAL	0	0.045	0.027	21.703	-0.008	-0.008	0.000	0.000	0.000	0.000
40	B	337	GLY	0	-0.044	-0.018	22.874	0.011	0.011	0.000	0.000	0.000	0.000
41	B	338	LYS	1	0.849	0.912	20.912	0.027	0.027	0.000	0.000	0.000	0.000
42	B	339	CYS	0	-0.025	0.006	21.114	-0.019	-0.019	0.000	0.000	0.000	0.000
43	B	340	VAL	0	0.023	0.004	19.358	0.014	0.014	0.000	0.000	0.000	0.000
44	B	341	ILE	0	0.070	0.046	19.364	-0.013	-0.013	0.000	0.000	0.000	0.000
45	B	342	PHE	0	-0.031	-0.024	16.642	0.017	0.017	0.000	0.000	0.000	0.000
46	B	343	GLU	-1	-0.824	-0.915	18.875	-0.006	-0.006	0.000	0.000	0.000	0.000
47	B	344	ILE	0	-0.050	-0.017	14.072	0.019	0.019	0.000	0.000	0.000	0.000
48	B	345	PRO	0	0.006	-0.014	18.572	-0.006	-0.006	0.000	0.000	0.000	0.000
49	B	346	GLY	0	-0.011	-0.002	20.742	0.012	0.012	0.000	0.000	0.000	0.000
50	B	347	ALA	0	-0.027	0.002	16.363	0.006	0.006	0.000	0.000	0.000	0.000
51	B	348	PRO	0	0.008	-0.008	15.770	-0.008	-0.008	0.000	0.000	0.000	0.000
52	B	349	ASP	-1	-0.742	-0.854	17.955	-0.031	-0.031	0.000	0.000	0.000	0.000
53	B	350	ASP	-1	-0.821	-0.893	15.722	-0.058	-0.058	0.000	0.000	0.000	0.000
54	B	351	GLU	-1	-0.877	-0.930	11.639	-0.137	-0.137	0.000	0.000	0.000	0.000
55	B	352	ALA	0	-0.031	0.002	14.994	0.006	0.006	0.000	0.000	0.000	0.000
56	B	353	VAL	0	0.044	0.040	17.676	0.011	0.011	0.000	0.000	0.000	0.000
57	B	354	ARG	1	0.771	0.870	9.905	-0.105	-0.105	0.000	0.000	0.000	0.000
58	B	355	ILE	0	0.074	0.036	16.110	0.016	0.016	0.000	0.000	0.000	0.000
59	B	356	PHE	0	-0.028	-0.024	12.329	-0.038	-0.038	0.000	0.000	0.000	0.000
60	B	357	LEU	0	0.057	0.014	16.452	0.018	0.018	0.000	0.000	0.000	0.000
61	B	358	GLU	-1	-0.791	-0.862	17.111	-0.061	-0.061	0.000	0.000	0.000	0.000
62	B	359	PHE	0	0.033	0.008	17.375	0.013	0.013	0.000	0.000	0.000	0.000
63	B	360	GLU	-1	-0.819	-0.912	20.534	-0.054	-0.054	0.000	0.000	0.000	0.000
64	B	361	ARG	1	0.895	0.951	21.060	0.097	0.097	0.000	0.000	0.000	0.000
65	B	362	VAL	0	0.065	0.038	14.734	-0.006	-0.006	0.000	0.000	0.000	0.000
66	B	363	GLU	-1	-0.866	-0.946	16.734	-0.185	-0.185	0.000	0.000	0.000	0.000
67	B	364	SER	0	-0.071	-0.053	19.251	-0.001	-0.001	0.000	0.000	0.000	0.000
68	B	365	ALA	0	0.043	0.029	14.667	-0.005	-0.005	0.000	0.000	0.000	0.000
69	B	366	ILE	0	-0.011	-0.019	13.519	-0.034	-0.034	0.000	0.000	0.000	0.000
70	B	367	LYS	1	0.834	0.923	15.042	0.139	0.139	0.000	0.000	0.000	0.000
71	B	368	ALA	0	0.050	0.029	16.455	0.004	0.004	0.000	0.000	0.000	0.000
72	B	369	VAL	0	-0.020	-0.008	10.358	0.004	0.004	0.000	0.000	0.000	0.000
73	B	370	VAL	0	-0.051	-0.036	13.673	0.001	0.001	0.000	0.000	0.000	0.000
74	B	371	ASP	-1	-0.835	-0.868	15.271	-0.130	-0.130	0.000	0.000	0.000	0.000
75	B	372	LEU	0	0.035	0.009	15.935	0.017	0.017	0.000	0.000	0.000	0.000
76	B	373	ASN	0	-0.024	-0.001	11.403	0.009	0.009	0.000	0.000	0.000	0.000
77	B	374	GLY	0	-0.022	-0.012	14.276	0.005	0.005	0.000	0.000	0.000	0.000
78	B	375	ARG	1	0.740	0.857	16.548	0.146	0.146	0.000	0.000	0.000	0.000
79	B	376	TYR	0	-0.017	-0.014	19.369	-0.003	-0.003	0.000	0.000	0.000	0.000
80	B	377	PHE	0	0.003	0.001	21.427	-0.004	-0.004	0.000	0.000	0.000	0.000
81	B	378	GLY	0	0.079	0.044	23.153	0.002	0.002	0.000	0.000	0.000	0.000
82	B	379	GLY	0	-0.053	-0.019	25.481	0.006	0.006	0.000	0.000	0.000	0.000
83	B	380	ARG	1	0.721	0.850	20.555	0.048	0.048	0.000	0.000	0.000	0.000
84	B	381	VAL	0	-0.025	-0.010	16.812	-0.006	-0.006	0.000	0.000	0.000	0.000
85	B	382	VAL	0	0.041	0.026	15.508	-0.002	-0.002	0.000	0.000	0.000	0.000
86	B	383	LYS	1	0.750	0.859	11.313	0.095	0.095	0.000	0.000	0.000	0.000
87	B	384	ALA	0	0.012	-0.003	12.050	0.016	0.016	0.000	0.000	0.000	0.000
88	B	385	CYS	0	-0.086	-0.014	7.265	-0.075	-0.075	0.000	0.000	0.000	0.000
89	B	386	PHE	0	0.052	0.019	7.946	0.190	0.190	0.000	0.000	0.000	0.000
90	B	387	TYR	0	0.043	-0.014	8.504	-0.097	-0.097	0.000	0.000	0.000	0.000
91	B	388	ASN	0	-0.048	-0.038	8.912	0.037	0.037	0.000	0.000	0.000	0.000
92	B	389	LEU	0	0.021	0.003	10.313	0.023	0.023	0.000	0.000	0.000	0.000
93	B	390	ASP	-1	-0.862	-0.923	13.729	0.138	0.138	0.000	0.000	0.000	0.000
94	B	391	LYS	1	0.805	0.871	10.770	-0.503	-0.503	0.000	0.000	0.000	0.000
95	B	392	PHE	0	-0.002	-0.002	13.713	-0.017	-0.017	0.000	0.000	0.000	0.000
96	B	393	ARG	1	0.798	0.881	15.234	-0.003	-0.003	0.000	0.000	0.000	0.000
97	B	394	VAL	0	-0.044	-0.012	16.406	-0.008	-0.008	0.000	0.000	0.000	0.000
98	B	395	LEU	0	0.000	0.006	17.809	0.004	0.004	0.000	0.000	0.000	0.000
99	B	396	ASP	-1	-0.768	-0.849	13.682	0.299	0.299	0.000	0.000	0.000	0.000
100	B	397	LEU	0	-0.046	-0.008	13.190	0.026	0.026	0.000	0.000	0.000	0.000
101	B	398	ALA	0	0.033	0.009	13.391	-0.037	-0.037	0.000	0.000	0.000	0.000
102	B	399	GLU	-1	-0.858	-0.897	8.672	0.643	0.643	0.000	0.000	0.000	0.000
103	B	400	GLN	0	0.022	0.007	6.085	-0.195	-0.195	0.000	0.000	0.000	0.000
104	B	401	VAL	0	-0.016	0.004	3.014	-1.964	-1.110	0.247	-0.546	-0.555	-0.005

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Interactive mode: IFIE and PIEDA for fragment #1(B:298:ALA)