FMO DATABASE

FMODB ID: YZGR2

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	OptHSide
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	-809312.682259
FMO2-HF: Nuclear repulsion	767877.351019
FMO2-HF: Total energy	-41435.33124
FMO2-MP2: Total energy	-41553.547518

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.
-1.055	2.554	0.419	-1.477	-2.552	-0.001

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 : -0.013 / q_NPA : -0.021

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	300	GLY	0	0.050	0.028	3.679	-0.848	0.637	-0.011	-0.632	-0.841	0.002
4	B	301	LYS	1	0.918	0.956	2.696	0.835	1.892	0.338	-0.311	-1.085	0.001
5	B	302	CYS	0	-0.017	0.002	4.782	0.423	0.573	-0.001	-0.015	-0.134	0.000
6	B	303	PRO	0	-0.011	-0.010	6.909	0.192	0.192	0.000	0.000	0.000	0.000
7	B	304	THR	0	-0.037	-0.034	10.081	0.112	0.112	0.000	0.000	0.000	0.000
8	B	305	LYS	1	0.894	0.921	12.831	0.098	0.098	0.000	0.000	0.000	0.000
9	B	306	VAL	0	-0.030	0.003	13.416	0.031	0.031	0.000	0.000	0.000	0.000
10	B	307	VAL	0	-0.013	-0.006	12.632	-0.087	-0.087	0.000	0.000	0.000	0.000
11	B	308	LEU	0	-0.032	-0.016	9.583	0.049	0.049	0.000	0.000	0.000	0.000
12	B	309	LEU	0	0.007	-0.002	11.940	-0.062	-0.062	0.000	0.000	0.000	0.000
13	B	310	ARG	1	0.853	0.886	7.877	0.345	0.345	0.000	0.000	0.000	0.000
14	B	311	ASN	0	-0.005	-0.026	14.437	0.003	0.003	0.000	0.000	0.000	0.000
15	B	312	MET	0	-0.013	0.011	17.141	-0.005	-0.005	0.000	0.000	0.000	0.000
16	B	313	VAL	0	0.024	0.012	19.644	0.004	0.004	0.000	0.000	0.000	0.000
17	B	314	GLY	0	-0.018	-0.012	20.508	-0.006	-0.006	0.000	0.000	0.000	0.000
18	B	315	ALA	0	-0.028	-0.035	22.288	0.002	0.002	0.000	0.000	0.000	0.000
19	B	316	GLY	0	-0.043	-0.032	23.309	0.001	0.001	0.000	0.000	0.000	0.000
20	B	317	GLU	-1	-0.922	-0.942	24.911	-0.051	-0.051	0.000	0.000	0.000	0.000
21	B	318	VAL	0	-0.014	-0.014	23.303	-0.007	-0.007	0.000	0.000	0.000	0.000
22	B	319	ASP	-1	-0.865	-0.940	25.892	-0.047	-0.047	0.000	0.000	0.000	0.000
23	B	320	GLU	-1	-0.966	-0.996	27.984	-0.031	-0.031	0.000	0.000	0.000	0.000
24	B	321	ASP	-1	-0.943	-0.966	29.992	-0.044	-0.044	0.000	0.000	0.000	0.000
25	B	322	LEU	0	0.006	0.025	22.790	-0.008	-0.008	0.000	0.000	0.000	0.000
26	B	323	GLU	-1	-0.946	-0.986	24.108	-0.067	-0.067	0.000	0.000	0.000	0.000
27	B	324	VAL	0	0.032	0.015	25.486	-0.007	-0.007	0.000	0.000	0.000	0.000
28	B	325	GLU	-1	-0.911	-0.939	26.637	-0.080	-0.080	0.000	0.000	0.000	0.000
29	B	326	THR	0	-0.050	-0.033	20.527	-0.012	-0.012	0.000	0.000	0.000	0.000
30	B	327	LYS	1	0.882	0.944	23.398	0.063	0.063	0.000	0.000	0.000	0.000
31	B	328	GLU	-1	-0.939	-0.992	24.548	-0.065	-0.065	0.000	0.000	0.000	0.000
32	B	329	GLU	-1	-0.749	-0.826	23.446	-0.118	-0.118	0.000	0.000	0.000	0.000
33	B	330	CYS	0	-0.064	-0.056	20.926	-0.014	-0.014	0.000	0.000	0.000	0.000
34	B	331	GLU	-1	-0.739	-0.888	22.916	-0.097	-0.097	0.000	0.000	0.000	0.000
35	B	332	LYS	1	0.769	0.906	23.486	0.133	0.133	0.000	0.000	0.000	0.000
36	B	333	TYR	0	-0.124	-0.088	20.706	-0.004	-0.004	0.000	0.000	0.000	0.000
37	B	334	GLY	0	-0.062	-0.044	22.778	-0.008	-0.008	0.000	0.000	0.000	0.000
38	B	335	LYS	1	0.843	0.924	24.417	0.067	0.067	0.000	0.000	0.000	0.000
39	B	336	VAL	0	0.007	0.010	21.984	-0.007	-0.007	0.000	0.000	0.000	0.000
40	B	337	GLY	0	-0.075	-0.035	22.788	0.012	0.012	0.000	0.000	0.000	0.000
41	B	338	LYS	1	0.827	0.894	21.182	0.059	0.059	0.000	0.000	0.000	0.000
42	B	339	CYS	0	-0.019	0.004	21.271	-0.020	-0.020	0.000	0.000	0.000	0.000
43	B	340	VAL	0	0.010	0.011	19.676	0.014	0.014	0.000	0.000	0.000	0.000
44	B	341	ILE	0	0.071	0.035	19.570	-0.018	-0.018	0.000	0.000	0.000	0.000
45	B	342	PHE	0	-0.034	-0.017	17.082	0.017	0.017	0.000	0.000	0.000	0.000
46	B	343	GLU	-1	-0.807	-0.897	18.728	-0.035	-0.035	0.000	0.000	0.000	0.000
47	B	344	ILE	0	-0.057	-0.039	14.337	0.016	0.016	0.000	0.000	0.000	0.000
48	B	345	PRO	0	0.003	-0.013	18.867	-0.003	-0.003	0.000	0.000	0.000	0.000
49	B	346	GLY	0	-0.022	-0.012	20.719	0.010	0.010	0.000	0.000	0.000	0.000
50	B	347	ALA	0	-0.028	0.007	16.945	0.006	0.006	0.000	0.000	0.000	0.000
51	B	348	PRO	0	0.007	-0.010	16.084	-0.003	-0.003	0.000	0.000	0.000	0.000
52	B	349	ASP	-1	-0.751	-0.865	18.367	-0.056	-0.056	0.000	0.000	0.000	0.000
53	B	350	ASP	-1	-0.857	-0.915	15.311	-0.088	-0.088	0.000	0.000	0.000	0.000
54	B	351	GLU	-1	-0.890	-0.950	11.757	-0.181	-0.181	0.000	0.000	0.000	0.000
55	B	352	ALA	0	-0.009	0.018	15.323	-0.001	-0.001	0.000	0.000	0.000	0.000
56	B	353	VAL	0	0.052	0.050	18.252	0.008	0.008	0.000	0.000	0.000	0.000
57	B	354	ARG	1	0.779	0.889	9.910	0.032	0.032	0.000	0.000	0.000	0.000
58	B	355	ILE	0	0.067	0.032	16.173	0.016	0.016	0.000	0.000	0.000	0.000
59	B	356	PHE	0	-0.034	-0.023	12.545	-0.040	-0.040	0.000	0.000	0.000	0.000
60	B	357	LEU	0	0.058	0.019	16.462	0.024	0.024	0.000	0.000	0.000	0.000
61	B	358	GLU	-1	-0.816	-0.880	17.097	-0.094	-0.094	0.000	0.000	0.000	0.000
62	B	359	PHE	0	0.070	0.029	17.529	0.015	0.015	0.000	0.000	0.000	0.000
63	B	360	GLU	-1	-0.789	-0.899	20.495	-0.066	-0.066	0.000	0.000	0.000	0.000
64	B	361	ARG	1	0.889	0.947	21.260	0.105	0.105	0.000	0.000	0.000	0.000
65	B	362	VAL	0	0.071	0.028	14.940	-0.007	-0.007	0.000	0.000	0.000	0.000
66	B	363	GLU	-1	-0.870	-0.947	16.748	-0.196	-0.196	0.000	0.000	0.000	0.000
67	B	364	SER	0	-0.064	-0.061	18.856	-0.006	-0.006	0.000	0.000	0.000	0.000
68	B	365	ALA	0	0.028	0.038	14.855	-0.001	-0.001	0.000	0.000	0.000	0.000
69	B	366	ILE	0	-0.012	-0.014	13.516	-0.033	-0.033	0.000	0.000	0.000	0.000
70	B	367	LYS	1	0.850	0.937	15.252	0.150	0.150	0.000	0.000	0.000	0.000
71	B	368	ALA	0	0.066	0.036	16.826	0.002	0.002	0.000	0.000	0.000	0.000
72	B	369	VAL	0	-0.002	0.011	10.654	0.006	0.006	0.000	0.000	0.000	0.000
73	B	370	VAL	0	-0.069	-0.042	13.890	-0.003	-0.003	0.000	0.000	0.000	0.000
74	B	371	ASP	-1	-0.866	-0.894	15.388	-0.151	-0.151	0.000	0.000	0.000	0.000
75	B	372	LEU	0	0.010	-0.007	16.049	0.016	0.016	0.000	0.000	0.000	0.000
76	B	373	ASN	0	-0.020	-0.004	11.922	0.004	0.004	0.000	0.000	0.000	0.000
77	B	374	GLY	0	-0.028	-0.015	14.506	0.010	0.010	0.000	0.000	0.000	0.000
78	B	375	ARG	1	0.765	0.876	16.890	0.157	0.157	0.000	0.000	0.000	0.000
79	B	376	TYR	0	-0.021	-0.020	19.463	-0.004	-0.004	0.000	0.000	0.000	0.000
80	B	377	PHE	0	0.006	-0.001	21.344	-0.003	-0.003	0.000	0.000	0.000	0.000
81	B	378	GLY	0	0.086	0.049	23.068	0.003	0.003	0.000	0.000	0.000	0.000
82	B	379	GLY	0	-0.049	-0.026	25.531	0.005	0.005	0.000	0.000	0.000	0.000
83	B	380	ARG	1	0.779	0.895	20.282	0.071	0.071	0.000	0.000	0.000	0.000
84	B	381	VAL	0	-0.014	0.000	16.628	-0.006	-0.006	0.000	0.000	0.000	0.000
85	B	382	VAL	0	0.046	0.036	15.357	-0.004	-0.004	0.000	0.000	0.000	0.000
86	B	383	LYS	1	0.779	0.887	10.984	0.135	0.135	0.000	0.000	0.000	0.000
87	B	384	ALA	0	0.016	0.007	11.988	0.008	0.008	0.000	0.000	0.000	0.000
88	B	385	CYS	0	-0.094	-0.024	7.024	-0.082	-0.082	0.000	0.000	0.000	0.000
89	B	386	PHE	0	0.047	0.026	7.875	0.195	0.195	0.000	0.000	0.000	0.000
90	B	387	TYR	0	0.032	-0.017	8.109	-0.159	-0.159	0.000	0.000	0.000	0.000
91	B	388	ASN	0	-0.015	-0.004	8.870	0.061	0.061	0.000	0.000	0.000	0.000
92	B	389	LEU	0	0.006	-0.002	10.383	0.022	0.022	0.000	0.000	0.000	0.000
93	B	390	ASP	-1	-0.860	-0.943	13.854	0.105	0.105	0.000	0.000	0.000	0.000
94	B	391	LYS	1	0.797	0.889	10.480	-0.369	-0.369	0.000	0.000	0.000	0.000
95	B	392	PHE	0	-0.002	0.000	13.632	-0.011	-0.011	0.000	0.000	0.000	0.000
96	B	393	ARG	1	0.821	0.892	15.328	0.033	0.033	0.000	0.000	0.000	0.000
97	B	394	VAL	0	-0.036	-0.004	16.338	-0.003	-0.003	0.000	0.000	0.000	0.000
98	B	395	LEU	0	-0.021	-0.006	17.853	0.004	0.004	0.000	0.000	0.000	0.000
99	B	396	ASP	-1	-0.790	-0.867	13.626	0.219	0.219	0.000	0.000	0.000	0.000
100	B	397	LEU	0	-0.019	0.003	13.330	-0.005	-0.005	0.000	0.000	0.000	0.000
101	B	398	ALA	0	0.032	0.011	13.164	-0.042	-0.042	0.000	0.000	0.000	0.000
102	B	399	GLU	-1	-0.841	-0.895	8.479	0.452	0.452	0.000	0.000	0.000	0.000
103	B	400	GLN	0	0.018	0.005	6.332	-0.169	-0.169	0.000	0.000	0.000	0.000
104	B	401	VAL	0	-0.002	0.001	3.194	-1.871	-0.954	0.093	-0.519	-0.492	-0.004

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