FMO DATABASE

FMODB ID: 52VGZ

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	OptH
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	-807333.736437
FMO2-HF: Nuclear repulsion	765899.061073
FMO2-HF: Total energy	-41434.675364
FMO2-MP2: Total energy	-41552.826441

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.
-1.366	2.39	0.649	-1.605	-2.799	-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 : -0.004 / q_NPA : -0.018

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	0.052	0.027	3.604	-0.796	0.683	-0.011	-0.628	-0.840	0.002
4	B	301	LYS	1	0.913	0.959	2.559	0.785	1.862	0.531	-0.362	-1.245	0.002
5	B	302	CYS	0	-0.030	-0.007	4.753	0.463	0.609	-0.001	-0.015	-0.130	0.000
6	B	303	PRO	0	0.001	-0.003	6.870	0.194	0.194	0.000	0.000	0.000	0.000
7	B	304	THR	0	-0.046	-0.046	10.040	0.103	0.103	0.000	0.000	0.000	0.000
8	B	305	LYS	1	0.932	0.950	12.831	0.117	0.117	0.000	0.000	0.000	0.000
9	B	306	VAL	0	-0.018	0.013	13.387	0.036	0.036	0.000	0.000	0.000	0.000
10	B	307	VAL	0	-0.016	-0.008	12.564	-0.095	-0.095	0.000	0.000	0.000	0.000
11	B	308	LEU	0	-0.035	-0.022	9.370	0.051	0.051	0.000	0.000	0.000	0.000
12	B	309	LEU	0	0.002	-0.005	11.868	-0.061	-0.061	0.000	0.000	0.000	0.000
13	B	310	ARG	1	0.901	0.938	7.814	0.351	0.351	0.000	0.000	0.000	0.000
14	B	311	ASN	0	-0.015	-0.040	14.365	0.003	0.003	0.000	0.000	0.000	0.000
15	B	312	MET	0	-0.030	0.002	17.077	-0.004	-0.004	0.000	0.000	0.000	0.000
16	B	313	VAL	0	0.037	0.021	19.578	0.004	0.004	0.000	0.000	0.000	0.000
17	B	314	GLY	0	-0.035	-0.013	20.435	-0.007	-0.007	0.000	0.000	0.000	0.000
18	B	315	ALA	0	-0.022	-0.029	22.282	0.001	0.001	0.000	0.000	0.000	0.000
19	B	316	GLY	0	-0.047	-0.029	23.231	0.002	0.002	0.000	0.000	0.000	0.000
20	B	317	GLU	-1	-0.955	-0.967	24.877	-0.052	-0.052	0.000	0.000	0.000	0.000
21	B	318	VAL	0	-0.017	-0.010	23.317	-0.008	-0.008	0.000	0.000	0.000	0.000
22	B	319	ASP	-1	-0.879	-0.942	25.808	-0.052	-0.052	0.000	0.000	0.000	0.000
23	B	320	GLU	-1	-0.978	-0.998	27.900	-0.035	-0.035	0.000	0.000	0.000	0.000
24	B	321	ASP	-1	-0.932	-0.967	29.908	-0.048	-0.048	0.000	0.000	0.000	0.000
25	B	322	LEU	0	0.037	0.035	22.514	-0.008	-0.008	0.000	0.000	0.000	0.000
26	B	323	GLU	-1	-0.965	-0.978	24.352	-0.074	-0.074	0.000	0.000	0.000	0.000
27	B	324	VAL	0	0.017	0.009	25.408	-0.008	-0.008	0.000	0.000	0.000	0.000
28	B	325	GLU	-1	-0.928	-0.943	26.503	-0.084	-0.084	0.000	0.000	0.000	0.000
29	B	326	THR	0	-0.064	-0.059	20.448	-0.012	-0.012	0.000	0.000	0.000	0.000
30	B	327	LYS	1	0.928	0.956	23.332	0.065	0.065	0.000	0.000	0.000	0.000
31	B	328	GLU	-1	-0.919	-0.986	24.477	-0.073	-0.073	0.000	0.000	0.000	0.000
32	B	329	GLU	-1	-0.848	-0.910	23.722	-0.119	-0.119	0.000	0.000	0.000	0.000
33	B	330	CYS	0	-0.091	-0.073	20.746	-0.016	-0.016	0.000	0.000	0.000	0.000
34	B	331	GLU	-1	-0.780	-0.907	22.859	-0.108	-0.108	0.000	0.000	0.000	0.000
35	B	332	LYS	1	0.826	0.941	24.205	0.133	0.133	0.000	0.000	0.000	0.000
36	B	333	TYR	0	-0.142	-0.093	20.663	-0.006	-0.006	0.000	0.000	0.000	0.000
37	B	334	GLY	0	-0.090	-0.063	22.741	-0.009	-0.009	0.000	0.000	0.000	0.000
38	B	335	LYS	1	0.857	0.939	24.371	0.078	0.078	0.000	0.000	0.000	0.000
39	B	336	VAL	0	0.020	0.026	22.151	-0.010	-0.010	0.000	0.000	0.000	0.000
40	B	337	GLY	0	-0.048	-0.018	22.724	0.012	0.012	0.000	0.000	0.000	0.000
41	B	338	LYS	1	0.876	0.924	21.276	0.065	0.065	0.000	0.000	0.000	0.000
42	B	339	CYS	0	-0.003	0.011	20.747	-0.016	-0.016	0.000	0.000	0.000	0.000
43	B	340	VAL	0	0.008	0.010	19.605	0.014	0.014	0.000	0.000	0.000	0.000
44	B	341	ILE	0	0.072	0.034	19.480	-0.020	-0.020	0.000	0.000	0.000	0.000
45	B	342	PHE	0	-0.030	-0.016	17.019	0.017	0.017	0.000	0.000	0.000	0.000
46	B	343	GLU	-1	-0.799	-0.889	18.635	-0.041	-0.041	0.000	0.000	0.000	0.000
47	B	344	ILE	0	-0.059	-0.044	14.390	0.016	0.016	0.000	0.000	0.000	0.000
48	B	345	PRO	0	-0.007	-0.018	18.852	-0.002	-0.002	0.000	0.000	0.000	0.000
49	B	346	GLY	0	-0.023	-0.013	20.709	0.010	0.010	0.000	0.000	0.000	0.000
50	B	347	ALA	0	-0.027	0.009	16.838	0.007	0.007	0.000	0.000	0.000	0.000
51	B	348	PRO	0	0.004	-0.009	16.001	-0.003	-0.003	0.000	0.000	0.000	0.000
52	B	349	ASP	-1	-0.795	-0.900	18.297	-0.054	-0.054	0.000	0.000	0.000	0.000
53	B	350	ASP	-1	-0.937	-0.969	16.026	-0.077	-0.077	0.000	0.000	0.000	0.000
54	B	351	GLU	-1	-0.963	-0.996	11.913	-0.154	-0.154	0.000	0.000	0.000	0.000
55	B	352	ALA	0	-0.027	0.001	15.250	-0.003	-0.003	0.000	0.000	0.000	0.000
56	B	353	VAL	0	0.049	0.050	18.171	0.007	0.007	0.000	0.000	0.000	0.000
57	B	354	ARG	1	0.795	0.906	9.979	0.047	0.047	0.000	0.000	0.000	0.000
58	B	355	ILE	0	0.067	0.035	16.089	0.017	0.017	0.000	0.000	0.000	0.000
59	B	356	PHE	0	-0.032	-0.026	12.529	-0.045	-0.045	0.000	0.000	0.000	0.000
60	B	357	LEU	0	0.050	0.015	16.381	0.028	0.028	0.000	0.000	0.000	0.000
61	B	358	GLU	-1	-0.904	-0.946	17.024	-0.121	-0.121	0.000	0.000	0.000	0.000
62	B	359	PHE	0	0.057	0.018	17.377	0.015	0.015	0.000	0.000	0.000	0.000
63	B	360	GLU	-1	-0.811	-0.917	20.454	-0.082	-0.082	0.000	0.000	0.000	0.000
64	B	361	ARG	1	0.889	0.934	21.239	0.119	0.119	0.000	0.000	0.000	0.000
65	B	362	VAL	0	0.071	0.026	14.876	-0.007	-0.007	0.000	0.000	0.000	0.000
66	B	363	GLU	-1	-0.889	-0.956	16.728	-0.217	-0.217	0.000	0.000	0.000	0.000
67	B	364	SER	0	-0.063	-0.047	18.832	-0.005	-0.005	0.000	0.000	0.000	0.000
68	B	365	ALA	0	0.035	0.040	14.783	0.000	0.000	0.000	0.000	0.000	0.000
69	B	366	ILE	0	-0.018	-0.015	13.701	-0.033	-0.033	0.000	0.000	0.000	0.000
70	B	367	LYS	1	0.884	0.950	15.224	0.165	0.165	0.000	0.000	0.000	0.000
71	B	368	ALA	0	0.081	0.042	16.756	0.004	0.004	0.000	0.000	0.000	0.000
72	B	369	VAL	0	-0.005	0.010	10.621	0.007	0.007	0.000	0.000	0.000	0.000
73	B	370	VAL	0	-0.073	-0.048	13.942	-0.002	-0.002	0.000	0.000	0.000	0.000
74	B	371	ASP	-1	-0.883	-0.901	15.376	-0.162	-0.162	0.000	0.000	0.000	0.000
75	B	372	LEU	0	-0.002	-0.011	16.038	0.018	0.018	0.000	0.000	0.000	0.000
76	B	373	ASN	0	-0.008	0.007	11.603	0.008	0.008	0.000	0.000	0.000	0.000
77	B	374	GLY	0	-0.034	-0.019	14.478	0.012	0.012	0.000	0.000	0.000	0.000
78	B	375	ARG	1	0.853	0.947	16.869	0.170	0.170	0.000	0.000	0.000	0.000
79	B	376	TYR	0	-0.032	-0.026	19.425	-0.004	-0.004	0.000	0.000	0.000	0.000
80	B	377	PHE	0	0.022	0.008	21.348	-0.004	-0.004	0.000	0.000	0.000	0.000
81	B	378	GLY	0	0.082	0.047	23.016	0.003	0.003	0.000	0.000	0.000	0.000
82	B	379	GLY	0	-0.043	-0.021	25.487	0.005	0.005	0.000	0.000	0.000	0.000
83	B	380	ARG	1	0.861	0.939	20.111	0.076	0.076	0.000	0.000	0.000	0.000
84	B	381	VAL	0	-0.020	-0.002	16.611	-0.007	-0.007	0.000	0.000	0.000	0.000
85	B	382	VAL	0	0.052	0.045	15.274	-0.004	-0.004	0.000	0.000	0.000	0.000
86	B	383	LYS	1	0.931	0.974	10.590	0.170	0.170	0.000	0.000	0.000	0.000
87	B	384	ALA	0	0.016	0.008	11.936	0.008	0.008	0.000	0.000	0.000	0.000
88	B	385	CYS	0	-0.098	-0.043	6.868	-0.084	-0.084	0.000	0.000	0.000	0.000
89	B	386	PHE	0	0.023	0.033	7.820	0.194	0.194	0.000	0.000	0.000	0.000
90	B	387	TYR	0	0.032	-0.020	8.031	-0.182	-0.182	0.000	0.000	0.000	0.000
91	B	388	ASN	0	0.003	0.005	8.733	0.075	0.075	0.000	0.000	0.000	0.000
92	B	389	LEU	0	0.029	0.006	10.383	0.034	0.034	0.000	0.000	0.000	0.000
93	B	390	ASP	-1	-0.878	-0.952	13.828	0.079	0.079	0.000	0.000	0.000	0.000
94	B	391	LYS	1	0.893	0.967	10.335	-0.462	-0.462	0.000	0.000	0.000	0.000
95	B	392	PHE	0	0.001	0.005	13.616	-0.006	-0.006	0.000	0.000	0.000	0.000
96	B	393	ARG	1	0.865	0.927	15.309	0.047	0.047	0.000	0.000	0.000	0.000
97	B	394	VAL	0	-0.033	-0.002	16.334	-0.002	-0.002	0.000	0.000	0.000	0.000
98	B	395	LEU	0	-0.026	-0.007	17.879	0.005	0.005	0.000	0.000	0.000	0.000
99	B	396	ASP	-1	-0.857	-0.906	13.765	0.188	0.188	0.000	0.000	0.000	0.000
100	B	397	LEU	0	-0.021	0.001	13.313	-0.010	-0.010	0.000	0.000	0.000	0.000
101	B	398	ALA	0	0.032	0.013	13.157	-0.044	-0.044	0.000	0.000	0.000	0.000
102	B	399	GLU	-1	-0.894	-0.943	8.500	0.460	0.460	0.000	0.000	0.000	0.000
103	B	400	GLN	0	0.010	-0.004	6.271	-0.150	-0.150	0.000	0.000	0.000	0.000
104	B	401	VAL	0	0.005	0.000	3.101	-2.166	-1.112	0.130	-0.600	-0.584	-0.005

Top

Graph

Manual

About

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