FMO DATABASE

FMODB ID: 76K3K

Calculation Name: 2F9D-P-Xray372

Preferred Name: Splicing factor 3B subunit 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2F9D

Chain ID: P

ChEMBL ID: CHEMBL1229013

UniProt ID: O75533

Base Structure: X-ray

Registration Date: 2023-09-23

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	39
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-151757.972119
FMO2-HF: Nuclear repulsion	134746.037456
FMO2-HF: Total energy	-17011.934663
FMO2-MP2: Total energy	-17060.566588

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(P:377:SER)

Summations of interaction energy for fragment #1(P:377:SER)

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.
-0.859	0.486	-0.002	-0.555	-0.789	0

Interaction energy analysis for fragmet #1(P:377:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : -0.030

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].
3	P	379	THR	0	0.060	0.016	3.661	-1.402	-0.057	-0.002	-0.555	-0.789
4	P	380	PRO	0	0.025	-0.008	5.598	0.966	0.966	0.000	0.000	0.000
5	P	381	GLU	-1	-0.880	-0.938	8.147	-0.947	-0.947	0.000	0.000	0.000
6	P	382	GLN	0	0.048	0.048	5.688	-0.646	-0.646	0.000	0.000	0.000
7	P	383	LEU	0	0.004	-0.012	5.612	0.370	0.370	0.000	0.000	0.000
8	P	384	GLN	0	0.010	0.016	8.785	0.251	0.251	0.000	0.000	0.000
9	P	385	ALA	0	-0.008	0.006	11.627	0.086	0.086	0.000	0.000	0.000
10	P	386	TRP	0	0.019	0.011	9.606	0.090	0.090	0.000	0.000	0.000
11	P	387	ARG	1	0.937	0.953	9.914	0.049	0.049	0.000	0.000	0.000
12	P	388	TRP	0	-0.004	-0.001	14.311	0.000	0.000	0.000	0.000	0.000
13	P	389	GLU	-1	-0.940	-0.970	14.280	0.197	0.197	0.000	0.000	0.000
14	P	390	ARG	1	0.833	0.918	13.099	-0.365	-0.365	0.000	0.000	0.000
15	P	391	GLU	-1	-0.926	-0.961	17.036	0.043	0.043	0.000	0.000	0.000
16	P	392	ILE	0	-0.021	-0.026	19.621	-0.014	-0.014	0.000	0.000	0.000
17	P	393	ASP	-1	-0.843	-0.917	18.405	0.255	0.255	0.000	0.000	0.000
18	P	394	GLU	-1	-0.949	-0.975	21.463	0.161	0.161	0.000	0.000	0.000
19	P	395	ARG	1	0.829	0.909	23.430	-0.071	-0.071	0.000	0.000	0.000
20	P	396	ASN	0	-0.037	-0.009	24.728	-0.020	-0.020	0.000	0.000	0.000
21	P	397	ARG	1	0.807	0.912	25.676	-0.115	-0.115	0.000	0.000	0.000
22	P	398	PRO	0	-0.044	-0.023	26.914	-0.011	-0.011	0.000	0.000	0.000
23	P	399	LEU	0	-0.006	0.001	30.311	0.003	0.003	0.000	0.000	0.000
24	P	400	SER	0	-0.011	0.002	33.185	-0.002	-0.002	0.000	0.000	0.000
25	P	401	ASP	-1	-0.855	-0.957	36.121	0.071	0.071	0.000	0.000	0.000
26	P	402	GLU	-1	-0.982	-0.973	38.850	0.074	0.074	0.000	0.000	0.000
27	P	403	GLU	-1	-0.836	-0.916	32.444	0.088	0.088	0.000	0.000	0.000
28	P	404	LEU	0	-0.014	-0.010	36.397	-0.005	-0.005	0.000	0.000	0.000
29	P	405	ASP	-1	-0.941	-0.980	38.532	0.051	0.051	0.000	0.000	0.000
30	P	406	ALA	0	-0.041	-0.007	39.499	-0.004	-0.004	0.000	0.000	0.000
31	P	407	MET	0	-0.076	-0.028	35.920	-0.002	-0.002	0.000	0.000	0.000
32	P	408	PHE	0	-0.070	-0.030	40.056	-0.005	-0.005	0.000	0.000	0.000
33	P	409	PRO	0	-0.020	0.006	43.619	0.000	0.000	0.000	0.000	0.000
34	P	410	GLU	-1	-0.904	-0.972	46.905	0.029	0.029	0.000	0.000	0.000
35	P	411	GLY	0	-0.047	-0.021	50.270	-0.001	-0.001	0.000	0.000	0.000
36	P	412	TYR	0	-0.005	0.003	47.907	-0.002	-0.002	0.000	0.000	0.000
37	P	413	LYS	1	0.899	0.948	49.878	-0.030	-0.030	0.000	0.000	0.000
38	P	414	VAL	0	0.074	0.045	45.355	-0.001	-0.001	0.000	0.000	0.000
39	P	415	LEU	0	-0.025	-0.012	47.022	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(P:377:SER)