FMO DATABASE

FMODB ID: 6Y4LZ

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:

Apendix: None

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	39
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-151618.077279
FMO2-HF: Nuclear repulsion	134605.685129
FMO2-HF: Total energy	-17012.39215
FMO2-MP2: Total energy	-17060.991821

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.
-1.234	0.605	-0.012	-0.945	-0.883	0.004

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 : 0.013 / q_NPA : 0.000

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	P	379	THR	0	0.016	-0.026	3.865	-1.080	0.759	-0.012	-0.945	-0.883	0.004
4	P	380	PRO	0	0.012	-0.008	6.467	0.699	0.699	0.000	0.000	0.000	0.000
5	P	381	GLU	-1	-0.805	-0.878	9.138	-1.078	-1.078	0.000	0.000	0.000	0.000
6	P	382	GLN	0	0.034	0.022	6.146	-0.656	-0.656	0.000	0.000	0.000	0.000
7	P	383	LEU	0	-0.003	-0.004	5.287	0.252	0.252	0.000	0.000	0.000	0.000
8	P	384	GLN	0	-0.012	0.009	9.065	0.129	0.129	0.000	0.000	0.000	0.000
9	P	385	ALA	0	-0.004	0.004	12.320	0.062	0.062	0.000	0.000	0.000	0.000
10	P	386	TRP	0	0.029	0.006	10.061	0.096	0.096	0.000	0.000	0.000	0.000
11	P	387	ARG	1	0.898	0.935	9.322	0.078	0.078	0.000	0.000	0.000	0.000
12	P	388	TRP	0	0.017	0.003	13.983	0.002	0.002	0.000	0.000	0.000	0.000
13	P	389	GLU	-1	-0.860	-0.924	14.425	0.174	0.174	0.000	0.000	0.000	0.000
14	P	390	ARG	1	0.733	0.826	13.686	-0.289	-0.289	0.000	0.000	0.000	0.000
15	P	391	GLU	-1	-0.916	-0.932	16.721	0.001	0.001	0.000	0.000	0.000	0.000
16	P	392	ILE	0	-0.046	-0.045	19.497	-0.010	-0.010	0.000	0.000	0.000	0.000
17	P	393	ASP	-1	-0.810	-0.865	18.535	0.230	0.230	0.000	0.000	0.000	0.000
18	P	394	GLU	-1	-0.860	-0.911	21.583	0.108	0.108	0.000	0.000	0.000	0.000
19	P	395	ARG	1	0.807	0.885	23.510	-0.027	-0.027	0.000	0.000	0.000	0.000
20	P	396	ASN	0	-0.049	-0.016	25.067	-0.022	-0.022	0.000	0.000	0.000	0.000
21	P	397	ARG	1	0.777	0.872	25.785	-0.089	-0.089	0.000	0.000	0.000	0.000
22	P	398	PRO	0	-0.066	-0.028	27.192	-0.010	-0.010	0.000	0.000	0.000	0.000
23	P	399	LEU	0	0.014	0.010	30.639	0.005	0.005	0.000	0.000	0.000	0.000
24	P	400	SER	0	-0.005	0.005	33.093	-0.001	-0.001	0.000	0.000	0.000	0.000
25	P	401	ASP	-1	-0.889	-0.961	35.968	0.052	0.052	0.000	0.000	0.000	0.000
26	P	402	GLU	-1	-0.954	-0.975	37.863	0.059	0.059	0.000	0.000	0.000	0.000
27	P	403	GLU	-1	-0.828	-0.900	31.766	0.072	0.072	0.000	0.000	0.000	0.000
28	P	404	LEU	0	-0.027	-0.015	36.709	-0.005	-0.005	0.000	0.000	0.000	0.000
29	P	405	ASP	-1	-0.910	-0.969	38.217	0.031	0.031	0.000	0.000	0.000	0.000
30	P	406	ALA	0	-0.070	-0.031	38.635	-0.004	-0.004	0.000	0.000	0.000	0.000
31	P	407	MET	0	-0.067	-0.021	35.529	-0.002	-0.002	0.000	0.000	0.000	0.000
32	P	408	PHE	0	-0.073	-0.028	39.598	-0.005	-0.005	0.000	0.000	0.000	0.000
33	P	409	PRO	0	-0.026	-0.002	43.306	0.001	0.001	0.000	0.000	0.000	0.000
34	P	410	GLU	-1	-0.907	-0.969	46.596	0.016	0.016	0.000	0.000	0.000	0.000
35	P	411	GLY	0	-0.028	-0.020	50.065	-0.002	-0.002	0.000	0.000	0.000	0.000
36	P	412	TYR	0	-0.029	0.001	47.232	-0.002	-0.002	0.000	0.000	0.000	0.000
37	P	413	LYS	1	0.853	0.912	49.634	-0.016	-0.016	0.000	0.000	0.000	0.000
38	P	414	VAL	0	0.090	0.049	45.755	-0.002	-0.002	0.000	0.000	0.000	0.000
39	P	415	LEU	0	0.014	0.018	46.939	-0.001	-0.001	0.000	0.000	0.000	0.000

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