FMO DATABASE

FMODB ID: QVGNY

Calculation Name: 2BAY-A-Xray372

Preferred Name: Pre-mRNA-splicing factor 19

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2BAY

Chain ID: A

ChEMBL ID: CHEMBL5058

UniProt ID: P32523

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	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	56
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-294815.816177
FMO2-HF: Nuclear repulsion	272905.067314
FMO2-HF: Total energy	-21910.748864
FMO2-MP2: Total energy	-21974.35918

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(A:1:MET)

Summations of interaction energy for fragment #1(A:1:MET)

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.
0.063	3.004	1.424	-1.296	-3.067	0.002

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.024

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	A	3	CYM	-1	-0.882	-0.816	3.813	0.528	1.955	-0.012	-0.591	-0.823	0.002
4	A	4	ALA	0	0.030	0.011	6.481	0.235	0.235	0.000	0.000	0.000	0.000
5	A	5	ILE	0	-0.013	-0.020	8.194	-0.115	-0.115	0.000	0.000	0.000	0.000
6	A	6	SER	0	-0.050	-0.103	9.938	-0.093	-0.093	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.025	0.014	8.315	-0.084	-0.084	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.902	0.952	8.317	0.129	0.129	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.043	0.018	4.823	-0.152	-0.152	0.000	0.000	0.000	0.000
10	A	10	PRO	0	-0.015	0.003	4.789	0.282	0.432	-0.001	-0.015	-0.133	0.000
11	A	11	ARG	1	0.933	0.961	7.764	0.365	0.365	0.000	0.000	0.000	0.000
12	A	12	ARG	1	0.874	0.928	10.327	0.277	0.277	0.000	0.000	0.000	0.000
13	A	13	PRO	0	0.013	0.017	5.340	0.188	0.188	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.022	0.010	7.391	0.005	0.005	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.009	-0.004	6.166	0.254	0.254	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.005	-0.014	8.376	-0.212	-0.212	0.000	0.000	0.000	0.000
17	A	17	PRO	0	-0.003	-0.019	11.184	0.194	0.194	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.779	0.889	12.808	-0.275	-0.275	0.000	0.000	0.000	0.000
19	A	19	SER	0	0.009	-0.026	11.557	0.096	0.096	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.867	0.941	9.602	-0.823	-0.823	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.017	-0.003	6.695	0.676	0.676	0.000	0.000	0.000	0.000
22	A	22	ILE	0	-0.006	-0.004	2.500	-1.870	-0.684	1.436	-0.671	-1.951	0.000
23	A	23	PHE	0	0.058	0.010	5.416	0.038	0.038	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.779	-0.927	8.019	-0.846	-0.846	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.808	0.894	10.158	0.321	0.321	0.000	0.000	0.000	0.000
26	A	26	SER	0	-0.013	-0.016	12.808	0.058	0.058	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.001	0.003	11.982	0.027	0.027	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.037	0.024	11.475	0.046	0.046	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.803	-0.900	13.994	-0.062	-0.062	0.000	0.000	0.000	0.000
30	A	30	GLN	0	-0.073	-0.024	17.206	-0.015	-0.015	0.000	0.000	0.000	0.000
31	A	31	TYR	0	0.052	0.019	15.071	0.003	0.003	0.000	0.000	0.000	0.000
32	A	32	VAL	0	0.004	0.017	16.847	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.812	0.887	19.488	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.973	-0.970	21.949	0.123	0.123	0.000	0.000	0.000	0.000
35	A	35	THR	0	-0.026	-0.029	20.825	0.011	0.011	0.000	0.000	0.000	0.000
36	A	36	GLY	0	-0.020	0.004	22.256	0.002	0.002	0.000	0.000	0.000	0.000
37	A	37	ASN	0	-0.007	-0.007	20.151	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.739	-0.820	13.741	0.706	0.706	0.000	0.000	0.000	0.000
39	A	39	PRO	0	-0.026	-0.017	13.684	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	40	ILE	0	-0.066	-0.027	11.278	0.021	0.021	0.000	0.000	0.000	0.000
41	A	41	THR	0	-0.050	-0.079	14.783	-0.020	-0.020	0.000	0.000	0.000	0.000
42	A	42	ASN	0	-0.057	-0.021	17.311	-0.057	-0.057	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.857	-0.888	17.498	0.458	0.458	0.000	0.000	0.000	0.000
44	A	44	PRO	0	0.041	0.018	19.650	0.005	0.005	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.070	-0.029	15.012	0.033	0.033	0.000	0.000	0.000	0.000
46	A	46	SER	0	-0.004	-0.010	19.377	-0.029	-0.029	0.000	0.000	0.000	0.000
47	A	47	ILE	0	0.009	-0.024	18.166	0.013	0.013	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.913	-0.968	17.312	0.033	0.033	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.812	-0.868	16.670	0.210	0.210	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.058	-0.018	12.225	0.044	0.044	0.000	0.000	0.000	0.000
51	A	51	VAL	0	-0.005	0.006	9.247	-0.064	-0.064	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.837	-0.917	9.357	-0.266	-0.266	0.000	0.000	0.000	0.000
53	A	53	ILE	0	-0.040	-0.016	3.787	-0.198	-0.020	0.001	-0.019	-0.160	0.000
54	A	54	VAL	0	-0.019	-0.008	7.672	-0.018	-0.018	0.000	0.000	0.000	0.000
55	A	55	PRO	0	-0.013	-0.010	7.834	-0.219	-0.219	0.000	0.000	0.000	0.000
56	A	56	SER	0	0.008	0.011	6.983	0.120	0.120	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)