FMO DATABASE

FMODB ID: KGL23

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	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	56
LigandResidueName
LigandFragmentNumber	0
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-296136.835525
FMO2-HF: Nuclear repulsion	274226.081132
FMO2-HF: Total energy	-21910.754393
FMO2-MP2: Total energy	-21974.410454

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.
-0.711	2.849	1.977	-1.653	-3.885	-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 : -0.002 / q_NPA : -0.015

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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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	-0.864	-0.782	3.857	0.439	1.802	-0.012	-0.567	-0.785	0.001
4	A	4	ALA	0	0.011	0.001	6.661	0.251	0.251	0.000	0.000	0.000	0.000
5	A	5	ILE	0	-0.018	-0.025	8.458	-0.136	-0.136	0.000	0.000	0.000	0.000
6	A	6	SER	0	-0.059	-0.123	10.097	-0.108	-0.108	0.000	0.000	0.000	0.000
7	A	7	GLY	0	-0.002	0.002	8.675	-0.109	-0.109	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.921	0.954	8.298	0.168	0.168	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.038	0.022	4.364	-0.244	-0.107	-0.001	-0.027	-0.109	0.000
10	A	10	PRO	0	-0.014	0.012	4.562	0.336	0.529	-0.001	-0.022	-0.170	0.000
11	A	11	ARG	1	0.918	0.955	7.568	0.483	0.483	0.000	0.000	0.000	0.000
12	A	12	ARG	1	0.862	0.918	10.092	0.473	0.473	0.000	0.000	0.000	0.000
13	A	13	PRO	0	0.021	0.016	4.740	0.113	0.186	-0.001	-0.004	-0.068	0.000
14	A	14	VAL	0	0.014	0.011	6.664	0.108	0.108	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.014	-0.003	5.799	0.084	0.084	0.000	0.000	0.000	0.000
16	A	16	SER	0	0.012	-0.004	7.780	-0.135	-0.135	0.000	0.000	0.000	0.000
17	A	17	PRO	0	-0.016	-0.023	10.764	0.183	0.183	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.784	0.900	12.417	-0.183	-0.183	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.012	-0.043	11.625	0.107	0.107	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.869	0.953	9.735	-0.683	-0.683	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.015	-0.007	6.888	0.663	0.663	0.000	0.000	0.000	0.000
22	A	22	ILE	0	-0.005	-0.008	2.248	-2.272	-0.809	1.979	-0.983	-2.459	-0.003
23	A	23	PHE	0	0.059	0.012	5.275	0.220	0.264	-0.001	-0.003	-0.040	0.000
24	A	24	GLU	-1	-0.745	-0.910	7.843	-1.195	-1.195	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.790	0.878	9.997	0.540	0.540	0.000	0.000	0.000	0.000
26	A	26	SER	0	-0.030	-0.023	12.155	0.086	0.086	0.000	0.000	0.000	0.000
27	A	27	LEU	0	0.003	0.008	11.972	0.042	0.042	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.032	0.025	11.339	0.064	0.064	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.797	-0.891	13.894	-0.182	-0.182	0.000	0.000	0.000	0.000
30	A	30	GLN	0	-0.063	-0.022	17.029	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	31	TYR	0	0.056	0.016	15.261	0.010	0.010	0.000	0.000	0.000	0.000
32	A	32	VAL	0	0.015	0.032	16.896	0.008	0.008	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.811	0.880	19.458	0.091	0.091	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.979	-0.970	21.731	0.082	0.082	0.000	0.000	0.000	0.000
35	A	35	THR	0	-0.036	-0.038	20.718	0.014	0.014	0.000	0.000	0.000	0.000
36	A	36	GLY	0	-0.009	0.011	22.478	0.005	0.005	0.000	0.000	0.000	0.000
37	A	37	ASN	0	-0.024	-0.015	20.202	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.688	-0.802	13.891	0.582	0.582	0.000	0.000	0.000	0.000
39	A	39	PRO	0	-0.027	-0.016	13.514	0.005	0.005	0.000	0.000	0.000	0.000
40	A	40	ILE	0	-0.077	-0.036	11.504	0.038	0.038	0.000	0.000	0.000	0.000
41	A	41	THR	0	-0.061	-0.075	15.002	0.003	0.003	0.000	0.000	0.000	0.000
42	A	42	ASN	0	-0.041	-0.011	17.540	-0.053	-0.053	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.849	-0.899	17.627	0.403	0.403	0.000	0.000	0.000	0.000
44	A	44	PRO	0	0.018	0.008	19.670	0.000	0.000	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.079	-0.036	14.935	0.022	0.022	0.000	0.000	0.000	0.000
46	A	46	SER	0	-0.013	-0.017	19.121	-0.025	-0.025	0.000	0.000	0.000	0.000
47	A	47	ILE	0	0.006	-0.019	17.581	0.003	0.003	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.897	-0.964	16.667	-0.068	-0.068	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.800	-0.854	15.933	0.127	0.127	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.050	-0.021	11.671	0.026	0.026	0.000	0.000	0.000	0.000
51	A	51	VAL	0	0.003	0.007	8.550	-0.064	-0.064	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.833	-0.919	8.530	-0.557	-0.557	0.000	0.000	0.000	0.000
53	A	53	ILE	0	-0.059	-0.022	3.336	-0.346	-0.059	0.014	-0.047	-0.254	0.000
54	A	54	VAL	0	-0.001	-0.006	7.392	-0.042	-0.042	0.000	0.000	0.000	0.000
55	A	55	PRO	0	-0.016	-0.009	7.948	-0.248	-0.248	0.000	0.000	0.000	0.000
56	A	56	SER	0	-0.001	0.009	6.515	0.167	0.167	0.000	0.000	0.000	0.000

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