FMO DATABASE

FMODB ID: R8GY8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-294307.399038
FMO2-HF: Nuclear repulsion	272396.883669
FMO2-HF: Total energy	-21910.51537
FMO2-MP2: Total energy	-21974.119238

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.
-0.219	2.903	0.98	-1.271	-2.832	0.001

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 : -0.020 / q_NPA : -0.027

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	-0.912	-0.844	3.813	0.401	1.908	-0.014	-0.648	-0.846	0.003
4	A	4	ALA	0	0.027	0.009	6.443	0.186	0.186	0.000	0.000	0.000	0.000
5	A	5	ILE	0	-0.011	-0.026	8.164	-0.125	-0.125	0.000	0.000	0.000	0.000
6	A	6	SER	0	-0.017	-0.056	9.783	-0.088	-0.088	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.038	0.022	8.316	-0.092	-0.092	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.903	0.952	8.369	0.015	0.015	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.033	0.014	4.964	-0.121	-0.121	0.000	0.000	0.000	0.000
10	A	10	PRO	0	-0.017	0.003	4.823	0.350	0.350	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.896	0.940	7.787	0.172	0.172	0.000	0.000	0.000	0.000
12	A	12	ARG	1	0.886	0.940	10.538	0.010	0.010	0.000	0.000	0.000	0.000
13	A	13	PRO	0	0.020	0.024	5.841	0.099	0.099	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.030	0.009	7.813	-0.055	-0.055	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.008	0.001	6.525	0.363	0.363	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.004	-0.005	8.831	-0.279	-0.279	0.000	0.000	0.000	0.000
17	A	17	PRO	0	-0.005	-0.021	11.276	0.170	0.170	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.832	0.937	13.187	-0.381	-0.381	0.000	0.000	0.000	0.000
19	A	19	SER	0	0.019	-0.016	11.517	0.072	0.072	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.865	0.943	9.662	-0.766	-0.766	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.017	-0.008	6.694	0.514	0.514	0.000	0.000	0.000	0.000
22	A	22	ILE	0	-0.001	-0.001	2.639	-1.771	-0.315	0.996	-0.609	-1.843	-0.002
23	A	23	PHE	0	0.066	0.010	5.395	-0.179	-0.165	-0.001	-0.003	-0.009	0.000
24	A	24	GLU	-1	-0.801	-0.938	7.986	-0.300	-0.300	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.857	0.924	10.123	-0.014	-0.014	0.000	0.000	0.000	0.000
26	A	26	SER	0	-0.001	-0.019	12.777	0.018	0.018	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.008	0.005	11.994	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.030	0.022	11.496	0.017	0.017	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.867	-0.952	13.963	0.126	0.126	0.000	0.000	0.000	0.000
30	A	30	GLN	0	-0.092	-0.038	17.176	-0.020	-0.020	0.000	0.000	0.000	0.000
31	A	31	TYR	0	0.047	0.017	15.076	-0.014	-0.014	0.000	0.000	0.000	0.000
32	A	32	VAL	0	0.010	0.021	16.814	-0.015	-0.015	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.889	0.934	19.461	-0.145	-0.145	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.978	-0.977	21.921	0.169	0.169	0.000	0.000	0.000	0.000
35	A	35	THR	0	-0.030	-0.021	20.735	0.002	0.002	0.000	0.000	0.000	0.000
36	A	36	GLY	0	-0.015	0.003	22.233	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	37	ASN	0	0.007	0.005	20.130	0.002	0.002	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.738	-0.836	13.746	0.765	0.765	0.000	0.000	0.000	0.000
39	A	39	PRO	0	-0.028	-0.017	13.644	-0.019	-0.019	0.000	0.000	0.000	0.000
40	A	40	ILE	0	-0.066	-0.026	11.306	0.006	0.006	0.000	0.000	0.000	0.000
41	A	41	THR	0	-0.053	-0.069	14.765	-0.033	-0.033	0.000	0.000	0.000	0.000
42	A	42	ASN	0	-0.065	-0.027	17.299	-0.054	-0.054	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.880	-0.911	17.537	0.452	0.452	0.000	0.000	0.000	0.000
44	A	44	PRO	0	0.035	0.017	19.635	0.014	0.014	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.064	-0.038	15.006	0.037	0.037	0.000	0.000	0.000	0.000
46	A	46	SER	0	-0.005	0.007	19.361	-0.028	-0.028	0.000	0.000	0.000	0.000
47	A	47	ILE	0	0.022	-0.017	18.657	0.029	0.029	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.919	-0.970	18.023	0.162	0.162	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.871	-0.926	17.395	0.295	0.295	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.046	-0.013	12.779	0.070	0.070	0.000	0.000	0.000	0.000
51	A	51	VAL	0	-0.009	0.004	9.790	-0.073	-0.073	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.861	-0.930	10.005	0.176	0.176	0.000	0.000	0.000	0.000
53	A	53	ILE	0	-0.038	-0.013	4.486	-0.142	0.003	-0.001	-0.011	-0.134	0.000
54	A	54	VAL	0	-0.019	-0.009	8.012	-0.052	-0.052	0.000	0.000	0.000	0.000
55	A	55	PRO	0	-0.011	-0.010	7.907	-0.169	-0.169	0.000	0.000	0.000	0.000
56	A	56	SER	0	0.002	0.008	6.761	0.029	0.029	0.000	0.000	0.000	0.000

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