FMO DATABASE

FMODB ID: YZL12

Calculation Name: 1URQ-A-Xray372

Preferred Name: Synaptosomal-associated protein 25

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1URQ

Chain ID: A

ChEMBL ID: CHEMBL1075243

UniProt ID: P60881

Base Structure: X-ray

Registration Date: 2023-09-20

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	57
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-207480.629988
FMO2-HF: Nuclear repulsion	185144.663767
FMO2-HF: Total energy	-22335.966221
FMO2-MP2: Total energy	-22398.305841

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:1052:ILE)

Summations of interaction energy for fragment #1(A:1052:ILE)

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.
-5.042	-1.292	0.079	-1.454	-2.375	0.004

Interaction energy analysis for fragmet #1(A:1052:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.048 / q_NPA : 0.011

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	1054	GLY	0	0.012	0.001	3.431	-4.024	-1.753	-0.003	-1.093	-1.175	0.003
4	A	1055	VAL	0	0.005	0.002	3.085	-1.293	-0.434	0.077	-0.181	-0.755	0.000
5	A	1056	LYS	1	0.874	0.935	3.688	-0.076	0.544	0.005	-0.180	-0.445	0.001
6	A	1057	GLY	0	0.022	0.006	5.626	0.156	0.156	0.000	0.000	0.000	0.000
7	A	1058	ALA	0	0.015	0.007	7.848	0.001	0.001	0.000	0.000	0.000	0.000
8	A	1059	ALA	0	-0.012	-0.005	8.375	0.021	0.021	0.000	0.000	0.000	0.000
9	A	1060	SER	0	-0.009	-0.011	9.250	0.056	0.056	0.000	0.000	0.000	0.000
10	A	1061	GLY	0	0.013	0.010	11.577	0.029	0.029	0.000	0.000	0.000	0.000
11	A	1062	VAL	0	0.016	0.006	13.219	0.009	0.009	0.000	0.000	0.000	0.000
12	A	1063	VAL	0	-0.020	-0.006	13.244	0.011	0.011	0.000	0.000	0.000	0.000
13	A	1064	GLY	0	0.017	0.013	15.674	0.013	0.013	0.000	0.000	0.000	0.000
14	A	1065	GLU	-1	-0.978	-0.993	17.916	0.005	0.005	0.000	0.000	0.000	0.000
15	A	1066	LEU	0	0.001	-0.004	18.552	0.005	0.005	0.000	0.000	0.000	0.000
16	A	1067	ALA	0	0.007	0.004	19.842	0.004	0.004	0.000	0.000	0.000	0.000
17	A	1068	ARG	1	0.963	0.974	21.580	0.003	0.003	0.000	0.000	0.000	0.000
18	A	1069	ALA	0	0.010	0.009	23.608	0.004	0.004	0.000	0.000	0.000	0.000
19	A	1070	ARG	1	0.830	0.916	23.626	0.075	0.075	0.000	0.000	0.000	0.000
20	A	1071	LEU	0	0.034	0.010	25.503	0.003	0.003	0.000	0.000	0.000	0.000
21	A	1072	ALA	0	0.035	0.020	27.755	0.003	0.003	0.000	0.000	0.000	0.000
22	A	1073	LEU	0	-0.067	-0.034	27.703	0.002	0.002	0.000	0.000	0.000	0.000
23	A	1074	ASP	-1	-0.822	-0.908	28.859	-0.057	-0.057	0.000	0.000	0.000	0.000
24	A	1075	GLU	-1	-0.932	-0.955	31.387	-0.016	-0.016	0.000	0.000	0.000	0.000
25	A	1076	ARG	1	0.902	0.948	33.084	0.044	0.044	0.000	0.000	0.000	0.000
26	A	1077	GLY	0	0.031	0.012	33.965	0.001	0.001	0.000	0.000	0.000	0.000
27	A	1078	GLN	0	0.017	0.013	35.544	0.002	0.002	0.000	0.000	0.000	0.000
28	A	1079	LYS	1	0.936	0.954	37.285	0.020	0.020	0.000	0.000	0.000	0.000
29	A	1080	LEU	0	-0.035	-0.016	36.537	0.001	0.001	0.000	0.000	0.000	0.000
30	A	1081	SER	0	0.017	0.025	39.839	0.000	0.000	0.000	0.000	0.000	0.000
31	A	1082	ASP	-1	-0.789	-0.874	41.630	-0.018	-0.018	0.000	0.000	0.000	0.000
32	A	1083	LEU	0	-0.032	-0.024	42.945	0.001	0.001	0.000	0.000	0.000	0.000
33	A	1084	GLU	-1	-0.943	-0.965	43.843	-0.031	-0.031	0.000	0.000	0.000	0.000
34	A	1085	GLU	-1	-0.924	-0.949	45.664	-0.020	-0.020	0.000	0.000	0.000	0.000
35	A	1086	ARG	1	0.793	0.859	45.979	0.017	0.017	0.000	0.000	0.000	0.000
36	A	1087	THR	0	-0.037	-0.024	47.551	0.002	0.002	0.000	0.000	0.000	0.000
37	A	1088	ALA	0	0.020	0.019	49.858	0.001	0.001	0.000	0.000	0.000	0.000
38	A	1089	ALA	0	-0.001	0.003	51.637	0.001	0.001	0.000	0.000	0.000	0.000
39	A	1090	MET	0	-0.028	-0.020	52.135	0.001	0.001	0.000	0.000	0.000	0.000
40	A	1091	MET	0	-0.003	-0.010	53.566	0.001	0.001	0.000	0.000	0.000	0.000
41	A	1092	SER	0	0.002	0.014	55.452	0.001	0.001	0.000	0.000	0.000	0.000
42	A	1093	SER	0	-0.001	-0.004	57.912	0.001	0.001	0.000	0.000	0.000	0.000
43	A	1094	ALA	0	-0.038	-0.018	58.213	0.001	0.001	0.000	0.000	0.000	0.000
44	A	1095	ASP	-1	-0.944	-0.959	59.450	-0.016	-0.016	0.000	0.000	0.000	0.000
45	A	1096	SER	0	0.028	0.007	61.211	0.001	0.001	0.000	0.000	0.000	0.000
46	A	1097	PHE	0	-0.030	-0.026	63.333	0.001	0.001	0.000	0.000	0.000	0.000
47	A	1098	SER	0	0.006	0.002	63.349	0.001	0.001	0.000	0.000	0.000	0.000
48	A	1099	LYS	1	0.900	0.961	65.292	0.013	0.013	0.000	0.000	0.000	0.000
49	A	1100	HIS	0	-0.042	-0.029	67.576	0.000	0.000	0.000	0.000	0.000	0.000
50	A	1101	ALA	0	0.016	0.009	68.178	0.000	0.000	0.000	0.000	0.000	0.000
51	A	1102	HIS	0	0.027	0.018	69.030	0.000	0.000	0.000	0.000	0.000	0.000
52	A	1103	GLU	-1	-0.838	-0.934	70.938	-0.011	-0.011	0.000	0.000	0.000	0.000
53	A	1104	MET	0	-0.095	-0.045	72.256	0.000	0.000	0.000	0.000	0.000	0.000
54	A	1105	MET	0	-0.013	-0.001	72.539	0.000	0.000	0.000	0.000	0.000	0.000
55	A	1106	LEU	0	0.003	-0.013	74.254	0.000	0.000	0.000	0.000	0.000	0.000
56	A	1107	LYS	1	0.846	0.942	76.269	0.009	0.009	0.000	0.000	0.000	0.000
57	A	1108	TYR	0	-0.031	0.008	78.130	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1052:ILE)