FMO DATABASE

FMODB ID: 17ZYZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-208129.843861
FMO2-HF: Nuclear repulsion	185793.563649
FMO2-HF: Total energy	-22336.280212
FMO2-MP2: Total energy	-22398.644775

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.
-4.896	-1.112	0.159	-1.48	-2.463	0.003

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 : 0.040 / 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	0.031	0.014	3.726	-2.031	-0.033	-0.004	-0.907	-1.088	0.002
4	A	1055	VAL	0	0.005	0.004	3.025	-2.166	-0.998	0.159	-0.354	-0.972	0.001
5	A	1056	LYS	1	0.866	0.918	3.591	-0.270	0.348	0.004	-0.219	-0.403	0.000
6	A	1057	GLY	0	0.023	0.025	5.511	0.035	0.035	0.000	0.000	0.000	0.000
7	A	1058	ALA	0	0.012	0.000	7.939	-0.117	-0.117	0.000	0.000	0.000	0.000
8	A	1059	ALA	0	-0.001	-0.002	8.344	-0.110	-0.110	0.000	0.000	0.000	0.000
9	A	1060	SER	0	-0.015	-0.026	9.057	-0.076	-0.076	0.000	0.000	0.000	0.000
10	A	1061	GLY	0	0.012	0.013	11.479	-0.022	-0.022	0.000	0.000	0.000	0.000
11	A	1062	VAL	0	-0.016	-0.010	13.103	-0.033	-0.033	0.000	0.000	0.000	0.000
12	A	1063	VAL	0	-0.003	-0.002	13.317	-0.028	-0.028	0.000	0.000	0.000	0.000
13	A	1064	GLY	0	0.024	0.019	15.658	-0.017	-0.017	0.000	0.000	0.000	0.000
14	A	1065	GLU	-1	-0.829	-0.892	17.684	0.147	0.147	0.000	0.000	0.000	0.000
15	A	1066	LEU	0	-0.020	-0.009	18.391	-0.013	-0.013	0.000	0.000	0.000	0.000
16	A	1067	ALA	0	0.007	0.004	19.717	-0.014	-0.014	0.000	0.000	0.000	0.000
17	A	1068	ARG	1	0.824	0.874	21.480	-0.133	-0.133	0.000	0.000	0.000	0.000
18	A	1069	ALA	0	-0.008	-0.002	23.356	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	1070	ARG	1	0.802	0.868	23.786	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	1071	LEU	0	0.040	0.016	25.397	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	1072	ALA	0	0.023	0.015	27.764	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	1073	LEU	0	-0.043	-0.018	27.659	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	1074	ASP	-1	-0.792	-0.866	28.564	0.004	0.004	0.000	0.000	0.000	0.000
24	A	1075	GLU	-1	-0.846	-0.907	31.497	0.028	0.028	0.000	0.000	0.000	0.000
25	A	1076	ARG	1	0.945	0.968	32.898	-0.032	-0.032	0.000	0.000	0.000	0.000
26	A	1077	GLY	0	0.003	-0.001	33.995	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	1078	GLN	0	-0.009	-0.008	35.547	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	1079	LYS	1	0.854	0.907	36.968	-0.030	-0.030	0.000	0.000	0.000	0.000
29	A	1080	LEU	0	-0.040	-0.013	36.523	0.000	0.000	0.000	0.000	0.000	0.000
30	A	1081	SER	0	0.034	0.022	40.005	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	1082	ASP	-1	-0.832	-0.892	41.894	0.014	0.014	0.000	0.000	0.000	0.000
32	A	1083	LEU	0	-0.025	-0.018	42.926	0.000	0.000	0.000	0.000	0.000	0.000
33	A	1084	GLU	-1	-0.946	-0.954	44.078	0.007	0.007	0.000	0.000	0.000	0.000
34	A	1085	GLU	-1	-0.916	-0.951	45.924	0.005	0.005	0.000	0.000	0.000	0.000
35	A	1086	ARG	1	0.822	0.882	46.332	-0.016	-0.016	0.000	0.000	0.000	0.000
36	A	1087	THR	0	-0.031	-0.032	47.661	0.001	0.001	0.000	0.000	0.000	0.000
37	A	1088	ALA	0	0.009	0.010	50.117	0.000	0.000	0.000	0.000	0.000	0.000
38	A	1089	ALA	0	0.020	0.013	51.967	0.000	0.000	0.000	0.000	0.000	0.000
39	A	1090	MET	0	-0.015	0.002	51.474	0.000	0.000	0.000	0.000	0.000	0.000
40	A	1091	MET	0	-0.004	-0.003	53.413	0.000	0.000	0.000	0.000	0.000	0.000
41	A	1092	SER	0	-0.012	0.000	55.563	0.000	0.000	0.000	0.000	0.000	0.000
42	A	1093	SER	0	-0.019	-0.028	57.922	0.000	0.000	0.000	0.000	0.000	0.000
43	A	1094	ALA	0	-0.025	-0.015	58.175	0.000	0.000	0.000	0.000	0.000	0.000
44	A	1095	ASP	-1	-0.933	-0.960	59.669	0.007	0.007	0.000	0.000	0.000	0.000
45	A	1096	SER	0	0.027	0.011	61.391	0.000	0.000	0.000	0.000	0.000	0.000
46	A	1097	PHE	0	-0.021	-0.009	63.197	0.000	0.000	0.000	0.000	0.000	0.000
47	A	1098	SER	0	-0.003	0.000	63.133	0.000	0.000	0.000	0.000	0.000	0.000
48	A	1099	LYS	1	0.840	0.918	65.168	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	1100	HIS	0	0.000	-0.014	67.377	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	1101	ALA	0	0.002	0.008	67.944	0.000	0.000	0.000	0.000	0.000	0.000
51	A	1102	HIS	0	0.019	0.011	69.034	0.000	0.000	0.000	0.000	0.000	0.000
52	A	1103	GLU	-1	-0.809	-0.915	70.877	0.005	0.005	0.000	0.000	0.000	0.000
53	A	1104	MET	0	-0.077	-0.025	72.726	0.000	0.000	0.000	0.000	0.000	0.000
54	A	1105	MET	0	0.014	0.016	72.671	0.000	0.000	0.000	0.000	0.000	0.000
55	A	1106	LEU	0	-0.001	-0.008	73.959	0.000	0.000	0.000	0.000	0.000	0.000
56	A	1107	LYS	1	0.840	0.930	76.135	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	1108	TYR	0	-0.079	-0.034	77.922	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)