FMO DATABASE

FMODB ID: V57N1

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	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	57
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-207712.515205
FMO2-HF: Nuclear repulsion	185376.282126
FMO2-HF: Total energy	-22336.233078
FMO2-MP2: Total energy	-22398.598979

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.
-5.899	-2.013	0.084	-1.575	-2.395	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 : 0.029 / q_NPA : 0.003

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	0.022	0.011	3.559	-3.220	-0.781	0.001	-1.197	-1.243	0.004
4	A	1055	VAL	0	0.007	-0.001	3.094	-2.168	-1.327	0.076	-0.189	-0.728	0.000
5	A	1056	LYS	1	0.870	0.927	3.522	-0.102	0.504	0.007	-0.189	-0.424	0.000
6	A	1057	GLY	0	0.028	0.022	5.505	-0.019	-0.019	0.000	0.000	0.000	0.000
7	A	1058	ALA	0	0.008	0.003	7.825	-0.122	-0.122	0.000	0.000	0.000	0.000
8	A	1059	ALA	0	-0.014	-0.006	8.381	-0.101	-0.101	0.000	0.000	0.000	0.000
9	A	1060	SER	0	-0.015	-0.027	9.020	-0.058	-0.058	0.000	0.000	0.000	0.000
10	A	1061	GLY	0	0.020	0.013	11.480	-0.019	-0.019	0.000	0.000	0.000	0.000
11	A	1062	VAL	0	-0.005	-0.005	13.209	-0.031	-0.031	0.000	0.000	0.000	0.000
12	A	1063	VAL	0	-0.008	-0.004	13.232	-0.025	-0.025	0.000	0.000	0.000	0.000
13	A	1064	GLY	0	0.023	0.019	15.688	-0.014	-0.014	0.000	0.000	0.000	0.000
14	A	1065	GLU	-1	-0.887	-0.932	17.816	0.157	0.157	0.000	0.000	0.000	0.000
15	A	1066	LEU	0	-0.019	-0.013	18.561	-0.011	-0.011	0.000	0.000	0.000	0.000
16	A	1067	ALA	0	0.005	0.003	19.836	-0.012	-0.012	0.000	0.000	0.000	0.000
17	A	1068	ARG	1	0.885	0.925	21.539	-0.117	-0.117	0.000	0.000	0.000	0.000
18	A	1069	ALA	0	0.012	0.009	23.649	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	1070	ARG	1	0.816	0.887	23.861	0.005	0.005	0.000	0.000	0.000	0.000
20	A	1071	LEU	0	0.030	0.011	25.385	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	1072	ALA	0	0.022	0.013	27.713	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	1073	LEU	0	-0.063	-0.032	27.719	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	1074	ASP	-1	-0.798	-0.881	28.582	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	1075	GLU	-1	-0.835	-0.904	31.476	0.024	0.024	0.000	0.000	0.000	0.000
25	A	1076	ARG	1	0.915	0.959	33.067	-0.023	-0.023	0.000	0.000	0.000	0.000
26	A	1077	GLY	0	0.026	0.012	34.135	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	1078	GLN	0	0.007	0.006	35.729	0.000	0.000	0.000	0.000	0.000	0.000
28	A	1079	LYS	1	0.847	0.902	36.880	-0.023	-0.023	0.000	0.000	0.000	0.000
29	A	1080	LEU	0	-0.029	-0.013	36.686	0.000	0.000	0.000	0.000	0.000	0.000
30	A	1081	SER	0	0.019	0.024	40.026	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	1082	ASP	-1	-0.790	-0.853	41.810	0.010	0.010	0.000	0.000	0.000	0.000
32	A	1083	LEU	0	-0.026	-0.022	43.017	0.000	0.000	0.000	0.000	0.000	0.000
33	A	1084	GLU	-1	-0.946	-0.960	43.990	0.001	0.001	0.000	0.000	0.000	0.000
34	A	1085	GLU	-1	-0.920	-0.952	45.818	0.001	0.001	0.000	0.000	0.000	0.000
35	A	1086	ARG	1	0.792	0.843	45.945	-0.012	-0.012	0.000	0.000	0.000	0.000
36	A	1087	THR	0	-0.045	-0.036	47.673	0.001	0.001	0.000	0.000	0.000	0.000
37	A	1088	ALA	0	0.012	0.015	50.013	0.000	0.000	0.000	0.000	0.000	0.000
38	A	1089	ALA	0	0.009	0.010	51.779	0.000	0.000	0.000	0.000	0.000	0.000
39	A	1090	MET	0	-0.017	-0.015	52.146	0.000	0.000	0.000	0.000	0.000	0.000
40	A	1091	MET	0	-0.005	-0.010	53.546	0.000	0.000	0.000	0.000	0.000	0.000
41	A	1092	SER	0	-0.010	0.012	55.583	0.000	0.000	0.000	0.000	0.000	0.000
42	A	1093	SER	0	-0.007	-0.013	58.050	0.000	0.000	0.000	0.000	0.000	0.000
43	A	1094	ALA	0	-0.032	-0.017	58.287	0.000	0.000	0.000	0.000	0.000	0.000
44	A	1095	ASP	-1	-0.919	-0.949	59.626	0.004	0.004	0.000	0.000	0.000	0.000
45	A	1096	SER	0	0.027	0.005	61.326	0.000	0.000	0.000	0.000	0.000	0.000
46	A	1097	PHE	0	-0.031	-0.020	63.438	0.000	0.000	0.000	0.000	0.000	0.000
47	A	1098	SER	0	0.009	0.004	63.372	0.000	0.000	0.000	0.000	0.000	0.000
48	A	1099	LYS	1	0.854	0.935	65.404	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	1100	HIS	0	-0.031	-0.024	67.447	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	1101	ALA	0	0.005	0.003	68.251	0.000	0.000	0.000	0.000	0.000	0.000
51	A	1102	HIS	0	0.030	0.018	69.129	0.000	0.000	0.000	0.000	0.000	0.000
52	A	1103	GLU	-1	-0.820	-0.923	71.033	0.003	0.003	0.000	0.000	0.000	0.000
53	A	1104	MET	0	-0.087	-0.044	72.679	0.000	0.000	0.000	0.000	0.000	0.000
54	A	1105	MET	0	-0.001	0.010	72.600	0.000	0.000	0.000	0.000	0.000	0.000
55	A	1106	LEU	0	-0.004	-0.017	74.119	0.000	0.000	0.000	0.000	0.000	0.000
56	A	1107	LYS	1	0.848	0.940	76.227	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	1108	TYR	0	-0.050	0.000	78.190	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)