FMO DATABASE

FMODB ID: LGY39

Calculation Name: 5KJ7-A-Xray547

Preferred Name: Synaptosomal-associated protein 25

Target Type: SINGLE PROTEIN

Ligand Name: calcium ion

Ligand 3-letter code: CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5KJ7

Chain ID: A

ChEMBL ID: CHEMBL1075243

UniProt ID: P60881

Base Structure: X-ray

Registration Date: 2025-10-04

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	63
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-261341.972669
FMO2-HF: Nuclear repulsion	236121.815696
FMO2-HF: Total energy	-25220.156973
FMO2-MP2: Total energy	-25294.118645

3D Structure Molmil

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:27:GLY)

Summations of interaction energy for fragment #1(A:27:GLY)

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.
75.325	77.083	0.028	-0.656	-1.13	-0.003

Interaction energy analysis for fragmet #1(A:27:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.889 / q_NPA : 0.929

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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Graph Options

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	29	ASN	0	0.108	0.044	3.852	4.265	5.153	-0.004	-0.359	-0.525	-0.001
4	A	30	ARG	1	0.950	0.987	2.966	49.326	50.068	0.033	-0.274	-0.501	-0.002
5	A	31	ARG	1	0.969	0.993	4.750	43.219	43.347	-0.001	-0.023	-0.104	0.000
6	A	32	LEU	0	0.036	0.034	6.208	4.976	4.976	0.000	0.000	0.000	0.000
7	A	33	GLN	0	0.043	0.020	8.409	3.612	3.612	0.000	0.000	0.000	0.000
8	A	34	GLN	0	-0.033	-0.016	7.567	-2.329	-2.329	0.000	0.000	0.000	0.000
9	A	35	THR	0	-0.024	-0.037	9.707	2.177	2.177	0.000	0.000	0.000	0.000
10	A	36	GLN	0	-0.064	-0.040	11.918	1.190	1.190	0.000	0.000	0.000	0.000
11	A	37	ALA	0	0.045	0.021	13.197	1.377	1.377	0.000	0.000	0.000	0.000
12	A	38	GLN	0	0.004	-0.007	12.642	-0.312	-0.312	0.000	0.000	0.000	0.000
13	A	39	VAL	0	-0.017	-0.002	15.732	1.133	1.133	0.000	0.000	0.000	0.000
14	A	40	ASP	-1	-0.834	-0.908	17.715	-16.094	-16.094	0.000	0.000	0.000	0.000
15	A	41	GLU	-1	-0.933	-0.958	17.766	-16.171	-16.171	0.000	0.000	0.000	0.000
16	A	42	VAL	0	-0.022	-0.020	19.788	0.922	0.922	0.000	0.000	0.000	0.000
17	A	43	VAL	0	-0.026	-0.012	21.776	0.860	0.860	0.000	0.000	0.000	0.000
18	A	44	ASP	-1	-0.900	-0.946	23.386	-12.445	-12.445	0.000	0.000	0.000	0.000
19	A	45	ILE	0	-0.044	-0.026	22.756	0.720	0.720	0.000	0.000	0.000	0.000
20	A	46	MET	0	-0.025	-0.023	25.669	0.596	0.596	0.000	0.000	0.000	0.000
21	A	47	ARG	1	0.953	0.987	26.735	11.829	11.829	0.000	0.000	0.000	0.000
22	A	48	VAL	0	0.030	0.010	29.202	0.451	0.451	0.000	0.000	0.000	0.000
23	A	49	ASN	0	-0.039	-0.034	29.104	0.547	0.547	0.000	0.000	0.000	0.000
24	A	50	VAL	0	0.003	0.004	31.583	0.322	0.322	0.000	0.000	0.000	0.000
25	A	51	ASP	-1	-0.870	-0.932	33.736	-9.067	-9.067	0.000	0.000	0.000	0.000
26	A	52	LYS	1	0.909	0.958	32.064	10.108	10.108	0.000	0.000	0.000	0.000
27	A	53	VAL	0	-0.044	-0.021	35.624	0.269	0.269	0.000	0.000	0.000	0.000
28	A	54	LEU	0	0.017	0.014	37.698	0.255	0.255	0.000	0.000	0.000	0.000
29	A	55	GLU	-1	-0.927	-0.962	39.781	-7.727	-7.727	0.000	0.000	0.000	0.000
30	A	56	ARG	1	0.880	0.935	39.797	8.084	8.084	0.000	0.000	0.000	0.000
31	A	57	ASP	-1	-0.932	-0.957	41.958	-7.189	-7.189	0.000	0.000	0.000	0.000
32	A	58	GLN	0	0.027	0.011	43.770	0.212	0.212	0.000	0.000	0.000	0.000
33	A	59	LYS	1	0.923	0.956	43.545	7.388	7.388	0.000	0.000	0.000	0.000
34	A	60	LEU	0	-0.051	-0.024	44.092	0.113	0.113	0.000	0.000	0.000	0.000
35	A	61	SER	0	0.029	0.022	47.680	0.188	0.188	0.000	0.000	0.000	0.000
36	A	62	GLU	-1	-0.820	-0.898	49.815	-6.122	-6.122	0.000	0.000	0.000	0.000
37	A	63	LEU	0	-0.085	-0.051	49.719	0.137	0.137	0.000	0.000	0.000	0.000
38	A	64	ASP	-1	-0.917	-0.955	51.747	-5.995	-5.995	0.000	0.000	0.000	0.000
39	A	65	ASP	-1	-0.885	-0.936	53.558	-5.826	-5.826	0.000	0.000	0.000	0.000
40	A	66	ARG	1	0.749	0.849	54.124	6.146	6.146	0.000	0.000	0.000	0.000
41	A	67	ALA	0	-0.017	-0.002	55.400	0.118	0.118	0.000	0.000	0.000	0.000
42	A	68	ASP	-1	-0.840	-0.914	57.348	-5.285	-5.285	0.000	0.000	0.000	0.000
43	A	69	ALA	0	0.007	0.005	59.635	0.130	0.130	0.000	0.000	0.000	0.000
44	A	70	LEU	0	-0.051	-0.017	59.158	0.117	0.117	0.000	0.000	0.000	0.000
45	A	71	GLN	0	-0.067	-0.041	61.010	0.161	0.161	0.000	0.000	0.000	0.000
46	A	72	ALA	0	0.043	0.029	63.022	0.108	0.108	0.000	0.000	0.000	0.000
47	A	73	GLY	0	0.009	0.000	65.181	0.105	0.105	0.000	0.000	0.000	0.000
48	A	74	ALA	0	-0.025	-0.017	65.051	0.096	0.096	0.000	0.000	0.000	0.000
49	A	75	SER	0	0.045	0.035	67.010	0.093	0.093	0.000	0.000	0.000	0.000
50	A	76	GLN	0	0.009	0.009	69.185	0.058	0.058	0.000	0.000	0.000	0.000
51	A	77	PHE	0	-0.022	-0.008	69.864	0.105	0.105	0.000	0.000	0.000	0.000
52	A	78	GLU	-1	-0.893	-0.945	70.650	-4.551	-4.551	0.000	0.000	0.000	0.000
53	A	79	THR	0	-0.032	-0.027	72.487	0.107	0.107	0.000	0.000	0.000	0.000
54	A	80	SER	0	-0.090	-0.058	74.770	0.104	0.104	0.000	0.000	0.000	0.000
55	A	81	ALA	0	0.015	0.005	74.787	0.075	0.075	0.000	0.000	0.000	0.000
56	A	82	ALA	0	-0.009	-0.005	76.503	0.064	0.064	0.000	0.000	0.000	0.000
57	A	83	LYS	1	0.904	0.945	78.239	4.194	4.194	0.000	0.000	0.000	0.000
58	A	84	LEU	0	-0.002	-0.003	78.659	0.064	0.064	0.000	0.000	0.000	0.000
59	A	85	LYS	1	0.956	0.983	78.425	4.189	4.189	0.000	0.000	0.000	0.000
60	A	86	ARG	1	0.923	0.962	80.321	4.073	4.073	0.000	0.000	0.000	0.000
61	A	87	LYS	1	0.912	0.970	84.224	3.803	3.803	0.000	0.000	0.000	0.000
62	A	88	TYR	0	-0.048	-0.040	83.788	0.058	0.058	0.000	0.000	0.000	0.000
63	A	89	TRP	-1	-0.911	-0.928	82.598	-3.806	-3.806	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:27:GLY)