FMO DATABASE

FMODB ID: Z7K2N

Calculation Name: 1N7S-C-Xray547

Preferred Name: Synaptosomal-associated protein 25

Target Type: SINGLE PROTEIN

Ligand Name: (4s)-2-methyl-2,4-pentanediol | calcium ion

Ligand 3-letter code: MPD | CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1N7S

Chain ID: C

ChEMBL ID: CHEMBL1075243

UniProt ID: P60881

Base Structure: X-ray

Registration Date: 2025-10-03

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	79
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-359923.77984
FMO2-HF: Nuclear repulsion	326383.416392
FMO2-HF: Total energy	-33540.363448
FMO2-MP2: Total energy	-33633.418901

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:5:GLY)

Summations of interaction energy for fragment #1(A:5: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.
-17.12	-15.294	0.005	-0.693	-1.137	-0.003

Interaction energy analysis for fragmet #1(A:5:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.895 / q_NPA : 0.932

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	7	MET	0	0.067	0.038	3.680	5.471	6.591	-0.001	-0.472	-0.647	-0.002
4	A	8	ARG	1	0.908	0.966	3.367	50.123	50.701	0.007	-0.211	-0.374	-0.001
5	A	9	ASN	0	0.000	-0.007	5.031	4.350	4.478	-0.001	-0.010	-0.116	0.000
6	A	10	GLU	-1	-0.815	-0.903	8.258	-24.612	-24.612	0.000	0.000	0.000	0.000
7	A	11	LEU	0	-0.025	-0.027	5.854	1.943	1.943	0.000	0.000	0.000	0.000
8	A	12	GLU	-1	-0.858	-0.911	9.192	-22.080	-22.080	0.000	0.000	0.000	0.000
9	A	13	GLU	-1	-0.962	-0.983	10.974	-21.372	-21.372	0.000	0.000	0.000	0.000
10	A	14	MET	0	-0.062	-0.029	11.451	1.552	1.552	0.000	0.000	0.000	0.000
11	A	15	GLN	0	-0.057	-0.028	13.139	0.779	0.779	0.000	0.000	0.000	0.000
12	A	16	ARG	1	0.926	0.944	13.499	23.518	23.518	0.000	0.000	0.000	0.000
13	A	17	ARG	1	0.899	0.965	16.797	15.434	15.434	0.000	0.000	0.000	0.000
14	A	18	ALA	0	0.006	-0.002	17.876	1.043	1.043	0.000	0.000	0.000	0.000
15	A	19	ASP	-1	-0.851	-0.919	18.256	-16.163	-16.163	0.000	0.000	0.000	0.000
16	A	20	GLN	0	-0.072	-0.049	20.846	0.453	0.453	0.000	0.000	0.000	0.000
17	A	21	LEU	0	-0.026	-0.013	21.859	0.698	0.698	0.000	0.000	0.000	0.000
18	A	22	ALA	0	-0.010	0.012	23.739	0.678	0.678	0.000	0.000	0.000	0.000
19	A	23	ASP	-1	-0.898	-0.951	25.229	-10.992	-10.992	0.000	0.000	0.000	0.000
20	A	24	GLU	-1	-0.831	-0.909	26.395	-11.784	-11.784	0.000	0.000	0.000	0.000
21	A	25	SER	0	-0.060	-0.045	27.985	0.607	0.607	0.000	0.000	0.000	0.000
22	A	26	LEU	0	-0.030	-0.006	29.602	0.519	0.519	0.000	0.000	0.000	0.000
23	A	27	GLU	-1	-0.896	-0.963	30.752	-9.865	-9.865	0.000	0.000	0.000	0.000
24	A	28	SER	0	-0.031	-0.014	32.701	0.482	0.482	0.000	0.000	0.000	0.000
25	A	29	THR	0	-0.036	-0.031	33.984	0.349	0.349	0.000	0.000	0.000	0.000
26	A	30	ARG	1	0.958	0.980	31.826	10.064	10.064	0.000	0.000	0.000	0.000
27	A	31	ARG	1	0.945	0.978	33.003	9.668	9.668	0.000	0.000	0.000	0.000
28	A	32	MET	0	-0.037	-0.013	36.407	0.232	0.232	0.000	0.000	0.000	0.000
29	A	33	LEU	0	0.008	0.003	39.292	0.225	0.225	0.000	0.000	0.000	0.000
30	A	34	GLN	0	0.005	0.006	41.867	0.070	0.070	0.000	0.000	0.000	0.000
31	A	35	LEU	0	0.031	0.017	41.812	0.189	0.189	0.000	0.000	0.000	0.000
32	A	36	VAL	0	-0.023	-0.004	44.444	0.192	0.192	0.000	0.000	0.000	0.000
33	A	37	GLU	-1	-0.880	-0.931	46.355	-6.522	-6.522	0.000	0.000	0.000	0.000
34	A	38	GLU	-1	-0.934	-0.960	47.953	-6.485	-6.485	0.000	0.000	0.000	0.000
35	A	39	SER	0	-0.035	-0.036	48.405	0.172	0.172	0.000	0.000	0.000	0.000
36	A	40	LYS	1	0.844	0.931	50.402	6.502	6.502	0.000	0.000	0.000	0.000
37	A	41	ASP	-1	-0.883	-0.946	52.371	-6.020	-6.020	0.000	0.000	0.000	0.000
38	A	42	ALA	0	-0.057	-0.034	53.668	0.148	0.148	0.000	0.000	0.000	0.000
39	A	43	GLY	0	0.009	0.019	54.919	0.127	0.127	0.000	0.000	0.000	0.000
40	A	44	ILE	0	-0.001	-0.008	55.608	0.122	0.122	0.000	0.000	0.000	0.000
41	A	45	ARG	1	0.948	0.974	54.739	5.923	5.923	0.000	0.000	0.000	0.000
42	A	46	THR	0	-0.020	-0.021	58.631	0.107	0.107	0.000	0.000	0.000	0.000
43	A	47	LEU	0	-0.022	-0.017	59.810	0.087	0.087	0.000	0.000	0.000	0.000
44	A	48	VAL	0	0.009	0.008	62.707	0.083	0.083	0.000	0.000	0.000	0.000
45	A	49	MET	0	-0.018	-0.003	61.896	0.074	0.074	0.000	0.000	0.000	0.000
46	A	50	LEU	0	-0.031	-0.023	63.453	0.075	0.075	0.000	0.000	0.000	0.000
47	A	51	ASP	-1	-0.956	-0.957	66.881	-4.664	-4.664	0.000	0.000	0.000	0.000
48	A	52	GLU	-1	-0.943	-0.969	68.788	-4.588	-4.588	0.000	0.000	0.000	0.000
49	A	53	GLN	0	-0.028	-0.035	67.612	0.028	0.028	0.000	0.000	0.000	0.000
50	A	54	GLY	0	-0.008	0.004	70.910	0.061	0.061	0.000	0.000	0.000	0.000
51	A	55	GLU	-1	-0.816	-0.911	72.593	-4.241	-4.241	0.000	0.000	0.000	0.000
52	A	56	GLN	0	-0.111	-0.061	73.002	0.044	0.044	0.000	0.000	0.000	0.000
53	A	57	LEU	0	-0.044	-0.023	72.715	0.065	0.065	0.000	0.000	0.000	0.000
54	A	58	ASP	-1	-0.858	-0.918	76.594	-4.214	-4.214	0.000	0.000	0.000	0.000
55	A	59	ARG	1	0.896	0.943	76.227	4.279	4.279	0.000	0.000	0.000	0.000
56	A	60	VAL	0	-0.061	-0.023	78.796	0.064	0.064	0.000	0.000	0.000	0.000
57	A	61	GLU	-1	-0.942	-0.965	80.416	-3.983	-3.983	0.000	0.000	0.000	0.000
58	A	62	GLU	-1	-0.936	-0.974	82.463	-3.865	-3.865	0.000	0.000	0.000	0.000
59	A	63	GLY	0	0.003	0.003	84.352	0.063	0.063	0.000	0.000	0.000	0.000
60	A	64	MET	0	-0.052	-0.034	83.795	0.064	0.064	0.000	0.000	0.000	0.000
61	A	65	ASN	0	-0.014	-0.013	85.208	0.077	0.077	0.000	0.000	0.000	0.000
62	A	66	HIS	0	-0.057	-0.028	88.458	0.028	0.028	0.000	0.000	0.000	0.000
63	A	67	ILE	0	-0.003	-0.007	87.971	0.055	0.055	0.000	0.000	0.000	0.000
64	A	68	ASN	0	-0.030	-0.018	90.501	0.067	0.067	0.000	0.000	0.000	0.000
65	A	69	GLN	0	-0.060	-0.022	92.282	0.048	0.048	0.000	0.000	0.000	0.000
66	A	70	ASP	-1	-0.827	-0.912	94.583	-3.402	-3.402	0.000	0.000	0.000	0.000
67	A	71	MET	0	-0.016	-0.017	94.007	0.047	0.047	0.000	0.000	0.000	0.000
68	A	72	LYS	1	0.918	0.967	95.829	3.430	3.430	0.000	0.000	0.000	0.000
69	A	73	GLU	-1	-0.823	-0.901	98.708	-3.131	-3.131	0.000	0.000	0.000	0.000
70	A	74	ALA	0	-0.015	-0.009	99.306	0.040	0.040	0.000	0.000	0.000	0.000
71	A	75	GLU	-1	-0.831	-0.894	99.954	-3.189	-3.189	0.000	0.000	0.000	0.000
72	A	76	LYS	1	0.822	0.908	101.894	3.154	3.154	0.000	0.000	0.000	0.000
73	A	77	ASN	0	0.017	-0.006	104.274	0.054	0.054	0.000	0.000	0.000	0.000
74	A	78	LEU	0	-0.028	-0.007	101.912	0.029	0.029	0.000	0.000	0.000	0.000
75	A	79	LYS	1	0.785	0.865	103.084	3.199	3.199	0.000	0.000	0.000	0.000
76	A	80	ASP	-1	-0.963	-0.971	107.820	-2.926	-2.926	0.000	0.000	0.000	0.000
77	A	81	LEU	0	-0.050	-0.020	108.318	0.028	0.028	0.000	0.000	0.000	0.000
78	A	82	GLY	0	-0.020	-0.007	110.412	0.016	0.016	0.000	0.000	0.000	0.000
79	A	83	LYS	0	-0.054	-0.013	111.291	-0.021	-0.021	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:GLY)