FMO DATABASE

FMODB ID: 9LZY2

Calculation Name: 1N7S-B-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: B

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	68
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-296615.442224
FMO2-HF: Nuclear repulsion	268141.084376
FMO2-HF: Total energy	-28474.357848
FMO2-MP2: Total energy	-28553.937374

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:189:GLY)

Summations of interaction energy for fragment #1(A:189: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.
-62.551	-61.937	-0.003	-0.276	-0.335	-0.001

Interaction energy analysis for fragmet #1(A:189:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.846 / q_NPA : 0.904

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

Sort

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	191	ALA	0	0.016	0.021	3.862	-0.538	0.076	-0.003	-0.276	-0.335	-0.001
4	A	192	LEU	0	0.051	0.007	5.790	3.039	3.039	0.000	0.000	0.000	0.000
5	A	193	SER	0	0.087	0.050	9.050	1.537	1.537	0.000	0.000	0.000	0.000
6	A	194	GLU	-1	-0.891	-0.937	5.883	-44.394	-44.394	0.000	0.000	0.000	0.000
7	A	195	ILE	0	-0.035	-0.018	6.994	2.494	2.494	0.000	0.000	0.000	0.000
8	A	196	GLU	-1	-0.934	-0.963	10.482	-18.458	-18.458	0.000	0.000	0.000	0.000
9	A	197	THR	0	-0.008	-0.019	13.097	2.220	2.220	0.000	0.000	0.000	0.000
10	A	198	ARG	1	0.942	0.965	11.664	24.421	24.421	0.000	0.000	0.000	0.000
11	A	199	HIS	0	0.012	0.007	14.259	0.673	0.673	0.000	0.000	0.000	0.000
12	A	200	SER	0	0.010	0.005	16.433	1.536	1.536	0.000	0.000	0.000	0.000
13	A	201	GLU	-1	-0.842	-0.914	17.587	-14.718	-14.718	0.000	0.000	0.000	0.000
14	A	202	ILE	0	-0.026	-0.007	15.999	0.673	0.673	0.000	0.000	0.000	0.000
15	A	203	ILE	0	0.019	0.012	19.792	0.802	0.802	0.000	0.000	0.000	0.000
16	A	204	LYS	1	0.834	0.906	21.150	15.393	15.393	0.000	0.000	0.000	0.000
17	A	205	LEU	0	0.004	0.018	21.740	0.604	0.604	0.000	0.000	0.000	0.000
18	A	206	GLU	-1	-0.842	-0.909	23.883	-12.167	-12.167	0.000	0.000	0.000	0.000
19	A	207	ASN	0	-0.019	-0.022	25.703	0.709	0.709	0.000	0.000	0.000	0.000
20	A	208	SER	0	0.017	0.004	27.231	0.479	0.479	0.000	0.000	0.000	0.000
21	A	209	ILE	0	-0.044	-0.023	25.828	0.352	0.352	0.000	0.000	0.000	0.000
22	A	210	ARG	1	0.811	0.890	28.212	11.429	11.429	0.000	0.000	0.000	0.000
23	A	211	GLU	-1	-0.892	-0.939	31.857	-9.334	-9.334	0.000	0.000	0.000	0.000
24	A	212	LEU	0	-0.022	-0.018	31.978	0.293	0.293	0.000	0.000	0.000	0.000
25	A	213	HIS	0	-0.081	-0.056	33.534	0.279	0.279	0.000	0.000	0.000	0.000
26	A	214	ASP	-1	-0.859	-0.919	35.197	-8.738	-8.738	0.000	0.000	0.000	0.000
27	A	215	MET	0	-0.002	0.003	36.052	0.323	0.323	0.000	0.000	0.000	0.000
28	A	216	PHE	0	-0.048	-0.026	35.747	0.243	0.243	0.000	0.000	0.000	0.000
29	A	217	MET	0	-0.037	-0.011	38.762	0.216	0.216	0.000	0.000	0.000	0.000
30	A	218	ASP	-1	-0.874	-0.936	41.345	-7.387	-7.387	0.000	0.000	0.000	0.000
31	A	219	MET	0	-0.061	-0.030	42.739	0.286	0.286	0.000	0.000	0.000	0.000
32	A	220	ALA	0	-0.023	-0.013	43.592	0.191	0.191	0.000	0.000	0.000	0.000
33	A	221	MET	0	0.020	0.015	45.358	0.205	0.205	0.000	0.000	0.000	0.000
34	A	222	LEU	0	-0.036	-0.017	46.668	0.197	0.197	0.000	0.000	0.000	0.000
35	A	223	VAL	0	-0.019	-0.018	47.798	0.179	0.179	0.000	0.000	0.000	0.000
36	A	224	GLU	-1	-0.960	-0.969	49.062	-6.435	-6.435	0.000	0.000	0.000	0.000
37	A	225	SER	0	-0.004	0.004	51.244	0.166	0.166	0.000	0.000	0.000	0.000
38	A	226	GLN	0	-0.038	-0.051	51.863	0.084	0.084	0.000	0.000	0.000	0.000
39	A	227	GLY	0	0.040	0.028	54.099	0.118	0.118	0.000	0.000	0.000	0.000
40	A	228	GLU	-1	-0.879	-0.936	55.596	-5.671	-5.671	0.000	0.000	0.000	0.000
41	A	229	MET	0	-0.139	-0.067	55.943	0.161	0.161	0.000	0.000	0.000	0.000
42	A	230	ILE	0	0.010	0.003	56.103	0.125	0.125	0.000	0.000	0.000	0.000
43	A	231	ASP	-1	-0.846	-0.912	59.277	-5.431	-5.431	0.000	0.000	0.000	0.000
44	A	232	ARG	1	0.882	0.934	60.244	5.464	5.464	0.000	0.000	0.000	0.000
45	A	233	ILE	0	-0.038	-0.011	61.362	0.119	0.119	0.000	0.000	0.000	0.000
46	A	234	GLU	-1	-0.913	-0.953	63.128	-5.089	-5.089	0.000	0.000	0.000	0.000
47	A	235	TYR	0	0.025	0.018	65.208	0.122	0.122	0.000	0.000	0.000	0.000
48	A	236	ASN	0	-0.060	-0.059	67.574	0.163	0.163	0.000	0.000	0.000	0.000
49	A	237	VAL	0	-0.023	-0.002	67.403	0.095	0.095	0.000	0.000	0.000	0.000
50	A	238	GLU	-1	-0.907	-0.957	67.891	-4.661	-4.661	0.000	0.000	0.000	0.000
51	A	239	HIS	1	0.843	0.916	70.731	4.580	4.580	0.000	0.000	0.000	0.000
52	A	240	ALA	0	-0.006	0.004	72.938	0.078	0.078	0.000	0.000	0.000	0.000
53	A	241	VAL	0	0.011	0.009	72.343	0.075	0.075	0.000	0.000	0.000	0.000
54	A	242	ASP	-1	-0.762	-0.855	75.191	-4.082	-4.082	0.000	0.000	0.000	0.000
55	A	243	TYR	0	-0.025	-0.021	75.962	0.065	0.065	0.000	0.000	0.000	0.000
56	A	244	VAL	0	-0.007	0.000	77.679	0.074	0.074	0.000	0.000	0.000	0.000
57	A	245	GLU	-1	-0.951	-0.966	78.991	-4.079	-4.079	0.000	0.000	0.000	0.000
58	A	246	ARG	1	0.830	0.892	80.093	4.103	4.103	0.000	0.000	0.000	0.000
59	A	247	ALA	0	0.057	0.046	82.988	0.064	0.064	0.000	0.000	0.000	0.000
60	A	248	VAL	0	-0.008	-0.002	82.543	0.065	0.065	0.000	0.000	0.000	0.000
61	A	249	SER	0	-0.090	-0.058	85.064	0.063	0.063	0.000	0.000	0.000	0.000
62	A	250	ASP	-1	-0.823	-0.912	86.921	-3.637	-3.637	0.000	0.000	0.000	0.000
63	A	251	THR	0	-0.030	-0.027	87.344	0.052	0.052	0.000	0.000	0.000	0.000
64	A	252	LYS	1	0.910	0.948	87.030	3.743	3.743	0.000	0.000	0.000	0.000
65	A	253	LYS	1	0.814	0.897	89.644	3.667	3.667	0.000	0.000	0.000	0.000
66	A	254	ALA	0	0.006	0.008	92.972	0.038	0.038	0.000	0.000	0.000	0.000
67	A	255	VAL	0	-0.081	-0.030	93.284	0.026	0.026	0.000	0.000	0.000	0.000
68	A	256	LYS	0	-0.005	0.022	93.472	0.185	0.185	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:189:GLY)