FMO DATABASE

FMODB ID: 4QVNN

Calculation Name: 1QB2-A-Xray547

Preferred Name: Signal recognition particle 54 kDa protein

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1QB2

Chain ID: A

ChEMBL ID: CHEMBL4295786

UniProt ID: P61011

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	106
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-759561.658074
FMO2-HF: Nuclear repulsion	715267.931396
FMO2-HF: Total energy	-44293.726678
FMO2-MP2: Total energy	-44415.73106

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:326:GLN)

Summations of interaction energy for fragment #1(A:326:GLN)

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.
-16.923	-15.071	-0.018	-0.813	-1.022	-0.003

Interaction energy analysis for fragmet #1(A:326:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.828 / q_NPA : 0.898

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	328	THR	0	-0.038	-0.033	3.840	5.940	7.792	-0.018	-0.813	-1.022	-0.003
4	A	329	LEU	0	0.060	0.011	5.778	2.376	2.376	0.000	0.000	0.000	0.000
5	A	330	ARG	1	0.942	0.988	8.698	26.956	26.956	0.000	0.000	0.000	0.000
6	A	331	ASP	-1	-0.722	-0.843	5.352	-50.547	-50.547	0.000	0.000	0.000	0.000
7	A	332	MET	0	-0.020	-0.011	8.952	2.071	2.071	0.000	0.000	0.000	0.000
8	A	333	TYR	0	-0.011	0.006	11.170	2.383	2.383	0.000	0.000	0.000	0.000
9	A	334	GLU	-1	-0.882	-0.955	11.516	-25.405	-25.405	0.000	0.000	0.000	0.000
10	A	335	GLN	0	-0.054	-0.028	10.470	2.759	2.759	0.000	0.000	0.000	0.000
11	A	336	PHE	0	0.010	-0.001	13.954	1.507	1.507	0.000	0.000	0.000	0.000
12	A	337	GLN	0	0.021	0.010	16.924	0.619	0.619	0.000	0.000	0.000	0.000
13	A	338	ASN	0	-0.014	-0.009	14.545	2.332	2.332	0.000	0.000	0.000	0.000
14	A	339	ILE	0	0.017	0.008	15.864	0.848	0.848	0.000	0.000	0.000	0.000
15	A	340	MET	0	-0.027	-0.021	19.504	0.749	0.749	0.000	0.000	0.000	0.000
16	A	341	LYS	1	0.893	0.953	19.155	17.014	17.014	0.000	0.000	0.000	0.000
17	A	342	MET	0	0.007	0.001	20.825	0.549	0.549	0.000	0.000	0.000	0.000
18	A	343	GLY	0	0.043	0.044	23.373	0.368	0.368	0.000	0.000	0.000	0.000
19	A	344	PRO	0	0.003	-0.008	25.385	0.391	0.391	0.000	0.000	0.000	0.000
20	A	345	PHE	0	0.027	0.017	26.255	0.306	0.306	0.000	0.000	0.000	0.000
21	A	346	SER	0	0.008	-0.016	24.793	0.220	0.220	0.000	0.000	0.000	0.000
22	A	347	GLN	0	-0.009	-0.006	27.369	0.132	0.132	0.000	0.000	0.000	0.000
23	A	348	ILE	0	0.007	0.007	30.322	0.351	0.351	0.000	0.000	0.000	0.000
24	A	349	LEU	0	-0.017	-0.008	27.597	0.279	0.279	0.000	0.000	0.000	0.000
25	A	350	GLY	0	0.002	0.006	30.960	0.242	0.242	0.000	0.000	0.000	0.000
26	A	351	MET	0	-0.041	-0.009	32.260	0.354	0.354	0.000	0.000	0.000	0.000
27	A	352	ILE	0	-0.044	-0.004	34.127	0.390	0.390	0.000	0.000	0.000	0.000
28	A	353	PRO	0	-0.026	-0.028	35.804	-0.134	-0.134	0.000	0.000	0.000	0.000
29	A	354	GLY	0	0.040	0.020	36.299	-0.013	-0.013	0.000	0.000	0.000	0.000
30	A	355	PHE	0	0.028	0.015	30.150	-0.163	-0.163	0.000	0.000	0.000	0.000
31	A	356	GLY	0	-0.029	-0.021	31.459	-0.250	-0.250	0.000	0.000	0.000	0.000
32	A	357	THR	0	-0.014	-0.039	32.409	-0.126	-0.126	0.000	0.000	0.000	0.000
33	A	358	ASP	-1	-0.852	-0.889	29.692	-10.156	-10.156	0.000	0.000	0.000	0.000
34	A	359	PHE	0	-0.005	0.003	26.115	-0.560	-0.560	0.000	0.000	0.000	0.000
35	A	360	MET	0	-0.049	-0.033	21.284	-0.245	-0.245	0.000	0.000	0.000	0.000
36	A	361	SER	0	-0.039	-0.011	24.176	-0.350	-0.350	0.000	0.000	0.000	0.000
37	A	362	LYS	1	0.947	0.953	22.608	12.277	12.277	0.000	0.000	0.000	0.000
38	A	363	GLY	0	-0.055	-0.032	22.920	0.535	0.535	0.000	0.000	0.000	0.000
39	A	364	ASN	0	0.021	0.034	24.257	0.456	0.456	0.000	0.000	0.000	0.000
40	A	365	GLU	-1	-0.778	-0.893	20.184	-14.645	-14.645	0.000	0.000	0.000	0.000
41	A	366	GLN	0	-0.020	-0.004	18.378	-0.158	-0.158	0.000	0.000	0.000	0.000
42	A	367	GLU	-1	-0.835	-0.930	22.297	-12.258	-12.258	0.000	0.000	0.000	0.000
43	A	368	SER	0	-0.010	-0.018	24.143	0.528	0.528	0.000	0.000	0.000	0.000
44	A	369	MET	0	-0.012	-0.012	18.044	-0.162	-0.162	0.000	0.000	0.000	0.000
45	A	370	ALA	0	-0.022	-0.001	23.052	0.183	0.183	0.000	0.000	0.000	0.000
46	A	371	ARG	1	0.840	0.918	25.615	10.552	10.552	0.000	0.000	0.000	0.000
47	A	372	LEU	0	0.017	0.018	23.577	0.299	0.299	0.000	0.000	0.000	0.000
48	A	373	LYS	1	0.975	0.989	23.321	12.826	12.826	0.000	0.000	0.000	0.000
49	A	374	LYS	1	0.894	0.956	25.795	9.559	9.559	0.000	0.000	0.000	0.000
50	A	375	LEU	0	0.030	0.013	29.519	0.270	0.270	0.000	0.000	0.000	0.000
51	A	376	MET	0	0.005	-0.005	22.960	0.085	0.085	0.000	0.000	0.000	0.000
52	A	377	THR	0	-0.023	-0.017	27.696	0.154	0.154	0.000	0.000	0.000	0.000
53	A	378	ILE	0	-0.043	-0.025	30.005	0.355	0.355	0.000	0.000	0.000	0.000
54	A	379	MET	0	-0.010	-0.024	30.528	0.220	0.220	0.000	0.000	0.000	0.000
55	A	380	ASP	-1	-0.866	-0.928	28.134	-11.269	-11.269	0.000	0.000	0.000	0.000
56	A	381	SER	0	-0.041	-0.012	31.156	0.230	0.230	0.000	0.000	0.000	0.000
57	A	382	MET	0	-0.103	-0.036	34.454	0.407	0.407	0.000	0.000	0.000	0.000
58	A	383	ASN	0	-0.018	-0.019	35.404	-0.058	-0.058	0.000	0.000	0.000	0.000
59	A	384	ASP	-1	-0.780	-0.894	35.113	-9.055	-9.055	0.000	0.000	0.000	0.000
60	A	385	GLN	0	-0.004	0.018	36.526	0.060	0.060	0.000	0.000	0.000	0.000
61	A	386	GLU	-1	-0.783	-0.862	38.262	-7.861	-7.861	0.000	0.000	0.000	0.000
62	A	387	LEU	0	-0.035	-0.012	32.264	-0.010	-0.010	0.000	0.000	0.000	0.000
63	A	388	ASP	-1	-0.874	-0.934	33.920	-9.533	-9.533	0.000	0.000	0.000	0.000
64	A	389	SER	0	-0.120	-0.062	36.306	0.220	0.220	0.000	0.000	0.000	0.000
65	A	390	THR	0	-0.003	-0.018	38.663	-0.148	-0.148	0.000	0.000	0.000	0.000
66	A	391	ASP	-1	-0.824	-0.923	40.183	-7.555	-7.555	0.000	0.000	0.000	0.000
67	A	392	GLY	0	0.085	0.050	39.211	0.154	0.154	0.000	0.000	0.000	0.000
68	A	393	ALA	0	0.003	0.002	40.228	0.107	0.107	0.000	0.000	0.000	0.000
69	A	394	LYS	1	0.917	0.947	42.588	6.954	6.954	0.000	0.000	0.000	0.000
70	A	395	VAL	0	-0.042	-0.001	42.046	0.205	0.205	0.000	0.000	0.000	0.000
71	A	396	PHE	0	0.033	-0.004	39.137	0.191	0.191	0.000	0.000	0.000	0.000
72	A	397	SER	0	-0.021	-0.018	44.699	0.115	0.115	0.000	0.000	0.000	0.000
73	A	398	LYS	1	0.926	0.973	47.855	6.786	6.786	0.000	0.000	0.000	0.000
74	A	399	GLN	0	0.013	0.021	47.373	0.046	0.046	0.000	0.000	0.000	0.000
75	A	400	PRO	0	0.094	0.047	47.146	-0.145	-0.145	0.000	0.000	0.000	0.000
76	A	401	GLY	0	-0.002	0.003	46.791	-0.096	-0.096	0.000	0.000	0.000	0.000
77	A	402	ARG	1	0.770	0.853	42.725	7.241	7.241	0.000	0.000	0.000	0.000
78	A	403	ILE	0	0.043	0.027	42.306	-0.179	-0.179	0.000	0.000	0.000	0.000
79	A	404	GLN	0	0.000	-0.007	42.254	-0.128	-0.128	0.000	0.000	0.000	0.000
80	A	405	ARG	1	0.716	0.825	38.616	7.975	7.975	0.000	0.000	0.000	0.000
81	A	406	VAL	0	0.031	0.018	36.899	-0.097	-0.097	0.000	0.000	0.000	0.000
82	A	407	ALA	0	-0.016	0.007	38.132	-0.200	-0.200	0.000	0.000	0.000	0.000
83	A	408	ARG	1	0.910	0.944	39.156	7.167	7.167	0.000	0.000	0.000	0.000
84	A	409	GLY	0	-0.032	0.001	37.791	-0.011	-0.011	0.000	0.000	0.000	0.000
85	A	410	SER	0	0.021	0.000	34.190	-0.168	-0.168	0.000	0.000	0.000	0.000
86	A	411	GLY	0	-0.037	-0.005	34.837	-0.175	-0.175	0.000	0.000	0.000	0.000
87	A	412	VAL	0	-0.043	-0.008	35.517	0.004	0.004	0.000	0.000	0.000	0.000
88	A	413	SER	0	-0.012	-0.043	37.947	0.312	0.312	0.000	0.000	0.000	0.000
89	A	414	THR	0	0.047	-0.005	40.413	-0.147	-0.147	0.000	0.000	0.000	0.000
90	A	415	ARG	1	0.962	0.983	40.954	7.634	7.634	0.000	0.000	0.000	0.000
91	A	416	ASP	-1	-0.769	-0.852	36.852	-8.502	-8.502	0.000	0.000	0.000	0.000
92	A	417	VAL	0	0.019	0.014	37.857	-0.152	-0.152	0.000	0.000	0.000	0.000
93	A	418	GLN	0	-0.011	-0.008	39.195	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	419	GLU	-1	-0.952	-0.951	36.052	-8.854	-8.854	0.000	0.000	0.000	0.000
95	A	420	LEU	0	0.073	0.048	33.093	0.006	0.006	0.000	0.000	0.000	0.000
96	A	421	LEU	0	0.013	0.009	36.703	-0.046	-0.046	0.000	0.000	0.000	0.000
97	A	422	THR	0	-0.065	-0.041	39.436	0.153	0.153	0.000	0.000	0.000	0.000
98	A	423	GLN	0	-0.085	-0.052	34.831	-0.085	-0.085	0.000	0.000	0.000	0.000
99	A	424	TYR	0	0.025	0.026	35.068	0.034	0.034	0.000	0.000	0.000	0.000
100	A	425	THR	0	-0.025	-0.028	36.642	0.029	0.029	0.000	0.000	0.000	0.000
101	A	426	LYS	1	0.872	0.937	37.965	8.021	8.021	0.000	0.000	0.000	0.000
102	A	427	PHE	0	0.038	0.007	30.698	0.016	0.016	0.000	0.000	0.000	0.000
103	A	428	ALA	0	0.009	0.002	36.149	-0.035	-0.035	0.000	0.000	0.000	0.000
104	A	429	GLN	0	-0.074	-0.042	37.736	0.069	0.069	0.000	0.000	0.000	0.000
105	A	430	MET	0	-0.090	-0.038	36.631	0.171	0.171	0.000	0.000	0.000	0.000
106	A	431	VAL	-1	-0.954	-0.944	33.216	-8.980	-8.980	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:326:GLN)