FMO DATABASE

FMODB ID: V5V11

Calculation Name: 1QB2-A-Xray372

Preferred Name: Signal recognition particle 54 kDa protein

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1QB2

Chain ID: A

ChEMBL ID: CHEMBL4295786

UniProt ID: P61011

Base Structure: X-ray

Registration Date: 2023-06-22

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	OptH
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	106
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-757994.142141
FMO2-HF: Nuclear repulsion	713700.857449
FMO2-HF: Total energy	-44293.284692
FMO2-MP2: Total energy	-44415.399114

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: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.
-1.769	-0.128	-0.018	-0.638	-0.985	0

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 : 0 / q_Mulliken : -0.038 / q_NPA : -0.042

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].
3	A	328	THR	0	0.001	0.007	3.821	-0.026	1.615	-0.018	-0.638	-0.985
4	A	329	LEU	0	0.061	0.005	5.649	-0.142	-0.142	0.000	0.000	0.000
5	A	330	ARG	1	0.929	0.974	8.771	-0.833	-0.833	0.000	0.000	0.000
6	A	331	ASP	-1	-0.755	-0.879	5.339	-0.961	-0.961	0.000	0.000	0.000
7	A	332	MET	0	-0.041	-0.024	8.940	-0.009	-0.009	0.000	0.000	0.000
8	A	333	TYR	0	-0.058	-0.024	10.880	-0.005	-0.005	0.000	0.000	0.000
9	A	334	GLU	-1	-0.884	-0.962	10.801	0.312	0.312	0.000	0.000	0.000
10	A	335	GLN	0	-0.030	-0.011	9.939	0.021	0.021	0.000	0.000	0.000
11	A	336	PHE	0	0.018	-0.001	13.343	0.001	0.001	0.000	0.000	0.000
12	A	337	GLN	0	-0.004	0.007	16.350	-0.001	-0.001	0.000	0.000	0.000
13	A	338	ASN	0	-0.037	-0.026	14.344	-0.002	-0.002	0.000	0.000	0.000
14	A	339	ILE	0	0.019	0.009	15.616	-0.008	-0.008	0.000	0.000	0.000
15	A	340	MET	0	-0.019	-0.005	18.977	-0.004	-0.004	0.000	0.000	0.000
16	A	341	LYS	1	0.932	0.975	19.620	-0.107	-0.107	0.000	0.000	0.000
17	A	342	MET	0	-0.015	-0.011	20.664	-0.007	-0.007	0.000	0.000	0.000
18	A	343	GLY	0	0.058	0.043	23.179	-0.004	-0.004	0.000	0.000	0.000
19	A	344	PRO	0	-0.003	-0.014	25.194	-0.005	-0.005	0.000	0.000	0.000
20	A	345	PHE	0	0.016	0.004	26.110	-0.004	-0.004	0.000	0.000	0.000
21	A	346	SER	0	0.023	-0.002	24.414	-0.005	-0.005	0.000	0.000	0.000
22	A	347	GLN	0	-0.007	0.004	27.161	0.000	0.000	0.000	0.000	0.000
23	A	348	ILE	0	-0.004	-0.009	30.165	-0.004	-0.004	0.000	0.000	0.000
24	A	349	LEU	0	-0.014	-0.009	27.475	-0.003	-0.003	0.000	0.000	0.000
25	A	350	GLY	0	0.010	0.019	31.134	-0.003	-0.003	0.000	0.000	0.000
26	A	351	MET	0	-0.059	-0.020	32.380	-0.003	-0.003	0.000	0.000	0.000
27	A	352	ILE	0	-0.082	-0.012	34.135	-0.004	-0.004	0.000	0.000	0.000
28	A	353	PRO	0	0.010	-0.011	35.653	0.000	0.000	0.000	0.000	0.000
29	A	354	GLY	0	0.031	0.007	36.425	-0.001	-0.001	0.000	0.000	0.000
30	A	355	PHE	0	0.046	0.033	30.178	-0.001	-0.001	0.000	0.000	0.000
31	A	356	GLY	0	-0.035	-0.019	31.216	0.002	0.002	0.000	0.000	0.000
32	A	357	THR	0	-0.006	-0.010	32.489	0.001	0.001	0.000	0.000	0.000
33	A	358	ASP	-1	-0.889	-0.927	29.684	0.064	0.064	0.000	0.000	0.000
34	A	359	PHE	0	-0.027	-0.024	25.963	0.004	0.004	0.000	0.000	0.000
35	A	360	MET	0	-0.047	-0.028	21.143	0.005	0.005	0.000	0.000	0.000
36	A	361	SER	0	-0.029	0.009	23.927	0.007	0.007	0.000	0.000	0.000
37	A	362	LYS	1	1.011	0.979	23.252	-0.101	-0.101	0.000	0.000	0.000
38	A	363	GLY	0	-0.083	-0.026	23.358	-0.007	-0.007	0.000	0.000	0.000
39	A	364	ASN	0	0.027	0.015	24.985	-0.007	-0.007	0.000	0.000	0.000
40	A	365	GLU	-1	-0.810	-0.910	19.947	0.119	0.119	0.000	0.000	0.000
41	A	366	GLN	0	0.008	-0.008	18.660	-0.012	-0.012	0.000	0.000	0.000
42	A	367	GLU	-1	-0.871	-0.928	22.598	0.066	0.066	0.000	0.000	0.000
43	A	368	SER	0	-0.012	-0.032	24.517	-0.009	-0.009	0.000	0.000	0.000
44	A	369	MET	0	-0.010	-0.005	18.461	-0.004	-0.004	0.000	0.000	0.000
45	A	370	ALA	0	-0.011	0.007	23.390	-0.008	-0.008	0.000	0.000	0.000
46	A	371	ARG	1	0.872	0.926	25.754	-0.050	-0.050	0.000	0.000	0.000
47	A	372	LEU	0	0.029	0.013	23.666	-0.005	-0.005	0.000	0.000	0.000
48	A	373	LYS	1	0.989	1.003	23.031	-0.020	-0.020	0.000	0.000	0.000
49	A	374	LYS	1	0.927	0.981	25.757	-0.025	-0.025	0.000	0.000	0.000
50	A	375	LEU	0	0.027	0.007	29.403	-0.004	-0.004	0.000	0.000	0.000
51	A	376	MET	0	-0.002	-0.005	22.799	0.000	0.000	0.000	0.000	0.000
52	A	377	THR	0	-0.030	-0.011	27.508	-0.003	-0.003	0.000	0.000	0.000
53	A	378	ILE	0	-0.043	-0.023	29.633	-0.003	-0.003	0.000	0.000	0.000
54	A	379	MET	0	-0.040	-0.047	30.339	-0.001	-0.001	0.000	0.000	0.000
55	A	380	ASP	-1	-0.838	-0.902	28.049	0.008	0.008	0.000	0.000	0.000
56	A	381	SER	0	-0.071	-0.034	31.128	-0.004	-0.004	0.000	0.000	0.000
57	A	382	MET	0	-0.099	-0.034	34.339	0.000	0.000	0.000	0.000	0.000
58	A	383	ASN	0	0.006	-0.004	35.169	0.000	0.000	0.000	0.000	0.000
59	A	384	ASP	-1	-0.781	-0.913	34.527	0.013	0.013	0.000	0.000	0.000
60	A	385	GLN	0	-0.010	0.022	36.481	0.001	0.001	0.000	0.000	0.000
61	A	386	GLU	-1	-0.800	-0.894	38.038	0.013	0.013	0.000	0.000	0.000
62	A	387	LEU	0	-0.022	-0.009	32.143	0.002	0.002	0.000	0.000	0.000
63	A	388	ASP	-1	-0.869	-0.931	34.091	0.027	0.027	0.000	0.000	0.000
64	A	389	SER	0	-0.118	-0.043	36.338	0.001	0.001	0.000	0.000	0.000
65	A	390	THR	0	-0.010	-0.016	38.505	0.001	0.001	0.000	0.000	0.000
66	A	391	ASP	-1	-0.850	-0.937	39.578	0.029	0.029	0.000	0.000	0.000
67	A	392	GLY	0	0.041	0.015	38.919	-0.002	-0.002	0.000	0.000	0.000
68	A	393	ALA	0	0.013	0.016	39.962	-0.002	-0.002	0.000	0.000	0.000
69	A	394	LYS	1	0.936	0.948	42.194	-0.024	-0.024	0.000	0.000	0.000
70	A	395	VAL	0	-0.024	0.003	41.997	-0.001	-0.001	0.000	0.000	0.000
71	A	396	PHE	0	0.038	-0.003	38.885	-0.002	-0.002	0.000	0.000	0.000
72	A	397	SER	0	-0.002	0.005	44.659	-0.001	-0.001	0.000	0.000	0.000
73	A	398	LYS	1	0.915	0.965	47.784	-0.019	-0.019	0.000	0.000	0.000
74	A	399	GLN	0	0.014	0.009	47.295	0.000	0.000	0.000	0.000	0.000
75	A	400	PRO	0	0.079	0.035	46.916	0.000	0.000	0.000	0.000	0.000
76	A	401	GLY	0	-0.013	0.003	46.996	0.000	0.000	0.000	0.000	0.000
77	A	402	ARG	1	0.753	0.861	42.562	-0.013	-0.013	0.000	0.000	0.000
78	A	403	ILE	0	0.056	0.034	42.209	-0.001	-0.001	0.000	0.000	0.000
79	A	404	GLN	0	0.003	-0.006	42.133	0.000	0.000	0.000	0.000	0.000
80	A	405	ARG	1	0.743	0.863	38.582	-0.009	-0.009	0.000	0.000	0.000
81	A	406	VAL	0	0.041	0.025	36.643	-0.001	-0.001	0.000	0.000	0.000
82	A	407	ALA	0	0.001	0.007	37.973	-0.001	-0.001	0.000	0.000	0.000
83	A	408	ARG	1	0.895	0.952	39.266	0.001	0.001	0.000	0.000	0.000
84	A	409	GLY	0	-0.037	-0.007	37.690	-0.002	-0.002	0.000	0.000	0.000
85	A	410	SER	0	0.004	0.000	33.960	-0.001	-0.001	0.000	0.000	0.000
86	A	411	GLY	0	-0.022	0.002	34.731	0.000	0.000	0.000	0.000	0.000
87	A	412	VAL	0	-0.041	-0.006	35.432	0.001	0.001	0.000	0.000	0.000
88	A	413	SER	0	-0.010	-0.013	37.758	-0.001	-0.001	0.000	0.000	0.000
89	A	414	THR	0	0.060	-0.005	40.132	0.001	0.001	0.000	0.000	0.000
90	A	415	ARG	1	0.961	0.984	41.495	-0.018	-0.018	0.000	0.000	0.000
91	A	416	ASP	-1	-0.797	-0.903	36.788	0.018	0.018	0.000	0.000	0.000
92	A	417	VAL	0	0.014	0.014	37.712	0.002	0.002	0.000	0.000	0.000
93	A	418	GLN	0	-0.019	-0.014	38.904	0.000	0.000	0.000	0.000	0.000
94	A	419	GLU	-1	-0.973	-0.983	36.112	0.030	0.030	0.000	0.000	0.000
95	A	420	LEU	0	0.084	0.053	33.144	0.002	0.002	0.000	0.000	0.000
96	A	421	LEU	0	0.002	-0.003	36.511	0.002	0.002	0.000	0.000	0.000
97	A	422	THR	0	-0.089	-0.052	38.972	0.001	0.001	0.000	0.000	0.000
98	A	423	GLN	0	-0.067	-0.041	35.082	0.001	0.001	0.000	0.000	0.000
99	A	424	TYR	0	0.035	0.022	34.855	0.001	0.001	0.000	0.000	0.000
100	A	425	THR	0	0.009	0.013	36.346	0.001	0.001	0.000	0.000	0.000
101	A	426	LYS	1	0.899	0.950	38.023	-0.032	-0.032	0.000	0.000	0.000
102	A	427	PHE	0	0.041	-0.002	30.486	0.001	0.001	0.000	0.000	0.000
103	A	428	ALA	0	0.000	0.000	35.978	0.002	0.002	0.000	0.000	0.000
104	A	429	GLN	0	-0.070	-0.039	37.155	0.001	0.001	0.000	0.000	0.000
105	A	430	MET	0	-0.051	-0.009	36.497	0.001	0.001	0.000	0.000	0.000
106	A	431	VAL	0	-0.041	0.007	32.918	0.003	0.003	0.000	0.000	0.000

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