FMO DATABASE

FMODB ID: 175GZ

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	OptHSide
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	-757302.922983
FMO2-HF: Nuclear repulsion	713009.019713
FMO2-HF: Total energy	-44293.90327
FMO2-MP2: Total energy	-44415.938645

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.
-2.583	-0.284	-0.022	-1.044	-1.233	0.004

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 : -0.014 / q_NPA : -0.013

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	-0.028	-0.054	3.821	0.041	2.340	-0.022	-1.044	-1.233	0.004
4	A	329	LEU	0	0.054	0.006	5.697	-0.381	-0.381	0.000	0.000	0.000	0.000
5	A	330	ARG	1	0.941	0.982	8.818	-0.690	-0.690	0.000	0.000	0.000	0.000
6	A	331	ASP	-1	-0.736	-0.830	5.330	-1.895	-1.895	0.000	0.000	0.000	0.000
7	A	332	MET	0	-0.025	-0.012	8.948	-0.079	-0.079	0.000	0.000	0.000	0.000
8	A	333	TYR	0	-0.037	-0.015	10.880	0.049	0.049	0.000	0.000	0.000	0.000
9	A	334	GLU	-1	-0.873	-0.958	11.330	-0.149	-0.149	0.000	0.000	0.000	0.000
10	A	335	GLN	0	-0.028	-0.007	10.261	0.096	0.096	0.000	0.000	0.000	0.000
11	A	336	PHE	0	0.016	-0.002	13.509	0.056	0.056	0.000	0.000	0.000	0.000
12	A	337	GLN	0	0.005	0.014	16.473	0.025	0.025	0.000	0.000	0.000	0.000
13	A	338	ASN	0	-0.042	-0.031	15.045	0.064	0.064	0.000	0.000	0.000	0.000
14	A	339	ILE	0	0.036	0.018	15.235	0.020	0.020	0.000	0.000	0.000	0.000
15	A	340	MET	0	-0.023	-0.008	19.003	0.031	0.031	0.000	0.000	0.000	0.000
16	A	341	LYS	1	0.884	0.950	19.128	0.264	0.264	0.000	0.000	0.000	0.000
17	A	342	MET	0	-0.005	-0.004	20.922	0.019	0.019	0.000	0.000	0.000	0.000
18	A	343	GLY	0	0.057	0.051	23.333	0.001	0.001	0.000	0.000	0.000	0.000
19	A	344	PRO	0	0.004	-0.015	25.198	0.005	0.005	0.000	0.000	0.000	0.000
20	A	345	PHE	0	0.011	0.003	26.194	0.005	0.005	0.000	0.000	0.000	0.000
21	A	346	SER	0	0.016	-0.018	24.556	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	347	GLN	0	-0.014	0.001	27.097	0.001	0.001	0.000	0.000	0.000	0.000
23	A	348	ILE	0	0.001	-0.003	30.046	0.006	0.006	0.000	0.000	0.000	0.000
24	A	349	LEU	0	-0.012	-0.007	27.524	0.005	0.005	0.000	0.000	0.000	0.000
25	A	350	GLY	0	0.014	0.019	30.973	0.002	0.002	0.000	0.000	0.000	0.000
26	A	351	MET	0	-0.056	-0.022	32.144	0.008	0.008	0.000	0.000	0.000	0.000
27	A	352	ILE	0	-0.073	-0.008	34.133	0.008	0.008	0.000	0.000	0.000	0.000
28	A	353	PRO	0	0.027	-0.001	35.449	-0.005	-0.005	0.000	0.000	0.000	0.000
29	A	354	GLY	0	0.036	0.012	36.157	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	355	PHE	0	0.024	0.015	30.044	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	356	GLY	0	-0.039	-0.018	30.880	-0.010	-0.010	0.000	0.000	0.000	0.000
32	A	357	THR	0	-0.009	-0.034	32.127	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	358	ASP	-1	-0.888	-0.908	29.293	-0.118	-0.118	0.000	0.000	0.000	0.000
34	A	359	PHE	0	-0.010	-0.012	26.006	-0.017	-0.017	0.000	0.000	0.000	0.000
35	A	360	MET	0	-0.049	-0.029	21.241	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	361	SER	0	-0.026	0.007	23.517	-0.007	-0.007	0.000	0.000	0.000	0.000
37	A	362	LYS	1	1.001	0.974	22.417	0.149	0.149	0.000	0.000	0.000	0.000
38	A	363	GLY	0	-0.096	-0.036	22.601	0.020	0.020	0.000	0.000	0.000	0.000
39	A	364	ASN	0	0.000	0.010	24.184	0.002	0.002	0.000	0.000	0.000	0.000
40	A	365	GLU	-1	-0.780	-0.889	19.511	-0.268	-0.268	0.000	0.000	0.000	0.000
41	A	366	GLN	0	0.001	-0.009	18.184	-0.012	-0.012	0.000	0.000	0.000	0.000
42	A	367	GLU	-1	-0.850	-0.931	22.005	-0.205	-0.205	0.000	0.000	0.000	0.000
43	A	368	SER	0	-0.009	-0.028	24.102	0.016	0.016	0.000	0.000	0.000	0.000
44	A	369	MET	0	-0.012	-0.006	17.954	-0.009	-0.009	0.000	0.000	0.000	0.000
45	A	370	ALA	0	-0.013	0.005	23.092	0.004	0.004	0.000	0.000	0.000	0.000
46	A	371	ARG	1	0.873	0.931	25.415	0.157	0.157	0.000	0.000	0.000	0.000
47	A	372	LEU	0	0.034	0.015	23.539	0.010	0.010	0.000	0.000	0.000	0.000
48	A	373	LYS	1	0.977	0.996	23.314	0.242	0.242	0.000	0.000	0.000	0.000
49	A	374	LYS	1	0.872	0.932	25.684	0.141	0.141	0.000	0.000	0.000	0.000
50	A	375	LEU	0	0.004	-0.012	29.324	0.010	0.010	0.000	0.000	0.000	0.000
51	A	376	MET	0	0.002	-0.002	22.954	0.003	0.003	0.000	0.000	0.000	0.000
52	A	377	THR	0	0.003	0.006	27.534	0.002	0.002	0.000	0.000	0.000	0.000
53	A	378	ILE	0	-0.058	-0.032	29.748	0.010	0.010	0.000	0.000	0.000	0.000
54	A	379	MET	0	-0.022	-0.037	30.626	0.006	0.006	0.000	0.000	0.000	0.000
55	A	380	ASP	-1	-0.844	-0.908	28.222	-0.179	-0.179	0.000	0.000	0.000	0.000
56	A	381	SER	0	-0.066	-0.029	31.309	0.006	0.006	0.000	0.000	0.000	0.000
57	A	382	MET	0	-0.105	-0.035	34.528	0.010	0.010	0.000	0.000	0.000	0.000
58	A	383	ASN	0	-0.008	-0.011	35.331	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	384	ASP	-1	-0.784	-0.915	34.977	-0.097	-0.097	0.000	0.000	0.000	0.000
60	A	385	GLN	0	0.000	0.025	36.624	0.001	0.001	0.000	0.000	0.000	0.000
61	A	386	GLU	-1	-0.770	-0.853	38.249	-0.084	-0.084	0.000	0.000	0.000	0.000
62	A	387	LEU	0	-0.031	-0.012	32.256	0.000	0.000	0.000	0.000	0.000	0.000
63	A	388	ASP	-1	-0.868	-0.928	34.197	-0.094	-0.094	0.000	0.000	0.000	0.000
64	A	389	SER	0	-0.123	-0.044	36.507	0.007	0.007	0.000	0.000	0.000	0.000
65	A	390	THR	0	-0.013	-0.019	38.705	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	391	ASP	-1	-0.845	-0.937	39.795	-0.067	-0.067	0.000	0.000	0.000	0.000
67	A	392	GLY	0	0.051	0.012	39.139	0.003	0.003	0.000	0.000	0.000	0.000
68	A	393	ALA	0	0.001	0.007	40.182	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	394	LYS	1	0.911	0.942	42.433	0.053	0.053	0.000	0.000	0.000	0.000
70	A	395	VAL	0	-0.016	0.006	42.190	0.003	0.003	0.000	0.000	0.000	0.000
71	A	396	PHE	0	0.046	0.000	39.250	0.002	0.002	0.000	0.000	0.000	0.000
72	A	397	SER	0	-0.029	-0.005	44.880	0.001	0.001	0.000	0.000	0.000	0.000
73	A	398	LYS	1	0.957	0.984	48.020	0.053	0.053	0.000	0.000	0.000	0.000
74	A	399	GLN	0	0.031	0.025	47.519	0.001	0.001	0.000	0.000	0.000	0.000
75	A	400	PRO	0	0.085	0.039	47.122	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	401	GLY	0	-0.023	-0.001	47.208	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	402	ARG	1	0.749	0.839	42.683	0.067	0.067	0.000	0.000	0.000	0.000
78	A	403	ILE	0	0.049	0.027	42.407	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	404	GLN	0	0.007	-0.003	42.279	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	405	ARG	1	0.725	0.838	38.720	0.088	0.088	0.000	0.000	0.000	0.000
81	A	406	VAL	0	0.038	0.023	36.820	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	407	ALA	0	-0.007	0.019	38.130	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	408	ARG	1	0.919	0.956	39.314	0.080	0.080	0.000	0.000	0.000	0.000
84	A	409	GLY	0	-0.038	-0.004	37.865	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	410	SER	0	0.006	-0.010	34.133	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	411	GLY	0	-0.035	-0.004	34.739	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	412	VAL	0	-0.046	-0.007	35.428	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	413	SER	0	-0.008	-0.039	37.686	0.008	0.008	0.000	0.000	0.000	0.000
89	A	414	THR	0	0.058	-0.005	40.084	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	415	ARG	1	0.864	0.921	39.934	0.091	0.091	0.000	0.000	0.000	0.000
91	A	416	ASP	-1	-0.762	-0.836	36.657	-0.111	-0.111	0.000	0.000	0.000	0.000
92	A	417	VAL	0	0.022	0.012	37.684	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	418	GLN	0	-0.014	-0.010	38.952	0.001	0.001	0.000	0.000	0.000	0.000
94	A	419	GLU	-1	-0.879	-0.913	36.614	-0.104	-0.104	0.000	0.000	0.000	0.000
95	A	420	LEU	0	0.037	0.028	33.020	0.001	0.001	0.000	0.000	0.000	0.000
96	A	421	LEU	0	0.011	0.001	36.548	0.001	0.001	0.000	0.000	0.000	0.000
97	A	422	THR	0	-0.061	-0.036	39.109	0.005	0.005	0.000	0.000	0.000	0.000
98	A	423	GLN	0	-0.045	-0.030	34.624	0.000	0.000	0.000	0.000	0.000	0.000
99	A	424	TYR	0	0.030	0.028	34.960	0.002	0.002	0.000	0.000	0.000	0.000
100	A	425	THR	0	0.009	0.007	36.519	0.002	0.002	0.000	0.000	0.000	0.000
101	A	426	LYS	1	0.875	0.941	38.057	0.081	0.081	0.000	0.000	0.000	0.000
102	A	427	PHE	0	0.044	0.006	30.689	0.003	0.003	0.000	0.000	0.000	0.000
103	A	428	ALA	0	0.004	0.001	36.126	0.003	0.003	0.000	0.000	0.000	0.000
104	A	429	GLN	0	-0.074	-0.042	37.422	0.002	0.002	0.000	0.000	0.000	0.000
105	A	430	MET	0	-0.054	-0.014	36.438	0.004	0.004	0.000	0.000	0.000	0.000
106	A	431	VAL	0	-0.034	0.012	33.133	0.004	0.004	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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