FMO DATABASE

FMODB ID: G68K1

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	OptAll
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	-760168.017558
FMO2-HF: Nuclear repulsion	715873.822846
FMO2-HF: Total energy	-44294.194713
FMO2-MP2: Total energy	-44416.209635

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.
-1.921	0.423	-0.018	-1.169	-1.158	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 : -0.001 / q_NPA : -0.007

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	-0.049	-0.053	3.869	0.116	2.460	-0.018	-1.169	-1.158	0.004
4	A	329	LEU	0	0.046	0.001	6.171	-0.433	-0.433	0.000	0.000	0.000	0.000
5	A	330	ARG	1	0.892	0.957	9.165	-0.573	-0.573	0.000	0.000	0.000	0.000
6	A	331	ASP	-1	-0.725	-0.836	5.622	-1.226	-1.226	0.000	0.000	0.000	0.000
7	A	332	MET	0	-0.006	0.005	9.320	-0.115	-0.115	0.000	0.000	0.000	0.000
8	A	333	TYR	0	-0.003	0.005	11.285	0.015	0.015	0.000	0.000	0.000	0.000
9	A	334	GLU	-1	-0.831	-0.923	11.865	-0.108	-0.108	0.000	0.000	0.000	0.000
10	A	335	GLN	0	-0.048	-0.021	11.047	-0.015	-0.015	0.000	0.000	0.000	0.000
11	A	336	PHE	0	0.003	-0.005	14.185	0.050	0.050	0.000	0.000	0.000	0.000
12	A	337	GLN	0	0.017	0.012	17.109	0.002	0.002	0.000	0.000	0.000	0.000
13	A	338	ASN	0	-0.032	-0.020	15.980	0.043	0.043	0.000	0.000	0.000	0.000
14	A	339	ILE	0	0.023	0.011	15.889	0.015	0.015	0.000	0.000	0.000	0.000
15	A	340	MET	0	-0.027	-0.021	19.686	0.032	0.032	0.000	0.000	0.000	0.000
16	A	341	LYS	1	0.869	0.936	19.675	0.338	0.338	0.000	0.000	0.000	0.000
17	A	342	MET	0	0.006	0.002	21.179	0.015	0.015	0.000	0.000	0.000	0.000
18	A	343	GLY	0	0.044	0.046	23.704	0.003	0.003	0.000	0.000	0.000	0.000
19	A	344	PRO	0	0.014	-0.003	25.593	0.005	0.005	0.000	0.000	0.000	0.000
20	A	345	PHE	0	0.015	0.008	26.419	0.005	0.005	0.000	0.000	0.000	0.000
21	A	346	SER	0	0.016	-0.014	25.004	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	347	GLN	0	-0.004	0.001	27.547	0.003	0.003	0.000	0.000	0.000	0.000
23	A	348	ILE	0	-0.005	-0.007	30.433	0.008	0.008	0.000	0.000	0.000	0.000
24	A	349	LEU	0	-0.016	-0.009	27.956	0.005	0.005	0.000	0.000	0.000	0.000
25	A	350	GLY	0	0.008	0.008	31.119	0.004	0.004	0.000	0.000	0.000	0.000
26	A	351	MET	0	-0.048	-0.013	32.359	0.011	0.011	0.000	0.000	0.000	0.000
27	A	352	ILE	0	-0.053	-0.007	34.389	0.009	0.009	0.000	0.000	0.000	0.000
28	A	353	PRO	0	-0.015	-0.022	36.005	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	354	GLY	0	0.048	0.024	36.473	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	355	PHE	0	-0.001	0.004	30.260	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	356	GLY	0	-0.008	-0.014	31.624	-0.010	-0.010	0.000	0.000	0.000	0.000
32	A	357	THR	0	-0.007	-0.035	32.531	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	358	ASP	-1	-0.861	-0.889	29.809	-0.139	-0.139	0.000	0.000	0.000	0.000
34	A	359	PHE	0	-0.011	0.001	26.577	-0.021	-0.021	0.000	0.000	0.000	0.000
35	A	360	MET	0	-0.059	-0.039	22.482	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	361	SER	0	-0.035	-0.010	24.030	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	362	LYS	1	0.917	0.925	22.473	0.167	0.167	0.000	0.000	0.000	0.000
38	A	363	GLY	0	-0.039	-0.015	23.135	0.028	0.028	0.000	0.000	0.000	0.000
39	A	364	ASN	0	0.018	0.036	24.505	0.013	0.013	0.000	0.000	0.000	0.000
40	A	365	GLU	-1	-0.771	-0.886	20.329	-0.315	-0.315	0.000	0.000	0.000	0.000
41	A	366	GLN	0	0.000	0.009	18.548	-0.025	-0.025	0.000	0.000	0.000	0.000
42	A	367	GLU	-1	-0.834	-0.931	22.347	-0.263	-0.263	0.000	0.000	0.000	0.000
43	A	368	SER	0	-0.014	-0.021	24.385	0.019	0.019	0.000	0.000	0.000	0.000
44	A	369	MET	0	-0.003	-0.011	18.150	-0.013	-0.013	0.000	0.000	0.000	0.000
45	A	370	ALA	0	-0.014	0.002	23.176	0.003	0.003	0.000	0.000	0.000	0.000
46	A	371	ARG	1	0.852	0.926	25.599	0.202	0.202	0.000	0.000	0.000	0.000
47	A	372	LEU	0	0.017	0.016	23.775	0.011	0.011	0.000	0.000	0.000	0.000
48	A	373	LYS	1	0.949	0.983	23.325	0.313	0.313	0.000	0.000	0.000	0.000
49	A	374	LYS	1	0.858	0.914	25.756	0.185	0.185	0.000	0.000	0.000	0.000
50	A	375	LEU	0	0.020	0.005	29.446	0.009	0.009	0.000	0.000	0.000	0.000
51	A	376	MET	0	0.008	-0.001	23.039	0.004	0.004	0.000	0.000	0.000	0.000
52	A	377	THR	0	0.021	0.002	28.261	0.002	0.002	0.000	0.000	0.000	0.000
53	A	378	ILE	0	-0.048	-0.024	30.169	0.013	0.013	0.000	0.000	0.000	0.000
54	A	379	MET	0	-0.011	-0.027	30.701	0.009	0.009	0.000	0.000	0.000	0.000
55	A	380	ASP	-1	-0.870	-0.928	28.257	-0.254	-0.254	0.000	0.000	0.000	0.000
56	A	381	SER	0	-0.035	-0.009	31.343	0.007	0.007	0.000	0.000	0.000	0.000
57	A	382	MET	0	-0.105	-0.037	34.726	0.015	0.015	0.000	0.000	0.000	0.000
58	A	383	ASN	0	-0.009	-0.014	35.885	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	384	ASP	-1	-0.780	-0.899	35.537	-0.146	-0.146	0.000	0.000	0.000	0.000
60	A	385	GLN	0	0.004	0.016	36.947	0.002	0.002	0.000	0.000	0.000	0.000
61	A	386	GLU	-1	-0.782	-0.857	38.592	-0.121	-0.121	0.000	0.000	0.000	0.000
62	A	387	LEU	0	-0.038	-0.017	32.574	0.001	0.001	0.000	0.000	0.000	0.000
63	A	388	ASP	-1	-0.870	-0.927	34.358	-0.147	-0.147	0.000	0.000	0.000	0.000
64	A	389	SER	0	-0.119	-0.059	36.675	0.010	0.010	0.000	0.000	0.000	0.000
65	A	390	THR	0	-0.005	-0.020	39.004	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	391	ASP	-1	-0.857	-0.934	40.628	-0.095	-0.095	0.000	0.000	0.000	0.000
67	A	392	GLY	0	0.108	0.054	39.589	0.003	0.003	0.000	0.000	0.000	0.000
68	A	393	ALA	0	0.008	0.007	40.613	0.001	0.001	0.000	0.000	0.000	0.000
69	A	394	LYS	1	0.874	0.933	42.793	0.080	0.080	0.000	0.000	0.000	0.000
70	A	395	VAL	0	-0.039	-0.007	42.652	0.005	0.005	0.000	0.000	0.000	0.000
71	A	396	PHE	0	0.035	-0.006	39.337	0.004	0.004	0.000	0.000	0.000	0.000
72	A	397	SER	0	-0.028	-0.017	44.906	0.003	0.003	0.000	0.000	0.000	0.000
73	A	398	LYS	1	0.942	0.980	48.062	0.081	0.081	0.000	0.000	0.000	0.000
74	A	399	GLN	0	0.020	0.022	47.792	0.000	0.000	0.000	0.000	0.000	0.000
75	A	400	PRO	0	0.088	0.043	47.493	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	401	GLY	0	0.000	0.005	46.927	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	402	ARG	1	0.778	0.857	43.013	0.099	0.099	0.000	0.000	0.000	0.000
78	A	403	ILE	0	0.040	0.025	42.455	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	404	GLN	0	0.003	-0.007	42.353	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	405	ARG	1	0.721	0.831	38.869	0.128	0.128	0.000	0.000	0.000	0.000
81	A	406	VAL	0	0.027	0.016	37.034	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	407	ALA	0	-0.014	0.010	38.242	-0.008	-0.008	0.000	0.000	0.000	0.000
83	A	408	ARG	1	0.920	0.950	39.273	0.112	0.112	0.000	0.000	0.000	0.000
84	A	409	GLY	0	-0.038	-0.002	37.991	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	410	SER	0	0.015	-0.002	34.331	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	411	GLY	0	-0.039	-0.004	34.962	-0.007	-0.007	0.000	0.000	0.000	0.000
87	A	412	VAL	0	-0.041	-0.008	35.936	0.000	0.000	0.000	0.000	0.000	0.000
88	A	413	SER	0	-0.007	-0.036	38.200	0.010	0.010	0.000	0.000	0.000	0.000
89	A	414	THR	0	0.051	-0.006	40.554	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	415	ARG	1	0.861	0.915	39.742	0.123	0.123	0.000	0.000	0.000	0.000
91	A	416	ASP	-1	-0.770	-0.845	36.981	-0.148	-0.148	0.000	0.000	0.000	0.000
92	A	417	VAL	0	0.018	0.015	37.913	-0.005	-0.005	0.000	0.000	0.000	0.000
93	A	418	GLN	0	-0.011	-0.008	39.350	0.001	0.001	0.000	0.000	0.000	0.000
94	A	419	GLU	-1	-0.890	-0.899	36.469	-0.142	-0.142	0.000	0.000	0.000	0.000
95	A	420	LEU	0	0.061	0.036	33.210	0.002	0.002	0.000	0.000	0.000	0.000
96	A	421	LEU	0	-0.003	-0.003	36.807	0.001	0.001	0.000	0.000	0.000	0.000
97	A	422	THR	0	-0.056	-0.045	39.390	0.006	0.006	0.000	0.000	0.000	0.000
98	A	423	GLN	0	-0.040	-0.031	35.074	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	424	TYR	0	0.024	0.031	35.200	0.004	0.004	0.000	0.000	0.000	0.000
100	A	425	THR	0	0.010	0.000	36.772	0.002	0.002	0.000	0.000	0.000	0.000
101	A	426	LYS	1	0.820	0.908	38.382	0.107	0.107	0.000	0.000	0.000	0.000
102	A	427	PHE	0	0.062	0.026	30.975	0.004	0.004	0.000	0.000	0.000	0.000
103	A	428	ALA	0	0.011	0.004	36.376	0.003	0.003	0.000	0.000	0.000	0.000
104	A	429	GLN	0	-0.043	-0.032	38.070	0.002	0.002	0.000	0.000	0.000	0.000
105	A	430	MET	0	-0.043	-0.005	36.854	0.007	0.007	0.000	0.000	0.000	0.000
106	A	431	VAL	0	-0.035	0.008	33.664	0.002	0.002	0.000	0.000	0.000	0.000

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