FMO DATABASE

FMODB ID: 2M4GR

Calculation Name: 2FH5-A-Xray547

Preferred Name: Signal recognition particle receptor subunit alpha

Target Type: SINGLE PROTEIN

Ligand Name: guanosine-5'-triphosphate | magnesium ion

Ligand 3-letter code: GTP | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2FH5

Chain ID: A

ChEMBL ID: CHEMBL4105934

UniProt ID: P08240

Base Structure: X-ray

Registration Date: 2025-10-05

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	130
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1174991.495144
FMO2-HF: Nuclear repulsion	1122618.968978
FMO2-HF: Total energy	-52372.526166
FMO2-MP2: Total energy	-52526.995043

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:0:HIS)

Summations of interaction energy for fragment #1(A:0:HIS)

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.
-102.416	-97.843	5.217	-3.365	-6.424	-0.025

Interaction energy analysis for fragmet #1(A:0:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.819 / q_NPA : 0.895

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	1	MET	0	-0.003	0.012	3.420	-10.211	-8.482	0.010	-0.840	-0.899	-0.002
5	A	3	ASP	-1	-0.796	-0.876	5.164	-52.630	-52.605	-0.001	-0.006	-0.018	0.000
41	A	40	GLU	-1	-0.846	-0.924	4.686	-45.157	-44.960	-0.001	-0.012	-0.183	0.000
42	A	41	ARG	1	0.848	0.925	2.379	57.816	60.020	5.211	-2.438	-4.977	-0.023
45	A	44	ASN	0	-0.086	-0.051	4.850	-5.381	-5.254	-0.001	-0.003	-0.123	0.000
72	A	71	GLN	0	0.022	-0.007	4.128	-5.352	-5.061	-0.001	-0.066	-0.224	0.000
4	A	2	VAL	0	-0.033	-0.026	5.889	4.101	4.101	0.000	0.000	0.000	0.000
6	A	4	PHE	0	-0.030	-0.031	8.092	2.857	2.857	0.000	0.000	0.000	0.000
7	A	5	PHE	0	0.054	0.014	11.885	-0.222	-0.222	0.000	0.000	0.000	0.000
8	A	6	THR	0	-0.025	-0.008	14.656	0.753	0.753	0.000	0.000	0.000	0.000
9	A	7	ILE	0	0.055	0.031	18.497	-0.112	-0.112	0.000	0.000	0.000	0.000
10	A	8	PHE	0	0.018	0.010	21.426	0.228	0.228	0.000	0.000	0.000	0.000
11	A	9	SER	0	0.057	0.025	25.039	-0.028	-0.028	0.000	0.000	0.000	0.000
12	A	10	LYS	1	0.885	0.922	28.432	10.250	10.250	0.000	0.000	0.000	0.000
13	A	11	GLY	0	-0.007	0.010	30.015	0.166	0.166	0.000	0.000	0.000	0.000
14	A	12	GLY	0	-0.027	-0.008	28.415	0.168	0.168	0.000	0.000	0.000	0.000
15	A	13	LEU	0	-0.028	-0.007	28.304	-0.216	-0.216	0.000	0.000	0.000	0.000
16	A	14	VAL	0	-0.011	-0.020	22.778	-0.228	-0.228	0.000	0.000	0.000	0.000
17	A	15	LEU	0	-0.040	-0.002	24.713	0.315	0.315	0.000	0.000	0.000	0.000
18	A	16	TRP	0	0.029	0.000	15.967	0.076	0.076	0.000	0.000	0.000	0.000
19	A	17	CYS	0	-0.120	-0.058	15.851	0.550	0.550	0.000	0.000	0.000	0.000
20	A	18	PHE	0	0.033	0.029	9.195	0.206	0.206	0.000	0.000	0.000	0.000
21	A	19	GLN	0	-0.013	-0.015	11.811	0.676	0.676	0.000	0.000	0.000	0.000
22	A	20	GLY	0	0.061	0.041	8.851	-0.531	-0.531	0.000	0.000	0.000	0.000
23	A	21	VAL	0	-0.044	-0.036	7.740	2.057	2.057	0.000	0.000	0.000	0.000
24	A	22	SER	0	-0.035	-0.023	9.435	0.523	0.523	0.000	0.000	0.000	0.000
25	A	23	ASP	-1	-0.796	-0.873	11.298	-16.949	-16.949	0.000	0.000	0.000	0.000
26	A	24	SER	0	-0.018	-0.003	14.428	-0.442	-0.442	0.000	0.000	0.000	0.000
27	A	26	THR	0	0.073	0.045	15.748	0.484	0.484	0.000	0.000	0.000	0.000
28	A	27	GLY	0	0.039	0.035	16.807	0.582	0.582	0.000	0.000	0.000	0.000
29	A	28	PRO	0	0.022	-0.006	14.141	-0.931	-0.931	0.000	0.000	0.000	0.000
30	A	29	VAL	0	0.032	0.020	13.672	-1.384	-1.384	0.000	0.000	0.000	0.000
31	A	30	ASN	0	0.000	-0.017	14.558	-0.921	-0.921	0.000	0.000	0.000	0.000
32	A	31	ALA	0	-0.010	0.011	10.603	-1.027	-1.027	0.000	0.000	0.000	0.000
33	A	32	LEU	0	0.028	0.010	9.662	-2.919	-2.919	0.000	0.000	0.000	0.000
34	A	33	ILE	0	0.005	-0.002	10.671	-1.492	-1.492	0.000	0.000	0.000	0.000
35	A	34	ARG	1	0.833	0.891	9.340	20.028	20.028	0.000	0.000	0.000	0.000
36	A	35	SER	0	-0.022	-0.007	5.556	-1.746	-1.746	0.000	0.000	0.000	0.000
37	A	36	VAL	0	-0.053	-0.009	5.741	-6.349	-6.349	0.000	0.000	0.000	0.000
38	A	37	LEU	0	0.031	0.011	8.214	0.601	0.601	0.000	0.000	0.000	0.000
39	A	38	LEU	0	-0.058	-0.026	10.909	0.621	0.621	0.000	0.000	0.000	0.000
40	A	39	GLN	0	-0.035	-0.013	6.571	-0.883	-0.883	0.000	0.000	0.000	0.000
43	A	42	GLY	0	0.009	0.011	6.107	0.503	0.503	0.000	0.000	0.000	0.000
44	A	43	GLY	0	0.043	0.023	9.515	1.465	1.465	0.000	0.000	0.000	0.000
46	A	45	ASN	0	0.003	-0.005	8.394	1.636	1.636	0.000	0.000	0.000	0.000
47	A	46	SER	0	-0.053	-0.039	10.803	2.759	2.759	0.000	0.000	0.000	0.000
48	A	47	PHE	0	-0.036	-0.002	13.538	1.008	1.008	0.000	0.000	0.000	0.000
49	A	48	THR	0	-0.069	-0.032	13.980	0.643	0.643	0.000	0.000	0.000	0.000
50	A	49	HIS	0	0.038	0.015	11.228	-1.264	-1.264	0.000	0.000	0.000	0.000
51	A	50	GLU	-1	-0.796	-0.897	5.840	-38.724	-38.724	0.000	0.000	0.000	0.000
52	A	51	ALA	0	-0.045	-0.003	8.960	0.405	0.405	0.000	0.000	0.000	0.000
53	A	52	LEU	0	-0.031	-0.015	8.422	-2.740	-2.740	0.000	0.000	0.000	0.000
54	A	53	THR	0	-0.030	-0.004	10.527	3.071	3.071	0.000	0.000	0.000	0.000
55	A	54	LEU	0	-0.011	-0.009	12.177	-1.157	-1.157	0.000	0.000	0.000	0.000
56	A	55	LYS	1	0.818	0.894	14.901	18.601	18.601	0.000	0.000	0.000	0.000
57	A	56	TYR	0	0.015	0.002	17.131	-0.437	-0.437	0.000	0.000	0.000	0.000
58	A	57	LYS	1	0.822	0.902	19.835	13.749	13.749	0.000	0.000	0.000	0.000
59	A	58	LEU	0	0.004	-0.003	21.839	0.085	0.085	0.000	0.000	0.000	0.000
60	A	59	ASP	-1	-0.793	-0.873	25.316	-11.055	-11.055	0.000	0.000	0.000	0.000
61	A	60	ASN	0	0.000	-0.025	27.711	0.064	0.064	0.000	0.000	0.000	0.000
62	A	61	GLN	0	-0.050	-0.004	31.102	0.473	0.473	0.000	0.000	0.000	0.000
63	A	62	PHE	0	0.008	-0.017	30.109	0.315	0.315	0.000	0.000	0.000	0.000
64	A	63	GLU	-1	-0.936	-0.952	30.832	-9.511	-9.511	0.000	0.000	0.000	0.000
65	A	64	LEU	0	0.018	0.014	25.588	-0.139	-0.139	0.000	0.000	0.000	0.000
66	A	65	VAL	0	-0.022	-0.012	22.710	0.095	0.095	0.000	0.000	0.000	0.000
67	A	66	PHE	0	0.003	0.015	19.369	-0.147	-0.147	0.000	0.000	0.000	0.000
68	A	67	VAL	0	-0.015	-0.019	16.935	0.107	0.107	0.000	0.000	0.000	0.000
69	A	68	VAL	0	0.000	0.008	11.757	-0.516	-0.516	0.000	0.000	0.000	0.000
70	A	69	GLY	0	0.016	0.001	11.663	0.985	0.985	0.000	0.000	0.000	0.000
71	A	70	PHE	0	-0.008	-0.008	7.770	-1.088	-1.088	0.000	0.000	0.000	0.000
73	A	72	LYS	1	0.915	0.938	5.835	38.690	38.690	0.000	0.000	0.000	0.000
74	A	73	ILE	0	0.060	0.030	8.338	0.490	0.490	0.000	0.000	0.000	0.000
75	A	74	LEU	0	0.009	-0.010	10.780	0.949	0.949	0.000	0.000	0.000	0.000
76	A	75	THR	0	-0.010	0.001	6.109	1.239	1.239	0.000	0.000	0.000	0.000
77	A	76	LEU	0	0.010	0.018	9.590	0.676	0.676	0.000	0.000	0.000	0.000
78	A	77	THR	0	-0.007	-0.009	12.724	0.833	0.833	0.000	0.000	0.000	0.000
79	A	78	TYR	0	-0.021	-0.008	10.366	0.905	0.905	0.000	0.000	0.000	0.000
80	A	79	VAL	0	0.039	0.022	9.589	0.604	0.604	0.000	0.000	0.000	0.000
81	A	80	ASP	-1	-0.777	-0.884	12.053	-17.130	-17.130	0.000	0.000	0.000	0.000
82	A	81	LYS	1	0.937	0.976	15.193	18.659	18.659	0.000	0.000	0.000	0.000
83	A	82	LEU	0	0.050	0.044	11.430	0.734	0.734	0.000	0.000	0.000	0.000
84	A	83	ILE	0	-0.036	-0.027	14.973	0.852	0.852	0.000	0.000	0.000	0.000
85	A	84	ASP	-1	-0.877	-0.928	17.280	-13.684	-13.684	0.000	0.000	0.000	0.000
86	A	85	ASP	-1	-0.918	-0.960	17.931	-15.449	-15.449	0.000	0.000	0.000	0.000
87	A	86	VAL	0	-0.031	-0.016	16.486	0.690	0.690	0.000	0.000	0.000	0.000
88	A	87	HIS	0	-0.052	-0.035	19.641	0.482	0.482	0.000	0.000	0.000	0.000
89	A	88	ARG	1	0.887	0.937	22.572	13.382	13.382	0.000	0.000	0.000	0.000
90	A	89	LEU	0	0.075	0.033	20.350	0.592	0.592	0.000	0.000	0.000	0.000
91	A	90	PHE	0	0.009	0.006	22.706	0.535	0.535	0.000	0.000	0.000	0.000
92	A	91	ARG	1	0.839	0.911	24.637	11.820	11.820	0.000	0.000	0.000	0.000
93	A	92	ASP	-1	-0.862	-0.917	27.290	-10.579	-10.579	0.000	0.000	0.000	0.000
94	A	93	LYS	1	0.806	0.909	22.802	13.347	13.347	0.000	0.000	0.000	0.000
95	A	94	TYR	0	0.027	0.020	23.975	-0.074	-0.074	0.000	0.000	0.000	0.000
96	A	95	ARG	1	0.880	0.935	29.402	10.147	10.147	0.000	0.000	0.000	0.000
97	A	96	THR	0	0.015	0.000	32.255	0.216	0.216	0.000	0.000	0.000	0.000
98	A	97	GLU	-1	-0.819	-0.914	31.053	-9.905	-9.905	0.000	0.000	0.000	0.000
99	A	98	ILE	0	-0.027	0.008	28.935	0.061	0.061	0.000	0.000	0.000	0.000
100	A	99	GLN	0	-0.058	-0.020	32.408	0.048	0.048	0.000	0.000	0.000	0.000
101	A	100	GLN	0	-0.074	-0.038	35.420	0.489	0.489	0.000	0.000	0.000	0.000
102	A	101	GLN	0	0.021	0.009	36.803	-0.115	-0.115	0.000	0.000	0.000	0.000
103	A	102	SER	0	0.003	0.006	38.745	-0.049	-0.049	0.000	0.000	0.000	0.000
104	A	103	ALA	0	0.103	0.040	35.943	-0.179	-0.179	0.000	0.000	0.000	0.000
105	A	104	LEU	0	-0.010	-0.013	35.719	-0.224	-0.224	0.000	0.000	0.000	0.000
106	A	105	SER	0	-0.048	-0.032	35.304	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	106	LEU	0	-0.008	-0.003	30.488	-0.266	-0.266	0.000	0.000	0.000	0.000
108	A	107	LEU	0	-0.030	-0.027	31.879	-0.217	-0.217	0.000	0.000	0.000	0.000
109	A	108	ASN	0	-0.047	-0.017	33.485	-0.015	-0.015	0.000	0.000	0.000	0.000
110	A	109	GLY	0	0.025	0.033	31.334	0.070	0.070	0.000	0.000	0.000	0.000
111	A	110	THR	0	-0.016	-0.012	28.117	-0.144	-0.144	0.000	0.000	0.000	0.000
112	A	111	PHE	0	0.008	0.000	24.995	-0.111	-0.111	0.000	0.000	0.000	0.000
113	A	112	ASP	-1	-0.916	-0.960	21.514	-14.275	-14.275	0.000	0.000	0.000	0.000
114	A	113	PHE	0	0.020	-0.010	18.725	0.077	0.077	0.000	0.000	0.000	0.000
115	A	114	GLN	0	0.067	0.044	14.201	-0.499	-0.499	0.000	0.000	0.000	0.000
116	A	115	ASN	0	0.020	-0.013	15.805	-1.654	-1.654	0.000	0.000	0.000	0.000
117	A	116	ASP	-1	-0.812	-0.870	16.569	-14.375	-14.375	0.000	0.000	0.000	0.000
118	A	117	PHE	0	0.014	0.012	12.067	-0.409	-0.409	0.000	0.000	0.000	0.000
119	A	118	LEU	0	0.015	-0.003	10.590	-1.454	-1.454	0.000	0.000	0.000	0.000
120	A	119	ARG	1	0.790	0.905	11.798	14.464	14.464	0.000	0.000	0.000	0.000
121	A	120	LEU	0	0.075	0.021	13.217	-0.813	-0.813	0.000	0.000	0.000	0.000
122	A	121	LEU	0	-0.025	-0.006	8.412	-0.113	-0.113	0.000	0.000	0.000	0.000
123	A	122	ARG	1	0.933	0.960	8.630	19.749	19.749	0.000	0.000	0.000	0.000
124	A	123	GLU	-1	-0.915	-0.957	9.695	-17.683	-17.683	0.000	0.000	0.000	0.000
125	A	124	ALA	0	0.008	0.003	11.855	0.473	0.473	0.000	0.000	0.000	0.000
126	A	125	GLU	-1	-0.832	-0.935	6.199	-43.050	-43.050	0.000	0.000	0.000	0.000
127	A	126	GLU	-1	-0.898	-0.917	9.310	-27.036	-27.036	0.000	0.000	0.000	0.000
128	A	127	SER	0	-0.073	-0.039	11.253	1.118	1.118	0.000	0.000	0.000	0.000
129	A	128	SER	0	-0.128	-0.076	8.666	-0.406	-0.406	0.000	0.000	0.000	0.000
130	A	129	LYS	0	-0.111	-0.052	7.140	7.969	7.969	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:HIS)