FMO DATABASE

FMODB ID: JK1L9

Calculation Name: 1RF8-B-Other549

Preferred Name:

Target Type:

Ligand Name: 7n-methyl-8-hydroguanosine-5'-diphosphate | s-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1h-pyrrol-3-yl)methyl] methanesulfonothioate

Ligand 3-letter code: M7G | MTN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1RF8

Chain ID: B

ChEMBL ID:

UniProt ID: P07260

Base Structure: SolutionNMR

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	100
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-606608.281434
FMO2-HF: Nuclear repulsion	568231.127016
FMO2-HF: Total energy	-38377.154418
FMO2-MP2: Total energy	-38490.706702

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(B:215:GLY)

Summations of interaction energy for fragment #1(B:215:GLY)

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.
-117.847	-116.947	-0.013	-0.296	-0.591	-0.001

Interaction energy analysis for fragmet #1(B:215:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.802 / q_NPA : 0.885

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	B	217	ILE	0	-0.061	-0.044	3.745	-1.593	-0.693	-0.013	-0.296	-0.591	-0.001
4	B	218	GLY	0	0.020	0.008	6.109	4.708	4.708	0.000	0.000	0.000	0.000
5	B	219	LEU	0	-0.008	0.001	9.359	-1.156	-1.156	0.000	0.000	0.000	0.000
6	B	220	GLU	-1	-0.819	-0.893	6.187	-46.335	-46.335	0.000	0.000	0.000	0.000
7	B	221	ALA	0	-0.075	-0.025	10.727	1.598	1.598	0.000	0.000	0.000	0.000
8	B	222	GLU	-1	-0.887	-0.937	14.100	-17.668	-17.668	0.000	0.000	0.000	0.000
9	B	223	ILE	0	-0.071	-0.037	16.531	0.442	0.442	0.000	0.000	0.000	0.000
10	B	224	GLU	-1	-0.939	-0.973	20.265	-14.414	-14.414	0.000	0.000	0.000	0.000
11	B	225	THR	0	-0.061	-0.036	22.730	0.349	0.349	0.000	0.000	0.000	0.000
12	B	226	THR	0	0.019	0.015	23.981	0.299	0.299	0.000	0.000	0.000	0.000
13	B	227	THR	0	-0.061	-0.045	26.740	0.488	0.488	0.000	0.000	0.000	0.000
14	B	228	ASP	-1	-0.937	-0.960	30.103	-10.180	-10.180	0.000	0.000	0.000	0.000
15	B	229	GLU	-1	-0.933	-0.956	31.938	-9.457	-9.457	0.000	0.000	0.000	0.000
16	B	230	THR	0	-0.084	-0.052	34.631	0.060	0.060	0.000	0.000	0.000	0.000
17	B	231	ASP	-1	-0.851	-0.906	38.246	-7.222	-7.222	0.000	0.000	0.000	0.000
18	B	232	ASP	-1	-0.908	-0.940	40.050	-7.890	-7.890	0.000	0.000	0.000	0.000
19	B	233	GLY	0	-0.044	-0.023	41.206	0.102	0.102	0.000	0.000	0.000	0.000
20	B	234	THR	0	-0.164	-0.092	42.078	0.246	0.246	0.000	0.000	0.000	0.000
21	B	235	ASN	0	0.017	0.015	44.223	-0.177	-0.177	0.000	0.000	0.000	0.000
22	B	236	THR	0	0.035	-0.001	46.663	0.156	0.156	0.000	0.000	0.000	0.000
23	B	237	VAL	0	-0.024	-0.009	49.119	-0.071	-0.071	0.000	0.000	0.000	0.000
24	B	238	SER	0	0.033	0.013	50.996	-0.069	-0.069	0.000	0.000	0.000	0.000
25	B	239	HIS	0	0.026	0.022	42.294	0.097	0.097	0.000	0.000	0.000	0.000
26	B	240	ILE	0	0.058	0.017	45.238	-0.101	-0.101	0.000	0.000	0.000	0.000
27	B	241	LEU	0	-0.069	-0.046	47.162	-0.011	-0.011	0.000	0.000	0.000	0.000
28	B	242	ASN	0	0.019	-0.007	47.213	0.154	0.154	0.000	0.000	0.000	0.000
29	B	243	VAL	0	0.032	0.027	43.444	-0.014	-0.014	0.000	0.000	0.000	0.000
30	B	244	LEU	0	-0.059	-0.030	45.534	-0.014	-0.014	0.000	0.000	0.000	0.000
31	B	245	LYS	1	0.844	0.925	48.158	6.543	6.543	0.000	0.000	0.000	0.000
32	B	246	ASP	-1	-0.952	-0.962	42.550	-7.567	-7.567	0.000	0.000	0.000	0.000
33	B	247	ALA	0	-0.006	0.021	43.727	-0.186	-0.186	0.000	0.000	0.000	0.000
34	B	248	THR	0	0.007	0.006	41.899	0.055	0.055	0.000	0.000	0.000	0.000
35	B	249	PRO	0	-0.048	-0.037	45.021	0.106	0.106	0.000	0.000	0.000	0.000
36	B	250	ILE	0	0.017	0.011	45.935	-0.134	-0.134	0.000	0.000	0.000	0.000
37	B	251	GLU	-1	-0.877	-0.950	44.743	-7.157	-7.157	0.000	0.000	0.000	0.000
38	B	252	ASP	-1	-0.817	-0.937	48.274	-6.273	-6.273	0.000	0.000	0.000	0.000
39	B	253	VAL	0	-0.073	-0.042	47.620	-0.138	-0.138	0.000	0.000	0.000	0.000
40	B	254	PHE	0	-0.063	-0.044	46.175	-0.067	-0.067	0.000	0.000	0.000	0.000
41	B	255	SER	0	-0.072	-0.026	45.769	-0.118	-0.118	0.000	0.000	0.000	0.000
42	B	256	PHE	0	0.018	0.021	42.584	-0.109	-0.109	0.000	0.000	0.000	0.000
43	B	257	ASN	0	-0.043	-0.033	39.167	0.156	0.156	0.000	0.000	0.000	0.000
44	B	258	TYR	0	0.001	-0.004	38.903	-0.171	-0.171	0.000	0.000	0.000	0.000
45	B	259	PRO	0	0.012	0.014	34.626	0.070	0.070	0.000	0.000	0.000	0.000
46	B	260	GLU	-1	-0.853	-0.937	35.320	-8.810	-8.810	0.000	0.000	0.000	0.000
47	B	261	GLY	0	-0.009	-0.003	35.782	0.139	0.139	0.000	0.000	0.000	0.000
48	B	262	ILE	0	-0.127	-0.050	36.989	0.282	0.282	0.000	0.000	0.000	0.000
49	B	263	GLU	-1	-0.809	-0.901	39.168	-8.400	-8.400	0.000	0.000	0.000	0.000
50	B	264	GLY	0	-0.034	-0.047	41.479	0.190	0.190	0.000	0.000	0.000	0.000
51	B	265	PRO	0	0.027	0.049	43.305	0.093	0.093	0.000	0.000	0.000	0.000
52	B	266	ASP	-1	-0.794	-0.915	45.207	-6.598	-6.598	0.000	0.000	0.000	0.000
53	B	267	ILE	0	-0.039	-0.017	46.657	0.200	0.200	0.000	0.000	0.000	0.000
54	B	268	LYS	1	0.821	0.908	49.738	6.057	6.057	0.000	0.000	0.000	0.000
55	B	269	TYR	0	0.070	0.062	50.871	0.127	0.127	0.000	0.000	0.000	0.000
56	B	270	LYS	1	0.861	0.910	50.391	6.482	6.482	0.000	0.000	0.000	0.000
57	B	271	LYS	1	0.842	0.924	54.969	5.715	5.715	0.000	0.000	0.000	0.000
58	B	272	GLU	-1	-0.872	-0.916	57.647	-5.096	-5.096	0.000	0.000	0.000	0.000
59	B	273	HIS	0	-0.002	-0.001	59.422	-0.018	-0.018	0.000	0.000	0.000	0.000
60	B	274	VAL	0	-0.021	-0.008	53.017	-0.055	-0.055	0.000	0.000	0.000	0.000
61	B	275	LYS	1	0.909	0.965	55.854	5.717	5.717	0.000	0.000	0.000	0.000
62	B	276	TYR	0	0.028	-0.013	53.888	-0.002	-0.002	0.000	0.000	0.000	0.000
63	B	277	THR	0	-0.035	-0.006	53.677	0.064	0.064	0.000	0.000	0.000	0.000
64	B	278	TYR	0	0.105	0.046	51.090	-0.127	-0.127	0.000	0.000	0.000	0.000
65	B	279	GLY	0	0.039	-0.004	50.249	0.115	0.115	0.000	0.000	0.000	0.000
66	B	280	PRO	0	-0.047	-0.024	51.314	0.008	0.008	0.000	0.000	0.000	0.000
67	B	281	THR	0	0.045	0.012	47.976	0.049	0.049	0.000	0.000	0.000	0.000
68	B	282	PHE	0	0.061	0.045	45.218	-0.013	-0.013	0.000	0.000	0.000	0.000
69	B	283	LEU	0	0.021	0.007	48.104	-0.047	-0.047	0.000	0.000	0.000	0.000
70	B	284	LEU	0	-0.032	-0.013	49.375	0.021	0.021	0.000	0.000	0.000	0.000
71	B	285	GLN	0	0.062	0.028	43.934	0.064	0.064	0.000	0.000	0.000	0.000
72	B	286	PHE	0	0.020	0.009	45.840	-0.083	-0.083	0.000	0.000	0.000	0.000
73	B	287	LYS	1	0.772	0.873	47.778	6.510	6.510	0.000	0.000	0.000	0.000
74	B	288	ASP	-1	-0.865	-0.918	45.222	-6.860	-6.860	0.000	0.000	0.000	0.000
75	B	289	LYS	1	0.908	0.958	40.226	7.855	7.855	0.000	0.000	0.000	0.000
76	B	290	LEU	0	-0.041	-0.027	45.679	0.013	0.013	0.000	0.000	0.000	0.000
77	B	291	ASN	0	-0.017	0.007	47.775	0.299	0.299	0.000	0.000	0.000	0.000
78	B	292	VAL	0	0.007	-0.002	49.094	-0.044	-0.044	0.000	0.000	0.000	0.000
79	B	293	LYS	1	0.946	0.966	51.859	5.816	5.816	0.000	0.000	0.000	0.000
80	B	294	ALA	0	-0.009	-0.007	54.795	0.025	0.025	0.000	0.000	0.000	0.000
81	B	295	ASP	-1	-0.909	-0.962	56.679	-5.158	-5.158	0.000	0.000	0.000	0.000
82	B	296	ALA	0	0.020	0.019	59.302	0.006	0.006	0.000	0.000	0.000	0.000
83	B	297	GLU	-1	-0.828	-0.911	54.000	-5.964	-5.964	0.000	0.000	0.000	0.000
84	B	298	TRP	0	0.024	0.004	54.981	-0.056	-0.056	0.000	0.000	0.000	0.000
85	B	299	VAL	0	-0.006	0.024	57.514	-0.026	-0.026	0.000	0.000	0.000	0.000
86	B	300	GLN	0	-0.041	-0.030	55.046	-0.005	-0.005	0.000	0.000	0.000	0.000
87	B	301	SER	0	0.047	0.026	52.215	-0.037	-0.037	0.000	0.000	0.000	0.000
88	B	302	THR	0	-0.116	-0.101	54.578	-0.032	-0.032	0.000	0.000	0.000	0.000
89	B	303	ALA	0	0.024	0.017	56.808	0.001	0.001	0.000	0.000	0.000	0.000
90	B	304	SER	0	0.000	0.008	53.432	0.013	0.013	0.000	0.000	0.000	0.000
91	B	305	LYS	1	0.816	0.911	51.522	6.136	6.136	0.000	0.000	0.000	0.000
92	B	306	ILE	0	0.016	0.033	50.205	0.110	0.110	0.000	0.000	0.000	0.000
93	B	307	VAL	0	-0.009	-0.011	53.090	-0.064	-0.064	0.000	0.000	0.000	0.000
94	B	308	ILE	0	0.045	0.023	50.499	0.080	0.080	0.000	0.000	0.000	0.000
95	B	309	PRO	0	-0.049	0.000	53.486	0.001	0.001	0.000	0.000	0.000	0.000
96	B	310	PRO	0	0.027	0.027	51.242	-0.051	-0.051	0.000	0.000	0.000	0.000
97	B	311	GLY	0	0.028	-0.010	51.703	0.143	0.143	0.000	0.000	0.000	0.000
98	B	312	MET	0	-0.032	0.000	47.748	-0.151	-0.151	0.000	0.000	0.000	0.000
99	B	313	GLY	0	-0.017	-0.001	50.696	0.016	0.016	0.000	0.000	0.000	0.000
100	B	314	ARG	0	-0.015	-0.005	51.315	0.166	0.166	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:215:GLY)