FMO DATABASE

FMODB ID: N6ZVQ

Calculation Name: 7LS2-A-Other547

Preferred Name:

Target Type:

Ligand Name: 2-methyl, 7-(3-methyl-pentane), guanosine-5'-monophosphate | (2~{r})-2-azanyl-4-[5-[(2~{s},3~{r},4~{s},5~{r})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic acid | guanosine-5'-diphosphate | n7-methyl-guanosine-5'-monophosphate | 7-propyl, guanosine-5'-monophosphate | 7-ethyl, guanosine-5'-monophosphate | 6-propyl, guanosine-5'-monophosphate | n(4)-acetylcytidine-5'-monophosphate | 6-ethyl, guanosine-5'-monophosphate | 2n-methylguanosine-5'-monophosphate | 6-methyl, guanosine-5'-monophosphate | 4-isopropyl, uridine-5'-monophosphate | 2'-methyl, 3-propyl, cytidine-5'-monophosphate | 6-hydro-1-methyladenosine-5'-monophosphate | n6-methyladenosine-5'-monophosphate | {3-[4-(2-amino-2-carboxy-ethyl)-1h-imidazol-2-yl]-1-carbamoyl-propyl}-trimethyl-ammonium | pseudouridine-5'-monophosphate | 5-methylcytidine-5'-monophosphate | 4-methyl, cytidine-5'-monophosphate | o2'-methylguanosine-5'-monophosphate | 3-methyluridine-5'-monophoshate | 3-methyl, cytidine-5'-monophosphate | o2'-methylycytidine-5'-monophosphate | o2'-methyluridine 5'-monophosphate | 2'-o-methyladenosine 5'-(dihydrogen phosphate) | n-methyl-lysine | magnesium ion | zinc ion

Ligand 3-letter code: MHG | B8N | GDP | G7M | P7G | E7G | B9B | 4AC | E6G | 2MG | B8W | I4U | B9H | 1MA | 6MZ | DDE | PSU | 5MC | B8T | OMG | UR3 | B8Q | OMC | OMU | A2M | MLZ | MG | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7LS2

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-06

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	134
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1181832.73771
FMO2-HF: Nuclear repulsion	1127137.172357
FMO2-HF: Total energy	-54695.565353
FMO2-MP2: Total energy	-54857.355892

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:1:MET)

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

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.
295.77	299.86	3.254	-2.65	-4.694	-0.025

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.891 / q_NPA : 0.945

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	3	PHE	0	0.123	0.042	2.809	-7.286	-3.366	3.255	-2.642	-4.534	-0.025
4	A	4	ASN	0	0.006	0.011	5.003	5.576	5.746	-0.001	-0.008	-0.160	0.000
5	A	5	PRO	0	0.085	0.039	8.629	-1.540	-1.540	0.000	0.000	0.000	0.000
6	A	6	PHE	0	0.065	0.031	10.585	0.575	0.575	0.000	0.000	0.000	0.000
7	A	7	VAL	0	-0.085	-0.024	9.553	1.139	1.139	0.000	0.000	0.000	0.000
8	A	8	THR	0	-0.003	-0.003	9.628	-2.201	-2.201	0.000	0.000	0.000	0.000
9	A	9	SER	0	0.035	0.001	7.157	-2.373	-2.373	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.799	-0.892	9.180	-20.938	-20.938	0.000	0.000	0.000	0.000
11	A	11	ARG	1	1.005	0.992	12.487	18.628	18.628	0.000	0.000	0.000	0.000
12	A	12	SER	0	0.038	0.023	14.321	0.302	0.302	0.000	0.000	0.000	0.000
13	A	13	LYS	1	1.012	1.008	15.138	18.395	18.395	0.000	0.000	0.000	0.000
14	A	14	ASN	0	-0.031	-0.023	11.759	0.518	0.518	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.960	0.981	15.516	15.045	15.045	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.956	0.988	18.520	13.039	13.039	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.957	0.975	15.060	18.545	18.545	0.000	0.000	0.000	0.000
18	A	18	HIS	0	0.019	0.020	18.262	0.205	0.205	0.000	0.000	0.000	0.000
19	A	19	PHE	0	0.031	0.002	20.114	0.543	0.543	0.000	0.000	0.000	0.000
20	A	20	ASN	0	0.011	0.007	23.264	0.620	0.620	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.017	0.033	21.660	0.024	0.024	0.000	0.000	0.000	0.000
22	A	22	PRO	0	0.062	0.038	23.396	0.451	0.451	0.000	0.000	0.000	0.000
23	A	23	SER	0	0.062	0.017	25.461	-0.467	-0.467	0.000	0.000	0.000	0.000
24	A	24	HIS	0	0.096	0.043	25.335	0.080	0.080	0.000	0.000	0.000	0.000
25	A	25	ILE	0	0.016	0.011	20.230	-0.360	-0.360	0.000	0.000	0.000	0.000
26	A	26	ARG	1	0.895	0.940	22.269	11.492	11.492	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.966	0.986	24.185	11.308	11.308	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.949	0.974	19.702	14.630	14.630	0.000	0.000	0.000	0.000
29	A	29	ILE	0	0.013	0.030	17.917	-0.491	-0.491	0.000	0.000	0.000	0.000
30	A	30	MET	0	-0.064	-0.002	20.537	-0.076	-0.076	0.000	0.000	0.000	0.000
31	A	31	SER	0	-0.043	-0.038	20.322	0.557	0.557	0.000	0.000	0.000	0.000
32	A	32	SER	0	0.009	0.010	22.476	0.009	0.009	0.000	0.000	0.000	0.000
33	A	33	PRO	0	-0.031	-0.023	22.066	-0.201	-0.201	0.000	0.000	0.000	0.000
34	A	34	LEU	0	0.006	0.009	23.562	0.455	0.455	0.000	0.000	0.000	0.000
35	A	35	SER	0	0.005	-0.031	26.103	-0.424	-0.424	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.928	0.960	26.863	10.880	10.880	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.718	-0.836	28.581	-10.052	-10.052	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.030	-0.017	29.330	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.851	0.925	23.195	12.707	12.707	0.000	0.000	0.000	0.000
40	A	40	GLN	0	0.017	0.027	26.635	-0.308	-0.308	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.939	0.985	29.191	9.054	9.054	0.000	0.000	0.000	0.000
42	A	42	TYR	0	0.031	0.006	28.460	0.215	0.215	0.000	0.000	0.000	0.000
43	A	43	ASN	0	0.121	0.084	22.878	-0.838	-0.838	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.002	-0.022	22.491	-0.631	-0.631	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.954	0.981	17.446	16.901	16.901	0.000	0.000	0.000	0.000
46	A	46	SER	0	0.018	-0.007	18.947	0.247	0.247	0.000	0.000	0.000	0.000
47	A	47	MET	0	0.028	0.009	21.968	-0.355	-0.355	0.000	0.000	0.000	0.000
48	A	48	PRO	0	-0.013	0.001	23.373	-0.013	-0.013	0.000	0.000	0.000	0.000
49	A	49	ILE	0	0.021	0.037	25.228	0.366	0.366	0.000	0.000	0.000	0.000
50	A	50	ARG	1	0.801	0.901	28.116	9.027	9.027	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.947	0.973	31.603	7.849	7.849	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.827	-0.916	34.987	-7.993	-7.993	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.783	-0.886	31.483	-9.716	-9.716	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.820	-0.896	34.486	-8.069	-8.069	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.040	-0.022	30.641	-0.326	-0.326	0.000	0.000	0.000	0.000
56	A	56	GLN	0	0.083	0.055	31.339	0.457	0.457	0.000	0.000	0.000	0.000
57	A	57	VAL	0	0.034	0.013	30.098	-0.505	-0.505	0.000	0.000	0.000	0.000
58	A	58	VAL	0	0.046	0.023	25.950	0.099	0.099	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.842	0.902	23.529	11.995	11.995	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.041	0.023	28.033	0.120	0.120	0.000	0.000	0.000	0.000
61	A	61	HIS	0	0.056	0.024	30.111	0.076	0.076	0.000	0.000	0.000	0.000
62	A	62	TYR	0	-0.005	-0.010	33.607	0.021	0.021	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.882	0.950	29.639	10.059	10.059	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.075	0.027	33.175	0.233	0.233	0.000	0.000	0.000	0.000
65	A	65	GLN	0	-0.003	-0.004	34.322	-0.065	-0.065	0.000	0.000	0.000	0.000
66	A	66	GLN	0	0.009	0.013	36.063	0.227	0.227	0.000	0.000	0.000	0.000
67	A	67	ILE	0	-0.015	-0.006	35.623	-0.197	-0.197	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.042	0.019	36.343	0.270	0.270	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.895	0.950	35.974	7.337	7.337	0.000	0.000	0.000	0.000
70	A	70	VAL	0	-0.047	-0.021	31.941	0.035	0.035	0.000	0.000	0.000	0.000
71	A	71	VAL	0	0.088	0.046	35.274	0.060	0.060	0.000	0.000	0.000	0.000
72	A	72	GLN	0	0.007	-0.003	35.310	0.191	0.191	0.000	0.000	0.000	0.000
73	A	73	VAL	0	0.012	-0.003	29.626	-0.246	-0.246	0.000	0.000	0.000	0.000
74	A	74	TYR	0	0.043	0.029	31.968	-0.110	-0.110	0.000	0.000	0.000	0.000
75	A	75	ARG	1	0.890	0.904	27.282	10.366	10.366	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.951	0.980	27.918	8.547	8.547	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.959	0.979	29.415	9.317	9.317	0.000	0.000	0.000	0.000
78	A	78	TYR	0	-0.057	-0.041	22.390	-0.130	-0.130	0.000	0.000	0.000	0.000
79	A	79	VAL	0	-0.008	0.006	26.621	-0.243	-0.243	0.000	0.000	0.000	0.000
80	A	80	ILE	0	-0.040	-0.028	28.978	0.118	0.118	0.000	0.000	0.000	0.000
81	A	81	TYR	0	0.019	0.021	31.419	-0.021	-0.021	0.000	0.000	0.000	0.000
82	A	82	ILE	0	0.008	-0.008	32.348	-0.048	-0.048	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.821	-0.915	36.418	-7.543	-7.543	0.000	0.000	0.000	0.000
84	A	84	ARG	1	1.005	1.000	39.070	7.472	7.472	0.000	0.000	0.000	0.000
85	A	85	VAL	0	-0.062	-0.017	34.481	0.020	0.020	0.000	0.000	0.000	0.000
86	A	86	GLN	0	0.032	0.009	37.809	-0.119	-0.119	0.000	0.000	0.000	0.000
87	A	87	ARG	1	0.882	0.952	39.403	7.545	7.545	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.698	-0.816	42.152	-6.701	-6.701	0.000	0.000	0.000	0.000
89	A	89	LYS	1	0.871	0.930	43.947	6.835	6.835	0.000	0.000	0.000	0.000
90	A	90	ALA	0	0.037	0.007	45.809	0.090	0.090	0.000	0.000	0.000	0.000
91	A	91	ASN	0	-0.025	-0.013	48.476	0.023	0.023	0.000	0.000	0.000	0.000
92	A	92	GLY	0	0.060	0.042	49.584	0.114	0.114	0.000	0.000	0.000	0.000
93	A	93	THR	0	0.013	0.026	47.030	0.048	0.048	0.000	0.000	0.000	0.000
94	A	94	THR	0	-0.008	-0.032	44.211	-0.125	-0.125	0.000	0.000	0.000	0.000
95	A	95	VAL	0	-0.045	-0.031	41.083	-0.027	-0.027	0.000	0.000	0.000	0.000
96	A	96	HIS	0	0.016	0.004	37.645	-0.169	-0.169	0.000	0.000	0.000	0.000
97	A	97	VAL	0	-0.014	0.000	34.005	-0.071	-0.071	0.000	0.000	0.000	0.000
98	A	98	GLY	0	-0.045	-0.025	32.844	-0.110	-0.110	0.000	0.000	0.000	0.000
99	A	99	ILE	0	0.036	0.021	29.713	-0.227	-0.227	0.000	0.000	0.000	0.000
100	A	100	HIS	0	0.087	0.063	21.498	-0.104	-0.104	0.000	0.000	0.000	0.000
101	A	101	PRO	0	0.034	0.017	24.088	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	102	SER	0	-0.023	-0.038	20.581	-0.155	-0.155	0.000	0.000	0.000	0.000
103	A	103	LYS	1	0.854	0.910	20.613	13.450	13.450	0.000	0.000	0.000	0.000
104	A	104	VAL	0	0.023	0.027	25.309	0.387	0.387	0.000	0.000	0.000	0.000
105	A	105	VAL	0	-0.039	-0.018	25.996	-0.567	-0.567	0.000	0.000	0.000	0.000
106	A	106	ILE	0	-0.028	-0.012	27.532	0.385	0.385	0.000	0.000	0.000	0.000
107	A	107	THR	0	-0.041	-0.041	29.785	-0.110	-0.110	0.000	0.000	0.000	0.000
108	A	108	ARG	1	0.959	0.962	32.899	8.176	8.176	0.000	0.000	0.000	0.000
109	A	109	LEU	0	-0.071	-0.019	30.456	-0.112	-0.112	0.000	0.000	0.000	0.000
110	A	110	LYS	1	0.928	0.948	33.607	8.224	8.224	0.000	0.000	0.000	0.000
111	A	111	LEU	0	-0.023	-0.015	34.689	-0.301	-0.301	0.000	0.000	0.000	0.000
112	A	112	ASP	-1	-0.738	-0.867	34.254	-9.099	-9.099	0.000	0.000	0.000	0.000
113	A	113	LYS	1	1.027	1.000	35.095	7.922	7.922	0.000	0.000	0.000	0.000
114	A	114	ASP	-1	-0.842	-0.910	31.896	-9.484	-9.484	0.000	0.000	0.000	0.000
115	A	115	ARG	1	0.733	0.857	28.738	9.842	9.842	0.000	0.000	0.000	0.000
116	A	116	LYS	1	0.975	0.986	30.174	9.162	9.162	0.000	0.000	0.000	0.000
117	A	117	LYS	1	0.998	1.011	30.079	9.786	9.786	0.000	0.000	0.000	0.000
118	A	118	ILE	0	-0.051	-0.043	24.305	-0.420	-0.420	0.000	0.000	0.000	0.000
119	A	119	LEU	0	-0.002	0.000	25.736	-0.564	-0.564	0.000	0.000	0.000	0.000
120	A	120	GLU	-1	-0.888	-0.937	26.575	-10.589	-10.589	0.000	0.000	0.000	0.000
121	A	121	ARG	1	0.928	0.963	24.124	11.928	11.928	0.000	0.000	0.000	0.000
122	A	122	LYS	1	0.843	0.929	20.617	13.771	13.771	0.000	0.000	0.000	0.000
123	A	123	ALA	0	0.030	0.027	22.167	-0.584	-0.584	0.000	0.000	0.000	0.000
124	A	124	LYS	1	1.053	1.030	23.894	10.912	10.912	0.000	0.000	0.000	0.000
125	A	125	SER	0	-0.081	-0.047	19.671	-0.486	-0.486	0.000	0.000	0.000	0.000
126	A	126	ARG	1	0.830	0.896	18.135	14.472	14.472	0.000	0.000	0.000	0.000
127	A	127	GLN	0	0.003	0.010	20.406	-0.275	-0.275	0.000	0.000	0.000	0.000
128	A	128	VAL	0	0.064	0.030	20.408	-0.119	-0.119	0.000	0.000	0.000	0.000
129	A	129	GLY	0	-0.045	-0.025	17.731	-0.353	-0.353	0.000	0.000	0.000	0.000
130	A	130	LYS	1	0.862	0.925	17.463	15.705	15.705	0.000	0.000	0.000	0.000
131	A	131	GLU	-1	-0.787	-0.886	20.213	-12.357	-12.357	0.000	0.000	0.000	0.000
132	A	132	LYS	1	0.931	0.971	13.896	19.723	19.723	0.000	0.000	0.000	0.000
133	A	133	GLY	0	-0.085	-0.045	17.520	-0.723	-0.723	0.000	0.000	0.000	0.000
134	A	134	LYS	0	-0.022	0.006	18.319	-1.406	-1.406	0.000	0.000	0.000	0.000

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