FMO DATABASE

FMODB ID: 74M9K

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	89
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-528128.83364
FMO2-HF: Nuclear repulsion	492332.884995
FMO2-HF: Total energy	-35795.948645
FMO2-MP2: Total energy	-35896.434626

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:4:ARG)

Summations of interaction energy for fragment #1(A:4:ARG)

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.
487.289	489.597	0.248	-1.444	-1.112	-0.009

Interaction energy analysis for fragmet #1(A:4:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.873 / q_NPA : 1.927

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	6	LYS	1	1.045	1.015	2.852	40.143	42.451	0.248	-1.444	-1.112	-0.009
4	A	7	LYS	1	1.041	1.012	5.672	46.028	46.028	0.000	0.000	0.000	0.000
5	A	8	VAL	0	-0.035	-0.007	6.859	4.979	4.979	0.000	0.000	0.000	0.000
6	A	9	GLY	0	0.016	0.003	6.553	5.713	5.713	0.000	0.000	0.000	0.000
7	A	10	ILE	0	0.064	0.014	6.852	-4.243	-4.243	0.000	0.000	0.000	0.000
8	A	11	VAL	0	-0.026	0.000	8.070	1.042	1.042	0.000	0.000	0.000	0.000
9	A	12	GLY	0	-0.005	-0.010	7.730	2.710	2.710	0.000	0.000	0.000	0.000
10	A	13	LYS	1	0.862	0.934	8.776	42.612	42.612	0.000	0.000	0.000	0.000
11	A	14	TYR	0	-0.023	-0.027	10.769	2.737	2.737	0.000	0.000	0.000	0.000
12	A	15	GLY	0	0.003	0.010	11.630	2.275	2.275	0.000	0.000	0.000	0.000
13	A	16	THR	0	-0.031	-0.035	12.664	-0.122	-0.122	0.000	0.000	0.000	0.000
14	A	17	ARG	1	0.969	1.000	14.417	37.864	37.864	0.000	0.000	0.000	0.000
15	A	18	TYR	0	0.088	0.049	17.049	0.554	0.554	0.000	0.000	0.000	0.000
16	A	19	GLY	0	0.101	0.057	17.944	-1.408	-1.408	0.000	0.000	0.000	0.000
17	A	20	ALA	0	0.009	-0.007	16.558	-1.170	-1.170	0.000	0.000	0.000	0.000
18	A	21	SER	0	-0.003	0.000	17.001	-1.752	-1.752	0.000	0.000	0.000	0.000
19	A	22	LEU	0	0.090	0.044	19.226	-0.954	-0.954	0.000	0.000	0.000	0.000
20	A	23	ARG	1	0.940	0.960	12.927	37.806	37.806	0.000	0.000	0.000	0.000
21	A	24	LYS	1	0.899	0.950	14.959	34.009	34.009	0.000	0.000	0.000	0.000
22	A	25	MET	0	0.052	0.019	16.136	-0.936	-0.936	0.000	0.000	0.000	0.000
23	A	26	VAL	0	0.046	0.030	15.335	-0.355	-0.355	0.000	0.000	0.000	0.000
24	A	27	LYS	1	0.878	0.944	10.463	47.701	47.701	0.000	0.000	0.000	0.000
25	A	28	LYS	1	0.940	0.971	14.255	30.735	30.735	0.000	0.000	0.000	0.000
26	A	29	ILE	0	0.072	0.045	16.732	0.119	0.119	0.000	0.000	0.000	0.000
27	A	30	GLU	-1	-0.793	-0.865	12.991	-39.298	-39.298	0.000	0.000	0.000	0.000
28	A	31	ILE	0	-0.018	-0.029	11.199	-1.482	-1.482	0.000	0.000	0.000	0.000
29	A	32	SER	0	-0.025	0.015	13.480	0.840	0.840	0.000	0.000	0.000	0.000
30	A	33	GLN	0	0.076	0.043	15.784	2.491	2.491	0.000	0.000	0.000	0.000
31	A	34	HIS	0	-0.039	-0.028	12.224	1.650	1.650	0.000	0.000	0.000	0.000
32	A	35	ALA	0	-0.036	0.001	13.909	-0.839	-0.839	0.000	0.000	0.000	0.000
33	A	36	LYS	1	0.907	0.959	13.953	37.439	37.439	0.000	0.000	0.000	0.000
34	A	37	TYR	0	0.024	-0.014	17.134	-0.395	-0.395	0.000	0.000	0.000	0.000
35	A	38	THR	0	0.015	-0.004	19.954	-0.142	-0.142	0.000	0.000	0.000	0.000
36	A	39	CYS	-1	-0.833	-0.740	22.446	-20.747	-20.747	0.000	0.000	0.000	0.000
37	A	40	SER	0	-0.007	-0.011	25.413	0.206	0.206	0.000	0.000	0.000	0.000
38	A	41	PHE	0	0.055	-0.021	28.684	0.639	0.639	0.000	0.000	0.000	0.000
39	A	42	CYS	0	-0.078	-0.105	27.303	0.122	0.122	0.000	0.000	0.000	0.000
40	A	43	GLY	0	0.084	0.051	26.431	-0.203	-0.203	0.000	0.000	0.000	0.000
41	A	44	LYS	1	0.901	0.933	22.905	20.296	20.296	0.000	0.000	0.000	0.000
42	A	45	THR	0	0.024	0.020	18.053	0.335	0.335	0.000	0.000	0.000	0.000
43	A	46	LYS	1	0.886	0.923	18.626	23.205	23.205	0.000	0.000	0.000	0.000
44	A	47	MET	0	0.024	0.041	20.758	0.475	0.475	0.000	0.000	0.000	0.000
45	A	48	LYS	1	0.979	0.984	16.547	29.453	29.453	0.000	0.000	0.000	0.000
46	A	49	ARG	1	0.859	0.936	19.249	28.210	28.210	0.000	0.000	0.000	0.000
47	A	50	ARG	1	0.894	0.944	20.691	20.454	20.454	0.000	0.000	0.000	0.000
48	A	51	ALA	0	0.058	0.022	23.363	-0.232	-0.232	0.000	0.000	0.000	0.000
49	A	52	VAL	0	0.014	-0.002	24.398	-0.673	-0.673	0.000	0.000	0.000	0.000
50	A	53	GLY	0	0.043	0.034	25.519	0.713	0.713	0.000	0.000	0.000	0.000
51	A	54	ILE	0	-0.014	0.014	26.026	0.513	0.513	0.000	0.000	0.000	0.000
52	A	55	TRP	0	-0.012	-0.010	19.350	-1.444	-1.444	0.000	0.000	0.000	0.000
53	A	56	HIS	0	-0.002	-0.016	23.720	1.142	1.142	0.000	0.000	0.000	0.000
54	A	57	CYS	0	-0.029	-0.036	23.381	-1.349	-1.349	0.000	0.000	0.000	0.000
55	A	58	GLY	0	-0.015	-0.015	23.125	0.669	0.669	0.000	0.000	0.000	0.000
56	A	59	SER	0	-0.066	-0.041	24.127	-0.013	-0.013	0.000	0.000	0.000	0.000
57	A	60	CYS	0	0.038	-0.005	26.298	0.442	0.442	0.000	0.000	0.000	0.000
58	A	61	MET	0	0.031	0.033	26.841	0.378	0.378	0.000	0.000	0.000	0.000
59	A	62	LYS	1	1.004	1.011	29.215	17.932	17.932	0.000	0.000	0.000	0.000
60	A	63	THR	0	0.012	0.001	28.234	-0.755	-0.755	0.000	0.000	0.000	0.000
61	A	64	VAL	0	-0.043	-0.025	27.965	0.624	0.624	0.000	0.000	0.000	0.000
62	A	65	ALA	0	0.039	0.030	28.443	-0.615	-0.615	0.000	0.000	0.000	0.000
63	A	66	GLY	0	0.033	0.005	27.312	0.228	0.228	0.000	0.000	0.000	0.000
64	A	67	GLY	0	-0.009	-0.004	26.045	0.361	0.361	0.000	0.000	0.000	0.000
65	A	68	ALA	0	-0.009	-0.004	25.028	-0.521	-0.521	0.000	0.000	0.000	0.000
66	A	69	TRP	0	0.002	-0.012	20.541	-0.963	-0.963	0.000	0.000	0.000	0.000
67	A	70	THR	0	0.010	0.000	20.112	-1.091	-1.091	0.000	0.000	0.000	0.000
68	A	71	TYR	0	0.016	0.020	22.152	0.913	0.913	0.000	0.000	0.000	0.000
69	A	72	ASN	0	0.032	0.015	24.075	1.360	1.360	0.000	0.000	0.000	0.000
70	A	73	THR	0	0.044	0.005	25.786	-0.508	-0.508	0.000	0.000	0.000	0.000
71	A	74	THR	0	0.072	0.022	28.271	0.328	0.328	0.000	0.000	0.000	0.000
72	A	75	SER	0	0.025	0.042	30.406	0.740	0.740	0.000	0.000	0.000	0.000
73	A	76	ALA	0	0.076	0.036	31.455	0.505	0.505	0.000	0.000	0.000	0.000
74	A	77	VAL	0	-0.046	-0.028	30.038	0.490	0.490	0.000	0.000	0.000	0.000
75	A	78	THR	0	0.033	0.009	33.195	0.440	0.440	0.000	0.000	0.000	0.000
76	A	79	VAL	0	0.044	0.023	36.084	0.449	0.449	0.000	0.000	0.000	0.000
77	A	80	LYS	1	0.907	0.960	33.809	18.083	18.083	0.000	0.000	0.000	0.000
78	A	81	SER	0	-0.064	-0.046	36.533	0.254	0.254	0.000	0.000	0.000	0.000
79	A	82	ALA	0	0.027	0.014	39.213	0.338	0.338	0.000	0.000	0.000	0.000
80	A	83	ILE	0	0.020	0.006	41.272	0.329	0.329	0.000	0.000	0.000	0.000
81	A	84	ARG	1	0.913	0.951	37.435	16.112	16.112	0.000	0.000	0.000	0.000
82	A	85	ARG	1	1.008	1.014	43.249	13.730	13.730	0.000	0.000	0.000	0.000
83	A	86	LEU	0	-0.007	-0.003	45.509	0.238	0.238	0.000	0.000	0.000	0.000
84	A	87	LYS	1	0.878	0.952	46.075	13.384	13.384	0.000	0.000	0.000	0.000
85	A	88	GLU	-1	-0.886	-0.948	47.323	-12.770	-12.770	0.000	0.000	0.000	0.000
86	A	89	LEU	0	0.010	-0.002	48.990	0.175	0.175	0.000	0.000	0.000	0.000
87	A	90	LYS	1	0.880	0.943	50.947	12.260	12.260	0.000	0.000	0.000	0.000
88	A	91	ASP	-1	-0.952	-0.974	50.137	-12.193	-12.193	0.000	0.000	0.000	0.000
89	A	92	GLN	-1	-0.984	-0.980	51.577	-11.510	-11.510	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:4:ARG)