FMO DATABASE

FMODB ID: G7R61

Calculation Name: 7OSM-A-Xray547

Preferred Name:

Target Type:

Ligand Name: wybutosine | guanosine-5'-triphosphate | {3-[4-(2-amino-2-carboxy-ethyl)-1h-imidazol-2-yl]-1-carbamoyl-propyl}-trimethyl-ammonium | magnesium ion | zinc ion

Ligand 3-letter code: YG | GTP | DDE | MG | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7OSM

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

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	50
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-246498.181738
FMO2-HF: Nuclear repulsion	224908.383424
FMO2-HF: Total energy	-21589.798314
FMO2-MP2: Total energy	-21652.804192

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:2:ALA)

Summations of interaction energy for fragment #1(A:2:ALA)

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.
229.67	231.458	11.388	-6.968	-6.208	-0.075

Interaction energy analysis for fragmet #1(A:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.790 / q_NPA : 0.870

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

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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	4	GLN	0	0.095	0.053	3.293	5.295	7.792	-0.002	-1.205	-1.290	-0.004
4	A	5	LYS	0	-0.047	-0.007	1.966	-41.616	-42.426	11.390	-5.736	-4.844	-0.071
5	A	6	SER	0	0.105	0.060	4.070	9.908	10.009	0.000	-0.027	-0.074	0.000
6	A	7	PHE	0	0.075	0.020	7.018	-2.391	-2.391	0.000	0.000	0.000	0.000
7	A	8	ARG	1	1.031	1.019	9.813	22.733	22.733	0.000	0.000	0.000	0.000
8	A	9	ILE	0	0.034	0.015	5.320	1.307	1.307	0.000	0.000	0.000	0.000
9	A	10	LYS	1	0.983	0.990	7.158	30.839	30.839	0.000	0.000	0.000	0.000
10	A	11	GLN	0	0.025	0.005	7.996	1.534	1.534	0.000	0.000	0.000	0.000
11	A	12	LYS	1	0.862	0.924	10.269	25.386	25.386	0.000	0.000	0.000	0.000
12	A	13	MET	0	0.008	-0.007	5.044	0.358	0.358	0.000	0.000	0.000	0.000
13	A	14	ALA	0	0.021	0.020	9.891	1.721	1.721	0.000	0.000	0.000	0.000
14	A	15	LYS	1	0.901	0.953	12.089	19.134	19.134	0.000	0.000	0.000	0.000
15	A	16	ALA	0	0.033	0.013	12.215	1.382	1.382	0.000	0.000	0.000	0.000
16	A	17	LYS	1	0.952	0.985	12.941	19.920	19.920	0.000	0.000	0.000	0.000
17	A	18	LYS	1	0.988	0.989	14.810	17.866	17.866	0.000	0.000	0.000	0.000
18	A	19	GLN	0	0.050	0.016	17.862	0.409	0.409	0.000	0.000	0.000	0.000
19	A	20	ASN	0	-0.067	-0.012	15.720	1.451	1.451	0.000	0.000	0.000	0.000
20	A	21	ARG	1	0.946	0.964	18.881	12.450	12.450	0.000	0.000	0.000	0.000
21	A	22	PRO	0	0.047	0.013	22.336	0.071	0.071	0.000	0.000	0.000	0.000
22	A	23	LEU	0	0.031	0.018	26.011	-0.243	-0.243	0.000	0.000	0.000	0.000
23	A	24	PRO	0	-0.020	-0.023	27.337	0.120	0.120	0.000	0.000	0.000	0.000
24	A	25	GLN	0	0.035	0.023	30.110	0.148	0.148	0.000	0.000	0.000	0.000
25	A	26	TRP	0	0.119	0.079	32.390	0.213	0.213	0.000	0.000	0.000	0.000
26	A	27	ILE	0	-0.022	-0.008	32.063	0.210	0.210	0.000	0.000	0.000	0.000
27	A	28	ARG	1	0.836	0.905	32.770	9.249	9.249	0.000	0.000	0.000	0.000
28	A	29	LEU	0	0.078	0.046	38.344	0.165	0.165	0.000	0.000	0.000	0.000
29	A	30	ARG	1	0.911	0.970	35.568	8.736	8.736	0.000	0.000	0.000	0.000
30	A	31	THR	0	0.066	0.003	39.945	-0.082	-0.082	0.000	0.000	0.000	0.000
31	A	32	ASN	0	0.029	0.032	42.960	-0.042	-0.042	0.000	0.000	0.000	0.000
32	A	33	ASN	0	-0.088	-0.050	36.905	-0.223	-0.223	0.000	0.000	0.000	0.000
33	A	34	THR	0	0.094	0.046	36.487	-0.056	-0.056	0.000	0.000	0.000	0.000
34	A	35	ILE	0	-0.023	-0.008	32.023	-0.173	-0.173	0.000	0.000	0.000	0.000
35	A	36	ARG	1	1.040	1.028	34.267	8.442	8.442	0.000	0.000	0.000	0.000
36	A	37	TYR	0	0.015	-0.005	28.269	-0.147	-0.147	0.000	0.000	0.000	0.000
37	A	38	ASN	0	-0.041	-0.026	23.232	0.099	0.099	0.000	0.000	0.000	0.000
38	A	39	ALA	0	0.063	0.029	26.329	-0.328	-0.328	0.000	0.000	0.000	0.000
39	A	40	LYS	1	0.965	0.992	22.723	12.299	12.299	0.000	0.000	0.000	0.000
40	A	41	ARG	1	0.861	0.954	20.653	13.506	13.506	0.000	0.000	0.000	0.000
41	A	42	ARG	1	0.962	0.970	12.154	21.909	21.909	0.000	0.000	0.000	0.000
42	A	43	ASN	0	-0.002	-0.017	17.343	-0.474	-0.474	0.000	0.000	0.000	0.000
43	A	44	TRP	0	0.076	0.028	11.300	-0.410	-0.410	0.000	0.000	0.000	0.000
44	A	45	ARG	1	0.978	0.998	12.938	16.966	16.966	0.000	0.000	0.000	0.000
45	A	46	ARG	1	0.971	0.993	14.581	14.368	14.368	0.000	0.000	0.000	0.000
46	A	47	THR	0	0.037	0.028	16.369	0.158	0.158	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.891	0.933	10.579	23.656	23.656	0.000	0.000	0.000	0.000
48	A	49	MET	0	-0.049	-0.037	9.418	0.948	0.948	0.000	0.000	0.000	0.000
49	A	50	ASN	0	0.017	0.024	11.660	-0.033	-0.033	0.000	0.000	0.000	0.000
50	A	51	ILE	-1	-0.801	-0.871	7.995	-27.068	-27.068	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ALA)