FMO DATABASE

FMODB ID: 4GJZN

Calculation Name: 3JCS-k-Other547

Preferred Name:

Target Type:

Ligand Name: o2'-methylguanosine-5'-monophosphate | 5,6-dihydrouridine-5'-monophosphate | o2'-methylycytidine-5'-monophosphate | o2'-methyluridine 5'-monophosphate | 2'-o-methyladenosine 5'-(dihydrogen phosphate)

Ligand 3-letter code: OMG | H2U | OMC | OMU | A2M

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3JCS

Chain ID: k

ChEMBL ID:

UniProt ID: P62885

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	58
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-329380.949182
FMO2-HF: Nuclear repulsion	305398.317667
FMO2-HF: Total energy	-23982.631514
FMO2-MP2: Total energy	-24051.793446

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:PRO)

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

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.
60.142	67.848	2.028	-3.904	-5.829	-0.028

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.834 / q_NPA : 0.893

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	GLU	-1	-0.758	-0.838	3.854	-32.533	-30.427	-0.017	-0.968	-1.121	-0.004
40	A	41	TYR	0	-0.053	-0.032	2.638	-7.945	-6.512	0.460	-0.759	-1.134	-0.006
41	A	42	LEU	0	-0.038	0.004	2.346	4.595	5.887	1.107	-0.605	-1.793	-0.003
42	A	43	TYR	0	0.037	0.003	2.919	-19.289	-16.540	0.479	-1.562	-1.666	-0.015
43	A	44	THR	0	-0.062	-0.072	4.557	0.628	0.754	-0.001	-0.010	-0.115	0.000
4	A	5	ILE	0	-0.072	-0.033	5.885	0.442	0.442	0.000	0.000	0.000	0.000
5	A	6	LYS	1	0.923	0.956	9.092	20.414	20.414	0.000	0.000	0.000	0.000
6	A	7	THR	-1	-0.748	-0.891	12.389	-20.830	-20.830	0.000	0.000	0.000	0.000
7	A	8	LEU	0	0.017	0.017	14.247	-0.728	-0.728	0.000	0.000	0.000	0.000
8	A	9	LYS	1	0.960	0.982	16.598	14.036	14.036	0.000	0.000	0.000	0.000
9	A	10	GLU	-1	-0.835	-0.900	11.730	-24.167	-24.167	0.000	0.000	0.000	0.000
10	A	11	PHE	0	-0.007	-0.014	10.179	-1.096	-1.096	0.000	0.000	0.000	0.000
11	A	12	LEU	0	0.084	0.038	13.201	-0.304	-0.304	0.000	0.000	0.000	0.000
12	A	13	ALA	0	-0.036	-0.015	15.740	0.398	0.398	0.000	0.000	0.000	0.000
13	A	14	ILE	0	-0.092	-0.050	9.030	-0.103	-0.103	0.000	0.000	0.000	0.000
14	A	15	CYS	-1	-0.911	-0.857	12.077	-21.204	-21.204	0.000	0.000	0.000	0.000
15	A	16	SER	0	0.043	0.026	13.339	0.544	0.544	0.000	0.000	0.000	0.000
16	A	17	ARG	1	0.745	0.833	10.941	23.731	23.731	0.000	0.000	0.000	0.000
17	A	18	LYS	1	0.952	0.953	15.476	14.059	14.059	0.000	0.000	0.000	0.000
18	A	19	ASP	-1	-0.793	-0.851	11.884	-23.462	-23.462	0.000	0.000	0.000	0.000
19	A	20	ALA	0	0.068	0.026	12.529	0.275	0.275	0.000	0.000	0.000	0.000
20	A	21	ARG	1	0.913	0.959	11.533	22.439	22.439	0.000	0.000	0.000	0.000
21	A	22	CYS	0	-0.065	-0.030	11.379	0.427	0.427	0.000	0.000	0.000	0.000
22	A	23	VAL	0	0.111	0.052	11.464	-2.120	-2.120	0.000	0.000	0.000	0.000
23	A	24	LYS	1	0.898	0.955	11.282	20.680	20.680	0.000	0.000	0.000	0.000
24	A	25	VAL	0	0.081	0.041	11.698	-1.740	-1.740	0.000	0.000	0.000	0.000
25	A	26	LYS	1	0.810	0.904	10.918	20.530	20.530	0.000	0.000	0.000	0.000
26	A	27	HIS	-1	-0.737	-0.854	13.861	-15.852	-15.852	0.000	0.000	0.000	0.000
27	A	28	ASN	0	-0.087	-0.062	13.514	-1.384	-1.384	0.000	0.000	0.000	0.000
28	A	29	PRO	0	0.091	0.038	16.370	0.325	0.325	0.000	0.000	0.000	0.000
29	A	30	SER	0	-0.003	-0.012	16.755	-0.749	-0.749	0.000	0.000	0.000	0.000
30	A	31	ALA	0	0.003	0.025	14.106	-0.206	-0.206	0.000	0.000	0.000	0.000
31	A	32	THR	0	-0.058	-0.024	14.818	0.404	0.404	0.000	0.000	0.000	0.000
32	A	33	LYS	1	0.850	0.918	7.153	30.221	30.221	0.000	0.000	0.000	0.000
33	A	34	PHE	0	0.055	0.042	10.880	0.061	0.061	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.882	0.940	6.390	28.904	28.904	0.000	0.000	0.000	0.000
35	A	36	VAL	0	0.114	0.062	7.765	1.925	1.925	0.000	0.000	0.000	0.000
36	A	37	ARG	1	0.843	0.902	6.134	30.312	30.312	0.000	0.000	0.000	0.000
37	A	38	CYS	-1	-0.717	-0.799	7.626	-25.720	-25.720	0.000	0.000	0.000	0.000
38	A	39	SER	0	-0.066	-0.083	8.728	-1.111	-1.111	0.000	0.000	0.000	0.000
39	A	40	ARG	1	0.911	0.968	5.828	38.120	38.120	0.000	0.000	0.000	0.000
44	A	45	LEU	0	0.083	0.074	6.434	-0.665	-0.665	0.000	0.000	0.000	0.000
45	A	46	VAL	0	-0.069	-0.037	9.732	0.633	0.633	0.000	0.000	0.000	0.000
46	A	47	VAL	0	0.025	0.013	11.271	0.470	0.470	0.000	0.000	0.000	0.000
47	A	48	ASN	0	0.010	-0.002	15.083	-0.524	-0.524	0.000	0.000	0.000	0.000
48	A	49	ASP	-1	-0.773	-0.893	18.252	-12.437	-12.437	0.000	0.000	0.000	0.000
49	A	50	LYS	1	0.964	0.985	20.245	10.375	10.375	0.000	0.000	0.000	0.000
50	A	51	LYS	0	0.041	0.015	17.503	-0.219	-0.219	0.000	0.000	0.000	0.000
51	A	52	LYS	1	0.775	0.891	16.067	16.027	16.027	0.000	0.000	0.000	0.000
52	A	53	ALA	0	-0.034	-0.041	18.565	-0.250	-0.250	0.000	0.000	0.000	0.000
53	A	54	ASP	-1	-0.947	-0.951	21.503	-12.307	-12.307	0.000	0.000	0.000	0.000
54	A	55	LYS	0	0.028	-0.002	14.471	0.099	0.099	0.000	0.000	0.000	0.000
55	A	56	ILE	0	-0.086	-0.045	18.045	-0.904	-0.904	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.981	-0.980	19.625	-11.330	-11.330	0.000	0.000	0.000	0.000
57	A	58	ARG	1	0.857	0.907	21.391	12.863	12.863	0.000	0.000	0.000	0.000
58	A	59	SER	-1	-0.894	-1.004	16.170	-14.616	-14.616	0.000	0.000	0.000	0.000

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