FMO DATABASE

FMODB ID: MZR1Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-250384.240029
FMO2-HF: Nuclear repulsion	228942.334945
FMO2-HF: Total energy	-21441.905083
FMO2-MP2: Total energy	-21505.755365

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:SER)

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

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.
287.844	287.545	11.101	-5.97	-4.832	-0.051

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.890 / q_NPA : 0.929

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	HIS	0	0.124	0.072	3.132	-1.503	0.486	0.119	-0.890	-1.218	-0.003
4	A	5	LYS	1	0.845	0.918	1.729	33.438	30.923	10.983	-5.014	-3.454	-0.048
5	A	6	THR	0	0.118	0.061	4.010	6.031	6.191	0.000	-0.063	-0.098	0.000
8	A	9	ILE	0	0.065	0.031	4.517	0.855	0.922	-0.001	-0.003	-0.062	0.000
6	A	7	PHE	0	0.085	0.027	7.544	-1.040	-1.040	0.000	0.000	0.000	0.000
7	A	8	ARG	1	1.011	1.004	10.630	21.814	21.814	0.000	0.000	0.000	0.000
9	A	10	LYS	1	0.985	0.998	8.263	26.715	26.715	0.000	0.000	0.000	0.000
10	A	11	ARG	1	0.960	0.979	9.329	18.853	18.853	0.000	0.000	0.000	0.000
11	A	12	PHE	0	0.060	0.029	10.738	1.805	1.805	0.000	0.000	0.000	0.000
12	A	13	LEU	0	0.016	-0.002	5.959	1.501	1.501	0.000	0.000	0.000	0.000
13	A	14	ALA	0	0.053	0.028	10.622	1.483	1.483	0.000	0.000	0.000	0.000
14	A	15	LYS	1	0.898	0.947	13.423	16.998	16.998	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.887	0.951	12.713	21.079	21.079	0.000	0.000	0.000	0.000
16	A	17	GLN	0	-0.006	0.001	13.037	-0.153	-0.153	0.000	0.000	0.000	0.000
17	A	18	LYS	1	0.986	0.982	14.927	17.151	17.151	0.000	0.000	0.000	0.000
18	A	19	GLN	0	-0.008	0.007	17.734	0.936	0.936	0.000	0.000	0.000	0.000
19	A	20	ASN	0	-0.036	-0.008	16.262	1.127	1.127	0.000	0.000	0.000	0.000
20	A	21	ARG	1	0.965	0.997	19.131	12.298	12.298	0.000	0.000	0.000	0.000
21	A	22	PRO	0	-0.012	-0.006	21.977	0.329	0.329	0.000	0.000	0.000	0.000
22	A	23	ILE	0	0.010	-0.002	24.971	-0.061	-0.061	0.000	0.000	0.000	0.000
23	A	24	PRO	0	-0.021	-0.004	28.322	-0.029	-0.029	0.000	0.000	0.000	0.000
24	A	25	GLN	0	0.080	0.035	30.759	0.256	0.256	0.000	0.000	0.000	0.000
25	A	26	TRP	0	0.128	0.042	31.794	0.038	0.038	0.000	0.000	0.000	0.000
26	A	27	ILE	0	-0.040	-0.022	32.059	0.156	0.156	0.000	0.000	0.000	0.000
27	A	28	ARG	1	0.922	0.954	34.333	8.695	8.695	0.000	0.000	0.000	0.000
28	A	29	MET	0	0.036	0.029	37.197	0.126	0.126	0.000	0.000	0.000	0.000
29	A	30	LYS	1	0.911	0.980	36.051	8.835	8.835	0.000	0.000	0.000	0.000
30	A	31	THR	0	0.087	0.036	40.317	0.013	0.013	0.000	0.000	0.000	0.000
31	A	32	GLY	0	0.044	0.025	42.112	-0.072	-0.072	0.000	0.000	0.000	0.000
32	A	33	ASN	0	-0.061	-0.030	36.003	-0.321	-0.321	0.000	0.000	0.000	0.000
33	A	34	LYS	1	1.003	1.000	37.304	7.878	7.878	0.000	0.000	0.000	0.000
34	A	35	ILE	0	-0.052	-0.012	31.098	-0.145	-0.145	0.000	0.000	0.000	0.000
35	A	36	ARG	1	1.007	1.003	34.115	8.517	8.517	0.000	0.000	0.000	0.000
36	A	37	TYR	0	0.026	0.000	27.985	-0.159	-0.159	0.000	0.000	0.000	0.000
37	A	38	ASN	0	-0.019	-0.010	23.926	0.083	0.083	0.000	0.000	0.000	0.000
38	A	39	SER	0	0.055	0.019	26.046	-0.213	-0.213	0.000	0.000	0.000	0.000
39	A	40	LYS	1	0.945	0.975	22.313	12.030	12.030	0.000	0.000	0.000	0.000
40	A	41	ARG	1	0.937	0.985	20.854	11.579	11.579	0.000	0.000	0.000	0.000
41	A	42	ARG	1	0.958	0.974	12.410	21.619	21.619	0.000	0.000	0.000	0.000
42	A	43	HIS	0	0.063	0.034	16.054	-1.143	-1.143	0.000	0.000	0.000	0.000
43	A	44	TRP	0	0.055	0.019	11.084	-0.666	-0.666	0.000	0.000	0.000	0.000
44	A	45	ARG	1	0.966	0.991	11.903	17.501	17.501	0.000	0.000	0.000	0.000
45	A	46	ARG	1	0.974	0.993	14.102	14.435	14.435	0.000	0.000	0.000	0.000
46	A	47	THR	0	0.017	0.006	15.945	0.619	0.619	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.914	0.954	9.741	26.692	26.692	0.000	0.000	0.000	0.000
48	A	49	LEU	0	-0.074	-0.049	9.601	1.788	1.788	0.000	0.000	0.000	0.000
49	A	50	GLY	0	0.040	0.019	12.677	-0.152	-0.152	0.000	0.000	0.000	0.000
50	A	51	LEU	-1	-0.920	-0.946	8.741	-29.772	-29.772	0.000	0.000	0.000	0.000

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