FMO DATABASE

FMODB ID: R4MN8

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	54
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-266456.51783
FMO2-HF: Nuclear repulsion	242924.894882
FMO2-HF: Total energy	-23531.622948
FMO2-MP2: Total energy	-23597.158749

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:3:HIS)

Summations of interaction energy for fragment #1(A:3:HIS)

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.
106.14	109.722	0.101	-1.355	-2.328	-0.004

Interaction energy analysis for fragmet #1(A:3:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.908 / q_NPA : 0.944

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	5	GLN	0	0.028	0.016	3.800	1.133	2.994	-0.008	-0.773	-1.080	-0.002
4	A	6	LEU	0	-0.004	0.006	2.753	2.720	3.821	0.108	-0.403	-0.806	-0.002
5	A	7	TYR	0	-0.032	-0.004	3.810	5.955	6.531	0.002	-0.175	-0.403	0.000
6	A	8	TRP	0	0.000	-0.006	5.092	4.338	4.382	-0.001	-0.004	-0.039	0.000
7	A	9	SER	0	-0.003	-0.002	7.296	2.995	2.995	0.000	0.000	0.000	0.000
8	A	10	HIS	0	0.038	0.030	8.995	1.389	1.389	0.000	0.000	0.000	0.000
9	A	11	PRO	0	0.004	-0.003	11.902	0.527	0.527	0.000	0.000	0.000	0.000
10	A	12	ARG	1	0.979	0.988	14.977	17.739	17.739	0.000	0.000	0.000	0.000
11	A	13	LYS	1	0.944	0.965	16.606	15.628	15.628	0.000	0.000	0.000	0.000
12	A	14	PHE	0	0.033	0.009	19.856	-0.060	-0.060	0.000	0.000	0.000	0.000
13	A	15	GLY	0	0.075	0.062	20.327	0.370	0.370	0.000	0.000	0.000	0.000
14	A	16	GLN	0	-0.028	-0.020	21.333	0.292	0.292	0.000	0.000	0.000	0.000
15	A	17	GLY	0	0.031	0.007	21.279	0.258	0.258	0.000	0.000	0.000	0.000
16	A	18	SER	0	-0.055	-0.039	19.237	-0.511	-0.511	0.000	0.000	0.000	0.000
17	A	19	ARG	1	0.925	0.975	20.299	11.683	11.683	0.000	0.000	0.000	0.000
18	A	20	SER	0	-0.010	-0.028	22.636	-0.291	-0.291	0.000	0.000	0.000	0.000
19	A	21	CYS	-1	-0.930	-0.748	24.754	-10.201	-10.201	0.000	0.000	0.000	0.000
20	A	22	ARG	1	0.918	0.942	26.711	9.494	9.494	0.000	0.000	0.000	0.000
21	A	23	VAL	0	0.048	-0.003	28.047	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	24	CYS	0	-0.024	-0.077	28.696	-0.011	-0.011	0.000	0.000	0.000	0.000
23	A	25	SER	0	0.016	0.012	22.768	-0.419	-0.419	0.000	0.000	0.000	0.000
24	A	26	ASN	0	0.001	-0.012	23.984	-0.408	-0.408	0.000	0.000	0.000	0.000
25	A	27	ARG	1	0.980	0.984	20.915	14.005	14.005	0.000	0.000	0.000	0.000
26	A	28	HIS	0	0.019	0.023	25.609	0.072	0.072	0.000	0.000	0.000	0.000
27	A	29	GLY	0	0.001	-0.008	28.904	0.189	0.189	0.000	0.000	0.000	0.000
28	A	30	LEU	0	-0.034	-0.001	26.982	0.193	0.193	0.000	0.000	0.000	0.000
29	A	31	ILE	0	0.022	0.013	30.909	0.094	0.094	0.000	0.000	0.000	0.000
30	A	32	ARG	1	0.972	0.963	29.020	10.168	10.168	0.000	0.000	0.000	0.000
31	A	33	LYS	1	0.941	0.984	32.471	7.572	7.572	0.000	0.000	0.000	0.000
32	A	34	TYR	0	0.065	0.005	36.060	-0.062	-0.062	0.000	0.000	0.000	0.000
33	A	35	GLY	0	0.046	0.050	32.980	0.023	0.023	0.000	0.000	0.000	0.000
34	A	36	LEU	0	0.031	0.021	33.322	-0.150	-0.150	0.000	0.000	0.000	0.000
35	A	37	ASN	0	-0.067	-0.042	28.166	0.035	0.035	0.000	0.000	0.000	0.000
36	A	38	MET	0	0.120	0.044	30.113	-0.220	-0.220	0.000	0.000	0.000	0.000
37	A	39	CYS	0	-0.027	-0.041	30.368	0.165	0.165	0.000	0.000	0.000	0.000
38	A	40	ARG	1	1.007	0.994	32.070	8.956	8.956	0.000	0.000	0.000	0.000
39	A	41	GLN	0	0.003	-0.013	34.274	0.208	0.208	0.000	0.000	0.000	0.000
40	A	42	CYS	0	0.020	-0.009	31.707	0.180	0.180	0.000	0.000	0.000	0.000
41	A	43	PHE	0	0.001	0.008	35.384	0.152	0.152	0.000	0.000	0.000	0.000
42	A	44	ARG	1	0.952	0.956	37.676	7.636	7.636	0.000	0.000	0.000	0.000
43	A	45	GLN	0	-0.067	-0.009	36.748	0.082	0.082	0.000	0.000	0.000	0.000
44	A	46	TYR	0	0.058	0.019	35.238	0.145	0.145	0.000	0.000	0.000	0.000
45	A	47	ALA	0	-0.037	-0.004	40.056	0.075	0.075	0.000	0.000	0.000	0.000
46	A	48	LYS	1	0.972	0.983	42.291	7.007	7.007	0.000	0.000	0.000	0.000
47	A	49	ASP	-1	-0.867	-0.937	41.407	-7.264	-7.264	0.000	0.000	0.000	0.000
48	A	50	ILE	0	-0.085	-0.044	38.186	-0.065	-0.065	0.000	0.000	0.000	0.000
49	A	51	GLY	0	0.040	0.032	42.235	0.051	0.051	0.000	0.000	0.000	0.000
50	A	52	PHE	0	-0.078	-0.051	41.313	0.073	0.073	0.000	0.000	0.000	0.000
51	A	53	ILE	0	0.007	0.001	45.911	-0.034	-0.034	0.000	0.000	0.000	0.000
52	A	54	LYS	1	0.878	0.938	48.248	6.374	6.374	0.000	0.000	0.000	0.000
53	A	55	LEU	0	-0.017	-0.020	49.969	0.070	0.070	0.000	0.000	0.000	0.000
54	A	56	ASP	-2	-1.863	-1.907	51.302	-12.203	-12.203	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:HIS)