FMO DATABASE

FMODB ID: 74YNK

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	83
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-458232.354717
FMO2-HF: Nuclear repulsion	425342.966707
FMO2-HF: Total energy	-32889.38801
FMO2-MP2: Total energy	-32982.257927

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:1:MET)

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

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.
-135.204	-125.985	15.761	-12.089	-12.891	-0.121

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.778 / q_NPA : 0.894

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	3	ASN	0	0.038	0.021	3.630	-1.729	0.110	-0.021	-0.883	-0.934	0.000
8	A	8	PHE	0	-0.033	-0.027	2.788	-13.914	-11.724	1.930	-1.159	-2.961	-0.014
9	A	9	VAL	0	-0.007	-0.006	4.294	1.555	2.017	0.000	-0.097	-0.365	0.000
10	A	10	ASP	-1	-0.851	-0.944	1.881	-142.390	-138.278	13.807	-9.832	-8.088	-0.106
11	A	11	LEU	0	-0.036	-0.003	3.492	10.643	10.795	0.023	-0.047	-0.128	-0.001
13	A	13	VAL	0	0.040	0.027	3.213	-5.905	-5.441	0.022	-0.071	-0.415	0.000
4	A	4	ASP	-1	-0.859	-0.934	6.866	-27.312	-27.312	0.000	0.000	0.000	0.000
5	A	5	ALA	0	-0.076	-0.032	10.036	2.420	2.420	0.000	0.000	0.000	0.000
6	A	6	GLY	0	0.005	0.011	8.261	1.991	1.991	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.922	-0.959	8.315	-29.664	-29.664	0.000	0.000	0.000	0.000
12	A	12	TYR	0	-0.022	-0.021	6.274	5.254	5.254	0.000	0.000	0.000	0.000
14	A	14	PRO	0	-0.031	-0.004	5.065	4.861	4.861	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.934	0.957	7.607	18.054	18.054	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.953	0.969	6.344	24.616	24.616	0.000	0.000	0.000	0.000
17	A	17	CYS	-1	-0.884	-0.741	11.081	-14.406	-14.406	0.000	0.000	0.000	0.000
18	A	18	SER	0	-0.023	-0.037	14.105	-0.136	-0.136	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.060	0.029	15.544	0.390	0.390	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.054	-0.146	17.045	0.048	0.048	0.000	0.000	0.000	0.000
21	A	21	ASN	0	-0.002	-0.005	10.979	-1.221	-1.221	0.000	0.000	0.000	0.000
22	A	22	ARG	1	0.950	0.975	11.950	14.456	14.456	0.000	0.000	0.000	0.000
23	A	23	ILE	0	0.012	-0.003	7.008	0.226	0.226	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.017	-0.006	10.881	1.520	1.520	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.010	0.005	12.476	-1.326	-1.326	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.026	0.007	13.560	1.076	1.076	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.946	0.962	15.136	16.983	16.983	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.755	-0.868	17.377	-14.361	-14.361	0.000	0.000	0.000	0.000
29	A	29	HIS	0	-0.004	-0.002	19.085	-0.132	-0.132	0.000	0.000	0.000	0.000
30	A	30	ALA	0	-0.023	0.008	21.809	0.578	0.578	0.000	0.000	0.000	0.000
31	A	31	SER	0	-0.056	-0.034	17.791	0.178	0.178	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.014	0.000	19.887	0.201	0.201	0.000	0.000	0.000	0.000
33	A	33	GLN	0	0.032	0.001	16.485	-1.300	-1.300	0.000	0.000	0.000	0.000
34	A	34	MET	0	-0.007	0.017	19.526	0.324	0.324	0.000	0.000	0.000	0.000
35	A	35	ASN	0	0.014	0.003	21.375	-0.670	-0.670	0.000	0.000	0.000	0.000
36	A	36	VAL	0	0.015	0.009	23.458	0.412	0.412	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.017	-0.009	25.500	-0.209	-0.209	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.855	-0.923	24.791	-10.586	-10.586	0.000	0.000	0.000	0.000
39	A	39	VAL	0	0.002	-0.023	28.980	0.147	0.147	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.882	-0.926	32.587	-8.441	-8.441	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.930	0.943	33.625	8.081	8.081	0.000	0.000	0.000	0.000
42	A	42	THR	0	0.001	0.009	36.180	0.076	0.076	0.000	0.000	0.000	0.000
43	A	43	THR	0	-0.022	-0.014	38.256	0.194	0.194	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.031	0.029	37.210	0.102	0.102	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.928	0.964	36.768	7.245	7.245	0.000	0.000	0.000	0.000
46	A	46	PHE	0	0.007	0.006	28.524	-0.060	-0.060	0.000	0.000	0.000	0.000
47	A	47	ASN	0	0.034	0.007	30.008	-0.037	-0.037	0.000	0.000	0.000	0.000
48	A	48	GLY	0	-0.022	-0.008	29.408	-0.063	-0.063	0.000	0.000	0.000	0.000
49	A	49	GLN	0	-0.015	0.004	25.244	-0.712	-0.712	0.000	0.000	0.000	0.000
50	A	50	PHE	0	-0.019	-0.022	21.232	0.235	0.235	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.873	0.970	20.302	11.235	11.235	0.000	0.000	0.000	0.000
52	A	52	THR	0	-0.042	-0.023	16.864	0.180	0.180	0.000	0.000	0.000	0.000
53	A	53	TYR	0	0.003	-0.032	18.461	-0.195	-0.195	0.000	0.000	0.000	0.000
54	A	54	GLY	0	-0.007	0.009	15.896	0.171	0.171	0.000	0.000	0.000	0.000
55	A	55	ILE	0	0.027	0.018	16.966	-0.068	-0.068	0.000	0.000	0.000	0.000
56	A	56	CYS	0	-0.049	-0.058	16.242	0.110	0.110	0.000	0.000	0.000	0.000
57	A	57	GLY	0	0.050	-0.002	18.073	0.739	0.739	0.000	0.000	0.000	0.000
58	A	58	ALA	0	-0.104	-0.059	19.646	0.570	0.570	0.000	0.000	0.000	0.000
59	A	59	ILE	0	0.077	0.017	19.814	0.437	0.437	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.909	0.953	22.316	11.986	11.986	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.894	0.950	22.858	12.583	12.583	0.000	0.000	0.000	0.000
62	A	62	MET	0	-0.029	-0.009	24.147	0.243	0.243	0.000	0.000	0.000	0.000
63	A	63	GLY	0	0.036	0.034	26.944	0.301	0.301	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.860	-0.936	24.949	-9.986	-9.986	0.000	0.000	0.000	0.000
65	A	65	SER	0	-0.057	-0.026	23.771	-0.271	-0.271	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.929	-0.952	24.765	-9.532	-9.532	0.000	0.000	0.000	0.000
67	A	67	ASP	-1	-0.737	-0.872	27.270	-10.065	-10.065	0.000	0.000	0.000	0.000
68	A	68	SER	0	-0.097	-0.072	21.861	-0.286	-0.286	0.000	0.000	0.000	0.000
69	A	69	ILE	0	0.003	-0.005	23.291	-0.257	-0.257	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.003	0.018	24.648	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.849	0.909	22.555	11.194	11.194	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.053	-0.016	19.023	-0.022	-0.022	0.000	0.000	0.000	0.000
73	A	73	ALA	0	0.061	0.033	22.939	0.088	0.088	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.914	0.971	25.696	9.242	9.242	0.000	0.000	0.000	0.000
75	A	75	ALA	0	-0.068	-0.029	23.146	0.218	0.218	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.836	-0.911	21.728	-11.901	-11.901	0.000	0.000	0.000	0.000
77	A	77	GLY	0	-0.047	-0.013	24.591	0.126	0.126	0.000	0.000	0.000	0.000
78	A	78	ILE	0	-0.040	-0.013	25.031	0.277	0.277	0.000	0.000	0.000	0.000
79	A	79	VAL	0	-0.033	-0.012	29.016	0.300	0.300	0.000	0.000	0.000	0.000
80	A	80	SER	0	0.014	0.004	30.855	-0.083	-0.083	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.977	0.976	32.478	7.912	7.912	0.000	0.000	0.000	0.000
82	A	82	ASN	0	-0.115	-0.063	33.452	-0.091	-0.091	0.000	0.000	0.000	0.000
83	A	83	PHE	-1	-0.834	-0.910	33.960	-7.647	-7.647	0.000	0.000	0.000	0.000

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