FMO DATABASE

FMODB ID: G7Y11

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	97
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-773666.263389
FMO2-HF: Nuclear repulsion	732930.579244
FMO2-HF: Total energy	-40735.684146
FMO2-MP2: Total energy	-40853.865402

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:LEU)

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

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.
186.262	189.354	0.127	-1.228	-1.991	-0.004

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.872 / 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

Sort

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	PRO	0	0.058	0.036	3.497	0.288	2.663	0.013	-1.016	-1.372	-0.003
43	A	44	HIS	0	-0.035	-0.035	4.594	-2.030	-1.873	-0.001	-0.028	-0.128	0.000
46	A	47	LYS	1	0.953	0.980	2.713	54.089	54.649	0.115	-0.184	-0.491	-0.001
4	A	5	LYS	1	1.014	1.005	5.554	23.879	23.879	0.000	0.000	0.000	0.000
5	A	6	LYS	1	1.029	1.013	7.494	20.880	20.880	0.000	0.000	0.000	0.000
6	A	7	ASN	0	0.037	0.014	8.017	3.025	3.025	0.000	0.000	0.000	0.000
7	A	8	ARG	1	0.877	0.920	5.482	37.602	37.602	0.000	0.000	0.000	0.000
8	A	9	ILE	0	0.023	0.015	9.730	1.141	1.141	0.000	0.000	0.000	0.000
9	A	10	ALA	0	0.032	0.019	12.750	1.084	1.084	0.000	0.000	0.000	0.000
10	A	11	ILE	0	-0.005	-0.004	10.112	0.695	0.695	0.000	0.000	0.000	0.000
11	A	12	TYR	0	0.000	-0.001	11.198	0.050	0.050	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.885	-0.950	15.513	-15.594	-15.594	0.000	0.000	0.000	0.000
13	A	14	LEU	0	-0.045	-0.007	17.399	0.692	0.692	0.000	0.000	0.000	0.000
14	A	15	LEU	0	-0.022	-0.023	14.839	0.643	0.643	0.000	0.000	0.000	0.000
15	A	16	PHE	0	-0.011	-0.014	18.938	0.697	0.697	0.000	0.000	0.000	0.000
16	A	17	LYS	1	0.960	0.991	21.436	14.598	14.598	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.909	-0.957	21.824	-13.355	-13.355	0.000	0.000	0.000	0.000
18	A	19	GLY	0	-0.027	-0.010	22.374	0.598	0.598	0.000	0.000	0.000	0.000
19	A	20	VAL	0	-0.054	-0.045	21.559	0.049	0.049	0.000	0.000	0.000	0.000
20	A	21	MET	0	0.043	0.029	14.995	-0.587	-0.587	0.000	0.000	0.000	0.000
21	A	22	VAL	0	0.027	0.017	19.029	0.277	0.277	0.000	0.000	0.000	0.000
22	A	23	ALA	0	0.001	0.008	14.900	-0.725	-0.725	0.000	0.000	0.000	0.000
23	A	24	LYS	1	0.970	1.003	16.590	16.023	16.023	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.921	0.954	15.656	15.506	15.506	0.000	0.000	0.000	0.000
25	A	26	ASP	-1	-0.907	-0.958	15.766	-18.577	-18.577	0.000	0.000	0.000	0.000
26	A	27	VAL	0	0.015	-0.002	10.929	-0.902	-0.902	0.000	0.000	0.000	0.000
27	A	28	HIS	0	0.028	0.017	11.560	-2.504	-2.504	0.000	0.000	0.000	0.000
28	A	29	MET	0	-0.026	0.005	14.129	0.506	0.506	0.000	0.000	0.000	0.000
29	A	30	PRO	0	0.039	0.010	13.625	-1.513	-1.513	0.000	0.000	0.000	0.000
30	A	31	LYS	1	0.812	0.902	13.712	20.052	20.052	0.000	0.000	0.000	0.000
31	A	32	HIS	0	-0.009	-0.011	14.400	0.400	0.400	0.000	0.000	0.000	0.000
32	A	33	PRO	0	-0.015	-0.026	16.144	0.306	0.306	0.000	0.000	0.000	0.000
33	A	34	GLU	-1	-0.845	-0.900	19.036	-14.576	-14.576	0.000	0.000	0.000	0.000
34	A	35	LEU	0	-0.023	-0.024	14.603	-0.136	-0.136	0.000	0.000	0.000	0.000
35	A	36	ALA	0	0.021	0.008	16.597	-1.067	-1.067	0.000	0.000	0.000	0.000
36	A	37	ASP	-1	-0.825	-0.902	18.324	-14.486	-14.486	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.837	0.906	14.645	16.249	16.249	0.000	0.000	0.000	0.000
38	A	39	ASN	0	0.000	-0.006	13.928	-1.628	-1.628	0.000	0.000	0.000	0.000
39	A	40	VAL	0	0.005	0.020	10.743	-1.969	-1.969	0.000	0.000	0.000	0.000
40	A	41	PRO	0	0.032	0.029	8.548	1.303	1.303	0.000	0.000	0.000	0.000
41	A	42	ASN	0	0.048	-0.005	10.343	-1.338	-1.338	0.000	0.000	0.000	0.000
42	A	43	LEU	0	0.062	0.028	6.676	-0.609	-0.609	0.000	0.000	0.000	0.000
44	A	45	VAL	0	0.047	0.032	7.055	-0.830	-0.830	0.000	0.000	0.000	0.000
45	A	46	MET	0	-0.020	0.001	9.828	0.429	0.429	0.000	0.000	0.000	0.000
47	A	48	ALA	0	-0.027	-0.013	7.230	-0.237	-0.237	0.000	0.000	0.000	0.000
48	A	49	MET	0	0.075	0.039	8.634	1.687	1.687	0.000	0.000	0.000	0.000
49	A	50	GLN	0	-0.017	0.005	9.257	-0.574	-0.574	0.000	0.000	0.000	0.000
50	A	51	SER	0	-0.064	-0.021	8.085	1.101	1.101	0.000	0.000	0.000	0.000
51	A	52	LEU	0	0.019	-0.003	10.184	1.105	1.105	0.000	0.000	0.000	0.000
52	A	53	LYS	1	0.822	0.908	13.458	19.684	19.684	0.000	0.000	0.000	0.000
53	A	54	SER	0	-0.060	-0.051	12.495	1.044	1.044	0.000	0.000	0.000	0.000
54	A	55	ARG	1	0.849	0.927	12.622	23.101	23.101	0.000	0.000	0.000	0.000
55	A	56	GLY	0	0.051	0.046	15.977	0.744	0.744	0.000	0.000	0.000	0.000
56	A	57	TYR	0	0.015	0.011	15.819	0.519	0.519	0.000	0.000	0.000	0.000
57	A	58	VAL	0	-0.030	-0.007	16.198	0.459	0.459	0.000	0.000	0.000	0.000
58	A	59	LYS	1	0.970	0.993	18.744	12.491	12.491	0.000	0.000	0.000	0.000
59	A	60	GLU	-1	-0.805	-0.905	17.151	-17.759	-17.759	0.000	0.000	0.000	0.000
60	A	61	GLN	0	0.062	0.036	20.040	0.519	0.519	0.000	0.000	0.000	0.000
61	A	62	PHE	0	-0.023	-0.017	18.930	-0.520	-0.520	0.000	0.000	0.000	0.000
62	A	63	ALA	0	0.057	0.020	21.676	0.588	0.588	0.000	0.000	0.000	0.000
63	A	64	TRP	0	0.066	0.031	23.747	-0.491	-0.491	0.000	0.000	0.000	0.000
64	A	65	ARG	1	0.900	0.951	20.377	13.892	13.892	0.000	0.000	0.000	0.000
65	A	66	HIS	0	0.012	-0.001	19.857	-0.918	-0.918	0.000	0.000	0.000	0.000
66	A	67	PHE	0	-0.012	-0.003	15.463	0.201	0.201	0.000	0.000	0.000	0.000
67	A	68	TYR	0	0.026	0.018	18.809	-0.067	-0.067	0.000	0.000	0.000	0.000
68	A	69	TRP	0	-0.009	-0.020	13.550	-0.690	-0.690	0.000	0.000	0.000	0.000
69	A	70	TYR	0	0.051	0.014	19.558	0.217	0.217	0.000	0.000	0.000	0.000
70	A	71	LEU	0	-0.039	0.000	18.642	-0.395	-0.395	0.000	0.000	0.000	0.000
71	A	72	THR	0	0.003	-0.009	21.249	0.757	0.757	0.000	0.000	0.000	0.000
72	A	73	ASN	0	0.051	0.004	23.065	-0.425	-0.425	0.000	0.000	0.000	0.000
73	A	74	GLU	-1	-0.874	-0.925	22.804	-12.674	-12.674	0.000	0.000	0.000	0.000
74	A	75	GLY	0	-0.001	-0.009	19.548	-0.493	-0.493	0.000	0.000	0.000	0.000
75	A	76	ILE	0	-0.045	-0.024	20.063	-0.495	-0.495	0.000	0.000	0.000	0.000
76	A	77	GLN	0	0.021	0.017	22.575	0.102	0.102	0.000	0.000	0.000	0.000
77	A	78	TYR	0	0.065	0.028	13.678	-1.267	-1.267	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.071	-0.041	15.947	-0.713	-0.713	0.000	0.000	0.000	0.000
79	A	80	ARG	1	0.866	0.938	18.928	11.507	11.507	0.000	0.000	0.000	0.000
80	A	81	ASP	-1	-0.902	-0.938	19.701	-14.390	-14.390	0.000	0.000	0.000	0.000
81	A	82	TYR	0	-0.064	-0.044	10.545	-1.497	-1.497	0.000	0.000	0.000	0.000
82	A	83	LEU	0	-0.091	-0.060	15.850	-0.740	-0.740	0.000	0.000	0.000	0.000
83	A	84	HIS	0	-0.013	0.011	18.016	0.902	0.902	0.000	0.000	0.000	0.000
84	A	85	LEU	0	-0.036	-0.009	21.578	0.530	0.530	0.000	0.000	0.000	0.000
85	A	86	PRO	0	0.043	0.026	24.090	-0.066	-0.066	0.000	0.000	0.000	0.000
86	A	87	PRO	0	-0.004	-0.021	27.670	-0.193	-0.193	0.000	0.000	0.000	0.000
87	A	88	GLU	-1	-0.878	-0.947	29.133	-9.859	-9.859	0.000	0.000	0.000	0.000
88	A	89	ILE	0	-0.026	0.006	26.657	0.087	0.087	0.000	0.000	0.000	0.000
89	A	90	VAL	0	-0.018	-0.018	27.774	-0.311	-0.311	0.000	0.000	0.000	0.000
90	A	91	PRO	0	0.028	0.024	24.125	0.097	0.097	0.000	0.000	0.000	0.000
91	A	92	ALA	0	0.059	0.033	26.407	0.467	0.467	0.000	0.000	0.000	0.000
92	A	93	THR	0	-0.057	-0.020	26.077	0.381	0.381	0.000	0.000	0.000	0.000
93	A	94	LEU	0	-0.002	0.018	27.762	0.331	0.331	0.000	0.000	0.000	0.000
94	A	95	ARG	1	0.881	0.931	31.024	9.282	9.282	0.000	0.000	0.000	0.000
95	A	96	ARG	1	0.929	0.950	28.758	10.173	10.173	0.000	0.000	0.000	0.000
96	A	97	SER	0	0.008	-0.002	35.291	0.178	0.178	0.000	0.000	0.000	0.000
97	A	98	ARG	0	0.046	0.043	38.515	0.255	0.255	0.000	0.000	0.000	0.000

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