FMO DATABASE

FMODB ID: N6Z6Q

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	100
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-637930.704092
FMO2-HF: Nuclear repulsion	597560.057816
FMO2-HF: Total energy	-40370.646276
FMO2-MP2: Total energy	-40486.86827

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:THR)

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

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.
321.232	322.769	-0.007	-0.578	-0.952	0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.968 / q_NPA : 0.974

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	LYS	1	0.992	0.999	3.843	38.732	40.222	-0.006	-0.577	-0.907	0.002
88	A	89	ARG	1	0.929	0.946	4.798	35.048	35.095	-0.001	-0.001	-0.045	0.000
4	A	5	ARG	1	0.983	0.981	5.445	30.527	30.527	0.000	0.000	0.000	0.000
5	A	6	ARG	1	1.068	1.044	8.812	19.266	19.266	0.000	0.000	0.000	0.000
6	A	7	ASN	0	0.033	0.010	10.891	0.286	0.286	0.000	0.000	0.000	0.000
7	A	8	ASN	0	0.039	0.017	10.105	-1.040	-1.040	0.000	0.000	0.000	0.000
8	A	9	GLY	0	-0.019	-0.018	11.318	0.347	0.347	0.000	0.000	0.000	0.000
9	A	10	ARG	1	0.822	0.897	13.448	18.490	18.490	0.000	0.000	0.000	0.000
10	A	11	ALA	0	0.056	0.018	16.717	-0.438	-0.438	0.000	0.000	0.000	0.000
11	A	12	LYS	1	0.846	0.940	17.152	17.715	17.715	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.861	0.926	14.130	19.205	19.205	0.000	0.000	0.000	0.000
13	A	14	GLY	0	0.094	0.041	19.725	0.580	0.580	0.000	0.000	0.000	0.000
14	A	15	ARG	1	0.975	0.999	21.601	13.726	13.726	0.000	0.000	0.000	0.000
15	A	16	GLY	0	0.076	0.043	21.009	-0.776	-0.776	0.000	0.000	0.000	0.000
16	A	17	HIS	0	0.052	0.019	20.553	-1.439	-1.439	0.000	0.000	0.000	0.000
17	A	18	VAL	0	-0.066	-0.041	21.980	0.242	0.242	0.000	0.000	0.000	0.000
18	A	19	GLN	0	0.075	0.055	23.573	-0.671	-0.671	0.000	0.000	0.000	0.000
19	A	20	PRO	0	-0.039	-0.031	23.611	-0.242	-0.242	0.000	0.000	0.000	0.000
20	A	21	ILE	0	0.001	-0.003	25.175	0.502	0.502	0.000	0.000	0.000	0.000
21	A	22	ARG	1	0.922	0.944	25.958	10.457	10.457	0.000	0.000	0.000	0.000
22	A	23	CYS	0	-0.124	0.017	24.554	0.059	0.059	0.000	0.000	0.000	0.000
23	A	24	THR	0	0.041	-0.007	26.638	0.262	0.262	0.000	0.000	0.000	0.000
24	A	25	ASN	0	0.074	0.013	26.840	-0.035	-0.035	0.000	0.000	0.000	0.000
25	A	26	CYS	0	0.050	-0.004	25.827	-0.388	-0.388	0.000	0.000	0.000	0.000
26	A	27	ALA	0	0.089	0.067	27.649	-0.103	-0.103	0.000	0.000	0.000	0.000
27	A	28	ARG	1	0.985	1.006	18.416	15.580	15.580	0.000	0.000	0.000	0.000
28	A	29	CYS	0	0.015	0.015	24.216	0.155	0.155	0.000	0.000	0.000	0.000
29	A	30	VAL	0	0.006	-0.006	20.427	-0.884	-0.884	0.000	0.000	0.000	0.000
30	A	31	PRO	0	0.028	0.006	18.322	0.467	0.467	0.000	0.000	0.000	0.000
31	A	32	LYS	1	1.030	1.024	21.511	10.836	10.836	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.744	-0.858	19.137	-16.263	-16.263	0.000	0.000	0.000	0.000
33	A	34	LYS	1	0.822	0.894	13.595	20.934	20.934	0.000	0.000	0.000	0.000
34	A	35	ALA	0	-0.006	0.023	18.968	-0.353	-0.353	0.000	0.000	0.000	0.000
35	A	36	ILE	0	0.003	-0.001	18.872	0.162	0.162	0.000	0.000	0.000	0.000
36	A	37	LYS	1	0.871	0.942	22.784	13.697	13.697	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.969	0.978	26.309	11.123	11.123	0.000	0.000	0.000	0.000
38	A	39	PHE	0	0.023	0.007	28.913	0.067	0.067	0.000	0.000	0.000	0.000
39	A	40	VAL	0	0.007	0.000	32.255	0.043	0.043	0.000	0.000	0.000	0.000
40	A	41	ILE	0	0.005	0.019	34.427	0.163	0.163	0.000	0.000	0.000	0.000
41	A	42	ARG	1	0.838	0.926	37.707	7.925	7.925	0.000	0.000	0.000	0.000
42	A	43	ASN	0	0.110	0.043	39.899	-0.041	-0.041	0.000	0.000	0.000	0.000
43	A	44	ILE	0	0.012	-0.001	43.018	-0.183	-0.183	0.000	0.000	0.000	0.000
44	A	45	VAL	0	0.031	0.023	44.548	-0.127	-0.127	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.943	-0.968	44.094	-7.100	-7.100	0.000	0.000	0.000	0.000
46	A	47	ALA	0	-0.007	-0.031	44.689	0.128	0.128	0.000	0.000	0.000	0.000
47	A	48	ALA	0	-0.011	0.011	46.492	0.108	0.108	0.000	0.000	0.000	0.000
48	A	49	ALA	0	0.092	0.040	49.039	0.105	0.105	0.000	0.000	0.000	0.000
49	A	50	VAL	0	-0.071	-0.031	48.512	0.066	0.066	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.967	0.990	51.396	6.040	6.040	0.000	0.000	0.000	0.000
51	A	52	ASP	-1	-0.813	-0.896	53.896	-5.833	-5.833	0.000	0.000	0.000	0.000
52	A	53	ILE	0	-0.044	-0.037	51.570	0.058	0.058	0.000	0.000	0.000	0.000
53	A	54	SER	0	-0.106	-0.061	55.515	0.057	0.057	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.885	-0.951	57.157	-5.209	-5.209	0.000	0.000	0.000	0.000
55	A	56	ALA	0	-0.049	-0.016	58.337	0.090	0.090	0.000	0.000	0.000	0.000
56	A	57	SER	0	-0.071	-0.023	58.296	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	58	VAL	0	0.016	0.002	60.129	0.075	0.075	0.000	0.000	0.000	0.000
58	A	59	PHE	0	-0.109	-0.050	58.866	0.058	0.058	0.000	0.000	0.000	0.000
59	A	60	ASP	-1	-0.872	-0.928	60.564	-5.156	-5.156	0.000	0.000	0.000	0.000
60	A	61	ALA	0	0.030	0.023	59.236	-0.088	-0.088	0.000	0.000	0.000	0.000
61	A	62	TYR	0	-0.007	-0.021	53.733	-0.072	-0.072	0.000	0.000	0.000	0.000
62	A	63	VAL	0	-0.010	-0.006	50.908	-0.064	-0.064	0.000	0.000	0.000	0.000
63	A	64	LEU	0	0.028	0.022	49.111	-0.031	-0.031	0.000	0.000	0.000	0.000
64	A	65	PRO	0	0.015	0.018	48.082	-0.175	-0.175	0.000	0.000	0.000	0.000
65	A	66	LYS	1	0.908	0.946	41.441	7.460	7.460	0.000	0.000	0.000	0.000
66	A	67	LEU	0	0.012	0.017	40.636	-0.024	-0.024	0.000	0.000	0.000	0.000
67	A	68	TYR	0	0.031	-0.002	38.461	-0.242	-0.242	0.000	0.000	0.000	0.000
68	A	69	VAL	0	0.032	0.021	34.729	-0.073	-0.073	0.000	0.000	0.000	0.000
69	A	70	LYS	1	0.920	0.967	30.324	9.956	9.956	0.000	0.000	0.000	0.000
70	A	71	LEU	0	0.040	0.030	30.118	-0.141	-0.141	0.000	0.000	0.000	0.000
71	A	72	HIS	0	-0.021	-0.025	26.620	-0.461	-0.461	0.000	0.000	0.000	0.000
72	A	73	TYR	0	0.053	0.019	23.966	0.148	0.148	0.000	0.000	0.000	0.000
73	A	74	CYS	-1	-0.918	-0.864	20.692	-15.848	-15.848	0.000	0.000	0.000	0.000
74	A	75	VAL	0	-0.009	-0.020	15.125	-0.050	-0.050	0.000	0.000	0.000	0.000
75	A	76	SER	0	0.001	-0.061	18.133	0.002	0.002	0.000	0.000	0.000	0.000
76	A	77	CYS	0	0.109	0.012	19.254	0.449	0.449	0.000	0.000	0.000	0.000
77	A	78	ALA	0	-0.020	-0.006	20.724	0.478	0.478	0.000	0.000	0.000	0.000
78	A	79	ILE	0	-0.032	-0.028	15.742	0.066	0.066	0.000	0.000	0.000	0.000
79	A	80	HIS	0	0.040	0.031	20.081	-0.147	-0.147	0.000	0.000	0.000	0.000
80	A	81	SER	0	-0.016	-0.018	22.769	0.579	0.579	0.000	0.000	0.000	0.000
81	A	82	LYS	1	0.925	0.963	22.865	12.120	12.120	0.000	0.000	0.000	0.000
82	A	83	VAL	0	-0.034	0.003	23.683	0.193	0.193	0.000	0.000	0.000	0.000
83	A	84	VAL	0	-0.041	-0.019	18.422	-0.132	-0.132	0.000	0.000	0.000	0.000
84	A	85	ARG	1	1.011	0.998	19.160	13.005	13.005	0.000	0.000	0.000	0.000
85	A	86	ASN	0	-0.041	-0.013	12.532	-0.972	-0.972	0.000	0.000	0.000	0.000
86	A	87	ARG	1	0.912	0.946	13.912	17.857	17.857	0.000	0.000	0.000	0.000
87	A	88	SER	0	0.105	0.043	12.514	-2.529	-2.529	0.000	0.000	0.000	0.000
89	A	90	GLU	-1	-0.852	-0.913	10.633	-18.889	-18.889	0.000	0.000	0.000	0.000
90	A	91	ALA	0	0.094	0.037	13.693	0.221	0.221	0.000	0.000	0.000	0.000
91	A	92	ARG	1	0.772	0.887	7.787	27.134	27.134	0.000	0.000	0.000	0.000
92	A	93	LYS	1	0.918	0.954	10.741	22.696	22.696	0.000	0.000	0.000	0.000
93	A	94	ASP	-1	-0.754	-0.867	14.547	-14.019	-14.019	0.000	0.000	0.000	0.000
94	A	95	ARG	1	0.838	0.912	17.127	15.028	15.028	0.000	0.000	0.000	0.000
95	A	96	THR	0	0.052	0.052	19.942	0.382	0.382	0.000	0.000	0.000	0.000
96	A	97	PRO	0	-0.041	-0.015	22.973	-0.445	-0.445	0.000	0.000	0.000	0.000
97	A	98	PRO	0	-0.009	-0.022	24.091	0.072	0.072	0.000	0.000	0.000	0.000
98	A	99	PRO	0	0.022	0.023	26.266	0.153	0.153	0.000	0.000	0.000	0.000
99	A	100	ARG	1	0.894	0.944	29.704	9.048	9.048	0.000	0.000	0.000	0.000
100	A	101	PHE	-1	-0.862	-0.916	32.315	-8.506	-8.506	0.000	0.000	0.000	0.000

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