FMO DATABASE

FMODB ID: 1V58Z

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	134
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1023537.050319
FMO2-HF: Nuclear repulsion	972654.306436
FMO2-HF: Total energy	-50882.743883
FMO2-MP2: Total energy	-51028.661701

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:18:GLY)

Summations of interaction energy for fragment #1(A:18:GLY)

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.
-32.806	-31.087	10.822	-6.482	-6.06	-0.083

Interaction energy analysis for fragmet #1(A:18:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.824 / q_NPA : 0.911

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	20	GLN	0	0.025	0.011	3.818	-10.166	-9.476	0.004	-0.327	-0.367	0.000
10	A	27	VAL	0	0.036	0.047	3.783	2.096	2.193	0.000	-0.028	-0.069	0.000
71	A	88	LEU	0	0.007	0.010	3.096	-6.835	-5.890	0.056	-0.515	-0.487	-0.003
72	A	89	GLY	0	0.020	0.014	1.816	-44.595	-46.229	10.553	-4.593	-4.326	-0.069
73	A	90	ILE	0	-0.047	-0.031	2.915	-5.420	-3.804	0.210	-1.016	-0.810	-0.011
74	A	91	THR	0	-0.033	-0.026	5.290	4.283	4.288	-0.001	-0.003	-0.001	0.000
4	A	21	VAL	0	-0.023	-0.011	5.646	4.411	4.411	0.000	0.000	0.000	0.000
5	A	22	ALA	0	0.009	-0.002	8.124	-0.303	-0.303	0.000	0.000	0.000	0.000
6	A	23	GLU	-1	-0.936	-0.979	10.052	-26.345	-26.345	0.000	0.000	0.000	0.000
7	A	24	GLY	0	-0.050	-0.018	11.429	1.030	1.030	0.000	0.000	0.000	0.000
8	A	25	GLU	-1	-0.880	-0.925	10.031	-25.144	-25.144	0.000	0.000	0.000	0.000
9	A	26	ASN	0	-0.063	-0.054	9.206	-0.325	-0.325	0.000	0.000	0.000	0.000
11	A	28	PHE	0	0.032	-0.005	6.999	1.289	1.289	0.000	0.000	0.000	0.000
12	A	29	GLY	0	0.030	0.015	9.155	-1.694	-1.694	0.000	0.000	0.000	0.000
13	A	30	VAL	0	-0.077	-0.039	10.909	1.829	1.829	0.000	0.000	0.000	0.000
14	A	31	CYS	0	-0.011	0.000	13.975	-0.566	-0.566	0.000	0.000	0.000	0.000
15	A	32	HIS	0	0.019	0.008	15.927	1.783	1.783	0.000	0.000	0.000	0.000
16	A	33	ILE	0	-0.001	-0.003	19.293	-0.244	-0.244	0.000	0.000	0.000	0.000
17	A	34	PHE	0	-0.014	-0.006	21.677	0.730	0.730	0.000	0.000	0.000	0.000
18	A	35	ALA	0	0.038	0.031	24.656	0.001	0.001	0.000	0.000	0.000	0.000
19	A	36	SER	0	-0.070	-0.059	27.359	0.549	0.549	0.000	0.000	0.000	0.000
20	A	37	PHE	0	0.013	-0.033	30.591	-0.011	-0.011	0.000	0.000	0.000	0.000
21	A	38	ASN	0	-0.077	-0.001	32.343	0.427	0.427	0.000	0.000	0.000	0.000
22	A	39	ASP	-1	-0.714	-0.859	26.842	-11.885	-11.885	0.000	0.000	0.000	0.000
23	A	40	THR	0	-0.090	-0.039	24.581	0.018	0.018	0.000	0.000	0.000	0.000
24	A	41	PHE	0	0.011	0.000	21.696	-0.355	-0.355	0.000	0.000	0.000	0.000
25	A	42	VAL	0	0.025	0.016	16.944	0.108	0.108	0.000	0.000	0.000	0.000
26	A	43	HIS	0	-0.040	-0.046	15.111	0.352	0.352	0.000	0.000	0.000	0.000
27	A	44	VAL	0	-0.003	0.004	10.625	0.516	0.516	0.000	0.000	0.000	0.000
28	A	45	THR	0	0.021	0.015	12.284	-0.167	-0.167	0.000	0.000	0.000	0.000
29	A	46	ASP	-1	-0.760	-0.895	10.523	-22.926	-22.926	0.000	0.000	0.000	0.000
30	A	47	LEU	0	0.002	-0.016	11.494	1.536	1.536	0.000	0.000	0.000	0.000
31	A	48	SER	0	-0.038	-0.004	14.158	1.671	1.671	0.000	0.000	0.000	0.000
32	A	49	GLY	0	-0.053	-0.019	14.967	1.100	1.100	0.000	0.000	0.000	0.000
33	A	50	LYS	1	0.854	0.931	15.724	18.318	18.318	0.000	0.000	0.000	0.000
34	A	51	GLU	-1	-0.826	-0.898	11.382	-20.181	-20.181	0.000	0.000	0.000	0.000
35	A	52	THR	0	-0.067	-0.054	12.111	1.268	1.268	0.000	0.000	0.000	0.000
36	A	53	ILE	0	-0.022	0.012	6.637	-1.036	-1.036	0.000	0.000	0.000	0.000
37	A	54	CYS	0	0.014	0.010	9.637	-0.191	-0.191	0.000	0.000	0.000	0.000
38	A	55	ARG	1	0.926	0.963	12.453	16.700	16.700	0.000	0.000	0.000	0.000
39	A	56	VAL	0	0.000	0.011	16.226	0.144	0.144	0.000	0.000	0.000	0.000
40	A	57	THR	0	0.013	-0.006	18.802	-0.082	-0.082	0.000	0.000	0.000	0.000
41	A	58	GLY	0	0.010	0.005	22.489	-0.168	-0.168	0.000	0.000	0.000	0.000
42	A	59	GLY	0	0.051	0.013	25.318	0.115	0.115	0.000	0.000	0.000	0.000
43	A	60	MET	0	-0.076	-0.012	20.948	-0.247	-0.247	0.000	0.000	0.000	0.000
44	A	61	LYS	1	0.791	0.890	19.221	15.225	15.225	0.000	0.000	0.000	0.000
45	A	62	VAL	0	-0.033	-0.009	24.253	0.183	0.183	0.000	0.000	0.000	0.000
46	A	63	LYS	1	0.953	0.969	28.087	10.053	10.053	0.000	0.000	0.000	0.000
47	A	64	ALA	0	0.039	0.019	30.961	0.173	0.173	0.000	0.000	0.000	0.000
48	A	65	ASP	-1	-0.825	-0.912	32.579	-9.506	-9.506	0.000	0.000	0.000	0.000
49	A	66	ARG	1	0.849	0.936	33.624	8.187	8.187	0.000	0.000	0.000	0.000
50	A	67	ASP	-1	-0.917	-0.969	31.920	-9.256	-9.256	0.000	0.000	0.000	0.000
51	A	68	GLU	-1	-0.830	-0.918	29.155	-10.581	-10.581	0.000	0.000	0.000	0.000
52	A	69	SER	0	-0.052	-0.038	28.290	-0.435	-0.435	0.000	0.000	0.000	0.000
53	A	70	SER	0	0.006	0.008	30.011	0.001	0.001	0.000	0.000	0.000	0.000
54	A	71	PRO	0	-0.003	-0.019	28.407	-0.456	-0.456	0.000	0.000	0.000	0.000
55	A	72	TYR	0	0.047	0.037	27.145	-0.480	-0.480	0.000	0.000	0.000	0.000
56	A	73	ALA	0	0.063	0.041	25.778	-0.486	-0.486	0.000	0.000	0.000	0.000
57	A	74	ALA	0	0.025	0.008	24.076	-0.597	-0.597	0.000	0.000	0.000	0.000
58	A	75	MET	0	-0.050	-0.014	22.465	-0.688	-0.688	0.000	0.000	0.000	0.000
59	A	76	LEU	0	0.008	0.000	21.258	-0.806	-0.806	0.000	0.000	0.000	0.000
60	A	77	ALA	0	0.010	0.009	19.900	-0.786	-0.786	0.000	0.000	0.000	0.000
61	A	78	ALA	0	0.004	-0.003	18.037	-1.016	-1.016	0.000	0.000	0.000	0.000
62	A	79	GLN	0	0.003	-0.009	16.647	-0.621	-0.621	0.000	0.000	0.000	0.000
63	A	80	ASP	-1	-0.811	-0.861	15.631	-19.668	-19.668	0.000	0.000	0.000	0.000
64	A	81	VAL	0	0.025	0.002	13.367	-1.594	-1.594	0.000	0.000	0.000	0.000
65	A	82	ALA	0	0.011	-0.001	12.058	-2.196	-2.196	0.000	0.000	0.000	0.000
66	A	83	GLN	0	-0.041	-0.023	11.256	-1.374	-1.374	0.000	0.000	0.000	0.000
67	A	84	ARG	1	0.972	0.952	9.602	18.611	18.611	0.000	0.000	0.000	0.000
68	A	85	CYS	0	-0.077	-0.033	7.715	-3.893	-3.893	0.000	0.000	0.000	0.000
69	A	86	LYS	1	0.896	0.941	6.457	17.989	17.989	0.000	0.000	0.000	0.000
70	A	87	GLU	-1	-0.927	-0.938	6.156	-34.056	-34.056	0.000	0.000	0.000	0.000
75	A	92	ALA	0	-0.007	-0.005	8.564	3.035	3.035	0.000	0.000	0.000	0.000
76	A	93	LEU	0	0.004	0.002	10.600	-0.830	-0.830	0.000	0.000	0.000	0.000
77	A	94	HIS	0	0.049	0.040	13.348	2.091	2.091	0.000	0.000	0.000	0.000
78	A	95	ILE	0	-0.028	-0.016	16.540	-0.456	-0.456	0.000	0.000	0.000	0.000
79	A	96	LYS	1	0.973	0.991	19.070	15.660	15.660	0.000	0.000	0.000	0.000
80	A	97	LEU	0	0.001	0.008	21.201	-0.119	-0.119	0.000	0.000	0.000	0.000
81	A	98	ARG	1	0.955	0.981	24.121	11.986	11.986	0.000	0.000	0.000	0.000
82	A	99	ALA	0	0.032	0.033	26.613	-0.046	-0.046	0.000	0.000	0.000	0.000
83	A	100	THR	0	-0.085	-0.069	29.486	0.016	0.016	0.000	0.000	0.000	0.000
84	A	101	GLY	0	0.068	0.034	31.460	-0.134	-0.134	0.000	0.000	0.000	0.000
85	A	102	GLY	0	0.023	0.013	33.143	0.191	0.191	0.000	0.000	0.000	0.000
86	A	103	ASN	0	0.022	0.007	35.771	0.064	0.064	0.000	0.000	0.000	0.000
87	A	104	ARG	1	0.914	0.965	35.146	8.906	8.906	0.000	0.000	0.000	0.000
88	A	105	THR	0	0.033	0.022	34.658	0.126	0.126	0.000	0.000	0.000	0.000
89	A	106	LYS	1	0.920	0.962	33.884	8.353	8.353	0.000	0.000	0.000	0.000
90	A	107	THR	0	0.026	0.028	33.247	-0.107	-0.107	0.000	0.000	0.000	0.000
91	A	108	PRO	0	0.020	0.004	28.628	0.029	0.029	0.000	0.000	0.000	0.000
92	A	109	GLY	0	-0.011	-0.003	30.139	0.282	0.282	0.000	0.000	0.000	0.000
93	A	110	PRO	0	0.030	-0.002	29.797	-0.285	-0.285	0.000	0.000	0.000	0.000
94	A	111	GLY	0	0.014	0.005	27.540	-0.178	-0.178	0.000	0.000	0.000	0.000
95	A	112	ALA	0	0.034	0.026	25.222	-0.544	-0.544	0.000	0.000	0.000	0.000
96	A	113	GLN	0	0.020	0.004	24.780	-0.675	-0.675	0.000	0.000	0.000	0.000
97	A	114	SER	0	-0.059	-0.042	25.628	-0.264	-0.264	0.000	0.000	0.000	0.000
98	A	115	ALA	0	0.056	0.030	21.517	-0.402	-0.402	0.000	0.000	0.000	0.000
99	A	116	LEU	0	0.047	0.023	20.544	-0.744	-0.744	0.000	0.000	0.000	0.000
100	A	117	ARG	1	0.960	0.966	21.154	10.823	10.823	0.000	0.000	0.000	0.000
101	A	118	ALA	0	-0.010	0.011	20.844	-0.162	-0.162	0.000	0.000	0.000	0.000
102	A	119	LEU	0	0.020	0.025	15.327	-0.680	-0.680	0.000	0.000	0.000	0.000
103	A	120	ALA	0	0.015	0.012	16.956	-0.784	-0.784	0.000	0.000	0.000	0.000
104	A	121	ARG	1	0.915	0.947	18.896	13.177	13.177	0.000	0.000	0.000	0.000
105	A	122	SER	0	-0.019	-0.011	15.584	0.023	0.023	0.000	0.000	0.000	0.000
106	A	123	GLY	0	-0.037	-0.019	15.369	-1.247	-1.247	0.000	0.000	0.000	0.000
107	A	124	MET	0	-0.049	-0.002	10.176	-1.896	-1.896	0.000	0.000	0.000	0.000
108	A	125	LYS	1	0.951	0.974	11.975	24.695	24.695	0.000	0.000	0.000	0.000
109	A	126	ILE	0	0.003	0.001	14.188	-0.694	-0.694	0.000	0.000	0.000	0.000
110	A	127	GLY	0	-0.001	0.007	16.753	0.181	0.181	0.000	0.000	0.000	0.000
111	A	128	ARG	1	0.930	0.952	17.517	14.320	14.320	0.000	0.000	0.000	0.000
112	A	129	ILE	0	0.003	-0.008	19.720	-0.648	-0.648	0.000	0.000	0.000	0.000
113	A	130	GLU	-1	-0.910	-0.943	22.411	-11.761	-11.761	0.000	0.000	0.000	0.000
114	A	131	ASP	-1	-0.843	-0.895	23.918	-11.115	-11.115	0.000	0.000	0.000	0.000
115	A	132	VAL	0	0.007	-0.004	23.312	0.050	0.050	0.000	0.000	0.000	0.000
116	A	133	THR	0	-0.037	-0.055	26.544	0.013	0.013	0.000	0.000	0.000	0.000
117	A	134	PRO	0	-0.058	-0.026	28.614	0.270	0.270	0.000	0.000	0.000	0.000
118	A	135	ILE	0	0.049	0.016	31.339	0.279	0.279	0.000	0.000	0.000	0.000
119	A	136	PRO	0	-0.067	-0.016	34.696	-0.058	-0.058	0.000	0.000	0.000	0.000
120	A	137	SER	0	0.033	0.004	37.046	0.016	0.016	0.000	0.000	0.000	0.000
121	A	138	ASP	-1	-0.843	-0.918	39.798	-6.975	-6.975	0.000	0.000	0.000	0.000
122	A	139	SER	0	-0.092	-0.055	39.509	-0.184	-0.184	0.000	0.000	0.000	0.000
123	A	140	THR	0	0.016	0.013	40.823	0.185	0.185	0.000	0.000	0.000	0.000
124	A	141	ARG	1	0.985	0.992	43.050	6.369	6.369	0.000	0.000	0.000	0.000
125	A	142	ARG	1	0.906	0.949	40.145	7.476	7.476	0.000	0.000	0.000	0.000
126	A	143	LYS	1	0.979	0.986	40.684	7.808	7.808	0.000	0.000	0.000	0.000
127	A	144	GLY	0	0.020	0.000	43.777	-0.110	-0.110	0.000	0.000	0.000	0.000
128	A	145	GLY	0	0.011	0.017	46.242	0.136	0.136	0.000	0.000	0.000	0.000
129	A	146	ARG	1	0.968	0.970	49.380	5.646	5.646	0.000	0.000	0.000	0.000
130	A	147	ARG	1	0.970	0.985	52.155	5.681	5.681	0.000	0.000	0.000	0.000
131	A	148	GLY	0	0.043	0.036	48.809	0.025	0.025	0.000	0.000	0.000	0.000
132	A	149	ARG	1	0.917	0.931	42.729	7.254	7.254	0.000	0.000	0.000	0.000
133	A	150	ARG	1	0.877	0.951	48.232	6.044	6.044	0.000	0.000	0.000	0.000
134	A	151	LEU	-1	-0.825	-0.888	46.332	-6.233	-6.233	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:18:GLY)