FMO DATABASE

FMODB ID: 9QLR2

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	141
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1218506.548915
FMO2-HF: Nuclear repulsion	1164428.422842
FMO2-HF: Total energy	-54078.126074
FMO2-MP2: Total energy	-54238.600777

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:4:VAL)

Summations of interaction energy for fragment #1(A:4:VAL)

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.
114.384	122.098	7.533	-5.957	-9.29	-0.063

Interaction energy analysis for fragmet #1(A:4:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.819 / q_NPA : 0.919

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	6	VAL	0	0.023	0.002	3.709	0.324	2.138	-0.010	-0.872	-0.933	0.000
5	A	8	ASP	-1	-0.780	-0.884	2.524	-81.483	-75.613	3.254	-4.360	-4.764	-0.056
6	A	9	VAL	0	0.003	0.013	4.076	0.436	0.686	-0.001	-0.017	-0.232	0.000
130	A	133	ARG	1	0.852	0.933	3.937	17.804	17.950	0.001	-0.057	-0.090	0.000
132	A	135	ALA	0	0.000	0.010	3.509	1.611	1.825	0.007	-0.044	-0.176	0.000
133	A	136	GLY	0	0.005	-0.002	2.240	-4.415	-4.058	3.120	-1.852	-1.625	-0.003
134	A	137	GLN	0	-0.023	-0.022	3.245	4.759	3.183	0.052	1.777	-0.253	-0.001
136	A	139	ALA	0	0.025	0.006	2.365	0.880	1.405	1.111	-0.511	-1.125	-0.003
137	A	140	ALA	0	-0.063	-0.026	4.324	2.086	2.200	-0.001	-0.021	-0.092	0.000
4	A	7	LYS	1	0.904	0.950	5.563	34.031	34.031	0.000	0.000	0.000	0.000
7	A	10	ASN	0	0.017	-0.008	6.538	2.506	2.506	0.000	0.000	0.000	0.000
8	A	11	GLN	0	-0.002	-0.011	9.010	1.522	1.522	0.000	0.000	0.000	0.000
9	A	12	GLN	0	0.017	0.005	12.053	0.670	0.670	0.000	0.000	0.000	0.000
10	A	13	GLU	-1	-0.804	-0.877	11.017	-21.365	-21.365	0.000	0.000	0.000	0.000
11	A	14	PHE	0	0.021	0.009	7.093	1.082	1.082	0.000	0.000	0.000	0.000
12	A	15	VAL	0	-0.008	-0.013	10.537	0.631	0.631	0.000	0.000	0.000	0.000
13	A	16	ARG	1	0.968	0.984	13.943	16.557	16.557	0.000	0.000	0.000	0.000
14	A	17	ALA	0	0.038	0.026	10.869	0.859	0.859	0.000	0.000	0.000	0.000
15	A	18	LEU	0	-0.006	0.005	11.831	0.673	0.673	0.000	0.000	0.000	0.000
16	A	19	ALA	0	0.000	-0.008	13.295	0.923	0.923	0.000	0.000	0.000	0.000
17	A	20	ALA	0	0.020	0.011	15.573	0.841	0.841	0.000	0.000	0.000	0.000
18	A	21	PHE	0	-0.002	0.006	13.428	0.462	0.462	0.000	0.000	0.000	0.000
19	A	22	LEU	0	-0.011	-0.005	15.542	0.829	0.829	0.000	0.000	0.000	0.000
20	A	23	LYS	1	0.926	0.964	18.165	12.396	12.396	0.000	0.000	0.000	0.000
21	A	24	LYS	1	0.932	0.965	17.131	15.555	15.555	0.000	0.000	0.000	0.000
22	A	25	SER	0	-0.024	-0.015	17.705	0.237	0.237	0.000	0.000	0.000	0.000
23	A	26	GLY	0	0.002	0.013	20.334	0.441	0.441	0.000	0.000	0.000	0.000
24	A	27	LYS	1	0.943	0.963	21.957	13.672	13.672	0.000	0.000	0.000	0.000
25	A	28	LEU	0	-0.007	0.010	21.135	0.035	0.035	0.000	0.000	0.000	0.000
26	A	29	LYS	1	0.970	0.981	23.821	10.135	10.135	0.000	0.000	0.000	0.000
27	A	30	VAL	0	0.001	0.003	26.231	-0.090	-0.090	0.000	0.000	0.000	0.000
28	A	31	PRO	0	-0.088	-0.044	28.359	0.282	0.282	0.000	0.000	0.000	0.000
29	A	32	GLU	-1	-0.844	-0.931	31.579	-8.296	-8.296	0.000	0.000	0.000	0.000
30	A	33	TRP	0	-0.006	-0.004	31.035	-0.120	-0.120	0.000	0.000	0.000	0.000
31	A	34	VAL	0	-0.025	-0.027	30.017	-0.183	-0.183	0.000	0.000	0.000	0.000
32	A	35	ASP	-1	-0.920	-0.970	31.172	-9.720	-9.720	0.000	0.000	0.000	0.000
33	A	36	THR	0	0.046	0.035	33.587	0.291	0.291	0.000	0.000	0.000	0.000
34	A	37	VAL	0	-0.044	-0.011	32.524	0.163	0.163	0.000	0.000	0.000	0.000
35	A	38	LYS	1	0.843	0.919	33.621	7.912	7.912	0.000	0.000	0.000	0.000
36	A	39	LEU	0	-0.024	-0.006	25.964	-0.016	-0.016	0.000	0.000	0.000	0.000
37	A	40	ALA	0	-0.004	-0.028	29.976	-0.228	-0.228	0.000	0.000	0.000	0.000
38	A	41	LYS	1	0.941	0.968	31.919	8.391	8.391	0.000	0.000	0.000	0.000
39	A	42	HIS	0	-0.058	-0.025	30.740	0.088	0.088	0.000	0.000	0.000	0.000
40	A	43	LYS	1	0.842	0.940	30.135	9.665	9.665	0.000	0.000	0.000	0.000
41	A	44	GLU	-1	-0.800	-0.893	35.017	-8.517	-8.517	0.000	0.000	0.000	0.000
42	A	45	LEU	0	0.066	0.038	35.331	0.197	0.197	0.000	0.000	0.000	0.000
43	A	46	ALA	0	0.037	0.019	33.908	-0.195	-0.195	0.000	0.000	0.000	0.000
44	A	47	PRO	0	-0.091	-0.075	28.372	-0.093	-0.093	0.000	0.000	0.000	0.000
45	A	48	TYR	0	0.021	0.022	27.872	0.260	0.260	0.000	0.000	0.000	0.000
46	A	49	ASP	-1	-0.865	-0.908	25.343	-11.232	-11.232	0.000	0.000	0.000	0.000
47	A	50	GLU	-1	-0.818	-0.913	27.332	-10.403	-10.403	0.000	0.000	0.000	0.000
48	A	51	ASN	0	-0.039	-0.042	23.284	-0.413	-0.413	0.000	0.000	0.000	0.000
49	A	52	TRP	0	0.066	0.040	23.324	-0.916	-0.916	0.000	0.000	0.000	0.000
50	A	53	PHE	0	-0.008	-0.003	23.648	-0.452	-0.452	0.000	0.000	0.000	0.000
51	A	54	TYR	0	0.040	0.017	20.215	-0.404	-0.404	0.000	0.000	0.000	0.000
52	A	55	THR	0	0.008	0.000	19.087	-0.796	-0.796	0.000	0.000	0.000	0.000
53	A	56	ARG	1	0.926	0.985	19.383	11.847	11.847	0.000	0.000	0.000	0.000
54	A	57	ALA	0	0.019	0.014	20.102	-0.253	-0.253	0.000	0.000	0.000	0.000
55	A	58	ALA	0	0.042	0.022	15.364	-0.555	-0.555	0.000	0.000	0.000	0.000
56	A	59	SER	0	-0.030	-0.032	15.458	-0.744	-0.744	0.000	0.000	0.000	0.000
57	A	60	THR	0	-0.038	-0.040	17.272	-0.137	-0.137	0.000	0.000	0.000	0.000
58	A	61	ALA	0	0.030	0.017	14.953	-0.129	-0.129	0.000	0.000	0.000	0.000
59	A	62	ARG	1	0.920	0.949	11.800	19.607	19.607	0.000	0.000	0.000	0.000
60	A	63	HIS	0	-0.052	-0.028	13.925	-0.852	-0.852	0.000	0.000	0.000	0.000
61	A	64	LEU	0	-0.010	-0.007	17.062	0.213	0.213	0.000	0.000	0.000	0.000
62	A	65	TYR	0	-0.037	-0.017	8.187	1.077	1.077	0.000	0.000	0.000	0.000
63	A	66	LEU	0	-0.063	-0.030	12.268	-0.462	-0.462	0.000	0.000	0.000	0.000
64	A	67	ARG	1	0.896	0.943	15.164	14.826	14.826	0.000	0.000	0.000	0.000
65	A	68	GLY	0	0.061	0.041	18.694	0.232	0.232	0.000	0.000	0.000	0.000
66	A	69	GLY	0	0.080	0.049	20.286	0.341	0.341	0.000	0.000	0.000	0.000
67	A	70	ALA	0	-0.035	-0.006	22.626	0.606	0.606	0.000	0.000	0.000	0.000
68	A	71	GLY	0	0.084	0.034	24.376	0.145	0.145	0.000	0.000	0.000	0.000
69	A	72	VAL	0	-0.001	-0.018	27.009	-0.158	-0.158	0.000	0.000	0.000	0.000
70	A	73	GLY	0	0.010	0.014	28.719	0.051	0.051	0.000	0.000	0.000	0.000
71	A	74	SER	0	-0.001	0.000	25.689	0.084	0.084	0.000	0.000	0.000	0.000
72	A	75	MET	0	0.028	0.026	20.788	-0.050	-0.050	0.000	0.000	0.000	0.000
73	A	76	THR	0	-0.054	-0.038	25.636	0.090	0.090	0.000	0.000	0.000	0.000
74	A	77	LYS	1	0.933	0.970	28.196	10.904	10.904	0.000	0.000	0.000	0.000
75	A	78	ILE	0	0.020	0.014	21.819	0.123	0.123	0.000	0.000	0.000	0.000
76	A	79	TYR	0	-0.053	-0.048	21.258	-0.135	-0.135	0.000	0.000	0.000	0.000
77	A	80	GLY	0	0.011	0.004	26.425	0.356	0.356	0.000	0.000	0.000	0.000
78	A	81	GLY	0	0.003	-0.008	28.611	-0.356	-0.356	0.000	0.000	0.000	0.000
79	A	82	ARG	1	0.985	1.002	30.977	8.877	8.877	0.000	0.000	0.000	0.000
80	A	83	GLN	0	0.034	0.018	33.839	-0.095	-0.095	0.000	0.000	0.000	0.000
81	A	84	ARG	1	0.996	0.997	36.976	8.000	8.000	0.000	0.000	0.000	0.000
82	A	85	ASN	0	-0.046	-0.024	39.520	0.095	0.095	0.000	0.000	0.000	0.000
83	A	86	GLY	0	0.042	0.025	42.899	0.179	0.179	0.000	0.000	0.000	0.000
84	A	87	VAL	0	0.062	0.032	44.555	-0.109	-0.109	0.000	0.000	0.000	0.000
85	A	88	ARG	1	0.934	0.977	44.602	6.921	6.921	0.000	0.000	0.000	0.000
86	A	89	PRO	0	0.062	0.024	43.048	-0.159	-0.159	0.000	0.000	0.000	0.000
87	A	90	SER	0	-0.063	-0.042	37.834	-0.090	-0.090	0.000	0.000	0.000	0.000
88	A	91	HIS	0	0.054	0.037	38.183	-0.161	-0.161	0.000	0.000	0.000	0.000
89	A	92	PHE	0	-0.004	0.001	29.930	-0.147	-0.147	0.000	0.000	0.000	0.000
90	A	93	SER	0	-0.026	-0.012	33.834	0.237	0.237	0.000	0.000	0.000	0.000
91	A	94	ARG	1	0.969	0.980	31.876	8.918	8.918	0.000	0.000	0.000	0.000
92	A	95	GLY	0	0.066	0.030	29.785	0.190	0.190	0.000	0.000	0.000	0.000
93	A	96	SER	0	-0.014	-0.008	30.751	0.223	0.223	0.000	0.000	0.000	0.000
94	A	97	LYS	1	1.025	0.986	30.336	8.402	8.402	0.000	0.000	0.000	0.000
95	A	98	SER	0	-0.036	-0.010	31.576	-0.220	-0.220	0.000	0.000	0.000	0.000
96	A	99	VAL	0	0.088	0.045	26.961	-0.146	-0.146	0.000	0.000	0.000	0.000
97	A	100	ALA	0	0.032	0.018	26.294	-0.312	-0.312	0.000	0.000	0.000	0.000
98	A	101	ARG	1	0.932	0.968	26.555	8.946	8.946	0.000	0.000	0.000	0.000
99	A	102	ARG	1	0.943	0.981	28.391	9.158	9.158	0.000	0.000	0.000	0.000
100	A	103	VAL	0	0.032	0.031	22.320	-0.122	-0.122	0.000	0.000	0.000	0.000
101	A	104	LEU	0	-0.002	-0.004	22.742	-0.328	-0.328	0.000	0.000	0.000	0.000
102	A	105	GLN	0	0.011	-0.002	24.857	-0.058	-0.058	0.000	0.000	0.000	0.000
103	A	106	ALA	0	0.005	0.013	24.262	-0.004	-0.004	0.000	0.000	0.000	0.000
104	A	107	LEU	0	0.011	-0.001	18.968	-0.222	-0.222	0.000	0.000	0.000	0.000
105	A	108	GLU	-1	-0.783	-0.865	21.949	-11.590	-11.590	0.000	0.000	0.000	0.000
106	A	109	GLY	0	-0.027	-0.009	24.625	0.082	0.082	0.000	0.000	0.000	0.000
107	A	110	LEU	0	-0.035	-0.027	19.216	0.124	0.124	0.000	0.000	0.000	0.000
108	A	111	LYS	1	0.879	0.938	20.644	11.588	11.588	0.000	0.000	0.000	0.000
109	A	112	MET	0	0.003	0.019	15.503	-0.675	-0.675	0.000	0.000	0.000	0.000
110	A	113	VAL	0	-0.053	-0.030	17.991	-0.696	-0.696	0.000	0.000	0.000	0.000
111	A	114	GLU	-1	-0.909	-0.950	20.706	-12.898	-12.898	0.000	0.000	0.000	0.000
112	A	115	LYS	1	0.889	0.942	23.547	10.225	10.225	0.000	0.000	0.000	0.000
113	A	116	ASP	-1	-0.827	-0.909	24.394	-13.613	-13.613	0.000	0.000	0.000	0.000
114	A	117	GLN	0	-0.007	-0.008	26.916	0.585	0.585	0.000	0.000	0.000	0.000
115	A	118	ASP	-1	-0.849	-0.901	28.777	-10.872	-10.872	0.000	0.000	0.000	0.000
116	A	119	GLY	0	-0.015	-0.024	29.450	0.392	0.392	0.000	0.000	0.000	0.000
117	A	120	GLY	0	-0.079	-0.029	26.695	-0.353	-0.353	0.000	0.000	0.000	0.000
118	A	121	ARG	1	0.784	0.871	23.050	11.866	11.866	0.000	0.000	0.000	0.000
119	A	122	LYS	1	0.927	0.953	20.054	13.808	13.808	0.000	0.000	0.000	0.000
120	A	123	LEU	0	-0.002	-0.005	13.628	0.422	0.422	0.000	0.000	0.000	0.000
121	A	124	THR	0	0.014	0.004	17.584	-0.230	-0.230	0.000	0.000	0.000	0.000
122	A	125	PRO	0	0.076	0.020	14.909	-1.121	-1.121	0.000	0.000	0.000	0.000
123	A	126	GLN	0	-0.001	-0.002	13.792	-1.719	-1.719	0.000	0.000	0.000	0.000
124	A	127	GLY	0	0.038	0.013	13.421	-1.099	-1.099	0.000	0.000	0.000	0.000
125	A	128	GLN	0	-0.027	-0.008	9.708	0.927	0.927	0.000	0.000	0.000	0.000
126	A	129	ARG	1	0.967	0.992	9.576	20.827	20.827	0.000	0.000	0.000	0.000
127	A	130	ASP	-1	-0.855	-0.912	8.897	-24.311	-24.311	0.000	0.000	0.000	0.000
128	A	131	LEU	0	-0.026	-0.015	8.851	-1.165	-1.165	0.000	0.000	0.000	0.000
129	A	132	ASP	-1	-0.757	-0.886	5.180	-44.370	-44.370	0.000	0.000	0.000	0.000
131	A	134	ILE	0	-0.042	-0.031	5.990	-0.086	-0.086	0.000	0.000	0.000	0.000
135	A	138	VAL	0	-0.005	0.001	5.973	2.117	2.117	0.000	0.000	0.000	0.000
138	A	141	ALA	0	0.032	0.012	6.524	1.902	1.902	0.000	0.000	0.000	0.000
139	A	142	ASN	0	-0.051	-0.041	7.641	1.717	1.717	0.000	0.000	0.000	0.000
140	A	143	LYS	1	0.885	0.951	5.352	36.083	36.083	0.000	0.000	0.000	0.000
141	A	144	LYS	0	0.018	0.026	9.342	2.004	2.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:VAL)