FMODB ID: LRQY9

Calculation Name: 7S1K-y-Other547

Preferred Name:

Target Type:

Ligand Name: radezolid | n7-methyl-guanosine-5'-monophosphate | 1n-methylguanosine-5'-monophosphate | 5'-o-(dihydroxyphosphanyl)-2,8-dimethyladenosine | 2n-methylguanosine-5'-monophosphate | n6-methyladenosine-5'-monophosphate | pseudouridine-5'-monophosphate | (1s)-1,4-anhydro-1-(3-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-o-phosphono-d-ribitol | 5-methylcytidine-5'-monophosphate | 5-methyluridine 5'-monophosphate | o2'-methylguanosine-5'-monophosphate | 5,6-dihydrouridine-5'-monophosphate | o2'-methylycytidine-5'-monophosphate | o2'-methyluridine 5'-monophosphate | (2s,3r)-2-azanyl-5-carbamimidamido-3-oxidanyl-pentanoic acid

Ligand 3-letter code: RD8 | G7M | 1MG | 8AH | 2MG | 6MZ | PSU | 3TD | 5MC | 5MU | OMG | H2U | OMC | OMU | 4D4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7S1K

Chain ID: y

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

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 method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	80
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

FMO2-HF: Electronic energy	-512990.829026
FMO2-HF: Nuclear repulsion	480708.828201
FMO2-HF: Total energy	-32282.000825
FMO2-MP2: Total energy	-32376.15993

Snapshot

Snapshot

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	ARG	1	0.971	0.979	2.665	51.390	54.725	0.629	-1.796	-2.168	-0.018
4	A	7	THR	0	-0.019	-0.028	4.448	4.920	5.045	-0.001	-0.007	-0.117	0.000
5	A	8	LEU	0	-0.051	-0.017	6.962	-1.923	-1.923	0.000	0.000	0.000	0.000
6	A	9	GLN	0	-0.010	-0.012	8.786	2.804	2.804	0.000	0.000	0.000	0.000
7	A	10	GLY	0	-0.012	-0.012	12.092	1.056	1.056	0.000	0.000	0.000	0.000
8	A	11	ARG	1	0.916	0.960	15.894	26.106	26.106	0.000	0.000	0.000	0.000
9	A	12	VAL	0	0.011	0.020	19.355	-0.038	-0.038	0.000	0.000	0.000	0.000
10	A	13	VAL	0	-0.072	-0.043	21.621	0.971	0.971	0.000	0.000	0.000	0.000
11	A	14	SER	0	-0.020	-0.028	24.401	1.118	1.118	0.000	0.000	0.000	0.000
12	A	15	ASP	-1	-0.778	-0.904	24.694	-22.888	-22.888	0.000	0.000	0.000	0.000
13	A	16	LYS	1	0.961	1.004	26.212	18.439	18.439	0.000	0.000	0.000	0.000
14	A	17	MET	0	-0.105	-0.058	25.467	0.944	0.944	0.000	0.000	0.000	0.000
15	A	18	GLU	-1	-0.848	-0.923	27.460	-20.426	-20.426	0.000	0.000	0.000	0.000
16	A	19	LYS	1	0.899	0.976	24.128	22.703	22.703	0.000	0.000	0.000	0.000
17	A	20	SER	0	-0.041	-0.037	23.192	-1.276	-1.276	0.000	0.000	0.000	0.000
18	A	21	ILE	0	0.069	0.059	18.697	0.658	0.658	0.000	0.000	0.000	0.000
19	A	22	VAL	0	-0.062	-0.032	21.731	-0.732	-0.732	0.000	0.000	0.000	0.000
20	A	23	VAL	0	0.043	0.019	16.507	0.272	0.272	0.000	0.000	0.000	0.000
21	A	24	ALA	0	-0.028	-0.014	19.647	0.041	0.041	0.000	0.000	0.000	0.000
22	A	25	ILE	0	0.031	0.016	14.507	-0.773	-0.773	0.000	0.000	0.000	0.000
23	A	26	GLU	-1	-0.796	-0.901	16.591	-26.136	-26.136	0.000	0.000	0.000	0.000
24	A	27	ARG	1	0.906	0.953	15.914	28.601	28.601	0.000	0.000	0.000	0.000
25	A	28	PHE	0	-0.002	-0.009	17.180	1.918	1.918	0.000	0.000	0.000	0.000
26	A	29	VAL	0	0.017	0.008	18.125	-1.288	-1.288	0.000	0.000	0.000	0.000
27	A	30	LYS	1	0.970	0.998	20.550	25.173	25.173	0.000	0.000	0.000	0.000
28	A	31	HIS	0	0.033	0.018	23.398	-0.400	-0.400	0.000	0.000	0.000	0.000
29	A	32	PRO	0	-0.023	-0.024	25.965	0.169	0.169	0.000	0.000	0.000	0.000
30	A	33	ILE	0	0.027	0.023	27.536	0.164	0.164	0.000	0.000	0.000	0.000
31	A	34	TYR	0	0.027	0.005	30.687	0.169	0.169	0.000	0.000	0.000	0.000
32	A	35	GLY	0	0.017	0.020	27.642	0.157	0.157	0.000	0.000	0.000	0.000
33	A	36	LYS	1	0.961	0.977	26.808	18.951	18.951	0.000	0.000	0.000	0.000
34	A	37	PHE	0	0.004	-0.001	20.019	-0.275	-0.275	0.000	0.000	0.000	0.000
35	A	38	ILE	0	-0.019	-0.008	23.979	0.735	0.735	0.000	0.000	0.000	0.000
36	A	39	LYS	1	0.881	0.928	19.195	27.072	27.072	0.000	0.000	0.000	0.000
37	A	40	ARG	1	0.863	0.928	21.301	24.376	24.376	0.000	0.000	0.000	0.000
38	A	41	THR	0	0.081	0.042	20.418	-0.978	-0.978	0.000	0.000	0.000	0.000
39	A	42	THR	0	-0.036	-0.021	18.363	0.947	0.947	0.000	0.000	0.000	0.000
40	A	43	LYS	1	0.952	0.989	19.526	22.190	22.190	0.000	0.000	0.000	0.000
41	A	44	LEU	0	0.017	0.015	15.715	0.299	0.299	0.000	0.000	0.000	0.000
42	A	45	HIS	0	0.026	0.022	19.800	-0.126	-0.126	0.000	0.000	0.000	0.000
43	A	46	VAL	0	-0.037	-0.021	16.636	-1.343	-1.343	0.000	0.000	0.000	0.000
44	A	47	HIS	0	-0.075	-0.056	18.641	1.706	1.706	0.000	0.000	0.000	0.000
45	A	48	ASP	-1	-0.826	-0.936	18.571	-28.761	-28.761	0.000	0.000	0.000	0.000
46	A	49	GLU	-1	-0.829	-0.938	20.637	-25.535	-25.535	0.000	0.000	0.000	0.000
47	A	50	ASN	0	-0.120	-0.062	22.332	0.574	0.574	0.000	0.000	0.000	0.000
48	A	51	ASN	0	0.013	0.013	24.773	0.634	0.634	0.000	0.000	0.000	0.000
49	A	52	GLU	-1	-0.801	-0.890	20.104	-29.506	-29.506	0.000	0.000	0.000	0.000
50	A	53	CYS	0	-0.100	-0.040	20.065	-1.140	-1.140	0.000	0.000	0.000	0.000
51	A	54	GLY	0	0.084	0.065	22.683	0.936	0.936	0.000	0.000	0.000	0.000
52	A	55	ILE	0	-0.057	-0.038	23.894	-0.907	-0.907	0.000	0.000	0.000	0.000
53	A	56	GLY	0	-0.003	0.003	24.260	0.530	0.530	0.000	0.000	0.000	0.000
54	A	57	ASP	-1	-0.787	-0.889	20.640	-26.266	-26.266	0.000	0.000	0.000	0.000
55	A	58	VAL	0	-0.051	-0.027	14.950	-0.504	-0.504	0.000	0.000	0.000	0.000
56	A	59	VAL	0	0.017	0.007	14.881	-0.558	-0.558	0.000	0.000	0.000	0.000
57	A	60	GLU	-1	-0.804	-0.869	8.293	-61.921	-61.921	0.000	0.000	0.000	0.000
58	A	61	ILE	0	0.010	0.005	11.102	0.919	0.919	0.000	0.000	0.000	0.000
59	A	62	ARG	1	0.922	0.971	8.823	42.368	42.368	0.000	0.000	0.000	0.000
60	A	63	GLU	-1	-0.887	-0.937	10.124	-40.661	-40.661	0.000	0.000	0.000	0.000
61	A	64	CYS	0	-0.109	-0.062	11.598	-2.511	-2.511	0.000	0.000	0.000	0.000
62	A	65	ARG	1	0.996	1.011	14.197	31.398	31.398	0.000	0.000	0.000	0.000
63	A	66	PRO	0	0.027	0.006	16.964	0.002	0.002	0.000	0.000	0.000	0.000
64	A	67	LEU	0	-0.015	-0.012	18.171	0.403	0.403	0.000	0.000	0.000	0.000
65	A	68	SER	0	0.025	0.010	22.149	1.302	1.302	0.000	0.000	0.000	0.000
66	A	69	LYS	1	0.972	0.992	24.233	19.138	19.138	0.000	0.000	0.000	0.000
67	A	70	THR	0	-0.016	-0.010	24.214	0.043	0.043	0.000	0.000	0.000	0.000
68	A	71	LYS	1	0.839	0.937	20.746	25.542	25.542	0.000	0.000	0.000	0.000
69	A	72	SER	0	0.019	-0.004	16.854	0.789	0.789	0.000	0.000	0.000	0.000
70	A	73	TRP	0	0.037	0.013	11.111	-3.429	-3.429	0.000	0.000	0.000	0.000
71	A	74	THR	0	-0.006	-0.011	13.819	1.953	1.953	0.000	0.000	0.000	0.000
72	A	75	LEU	0	0.049	0.034	13.384	-3.336	-3.336	0.000	0.000	0.000	0.000
73	A	76	VAL	0	-0.107	-0.049	8.144	-2.048	-2.048	0.000	0.000	0.000	0.000
74	A	77	ARG	1	0.857	0.897	8.801	52.622	52.622	0.000	0.000	0.000	0.000
75	A	78	VAL	0	0.074	0.039	13.530	-0.819	-0.819	0.000	0.000	0.000	0.000
76	A	79	VAL	0	-0.107	-0.065	13.442	-0.301	-0.301	0.000	0.000	0.000	0.000
77	A	80	GLU	-1	-0.892	-0.967	16.517	-30.713	-30.713	0.000	0.000	0.000	0.000
78	A	81	LYS	1	0.938	0.965	18.429	30.222	30.222	0.000	0.000	0.000	0.000
79	A	82	ALA	0	-0.043	0.006	22.226	0.776	0.776	0.000	0.000	0.000	0.000
80	A	83	VAL	-1	-0.939	-0.958	24.581	-21.187	-21.187	0.000	0.000	0.000	0.000