FMODB ID: VZK41

Calculation Name: 7S1K-f-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: f

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	77
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

FMO2-HF: Electronic energy	-458067.352639
FMO2-HF: Nuclear repulsion	427241.938631
FMO2-HF: Total energy	-30825.414007
FMO2-MP2: Total energy	-30916.132084

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	4	VAL	0	0.012	-0.018	2.743	1.666	3.638	0.410	-0.813	-1.569	-0.002
4	A	5	CYS	-1	-0.902	-0.688	4.731	-25.367	-25.344	-0.001	-0.006	-0.016	0.000
49	A	50	ARG	1	0.935	0.972	4.767	46.068	46.231	-0.001	-0.027	-0.136	0.000
5	A	6	GLN	0	0.089	0.042	7.144	0.028	0.028	0.000	0.000	0.000	0.000
6	A	7	VAL	0	0.073	0.045	8.636	1.368	1.368	0.000	0.000	0.000	0.000
7	A	8	THR	0	0.013	-0.121	11.411	0.371	0.371	0.000	0.000	0.000	0.000
8	A	9	GLY	0	0.058	0.041	8.351	0.862	0.862	0.000	0.000	0.000	0.000
9	A	10	LYS	1	0.889	0.947	8.639	19.426	19.426	0.000	0.000	0.000	0.000
10	A	11	ARG	1	1.007	1.005	5.347	35.327	35.327	0.000	0.000	0.000	0.000
11	A	12	PRO	0	-0.069	-0.035	4.980	3.205	3.205	0.000	0.000	0.000	0.000
12	A	13	VAL	0	0.035	0.030	8.057	-0.927	-0.927	0.000	0.000	0.000	0.000
13	A	14	THR	0	-0.032	-0.026	11.101	0.301	0.301	0.000	0.000	0.000	0.000
14	A	15	GLY	0	0.046	0.018	13.700	0.577	0.577	0.000	0.000	0.000	0.000
15	A	16	ASN	0	0.018	0.011	17.407	-0.869	-0.869	0.000	0.000	0.000	0.000
16	A	17	ASN	0	0.005	0.003	20.488	-0.589	-0.589	0.000	0.000	0.000	0.000
17	A	18	ARG	1	0.851	0.914	22.174	11.707	11.707	0.000	0.000	0.000	0.000
18	A	19	SER	0	0.015	0.007	25.997	-0.041	-0.041	0.000	0.000	0.000	0.000
19	A	20	HIS	0	0.092	0.028	28.629	-0.069	-0.069	0.000	0.000	0.000	0.000
20	A	21	ALA	0	0.025	0.031	31.831	0.250	0.250	0.000	0.000	0.000	0.000
21	A	22	LEU	0	0.031	0.010	29.770	-0.115	-0.115	0.000	0.000	0.000	0.000
22	A	23	ASN	0	0.057	0.052	28.009	-0.274	-0.274	0.000	0.000	0.000	0.000
23	A	24	ALA	0	-0.017	-0.015	24.752	-0.347	-0.347	0.000	0.000	0.000	0.000
24	A	25	THR	0	0.040	0.035	20.750	-0.055	-0.055	0.000	0.000	0.000	0.000
25	A	26	LYS	1	0.921	0.956	17.349	16.070	16.070	0.000	0.000	0.000	0.000
26	A	27	ARG	1	0.934	0.967	15.610	17.578	17.578	0.000	0.000	0.000	0.000
27	A	28	ARG	1	0.963	0.966	6.672	33.684	33.684	0.000	0.000	0.000	0.000
28	A	29	PHE	0	0.024	0.028	12.511	1.303	1.303	0.000	0.000	0.000	0.000
29	A	30	LEU	0	0.002	-0.010	8.248	-2.819	-2.819	0.000	0.000	0.000	0.000
30	A	31	PRO	0	-0.006	0.008	7.566	2.345	2.345	0.000	0.000	0.000	0.000
31	A	32	ASN	0	0.060	0.029	10.388	-2.156	-2.156	0.000	0.000	0.000	0.000
32	A	33	LEU	0	-0.088	-0.043	6.708	0.217	0.217	0.000	0.000	0.000	0.000
33	A	34	HIS	0	0.031	0.009	10.916	-0.024	-0.024	0.000	0.000	0.000	0.000
34	A	35	SER	0	-0.011	-0.005	11.457	-1.466	-1.466	0.000	0.000	0.000	0.000
35	A	36	HIS	0	0.002	0.000	12.694	1.646	1.646	0.000	0.000	0.000	0.000
36	A	37	ARG	1	0.950	0.984	15.229	14.088	14.088	0.000	0.000	0.000	0.000
37	A	38	PHE	0	0.041	0.014	14.838	0.669	0.669	0.000	0.000	0.000	0.000
38	A	39	TRP	0	0.019	0.012	19.379	-0.326	-0.326	0.000	0.000	0.000	0.000
39	A	40	VAL	0	-0.011	-0.008	20.511	0.048	0.048	0.000	0.000	0.000	0.000
40	A	41	GLU	-1	-0.820	-0.923	23.487	-10.079	-10.079	0.000	0.000	0.000	0.000
41	A	42	SER	0	0.010	-0.008	25.120	0.182	0.182	0.000	0.000	0.000	0.000
42	A	43	GLU	-1	-0.852	-0.914	21.739	-13.891	-13.891	0.000	0.000	0.000	0.000
43	A	44	LYS	1	0.920	0.962	25.631	10.604	10.604	0.000	0.000	0.000	0.000
44	A	45	ARG	1	0.825	0.933	17.456	15.242	15.242	0.000	0.000	0.000	0.000
45	A	46	PHE	0	0.005	-0.012	19.767	-0.190	-0.190	0.000	0.000	0.000	0.000
46	A	47	VAL	0	0.015	0.016	15.332	-0.370	-0.370	0.000	0.000	0.000	0.000
47	A	48	THR	0	-0.018	-0.016	12.837	0.430	0.430	0.000	0.000	0.000	0.000
48	A	49	LEU	0	0.021	0.017	11.146	-1.247	-1.247	0.000	0.000	0.000	0.000
50	A	51	VAL	0	0.051	0.013	8.731	-1.838	-1.838	0.000	0.000	0.000	0.000
51	A	52	SER	0	-0.027	-0.131	11.080	0.819	0.819	0.000	0.000	0.000	0.000
52	A	53	ALA	0	0.060	0.018	12.395	1.141	1.141	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.890	0.941	15.535	16.867	16.867	0.000	0.000	0.000	0.000
54	A	55	GLY	0	0.053	0.003	14.013	0.862	0.862	0.000	0.000	0.000	0.000
55	A	56	MET	0	0.013	0.015	15.086	0.359	0.359	0.000	0.000	0.000	0.000
56	A	57	ARG	1	1.001	1.001	16.952	14.217	14.217	0.000	0.000	0.000	0.000
57	A	58	VAL	0	-0.094	-0.038	17.450	0.708	0.708	0.000	0.000	0.000	0.000
58	A	59	ILE	0	0.010	0.008	16.260	0.434	0.434	0.000	0.000	0.000	0.000
59	A	60	ASP	-1	-0.877	-0.944	20.029	-13.286	-13.286	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.902	0.957	22.962	13.006	13.006	0.000	0.000	0.000	0.000
61	A	62	LYS	1	0.816	0.905	19.432	15.043	15.043	0.000	0.000	0.000	0.000
62	A	63	GLY	0	0.105	0.089	23.116	0.373	0.373	0.000	0.000	0.000	0.000
63	A	64	ILE	0	-0.025	-0.027	17.786	-0.690	-0.690	0.000	0.000	0.000	0.000
64	A	65	ASP	-1	-0.835	-0.921	19.827	-12.917	-12.917	0.000	0.000	0.000	0.000
65	A	66	THR	0	-0.030	-0.041	21.428	-0.617	-0.617	0.000	0.000	0.000	0.000
66	A	67	VAL	0	-0.009	-0.003	15.868	-0.533	-0.533	0.000	0.000	0.000	0.000
67	A	68	LEU	0	-0.014	-0.002	16.108	-1.023	-1.023	0.000	0.000	0.000	0.000
68	A	69	ALA	0	0.006	-0.001	17.510	-0.374	-0.374	0.000	0.000	0.000	0.000
69	A	70	GLU	-1	-0.836	-0.912	16.832	-15.641	-15.641	0.000	0.000	0.000	0.000
70	A	71	LEU	0	-0.068	-0.045	11.140	-1.034	-1.034	0.000	0.000	0.000	0.000
71	A	72	ARG	1	0.960	0.981	14.062	13.798	13.798	0.000	0.000	0.000	0.000
72	A	73	ALA	0	-0.020	0.006	16.620	-0.051	-0.051	0.000	0.000	0.000	0.000
73	A	74	ARG	1	0.751	0.876	8.601	25.762	25.762	0.000	0.000	0.000	0.000
74	A	75	GLY	0	0.041	0.032	13.249	-1.092	-1.092	0.000	0.000	0.000	0.000
75	A	76	GLU	-1	-0.900	-0.942	8.333	-32.368	-32.368	0.000	0.000	0.000	0.000
76	A	77	LYS	1	0.843	0.911	10.028	23.655	23.655	0.000	0.000	0.000	0.000
77	A	78	TYR	-1	-0.892	-0.947	10.590	-20.937	-20.937	0.000	0.000	0.000	0.000