FMO DATABASE

FMODB ID: JK3J9

Calculation Name: 6YAL-j-Other547

Preferred Name:

Target Type:

Ligand Name: phosphoaminophosphonic acid-guanylate ester | n-[n-(9-b-d-ribofuranosylpurin-6-yl)carbamoyl]threonine-5'-monophosphate | (5s)-5-{3-[(3s)-3-amino-3-carboxypropyl]-1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl}-2,5-anhydro-1-o-phosphono-l-arabinitol | iron/sulfur cluster | magnesium ion

Ligand 3-letter code: GNP | T6A | C4J | SF4 | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6YAL

Chain ID: j

ChEMBL ID:

UniProt ID: G1TZ76

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	109
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-831984.301608
FMO2-HF: Nuclear repulsion	787803.12188
FMO2-HF: Total energy	-44181.179728
FMO2-MP2: Total energy	-44309.340212

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:7:LYS)

Summations of interaction energy for fragment #1(A:7:LYS)

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.
345.231	349.326	1.013	-1.427	-3.681	-0.007

Interaction energy analysis for fragmet #1(A:7:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.839 / q_NPA : 1.907

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	9	GLY	0	0.077	0.047	3.657	6.100	7.950	0.009	-0.719	-1.139	-0.003
4	A	10	LYS	1	0.895	0.952	2.385	84.994	87.042	1.006	-0.689	-2.366	-0.004
5	A	11	ASN	0	0.142	0.061	4.721	6.718	6.770	-0.001	-0.012	-0.039	0.000
7	A	13	ARG	1	0.763	0.856	4.429	70.454	70.599	-0.001	-0.007	-0.137	0.000
6	A	12	ARG	1	0.958	0.967	6.139	47.944	47.944	0.000	0.000	0.000	0.000
8	A	14	ARG	1	1.066	1.027	7.258	42.964	42.964	0.000	0.000	0.000	0.000
9	A	15	GLY	0	-0.002	0.037	10.766	3.039	3.039	0.000	0.000	0.000	0.000
10	A	16	LYS	1	0.852	0.884	10.927	44.697	44.697	0.000	0.000	0.000	0.000
11	A	17	ASN	0	0.043	0.032	12.802	-0.873	-0.873	0.000	0.000	0.000	0.000
12	A	18	GLU	-1	-0.852	-0.903	10.556	-51.687	-51.687	0.000	0.000	0.000	0.000
13	A	19	ASN	0	0.044	0.022	9.186	3.535	3.535	0.000	0.000	0.000	0.000
14	A	20	GLU	-1	-0.958	-0.982	10.499	-42.422	-42.422	0.000	0.000	0.000	0.000
15	A	21	SER	0	-0.037	-0.004	12.651	-0.564	-0.564	0.000	0.000	0.000	0.000
16	A	22	GLU	-1	-0.964	-0.981	15.470	-28.459	-28.459	0.000	0.000	0.000	0.000
17	A	23	LYS	1	0.904	0.937	17.170	30.503	30.503	0.000	0.000	0.000	0.000
18	A	24	ARG	1	0.927	0.966	19.447	27.041	27.041	0.000	0.000	0.000	0.000
19	A	25	GLU	-1	-0.845	-0.922	21.635	-21.807	-21.807	0.000	0.000	0.000	0.000
20	A	26	LEU	0	0.013	-0.009	24.293	-0.392	-0.392	0.000	0.000	0.000	0.000
21	A	27	VAL	0	-0.053	0.010	25.395	0.670	0.670	0.000	0.000	0.000	0.000
22	A	28	PHE	0	0.043	0.033	26.373	-0.745	-0.745	0.000	0.000	0.000	0.000
23	A	29	LYS	1	0.905	0.944	27.828	18.144	18.144	0.000	0.000	0.000	0.000
24	A	30	GLU	-1	-0.954	-0.972	29.766	-17.940	-17.940	0.000	0.000	0.000	0.000
25	A	31	ASP	-1	-0.882	-0.951	32.208	-16.756	-16.756	0.000	0.000	0.000	0.000
26	A	32	GLY	0	0.007	0.017	33.160	-0.356	-0.356	0.000	0.000	0.000	0.000
27	A	33	GLN	0	-0.043	-0.024	27.199	-1.480	-1.480	0.000	0.000	0.000	0.000
28	A	34	GLU	-1	-0.793	-0.893	28.168	-19.264	-19.264	0.000	0.000	0.000	0.000
29	A	35	TYR	0	0.025	0.010	25.403	-1.099	-1.099	0.000	0.000	0.000	0.000
30	A	36	ALA	0	0.018	0.012	23.918	0.738	0.738	0.000	0.000	0.000	0.000
31	A	37	GLN	0	0.026	0.008	22.312	-1.215	-1.215	0.000	0.000	0.000	0.000
32	A	38	VAL	0	-0.058	-0.029	17.577	0.489	0.489	0.000	0.000	0.000	0.000
33	A	39	ILE	0	-0.010	0.006	20.698	-0.043	-0.043	0.000	0.000	0.000	0.000
34	A	40	LYS	1	0.881	0.931	20.867	28.616	28.616	0.000	0.000	0.000	0.000
35	A	41	MET	0	0.056	0.015	13.675	-0.795	-0.795	0.000	0.000	0.000	0.000
36	A	42	LEU	0	-0.013	0.005	18.240	1.047	1.047	0.000	0.000	0.000	0.000
37	A	43	GLY	0	0.073	0.047	16.150	-2.088	-2.088	0.000	0.000	0.000	0.000
38	A	44	ASN	0	-0.030	-0.034	16.356	0.429	0.429	0.000	0.000	0.000	0.000
39	A	45	GLY	0	-0.078	-0.045	16.277	-0.641	-0.641	0.000	0.000	0.000	0.000
40	A	46	ARG	1	0.916	0.974	17.253	26.807	26.807	0.000	0.000	0.000	0.000
41	A	47	LEU	0	-0.026	-0.015	16.958	-1.127	-1.127	0.000	0.000	0.000	0.000
42	A	48	GLU	-1	-0.821	-0.925	20.616	-22.709	-22.709	0.000	0.000	0.000	0.000
43	A	49	ALA	0	-0.042	-0.040	21.574	-1.342	-1.342	0.000	0.000	0.000	0.000
44	A	50	MET	0	0.005	0.032	23.528	0.626	0.626	0.000	0.000	0.000	0.000
45	A	51	CYS	0	-0.016	0.002	26.463	-0.870	-0.870	0.000	0.000	0.000	0.000
46	A	52	PHE	0	-0.003	-0.022	24.840	0.166	0.166	0.000	0.000	0.000	0.000
47	A	53	ASP	-1	-0.807	-0.883	29.760	-18.210	-18.210	0.000	0.000	0.000	0.000
48	A	54	GLY	0	0.013	0.015	32.235	0.541	0.541	0.000	0.000	0.000	0.000
49	A	55	VAL	0	-0.022	-0.013	33.445	-0.036	-0.036	0.000	0.000	0.000	0.000
50	A	56	LYS	1	0.897	0.944	29.056	19.910	19.910	0.000	0.000	0.000	0.000
51	A	57	ARG	1	0.878	0.919	28.870	18.923	18.923	0.000	0.000	0.000	0.000
52	A	58	LEU	0	0.010	0.027	24.865	-0.594	-0.594	0.000	0.000	0.000	0.000
53	A	59	CYS	0	0.004	0.025	22.582	0.251	0.251	0.000	0.000	0.000	0.000
54	A	60	HIS	0	0.020	-0.012	21.921	-1.082	-1.082	0.000	0.000	0.000	0.000
55	A	61	ILE	0	-0.006	0.013	16.391	-0.055	-0.055	0.000	0.000	0.000	0.000
56	A	62	ARG	1	1.000	1.025	19.072	28.004	28.004	0.000	0.000	0.000	0.000
57	A	63	GLY	0	0.005	-0.016	18.524	-1.937	-1.937	0.000	0.000	0.000	0.000
58	A	64	LYS	1	0.952	0.962	17.234	29.184	29.184	0.000	0.000	0.000	0.000
59	A	65	LEU	0	0.087	0.034	14.578	-2.750	-2.750	0.000	0.000	0.000	0.000
60	A	66	ARG	1	0.970	0.994	13.243	32.704	32.704	0.000	0.000	0.000	0.000
61	A	67	LYS	1	0.926	0.957	9.537	46.785	46.785	0.000	0.000	0.000	0.000
62	A	68	LYS	1	0.872	0.929	9.930	45.710	45.710	0.000	0.000	0.000	0.000
63	A	69	VAL	0	0.048	0.036	10.015	-2.358	-2.358	0.000	0.000	0.000	0.000
64	A	70	TRP	0	-0.045	-0.008	7.430	-1.888	-1.888	0.000	0.000	0.000	0.000
65	A	71	ILE	0	0.040	0.019	9.762	0.922	0.922	0.000	0.000	0.000	0.000
66	A	72	ASN	0	-0.011	-0.012	9.392	-1.832	-1.832	0.000	0.000	0.000	0.000
67	A	73	THR	0	0.025	-0.006	12.914	1.286	1.286	0.000	0.000	0.000	0.000
68	A	74	SER	0	-0.023	0.005	16.052	-0.740	-0.740	0.000	0.000	0.000	0.000
69	A	75	ASP	-1	-0.851	-0.909	16.257	-34.263	-34.263	0.000	0.000	0.000	0.000
70	A	76	ILE	0	-0.011	-0.016	18.422	1.133	1.133	0.000	0.000	0.000	0.000
71	A	77	ILE	0	-0.063	-0.041	17.452	-1.667	-1.667	0.000	0.000	0.000	0.000
72	A	78	LEU	0	0.042	0.038	20.709	0.737	0.737	0.000	0.000	0.000	0.000
73	A	79	VAL	0	-0.041	-0.048	22.350	-1.395	-1.395	0.000	0.000	0.000	0.000
74	A	80	GLY	0	0.054	0.049	24.857	0.793	0.793	0.000	0.000	0.000	0.000
75	A	81	LEU	0	-0.001	-0.007	27.789	-0.628	-0.628	0.000	0.000	0.000	0.000
76	A	82	ARG	1	0.825	0.901	27.967	21.581	21.581	0.000	0.000	0.000	0.000
77	A	83	ASP	-1	-0.856	-0.936	32.132	-17.924	-17.924	0.000	0.000	0.000	0.000
78	A	84	TYR	0	-0.013	-0.007	33.837	0.281	0.281	0.000	0.000	0.000	0.000
79	A	85	GLN	0	-0.115	-0.070	32.930	-0.107	-0.107	0.000	0.000	0.000	0.000
80	A	86	ASP	-1	-0.854	-0.909	33.423	-18.040	-18.040	0.000	0.000	0.000	0.000
81	A	87	ASN	0	0.017	-0.011	32.537	-0.641	-0.641	0.000	0.000	0.000	0.000
82	A	88	LYS	1	0.853	0.933	28.927	20.152	20.152	0.000	0.000	0.000	0.000
83	A	89	ALA	0	0.111	0.064	26.966	0.490	0.490	0.000	0.000	0.000	0.000
84	A	90	ASP	-1	-0.944	-0.980	24.680	-22.971	-22.971	0.000	0.000	0.000	0.000
85	A	91	VAL	0	-0.010	-0.001	18.519	-0.065	-0.065	0.000	0.000	0.000	0.000
86	A	92	ILE	0	-0.047	-0.035	22.034	-0.493	-0.493	0.000	0.000	0.000	0.000
87	A	93	LEU	0	-0.034	-0.034	19.916	-1.389	-1.389	0.000	0.000	0.000	0.000
88	A	94	LYS	1	0.781	0.912	12.090	40.255	40.255	0.000	0.000	0.000	0.000
89	A	95	TYR	0	0.084	0.040	18.002	1.138	1.138	0.000	0.000	0.000	0.000
90	A	96	ASN	0	-0.024	-0.028	14.692	-3.537	-3.537	0.000	0.000	0.000	0.000
91	A	97	ALA	0	0.082	0.042	16.160	1.601	1.601	0.000	0.000	0.000	0.000
92	A	98	ASP	-1	-0.896	-0.959	17.175	-29.148	-29.148	0.000	0.000	0.000	0.000
93	A	99	GLU	-1	-0.863	-0.904	19.675	-27.284	-27.284	0.000	0.000	0.000	0.000
94	A	100	ALA	0	0.035	0.013	20.785	1.198	1.198	0.000	0.000	0.000	0.000
95	A	101	ARG	1	0.852	0.911	20.140	27.600	27.600	0.000	0.000	0.000	0.000
96	A	102	SER	0	-0.019	-0.013	23.684	0.964	0.964	0.000	0.000	0.000	0.000
97	A	103	LEU	0	0.039	0.006	24.774	0.700	0.700	0.000	0.000	0.000	0.000
98	A	104	LYS	1	0.852	0.940	26.230	22.426	22.426	0.000	0.000	0.000	0.000
99	A	105	ALA	0	-0.042	-0.015	27.963	0.616	0.616	0.000	0.000	0.000	0.000
100	A	106	TYR	0	-0.053	-0.026	28.065	0.550	0.550	0.000	0.000	0.000	0.000
101	A	107	GLY	0	0.028	0.044	31.393	0.577	0.577	0.000	0.000	0.000	0.000
102	A	108	GLU	-1	-0.904	-0.960	30.395	-18.736	-18.736	0.000	0.000	0.000	0.000
103	A	109	LEU	0	-0.137	-0.065	25.884	-0.151	-0.151	0.000	0.000	0.000	0.000
104	A	110	PRO	0	0.035	0.016	30.264	0.235	0.235	0.000	0.000	0.000	0.000
105	A	111	GLU	-1	-0.832	-0.925	29.976	-19.849	-19.849	0.000	0.000	0.000	0.000
106	A	112	HIS	0	-0.060	-0.041	30.330	-0.072	-0.072	0.000	0.000	0.000	0.000
107	A	113	ALA	0	-0.007	0.013	25.014	-0.124	-0.124	0.000	0.000	0.000	0.000
108	A	114	LYS	1	0.811	0.886	23.591	24.448	24.448	0.000	0.000	0.000	0.000
109	A	115	ILE	-1	-0.822	-0.898	18.866	-27.545	-27.545	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:7:LYS)