FMO DATABASE

FMODB ID: 8KG6Y

Calculation Name: 7S0S-N-Other547

Preferred Name:

Target Type:

Ligand Name: (2~{s})-4-[2-[(2~{r},3~{s},4~{r},5~{r})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]ethyl-[2-[(2~{r},3~{r},4~{r},5~{r})-2-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-5-[bis(oxidanyl)phosphanyloxymethyl]-4-oxidanyl-oxolan-3-yl]oxyethyl]amino]-2-azanyl-butanoic acid | magnesium ion | zinc ion

Ligand 3-letter code: AI5 | MG | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7S0S

Chain ID: N

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	145
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-875371.693269
FMO2-HF: Nuclear repulsion	822152.241905
FMO2-HF: Total energy	-53219.451364
FMO2-MP2: Total energy	-53375.885833

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:3:VAL)

Summations of interaction energy for fragment #1(A:3: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.
131.847	134.681	0.413	-1.209	-2.037	-0.007

Interaction energy analysis for fragmet #1(A:3:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.867 / 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	5	LYS	1	0.931	0.962	2.869	42.984	45.767	0.414	-1.204	-1.993	-0.007
4	A	6	LEU	0	0.060	0.009	4.986	1.802	1.853	-0.001	-0.005	-0.044	0.000
5	A	7	HIS	0	-0.002	0.005	7.286	4.111	4.111	0.000	0.000	0.000	0.000
6	A	8	ASP	-1	-0.843	-0.917	5.942	-46.595	-46.595	0.000	0.000	0.000	0.000
7	A	9	LEU	0	-0.060	-0.021	8.639	1.095	1.095	0.000	0.000	0.000	0.000
8	A	10	LYS	1	0.945	0.961	11.137	26.023	26.023	0.000	0.000	0.000	0.000
9	A	11	PRO	0	-0.023	0.006	14.734	-0.159	-0.159	0.000	0.000	0.000	0.000
10	A	12	ALA	0	0.056	0.030	17.335	-0.514	-0.514	0.000	0.000	0.000	0.000
11	A	13	PRO	0	0.009	-0.017	17.741	0.740	0.740	0.000	0.000	0.000	0.000
12	A	14	GLY	0	0.006	0.010	20.772	0.415	0.415	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.847	-0.896	20.328	-14.794	-14.794	0.000	0.000	0.000	0.000
14	A	16	LYS	1	0.850	0.908	20.807	14.900	14.900	0.000	0.000	0.000	0.000
15	A	17	LYS	1	0.977	0.993	24.744	10.383	10.383	0.000	0.000	0.000	0.000
16	A	18	ALA	0	0.040	0.023	28.258	0.040	0.040	0.000	0.000	0.000	0.000
17	A	19	LYS	1	0.944	0.966	29.555	9.448	9.448	0.000	0.000	0.000	0.000
18	A	20	THR	0	0.037	0.010	32.347	0.075	0.075	0.000	0.000	0.000	0.000
19	A	21	ARG	1	0.918	0.957	33.227	9.200	9.200	0.000	0.000	0.000	0.000
20	A	22	VAL	0	0.025	0.027	37.083	0.076	0.076	0.000	0.000	0.000	0.000
21	A	23	GLY	0	0.023	0.017	40.822	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	24	ARG	1	0.844	0.909	38.966	7.833	7.833	0.000	0.000	0.000	0.000
23	A	25	GLY	0	0.109	0.063	41.816	-0.104	-0.104	0.000	0.000	0.000	0.000
24	A	26	GLU	-1	-0.888	-0.979	44.251	-6.803	-6.803	0.000	0.000	0.000	0.000
25	A	27	GLY	0	0.013	0.033	42.549	0.028	0.028	0.000	0.000	0.000	0.000
26	A	28	SER	0	-0.028	-0.011	39.941	-0.090	-0.090	0.000	0.000	0.000	0.000
27	A	29	LYS	1	0.959	0.969	41.142	7.858	7.858	0.000	0.000	0.000	0.000
28	A	30	GLY	0	0.054	0.049	44.223	-0.073	-0.073	0.000	0.000	0.000	0.000
29	A	31	LYS	1	1.051	1.019	46.643	6.165	6.165	0.000	0.000	0.000	0.000
30	A	32	THR	0	-0.050	-0.024	48.777	0.085	0.085	0.000	0.000	0.000	0.000
31	A	33	ALA	0	-0.033	-0.030	44.971	0.000	0.000	0.000	0.000	0.000	0.000
32	A	34	GLY	0	0.004	0.003	45.473	-0.139	-0.139	0.000	0.000	0.000	0.000
33	A	35	ARG	1	0.840	0.916	47.278	6.578	6.578	0.000	0.000	0.000	0.000
34	A	36	GLY	0	0.025	0.031	49.990	0.104	0.104	0.000	0.000	0.000	0.000
35	A	37	THR	0	0.022	0.003	52.710	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	38	LYS	1	0.974	0.974	55.627	5.195	5.195	0.000	0.000	0.000	0.000
37	A	39	GLY	0	0.088	0.038	57.988	0.028	0.028	0.000	0.000	0.000	0.000
38	A	40	THR	0	0.005	-0.006	56.648	-0.045	-0.045	0.000	0.000	0.000	0.000
39	A	41	LYS	1	1.025	0.996	51.295	6.157	6.157	0.000	0.000	0.000	0.000
40	A	42	ALA	0	0.008	0.034	52.208	-0.144	-0.144	0.000	0.000	0.000	0.000
41	A	43	ARG	1	0.930	0.963	52.204	5.617	5.617	0.000	0.000	0.000	0.000
42	A	44	LYS	1	0.973	1.000	51.441	5.553	5.553	0.000	0.000	0.000	0.000
43	A	45	ASN	0	0.008	0.000	48.140	-0.144	-0.144	0.000	0.000	0.000	0.000
44	A	46	VAL	0	0.021	0.002	52.467	0.121	0.121	0.000	0.000	0.000	0.000
45	A	47	PRO	0	0.000	0.010	53.472	-0.124	-0.124	0.000	0.000	0.000	0.000
46	A	48	VAL	0	0.045	0.003	51.375	0.085	0.085	0.000	0.000	0.000	0.000
47	A	49	MET	0	0.033	0.032	53.974	0.014	0.014	0.000	0.000	0.000	0.000
48	A	50	PHE	0	0.004	0.014	57.206	0.112	0.112	0.000	0.000	0.000	0.000
49	A	51	GLU	-1	-0.750	-0.846	59.036	-5.338	-5.338	0.000	0.000	0.000	0.000
50	A	52	GLY	0	-0.001	-0.017	61.593	0.063	0.063	0.000	0.000	0.000	0.000
51	A	53	GLY	0	-0.014	-0.004	63.450	0.065	0.065	0.000	0.000	0.000	0.000
52	A	54	GLN	0	-0.022	-0.002	63.887	0.141	0.141	0.000	0.000	0.000	0.000
53	A	55	MET	0	0.036	0.013	65.686	-0.090	-0.090	0.000	0.000	0.000	0.000
54	A	56	PRO	0	0.016	0.014	61.598	-0.019	-0.019	0.000	0.000	0.000	0.000
55	A	57	ILE	0	0.012	0.000	58.808	0.059	0.059	0.000	0.000	0.000	0.000
56	A	58	HIS	0	-0.066	-0.049	59.342	0.042	0.042	0.000	0.000	0.000	0.000
57	A	59	MET	0	-0.047	-0.032	61.691	0.028	0.028	0.000	0.000	0.000	0.000
58	A	60	ARG	1	0.828	0.897	62.650	5.161	5.161	0.000	0.000	0.000	0.000
59	A	61	LEU	0	-0.004	0.011	62.158	0.040	0.040	0.000	0.000	0.000	0.000
60	A	62	PRO	0	0.007	0.005	66.060	0.004	0.004	0.000	0.000	0.000	0.000
61	A	63	LYS	1	0.963	0.980	64.459	4.827	4.827	0.000	0.000	0.000	0.000
62	A	64	LEU	0	0.008	0.003	59.637	0.053	0.053	0.000	0.000	0.000	0.000
63	A	65	LYS	1	0.995	1.002	64.169	4.771	4.771	0.000	0.000	0.000	0.000
64	A	66	GLY	0	0.012	0.011	65.160	-0.061	-0.061	0.000	0.000	0.000	0.000
65	A	67	PHE	0	0.031	-0.003	64.859	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	68	LYS	1	0.966	0.962	56.635	5.575	5.575	0.000	0.000	0.000	0.000
67	A	69	ASN	0	0.011	0.022	60.734	-0.023	-0.023	0.000	0.000	0.000	0.000
68	A	70	ARG	1	0.954	0.967	60.250	4.982	4.982	0.000	0.000	0.000	0.000
69	A	71	PHE	0	0.050	0.033	60.242	-0.050	-0.050	0.000	0.000	0.000	0.000
70	A	72	ARG	1	0.805	0.897	56.454	5.610	5.610	0.000	0.000	0.000	0.000
71	A	73	THR	0	0.023	0.021	58.037	-0.062	-0.062	0.000	0.000	0.000	0.000
72	A	74	GLU	-1	-0.851	-0.919	53.229	-5.852	-5.852	0.000	0.000	0.000	0.000
73	A	75	TYR	0	0.012	-0.007	53.593	0.070	0.070	0.000	0.000	0.000	0.000
74	A	76	GLN	0	-0.052	-0.018	47.249	-0.204	-0.204	0.000	0.000	0.000	0.000
75	A	77	VAL	0	-0.012	-0.009	49.877	0.085	0.085	0.000	0.000	0.000	0.000
76	A	78	VAL	0	0.052	0.031	47.814	-0.137	-0.137	0.000	0.000	0.000	0.000
77	A	79	ASN	0	0.036	0.014	48.852	0.274	0.274	0.000	0.000	0.000	0.000
78	A	80	VAL	0	0.010	-0.004	49.518	-0.114	-0.114	0.000	0.000	0.000	0.000
79	A	81	GLY	0	-0.005	0.006	49.434	-0.014	-0.014	0.000	0.000	0.000	0.000
80	A	82	ASP	-1	-0.903	-0.950	45.073	-7.101	-7.101	0.000	0.000	0.000	0.000
81	A	83	ILE	0	-0.002	0.002	45.620	-0.146	-0.146	0.000	0.000	0.000	0.000
82	A	84	ASN	0	0.027	-0.014	47.282	0.040	0.040	0.000	0.000	0.000	0.000
83	A	85	LYS	1	0.932	0.971	40.096	7.632	7.632	0.000	0.000	0.000	0.000
84	A	86	ALA	0	-0.047	-0.012	42.243	-0.202	-0.202	0.000	0.000	0.000	0.000
85	A	87	PHE	0	0.032	0.005	43.124	-0.152	-0.152	0.000	0.000	0.000	0.000
86	A	88	PRO	0	0.024	0.017	42.561	0.152	0.152	0.000	0.000	0.000	0.000
87	A	89	GLN	0	0.008	-0.004	44.485	0.031	0.031	0.000	0.000	0.000	0.000
88	A	90	GLY	0	-0.044	-0.015	48.622	0.147	0.147	0.000	0.000	0.000	0.000
89	A	91	GLY	0	0.015	0.004	49.184	-0.125	-0.125	0.000	0.000	0.000	0.000
90	A	92	THR	0	-0.008	-0.005	50.316	0.116	0.116	0.000	0.000	0.000	0.000
91	A	93	VAL	0	-0.036	-0.022	48.617	-0.161	-0.161	0.000	0.000	0.000	0.000
92	A	94	GLY	0	0.069	0.042	50.576	0.135	0.135	0.000	0.000	0.000	0.000
93	A	95	VAL	0	-0.010	-0.020	48.746	-0.093	-0.093	0.000	0.000	0.000	0.000
94	A	96	ASP	-1	-0.907	-0.953	45.831	-6.779	-6.779	0.000	0.000	0.000	0.000
95	A	97	GLU	-1	-0.794	-0.899	44.560	-6.693	-6.693	0.000	0.000	0.000	0.000
96	A	98	LEU	0	-0.010	0.002	44.662	-0.134	-0.134	0.000	0.000	0.000	0.000
97	A	99	VAL	0	-0.055	-0.037	42.143	-0.163	-0.163	0.000	0.000	0.000	0.000
98	A	100	ALA	0	-0.030	-0.008	40.307	-0.218	-0.218	0.000	0.000	0.000	0.000
99	A	101	LYS	1	0.844	0.932	39.377	7.580	7.580	0.000	0.000	0.000	0.000
100	A	102	GLY	0	-0.029	-0.006	39.550	-0.087	-0.087	0.000	0.000	0.000	0.000
101	A	103	LEU	0	-0.009	-0.004	40.509	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	104	VAL	0	0.007	0.005	43.871	0.155	0.155	0.000	0.000	0.000	0.000
103	A	105	ARG	1	0.912	0.954	43.053	7.044	7.044	0.000	0.000	0.000	0.000
104	A	106	LYS	1	0.973	0.983	39.193	7.873	7.873	0.000	0.000	0.000	0.000
105	A	107	ASN	0	0.034	0.024	44.213	0.013	0.013	0.000	0.000	0.000	0.000
106	A	108	SER	0	-0.046	-0.035	47.376	0.046	0.046	0.000	0.000	0.000	0.000
107	A	109	LEU	0	0.040	0.039	49.948	0.019	0.019	0.000	0.000	0.000	0.000
108	A	110	VAL	0	0.042	0.020	49.953	-0.045	-0.045	0.000	0.000	0.000	0.000
109	A	111	LYS	1	0.898	0.951	52.570	5.622	5.622	0.000	0.000	0.000	0.000
110	A	112	VAL	0	0.042	0.034	52.769	-0.115	-0.115	0.000	0.000	0.000	0.000
111	A	113	LEU	0	-0.011	-0.031	53.071	0.186	0.186	0.000	0.000	0.000	0.000
112	A	114	GLY	0	0.023	0.001	53.933	-0.102	-0.102	0.000	0.000	0.000	0.000
113	A	115	ASP	-1	-0.953	-0.954	51.299	-6.122	-6.122	0.000	0.000	0.000	0.000
114	A	116	GLY	0	0.017	0.005	51.178	0.010	0.010	0.000	0.000	0.000	0.000
115	A	117	LYS	1	0.952	0.964	51.898	5.806	5.806	0.000	0.000	0.000	0.000
116	A	118	LEU	0	-0.010	0.012	51.845	-0.149	-0.149	0.000	0.000	0.000	0.000
117	A	119	THR	0	-0.055	-0.036	51.157	0.081	0.081	0.000	0.000	0.000	0.000
118	A	120	VAL	0	0.011	0.020	49.204	0.068	0.068	0.000	0.000	0.000	0.000
119	A	121	LYS	1	0.893	0.961	52.634	5.582	5.582	0.000	0.000	0.000	0.000
120	A	122	VAL	0	-0.011	0.001	51.319	-0.085	-0.085	0.000	0.000	0.000	0.000
121	A	123	ASP	-1	-0.860	-0.922	53.865	-5.489	-5.489	0.000	0.000	0.000	0.000
122	A	124	VAL	0	-0.052	-0.030	52.733	-0.104	-0.104	0.000	0.000	0.000	0.000
123	A	125	THR	0	-0.008	-0.008	53.875	0.119	0.119	0.000	0.000	0.000	0.000
124	A	126	ALA	0	0.011	-0.003	53.480	-0.141	-0.141	0.000	0.000	0.000	0.000
125	A	127	ASN	0	0.035	0.021	54.378	0.003	0.003	0.000	0.000	0.000	0.000
126	A	128	LYS	1	0.840	0.920	56.707	5.302	5.302	0.000	0.000	0.000	0.000
127	A	129	PHE	0	0.062	0.034	56.111	-0.112	-0.112	0.000	0.000	0.000	0.000
128	A	130	SER	0	-0.051	-0.024	58.236	0.132	0.132	0.000	0.000	0.000	0.000
129	A	131	GLY	0	0.033	0.015	60.035	0.000	0.000	0.000	0.000	0.000	0.000
130	A	132	SER	0	0.114	0.045	59.652	-0.006	-0.006	0.000	0.000	0.000	0.000
131	A	133	ALA	0	-0.074	-0.026	56.691	-0.068	-0.068	0.000	0.000	0.000	0.000
132	A	134	ARG	1	0.889	0.930	58.196	5.102	5.102	0.000	0.000	0.000	0.000
133	A	135	GLU	-1	-0.904	-0.932	60.748	-5.004	-5.004	0.000	0.000	0.000	0.000
134	A	136	ALA	0	-0.023	-0.011	56.758	-0.007	-0.007	0.000	0.000	0.000	0.000
135	A	137	ILE	0	-0.028	-0.020	54.983	-0.046	-0.046	0.000	0.000	0.000	0.000
136	A	138	THR	0	-0.016	-0.014	58.076	0.024	0.024	0.000	0.000	0.000	0.000
137	A	139	ALA	0	-0.018	-0.006	60.968	0.045	0.045	0.000	0.000	0.000	0.000
138	A	140	ALA	0	-0.033	-0.004	56.397	0.004	0.004	0.000	0.000	0.000	0.000
139	A	141	GLY	0	-0.004	-0.010	58.263	-0.050	-0.050	0.000	0.000	0.000	0.000
140	A	142	GLY	0	-0.019	-0.007	57.828	-0.012	-0.012	0.000	0.000	0.000	0.000
141	A	143	SER	0	-0.010	-0.016	58.635	0.112	0.112	0.000	0.000	0.000	0.000
142	A	144	ALA	0	0.019	-0.001	58.100	-0.115	-0.115	0.000	0.000	0.000	0.000
143	A	145	THR	0	-0.022	0.001	58.672	0.081	0.081	0.000	0.000	0.000	0.000
144	A	146	GLU	-1	-0.823	-0.921	58.494	-5.255	-5.255	0.000	0.000	0.000	0.000
145	A	147	LEU	-1	-0.931	-0.956	54.622	-5.295	-5.295	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:VAL)