FMO DATABASE

FMODB ID: MRY2Z

Calculation Name: 1UNN-C-Xray547

Preferred Name: DNA polymerase III subunit beta

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1UNN

Chain ID: C

ChEMBL ID: CHEMBL3562169

UniProt ID: P0A988

Base Structure: X-ray

Registration Date: 2025-10-03

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	111
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-898891.623572
FMO2-HF: Nuclear repulsion	853760.331339
FMO2-HF: Total energy	-45131.292233
FMO2-MP2: Total energy	-45264.239838

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:241:HIS)

Summations of interaction energy for fragment #1(A:241:HIS)

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.
-41.646	-33.477	1.749	-3.99	-5.928	-0.025

Interaction energy analysis for fragmet #1(A:241:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.930 / q_NPA : 0.962

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	243	VAL	0	0.020	0.027	3.865	2.486	4.477	-0.021	-0.977	-0.993	-0.001
97	A	337	THR	0	-0.075	-0.069	3.099	-7.408	-6.997	0.028	-0.132	-0.306	-0.001
98	A	338	LEU	0	0.007	-0.006	2.470	5.420	6.967	1.122	-0.779	-1.890	-0.004
99	A	339	LEU	0	0.021	0.008	3.535	-8.422	-7.780	0.001	-0.360	-0.283	-0.003
100	A	340	ASP	-1	-0.919	-0.951	3.073	-91.242	-88.608	0.157	-1.368	-1.423	-0.012
101	A	341	PRO	0	-0.048	-0.032	2.455	5.294	6.238	0.462	-0.374	-1.033	-0.004
4	A	244	GLY	0	0.033	0.004	6.565	0.198	0.198	0.000	0.000	0.000	0.000
5	A	245	VAL	0	-0.014	0.010	10.186	0.357	0.357	0.000	0.000	0.000	0.000
6	A	246	GLU	-1	-0.847	-0.930	13.772	-18.557	-18.557	0.000	0.000	0.000	0.000
7	A	247	ARG	1	0.960	0.999	16.881	12.568	12.568	0.000	0.000	0.000	0.000
8	A	248	THR	0	0.042	0.009	20.675	-0.117	-0.117	0.000	0.000	0.000	0.000
9	A	249	MET	0	-0.109	-0.035	22.628	-0.039	-0.039	0.000	0.000	0.000	0.000
10	A	250	ALA	0	-0.016	0.005	26.246	-0.068	-0.068	0.000	0.000	0.000	0.000
11	A	251	GLU	-1	-0.874	-0.940	29.595	-9.160	-9.160	0.000	0.000	0.000	0.000
12	A	252	ASP	-1	-0.876	-0.922	28.567	-10.954	-10.954	0.000	0.000	0.000	0.000
13	A	253	ILE	0	-0.042	-0.020	25.471	0.247	0.247	0.000	0.000	0.000	0.000
14	A	254	HIS	0	0.029	-0.004	29.400	-0.186	-0.186	0.000	0.000	0.000	0.000
15	A	255	HIS	0	-0.018	-0.012	31.361	0.038	0.038	0.000	0.000	0.000	0.000
16	A	256	TRP	0	-0.017	-0.017	23.904	-0.384	-0.384	0.000	0.000	0.000	0.000
17	A	257	SER	0	0.061	0.015	28.069	-0.327	-0.327	0.000	0.000	0.000	0.000
18	A	258	GLU	-1	-0.823	-0.905	29.047	-10.013	-10.013	0.000	0.000	0.000	0.000
19	A	259	CYS	0	0.004	0.002	23.225	-0.553	-0.553	0.000	0.000	0.000	0.000
20	A	260	GLU	-1	-0.877	-0.928	24.071	-11.985	-11.985	0.000	0.000	0.000	0.000
21	A	261	ALA	0	0.027	0.004	24.978	-0.361	-0.361	0.000	0.000	0.000	0.000
22	A	262	ILE	0	-0.042	-0.025	21.918	-0.131	-0.131	0.000	0.000	0.000	0.000
23	A	263	ILE	0	0.002	-0.007	19.893	-0.639	-0.639	0.000	0.000	0.000	0.000
24	A	264	GLU	-1	-0.793	-0.890	20.757	-13.114	-13.114	0.000	0.000	0.000	0.000
25	A	265	ARG	1	0.899	0.961	22.454	11.666	11.666	0.000	0.000	0.000	0.000
26	A	266	LEU	0	0.021	0.010	17.428	-0.371	-0.371	0.000	0.000	0.000	0.000
27	A	267	TYR	0	-0.012	-0.012	16.522	-1.155	-1.155	0.000	0.000	0.000	0.000
28	A	268	PRO	0	0.021	-0.004	16.800	-0.809	-0.809	0.000	0.000	0.000	0.000
29	A	269	GLU	-1	-0.956	-0.974	16.728	-14.934	-14.934	0.000	0.000	0.000	0.000
30	A	270	LEU	0	-0.036	-0.016	10.512	-0.922	-0.922	0.000	0.000	0.000	0.000
31	A	271	GLU	-1	-0.846	-0.926	12.369	-17.984	-17.984	0.000	0.000	0.000	0.000
32	A	272	ARG	1	0.946	0.977	13.947	14.277	14.277	0.000	0.000	0.000	0.000
33	A	273	ARG	1	0.885	0.932	7.453	25.451	25.451	0.000	0.000	0.000	0.000
34	A	274	LEU	0	-0.030	0.000	8.001	-1.830	-1.830	0.000	0.000	0.000	0.000
35	A	275	ALA	0	0.061	0.024	10.163	-0.930	-0.930	0.000	0.000	0.000	0.000
36	A	276	LYS	1	0.881	0.944	11.575	18.427	18.427	0.000	0.000	0.000	0.000
37	A	277	VAL	0	-0.035	-0.022	6.201	0.092	0.092	0.000	0.000	0.000	0.000
38	A	278	LYS	1	0.821	0.909	7.432	26.976	26.976	0.000	0.000	0.000	0.000
39	A	279	PRO	0	0.051	0.016	9.791	0.520	0.520	0.000	0.000	0.000	0.000
40	A	280	ASP	-1	-0.795	-0.870	11.769	-23.490	-23.490	0.000	0.000	0.000	0.000
41	A	281	LEU	0	-0.019	-0.012	11.614	0.380	0.380	0.000	0.000	0.000	0.000
42	A	282	LEU	0	-0.020	-0.010	11.249	-0.520	-0.520	0.000	0.000	0.000	0.000
43	A	283	ILE	0	-0.120	-0.059	7.744	-3.630	-3.630	0.000	0.000	0.000	0.000
44	A	284	ALA	0	0.028	0.017	6.155	2.432	2.432	0.000	0.000	0.000	0.000
45	A	285	ARG	1	0.879	0.921	7.651	33.346	33.346	0.000	0.000	0.000	0.000
46	A	286	GLN	0	0.012	-0.005	8.695	-3.366	-3.366	0.000	0.000	0.000	0.000
47	A	287	GLY	0	0.015	-0.002	11.189	1.236	1.236	0.000	0.000	0.000	0.000
48	A	288	VAL	0	-0.002	0.019	13.137	-0.147	-0.147	0.000	0.000	0.000	0.000
49	A	289	LYS	1	0.813	0.888	13.237	19.644	19.644	0.000	0.000	0.000	0.000
50	A	290	LEU	0	0.004	0.015	16.386	0.513	0.513	0.000	0.000	0.000	0.000
51	A	291	LYS	1	0.952	0.978	18.353	14.611	14.611	0.000	0.000	0.000	0.000
52	A	292	PHE	0	0.027	0.002	21.417	0.195	0.195	0.000	0.000	0.000	0.000
53	A	293	ASP	-1	-0.771	-0.894	25.112	-10.508	-10.508	0.000	0.000	0.000	0.000
54	A	294	ASP	-1	-0.805	-0.870	26.480	-11.499	-11.499	0.000	0.000	0.000	0.000
55	A	295	PHE	0	-0.056	-0.032	24.571	-0.079	-0.079	0.000	0.000	0.000	0.000
56	A	296	GLN	0	-0.046	-0.009	22.758	-0.951	-0.951	0.000	0.000	0.000	0.000
57	A	297	GLN	0	-0.014	-0.028	15.227	0.096	0.096	0.000	0.000	0.000	0.000
58	A	298	THR	0	-0.017	-0.003	17.997	0.115	0.115	0.000	0.000	0.000	0.000
59	A	299	THR	0	-0.084	-0.043	12.084	-0.110	-0.110	0.000	0.000	0.000	0.000
60	A	300	GLN	0	0.022	0.016	14.952	0.766	0.766	0.000	0.000	0.000	0.000
61	A	301	GLU	-1	-0.762	-0.857	8.137	-36.336	-36.336	0.000	0.000	0.000	0.000
62	A	302	HIS	1	0.781	0.879	12.657	20.424	20.424	0.000	0.000	0.000	0.000
63	A	303	VAL	0	0.034	0.014	11.286	-1.534	-1.534	0.000	0.000	0.000	0.000
64	A	304	TRP	0	-0.016	-0.020	11.713	2.355	2.355	0.000	0.000	0.000	0.000
65	A	305	PRO	0	0.047	0.034	11.567	-1.945	-1.945	0.000	0.000	0.000	0.000
66	A	306	ARG	1	0.969	0.977	12.526	15.766	15.766	0.000	0.000	0.000	0.000
67	A	307	LEU	0	0.035	0.033	12.113	0.110	0.110	0.000	0.000	0.000	0.000
68	A	308	ASN	0	-0.066	-0.045	13.644	1.803	1.803	0.000	0.000	0.000	0.000
69	A	309	LYS	1	0.900	0.938	17.248	12.641	12.641	0.000	0.000	0.000	0.000
70	A	310	ALA	0	0.028	0.020	19.689	0.142	0.142	0.000	0.000	0.000	0.000
71	A	311	ASP	-1	-0.760	-0.846	16.642	-17.956	-17.956	0.000	0.000	0.000	0.000
72	A	312	LEU	0	0.000	0.010	14.151	-0.050	-0.050	0.000	0.000	0.000	0.000
73	A	313	ILE	0	0.028	0.016	18.169	0.090	0.090	0.000	0.000	0.000	0.000
74	A	314	ALA	0	0.014	0.006	21.527	0.383	0.383	0.000	0.000	0.000	0.000
75	A	315	THR	0	-0.038	-0.031	16.202	0.090	0.090	0.000	0.000	0.000	0.000
76	A	316	ALA	0	-0.018	0.002	19.627	0.124	0.124	0.000	0.000	0.000	0.000
77	A	317	ARG	1	0.857	0.927	21.062	11.327	11.327	0.000	0.000	0.000	0.000
78	A	318	LYS	1	0.886	0.919	21.990	13.551	13.551	0.000	0.000	0.000	0.000
79	A	319	THR	0	-0.038	-0.039	19.166	0.068	0.068	0.000	0.000	0.000	0.000
80	A	320	TRP	0	-0.026	-0.020	21.972	0.023	0.023	0.000	0.000	0.000	0.000
81	A	321	ASP	-1	-0.843	-0.912	24.915	-10.505	-10.505	0.000	0.000	0.000	0.000
82	A	322	GLU	-1	-0.879	-0.918	24.102	-12.411	-12.411	0.000	0.000	0.000	0.000
83	A	323	ARG	1	0.899	0.948	19.340	14.533	14.533	0.000	0.000	0.000	0.000
84	A	324	ARG	1	0.888	0.964	24.712	10.377	10.377	0.000	0.000	0.000	0.000
85	A	325	GLY	0	0.030	0.017	26.571	0.107	0.107	0.000	0.000	0.000	0.000
86	A	326	GLY	0	-0.031	-0.017	29.780	0.207	0.207	0.000	0.000	0.000	0.000
87	A	327	ARG	1	0.831	0.915	24.811	11.815	11.815	0.000	0.000	0.000	0.000
88	A	328	GLY	0	0.048	0.033	29.415	-0.130	-0.130	0.000	0.000	0.000	0.000
89	A	329	VAL	0	-0.066	-0.045	23.331	-0.392	-0.392	0.000	0.000	0.000	0.000
90	A	330	ARG	1	0.894	0.934	24.188	11.120	11.120	0.000	0.000	0.000	0.000
91	A	331	LEU	0	-0.062	-0.043	17.320	-0.100	-0.100	0.000	0.000	0.000	0.000
92	A	332	VAL	0	0.052	0.033	19.693	-0.216	-0.216	0.000	0.000	0.000	0.000
93	A	333	GLY	0	0.002	-0.008	15.835	-0.040	-0.040	0.000	0.000	0.000	0.000
94	A	334	LEU	0	-0.020	0.009	14.534	-0.085	-0.085	0.000	0.000	0.000	0.000
95	A	335	HIS	0	-0.022	-0.023	9.194	-0.975	-0.975	0.000	0.000	0.000	0.000
96	A	336	VAL	0	0.053	0.027	6.938	1.585	1.585	0.000	0.000	0.000	0.000
102	A	342	GLN	0	0.017	0.008	5.401	2.952	2.952	0.000	0.000	0.000	0.000
103	A	343	MET	0	-0.013	-0.006	9.187	-0.368	-0.368	0.000	0.000	0.000	0.000
104	A	344	GLU	-1	-0.880	-0.937	11.075	-20.206	-20.206	0.000	0.000	0.000	0.000
105	A	345	ARG	1	0.852	0.930	12.532	19.675	19.675	0.000	0.000	0.000	0.000
106	A	346	GLN	0	0.018	0.009	14.149	-0.918	-0.918	0.000	0.000	0.000	0.000
107	A	347	LEU	0	-0.024	-0.015	15.746	0.341	0.341	0.000	0.000	0.000	0.000
108	A	348	VAL	0	0.020	0.002	18.917	0.333	0.333	0.000	0.000	0.000	0.000
109	A	349	LEU	0	-0.008	-0.021	22.731	-0.236	-0.236	0.000	0.000	0.000	0.000
110	A	350	GLY	0	-0.046	-0.003	25.255	0.122	0.122	0.000	0.000	0.000	0.000
111	A	351	LEU	-1	-0.921	-0.946	26.672	-9.763	-9.763	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:241:HIS)