FMO DATABASE

FMODB ID: Z67JN

Calculation Name: 1JQL-B-Xray372

Preferred Name: DNA polymerase III subunit beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1JQL

Chain ID: B

ChEMBL ID: CHEMBL3562169

UniProt ID: P0A988

Base Structure: X-ray

Registration Date: 2023-06-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	140
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1281923.298687
FMO2-HF: Nuclear repulsion	1227518.428099
FMO2-HF: Total energy	-54404.870589
FMO2-MP2: Total energy	-54564.180704

3D Structure

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(B:1:MET)

Summations of interaction energy for fragment #1(B:1:MET)

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.
-23.001	-9.387	13.059	-7.66	-19.012	-0.058

Interaction energy analysis for fragmet #1(B:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.028 / q_NPA : -0.002

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	B	3	ARG	1	0.830	0.896	3.090	-8.558	-5.233	0.214	-1.491	-2.049	0.001
4	B	4	LEU	0	-0.007	-0.003	5.192	0.085	0.150	-0.001	-0.004	-0.060	0.000
5	B	5	TYR	0	0.032	0.016	8.536	0.044	0.044	0.000	0.000	0.000	0.000
6	B	6	PRO	0	0.039	0.005	11.704	-0.070	-0.070	0.000	0.000	0.000	0.000
7	B	7	GLU	-1	-0.931	-0.962	13.550	-0.066	-0.066	0.000	0.000	0.000	0.000
8	B	8	GLN	0	0.027	0.010	12.310	-0.017	-0.017	0.000	0.000	0.000	0.000
9	B	9	LEU	0	-0.021	0.012	9.990	-0.044	-0.044	0.000	0.000	0.000	0.000
10	B	10	ARG	1	0.896	0.918	12.688	0.149	0.149	0.000	0.000	0.000	0.000
11	B	11	ALA	0	-0.011	0.020	14.806	0.018	0.018	0.000	0.000	0.000	0.000
12	B	12	GLN	0	0.022	-0.011	9.451	-0.126	-0.126	0.000	0.000	0.000	0.000
13	B	13	LEU	0	-0.040	-0.013	11.758	-0.084	-0.084	0.000	0.000	0.000	0.000
14	B	14	ASN	0	-0.038	-0.012	13.192	0.022	0.022	0.000	0.000	0.000	0.000
15	B	15	GLU	-1	-0.923	-0.956	12.432	-0.179	-0.179	0.000	0.000	0.000	0.000
16	B	16	GLY	0	0.015	0.002	11.724	0.050	0.050	0.000	0.000	0.000	0.000
17	B	17	LEU	0	0.021	0.027	11.146	-0.180	-0.180	0.000	0.000	0.000	0.000
18	B	18	ARG	1	0.819	0.905	6.680	0.856	0.856	0.000	0.000	0.000	0.000
19	B	19	ALA	0	0.068	0.032	9.969	0.024	0.024	0.000	0.000	0.000	0.000
20	B	20	ALA	0	0.009	-0.001	6.194	0.049	0.049	0.000	0.000	0.000	0.000
21	B	21	TYR	0	0.019	0.017	5.591	-0.726	-0.726	0.000	0.000	0.000	0.000
22	B	22	LEU	0	-0.026	-0.016	2.356	-0.177	0.117	1.753	-0.336	-1.710	0.000
23	B	23	LEU	0	0.007	0.002	5.264	0.382	0.415	-0.001	0.000	-0.032	0.000
24	B	24	LEU	0	0.019	-0.003	5.027	0.160	0.160	0.000	0.000	0.000	0.000
25	B	25	GLY	0	-0.020	-0.026	8.732	0.134	0.134	0.000	0.000	0.000	0.000
26	B	26	ASN	0	-0.009	-0.029	12.172	-0.021	-0.021	0.000	0.000	0.000	0.000
27	B	27	ASP	-1	-0.834	-0.894	15.681	-0.042	-0.042	0.000	0.000	0.000	0.000
28	B	28	PRO	0	0.011	0.002	16.974	-0.028	-0.028	0.000	0.000	0.000	0.000
29	B	29	LEU	0	0.008	0.008	19.285	-0.024	-0.024	0.000	0.000	0.000	0.000
30	B	30	LEU	0	0.028	-0.001	15.291	-0.032	-0.032	0.000	0.000	0.000	0.000
31	B	31	LEU	0	-0.043	0.003	12.419	-0.063	-0.063	0.000	0.000	0.000	0.000
32	B	32	GLN	0	0.005	0.011	14.596	-0.056	-0.056	0.000	0.000	0.000	0.000
33	B	33	GLU	-1	-0.849	-0.920	16.850	-0.193	-0.193	0.000	0.000	0.000	0.000
34	B	34	SER	0	-0.030	-0.035	11.484	-0.034	-0.034	0.000	0.000	0.000	0.000
35	B	35	GLN	0	-0.016	-0.036	13.128	-0.086	-0.086	0.000	0.000	0.000	0.000
36	B	36	ASP	-1	-0.826	-0.895	14.006	-0.296	-0.296	0.000	0.000	0.000	0.000
37	B	37	ALA	0	-0.006	0.013	14.909	0.024	0.024	0.000	0.000	0.000	0.000
38	B	38	VAL	0	-0.004	-0.011	10.744	0.002	0.002	0.000	0.000	0.000	0.000
39	B	39	ARG	1	0.838	0.902	14.075	0.377	0.377	0.000	0.000	0.000	0.000
40	B	40	GLN	0	-0.063	-0.025	16.937	0.046	0.046	0.000	0.000	0.000	0.000
41	B	41	VAL	0	-0.004	-0.019	16.137	0.025	0.025	0.000	0.000	0.000	0.000
42	B	42	ALA	0	0.023	0.019	15.926	0.010	0.010	0.000	0.000	0.000	0.000
43	B	43	ALA	0	-0.002	0.009	17.655	0.025	0.025	0.000	0.000	0.000	0.000
44	B	44	ALA	0	-0.053	-0.019	20.913	0.025	0.025	0.000	0.000	0.000	0.000
45	B	45	GLN	0	-0.047	-0.030	18.528	-0.006	-0.006	0.000	0.000	0.000	0.000
46	B	46	GLY	0	0.047	0.018	21.077	-0.016	-0.016	0.000	0.000	0.000	0.000
47	B	47	PHE	0	-0.041	-0.013	16.455	-0.001	-0.001	0.000	0.000	0.000	0.000
48	B	48	GLU	-1	-0.918	-0.964	20.823	-0.202	-0.202	0.000	0.000	0.000	0.000
49	B	49	GLU	-1	-0.834	-0.881	22.224	-0.252	-0.252	0.000	0.000	0.000	0.000
50	B	50	HIS	0	-0.031	-0.020	18.747	-0.064	-0.064	0.000	0.000	0.000	0.000
51	B	51	HIS	0	0.020	0.007	18.927	0.036	0.036	0.000	0.000	0.000	0.000
52	B	52	THR	0	-0.050	-0.054	17.662	-0.038	-0.038	0.000	0.000	0.000	0.000
53	B	53	PHE	0	0.033	0.031	17.315	0.031	0.031	0.000	0.000	0.000	0.000
54	B	54	SER	0	0.008	-0.006	17.029	-0.031	-0.031	0.000	0.000	0.000	0.000
55	B	55	ILE	0	-0.036	-0.001	14.181	0.014	0.014	0.000	0.000	0.000	0.000
56	B	56	ASP	-1	-0.755	-0.873	17.400	-0.092	-0.092	0.000	0.000	0.000	0.000
57	B	57	PRO	0	-0.081	-0.049	20.204	-0.009	-0.009	0.000	0.000	0.000	0.000
58	B	58	ASN	0	-0.065	-0.040	22.743	0.010	0.010	0.000	0.000	0.000	0.000
59	B	59	THR	0	-0.026	-0.016	18.896	-0.011	-0.011	0.000	0.000	0.000	0.000
60	B	60	ASP	-1	-0.796	-0.888	22.266	-0.164	-0.164	0.000	0.000	0.000	0.000
61	B	61	TRP	0	0.048	-0.002	14.963	-0.034	-0.034	0.000	0.000	0.000	0.000
62	B	62	ASN	0	-0.059	-0.023	20.810	-0.021	-0.021	0.000	0.000	0.000	0.000
63	B	63	ALA	0	0.015	0.030	23.097	-0.013	-0.013	0.000	0.000	0.000	0.000
64	B	64	ILE	0	-0.009	0.011	16.564	-0.019	-0.019	0.000	0.000	0.000	0.000
65	B	65	PHE	0	0.025	-0.009	15.953	-0.027	-0.027	0.000	0.000	0.000	0.000
66	B	66	SER	0	-0.052	-0.051	19.540	-0.008	-0.008	0.000	0.000	0.000	0.000
67	B	67	LEU	0	0.023	0.013	20.323	0.006	0.006	0.000	0.000	0.000	0.000
68	B	68	CYS	0	-0.064	-0.021	16.552	-0.030	-0.030	0.000	0.000	0.000	0.000
69	B	69	GLN	0	-0.005	-0.011	18.604	-0.017	-0.017	0.000	0.000	0.000	0.000
70	B	70	ALA	0	-0.048	0.005	21.595	0.023	0.023	0.000	0.000	0.000	0.000
71	B	71	MET	0	-0.021	-0.021	22.736	-0.019	-0.019	0.000	0.000	0.000	0.000
72	B	72	SER	0	0.017	-0.002	25.211	0.025	0.025	0.000	0.000	0.000	0.000
73	B	73	LEU	0	-0.019	-0.025	27.007	0.004	0.004	0.000	0.000	0.000	0.000
74	B	74	PHE	0	-0.039	-0.027	29.213	0.014	0.014	0.000	0.000	0.000	0.000
75	B	75	ALA	0	-0.024	-0.005	26.247	-0.001	-0.001	0.000	0.000	0.000	0.000
76	B	76	SER	0	-0.014	0.016	24.934	-0.007	-0.007	0.000	0.000	0.000	0.000
77	B	77	ARG	1	0.856	0.933	18.163	0.377	0.377	0.000	0.000	0.000	0.000
78	B	78	GLN	0	-0.002	-0.015	18.337	-0.005	-0.005	0.000	0.000	0.000	0.000
79	B	79	THR	0	-0.018	-0.013	14.875	-0.080	-0.080	0.000	0.000	0.000	0.000
80	B	80	LEU	0	0.003	0.002	14.536	0.060	0.060	0.000	0.000	0.000	0.000
81	B	81	LEU	0	-0.026	-0.008	12.943	-0.102	-0.102	0.000	0.000	0.000	0.000
82	B	82	LEU	0	-0.019	-0.017	11.714	0.070	0.070	0.000	0.000	0.000	0.000
83	B	83	LEU	0	-0.011	-0.011	12.425	-0.035	-0.035	0.000	0.000	0.000	0.000
84	B	84	LEU	0	-0.007	-0.014	9.453	0.031	0.031	0.000	0.000	0.000	0.000
85	B	85	PRO	0	0.025	0.021	13.689	0.017	0.017	0.000	0.000	0.000	0.000
86	B	86	GLU	-1	-0.848	-0.914	14.900	-0.032	-0.032	0.000	0.000	0.000	0.000
87	B	87	ASN	0	-0.072	-0.022	16.626	0.021	0.021	0.000	0.000	0.000	0.000
88	B	88	GLY	0	-0.016	-0.011	12.648	0.051	0.051	0.000	0.000	0.000	0.000
89	B	89	PRO	0	-0.031	-0.014	10.579	-0.030	-0.030	0.000	0.000	0.000	0.000
90	B	90	ASN	0	0.077	0.020	13.482	0.055	0.055	0.000	0.000	0.000	0.000
91	B	91	ALA	0	0.004	-0.007	16.343	-0.017	-0.017	0.000	0.000	0.000	0.000
92	B	92	ALA	0	0.095	0.051	16.934	0.006	0.006	0.000	0.000	0.000	0.000
93	B	93	ILE	0	-0.005	0.014	13.349	-0.024	-0.024	0.000	0.000	0.000	0.000
94	B	94	ASN	0	-0.033	-0.027	12.060	-0.046	-0.046	0.000	0.000	0.000	0.000
95	B	95	GLU	-1	-0.881	-0.946	13.212	-0.100	-0.100	0.000	0.000	0.000	0.000
96	B	96	GLN	0	-0.016	0.009	15.675	-0.036	-0.036	0.000	0.000	0.000	0.000
97	B	97	LEU	0	0.057	0.009	9.182	-0.043	-0.043	0.000	0.000	0.000	0.000
98	B	98	LEU	0	-0.035	-0.002	11.426	-0.101	-0.101	0.000	0.000	0.000	0.000
99	B	99	THR	0	-0.001	-0.003	12.455	-0.040	-0.040	0.000	0.000	0.000	0.000
100	B	100	LEU	0	0.000	-0.004	12.027	-0.012	-0.012	0.000	0.000	0.000	0.000
101	B	101	THR	0	-0.113	-0.074	8.245	-0.042	-0.042	0.000	0.000	0.000	0.000
102	B	102	GLY	0	-0.012	0.005	11.024	-0.036	-0.036	0.000	0.000	0.000	0.000
103	B	103	LEU	0	-0.043	-0.017	14.421	0.030	0.030	0.000	0.000	0.000	0.000
104	B	104	LEU	0	-0.033	0.005	9.198	-0.008	-0.008	0.000	0.000	0.000	0.000
105	B	105	HIS	0	0.067	0.041	13.245	-0.080	-0.080	0.000	0.000	0.000	0.000
106	B	106	ASP	-1	-0.845	-0.934	13.822	-0.769	-0.769	0.000	0.000	0.000	0.000
107	B	107	ASP	-1	-0.847	-0.898	15.645	-0.353	-0.353	0.000	0.000	0.000	0.000
108	B	108	LEU	0	-0.063	-0.019	13.870	0.026	0.026	0.000	0.000	0.000	0.000
109	B	109	LEU	0	-0.008	0.008	11.204	-0.121	-0.121	0.000	0.000	0.000	0.000
110	B	110	LEU	0	0.004	0.000	8.107	0.063	0.063	0.000	0.000	0.000	0.000
111	B	111	ILE	0	-0.018	-0.017	9.279	-0.218	-0.218	0.000	0.000	0.000	0.000
112	B	112	VAL	0	0.014	0.007	7.190	0.161	0.161	0.000	0.000	0.000	0.000
113	B	113	ARG	1	0.883	0.931	8.503	0.172	0.172	0.000	0.000	0.000	0.000
114	B	114	GLY	0	0.042	0.023	10.870	0.034	0.034	0.000	0.000	0.000	0.000
115	B	115	ASN	0	-0.033	-0.017	11.361	-0.019	-0.019	0.000	0.000	0.000	0.000
116	B	116	LYS	1	0.799	0.893	9.495	-1.008	-1.008	0.000	0.000	0.000	0.000
117	B	117	LEU	0	0.056	0.032	5.280	-0.093	-0.093	0.000	0.000	0.000	0.000
118	B	118	SER	0	0.034	0.000	9.211	0.096	0.096	0.000	0.000	0.000	0.000
119	B	119	LYS	1	0.923	0.964	12.607	-0.296	-0.296	0.000	0.000	0.000	0.000
120	B	120	ALA	0	0.048	0.017	12.129	0.133	0.133	0.000	0.000	0.000	0.000
121	B	121	GLN	0	0.014	0.009	11.881	0.016	0.016	0.000	0.000	0.000	0.000
122	B	122	GLU	-1	-0.825	-0.892	6.748	2.210	2.210	0.000	0.000	0.000	0.000
123	B	123	ASN	0	-0.033	-0.015	7.790	0.060	0.060	0.000	0.000	0.000	0.000
124	B	124	ALA	0	0.041	0.036	9.557	-0.140	-0.140	0.000	0.000	0.000	0.000
125	B	125	ALA	0	0.020	0.000	9.246	0.028	0.028	0.000	0.000	0.000	0.000
126	B	126	TRP	0	0.018	0.009	5.718	-0.061	-0.061	0.000	0.000	0.000	0.000
127	B	127	PHE	0	0.017	0.010	2.411	-2.084	-1.569	3.753	-0.822	-3.447	-0.007
128	B	128	THR	0	-0.031	-0.029	4.527	-0.158	-0.026	-0.001	-0.006	-0.125	0.000
129	B	129	ALA	0	-0.009	0.010	7.006	-0.177	-0.177	0.000	0.000	0.000	0.000
130	B	130	LEU	0	0.007	-0.005	3.721	-0.405	-0.147	0.005	-0.036	-0.226	0.000
131	B	131	ALA	0	0.002	0.025	2.501	-3.142	-1.648	1.755	-1.077	-2.172	0.000
132	B	132	ASN	0	-0.034	-0.030	2.606	-5.780	-3.544	2.703	-1.376	-3.563	-0.031
133	B	133	ARG	1	0.770	0.868	4.309	1.988	2.120	-0.001	-0.006	-0.125	0.000
134	B	134	SER	0	-0.033	-0.028	2.596	-3.344	-1.795	1.533	-1.162	-1.920	-0.013
135	B	135	VAL	0	-0.016	-0.001	3.405	-2.251	-0.863	0.087	-0.561	-0.914	-0.003
136	B	136	GLN	0	0.039	0.026	2.457	1.684	3.751	1.252	-0.759	-2.560	-0.005
137	B	137	VAL	0	0.017	0.001	3.852	0.185	0.311	0.008	-0.024	-0.109	0.000
138	B	138	THR	0	0.001	0.000	7.662	0.214	0.214	0.000	0.000	0.000	0.000
139	B	139	CYS	0	-0.031	0.004	9.875	-0.044	-0.044	0.000	0.000	0.000	0.000
140	B	140	GLN	0	-0.025	-0.013	12.475	0.057	0.057	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1:MET)