FMO DATABASE

FMODB ID: 2J4YR

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	OptH
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	-1282779.244183
FMO2-HF: Nuclear repulsion	1228377.130083
FMO2-HF: Total energy	-54402.114101
FMO2-MP2: Total energy	-54561.866865

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.
-15.027	-10.59	25.948	-9.225	-21.162	-0.082

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 : -0.050 / q_NPA : -0.006

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	0.937	0.961	2.585	-7.007	-4.065	0.893	-1.579	-2.256	-0.006
4	B	4	LEU	0	-0.045	-0.020	4.899	0.197	0.266	-0.001	-0.006	-0.062	0.000
5	B	5	TYR	0	0.020	0.006	8.181	0.067	0.067	0.000	0.000	0.000	0.000
6	B	6	PRO	0	0.053	0.033	11.139	-0.059	-0.059	0.000	0.000	0.000	0.000
7	B	7	GLU	-1	-0.938	-0.967	13.453	0.022	0.022	0.000	0.000	0.000	0.000
8	B	8	GLN	0	0.043	0.013	11.583	-0.026	-0.026	0.000	0.000	0.000	0.000
9	B	9	LEU	0	0.015	0.045	10.872	-0.028	-0.028	0.000	0.000	0.000	0.000
10	B	10	ARG	1	0.958	0.956	13.021	0.050	0.050	0.000	0.000	0.000	0.000
11	B	11	ALA	0	-0.019	0.011	14.728	0.006	0.006	0.000	0.000	0.000	0.000
12	B	12	GLN	0	0.089	0.016	10.104	0.011	0.011	0.000	0.000	0.000	0.000
13	B	13	LEU	0	-0.050	-0.008	11.630	-0.049	-0.049	0.000	0.000	0.000	0.000
14	B	14	ASN	0	-0.065	-0.019	13.109	0.001	0.001	0.000	0.000	0.000	0.000
15	B	15	GLU	-1	-1.012	-0.982	11.756	-0.008	-0.008	0.000	0.000	0.000	0.000
16	B	16	GLY	0	-0.014	-0.011	11.299	0.032	0.032	0.000	0.000	0.000	0.000
17	B	17	LEU	0	0.010	0.015	11.457	-0.090	-0.090	0.000	0.000	0.000	0.000
18	B	18	ARG	1	0.883	0.947	5.398	0.306	0.306	0.000	0.000	0.000	0.000
19	B	19	ALA	0	0.089	0.051	8.810	0.096	0.096	0.000	0.000	0.000	0.000
20	B	20	ALA	0	0.006	-0.023	5.160	-0.042	-0.042	0.000	0.000	0.000	0.000
21	B	21	TYR	0	0.021	0.010	5.827	-0.367	-0.367	0.000	0.000	0.000	0.000
22	B	22	LEU	0	-0.031	-0.007	2.492	-0.323	0.129	0.785	-0.201	-1.037	0.000
23	B	23	LEU	0	0.030	0.009	5.639	0.503	0.503	0.000	0.000	0.000	0.000
24	B	24	LEU	0	-0.011	-0.002	6.592	0.029	0.029	0.000	0.000	0.000	0.000
25	B	25	GLY	0	0.037	-0.002	9.895	0.032	0.032	0.000	0.000	0.000	0.000
26	B	26	ASN	0	-0.009	-0.024	13.333	-0.021	-0.021	0.000	0.000	0.000	0.000
27	B	27	ASP	-1	-0.857	-0.906	16.227	0.036	0.036	0.000	0.000	0.000	0.000
28	B	28	PRO	0	-0.008	-0.012	17.466	-0.016	-0.016	0.000	0.000	0.000	0.000
29	B	29	LEU	0	-0.020	-0.002	19.469	-0.018	-0.018	0.000	0.000	0.000	0.000
30	B	30	LEU	0	0.055	0.029	15.534	-0.018	-0.018	0.000	0.000	0.000	0.000
31	B	31	LEU	0	-0.052	-0.027	12.877	-0.033	-0.033	0.000	0.000	0.000	0.000
32	B	32	GLN	0	-0.031	-0.015	14.822	-0.049	-0.049	0.000	0.000	0.000	0.000
33	B	33	GLU	-1	-0.817	-0.930	17.008	-0.061	-0.061	0.000	0.000	0.000	0.000
34	B	34	SER	0	0.002	-0.031	12.327	-0.021	-0.021	0.000	0.000	0.000	0.000
35	B	35	GLN	0	0.039	0.002	13.586	-0.065	-0.065	0.000	0.000	0.000	0.000
36	B	36	ASP	-1	-0.940	-0.966	14.450	-0.163	-0.163	0.000	0.000	0.000	0.000
37	B	37	ALA	0	-0.021	-0.009	15.165	0.010	0.010	0.000	0.000	0.000	0.000
38	B	38	VAL	0	0.017	-0.008	11.340	-0.006	-0.006	0.000	0.000	0.000	0.000
39	B	39	ARG	1	0.904	0.954	14.597	0.243	0.243	0.000	0.000	0.000	0.000
40	B	40	GLN	0	-0.071	-0.020	17.240	0.033	0.033	0.000	0.000	0.000	0.000
41	B	41	VAL	0	-0.009	-0.025	16.255	0.016	0.016	0.000	0.000	0.000	0.000
42	B	42	ALA	0	-0.009	0.013	16.088	0.004	0.004	0.000	0.000	0.000	0.000
43	B	43	ALA	0	-0.029	-0.010	17.780	0.016	0.016	0.000	0.000	0.000	0.000
44	B	44	ALA	0	-0.046	-0.009	20.454	0.016	0.016	0.000	0.000	0.000	0.000
45	B	45	GLN	0	-0.054	-0.038	18.135	-0.004	-0.004	0.000	0.000	0.000	0.000
46	B	46	GLY	0	0.054	0.017	20.935	-0.019	-0.019	0.000	0.000	0.000	0.000
47	B	47	PHE	0	-0.056	-0.020	15.970	0.007	0.007	0.000	0.000	0.000	0.000
48	B	48	GLU	-1	-0.923	-0.969	21.006	-0.143	-0.143	0.000	0.000	0.000	0.000
49	B	49	GLU	-1	-0.879	-0.911	21.759	-0.200	-0.200	0.000	0.000	0.000	0.000
50	B	50	HIS	0	-0.023	-0.020	19.407	-0.049	-0.049	0.000	0.000	0.000	0.000
51	B	51	HIS	0	-0.012	-0.003	18.648	0.022	0.022	0.000	0.000	0.000	0.000
52	B	52	THR	0	-0.072	-0.069	17.406	-0.014	-0.014	0.000	0.000	0.000	0.000
53	B	53	PHE	0	0.035	0.028	17.277	0.016	0.016	0.000	0.000	0.000	0.000
54	B	54	SER	0	0.028	0.012	17.432	-0.018	-0.018	0.000	0.000	0.000	0.000
55	B	55	ILE	0	-0.014	0.003	14.428	0.005	0.005	0.000	0.000	0.000	0.000
56	B	56	ASP	-1	-0.751	-0.887	17.787	-0.099	-0.099	0.000	0.000	0.000	0.000
57	B	57	PRO	0	-0.119	-0.070	20.437	-0.013	-0.013	0.000	0.000	0.000	0.000
58	B	58	ASN	0	-0.039	-0.019	22.782	0.008	0.008	0.000	0.000	0.000	0.000
59	B	59	THR	0	-0.031	-0.002	19.388	-0.006	-0.006	0.000	0.000	0.000	0.000
60	B	60	ASP	-1	-0.860	-0.931	22.330	-0.163	-0.163	0.000	0.000	0.000	0.000
61	B	61	TRP	0	0.052	-0.010	14.598	-0.034	-0.034	0.000	0.000	0.000	0.000
62	B	62	ASN	0	0.000	0.018	20.352	-0.031	-0.031	0.000	0.000	0.000	0.000
63	B	63	ALA	0	0.024	0.057	22.759	-0.010	-0.010	0.000	0.000	0.000	0.000
64	B	64	ILE	0	0.032	0.017	16.275	-0.012	-0.012	0.000	0.000	0.000	0.000
65	B	65	PHE	0	0.006	-0.005	15.852	-0.018	-0.018	0.000	0.000	0.000	0.000
66	B	66	SER	0	-0.064	-0.071	19.336	-0.007	-0.007	0.000	0.000	0.000	0.000
67	B	67	LEU	0	0.019	0.007	19.355	0.009	0.009	0.000	0.000	0.000	0.000
68	B	68	CYS	0	-0.105	-0.065	16.519	-0.023	-0.023	0.000	0.000	0.000	0.000
69	B	69	GLN	0	0.001	0.003	18.520	0.003	0.003	0.000	0.000	0.000	0.000
70	B	70	ALA	0	-0.042	0.014	21.612	0.019	0.019	0.000	0.000	0.000	0.000
71	B	71	MET	0	-0.007	-0.006	22.834	-0.012	-0.012	0.000	0.000	0.000	0.000
72	B	72	SER	0	0.032	0.018	25.174	0.018	0.018	0.000	0.000	0.000	0.000
73	B	73	LEU	0	-0.031	-0.027	26.848	0.004	0.004	0.000	0.000	0.000	0.000
74	B	74	PHE	0	-0.013	-0.017	29.027	0.011	0.011	0.000	0.000	0.000	0.000
75	B	75	ALA	0	-0.045	-0.013	26.084	0.000	0.000	0.000	0.000	0.000	0.000
76	B	76	SER	0	0.038	0.023	24.422	-0.006	-0.006	0.000	0.000	0.000	0.000
77	B	77	ARG	1	0.884	0.983	18.675	0.247	0.247	0.000	0.000	0.000	0.000
78	B	78	GLN	0	0.086	0.033	18.152	0.020	0.020	0.000	0.000	0.000	0.000
79	B	79	THR	0	-0.025	-0.020	14.701	-0.062	-0.062	0.000	0.000	0.000	0.000
80	B	80	LEU	0	-0.025	-0.003	13.728	0.040	0.040	0.000	0.000	0.000	0.000
81	B	81	LEU	0	0.012	0.010	12.797	-0.083	-0.083	0.000	0.000	0.000	0.000
82	B	82	LEU	0	-0.058	-0.046	12.216	0.022	0.022	0.000	0.000	0.000	0.000
83	B	83	LEU	0	-0.039	-0.034	13.087	-0.005	-0.005	0.000	0.000	0.000	0.000
84	B	84	LEU	0	-0.018	-0.012	10.012	0.011	0.011	0.000	0.000	0.000	0.000
85	B	85	PRO	0	0.000	0.024	14.284	0.020	0.020	0.000	0.000	0.000	0.000
86	B	86	GLU	-1	-0.818	-0.927	15.442	-0.014	-0.014	0.000	0.000	0.000	0.000
87	B	87	ASN	0	-0.090	-0.029	17.241	0.026	0.026	0.000	0.000	0.000	0.000
88	B	88	GLY	0	-0.044	-0.019	12.889	0.022	0.022	0.000	0.000	0.000	0.000
89	B	89	PRO	0	-0.030	-0.009	10.682	-0.023	-0.023	0.000	0.000	0.000	0.000
90	B	90	ASN	0	0.072	0.038	13.495	0.044	0.044	0.000	0.000	0.000	0.000
91	B	91	ALA	0	-0.006	-0.029	16.041	-0.020	-0.020	0.000	0.000	0.000	0.000
92	B	92	ALA	0	0.087	0.043	17.196	-0.001	-0.001	0.000	0.000	0.000	0.000
93	B	93	ILE	0	-0.005	0.024	12.950	-0.025	-0.025	0.000	0.000	0.000	0.000
94	B	94	ASN	0	0.005	-0.044	11.958	-0.068	-0.068	0.000	0.000	0.000	0.000
95	B	95	GLU	-1	-0.927	-0.960	12.754	-0.218	-0.218	0.000	0.000	0.000	0.000
96	B	96	GLN	0	0.029	0.016	14.694	-0.046	-0.046	0.000	0.000	0.000	0.000
97	B	97	LEU	0	0.060	0.032	9.554	-0.036	-0.036	0.000	0.000	0.000	0.000
98	B	98	LEU	0	0.009	0.000	10.745	-0.134	-0.134	0.000	0.000	0.000	0.000
99	B	99	THR	0	-0.019	0.002	11.985	-0.024	-0.024	0.000	0.000	0.000	0.000
100	B	100	LEU	0	-0.013	-0.017	11.614	-0.005	-0.005	0.000	0.000	0.000	0.000
101	B	101	THR	0	-0.136	-0.090	7.813	-0.041	-0.041	0.000	0.000	0.000	0.000
102	B	102	GLY	0	-0.022	-0.012	10.721	-0.047	-0.047	0.000	0.000	0.000	0.000
103	B	103	LEU	0	-0.065	-0.031	13.831	0.037	0.037	0.000	0.000	0.000	0.000
104	B	104	LEU	0	-0.037	0.001	9.265	0.012	0.012	0.000	0.000	0.000	0.000
105	B	105	HIS	0	-0.006	-0.008	13.422	0.020	0.020	0.000	0.000	0.000	0.000
106	B	106	ASP	-1	-0.963	-1.014	14.283	-0.502	-0.502	0.000	0.000	0.000	0.000
107	B	107	ASP	-1	-0.868	-0.906	15.838	-0.273	-0.273	0.000	0.000	0.000	0.000
108	B	108	LEU	0	-0.069	-0.027	13.726	0.009	0.009	0.000	0.000	0.000	0.000
109	B	109	LEU	0	0.000	0.009	10.603	-0.100	-0.100	0.000	0.000	0.000	0.000
110	B	110	LEU	0	-0.033	-0.015	7.893	0.029	0.029	0.000	0.000	0.000	0.000
111	B	111	ILE	0	-0.023	-0.012	9.179	-0.151	-0.151	0.000	0.000	0.000	0.000
112	B	112	VAL	0	0.022	0.010	7.492	0.105	0.105	0.000	0.000	0.000	0.000
113	B	113	ARG	1	0.937	0.982	9.147	0.123	0.123	0.000	0.000	0.000	0.000
114	B	114	GLY	0	0.064	0.027	11.217	-0.012	-0.012	0.000	0.000	0.000	0.000
115	B	115	ASN	0	-0.025	-0.040	13.091	0.008	0.008	0.000	0.000	0.000	0.000
116	B	116	LYS	1	0.804	0.919	9.861	-0.836	-0.836	0.000	0.000	0.000	0.000
117	B	117	LEU	0	0.019	0.023	5.516	-0.085	-0.085	0.000	0.000	0.000	0.000
118	B	118	SER	0	0.047	0.009	9.727	0.030	0.030	0.000	0.000	0.000	0.000
119	B	119	LYS	1	0.931	0.951	11.809	-0.253	-0.253	0.000	0.000	0.000	0.000
120	B	120	ALA	0	0.098	0.065	12.292	0.077	0.077	0.000	0.000	0.000	0.000
121	B	121	GLN	0	0.015	0.003	11.579	-0.020	-0.020	0.000	0.000	0.000	0.000
122	B	122	GLU	-1	-0.935	-0.984	6.962	0.952	0.952	0.000	0.000	0.000	0.000
123	B	123	ASN	0	-0.015	-0.024	7.269	-0.153	-0.153	0.000	0.000	0.000	0.000
124	B	124	ALA	0	0.000	0.030	9.165	-0.092	-0.092	0.000	0.000	0.000	0.000
125	B	125	ALA	0	0.042	0.008	8.667	-0.099	-0.099	0.000	0.000	0.000	0.000
126	B	126	TRP	0	0.022	0.032	6.066	-0.119	-0.119	0.000	0.000	0.000	0.000
127	B	127	PHE	0	0.007	0.006	2.793	-2.831	-2.059	2.883	-0.710	-2.945	-0.006
128	B	128	THR	0	-0.035	-0.024	4.072	-0.779	-0.631	0.000	-0.036	-0.112	0.000
129	B	129	ALA	0	-0.002	0.008	6.304	-0.256	-0.256	0.000	0.000	0.000	0.000
130	B	130	LEU	0	-0.034	-0.022	3.764	-0.362	-0.030	0.010	-0.049	-0.294	0.000
131	B	131	ALA	0	0.005	0.004	2.059	-1.550	-1.190	3.073	-1.589	-1.844	0.001
132	B	132	ASN	0	-0.001	-0.012	2.120	-0.523	-5.390	11.697	-1.724	-5.106	-0.042
133	B	133	ARG	1	0.951	0.986	3.414	2.635	3.113	0.004	-0.037	-0.445	-0.001
134	B	134	SER	0	-0.032	-0.019	2.749	-1.686	-0.385	0.973	-0.777	-1.497	-0.007
135	B	135	VAL	0	0.031	0.009	2.760	-4.031	-1.666	0.994	-1.422	-1.937	-0.016
136	B	136	GLN	0	0.005	-0.003	2.993	3.626	3.557	4.634	-1.044	-3.521	-0.005
137	B	137	VAL	0	0.011	0.012	4.477	-0.253	-0.099	0.003	-0.051	-0.106	0.000
138	B	138	THR	0	-0.041	-0.032	7.939	0.248	0.248	0.000	0.000	0.000	0.000
139	B	139	CYS	0	-0.046	-0.001	9.816	-0.106	-0.106	0.000	0.000	0.000	0.000
140	B	140	GLN	0	0.025	0.036	12.679	0.037	0.037	0.000	0.000	0.000	0.000

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