FMO DATABASE

FMODB ID: 6NZMZ

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	OptHSide
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	-1282074.210117
FMO2-HF: Nuclear repulsion	1227670.453443
FMO2-HF: Total energy	-54403.756674
FMO2-MP2: Total energy	-54563.239139

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.
-21.212	-9.427	18.577	-9.24	-21.121	-0.077

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 : -0.052 / q_NPA : -0.004

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	0.871	0.922	2.927	-8.014	-4.704	0.224	-1.609	-1.924	0.000
4	B	4	LEU	0	-0.017	-0.008	5.441	0.232	0.232	0.000	0.000	0.000	0.000
5	B	5	TYR	0	0.039	0.020	8.547	0.006	0.006	0.000	0.000	0.000	0.000
6	B	6	PRO	0	0.033	0.027	11.495	-0.063	-0.063	0.000	0.000	0.000	0.000
7	B	7	GLU	-1	-0.927	-0.969	13.638	-0.031	-0.031	0.000	0.000	0.000	0.000
8	B	8	GLN	0	0.006	0.001	12.448	-0.023	-0.023	0.000	0.000	0.000	0.000
9	B	9	LEU	0	0.004	0.027	10.409	-0.031	-0.031	0.000	0.000	0.000	0.000
10	B	10	ARG	1	0.912	0.938	13.033	0.114	0.114	0.000	0.000	0.000	0.000
11	B	11	ALA	0	-0.002	0.019	14.866	0.010	0.010	0.000	0.000	0.000	0.000
12	B	12	GLN	0	0.006	-0.028	9.530	-0.062	-0.062	0.000	0.000	0.000	0.000
13	B	13	LEU	0	-0.036	-0.013	11.675	-0.066	-0.066	0.000	0.000	0.000	0.000
14	B	14	ASN	0	-0.046	-0.011	13.102	0.014	0.014	0.000	0.000	0.000	0.000
15	B	15	GLU	-1	-0.957	-0.959	12.415	-0.068	-0.068	0.000	0.000	0.000	0.000
16	B	16	GLY	0	-0.007	-0.004	11.345	0.038	0.038	0.000	0.000	0.000	0.000
17	B	17	LEU	0	0.008	0.007	11.493	-0.107	-0.107	0.000	0.000	0.000	0.000
18	B	18	ARG	1	0.885	0.938	6.059	0.606	0.606	0.000	0.000	0.000	0.000
19	B	19	ALA	0	0.091	0.050	8.717	0.133	0.133	0.000	0.000	0.000	0.000
20	B	20	ALA	0	-0.006	-0.025	5.516	-0.018	-0.018	0.000	0.000	0.000	0.000
21	B	21	TYR	0	0.028	0.020	5.524	-0.483	-0.483	0.000	0.000	0.000	0.000
22	B	22	LEU	0	-0.023	-0.008	2.220	0.244	0.014	2.326	-0.379	-1.717	0.000
23	B	23	LEU	0	0.019	0.009	5.481	0.398	0.398	0.000	0.000	0.000	0.000
24	B	24	LEU	0	0.007	0.002	5.512	0.121	0.121	0.000	0.000	0.000	0.000
25	B	25	GLY	0	0.033	-0.001	9.281	0.034	0.034	0.000	0.000	0.000	0.000
26	B	26	ASN	0	-0.026	-0.033	12.664	-0.019	-0.019	0.000	0.000	0.000	0.000
27	B	27	ASP	-1	-0.847	-0.910	15.703	-0.014	-0.014	0.000	0.000	0.000	0.000
28	B	28	PRO	0	-0.006	-0.006	17.114	-0.024	-0.024	0.000	0.000	0.000	0.000
29	B	29	LEU	0	0.012	0.006	19.195	-0.022	-0.022	0.000	0.000	0.000	0.000
30	B	30	LEU	0	0.035	0.009	15.511	-0.028	-0.028	0.000	0.000	0.000	0.000
31	B	31	LEU	0	-0.016	0.010	12.513	-0.053	-0.053	0.000	0.000	0.000	0.000
32	B	32	GLN	0	-0.011	-0.005	14.506	-0.054	-0.054	0.000	0.000	0.000	0.000
33	B	33	GLU	-1	-0.847	-0.930	16.678	-0.151	-0.151	0.000	0.000	0.000	0.000
34	B	34	SER	0	-0.033	-0.041	11.943	-0.021	-0.021	0.000	0.000	0.000	0.000
35	B	35	GLN	0	0.004	-0.012	13.295	-0.080	-0.080	0.000	0.000	0.000	0.000
36	B	36	ASP	-1	-0.874	-0.924	14.145	-0.242	-0.242	0.000	0.000	0.000	0.000
37	B	37	ALA	0	0.008	0.011	14.925	0.019	0.019	0.000	0.000	0.000	0.000
38	B	38	VAL	0	0.001	-0.009	10.888	-0.002	-0.002	0.000	0.000	0.000	0.000
39	B	39	ARG	1	0.842	0.911	14.250	0.333	0.333	0.000	0.000	0.000	0.000
40	B	40	GLN	0	-0.069	-0.029	16.974	0.048	0.048	0.000	0.000	0.000	0.000
41	B	41	VAL	0	-0.013	-0.022	16.191	0.023	0.023	0.000	0.000	0.000	0.000
42	B	42	ALA	0	-0.007	0.017	15.780	0.005	0.005	0.000	0.000	0.000	0.000
43	B	43	ALA	0	-0.028	-0.012	17.510	0.022	0.022	0.000	0.000	0.000	0.000
44	B	44	ALA	0	-0.045	-0.008	20.566	0.022	0.022	0.000	0.000	0.000	0.000
45	B	45	GLN	0	-0.047	-0.032	18.525	0.003	0.003	0.000	0.000	0.000	0.000
46	B	46	GLY	0	0.049	0.010	20.748	-0.021	-0.021	0.000	0.000	0.000	0.000
47	B	47	PHE	0	-0.035	-0.009	15.991	0.008	0.008	0.000	0.000	0.000	0.000
48	B	48	GLU	-1	-0.921	-0.968	20.863	-0.175	-0.175	0.000	0.000	0.000	0.000
49	B	49	GLU	-1	-0.865	-0.904	22.306	-0.231	-0.231	0.000	0.000	0.000	0.000
50	B	50	HIS	0	-0.014	-0.008	19.004	-0.064	-0.064	0.000	0.000	0.000	0.000
51	B	51	HIS	0	0.006	-0.007	18.633	0.031	0.031	0.000	0.000	0.000	0.000
52	B	52	THR	0	-0.058	-0.056	17.366	-0.027	-0.027	0.000	0.000	0.000	0.000
53	B	53	PHE	0	0.051	0.036	17.116	0.023	0.023	0.000	0.000	0.000	0.000
54	B	54	SER	0	0.020	0.009	17.125	-0.024	-0.024	0.000	0.000	0.000	0.000
55	B	55	ILE	0	-0.035	-0.007	14.037	0.013	0.013	0.000	0.000	0.000	0.000
56	B	56	ASP	-1	-0.710	-0.849	17.305	-0.095	-0.095	0.000	0.000	0.000	0.000
57	B	57	PRO	0	-0.099	-0.053	20.025	-0.010	-0.010	0.000	0.000	0.000	0.000
58	B	58	ASN	0	-0.080	-0.052	22.511	0.011	0.011	0.000	0.000	0.000	0.000
59	B	59	THR	0	-0.034	-0.013	18.772	-0.009	-0.009	0.000	0.000	0.000	0.000
60	B	60	ASP	-1	-0.809	-0.902	22.005	-0.165	-0.165	0.000	0.000	0.000	0.000
61	B	61	TRP	0	0.048	-0.006	14.582	-0.033	-0.033	0.000	0.000	0.000	0.000
62	B	62	ASN	0	-0.050	-0.016	20.313	-0.026	-0.026	0.000	0.000	0.000	0.000
63	B	63	ALA	0	0.024	0.048	22.674	-0.012	-0.012	0.000	0.000	0.000	0.000
64	B	64	ILE	0	0.020	0.012	16.175	-0.015	-0.015	0.000	0.000	0.000	0.000
65	B	65	PHE	0	0.016	0.004	15.867	-0.019	-0.019	0.000	0.000	0.000	0.000
66	B	66	SER	0	-0.064	-0.062	19.136	-0.008	-0.008	0.000	0.000	0.000	0.000
67	B	67	LEU	0	0.029	0.012	19.809	0.011	0.011	0.000	0.000	0.000	0.000
68	B	68	CYS	0	-0.106	-0.048	16.449	-0.026	-0.026	0.000	0.000	0.000	0.000
69	B	69	GLN	0	0.002	-0.006	18.438	-0.004	-0.004	0.000	0.000	0.000	0.000
70	B	70	ALA	0	-0.038	0.017	21.384	0.020	0.020	0.000	0.000	0.000	0.000
71	B	71	MET	0	-0.003	-0.005	22.795	-0.016	-0.016	0.000	0.000	0.000	0.000
72	B	72	SER	0	0.018	-0.001	25.341	0.020	0.020	0.000	0.000	0.000	0.000
73	B	73	LEU	0	-0.022	-0.022	26.923	0.004	0.004	0.000	0.000	0.000	0.000
74	B	74	PHE	0	-0.026	-0.025	29.056	0.012	0.012	0.000	0.000	0.000	0.000
75	B	75	ALA	0	-0.033	-0.009	26.082	-0.002	-0.002	0.000	0.000	0.000	0.000
76	B	76	SER	0	0.018	0.045	24.504	-0.007	-0.007	0.000	0.000	0.000	0.000
77	B	77	ARG	1	0.851	0.926	18.679	0.324	0.324	0.000	0.000	0.000	0.000
78	B	78	GLN	0	0.053	0.003	18.612	-0.004	-0.004	0.000	0.000	0.000	0.000
79	B	79	THR	0	-0.021	-0.009	14.560	-0.071	-0.071	0.000	0.000	0.000	0.000
80	B	80	LEU	0	-0.004	-0.001	14.183	0.048	0.048	0.000	0.000	0.000	0.000
81	B	81	LEU	0	-0.011	0.005	12.807	-0.093	-0.093	0.000	0.000	0.000	0.000
82	B	82	LEU	0	-0.024	-0.026	11.638	0.041	0.041	0.000	0.000	0.000	0.000
83	B	83	LEU	0	-0.044	-0.037	12.800	-0.020	-0.020	0.000	0.000	0.000	0.000
84	B	84	LEU	0	-0.019	-0.012	9.457	0.026	0.026	0.000	0.000	0.000	0.000
85	B	85	PRO	0	0.030	0.018	13.631	0.018	0.018	0.000	0.000	0.000	0.000
86	B	86	GLU	-1	-0.870	-0.934	14.779	-0.032	-0.032	0.000	0.000	0.000	0.000
87	B	87	ASN	0	-0.083	-0.026	16.640	0.022	0.022	0.000	0.000	0.000	0.000
88	B	88	GLY	0	-0.028	-0.006	12.367	0.032	0.032	0.000	0.000	0.000	0.000
89	B	89	PRO	0	-0.014	-0.005	10.437	-0.026	-0.026	0.000	0.000	0.000	0.000
90	B	90	ASN	0	0.062	0.023	13.215	0.050	0.050	0.000	0.000	0.000	0.000
91	B	91	ALA	0	-0.016	-0.025	16.013	-0.008	-0.008	0.000	0.000	0.000	0.000
92	B	92	ALA	0	0.100	0.049	17.428	0.008	0.008	0.000	0.000	0.000	0.000
93	B	93	ILE	0	-0.011	0.019	12.819	-0.022	-0.022	0.000	0.000	0.000	0.000
94	B	94	ASN	0	0.021	-0.014	11.954	-0.059	-0.059	0.000	0.000	0.000	0.000
95	B	95	GLU	-1	-0.915	-0.960	13.111	-0.127	-0.127	0.000	0.000	0.000	0.000
96	B	96	GLN	0	0.038	0.026	14.993	-0.041	-0.041	0.000	0.000	0.000	0.000
97	B	97	LEU	0	0.064	0.031	9.056	-0.043	-0.043	0.000	0.000	0.000	0.000
98	B	98	LEU	0	-0.013	-0.006	10.844	-0.119	-0.119	0.000	0.000	0.000	0.000
99	B	99	THR	0	-0.012	-0.015	12.172	-0.031	-0.031	0.000	0.000	0.000	0.000
100	B	100	LEU	0	0.001	-0.010	11.785	-0.012	-0.012	0.000	0.000	0.000	0.000
101	B	101	THR	0	-0.144	-0.072	7.704	-0.050	-0.050	0.000	0.000	0.000	0.000
102	B	102	GLY	0	-0.030	-0.016	10.403	-0.056	-0.056	0.000	0.000	0.000	0.000
103	B	103	LEU	0	-0.055	-0.028	13.633	0.026	0.026	0.000	0.000	0.000	0.000
104	B	104	LEU	0	-0.045	-0.009	9.122	0.000	0.000	0.000	0.000	0.000	0.000
105	B	105	HIS	0	0.015	0.006	13.213	0.003	0.003	0.000	0.000	0.000	0.000
106	B	106	ASP	-1	-0.877	-0.968	14.098	-0.634	-0.634	0.000	0.000	0.000	0.000
107	B	107	ASP	-1	-0.861	-0.885	15.832	-0.331	-0.331	0.000	0.000	0.000	0.000
108	B	108	LEU	0	-0.058	-0.019	14.025	0.004	0.004	0.000	0.000	0.000	0.000
109	B	109	LEU	0	-0.005	0.005	10.678	-0.112	-0.112	0.000	0.000	0.000	0.000
110	B	110	LEU	0	-0.029	-0.012	7.942	0.040	0.040	0.000	0.000	0.000	0.000
111	B	111	ILE	0	-0.016	-0.014	9.071	-0.198	-0.198	0.000	0.000	0.000	0.000
112	B	112	VAL	0	-0.001	0.006	7.258	0.150	0.150	0.000	0.000	0.000	0.000
113	B	113	ARG	1	0.895	0.945	9.066	0.171	0.171	0.000	0.000	0.000	0.000
114	B	114	GLY	0	0.055	0.027	10.868	0.016	0.016	0.000	0.000	0.000	0.000
115	B	115	ASN	0	-0.028	-0.047	12.386	-0.006	-0.006	0.000	0.000	0.000	0.000
116	B	116	LYS	1	0.809	0.919	9.871	-0.852	-0.852	0.000	0.000	0.000	0.000
117	B	117	LEU	0	0.026	0.020	5.126	-0.104	-0.104	0.000	0.000	0.000	0.000
118	B	118	SER	0	0.052	0.007	9.177	0.039	0.039	0.000	0.000	0.000	0.000
119	B	119	LYS	1	0.917	0.949	11.657	-0.234	-0.234	0.000	0.000	0.000	0.000
120	B	120	ALA	0	0.072	0.045	12.192	0.093	0.093	0.000	0.000	0.000	0.000
121	B	121	GLN	0	0.022	-0.005	11.879	0.015	0.015	0.000	0.000	0.000	0.000
122	B	122	GLU	-1	-0.909	-0.955	7.014	1.633	1.633	0.000	0.000	0.000	0.000
123	B	123	ASN	0	-0.014	-0.009	7.699	-0.019	-0.019	0.000	0.000	0.000	0.000
124	B	124	ALA	0	-0.006	0.023	9.498	-0.099	-0.099	0.000	0.000	0.000	0.000
125	B	125	ALA	0	0.047	0.004	9.308	-0.012	-0.012	0.000	0.000	0.000	0.000
126	B	126	TRP	0	0.000	0.016	5.513	-0.057	-0.057	0.000	0.000	0.000	0.000
127	B	127	PHE	0	0.011	0.003	2.335	-2.044	-1.554	3.471	-0.754	-3.206	-0.008
128	B	128	THR	0	-0.029	-0.016	4.396	-0.235	-0.115	-0.001	-0.009	-0.110	0.000
129	B	129	ALA	0	-0.001	0.010	6.497	-0.233	-0.233	0.000	0.000	0.000	0.000
130	B	130	LEU	0	-0.030	-0.018	3.451	-0.450	-0.118	0.015	-0.051	-0.297	0.000
131	B	131	ALA	0	0.006	0.006	2.490	-2.882	-1.322	0.950	-0.827	-1.684	0.000
132	B	132	ASN	0	-0.016	-0.020	2.279	-6.065	-5.970	7.299	-2.476	-4.919	-0.041
133	B	133	ARG	1	0.875	0.943	3.413	2.491	2.978	0.004	-0.040	-0.450	-0.001
134	B	134	SER	0	-0.041	-0.011	2.677	-1.703	-0.399	1.803	-1.085	-2.022	-0.011
135	B	135	VAL	0	0.020	0.009	2.759	-3.935	-1.564	0.772	-1.239	-1.904	-0.012
136	B	136	GLN	0	0.031	0.019	2.646	2.271	4.066	1.713	-0.729	-2.778	-0.004
137	B	137	VAL	0	0.021	0.016	4.266	0.172	0.323	0.001	-0.042	-0.110	0.000
138	B	138	THR	0	-0.033	-0.022	8.012	0.227	0.227	0.000	0.000	0.000	0.000
139	B	139	CYS	0	-0.021	-0.003	10.141	-0.063	-0.063	0.000	0.000	0.000	0.000
140	B	140	GLN	0	0.035	0.039	12.553	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)