FMO DATABASE

FMODB ID: LJVG9

Calculation Name: 3E0J-B-Xray372

Preferred Name: DNA polymerase (alpha/delta/epsilon)

Target Type: PROTEIN FAMILY

Ligand Name:

ligand 3-letter code:

PDB ID: 3E0J

Chain ID: B

ChEMBL ID: CHEMBL2363042

UniProt ID: P49005

Base Structure: X-ray

Registration Date: 2023-03-14

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	143
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1257730.798267
FMO2-HF: Nuclear repulsion	1201234.096317
FMO2-HF: Total energy	-56496.70195
FMO2-MP2: Total energy	-56661.265709

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:2:ALA)

Summations of interaction energy for fragment #1(B:2:ALA)

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.
0.55	4.105	0.041	-1.5	-2.096	0.003

Interaction energy analysis for fragmet #1(B:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.040 / q_NPA : 0.010

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	4	GLN	0	-0.036	-0.027	3.809	-1.182	1.038	-0.006	-1.035	-1.179	0.004
4	B	5	LEU	0	0.015	0.029	2.905	0.112	1.232	0.048	-0.442	-0.726	-0.001
5	B	6	TYR	0	-0.017	-0.039	4.591	1.104	1.319	-0.001	-0.023	-0.191	0.000
6	B	7	LEU	0	-0.055	-0.025	7.174	0.682	0.682	0.000	0.000	0.000	0.000
7	B	8	GLU	-1	-0.904	-0.941	8.127	-1.116	-1.116	0.000	0.000	0.000	0.000
8	B	9	ASN	0	-0.038	-0.015	8.362	0.108	0.108	0.000	0.000	0.000	0.000
9	B	10	ILE	0	-0.018	-0.017	10.793	0.217	0.217	0.000	0.000	0.000	0.000
10	B	11	ASP	-1	-0.766	-0.851	12.662	-0.465	-0.465	0.000	0.000	0.000	0.000
11	B	12	GLU	-1	-0.847	-0.934	11.671	-0.624	-0.624	0.000	0.000	0.000	0.000
12	B	13	PHE	0	-0.060	-0.035	13.610	0.090	0.090	0.000	0.000	0.000	0.000
13	B	14	VAL	0	-0.010	-0.017	17.139	0.076	0.076	0.000	0.000	0.000	0.000
14	B	15	THR	0	-0.041	-0.036	17.595	0.063	0.063	0.000	0.000	0.000	0.000
15	B	16	ASP	-1	-0.877	-0.924	17.882	-0.338	-0.338	0.000	0.000	0.000	0.000
16	B	17	GLN	0	-0.036	-0.019	16.872	0.078	0.078	0.000	0.000	0.000	0.000
17	B	18	ASN	0	-0.066	0.000	21.119	0.040	0.040	0.000	0.000	0.000	0.000
18	B	19	LYS	1	0.885	0.943	19.976	0.302	0.302	0.000	0.000	0.000	0.000
19	B	20	ILE	0	-0.050	-0.028	21.597	-0.021	-0.021	0.000	0.000	0.000	0.000
20	B	21	VAL	0	0.035	0.016	16.505	0.010	0.010	0.000	0.000	0.000	0.000
21	B	22	THR	0	-0.012	-0.043	19.892	-0.010	-0.010	0.000	0.000	0.000	0.000
22	B	23	TYR	0	0.015	0.000	17.578	-0.009	-0.009	0.000	0.000	0.000	0.000
23	B	24	LYS	1	0.958	0.991	17.690	0.120	0.120	0.000	0.000	0.000	0.000
24	B	25	TRP	0	0.075	0.034	16.644	0.000	0.000	0.000	0.000	0.000	0.000
25	B	26	LEU	0	0.025	0.027	12.391	0.006	0.006	0.000	0.000	0.000	0.000
26	B	27	SER	0	-0.111	-0.058	14.527	-0.010	-0.010	0.000	0.000	0.000	0.000
27	B	28	TYR	0	-0.052	-0.048	15.219	0.013	0.013	0.000	0.000	0.000	0.000
28	B	29	THR	0	-0.053	-0.023	14.580	0.027	0.027	0.000	0.000	0.000	0.000
29	B	30	LEU	0	-0.012	-0.009	9.452	0.002	0.002	0.000	0.000	0.000	0.000
30	B	31	GLY	0	-0.016	-0.001	11.289	0.031	0.031	0.000	0.000	0.000	0.000
31	B	32	VAL	0	-0.026	-0.023	9.664	0.038	0.038	0.000	0.000	0.000	0.000
32	B	33	HIS	0	0.047	0.040	12.749	-0.017	-0.017	0.000	0.000	0.000	0.000
33	B	34	VAL	0	0.036	0.012	14.759	-0.050	-0.050	0.000	0.000	0.000	0.000
34	B	35	ASN	0	0.009	-0.020	16.418	-0.033	-0.033	0.000	0.000	0.000	0.000
35	B	36	GLN	0	0.056	0.033	8.064	0.002	0.002	0.000	0.000	0.000	0.000
36	B	37	ALA	0	0.049	0.029	12.034	-0.096	-0.096	0.000	0.000	0.000	0.000
37	B	38	LYS	1	0.854	0.933	13.931	0.139	0.139	0.000	0.000	0.000	0.000
38	B	39	GLN	0	-0.046	-0.032	12.343	-0.019	-0.019	0.000	0.000	0.000	0.000
39	B	40	MET	0	0.003	0.022	7.546	-0.005	-0.005	0.000	0.000	0.000	0.000
40	B	41	LEU	0	-0.033	-0.010	11.888	-0.041	-0.041	0.000	0.000	0.000	0.000
41	B	42	TYR	0	-0.075	-0.068	14.929	0.011	0.011	0.000	0.000	0.000	0.000
42	B	43	ASP	-1	-0.738	-0.839	10.036	-1.037	-1.037	0.000	0.000	0.000	0.000
43	B	44	TYR	0	-0.002	-0.033	12.681	0.047	0.047	0.000	0.000	0.000	0.000
44	B	45	VAL	0	-0.024	-0.013	13.828	0.046	0.046	0.000	0.000	0.000	0.000
45	B	46	GLU	-1	-0.805	-0.878	15.969	-0.316	-0.316	0.000	0.000	0.000	0.000
46	B	47	ARG	1	0.767	0.873	8.017	1.296	1.296	0.000	0.000	0.000	0.000
47	B	48	LYS	1	0.880	0.924	15.548	0.633	0.633	0.000	0.000	0.000	0.000
48	B	49	ARG	1	0.733	0.819	17.639	0.336	0.336	0.000	0.000	0.000	0.000
49	B	50	LYS	1	0.855	0.930	16.461	0.404	0.404	0.000	0.000	0.000	0.000
50	B	51	GLU	-1	-0.895	-0.935	16.349	-0.500	-0.500	0.000	0.000	0.000	0.000
51	B	52	ASN	0	-0.013	-0.015	19.109	0.049	0.049	0.000	0.000	0.000	0.000
52	B	53	SER	0	-0.015	0.004	22.241	0.030	0.030	0.000	0.000	0.000	0.000
53	B	54	GLY	0	-0.026	-0.022	24.269	0.023	0.023	0.000	0.000	0.000	0.000
54	B	55	ALA	0	0.016	0.033	21.926	0.008	0.008	0.000	0.000	0.000	0.000
55	B	56	GLN	0	-0.036	-0.029	23.826	-0.003	-0.003	0.000	0.000	0.000	0.000
56	B	57	LEU	0	-0.012	0.004	19.243	-0.013	-0.013	0.000	0.000	0.000	0.000
57	B	58	HIS	0	-0.039	-0.023	23.605	0.030	0.030	0.000	0.000	0.000	0.000
58	B	59	VAL	0	0.023	0.024	21.644	-0.016	-0.016	0.000	0.000	0.000	0.000
59	B	60	THR	0	-0.061	-0.051	23.816	0.029	0.029	0.000	0.000	0.000	0.000
60	B	61	TYR	0	0.046	0.013	22.038	-0.022	-0.022	0.000	0.000	0.000	0.000
61	B	62	LEU	0	-0.022	0.004	24.687	0.015	0.015	0.000	0.000	0.000	0.000
62	B	63	VAL	0	0.008	-0.009	26.068	-0.003	-0.003	0.000	0.000	0.000	0.000
63	B	64	SER	0	-0.010	-0.015	28.403	0.009	0.009	0.000	0.000	0.000	0.000
64	B	65	GLY	0	0.048	0.029	30.516	-0.001	-0.001	0.000	0.000	0.000	0.000
65	B	66	SER	0	-0.021	0.021	33.240	0.002	0.002	0.000	0.000	0.000	0.000
66	B	67	LEU	0	0.031	0.003	36.858	-0.003	-0.003	0.000	0.000	0.000	0.000
67	B	68	ILE	0	-0.016	-0.004	39.523	0.002	0.002	0.000	0.000	0.000	0.000
68	B	69	GLN	0	-0.019	0.009	43.084	-0.005	-0.005	0.000	0.000	0.000	0.000
69	B	70	ASN	0	0.041	-0.001	45.858	0.000	0.000	0.000	0.000	0.000	0.000
70	B	71	GLY	0	0.020	0.047	48.209	0.002	0.002	0.000	0.000	0.000	0.000
71	B	72	HIS	0	0.035	-0.006	46.544	-0.001	-0.001	0.000	0.000	0.000	0.000
72	B	73	SER	0	0.006	-0.010	40.588	-0.004	-0.004	0.000	0.000	0.000	0.000
73	B	74	CYS	0	0.016	0.038	39.373	0.001	0.001	0.000	0.000	0.000	0.000
74	B	75	HIS	0	0.047	0.028	31.881	0.001	0.001	0.000	0.000	0.000	0.000
75	B	76	LYS	1	0.834	0.886	35.381	0.064	0.064	0.000	0.000	0.000	0.000
76	B	77	VAL	0	0.032	0.003	29.854	-0.004	-0.004	0.000	0.000	0.000	0.000
77	B	78	ALA	0	-0.015	-0.007	31.173	0.003	0.003	0.000	0.000	0.000	0.000
78	B	79	VAL	0	0.024	0.030	27.261	-0.006	-0.006	0.000	0.000	0.000	0.000
79	B	80	VAL	0	-0.048	-0.024	28.878	0.008	0.008	0.000	0.000	0.000	0.000
80	B	81	ARG	1	0.899	0.934	28.557	0.122	0.122	0.000	0.000	0.000	0.000
81	B	82	GLU	-1	-0.744	-0.855	24.867	-0.240	-0.240	0.000	0.000	0.000	0.000
82	B	83	ASP	-1	-0.807	-0.898	28.292	-0.130	-0.130	0.000	0.000	0.000	0.000
83	B	84	LYS	1	0.849	0.898	31.530	0.119	0.119	0.000	0.000	0.000	0.000
84	B	85	LEU	0	0.021	0.035	26.296	0.010	0.010	0.000	0.000	0.000	0.000
85	B	86	GLU	-1	-0.768	-0.876	29.162	-0.129	-0.129	0.000	0.000	0.000	0.000
86	B	87	ALA	0	0.007	0.009	32.274	0.008	0.008	0.000	0.000	0.000	0.000
87	B	88	VAL	0	-0.043	-0.018	32.892	0.007	0.007	0.000	0.000	0.000	0.000
88	B	89	LYS	1	0.852	0.901	28.434	0.138	0.138	0.000	0.000	0.000	0.000
89	B	90	SER	0	-0.058	-0.034	32.750	0.007	0.007	0.000	0.000	0.000	0.000
90	B	91	LYS	1	0.923	0.958	35.958	0.087	0.087	0.000	0.000	0.000	0.000
91	B	92	LEU	0	-0.062	-0.014	32.658	0.004	0.004	0.000	0.000	0.000	0.000
92	B	93	ALA	0	-0.003	0.010	36.683	0.001	0.001	0.000	0.000	0.000	0.000
93	B	94	VAL	0	0.041	0.012	33.599	0.000	0.000	0.000	0.000	0.000	0.000
94	B	95	THR	0	-0.004	-0.009	29.501	-0.002	-0.002	0.000	0.000	0.000	0.000
95	B	96	ALA	0	-0.010	-0.006	29.483	0.002	0.002	0.000	0.000	0.000	0.000
96	B	97	SER	0	-0.074	-0.044	25.065	-0.002	-0.002	0.000	0.000	0.000	0.000
97	B	98	ILE	0	0.046	0.014	24.011	0.002	0.002	0.000	0.000	0.000	0.000
98	B	99	HIS	0	-0.026	-0.013	19.927	0.010	0.010	0.000	0.000	0.000	0.000
99	B	100	VAL	0	0.056	0.036	18.643	0.019	0.019	0.000	0.000	0.000	0.000
100	B	101	TYR	0	-0.089	-0.031	20.930	0.012	0.012	0.000	0.000	0.000	0.000
101	B	102	SER	0	-0.006	-0.033	21.282	0.000	0.000	0.000	0.000	0.000	0.000
102	B	103	ILE	0	0.044	0.048	17.132	0.003	0.003	0.000	0.000	0.000	0.000
103	B	104	GLN	0	0.054	0.037	21.271	-0.008	-0.008	0.000	0.000	0.000	0.000
104	B	105	LYS	1	0.951	0.988	22.894	0.260	0.260	0.000	0.000	0.000	0.000
105	B	106	ALA	0	0.001	0.007	24.281	0.014	0.014	0.000	0.000	0.000	0.000
106	B	107	MET	0	-0.029	-0.007	27.892	0.001	0.001	0.000	0.000	0.000	0.000
107	B	108	LEU	0	0.015	0.015	27.227	0.006	0.006	0.000	0.000	0.000	0.000
108	B	109	LYS	1	0.972	0.977	31.136	0.113	0.113	0.000	0.000	0.000	0.000
109	B	110	ASP	-1	-0.822	-0.912	34.272	-0.111	-0.111	0.000	0.000	0.000	0.000
110	B	111	SER	0	0.031	0.000	31.035	-0.006	-0.006	0.000	0.000	0.000	0.000
111	B	112	GLY	0	0.048	0.034	30.898	-0.005	-0.005	0.000	0.000	0.000	0.000
112	B	113	PRO	0	0.037	0.020	29.003	-0.002	-0.002	0.000	0.000	0.000	0.000
113	B	114	LEU	0	-0.006	-0.004	25.615	-0.007	-0.007	0.000	0.000	0.000	0.000
114	B	115	PHE	0	-0.053	-0.007	27.239	-0.002	-0.002	0.000	0.000	0.000	0.000
115	B	116	ASN	0	0.032	0.005	28.413	-0.002	-0.002	0.000	0.000	0.000	0.000
116	B	117	THR	0	0.011	0.009	23.477	0.000	0.000	0.000	0.000	0.000	0.000
117	B	118	ASP	-1	-0.777	-0.874	23.636	-0.187	-0.187	0.000	0.000	0.000	0.000
118	B	119	TYR	0	-0.069	-0.047	25.449	0.009	0.009	0.000	0.000	0.000	0.000
119	B	120	ASP	-1	-0.829	-0.924	26.973	-0.106	-0.106	0.000	0.000	0.000	0.000
120	B	121	ILE	0	-0.002	0.005	20.360	0.009	0.009	0.000	0.000	0.000	0.000
121	B	122	LEU	0	0.001	0.010	24.050	0.008	0.008	0.000	0.000	0.000	0.000
122	B	123	LYS	1	0.844	0.927	26.021	0.104	0.104	0.000	0.000	0.000	0.000
123	B	124	SER	0	-0.003	0.008	24.471	0.007	0.007	0.000	0.000	0.000	0.000
124	B	125	ASN	0	-0.048	-0.041	21.214	0.014	0.014	0.000	0.000	0.000	0.000
125	B	126	LEU	0	-0.074	-0.030	24.589	0.008	0.008	0.000	0.000	0.000	0.000
126	B	127	GLN	0	-0.006	0.007	25.639	0.008	0.008	0.000	0.000	0.000	0.000
127	B	128	ASN	0	-0.029	-0.032	23.244	0.004	0.004	0.000	0.000	0.000	0.000
128	B	129	CYS	0	0.039	0.034	23.303	-0.007	-0.007	0.000	0.000	0.000	0.000
129	B	130	SER	0	0.015	-0.003	23.553	-0.015	-0.015	0.000	0.000	0.000	0.000
130	B	131	LYS	1	0.956	1.009	17.496	0.039	0.039	0.000	0.000	0.000	0.000
131	B	132	PHE	0	0.047	0.022	15.258	0.012	0.012	0.000	0.000	0.000	0.000
132	B	133	SER	0	0.026	0.023	19.016	-0.021	-0.021	0.000	0.000	0.000	0.000
133	B	134	ALA	0	-0.026	-0.015	20.539	0.008	0.008	0.000	0.000	0.000	0.000
134	B	135	ILE	0	-0.018	-0.020	21.442	0.011	0.011	0.000	0.000	0.000	0.000
135	B	136	GLN	0	-0.004	-0.001	21.891	0.003	0.003	0.000	0.000	0.000	0.000
136	B	137	CYS	0	-0.031	-0.014	25.755	0.004	0.004	0.000	0.000	0.000	0.000
137	B	138	ALA	0	0.043	0.022	29.478	0.001	0.001	0.000	0.000	0.000	0.000
138	B	139	ALA	0	0.013	-0.004	31.138	0.002	0.002	0.000	0.000	0.000	0.000
139	B	140	ALA	0	-0.012	0.003	30.342	0.000	0.000	0.000	0.000	0.000	0.000
140	B	141	VAL	0	0.026	0.006	30.404	0.000	0.000	0.000	0.000	0.000	0.000
141	B	142	PRO	0	-0.049	-0.035	31.480	0.000	0.000	0.000	0.000	0.000	0.000
142	B	143	ARG	1	0.986	1.001	34.412	-0.003	-0.003	0.000	0.000	0.000	0.000
143	B	144	ALA	0	0.009	0.021	37.871	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:ALA)