FMO DATABASE

FMODB ID: 9Y5N2

Calculation Name: 3E0J-B-Xray312

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	144
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1262927.547175
FMO2-HF: Nuclear repulsion	1206281.012902
FMO2-HF: Total energy	-56646.534273
FMO2-MP2: Total energy	-56811.699811

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:ACE )

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

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.
1.554	2.548	-0.004	-0.377	-0.612	0

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : 0.000

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].
3	B	3	ASP	-1	-0.815	-0.916	3.846	0.152	1.011	-0.005	-0.352	-0.502
4	B	4	GLN	0	-0.039	-0.034	5.333	0.135	0.135	0.000	0.000	0.000
5	B	5	LEU	0	-0.003	0.017	3.935	0.040	0.175	0.001	-0.025	-0.110
6	B	6	TYR	0	0.003	0.009	5.837	0.135	0.135	0.000	0.000	0.000
7	B	7	LEU	0	-0.054	-0.024	8.825	0.109	0.109	0.000	0.000	0.000
8	B	8	GLU	-1	-0.892	-0.936	7.909	0.534	0.534	0.000	0.000	0.000
9	B	9	ASN	0	0.016	0.005	9.125	-0.097	-0.097	0.000	0.000	0.000
10	B	10	ILE	0	-0.022	-0.023	11.822	0.016	0.016	0.000	0.000	0.000
11	B	11	ASP	-1	-0.774	-0.863	13.791	0.050	0.050	0.000	0.000	0.000
12	B	12	GLU	-1	-0.872	-0.941	12.146	0.088	0.088	0.000	0.000	0.000
13	B	13	PHE	0	-0.063	-0.032	15.087	-0.003	-0.003	0.000	0.000	0.000
14	B	14	VAL	0	-0.014	-0.016	18.168	0.005	0.005	0.000	0.000	0.000
15	B	15	THR	0	-0.060	-0.050	18.437	0.009	0.009	0.000	0.000	0.000
16	B	16	ASP	-1	-0.886	-0.926	17.861	0.073	0.073	0.000	0.000	0.000
17	B	17	GLN	0	-0.074	-0.039	17.683	-0.007	-0.007	0.000	0.000	0.000
18	B	18	ASN	0	-0.076	-0.027	21.834	-0.005	-0.005	0.000	0.000	0.000
19	B	19	LYS	1	0.917	0.963	21.026	0.025	0.025	0.000	0.000	0.000
20	B	20	ILE	0	-0.042	-0.029	22.937	-0.003	-0.003	0.000	0.000	0.000
21	B	21	VAL	0	0.039	0.019	18.655	-0.006	-0.006	0.000	0.000	0.000
22	B	22	THR	0	-0.010	-0.036	21.939	-0.005	-0.005	0.000	0.000	0.000
23	B	23	TYR	0	0.017	0.008	20.686	-0.010	-0.010	0.000	0.000	0.000
24	B	24	LYS	1	0.971	0.987	20.866	0.076	0.076	0.000	0.000	0.000
25	B	25	TRP	0	0.047	0.027	18.254	-0.013	-0.013	0.000	0.000	0.000
26	B	26	LEU	0	0.020	0.011	15.260	0.000	0.000	0.000	0.000	0.000
27	B	27	SER	0	-0.112	-0.050	17.388	-0.017	-0.017	0.000	0.000	0.000
28	B	28	TYR	0	-0.028	-0.033	18.373	-0.014	-0.014	0.000	0.000	0.000
29	B	29	THR	0	-0.058	-0.010	16.146	0.001	0.001	0.000	0.000	0.000
30	B	30	LEU	0	-0.009	-0.012	12.183	0.006	0.006	0.000	0.000	0.000
31	B	31	GLY	0	-0.017	0.007	14.118	-0.044	-0.044	0.000	0.000	0.000
32	B	32	VAL	0	-0.012	-0.021	13.388	-0.041	-0.041	0.000	0.000	0.000
33	B	33	HIS	0	0.048	0.049	16.435	0.042	0.042	0.000	0.000	0.000
34	B	34	VAL	0	0.072	0.022	18.869	-0.006	-0.006	0.000	0.000	0.000
35	B	35	ASN	0	0.012	-0.029	21.109	0.018	0.018	0.000	0.000	0.000
36	B	36	GLN	0	0.035	0.032	13.302	0.016	0.016	0.000	0.000	0.000
37	B	37	ALA	0	0.052	0.031	16.259	-0.016	-0.016	0.000	0.000	0.000
38	B	38	LYS	1	0.837	0.921	17.586	0.155	0.155	0.000	0.000	0.000
39	B	39	GLN	0	-0.043	-0.032	17.016	-0.013	-0.013	0.000	0.000	0.000
40	B	40	MET	0	0.031	0.024	11.619	0.014	0.014	0.000	0.000	0.000
41	B	41	LEU	0	-0.025	-0.004	15.400	0.024	0.024	0.000	0.000	0.000
42	B	42	TYR	0	-0.028	-0.019	18.082	0.021	0.021	0.000	0.000	0.000
43	B	43	ASP	-1	-0.820	-0.923	13.420	-0.209	-0.209	0.000	0.000	0.000
44	B	44	TYR	0	0.013	-0.033	14.306	0.025	0.025	0.000	0.000	0.000
45	B	45	VAL	0	-0.040	-0.021	15.998	0.030	0.030	0.000	0.000	0.000
46	B	46	GLU	-1	-0.924	-0.962	18.499	-0.066	-0.066	0.000	0.000	0.000
47	B	47	ARG	1	0.871	0.954	10.781	0.163	0.163	0.000	0.000	0.000
48	B	48	LYS	1	0.937	0.975	17.258	-0.023	-0.023	0.000	0.000	0.000
49	B	49	ARG	1	0.755	0.855	19.003	0.044	0.044	0.000	0.000	0.000
50	B	50	LYS	1	0.907	0.959	18.832	0.057	0.057	0.000	0.000	0.000
51	B	51	GLU	-1	-0.955	-0.976	16.851	0.066	0.066	0.000	0.000	0.000
52	B	52	ASN	0	-0.011	-0.010	20.340	0.002	0.002	0.000	0.000	0.000
53	B	53	SER	0	-0.007	0.006	23.356	-0.001	-0.001	0.000	0.000	0.000
54	B	54	GLY	0	-0.019	-0.021	25.525	-0.004	-0.004	0.000	0.000	0.000
55	B	55	ALA	0	-0.014	0.017	22.919	0.004	0.004	0.000	0.000	0.000
56	B	56	GLN	0	-0.025	-0.021	24.858	-0.004	-0.004	0.000	0.000	0.000
57	B	57	LEU	0	-0.006	0.006	21.066	-0.002	-0.002	0.000	0.000	0.000
58	B	58	HIS	0	-0.019	-0.008	24.977	0.000	0.000	0.000	0.000	0.000
59	B	59	VAL	0	0.051	0.038	23.616	-0.005	-0.005	0.000	0.000	0.000
60	B	60	THR	0	-0.080	-0.088	26.298	0.004	0.004	0.000	0.000	0.000
61	B	61	TYR	0	0.045	0.016	25.809	-0.011	-0.011	0.000	0.000	0.000
62	B	62	LEU	0	-0.035	0.005	28.420	0.007	0.007	0.000	0.000	0.000
63	B	63	VAL	0	0.011	-0.015	30.179	-0.004	-0.004	0.000	0.000	0.000
64	B	64	SER	0	0.001	-0.011	32.942	0.003	0.003	0.000	0.000	0.000
65	B	65	GLY	0	0.054	0.034	35.078	-0.003	-0.003	0.000	0.000	0.000
66	B	66	SER	0	-0.034	0.018	37.971	0.002	0.002	0.000	0.000	0.000
67	B	67	LEU	0	0.055	0.011	41.676	0.000	0.000	0.000	0.000	0.000
68	B	68	ILE	0	-0.030	-0.010	44.104	0.001	0.001	0.000	0.000	0.000
69	B	69	GLN	0	-0.018	-0.006	47.288	0.000	0.000	0.000	0.000	0.000
70	B	70	ASN	0	0.055	0.002	50.311	0.001	0.001	0.000	0.000	0.000
71	B	71	GLY	0	0.018	0.044	52.977	0.000	0.000	0.000	0.000	0.000
72	B	72	HIS	0	-0.025	-0.019	50.829	-0.001	-0.001	0.000	0.000	0.000
73	B	73	SER	0	0.047	-0.002	45.624	0.000	0.000	0.000	0.000	0.000
74	B	74	CYS	0	-0.038	0.002	43.461	-0.001	-0.001	0.000	0.000	0.000
75	B	75	HIS	0	0.037	0.026	36.478	0.001	0.001	0.000	0.000	0.000
76	B	76	LYS	1	0.914	0.949	39.833	0.039	0.039	0.000	0.000	0.000
77	B	77	VAL	0	0.033	0.007	34.063	-0.003	-0.003	0.000	0.000	0.000
78	B	78	ALA	0	-0.022	-0.017	35.131	0.003	0.003	0.000	0.000	0.000
79	B	79	VAL	0	0.021	0.036	30.480	-0.004	-0.004	0.000	0.000	0.000
80	B	80	VAL	0	-0.050	-0.032	32.119	0.006	0.006	0.000	0.000	0.000
81	B	81	ARG	1	0.879	0.929	31.420	0.025	0.025	0.000	0.000	0.000
82	B	82	GLU	-1	-0.787	-0.901	27.630	-0.043	-0.043	0.000	0.000	0.000
83	B	83	ASP	-1	-0.830	-0.914	30.869	-0.030	-0.030	0.000	0.000	0.000
84	B	84	LYS	1	0.884	0.924	34.114	0.025	0.025	0.000	0.000	0.000
85	B	85	LEU	0	0.023	0.040	29.900	0.000	0.000	0.000	0.000	0.000
86	B	86	GLU	-1	-0.828	-0.932	32.912	-0.047	-0.047	0.000	0.000	0.000
87	B	87	ALA	0	-0.020	-0.003	35.851	0.001	0.001	0.000	0.000	0.000
88	B	88	VAL	0	-0.057	-0.008	36.526	0.001	0.001	0.000	0.000	0.000
89	B	89	LYS	1	0.960	0.980	32.224	0.055	0.055	0.000	0.000	0.000
90	B	90	SER	0	-0.077	-0.059	36.898	0.000	0.000	0.000	0.000	0.000
91	B	91	LYS	1	0.924	0.953	40.140	0.033	0.033	0.000	0.000	0.000
92	B	92	LEU	0	-0.069	-0.013	37.234	0.000	0.000	0.000	0.000	0.000
93	B	93	ALA	0	0.003	0.012	41.199	0.001	0.001	0.000	0.000	0.000
94	B	94	VAL	0	0.039	0.013	38.680	-0.001	-0.001	0.000	0.000	0.000
95	B	95	THR	0	-0.040	-0.024	34.446	-0.001	-0.001	0.000	0.000	0.000
96	B	96	ALA	0	0.010	-0.003	34.479	-0.002	-0.002	0.000	0.000	0.000
97	B	97	SER	0	-0.073	-0.045	29.966	-0.008	-0.008	0.000	0.000	0.000
98	B	98	ILE	0	0.059	0.024	27.817	0.007	0.007	0.000	0.000	0.000
99	B	99	HIS	0	-0.076	-0.043	24.186	-0.007	-0.007	0.000	0.000	0.000
100	B	100	VAL	0	0.069	0.042	21.673	0.009	0.009	0.000	0.000	0.000
101	B	101	TYR	0	-0.062	-0.009	24.395	-0.009	-0.009	0.000	0.000	0.000
102	B	102	SER	0	0.015	0.015	23.838	-0.005	-0.005	0.000	0.000	0.000
103	B	103	ILE	0	0.060	0.058	19.480	0.002	0.002	0.000	0.000	0.000
104	B	104	GLN	0	0.043	0.015	23.250	-0.005	-0.005	0.000	0.000	0.000
105	B	105	LYS	1	0.979	1.018	23.872	-0.014	-0.014	0.000	0.000	0.000
106	B	106	ALA	0	0.009	0.004	25.525	0.002	0.002	0.000	0.000	0.000
107	B	107	MET	0	-0.051	-0.020	29.237	-0.004	-0.004	0.000	0.000	0.000
108	B	108	LEU	0	0.008	0.012	29.144	0.001	0.001	0.000	0.000	0.000
109	B	109	LYS	1	0.981	0.982	32.827	0.013	0.013	0.000	0.000	0.000
110	B	110	ASP	-1	-0.813	-0.898	36.270	-0.028	-0.028	0.000	0.000	0.000
111	B	111	SER	0	-0.008	-0.021	33.414	0.000	0.000	0.000	0.000	0.000
112	B	112	GLY	0	0.105	0.046	33.359	-0.003	-0.003	0.000	0.000	0.000
113	B	113	PRO	0	-0.014	0.005	30.882	-0.003	-0.003	0.000	0.000	0.000
114	B	114	LEU	0	-0.002	-0.012	28.074	-0.003	-0.003	0.000	0.000	0.000
115	B	115	PHE	0	-0.055	-0.006	29.874	-0.006	-0.006	0.000	0.000	0.000
116	B	116	ASN	0	0.059	0.014	30.939	-0.006	-0.006	0.000	0.000	0.000
117	B	117	THR	0	0.002	0.007	25.576	0.000	0.000	0.000	0.000	0.000
118	B	118	ASP	-1	-0.803	-0.894	26.237	-0.087	-0.087	0.000	0.000	0.000
119	B	119	TYR	0	-0.066	-0.040	28.093	-0.002	-0.002	0.000	0.000	0.000
120	B	120	ASP	-1	-0.895	-0.964	28.923	-0.040	-0.040	0.000	0.000	0.000
121	B	121	ILE	0	-0.007	-0.005	22.612	-0.001	-0.001	0.000	0.000	0.000
122	B	122	LEU	0	-0.007	0.011	26.451	-0.006	-0.006	0.000	0.000	0.000
123	B	123	LYS	1	0.923	0.969	28.705	0.038	0.038	0.000	0.000	0.000
124	B	124	SER	0	-0.004	0.007	26.596	0.003	0.003	0.000	0.000	0.000
125	B	125	ASN	0	-0.047	-0.032	23.607	-0.006	-0.006	0.000	0.000	0.000
126	B	126	LEU	0	-0.079	-0.033	27.172	-0.004	-0.004	0.000	0.000	0.000
127	B	127	GLN	0	0.034	0.029	28.219	0.005	0.005	0.000	0.000	0.000
128	B	128	ASN	0	-0.049	-0.040	26.236	0.001	0.001	0.000	0.000	0.000
129	B	129	CYS	0	0.031	0.016	26.557	-0.010	-0.010	0.000	0.000	0.000
130	B	130	SER	0	0.010	-0.006	27.082	-0.007	-0.007	0.000	0.000	0.000
131	B	131	LYS	1	0.957	1.012	20.944	0.156	0.156	0.000	0.000	0.000
132	B	132	PHE	0	0.049	0.020	18.634	-0.010	-0.010	0.000	0.000	0.000
133	B	133	SER	0	0.035	0.036	22.823	-0.007	-0.007	0.000	0.000	0.000
134	B	134	ALA	0	-0.018	-0.012	25.050	-0.010	-0.010	0.000	0.000	0.000
135	B	135	ILE	0	-0.044	-0.035	26.115	0.004	0.004	0.000	0.000	0.000
136	B	136	GLN	0	-0.019	-0.011	26.834	0.007	0.007	0.000	0.000	0.000
137	B	137	CYS	0	-0.030	-0.013	30.049	0.005	0.005	0.000	0.000	0.000
138	B	138	ALA	0	0.040	0.020	33.686	0.001	0.001	0.000	0.000	0.000
139	B	139	ALA	0	0.017	-0.005	35.193	0.002	0.002	0.000	0.000	0.000
140	B	140	ALA	0	-0.017	0.004	34.102	0.003	0.003	0.000	0.000	0.000
141	B	141	VAL	0	0.012	-0.003	34.066	-0.005	-0.005	0.000	0.000	0.000
142	B	142	PRO	0	-0.060	-0.039	34.745	0.004	0.004	0.000	0.000	0.000
143	B	143	ARG	1	0.949	0.980	37.723	0.049	0.049	0.000	0.000	0.000
144	B	144	ALA	-1	-0.923	-0.943	41.200	-0.040	-0.040	0.000	0.000	0.000

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