FMO DATABASE

FMODB ID: 9GR72

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1259196.243047
FMO2-HF: Nuclear repulsion	1202698.701491
FMO2-HF: Total energy	-56497.541555
FMO2-MP2: Total energy	-56661.990607

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.
2.107	4.858	0.007	-1.102	-1.657	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 : 0.033 / q_NPA : 0.013

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	-0.028	-0.030	3.534	-0.266	1.700	-0.001	-0.920	-1.045	0.003
4	B	5	LEU	0	0.046	0.051	3.292	0.676	1.280	0.009	-0.164	-0.450	0.000
5	B	6	TYR	0	-0.005	-0.035	4.886	0.879	1.060	-0.001	-0.018	-0.162	0.000
6	B	7	LEU	0	-0.061	-0.026	7.221	0.705	0.705	0.000	0.000	0.000	0.000
7	B	8	GLU	-1	-0.898	-0.948	7.069	-1.202	-1.202	0.000	0.000	0.000	0.000
8	B	9	ASN	0	-0.030	-0.026	8.865	0.123	0.123	0.000	0.000	0.000	0.000
9	B	10	ILE	0	-0.046	-0.026	11.044	0.216	0.216	0.000	0.000	0.000	0.000
10	B	11	ASP	-1	-0.722	-0.816	12.628	-0.514	-0.514	0.000	0.000	0.000	0.000
11	B	12	GLU	-1	-0.842	-0.907	11.786	-0.563	-0.563	0.000	0.000	0.000	0.000
12	B	13	PHE	0	-0.064	-0.043	13.405	0.093	0.093	0.000	0.000	0.000	0.000
13	B	14	VAL	0	-0.007	-0.004	16.955	0.073	0.073	0.000	0.000	0.000	0.000
14	B	15	THR	0	-0.061	-0.073	17.100	0.064	0.064	0.000	0.000	0.000	0.000
15	B	16	ASP	-1	-0.854	-0.913	17.676	-0.319	-0.319	0.000	0.000	0.000	0.000
16	B	17	GLN	0	-0.029	-0.017	16.705	0.068	0.068	0.000	0.000	0.000	0.000
17	B	18	ASN	0	-0.086	-0.023	20.978	0.035	0.035	0.000	0.000	0.000	0.000
18	B	19	LYS	1	0.895	0.952	19.776	0.324	0.324	0.000	0.000	0.000	0.000
19	B	20	ILE	0	-0.037	-0.017	21.870	-0.018	-0.018	0.000	0.000	0.000	0.000
20	B	21	VAL	0	0.018	0.013	16.412	0.004	0.004	0.000	0.000	0.000	0.000
21	B	22	THR	0	-0.018	-0.046	19.797	-0.017	-0.017	0.000	0.000	0.000	0.000
22	B	23	TYR	0	0.012	-0.007	17.590	-0.025	-0.025	0.000	0.000	0.000	0.000
23	B	24	LYS	1	0.857	0.935	17.709	0.151	0.151	0.000	0.000	0.000	0.000
24	B	25	TRP	0	0.028	0.010	16.695	0.003	0.003	0.000	0.000	0.000	0.000
25	B	26	LEU	0	0.029	0.027	12.409	0.012	0.012	0.000	0.000	0.000	0.000
26	B	27	SER	0	-0.081	-0.044	14.627	-0.012	-0.012	0.000	0.000	0.000	0.000
27	B	28	TYR	0	-0.050	-0.057	15.513	0.012	0.012	0.000	0.000	0.000	0.000
28	B	29	THR	0	-0.055	-0.031	15.103	0.032	0.032	0.000	0.000	0.000	0.000
29	B	30	LEU	0	-0.001	-0.004	9.572	-0.002	-0.002	0.000	0.000	0.000	0.000
30	B	31	GLY	0	-0.024	0.003	11.466	0.014	0.014	0.000	0.000	0.000	0.000
31	B	32	VAL	0	-0.015	-0.008	10.020	0.039	0.039	0.000	0.000	0.000	0.000
32	B	33	HIS	0	0.043	0.024	12.830	0.005	0.005	0.000	0.000	0.000	0.000
33	B	34	VAL	0	0.015	0.004	14.671	-0.057	-0.057	0.000	0.000	0.000	0.000
34	B	35	ASN	0	0.021	-0.015	16.539	-0.022	-0.022	0.000	0.000	0.000	0.000
35	B	36	GLN	0	0.044	0.027	8.375	0.005	0.005	0.000	0.000	0.000	0.000
36	B	37	ALA	0	0.047	0.024	11.967	-0.110	-0.110	0.000	0.000	0.000	0.000
37	B	38	LYS	1	0.837	0.921	13.749	0.201	0.201	0.000	0.000	0.000	0.000
38	B	39	GLN	0	-0.017	-0.006	11.980	-0.019	-0.019	0.000	0.000	0.000	0.000
39	B	40	MET	0	0.002	0.024	7.267	0.003	0.003	0.000	0.000	0.000	0.000
40	B	41	LEU	0	-0.011	-0.001	11.346	-0.041	-0.041	0.000	0.000	0.000	0.000
41	B	42	TYR	0	-0.085	-0.069	14.908	0.027	0.027	0.000	0.000	0.000	0.000
42	B	43	ASP	-1	-0.749	-0.832	9.336	-1.291	-1.291	0.000	0.000	0.000	0.000
43	B	44	TYR	0	0.003	-0.027	12.485	0.065	0.065	0.000	0.000	0.000	0.000
44	B	45	VAL	0	-0.017	-0.012	13.598	0.066	0.066	0.000	0.000	0.000	0.000
45	B	46	GLU	-1	-0.827	-0.891	15.459	-0.344	-0.344	0.000	0.000	0.000	0.000
46	B	47	ARG	1	0.724	0.837	7.320	1.617	1.617	0.000	0.000	0.000	0.000
47	B	48	LYS	1	0.820	0.882	14.552	0.654	0.654	0.000	0.000	0.000	0.000
48	B	49	ARG	1	0.760	0.832	16.853	0.366	0.366	0.000	0.000	0.000	0.000
49	B	50	LYS	1	0.872	0.927	16.040	0.454	0.454	0.000	0.000	0.000	0.000
50	B	51	GLU	-1	-0.889	-0.914	15.633	-0.504	-0.504	0.000	0.000	0.000	0.000
51	B	52	ASN	0	0.009	-0.009	18.129	0.048	0.048	0.000	0.000	0.000	0.000
52	B	53	SER	0	-0.018	-0.004	21.609	0.033	0.033	0.000	0.000	0.000	0.000
53	B	54	GLY	0	-0.035	-0.014	23.893	0.015	0.015	0.000	0.000	0.000	0.000
54	B	55	ALA	0	0.009	0.020	21.544	0.010	0.010	0.000	0.000	0.000	0.000
55	B	56	GLN	0	-0.037	-0.024	23.548	0.000	0.000	0.000	0.000	0.000	0.000
56	B	57	LEU	0	0.009	0.009	19.072	-0.018	-0.018	0.000	0.000	0.000	0.000
57	B	58	HIS	0	-0.053	-0.025	23.211	0.032	0.032	0.000	0.000	0.000	0.000
58	B	59	VAL	0	0.016	0.020	21.326	-0.018	-0.018	0.000	0.000	0.000	0.000
59	B	60	THR	0	-0.069	-0.053	23.578	0.035	0.035	0.000	0.000	0.000	0.000
60	B	61	TYR	0	0.035	-0.001	21.975	-0.029	-0.029	0.000	0.000	0.000	0.000
61	B	62	LEU	0	-0.014	0.008	24.329	0.019	0.019	0.000	0.000	0.000	0.000
62	B	63	VAL	0	-0.001	-0.011	25.925	-0.006	-0.006	0.000	0.000	0.000	0.000
63	B	64	SER	0	-0.017	-0.013	28.326	0.009	0.009	0.000	0.000	0.000	0.000
64	B	65	GLY	0	0.050	0.022	30.569	-0.003	-0.003	0.000	0.000	0.000	0.000
65	B	66	SER	0	-0.022	0.007	33.164	0.003	0.003	0.000	0.000	0.000	0.000
66	B	67	LEU	0	0.040	0.005	36.888	-0.003	-0.003	0.000	0.000	0.000	0.000
67	B	68	ILE	0	-0.008	0.002	39.598	0.002	0.002	0.000	0.000	0.000	0.000
68	B	69	GLN	0	-0.039	0.004	43.208	-0.005	-0.005	0.000	0.000	0.000	0.000
69	B	70	ASN	0	0.019	-0.011	45.764	0.000	0.000	0.000	0.000	0.000	0.000
70	B	71	GLY	0	0.040	0.039	48.069	0.002	0.002	0.000	0.000	0.000	0.000
71	B	72	HIS	0	0.052	0.019	46.330	-0.002	-0.002	0.000	0.000	0.000	0.000
72	B	73	SER	0	0.027	0.011	40.652	-0.004	-0.004	0.000	0.000	0.000	0.000
73	B	74	CYS	0	-0.007	0.010	39.470	0.002	0.002	0.000	0.000	0.000	0.000
74	B	75	HIS	0	0.046	0.027	31.899	0.001	0.001	0.000	0.000	0.000	0.000
75	B	76	LYS	1	0.847	0.899	35.190	0.080	0.080	0.000	0.000	0.000	0.000
76	B	77	VAL	0	0.025	-0.004	29.589	-0.004	-0.004	0.000	0.000	0.000	0.000
77	B	78	ALA	0	-0.012	0.006	30.912	0.005	0.005	0.000	0.000	0.000	0.000
78	B	79	VAL	0	0.024	0.011	26.956	-0.009	-0.009	0.000	0.000	0.000	0.000
79	B	80	VAL	0	-0.047	-0.015	28.598	0.010	0.010	0.000	0.000	0.000	0.000
80	B	81	ARG	1	0.916	0.934	28.235	0.135	0.135	0.000	0.000	0.000	0.000
81	B	82	GLU	-1	-0.724	-0.833	24.363	-0.269	-0.269	0.000	0.000	0.000	0.000
82	B	83	ASP	-1	-0.818	-0.900	28.113	-0.146	-0.146	0.000	0.000	0.000	0.000
83	B	84	LYS	1	0.828	0.897	31.467	0.139	0.139	0.000	0.000	0.000	0.000
84	B	85	LEU	0	0.024	0.026	25.938	0.009	0.009	0.000	0.000	0.000	0.000
85	B	86	GLU	-1	-0.734	-0.858	28.925	-0.152	-0.152	0.000	0.000	0.000	0.000
86	B	87	ALA	0	0.000	0.018	32.169	0.010	0.010	0.000	0.000	0.000	0.000
87	B	88	VAL	0	-0.029	-0.009	32.624	0.009	0.009	0.000	0.000	0.000	0.000
88	B	89	LYS	1	0.856	0.898	27.957	0.166	0.166	0.000	0.000	0.000	0.000
89	B	90	SER	0	-0.031	-0.031	32.484	0.007	0.007	0.000	0.000	0.000	0.000
90	B	91	LYS	1	0.867	0.934	35.764	0.105	0.105	0.000	0.000	0.000	0.000
91	B	92	LEU	0	-0.068	-0.015	32.320	0.005	0.005	0.000	0.000	0.000	0.000
92	B	93	ALA	0	0.004	0.008	36.306	0.000	0.000	0.000	0.000	0.000	0.000
93	B	94	VAL	0	0.019	0.003	33.342	0.002	0.002	0.000	0.000	0.000	0.000
94	B	95	THR	0	0.002	0.002	29.258	-0.002	-0.002	0.000	0.000	0.000	0.000
95	B	96	ALA	0	-0.011	-0.012	29.585	0.003	0.003	0.000	0.000	0.000	0.000
96	B	97	SER	0	-0.044	-0.028	25.190	-0.005	-0.005	0.000	0.000	0.000	0.000
97	B	98	ILE	0	-0.002	-0.001	24.131	0.005	0.005	0.000	0.000	0.000	0.000
98	B	99	HIS	0	-0.012	-0.009	19.861	0.009	0.009	0.000	0.000	0.000	0.000
99	B	100	VAL	0	0.072	0.044	18.629	0.024	0.024	0.000	0.000	0.000	0.000
100	B	101	TYR	0	-0.118	-0.068	20.412	0.000	0.000	0.000	0.000	0.000	0.000
101	B	102	SER	0	0.000	-0.027	20.950	-0.002	-0.002	0.000	0.000	0.000	0.000
102	B	103	ILE	0	0.025	0.039	16.852	0.010	0.010	0.000	0.000	0.000	0.000
103	B	104	GLN	0	0.060	0.037	21.002	-0.002	-0.002	0.000	0.000	0.000	0.000
104	B	105	LYS	1	0.951	0.993	22.297	0.266	0.266	0.000	0.000	0.000	0.000
105	B	106	ALA	0	0.001	0.013	23.938	0.015	0.015	0.000	0.000	0.000	0.000
106	B	107	MET	0	-0.021	-0.007	27.417	-0.004	-0.004	0.000	0.000	0.000	0.000
107	B	108	LEU	0	0.011	0.017	27.017	0.010	0.010	0.000	0.000	0.000	0.000
108	B	109	LYS	1	0.982	0.983	30.743	0.123	0.123	0.000	0.000	0.000	0.000
109	B	110	ASP	-1	-0.839	-0.917	33.710	-0.127	-0.127	0.000	0.000	0.000	0.000
110	B	111	SER	0	0.066	0.018	31.063	-0.007	-0.007	0.000	0.000	0.000	0.000
111	B	112	GLY	0	-0.003	0.013	30.986	-0.006	-0.006	0.000	0.000	0.000	0.000
112	B	113	PRO	0	0.021	-0.003	29.368	-0.002	-0.002	0.000	0.000	0.000	0.000
113	B	114	LEU	0	0.009	0.016	25.495	-0.011	-0.011	0.000	0.000	0.000	0.000
114	B	115	PHE	0	0.008	0.014	27.129	-0.006	-0.006	0.000	0.000	0.000	0.000
115	B	116	ASN	0	0.012	-0.008	28.985	0.001	0.001	0.000	0.000	0.000	0.000
116	B	117	THR	0	0.022	0.011	23.242	0.000	0.000	0.000	0.000	0.000	0.000
117	B	118	ASP	-1	-0.766	-0.858	23.915	-0.226	-0.226	0.000	0.000	0.000	0.000
118	B	119	TYR	0	-0.007	0.004	25.647	0.010	0.010	0.000	0.000	0.000	0.000
119	B	120	ASP	-1	-0.827	-0.923	27.076	-0.125	-0.125	0.000	0.000	0.000	0.000
120	B	121	ILE	0	-0.006	0.009	20.319	0.009	0.009	0.000	0.000	0.000	0.000
121	B	122	LEU	0	-0.009	0.003	24.206	0.006	0.006	0.000	0.000	0.000	0.000
122	B	123	LYS	1	0.816	0.902	26.102	0.123	0.123	0.000	0.000	0.000	0.000
123	B	124	SER	0	-0.006	0.005	24.258	0.009	0.009	0.000	0.000	0.000	0.000
124	B	125	ASN	0	-0.042	-0.033	21.395	0.006	0.006	0.000	0.000	0.000	0.000
125	B	126	LEU	0	-0.019	-0.009	24.702	0.005	0.005	0.000	0.000	0.000	0.000
126	B	127	GLN	0	-0.016	-0.003	26.208	0.008	0.008	0.000	0.000	0.000	0.000
127	B	128	ASN	0	-0.022	-0.024	24.017	0.004	0.004	0.000	0.000	0.000	0.000
128	B	129	CYS	0	0.041	0.042	23.869	-0.008	-0.008	0.000	0.000	0.000	0.000
129	B	130	SER	0	0.057	0.025	23.855	-0.018	-0.018	0.000	0.000	0.000	0.000
130	B	131	LYS	1	0.936	1.001	17.892	0.097	0.097	0.000	0.000	0.000	0.000
131	B	132	PHE	0	0.047	0.030	15.678	0.010	0.010	0.000	0.000	0.000	0.000
132	B	133	SER	0	0.010	0.006	18.687	-0.026	-0.026	0.000	0.000	0.000	0.000
133	B	134	ALA	0	-0.019	-0.022	20.474	0.006	0.006	0.000	0.000	0.000	0.000
134	B	135	ILE	0	-0.018	0.004	21.364	0.012	0.012	0.000	0.000	0.000	0.000
135	B	136	GLN	0	0.007	0.001	21.754	0.003	0.003	0.000	0.000	0.000	0.000
136	B	137	CYS	0	-0.010	-0.008	25.889	0.006	0.006	0.000	0.000	0.000	0.000
137	B	138	ALA	0	0.050	0.023	29.539	0.001	0.001	0.000	0.000	0.000	0.000
138	B	139	ALA	0	0.024	0.004	31.200	0.003	0.003	0.000	0.000	0.000	0.000
139	B	140	ALA	0	-0.054	-0.013	30.131	0.000	0.000	0.000	0.000	0.000	0.000
140	B	141	VAL	0	0.011	0.003	30.900	-0.002	-0.002	0.000	0.000	0.000	0.000
141	B	142	PRO	0	-0.024	-0.030	31.902	0.001	0.001	0.000	0.000	0.000	0.000
142	B	143	ARG	1	0.986	1.005	34.947	0.015	0.015	0.000	0.000	0.000	0.000
143	B	144	ALA	0	0.001	0.015	38.265	0.001	0.001	0.000	0.000	0.000	0.000

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