FMO DATABASE

FMODB ID: 3QMZL

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1258543.538969
FMO2-HF: Nuclear repulsion	1202048.262602
FMO2-HF: Total energy	-56495.276367
FMO2-MP2: Total energy	-56660.023893

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.
-2.157	0.841	0.082	-1.124	-1.957	-0.002

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 : 0.002 / q_NPA : -0.018

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	-0.026	-0.027	3.809	-2.074	-0.514	0.013	-0.608	-0.965	0.000
4	B	5	LEU	0	0.001	0.018	2.810	-0.942	0.278	0.070	-0.492	-0.799	-0.002
5	B	6	TYR	0	-0.001	0.008	4.557	0.796	1.014	-0.001	-0.024	-0.193	0.000
6	B	7	LEU	0	-0.053	-0.024	7.125	0.464	0.464	0.000	0.000	0.000	0.000
7	B	8	GLU	-1	-0.890	-0.935	7.705	-0.358	-0.358	0.000	0.000	0.000	0.000
8	B	9	ASN	0	0.014	0.004	7.985	-0.176	-0.176	0.000	0.000	0.000	0.000
9	B	10	ILE	0	-0.026	-0.024	10.773	0.150	0.150	0.000	0.000	0.000	0.000
10	B	11	ASP	-1	-0.773	-0.861	12.615	-0.134	-0.134	0.000	0.000	0.000	0.000
11	B	12	GLU	-1	-0.870	-0.941	11.727	-0.507	-0.507	0.000	0.000	0.000	0.000
12	B	13	PHE	0	-0.065	-0.034	13.537	0.044	0.044	0.000	0.000	0.000	0.000
13	B	14	VAL	0	-0.013	-0.017	16.861	0.048	0.048	0.000	0.000	0.000	0.000
14	B	15	THR	0	-0.060	-0.050	17.548	0.033	0.033	0.000	0.000	0.000	0.000
15	B	16	ASP	-1	-0.884	-0.926	17.506	-0.190	-0.190	0.000	0.000	0.000	0.000
16	B	17	GLN	0	-0.074	-0.039	16.977	0.044	0.044	0.000	0.000	0.000	0.000
17	B	18	ASN	0	-0.076	-0.026	21.098	0.028	0.028	0.000	0.000	0.000	0.000
18	B	19	LYS	1	0.919	0.963	19.987	0.256	0.256	0.000	0.000	0.000	0.000
19	B	20	ILE	0	-0.047	-0.031	21.571	-0.003	-0.003	0.000	0.000	0.000	0.000
20	B	21	VAL	0	0.045	0.021	16.598	-0.007	-0.007	0.000	0.000	0.000	0.000
21	B	22	THR	0	-0.011	-0.036	19.906	0.003	0.003	0.000	0.000	0.000	0.000
22	B	23	TYR	0	0.021	0.008	17.571	-0.019	-0.019	0.000	0.000	0.000	0.000
23	B	24	LYS	1	0.965	0.984	17.683	0.111	0.111	0.000	0.000	0.000	0.000
24	B	25	TRP	0	0.049	0.027	16.490	-0.019	-0.019	0.000	0.000	0.000	0.000
25	B	26	LEU	0	0.022	0.013	12.518	-0.014	-0.014	0.000	0.000	0.000	0.000
26	B	27	SER	0	-0.111	-0.050	14.531	-0.037	-0.037	0.000	0.000	0.000	0.000
27	B	28	TYR	0	-0.030	-0.036	15.214	-0.015	-0.015	0.000	0.000	0.000	0.000
28	B	29	THR	0	-0.045	-0.005	14.277	-0.003	-0.003	0.000	0.000	0.000	0.000
29	B	30	LEU	0	-0.020	-0.014	9.547	-0.014	-0.014	0.000	0.000	0.000	0.000
30	B	31	GLY	0	-0.016	0.006	11.294	-0.041	-0.041	0.000	0.000	0.000	0.000
31	B	32	VAL	0	-0.013	-0.021	9.850	-0.004	-0.004	0.000	0.000	0.000	0.000
32	B	33	HIS	0	0.045	0.048	12.730	0.031	0.031	0.000	0.000	0.000	0.000
33	B	34	VAL	0	0.071	0.021	14.680	-0.019	-0.019	0.000	0.000	0.000	0.000
34	B	35	ASN	0	0.014	-0.028	16.147	-0.005	-0.005	0.000	0.000	0.000	0.000
35	B	36	GLN	0	0.036	0.032	8.247	-0.031	-0.031	0.000	0.000	0.000	0.000
36	B	37	ALA	0	0.048	0.029	11.885	-0.044	-0.044	0.000	0.000	0.000	0.000
37	B	38	LYS	1	0.843	0.923	13.798	0.125	0.125	0.000	0.000	0.000	0.000
38	B	39	GLN	0	-0.045	-0.033	12.098	-0.009	-0.009	0.000	0.000	0.000	0.000
39	B	40	MET	0	0.032	0.024	7.811	0.007	0.007	0.000	0.000	0.000	0.000
40	B	41	LEU	0	-0.026	-0.004	11.690	0.015	0.015	0.000	0.000	0.000	0.000
41	B	42	TYR	0	-0.028	-0.020	14.408	0.015	0.015	0.000	0.000	0.000	0.000
42	B	43	ASP	-1	-0.821	-0.924	10.495	-0.087	-0.087	0.000	0.000	0.000	0.000
43	B	44	TYR	0	0.012	-0.034	12.744	0.059	0.059	0.000	0.000	0.000	0.000
44	B	45	VAL	0	-0.036	-0.019	13.828	0.032	0.032	0.000	0.000	0.000	0.000
45	B	46	GLU	-1	-0.924	-0.962	15.651	0.050	0.050	0.000	0.000	0.000	0.000
46	B	47	ARG	1	0.869	0.953	8.308	-0.067	-0.067	0.000	0.000	0.000	0.000
47	B	48	LYS	1	0.943	0.977	15.392	0.169	0.169	0.000	0.000	0.000	0.000
48	B	49	ARG	1	0.750	0.853	17.698	0.075	0.075	0.000	0.000	0.000	0.000
49	B	50	LYS	1	0.908	0.959	16.295	-0.080	-0.080	0.000	0.000	0.000	0.000
50	B	51	GLU	-1	-0.956	-0.977	15.965	-0.050	-0.050	0.000	0.000	0.000	0.000
51	B	52	ASN	0	-0.007	-0.009	19.422	0.008	0.008	0.000	0.000	0.000	0.000
52	B	53	SER	0	-0.008	0.005	22.418	0.007	0.007	0.000	0.000	0.000	0.000
53	B	54	GLY	0	-0.018	-0.021	24.413	0.001	0.001	0.000	0.000	0.000	0.000
54	B	55	ALA	0	-0.016	0.017	21.847	-0.002	-0.002	0.000	0.000	0.000	0.000
55	B	56	GLN	0	-0.022	-0.021	23.757	-0.006	-0.006	0.000	0.000	0.000	0.000
56	B	57	LEU	0	-0.007	0.005	19.520	-0.014	-0.014	0.000	0.000	0.000	0.000
57	B	58	HIS	0	-0.018	-0.008	23.547	0.019	0.019	0.000	0.000	0.000	0.000
58	B	59	VAL	0	0.050	0.038	21.337	-0.015	-0.015	0.000	0.000	0.000	0.000
59	B	60	THR	0	-0.079	-0.087	23.678	0.012	0.012	0.000	0.000	0.000	0.000
60	B	61	TYR	0	0.046	0.016	22.052	-0.013	-0.013	0.000	0.000	0.000	0.000
61	B	62	LEU	0	-0.037	0.003	24.489	0.004	0.004	0.000	0.000	0.000	0.000
62	B	63	VAL	0	0.011	-0.015	25.881	0.003	0.003	0.000	0.000	0.000	0.000
63	B	64	SER	0	0.004	-0.011	28.376	0.001	0.001	0.000	0.000	0.000	0.000
64	B	65	GLY	0	0.050	0.033	30.345	0.003	0.003	0.000	0.000	0.000	0.000
65	B	66	SER	0	-0.029	0.020	33.071	-0.001	-0.001	0.000	0.000	0.000	0.000
66	B	67	LEU	0	0.046	0.007	36.692	0.001	0.001	0.000	0.000	0.000	0.000
67	B	68	ILE	0	-0.020	-0.005	39.345	-0.001	-0.001	0.000	0.000	0.000	0.000
68	B	69	GLN	0	-0.048	-0.011	42.885	-0.002	-0.002	0.000	0.000	0.000	0.000
69	B	70	ASN	0	0.042	-0.011	45.680	0.000	0.000	0.000	0.000	0.000	0.000
70	B	71	GLY	0	0.012	0.043	48.032	0.000	0.000	0.000	0.000	0.000	0.000
71	B	72	HIS	0	0.032	-0.001	46.453	0.000	0.000	0.000	0.000	0.000	0.000
72	B	73	SER	0	0.043	0.002	40.535	-0.001	-0.001	0.000	0.000	0.000	0.000
73	B	74	CYS	0	-0.043	-0.001	38.897	-0.001	-0.001	0.000	0.000	0.000	0.000
74	B	75	HIS	0	0.035	0.024	31.669	0.003	0.003	0.000	0.000	0.000	0.000
75	B	76	LYS	1	0.912	0.947	35.226	0.031	0.031	0.000	0.000	0.000	0.000
76	B	77	VAL	0	0.030	0.005	29.834	0.000	0.000	0.000	0.000	0.000	0.000
77	B	78	ALA	0	-0.019	-0.016	31.002	-0.001	-0.001	0.000	0.000	0.000	0.000
78	B	79	VAL	0	0.023	0.036	27.321	-0.001	-0.001	0.000	0.000	0.000	0.000
79	B	80	VAL	0	-0.052	-0.032	28.684	0.004	0.004	0.000	0.000	0.000	0.000
80	B	81	ARG	1	0.880	0.930	28.349	0.055	0.055	0.000	0.000	0.000	0.000
81	B	82	GLU	-1	-0.789	-0.902	25.087	-0.063	-0.063	0.000	0.000	0.000	0.000
82	B	83	ASP	-1	-0.828	-0.914	28.063	-0.043	-0.043	0.000	0.000	0.000	0.000
83	B	84	LYS	1	0.885	0.924	31.294	0.038	0.038	0.000	0.000	0.000	0.000
84	B	85	LEU	0	0.021	0.039	25.951	0.003	0.003	0.000	0.000	0.000	0.000
85	B	86	GLU	-1	-0.828	-0.932	29.147	-0.017	-0.017	0.000	0.000	0.000	0.000
86	B	87	ALA	0	-0.019	-0.002	32.043	0.003	0.003	0.000	0.000	0.000	0.000
87	B	88	VAL	0	-0.060	-0.009	32.567	0.002	0.002	0.000	0.000	0.000	0.000
88	B	89	LYS	1	0.960	0.980	28.021	0.020	0.020	0.000	0.000	0.000	0.000
89	B	90	SER	0	-0.075	-0.058	32.539	0.003	0.003	0.000	0.000	0.000	0.000
90	B	91	LYS	1	0.924	0.953	35.743	0.029	0.029	0.000	0.000	0.000	0.000
91	B	92	LEU	0	-0.066	-0.012	32.623	0.000	0.000	0.000	0.000	0.000	0.000
92	B	93	ALA	0	0.002	0.012	36.490	0.002	0.002	0.000	0.000	0.000	0.000
93	B	94	VAL	0	0.039	0.013	33.415	0.002	0.002	0.000	0.000	0.000	0.000
94	B	95	THR	0	-0.044	-0.025	29.558	-0.005	-0.005	0.000	0.000	0.000	0.000
95	B	96	ALA	0	0.016	-0.001	29.282	0.003	0.003	0.000	0.000	0.000	0.000
96	B	97	SER	0	-0.074	-0.046	25.087	-0.003	-0.003	0.000	0.000	0.000	0.000
97	B	98	ILE	0	0.057	0.024	23.295	0.000	0.000	0.000	0.000	0.000	0.000
98	B	99	HIS	0	-0.075	-0.042	19.701	0.007	0.007	0.000	0.000	0.000	0.000
99	B	100	VAL	0	0.072	0.042	18.146	0.006	0.006	0.000	0.000	0.000	0.000
100	B	101	TYR	0	-0.062	-0.010	20.728	-0.005	-0.005	0.000	0.000	0.000	0.000
101	B	102	SER	0	0.014	0.015	21.302	-0.012	-0.012	0.000	0.000	0.000	0.000
102	B	103	ILE	0	0.054	0.057	17.317	0.013	0.013	0.000	0.000	0.000	0.000
103	B	104	GLN	0	0.048	0.017	21.271	-0.021	-0.021	0.000	0.000	0.000	0.000
104	B	105	LYS	1	0.977	1.019	22.886	0.135	0.135	0.000	0.000	0.000	0.000
105	B	106	ALA	0	0.010	0.004	24.236	0.013	0.013	0.000	0.000	0.000	0.000
106	B	107	MET	0	-0.051	-0.019	27.852	-0.004	-0.004	0.000	0.000	0.000	0.000
107	B	108	LEU	0	0.008	0.012	27.154	0.000	0.000	0.000	0.000	0.000	0.000
108	B	109	LYS	1	0.983	0.983	31.149	0.065	0.065	0.000	0.000	0.000	0.000
109	B	110	ASP	-1	-0.814	-0.898	34.342	-0.067	-0.067	0.000	0.000	0.000	0.000
110	B	111	SER	0	-0.006	-0.020	31.036	-0.004	-0.004	0.000	0.000	0.000	0.000
111	B	112	GLY	0	0.102	0.046	30.901	-0.006	-0.006	0.000	0.000	0.000	0.000
112	B	113	PRO	0	-0.012	0.005	29.003	-0.005	-0.005	0.000	0.000	0.000	0.000
113	B	114	LEU	0	-0.002	-0.012	25.554	-0.009	-0.009	0.000	0.000	0.000	0.000
114	B	115	PHE	0	-0.055	-0.005	27.241	-0.006	-0.006	0.000	0.000	0.000	0.000
115	B	116	ASN	0	0.055	0.012	28.418	-0.006	-0.006	0.000	0.000	0.000	0.000
116	B	117	THR	0	0.004	0.008	23.486	-0.005	-0.005	0.000	0.000	0.000	0.000
117	B	118	ASP	-1	-0.804	-0.894	23.405	-0.170	-0.170	0.000	0.000	0.000	0.000
118	B	119	TYR	0	-0.066	-0.041	25.453	-0.001	-0.001	0.000	0.000	0.000	0.000
119	B	120	ASP	-1	-0.893	-0.963	26.936	-0.122	-0.122	0.000	0.000	0.000	0.000
120	B	121	ILE	0	-0.009	-0.005	20.540	0.000	0.000	0.000	0.000	0.000	0.000
121	B	122	LEU	0	-0.005	0.012	24.059	-0.004	-0.004	0.000	0.000	0.000	0.000
122	B	123	LYS	1	0.921	0.967	26.025	0.105	0.105	0.000	0.000	0.000	0.000
123	B	124	SER	0	-0.002	0.007	24.560	0.003	0.003	0.000	0.000	0.000	0.000
124	B	125	ASN	0	-0.046	-0.030	21.171	-0.009	-0.009	0.000	0.000	0.000	0.000
125	B	126	LEU	0	-0.079	-0.033	24.594	0.004	0.004	0.000	0.000	0.000	0.000
126	B	127	GLN	0	0.030	0.026	25.647	0.009	0.009	0.000	0.000	0.000	0.000
127	B	128	ASN	0	-0.053	-0.042	23.147	0.012	0.012	0.000	0.000	0.000	0.000
128	B	129	CYS	0	0.029	0.016	23.291	-0.013	-0.013	0.000	0.000	0.000	0.000
129	B	130	SER	0	0.010	-0.006	23.535	-0.010	-0.010	0.000	0.000	0.000	0.000
130	B	131	LYS	1	0.956	1.010	17.701	0.222	0.222	0.000	0.000	0.000	0.000
131	B	132	PHE	0	0.051	0.022	15.178	-0.002	-0.002	0.000	0.000	0.000	0.000
132	B	133	SER	0	0.034	0.036	18.990	-0.001	-0.001	0.000	0.000	0.000	0.000
133	B	134	ALA	0	-0.014	-0.010	20.503	-0.002	-0.002	0.000	0.000	0.000	0.000
134	B	135	ILE	0	-0.044	-0.035	21.398	0.012	0.012	0.000	0.000	0.000	0.000
135	B	136	GLN	0	-0.017	-0.009	22.675	-0.003	-0.003	0.000	0.000	0.000	0.000
136	B	137	CYS	0	-0.027	-0.011	25.769	0.009	0.009	0.000	0.000	0.000	0.000
137	B	138	ALA	0	0.044	0.022	29.498	-0.002	-0.002	0.000	0.000	0.000	0.000
138	B	139	ALA	0	0.016	-0.005	31.185	-0.001	-0.001	0.000	0.000	0.000	0.000
139	B	140	ALA	0	-0.018	0.003	30.266	0.000	0.000	0.000	0.000	0.000	0.000
140	B	141	VAL	0	0.025	0.006	30.499	-0.006	-0.006	0.000	0.000	0.000	0.000
141	B	142	PRO	0	-0.051	-0.032	31.320	0.004	0.004	0.000	0.000	0.000	0.000
142	B	143	ARG	1	0.998	1.007	34.391	0.043	0.043	0.000	0.000	0.000	0.000
143	B	144	ALA	0	-0.002	0.011	37.848	0.003	0.003	0.000	0.000	0.000	0.000

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