FMO DATABASE

FMODB ID: R5G98

Calculation Name: 3PC7-A-Xray372

Preferred Name: DNA ligase 3

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3PC7

Chain ID: A

ChEMBL ID: CHEMBL4295773

UniProt ID: P49916

Base Structure: X-ray

Registration Date: 2023-06-19

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	81
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-537187.758023
FMO2-HF: Nuclear repulsion	505012.631362
FMO2-HF: Total energy	-32175.126661
FMO2-MP2: Total energy	-32269.975605

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(A:842:SER)

Summations of interaction energy for fragment #1(A:842:SER)

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.
2.673	4.353	-0.007	-0.724	-0.95	0.003

Interaction energy analysis for fragmet #1(A:842:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / 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

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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	A	844	THR	0	0.032	0.005	3.785	-1.475	-0.057	-0.013	-0.657	-0.748	0.003
4	A	845	LYS	1	0.893	0.937	3.157	3.569	3.831	0.006	-0.067	-0.202	0.000
5	A	846	VAL	0	0.003	0.011	8.306	0.227	0.227	0.000	0.000	0.000	0.000
6	A	847	LEU	0	-0.039	-0.010	11.495	-0.083	-0.083	0.000	0.000	0.000	0.000
7	A	848	LEU	0	-0.025	-0.024	12.690	-0.003	-0.003	0.000	0.000	0.000	0.000
8	A	849	ASP	-1	-0.837	-0.914	15.829	-0.352	-0.352	0.000	0.000	0.000	0.000
9	A	850	ILE	0	-0.126	-0.049	18.161	0.016	0.016	0.000	0.000	0.000	0.000
10	A	851	PHE	0	-0.064	-0.058	21.189	0.026	0.026	0.000	0.000	0.000	0.000
11	A	852	THR	0	0.069	0.027	22.981	0.014	0.014	0.000	0.000	0.000	0.000
12	A	853	GLY	0	-0.045	-0.018	25.104	0.009	0.009	0.000	0.000	0.000	0.000
13	A	854	VAL	0	-0.090	-0.037	27.704	0.013	0.013	0.000	0.000	0.000	0.000
14	A	855	ARG	1	0.844	0.911	29.599	0.101	0.101	0.000	0.000	0.000	0.000
15	A	856	LEU	0	-0.008	-0.009	30.361	0.008	0.008	0.000	0.000	0.000	0.000
16	A	857	TYR	0	-0.027	-0.025	32.755	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	858	LEU	0	-0.032	-0.020	29.778	0.001	0.001	0.000	0.000	0.000	0.000
18	A	859	PRO	0	0.046	0.023	33.811	0.001	0.001	0.000	0.000	0.000	0.000
19	A	860	PRO	0	0.056	0.030	35.091	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	861	SER	0	-0.008	0.003	36.047	0.000	0.000	0.000	0.000	0.000	0.000
21	A	862	THR	0	-0.074	-0.046	33.211	0.002	0.002	0.000	0.000	0.000	0.000
22	A	863	PRO	0	0.049	0.018	34.251	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	864	ASP	-1	-0.778	-0.879	28.145	-0.097	-0.097	0.000	0.000	0.000	0.000
24	A	865	PHE	0	0.045	0.037	29.261	-0.010	-0.010	0.000	0.000	0.000	0.000
25	A	866	SER	0	-0.012	-0.003	27.701	-0.012	-0.012	0.000	0.000	0.000	0.000
26	A	867	ARG	1	0.853	0.879	24.269	0.077	0.077	0.000	0.000	0.000	0.000
27	A	868	LEU	0	0.032	0.025	24.526	-0.016	-0.016	0.000	0.000	0.000	0.000
28	A	869	ARG	1	1.001	1.003	25.857	0.111	0.111	0.000	0.000	0.000	0.000
29	A	870	ARG	1	0.914	0.962	17.448	0.162	0.162	0.000	0.000	0.000	0.000
30	A	871	TYR	0	-0.016	-0.029	18.182	-0.014	-0.014	0.000	0.000	0.000	0.000
31	A	872	PHE	0	-0.007	0.012	21.624	-0.023	-0.023	0.000	0.000	0.000	0.000
32	A	873	VAL	0	0.015	0.005	22.466	-0.009	-0.009	0.000	0.000	0.000	0.000
33	A	874	ALA	0	-0.058	-0.021	17.928	-0.015	-0.015	0.000	0.000	0.000	0.000
34	A	875	PHE	0	-0.060	-0.044	15.613	-0.036	-0.036	0.000	0.000	0.000	0.000
35	A	876	ASP	-1	-0.759	-0.864	20.148	-0.235	-0.235	0.000	0.000	0.000	0.000
36	A	877	GLY	0	-0.004	0.012	22.517	0.015	0.015	0.000	0.000	0.000	0.000
37	A	878	ASP	-1	-0.862	-0.917	25.819	-0.132	-0.132	0.000	0.000	0.000	0.000
38	A	879	LEU	0	-0.054	-0.039	28.219	0.010	0.010	0.000	0.000	0.000	0.000
39	A	880	VAL	0	0.019	0.019	30.583	0.001	0.001	0.000	0.000	0.000	0.000
40	A	881	GLN	0	-0.006	-0.021	33.262	0.006	0.006	0.000	0.000	0.000	0.000
41	A	882	GLU	-1	-0.823	-0.900	36.492	-0.061	-0.061	0.000	0.000	0.000	0.000
42	A	883	PHE	0	-0.032	-0.027	38.141	0.001	0.001	0.000	0.000	0.000	0.000
43	A	884	ASP	-1	-0.818	-0.892	37.297	-0.084	-0.084	0.000	0.000	0.000	0.000
44	A	885	MET	0	0.000	0.013	38.674	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	886	THR	0	-0.036	-0.025	39.750	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	887	SER	0	-0.065	-0.040	38.189	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	888	ALA	0	-0.051	-0.009	36.090	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	889	THR	0	0.051	0.007	33.162	0.003	0.003	0.000	0.000	0.000	0.000
49	A	890	HIS	0	-0.011	0.014	31.354	0.004	0.004	0.000	0.000	0.000	0.000
50	A	891	VAL	0	0.018	-0.002	35.131	0.001	0.001	0.000	0.000	0.000	0.000
51	A	892	LEU	0	0.003	0.023	33.008	0.000	0.000	0.000	0.000	0.000	0.000
52	A	893	GLY	0	0.003	0.000	37.072	0.003	0.003	0.000	0.000	0.000	0.000
53	A	894	SER	0	-0.024	-0.048	40.593	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	895	ARG	1	0.916	0.954	40.834	0.058	0.058	0.000	0.000	0.000	0.000
55	A	896	ASP	-1	-0.874	-0.900	43.597	-0.048	-0.048	0.000	0.000	0.000	0.000
56	A	897	LYS	1	0.901	0.947	43.800	0.058	0.058	0.000	0.000	0.000	0.000
57	A	898	ASN	0	-0.024	-0.017	40.101	0.001	0.001	0.000	0.000	0.000	0.000
58	A	899	PRO	0	0.060	0.031	42.529	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	900	ALA	0	-0.005	0.005	41.658	0.000	0.000	0.000	0.000	0.000	0.000
60	A	901	ALA	0	0.004	0.033	38.228	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	902	GLN	0	-0.019	-0.022	34.424	0.005	0.005	0.000	0.000	0.000	0.000
62	A	903	GLN	0	-0.039	-0.035	36.314	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	904	VAL	0	-0.014	-0.004	32.098	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	905	SER	0	-0.012	-0.045	32.885	0.004	0.004	0.000	0.000	0.000	0.000
65	A	906	PRO	0	0.069	0.022	30.653	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	907	GLU	-1	-0.846	-0.909	29.297	-0.090	-0.090	0.000	0.000	0.000	0.000
67	A	908	TRP	0	-0.001	0.003	28.768	-0.009	-0.009	0.000	0.000	0.000	0.000
68	A	909	ILE	0	0.049	0.035	25.647	-0.012	-0.012	0.000	0.000	0.000	0.000
69	A	910	TRP	0	0.009	-0.008	22.433	-0.022	-0.022	0.000	0.000	0.000	0.000
70	A	911	ALA	0	-0.051	-0.030	23.777	-0.013	-0.013	0.000	0.000	0.000	0.000
71	A	912	CYS	0	0.022	0.029	23.782	-0.008	-0.008	0.000	0.000	0.000	0.000
72	A	913	ILE	0	-0.021	0.000	19.353	-0.023	-0.023	0.000	0.000	0.000	0.000
73	A	914	ARG	1	0.896	0.953	19.184	0.099	0.099	0.000	0.000	0.000	0.000
74	A	915	LYS	1	0.918	0.960	19.294	0.129	0.129	0.000	0.000	0.000	0.000
75	A	916	ARG	1	0.915	0.965	11.223	0.621	0.621	0.000	0.000	0.000	0.000
76	A	917	ARG	1	0.963	0.986	18.540	0.215	0.215	0.000	0.000	0.000	0.000
77	A	918	LEU	0	0.065	0.033	21.576	0.013	0.013	0.000	0.000	0.000	0.000
78	A	919	VAL	0	-0.052	-0.035	25.033	0.003	0.003	0.000	0.000	0.000	0.000
79	A	920	ALA	0	0.031	0.015	27.349	0.002	0.002	0.000	0.000	0.000	0.000
80	A	921	PRO	0	0.005	0.002	31.118	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	922	SER	0	0.002	0.006	31.794	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:842:SER)