FMO DATABASE

FMODB ID: Q1GYY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-538239.516071
FMO2-HF: Nuclear repulsion	506064.290558
FMO2-HF: Total energy	-32175.225513
FMO2-MP2: Total energy	-32270.076231

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.
-1.661	-0.238	-0.005	-0.607	-0.811	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 : 0.029 / q_NPA : 0.001

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	0.027	0.006	3.859	0.226	1.451	-0.006	-0.562	-0.657	0.003
4	A	845	LYS	1	0.875	0.920	3.901	-2.738	-2.540	0.001	-0.045	-0.154	0.000
5	A	846	VAL	0	0.018	0.026	8.670	0.131	0.131	0.000	0.000	0.000	0.000
6	A	847	LEU	0	-0.028	-0.006	11.499	-0.163	-0.163	0.000	0.000	0.000	0.000
7	A	848	LEU	0	-0.017	-0.019	12.341	-0.044	-0.044	0.000	0.000	0.000	0.000
8	A	849	ASP	-1	-0.830	-0.908	15.733	-0.183	-0.183	0.000	0.000	0.000	0.000
9	A	850	ILE	0	-0.134	-0.058	17.890	0.000	0.000	0.000	0.000	0.000	0.000
10	A	851	PHE	0	-0.047	-0.046	20.849	0.007	0.007	0.000	0.000	0.000	0.000
11	A	852	THR	0	0.049	0.014	22.799	0.009	0.009	0.000	0.000	0.000	0.000
12	A	853	GLY	0	-0.029	-0.006	24.860	0.001	0.001	0.000	0.000	0.000	0.000
13	A	854	VAL	0	-0.080	-0.040	27.512	0.006	0.006	0.000	0.000	0.000	0.000
14	A	855	ARG	1	0.811	0.896	29.501	0.039	0.039	0.000	0.000	0.000	0.000
15	A	856	LEU	0	-0.017	-0.012	30.390	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	857	TYR	0	-0.022	-0.038	33.179	0.002	0.002	0.000	0.000	0.000	0.000
17	A	858	LEU	0	-0.038	-0.022	30.254	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	859	PRO	0	0.043	0.023	34.394	0.004	0.004	0.000	0.000	0.000	0.000
19	A	860	PRO	0	0.050	0.025	35.941	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	861	SER	0	-0.008	0.005	36.713	0.000	0.000	0.000	0.000	0.000	0.000
21	A	862	THR	0	-0.058	-0.035	33.726	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	863	PRO	0	0.034	0.009	34.543	0.002	0.002	0.000	0.000	0.000	0.000
23	A	864	ASP	-1	-0.769	-0.879	28.188	-0.084	-0.084	0.000	0.000	0.000	0.000
24	A	865	PHE	0	0.035	0.034	29.753	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	866	SER	0	-0.008	-0.002	28.716	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	867	ARG	1	0.846	0.882	24.573	0.086	0.086	0.000	0.000	0.000	0.000
27	A	868	LEU	0	0.023	0.014	25.228	-0.010	-0.010	0.000	0.000	0.000	0.000
28	A	869	ARG	1	1.003	1.000	26.491	0.013	0.013	0.000	0.000	0.000	0.000
29	A	870	ARG	1	0.892	0.955	18.704	0.047	0.047	0.000	0.000	0.000	0.000
30	A	871	TYR	0	-0.004	-0.027	18.240	0.013	0.013	0.000	0.000	0.000	0.000
31	A	872	PHE	0	0.002	0.026	22.074	-0.021	-0.021	0.000	0.000	0.000	0.000
32	A	873	VAL	0	0.032	0.018	23.474	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	874	ALA	0	-0.070	-0.033	18.723	0.001	0.001	0.000	0.000	0.000	0.000
34	A	875	PHE	0	-0.056	-0.046	15.780	-0.036	-0.036	0.000	0.000	0.000	0.000
35	A	876	ASP	-1	-0.773	-0.868	20.214	-0.108	-0.108	0.000	0.000	0.000	0.000
36	A	877	GLY	0	0.007	0.011	22.718	0.004	0.004	0.000	0.000	0.000	0.000
37	A	878	ASP	-1	-0.863	-0.921	25.948	-0.034	-0.034	0.000	0.000	0.000	0.000
38	A	879	LEU	0	-0.038	-0.027	28.769	0.000	0.000	0.000	0.000	0.000	0.000
39	A	880	VAL	0	0.029	0.021	31.290	0.007	0.007	0.000	0.000	0.000	0.000
40	A	881	GLN	0	-0.022	-0.017	34.040	0.002	0.002	0.000	0.000	0.000	0.000
41	A	882	GLU	-1	-0.836	-0.899	37.208	-0.026	-0.026	0.000	0.000	0.000	0.000
42	A	883	PHE	0	-0.021	-0.028	38.912	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	884	ASP	-1	-0.797	-0.874	37.339	-0.026	-0.026	0.000	0.000	0.000	0.000
44	A	885	MET	0	-0.010	0.008	38.861	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	886	THR	0	-0.018	-0.014	39.941	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	887	SER	0	-0.057	-0.032	38.424	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	888	ALA	0	-0.026	0.002	35.791	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	889	THR	0	0.031	-0.002	32.843	0.002	0.002	0.000	0.000	0.000	0.000
49	A	890	HIS	0	-0.003	0.013	31.436	0.001	0.001	0.000	0.000	0.000	0.000
50	A	891	VAL	0	0.021	-0.002	34.915	0.004	0.004	0.000	0.000	0.000	0.000
51	A	892	LEU	0	0.004	0.016	33.175	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	893	GLY	0	-0.003	0.001	37.224	0.005	0.005	0.000	0.000	0.000	0.000
53	A	894	SER	0	-0.036	-0.050	40.718	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	895	ARG	1	0.897	0.940	40.997	0.050	0.050	0.000	0.000	0.000	0.000
55	A	896	ASP	-1	-0.882	-0.909	43.444	-0.036	-0.036	0.000	0.000	0.000	0.000
56	A	897	LYS	1	0.925	0.958	43.680	0.037	0.037	0.000	0.000	0.000	0.000
57	A	898	ASN	0	-0.026	-0.018	39.765	0.002	0.002	0.000	0.000	0.000	0.000
58	A	899	PRO	0	0.039	0.022	42.315	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	900	ALA	0	0.001	0.013	41.618	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	901	ALA	0	0.006	0.030	37.849	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	902	GLN	0	-0.049	-0.042	34.485	0.002	0.002	0.000	0.000	0.000	0.000
62	A	903	GLN	0	-0.015	-0.024	36.141	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	904	VAL	0	-0.014	0.003	32.166	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	905	SER	0	-0.004	-0.020	33.284	0.005	0.005	0.000	0.000	0.000	0.000
65	A	906	PRO	0	0.054	0.009	30.833	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	907	GLU	-1	-0.838	-0.897	29.229	-0.102	-0.102	0.000	0.000	0.000	0.000
67	A	908	TRP	0	0.000	-0.002	28.644	-0.014	-0.014	0.000	0.000	0.000	0.000
68	A	909	ILE	0	0.046	0.037	25.828	-0.015	-0.015	0.000	0.000	0.000	0.000
69	A	910	TRP	0	0.011	-0.010	22.505	-0.025	-0.025	0.000	0.000	0.000	0.000
70	A	911	ALA	0	-0.057	-0.028	23.877	-0.024	-0.024	0.000	0.000	0.000	0.000
71	A	912	CYS	0	0.014	0.020	23.714	-0.019	-0.019	0.000	0.000	0.000	0.000
72	A	913	ILE	0	-0.014	0.005	19.296	-0.031	-0.031	0.000	0.000	0.000	0.000
73	A	914	ARG	1	0.891	0.949	19.250	0.145	0.145	0.000	0.000	0.000	0.000
74	A	915	LYS	1	0.919	0.962	19.955	0.219	0.219	0.000	0.000	0.000	0.000
75	A	916	ARG	1	0.912	0.963	10.952	0.788	0.788	0.000	0.000	0.000	0.000
76	A	917	ARG	1	0.946	0.981	18.419	0.279	0.279	0.000	0.000	0.000	0.000
77	A	918	LEU	0	0.078	0.044	21.342	0.007	0.007	0.000	0.000	0.000	0.000
78	A	919	VAL	0	-0.036	-0.032	24.857	-0.009	-0.009	0.000	0.000	0.000	0.000
79	A	920	ALA	0	0.039	0.023	27.318	0.009	0.009	0.000	0.000	0.000	0.000
80	A	921	PRO	0	0.011	0.012	31.141	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	922	SER	0	-0.012	-0.023	31.680	0.001	0.001	0.000	0.000	0.000	0.000

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