FMO DATABASE

FMODB ID: 4NMQN

Calculation Name: 3PC7-A-Xray313

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: 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:

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	82
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-539520.649721
FMO2-HF: Nuclear repulsion	507194.411736
FMO2-HF: Total energy	-32326.237985
FMO2-MP2: Total energy	-32421.519044

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:841:ACE )

Summations of interaction energy for fragment #1(A:841: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.
-0.711	1.472	0.446	-1.348	-1.281	-0.007

Interaction energy analysis for fragmet #1(A:841:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : -0.008

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	A	843	GLN	0	-0.001	0.032	2.946	-1.446	0.696	0.446	-1.341	-1.247	-0.007
4	A	844	THR	0	0.022	0.002	5.719	-0.149	-0.149	0.000	0.000	0.000	0.000
5	A	845	LYS	1	0.944	0.964	4.241	0.944	0.985	0.000	-0.007	-0.034	0.000
6	A	846	VAL	0	0.001	0.010	9.494	0.057	0.057	0.000	0.000	0.000	0.000
7	A	847	LEU	0	-0.038	-0.010	13.052	0.000	0.000	0.000	0.000	0.000	0.000
8	A	848	LEU	0	-0.037	-0.032	15.662	-0.017	-0.017	0.000	0.000	0.000	0.000
9	A	849	ASP	-1	-0.816	-0.898	18.059	-0.066	-0.066	0.000	0.000	0.000	0.000
10	A	850	ILE	0	-0.140	-0.061	20.518	-0.003	-0.003	0.000	0.000	0.000	0.000
11	A	851	PHE	0	-0.064	-0.055	23.711	0.002	0.002	0.000	0.000	0.000	0.000
12	A	852	THR	0	0.075	0.021	25.060	0.003	0.003	0.000	0.000	0.000	0.000
13	A	853	GLY	0	-0.040	-0.016	27.264	-0.001	-0.001	0.000	0.000	0.000	0.000
14	A	854	VAL	0	-0.078	-0.032	29.752	0.003	0.003	0.000	0.000	0.000	0.000
15	A	855	ARG	1	0.874	0.928	30.908	0.013	0.013	0.000	0.000	0.000	0.000
16	A	856	LEU	0	0.002	-0.001	31.387	0.001	0.001	0.000	0.000	0.000	0.000
17	A	857	TYR	0	0.033	0.023	33.738	0.002	0.002	0.000	0.000	0.000	0.000
18	A	858	LEU	0	-0.016	-0.010	30.482	0.000	0.000	0.000	0.000	0.000	0.000
19	A	859	PRO	0	0.042	0.020	34.584	0.002	0.002	0.000	0.000	0.000	0.000
20	A	860	PRO	0	0.051	0.045	35.500	0.002	0.002	0.000	0.000	0.000	0.000
21	A	861	SER	0	-0.037	-0.009	36.388	0.002	0.002	0.000	0.000	0.000	0.000
22	A	862	THR	0	-0.051	-0.053	33.820	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	863	PRO	0	0.055	0.019	34.687	0.003	0.003	0.000	0.000	0.000	0.000
24	A	864	ASP	-1	-0.799	-0.912	28.784	0.046	0.046	0.000	0.000	0.000	0.000
25	A	865	PHE	0	0.017	0.027	29.689	0.003	0.003	0.000	0.000	0.000	0.000
26	A	866	SER	0	-0.015	-0.005	27.582	0.000	0.000	0.000	0.000	0.000	0.000
27	A	867	ARG	1	0.884	0.916	24.392	-0.060	-0.060	0.000	0.000	0.000	0.000
28	A	868	LEU	0	0.060	0.034	25.057	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	869	ARG	1	1.002	1.004	26.076	-0.041	-0.041	0.000	0.000	0.000	0.000
30	A	870	ARG	1	0.900	0.956	17.591	-0.111	-0.111	0.000	0.000	0.000	0.000
31	A	871	TYR	0	-0.019	-0.027	18.607	0.005	0.005	0.000	0.000	0.000	0.000
32	A	872	PHE	0	-0.008	0.013	22.595	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	873	VAL	0	0.013	0.006	23.016	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	874	ALA	0	-0.066	-0.025	18.786	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	875	PHE	0	-0.068	-0.048	17.022	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	876	ASP	-1	-0.757	-0.857	21.399	-0.051	-0.051	0.000	0.000	0.000	0.000
37	A	877	GLY	0	-0.019	0.004	23.799	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	878	ASP	-1	-0.866	-0.924	27.029	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	879	LEU	0	-0.048	-0.042	28.934	0.003	0.003	0.000	0.000	0.000	0.000
40	A	880	VAL	0	0.012	0.018	31.498	0.000	0.000	0.000	0.000	0.000	0.000
41	A	881	GLN	0	0.006	-0.021	33.951	0.003	0.003	0.000	0.000	0.000	0.000
42	A	882	GLU	-1	-0.899	-0.957	37.216	0.008	0.008	0.000	0.000	0.000	0.000
43	A	883	PHE	0	-0.037	-0.024	38.692	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	884	ASP	-1	-0.845	-0.928	38.837	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	885	MET	0	-0.065	-0.014	39.680	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	886	THR	0	-0.052	-0.029	40.747	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	887	SER	0	-0.004	0.012	39.243	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	888	ALA	0	-0.053	-0.015	37.333	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	889	THR	0	0.055	-0.002	35.095	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	890	HIS	0	-0.001	0.033	34.090	0.000	0.000	0.000	0.000	0.000	0.000
51	A	891	VAL	0	0.010	-0.004	36.785	0.002	0.002	0.000	0.000	0.000	0.000
52	A	892	LEU	0	0.007	0.027	34.042	0.000	0.000	0.000	0.000	0.000	0.000
53	A	893	GLY	0	0.004	0.000	38.114	0.001	0.001	0.000	0.000	0.000	0.000
54	A	894	SER	0	-0.010	-0.012	41.613	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	895	ARG	1	0.925	0.953	43.179	0.007	0.007	0.000	0.000	0.000	0.000
56	A	896	ASP	-1	-0.882	-0.940	45.069	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	897	LYS	1	0.894	0.944	44.979	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	898	ASN	0	-0.032	-0.025	41.335	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	899	PRO	0	0.041	0.026	44.204	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	900	ALA	0	0.011	0.012	44.005	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	901	ALA	0	0.000	0.031	39.876	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	902	GLN	0	-0.017	-0.017	36.778	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	903	GLN	0	-0.059	-0.040	38.199	0.000	0.000	0.000	0.000	0.000	0.000
64	A	904	VAL	0	0.001	0.006	33.878	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	905	SER	0	0.032	-0.007	34.494	0.003	0.003	0.000	0.000	0.000	0.000
66	A	906	PRO	0	0.025	-0.006	31.596	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	907	GLU	-1	-0.881	-0.950	30.291	0.014	0.014	0.000	0.000	0.000	0.000
68	A	908	TRP	0	-0.005	0.005	30.344	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	909	ILE	0	0.030	0.021	26.694	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	910	TRP	0	0.008	-0.008	23.290	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	911	ALA	0	-0.050	-0.026	25.441	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	912	CYS	0	-0.004	0.023	26.253	-0.007	-0.007	0.000	0.000	0.000	0.000
73	A	913	ILE	0	0.008	0.009	20.613	-0.007	-0.007	0.000	0.000	0.000	0.000
74	A	914	ARG	1	0.895	0.950	21.403	-0.010	-0.010	0.000	0.000	0.000	0.000
75	A	915	LYS	1	0.898	0.952	22.004	0.028	0.028	0.000	0.000	0.000	0.000
76	A	916	ARG	1	0.910	0.967	15.073	0.110	0.110	0.000	0.000	0.000	0.000
77	A	917	ARG	1	0.969	0.985	21.741	0.064	0.064	0.000	0.000	0.000	0.000
78	A	918	LEU	0	0.070	0.033	25.007	0.008	0.008	0.000	0.000	0.000	0.000
79	A	919	VAL	0	-0.057	-0.037	28.207	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	920	ALA	0	0.003	-0.002	30.657	0.001	0.001	0.000	0.000	0.000	0.000
81	A	921	PRO	0	-0.014	-0.014	34.211	0.002	0.002	0.000	0.000	0.000	0.000
82	A	922	SER	-1	-0.838	-0.905	34.522	-0.003	-0.003	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:841:ACE )