FMO DATABASE

FMODB ID: ZY56N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-537278.314839
FMO2-HF: Nuclear repulsion	505103.396112
FMO2-HF: Total energy	-32174.918727
FMO2-MP2: Total energy	-32269.769261

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.
2.391	3.985	-0.016	-0.681	-0.897	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 : 0.007 / q_NPA : -0.021

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	0.022	0.002	3.785	-1.505	-0.035	-0.015	-0.668	-0.787	0.003
4	A	845	LYS	1	0.947	0.966	3.918	3.454	3.578	-0.001	-0.013	-0.110	0.000
5	A	846	VAL	0	0.001	0.010	8.294	0.247	0.247	0.000	0.000	0.000	0.000
6	A	847	LEU	0	-0.038	-0.010	11.490	-0.070	-0.070	0.000	0.000	0.000	0.000
7	A	848	LEU	0	-0.037	-0.032	12.921	0.008	0.008	0.000	0.000	0.000	0.000
8	A	849	ASP	-1	-0.814	-0.897	15.525	-0.321	-0.321	0.000	0.000	0.000	0.000
9	A	850	ILE	0	-0.141	-0.061	17.834	0.022	0.022	0.000	0.000	0.000	0.000
10	A	851	PHE	0	-0.072	-0.060	20.882	0.028	0.028	0.000	0.000	0.000	0.000
11	A	852	THR	0	0.081	0.024	22.694	0.012	0.012	0.000	0.000	0.000	0.000
12	A	853	GLY	0	-0.038	-0.014	24.843	0.012	0.012	0.000	0.000	0.000	0.000
13	A	854	VAL	0	-0.085	-0.036	27.472	0.014	0.014	0.000	0.000	0.000	0.000
14	A	855	ARG	1	0.879	0.931	29.282	0.097	0.097	0.000	0.000	0.000	0.000
15	A	856	LEU	0	0.000	-0.004	30.335	0.009	0.009	0.000	0.000	0.000	0.000
16	A	857	TYR	0	0.039	0.027	32.733	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	858	LEU	0	-0.026	-0.016	29.704	0.002	0.002	0.000	0.000	0.000	0.000
18	A	859	PRO	0	0.044	0.021	33.787	0.000	0.000	0.000	0.000	0.000	0.000
19	A	860	PRO	0	0.055	0.047	35.073	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	861	SER	0	-0.033	-0.007	36.021	0.000	0.000	0.000	0.000	0.000	0.000
21	A	862	THR	0	-0.054	-0.055	33.089	0.004	0.004	0.000	0.000	0.000	0.000
22	A	863	PRO	0	0.054	0.019	34.224	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	864	ASP	-1	-0.800	-0.913	28.315	-0.089	-0.089	0.000	0.000	0.000	0.000
24	A	865	PHE	0	0.019	0.026	29.233	-0.011	-0.011	0.000	0.000	0.000	0.000
25	A	866	SER	0	-0.014	-0.003	27.494	-0.013	-0.013	0.000	0.000	0.000	0.000
26	A	867	ARG	1	0.888	0.920	24.131	0.071	0.071	0.000	0.000	0.000	0.000
27	A	868	LEU	0	0.051	0.029	24.499	-0.016	-0.016	0.000	0.000	0.000	0.000
28	A	869	ARG	1	1.004	1.005	25.831	0.127	0.127	0.000	0.000	0.000	0.000
29	A	870	ARG	1	0.904	0.959	17.481	0.186	0.186	0.000	0.000	0.000	0.000
30	A	871	TYR	0	-0.017	-0.027	18.088	-0.017	-0.017	0.000	0.000	0.000	0.000
31	A	872	PHE	0	-0.013	0.010	21.599	-0.022	-0.022	0.000	0.000	0.000	0.000
32	A	873	VAL	0	0.017	0.008	22.290	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	874	ALA	0	-0.064	-0.024	17.910	-0.017	-0.017	0.000	0.000	0.000	0.000
34	A	875	PHE	0	-0.065	-0.047	15.488	-0.039	-0.039	0.000	0.000	0.000	0.000
35	A	876	ASP	-1	-0.758	-0.857	20.048	-0.230	-0.230	0.000	0.000	0.000	0.000
36	A	877	GLY	0	-0.023	0.002	22.434	0.017	0.017	0.000	0.000	0.000	0.000
37	A	878	ASP	-1	-0.864	-0.923	25.750	-0.136	-0.136	0.000	0.000	0.000	0.000
38	A	879	LEU	0	-0.047	-0.043	28.231	0.011	0.011	0.000	0.000	0.000	0.000
39	A	880	VAL	0	0.011	0.018	30.563	0.000	0.000	0.000	0.000	0.000	0.000
40	A	881	GLN	0	0.008	-0.018	33.339	0.006	0.006	0.000	0.000	0.000	0.000
41	A	882	GLU	-1	-0.901	-0.958	36.472	-0.060	-0.060	0.000	0.000	0.000	0.000
42	A	883	PHE	0	-0.033	-0.022	38.040	0.002	0.002	0.000	0.000	0.000	0.000
43	A	884	ASP	-1	-0.844	-0.927	37.853	-0.080	-0.080	0.000	0.000	0.000	0.000
44	A	885	MET	0	-0.067	-0.015	38.654	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	886	THR	0	-0.051	-0.029	39.729	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	887	SER	0	0.000	0.014	38.086	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	888	ALA	0	-0.052	-0.014	35.843	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	889	THR	0	0.060	0.002	32.859	0.003	0.003	0.000	0.000	0.000	0.000
49	A	890	HIS	0	-0.009	0.027	31.294	0.003	0.003	0.000	0.000	0.000	0.000
50	A	891	VAL	0	0.018	0.002	34.790	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	892	LEU	0	0.001	0.020	32.923	0.001	0.001	0.000	0.000	0.000	0.000
52	A	893	GLY	0	0.005	0.001	36.830	0.002	0.002	0.000	0.000	0.000	0.000
53	A	894	SER	0	-0.006	-0.010	40.308	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	895	ARG	1	0.924	0.951	40.750	0.047	0.047	0.000	0.000	0.000	0.000
55	A	896	ASP	-1	-0.880	-0.939	43.234	-0.041	-0.041	0.000	0.000	0.000	0.000
56	A	897	LYS	1	0.899	0.946	43.978	0.052	0.052	0.000	0.000	0.000	0.000
57	A	898	ASN	0	-0.034	-0.024	39.590	0.001	0.001	0.000	0.000	0.000	0.000
58	A	899	PRO	0	0.047	0.028	42.195	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	900	ALA	0	0.014	0.014	41.347	0.001	0.001	0.000	0.000	0.000	0.000
60	A	901	ALA	0	0.003	0.033	37.841	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	902	GLN	0	-0.017	-0.016	33.903	0.005	0.005	0.000	0.000	0.000	0.000
62	A	903	GLN	0	-0.043	-0.031	35.964	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	904	VAL	0	-0.006	-0.002	31.734	0.000	0.000	0.000	0.000	0.000	0.000
64	A	905	SER	0	-0.005	-0.016	32.450	0.004	0.004	0.000	0.000	0.000	0.000
65	A	906	PRO	0	0.066	0.015	30.496	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	907	GLU	-1	-0.871	-0.945	28.938	-0.073	-0.073	0.000	0.000	0.000	0.000
67	A	908	TRP	0	-0.029	-0.010	28.348	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	909	ILE	0	0.047	0.030	25.468	-0.009	-0.009	0.000	0.000	0.000	0.000
69	A	910	TRP	0	0.018	-0.002	22.494	-0.020	-0.020	0.000	0.000	0.000	0.000
70	A	911	ALA	0	-0.054	-0.029	23.354	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	912	CYS	0	0.020	0.030	23.397	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	913	ILE	0	-0.015	0.003	18.880	-0.017	-0.017	0.000	0.000	0.000	0.000
73	A	914	ARG	1	0.900	0.952	18.781	0.066	0.066	0.000	0.000	0.000	0.000
74	A	915	LYS	1	0.901	0.953	18.911	0.076	0.076	0.000	0.000	0.000	0.000
75	A	916	ARG	1	0.920	0.971	11.176	0.496	0.496	0.000	0.000	0.000	0.000
76	A	917	ARG	1	0.976	0.988	18.201	0.128	0.128	0.000	0.000	0.000	0.000
77	A	918	LEU	0	0.071	0.034	21.274	0.011	0.011	0.000	0.000	0.000	0.000
78	A	919	VAL	0	-0.057	-0.035	24.754	0.007	0.007	0.000	0.000	0.000	0.000
79	A	920	ALA	0	0.024	0.010	27.029	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	921	PRO	0	0.005	-0.002	30.804	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	922	SER	0	0.033	0.029	31.243	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)