FMO DATABASE

FMODB ID: J27N9

Calculation Name: 3PC7-A-Xray540

Preferred Name: DNA ligase 3

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3PC7

Chain ID: A

ChEMBL ID: CHEMBL4295773

UniProt ID: P49916

Base Structure: X-ray

Registration Date: 2025-07-08

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	153
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-538223.76097
FMO2-HF: Nuclear repulsion	506064.290558
FMO2-HF: Total energy	-32159.470412
FMO2-MP2: Total energy	-32253.925427

3D Structure Molmil

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.
-3.662	-1.134	0.117	-1.2	-1.445	0.004

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 : 0.125 / q_NPA : 0.047

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].
4	A	843	GLN	0	-0.047	0.109	3.778	2.575	3.841	0.118	-0.590	-0.794	0.002
5	A	844	THR	0	0.056	-0.058	3.859	0.325	1.424	-0.002	-0.559	-0.538	0.002
6	A	844	THR	0	0.011	0.067	7.768	-0.028	-0.028	0.000	0.000	0.000	0.000
7	A	845	LYS	0	0.030	-0.085	6.627	0.658	0.658	0.000	0.000	0.000	0.000
8	A	845	LYS	1	0.815	1.019	3.901	-7.378	-7.215	0.001	-0.051	-0.113	0.000
9	A	846	VAL	0	0.043	-0.128	8.670	0.045	0.045	0.000	0.000	0.000	0.000
10	A	846	VAL	0	-0.039	0.125	10.178	-0.008	-0.008	0.000	0.000	0.000	0.000
11	A	847	LEU	0	0.030	-0.099	11.668	-0.066	-0.066	0.000	0.000	0.000	0.000
12	A	847	LEU	0	-0.042	0.106	13.666	0.012	0.012	0.000	0.000	0.000	0.000
13	A	848	LEU	0	0.074	-0.086	14.353	-0.039	-0.039	0.000	0.000	0.000	0.000
14	A	848	LEU	0	-0.106	0.052	13.307	-0.030	-0.030	0.000	0.000	0.000	0.000
15	A	849	ASP	0	0.121	-0.068	16.407	0.041	0.041	0.000	0.000	0.000	0.000
16	A	849	ASP	-1	-0.953	-0.825	18.123	0.013	0.013	0.000	0.000	0.000	0.000
17	A	850	ILE	0	0.083	-0.097	19.819	-0.030	-0.030	0.000	0.000	0.000	0.000
18	A	850	ILE	0	-0.175	0.046	18.491	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	851	PHE	0	-0.028	-0.111	21.671	-0.023	-0.023	0.000	0.000	0.000	0.000
20	A	851	PHE	0	-0.122	0.055	23.152	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	852	THR	0	0.190	-0.051	24.071	0.012	0.012	0.000	0.000	0.000	0.000
22	A	852	THR	0	-0.071	0.050	23.452	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	853	GLY	0	-0.049	-0.106	25.542	-0.014	-0.014	0.000	0.000	0.000	0.000
24	A	854	VAL	0	0.040	-0.001	28.432	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	854	VAL	0	-0.136	0.065	28.307	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	855	ARG	0	0.202	-0.065	29.914	0.013	0.013	0.000	0.000	0.000	0.000
27	A	855	ARG	1	0.673	0.961	32.159	-0.059	-0.059	0.000	0.000	0.000	0.000
28	A	856	LEU	0	0.085	-0.104	32.261	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	856	LEU	0	-0.147	0.082	30.533	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	857	TYR	0	0.109	-0.060	33.305	0.010	0.010	0.000	0.000	0.000	0.000
31	A	857	TYR	0	-0.095	0.032	36.530	0.000	0.000	0.000	0.000	0.000	0.000
32	A	858	LEU	0	0.047	-0.122	32.884	-0.009	-0.009	0.000	0.000	0.000	0.000
33	A	858	LEU	0	-0.142	0.095	30.254	0.001	0.001	0.000	0.000	0.000	0.000
34	A	859	PRO	0	0.031	-0.089	34.394	0.009	0.009	0.000	0.000	0.000	0.000
35	A	860	PRO	0	0.072	0.024	35.941	0.003	0.003	0.000	0.000	0.000	0.000
36	A	861	SER	0	0.038	0.018	36.713	0.007	0.007	0.000	0.000	0.000	0.000
37	A	861	SER	0	-0.024	0.090	40.257	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	862	THR	0	-0.045	-0.116	35.092	-0.006	-0.006	0.000	0.000	0.000	0.000
39	A	862	THR	0	-0.047	0.065	33.726	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	863	PRO	0	0.036	-0.079	34.543	0.010	0.010	0.000	0.000	0.000	0.000
41	A	864	ASP	0	0.094	0.020	30.417	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	864	ASP	-1	-0.874	-0.772	28.188	0.138	0.138	0.000	0.000	0.000	0.000
43	A	865	PHE	0	0.123	-0.109	29.753	0.010	0.010	0.000	0.000	0.000	0.000
44	A	865	PHE	0	-0.059	0.121	33.037	0.003	0.003	0.000	0.000	0.000	0.000
45	A	866	SER	0	0.086	-0.050	29.396	0.001	0.001	0.000	0.000	0.000	0.000
46	A	866	SER	0	-0.047	0.059	28.716	0.006	0.006	0.000	0.000	0.000	0.000
47	A	867	ARG	0	0.045	-0.096	25.521	0.019	0.019	0.000	0.000	0.000	0.000
48	A	867	ARG	1	0.776	0.969	24.573	-0.156	-0.156	0.000	0.000	0.000	0.000
49	A	868	LEU	0	0.081	-0.097	25.228	0.016	0.016	0.000	0.000	0.000	0.000
50	A	868	LEU	0	-0.062	0.104	27.606	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	869	ARG	0	0.161	-0.062	26.491	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	869	ARG	1	0.839	1.066	27.793	-0.193	-0.193	0.000	0.000	0.000	0.000
53	A	870	ARG	0	0.090	-0.054	24.012	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	870	ARG	1	0.800	1.017	18.704	-0.382	-0.382	0.000	0.000	0.000	0.000
55	A	871	TYR	0	0.049	-0.087	21.466	0.023	0.023	0.000	0.000	0.000	0.000
56	A	871	TYR	0	-0.102	0.055	18.240	0.021	0.021	0.000	0.000	0.000	0.000
57	A	872	PHE	0	0.163	-0.053	22.074	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	872	PHE	0	-0.112	0.082	26.210	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	873	VAL	0	0.076	-0.093	23.797	-0.016	-0.016	0.000	0.000	0.000	0.000
60	A	873	VAL	0	-0.086	0.094	23.474	0.003	0.003	0.000	0.000	0.000	0.000
61	A	874	ALA	0	0.092	-0.079	19.811	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	874	ALA	0	-0.109	0.068	18.723	0.008	0.008	0.000	0.000	0.000	0.000
63	A	875	PHE	0	-0.020	-0.067	18.690	0.034	0.034	0.000	0.000	0.000	0.000
64	A	875	PHE	0	-0.153	0.018	15.832	0.000	0.000	0.000	0.000	0.000	0.000
65	A	876	ASP	0	0.141	-0.079	20.435	-0.029	-0.029	0.000	0.000	0.000	0.000
66	A	876	ASP	-1	-0.866	-0.776	21.361	0.075	0.075	0.000	0.000	0.000	0.000
67	A	877	GLY	0	0.049	-0.115	22.927	-0.020	-0.020	0.000	0.000	0.000	0.000
68	A	878	ASP	0	0.094	-0.014	26.184	0.023	0.023	0.000	0.000	0.000	0.000
69	A	878	ASP	-1	-0.940	-0.791	28.940	0.078	0.078	0.000	0.000	0.000	0.000
70	A	879	LEU	0	0.084	-0.089	29.200	-0.015	-0.015	0.000	0.000	0.000	0.000
71	A	879	LEU	0	-0.145	0.064	28.769	0.003	0.003	0.000	0.000	0.000	0.000
72	A	880	VAL	0	0.107	-0.093	31.290	0.011	0.011	0.000	0.000	0.000	0.000
73	A	880	VAL	0	-0.083	0.114	34.197	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	881	GLN	0	0.094	-0.105	34.772	0.002	0.002	0.000	0.000	0.000	0.000
75	A	881	GLN	0	-0.093	0.087	34.040	0.001	0.001	0.000	0.000	0.000	0.000
76	A	882	GLU	0	0.139	-0.089	37.208	-0.006	-0.006	0.000	0.000	0.000	0.000
77	A	882	GLU	-1	-0.963	-0.803	40.406	0.068	0.068	0.000	0.000	0.000	0.000
78	A	883	PHE	0	0.056	-0.099	40.430	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	883	PHE	0	-0.067	0.082	38.912	0.001	0.001	0.000	0.000	0.000	0.000
80	A	884	ASP	0	0.071	-0.102	39.066	-0.004	-0.004	0.000	0.000	0.000	0.000
81	A	884	ASP	-1	-0.890	-0.778	37.339	0.062	0.062	0.000	0.000	0.000	0.000
82	A	885	MET	0	0.095	-0.089	39.000	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	885	MET	0	-0.088	0.090	40.223	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	886	THR	0	-0.010	-0.113	40.068	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	886	THR	0	-0.037	0.088	43.488	0.001	0.001	0.000	0.000	0.000	0.000
86	A	887	SER	0	-0.003	-0.070	39.575	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	887	SER	0	-0.053	0.053	38.601	0.001	0.001	0.000	0.000	0.000	0.000
88	A	888	ALA	0	0.139	-0.095	36.158	0.001	0.001	0.000	0.000	0.000	0.000
89	A	888	ALA	0	-0.091	0.101	36.439	0.001	0.001	0.000	0.000	0.000	0.000
90	A	889	THR	0	-0.008	-0.105	34.956	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	889	THR	0	-0.020	0.077	33.545	0.001	0.001	0.000	0.000	0.000	0.000
92	A	890	HIS	0	0.036	-0.086	34.001	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	890	HIS	0	-0.060	0.103	32.289	0.004	0.004	0.000	0.000	0.000	0.000
94	A	891	VAL	0	0.110	-0.095	35.468	0.008	0.008	0.000	0.000	0.000	0.000
95	A	891	VAL	0	-0.054	0.114	38.649	0.000	0.000	0.000	0.000	0.000	0.000
96	A	892	LEU	0	0.079	-0.103	36.672	-0.007	-0.007	0.000	0.000	0.000	0.000
97	A	892	LEU	0	-0.068	0.115	33.338	0.001	0.001	0.000	0.000	0.000	0.000
98	A	893	GLY	0	-0.013	-0.100	37.414	0.003	0.003	0.000	0.000	0.000	0.000
99	A	894	SER	0	0.038	-0.003	40.913	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	894	SER	0	-0.024	0.050	45.430	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	895	ARG	0	0.070	-0.098	42.991	0.005	0.005	0.000	0.000	0.000	0.000
102	A	895	ARG	1	0.762	1.036	41.713	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	896	ASP	0	0.048	-0.100	43.921	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	896	ASP	-1	-0.889	-0.803	48.031	0.018	0.018	0.000	0.000	0.000	0.000
105	A	897	LYS	0	0.015	-0.090	45.550	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	897	LYS	1	0.887	1.054	43.792	-0.035	-0.035	0.000	0.000	0.000	0.000
107	A	898	ASN	0	0.105	-0.094	42.562	0.002	0.002	0.000	0.000	0.000	0.000
108	A	898	ASN	0	-0.137	0.076	40.286	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	899	PRO	0	0.022	-0.095	42.910	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	900	ALA	0	0.129	0.016	42.889	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	900	ALA	0	-0.057	0.116	42.508	0.000	0.000	0.000	0.000	0.000	0.000
112	A	901	ALA	0	0.097	-0.091	38.921	-0.005	-0.005	0.000	0.000	0.000	0.000
113	A	901	ALA	0	-0.111	0.111	38.429	0.001	0.001	0.000	0.000	0.000	0.000
114	A	902	GLN	0	0.060	-0.119	36.548	0.000	0.000	0.000	0.000	0.000	0.000
115	A	902	GLN	0	-0.139	0.075	35.379	-0.004	-0.004	0.000	0.000	0.000	0.000
116	A	903	GLN	0	0.113	-0.100	36.755	0.006	0.006	0.000	0.000	0.000	0.000
117	A	903	GLN	0	-0.094	0.076	39.425	-0.004	-0.004	0.000	0.000	0.000	0.000
118	A	904	VAL	0	-0.018	-0.080	33.833	-0.009	-0.009	0.000	0.000	0.000	0.000
119	A	904	VAL	0	-0.083	0.087	32.665	0.000	0.000	0.000	0.000	0.000	0.000
120	A	905	SER	0	0.058	-0.088	33.695	0.006	0.006	0.000	0.000	0.000	0.000
121	A	905	SER	0	-0.035	0.064	34.309	-0.004	-0.004	0.000	0.000	0.000	0.000
122	A	906	PRO	0	0.071	-0.096	30.872	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	907	GLU	0	0.026	-0.041	29.343	0.007	0.007	0.000	0.000	0.000	0.000
124	A	907	GLU	-1	-0.848	-0.750	31.494	0.028	0.028	0.000	0.000	0.000	0.000
125	A	908	TRP	0	0.075	-0.100	29.007	-0.009	-0.009	0.000	0.000	0.000	0.000
126	A	908	TRP	0	-0.076	0.095	29.689	0.005	0.005	0.000	0.000	0.000	0.000
127	A	909	ILE	0	0.129	-0.059	27.267	-0.016	-0.016	0.000	0.000	0.000	0.000
128	A	909	ILE	0	-0.069	0.109	25.924	0.002	0.002	0.000	0.000	0.000	0.000
129	A	910	TRP	0	0.071	-0.093	24.677	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	910	TRP	0	-0.108	0.070	22.505	0.003	0.003	0.000	0.000	0.000	0.000
131	A	911	ALA	0	0.075	-0.109	24.214	-0.005	-0.005	0.000	0.000	0.000	0.000
132	A	911	ALA	0	-0.058	0.095	27.521	-0.002	-0.002	0.000	0.000	0.000	0.000
133	A	912	CYS	0	0.104	-0.118	24.427	-0.026	-0.026	0.000	0.000	0.000	0.000
134	A	912	CYS	0	-0.099	0.120	24.515	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	913	ILE	0	0.089	-0.077	20.776	-0.031	-0.031	0.000	0.000	0.000	0.000
136	A	913	ILE	0	-0.127	0.097	19.483	0.006	0.006	0.000	0.000	0.000	0.000
137	A	914	ARG	0	0.059	-0.105	19.819	-0.020	-0.020	0.000	0.000	0.000	0.000
138	A	914	ARG	1	0.814	1.046	21.853	0.020	0.020	0.000	0.000	0.000	0.000
139	A	915	LYS	0	-0.043	-0.106	20.740	-0.035	-0.035	0.000	0.000	0.000	0.000
140	A	915	LYS	1	0.919	1.081	22.954	0.163	0.163	0.000	0.000	0.000	0.000
141	A	916	ARG	0	0.090	-0.049	18.068	-0.026	-0.026	0.000	0.000	0.000	0.000
142	A	916	ARG	1	0.838	1.030	12.078	0.374	0.374	0.000	0.000	0.000	0.000
143	A	917	ARG	0	0.143	-0.085	19.409	-0.024	-0.024	0.000	0.000	0.000	0.000
144	A	917	ARG	1	0.821	1.027	20.431	0.220	0.220	0.000	0.000	0.000	0.000
145	A	918	LEU	0	0.132	-0.084	22.496	0.010	0.010	0.000	0.000	0.000	0.000
146	A	918	LEU	0	-0.025	0.143	25.918	-0.001	-0.001	0.000	0.000	0.000	0.000
147	A	919	VAL	0	-0.002	-0.096	26.163	-0.021	-0.021	0.000	0.000	0.000	0.000
148	A	919	VAL	0	-0.084	0.060	25.886	-0.003	-0.003	0.000	0.000	0.000	0.000
149	A	920	ALA	0	0.156	-0.083	28.426	0.011	0.011	0.000	0.000	0.000	0.000
150	A	920	ALA	0	-0.058	0.119	32.782	-0.001	-0.001	0.000	0.000	0.000	0.000
151	A	921	PRO	0	-0.027	-0.102	32.145	0.003	0.003	0.000	0.000	0.000	0.000
152	A	922	SER	0	-0.059	-0.077	33.545	0.001	0.001	0.000	0.000	0.000	0.000
153	A	922	SER	0	0.053	0.057	32.473	0.000	0.000	0.000	0.000	0.000	0.000

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