FMO DATABASE

FMODB ID: 378LL

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	OptH
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	-537261.899218
FMO2-HF: Nuclear repulsion	505103.396112
FMO2-HF: Total energy	-32158.503106
FMO2-MP2: Total energy	-32252.964255

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.
-4.734	-1.461	0.929	-1.969	-2.233	-0.008

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 : 0.107 / q_NPA : 0.019

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	-0.054	0.097	2.567	-2.568	-0.667	0.938	-1.295	-1.543	-0.011
5	A	844	THR	0	0.063	-0.077	3.785	-1.192	0.089	-0.008	-0.663	-0.611	0.003
6	A	844	THR	0	-0.001	0.078	7.585	-0.007	-0.007	0.000	0.000	0.000	0.000
7	A	845	LYS	0	0.058	-0.105	6.516	0.349	0.349	0.000	0.000	0.000	0.000
8	A	845	LYS	1	0.862	1.086	3.918	-1.275	-1.184	-0.001	-0.011	-0.079	0.000
9	A	846	VAL	0	0.051	-0.131	8.294	0.073	0.073	0.000	0.000	0.000	0.000
10	A	846	VAL	0	-0.057	0.117	9.967	-0.012	-0.012	0.000	0.000	0.000	0.000
11	A	847	LEU	0	0.029	-0.141	11.490	-0.034	-0.034	0.000	0.000	0.000	0.000
12	A	847	LEU	0	-0.028	0.135	13.860	0.011	0.011	0.000	0.000	0.000	0.000
13	A	848	LEU	0	0.055	-0.095	14.295	-0.028	-0.028	0.000	0.000	0.000	0.000
14	A	848	LEU	0	-0.121	0.058	14.071	-0.012	-0.012	0.000	0.000	0.000	0.000
15	A	849	ASP	0	0.163	-0.111	16.163	0.033	0.033	0.000	0.000	0.000	0.000
16	A	849	ASP	-1	-0.973	-0.797	19.042	-0.039	-0.039	0.000	0.000	0.000	0.000
17	A	850	ILE	0	0.062	-0.090	19.640	-0.021	-0.021	0.000	0.000	0.000	0.000
18	A	850	ILE	0	-0.173	0.052	18.653	0.000	0.000	0.000	0.000	0.000	0.000
19	A	851	PHE	0	-0.041	-0.119	21.731	-0.010	-0.010	0.000	0.000	0.000	0.000
20	A	851	PHE	0	-0.129	0.051	23.112	0.001	0.001	0.000	0.000	0.000	0.000
21	A	852	THR	0	0.195	-0.050	23.917	0.011	0.011	0.000	0.000	0.000	0.000
22	A	852	THR	0	-0.047	0.065	23.105	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	853	GLY	0	-0.066	-0.113	25.378	-0.007	-0.007	0.000	0.000	0.000	0.000
24	A	854	VAL	0	0.039	-0.012	28.249	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	854	VAL	0	-0.140	0.074	28.230	0.000	0.000	0.000	0.000	0.000	0.000
26	A	855	ARG	0	0.144	-0.083	29.594	0.006	0.006	0.000	0.000	0.000	0.000
27	A	855	ARG	1	0.759	0.996	32.371	-0.016	-0.016	0.000	0.000	0.000	0.000
28	A	856	LEU	0	0.136	-0.089	31.885	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	856	LEU	0	-0.135	0.097	30.335	0.000	0.000	0.000	0.000	0.000	0.000
30	A	857	TYR	0	0.088	-0.070	32.733	0.005	0.005	0.000	0.000	0.000	0.000
31	A	857	TYR	0	-0.039	0.102	36.180	0.001	0.001	0.000	0.000	0.000	0.000
32	A	858	LEU	0	0.125	-0.131	32.338	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	858	LEU	0	-0.174	0.110	29.704	0.001	0.001	0.000	0.000	0.000	0.000
34	A	859	PRO	0	0.030	-0.082	33.787	0.004	0.004	0.000	0.000	0.000	0.000
35	A	860	PRO	0	0.075	0.049	35.073	0.003	0.003	0.000	0.000	0.000	0.000
36	A	861	SER	0	0.049	0.029	36.021	0.005	0.005	0.000	0.000	0.000	0.000
37	A	861	SER	0	-0.035	0.073	39.546	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	862	THR	0	-0.020	-0.121	34.453	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	862	THR	0	-0.090	0.035	33.089	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	863	PRO	0	0.045	-0.066	34.224	0.006	0.006	0.000	0.000	0.000	0.000
41	A	864	ASP	0	0.104	-0.014	30.249	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	864	ASP	-1	-0.912	-0.790	28.315	0.101	0.101	0.000	0.000	0.000	0.000
43	A	865	PHE	0	0.123	-0.098	29.233	0.006	0.006	0.000	0.000	0.000	0.000
44	A	865	PHE	0	-0.085	0.116	31.631	0.002	0.002	0.000	0.000	0.000	0.000
45	A	866	SER	0	0.086	-0.058	28.461	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	866	SER	0	-0.048	0.063	27.494	0.003	0.003	0.000	0.000	0.000	0.000
47	A	867	ARG	0	0.028	-0.099	24.763	0.006	0.006	0.000	0.000	0.000	0.000
48	A	867	ARG	1	0.833	1.019	24.131	-0.125	-0.125	0.000	0.000	0.000	0.000
49	A	868	LEU	0	0.109	-0.110	24.499	0.009	0.009	0.000	0.000	0.000	0.000
50	A	868	LEU	0	-0.052	0.128	27.075	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	869	ARG	0	0.135	-0.074	25.831	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	869	ARG	1	0.854	1.073	25.864	-0.106	-0.106	0.000	0.000	0.000	0.000
53	A	870	ARG	0	0.085	-0.070	22.956	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	870	ARG	1	0.849	1.041	17.481	-0.249	-0.249	0.000	0.000	0.000	0.000
55	A	871	TYR	0	0.040	-0.081	20.845	0.009	0.009	0.000	0.000	0.000	0.000
56	A	871	TYR	0	-0.109	0.055	18.088	0.009	0.009	0.000	0.000	0.000	0.000
57	A	872	PHE	0	0.121	-0.054	21.599	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	872	PHE	0	-0.092	0.071	25.827	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	873	VAL	0	0.076	-0.080	23.490	-0.013	-0.013	0.000	0.000	0.000	0.000
60	A	873	VAL	0	-0.101	0.073	22.290	0.002	0.002	0.000	0.000	0.000	0.000
61	A	874	ALA	0	0.095	-0.063	18.991	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	874	ALA	0	-0.118	0.059	17.910	0.006	0.006	0.000	0.000	0.000	0.000
63	A	875	PHE	0	0.045	-0.035	18.659	0.002	0.002	0.000	0.000	0.000	0.000
64	A	875	PHE	0	-0.232	-0.002	15.692	0.007	0.007	0.000	0.000	0.000	0.000
65	A	876	ASP	0	0.154	-0.101	20.126	-0.015	-0.015	0.000	0.000	0.000	0.000
66	A	876	ASP	-1	-0.866	-0.771	20.973	0.001	0.001	0.000	0.000	0.000	0.000
67	A	877	GLY	0	0.020	-0.107	22.498	-0.010	-0.010	0.000	0.000	0.000	0.000
68	A	878	ASP	0	0.104	-0.022	25.798	0.011	0.011	0.000	0.000	0.000	0.000
69	A	878	ASP	-1	-0.955	-0.803	28.902	0.022	0.022	0.000	0.000	0.000	0.000
70	A	879	LEU	0	0.062	-0.115	28.758	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	879	LEU	0	-0.126	0.066	28.231	0.003	0.003	0.000	0.000	0.000	0.000
72	A	880	VAL	0	0.072	-0.098	30.563	0.003	0.003	0.000	0.000	0.000	0.000
73	A	880	VAL	0	-0.070	0.134	33.714	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	881	GLN	0	0.081	-0.118	34.146	0.003	0.003	0.000	0.000	0.000	0.000
75	A	881	GLN	0	-0.057	0.101	33.339	0.000	0.000	0.000	0.000	0.000	0.000
76	A	882	GLU	0	0.152	-0.124	36.472	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	882	GLU	-1	-1.023	-0.836	39.756	0.035	0.035	0.000	0.000	0.000	0.000
78	A	883	PHE	0	0.025	-0.102	39.677	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	883	PHE	0	-0.047	0.097	38.040	0.001	0.001	0.000	0.000	0.000	0.000
80	A	884	ASP	0	0.085	-0.121	38.686	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	884	ASP	-1	-1.005	-0.836	37.853	0.023	0.023	0.000	0.000	0.000	0.000
82	A	885	MET	0	0.102	-0.075	38.654	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	885	MET	0	-0.095	0.088	39.794	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	886	THR	0	-0.028	-0.112	39.729	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	886	THR	0	-0.035	0.065	43.510	0.000	0.000	0.000	0.000	0.000	0.000
86	A	887	SER	0	-0.006	-0.072	39.052	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	887	SER	0	-0.030	0.085	38.086	0.000	0.000	0.000	0.000	0.000	0.000
88	A	888	ALA	0	0.078	-0.094	36.080	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	888	ALA	0	-0.066	0.100	36.172	0.001	0.001	0.000	0.000	0.000	0.000
90	A	889	THR	0	0.019	-0.089	34.970	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	889	THR	0	-0.013	0.066	33.529	0.000	0.000	0.000	0.000	0.000	0.000
92	A	890	HIS	0	0.027	-0.083	33.925	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	890	HIS	0	-0.039	0.113	32.213	0.002	0.002	0.000	0.000	0.000	0.000
94	A	891	VAL	0	0.079	-0.102	35.405	0.004	0.004	0.000	0.000	0.000	0.000
95	A	891	VAL	0	-0.016	0.124	38.716	0.000	0.000	0.000	0.000	0.000	0.000
96	A	892	LEU	0	0.058	-0.114	36.289	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	892	LEU	0	-0.068	0.137	33.113	0.001	0.001	0.000	0.000	0.000	0.000
98	A	893	GLY	0	-0.015	-0.098	37.045	0.001	0.001	0.000	0.000	0.000	0.000
99	A	894	SER	0	0.097	0.028	40.567	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	894	SER	0	-0.037	0.072	44.782	0.000	0.000	0.000	0.000	0.000	0.000
101	A	895	ARG	0	0.047	-0.109	42.715	0.002	0.002	0.000	0.000	0.000	0.000
102	A	895	ARG	1	0.815	1.031	41.580	0.001	0.001	0.000	0.000	0.000	0.000
103	A	896	ASP	0	0.106	-0.083	43.818	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	896	ASP	-1	-0.988	-0.838	47.667	0.009	0.009	0.000	0.000	0.000	0.000
105	A	897	LYS	0	-0.005	-0.117	45.428	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	897	LYS	1	0.894	1.059	43.978	-0.019	-0.019	0.000	0.000	0.000	0.000
107	A	898	ASN	0	0.118	-0.107	42.552	0.000	0.000	0.000	0.000	0.000	0.000
108	A	898	ASN	0	-0.137	0.089	40.033	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	899	PRO	0	0.016	-0.084	42.833	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	900	ALA	0	0.123	0.021	42.744	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	900	ALA	0	-0.039	0.112	42.196	0.000	0.000	0.000	0.000	0.000	0.000
112	A	901	ALA	0	0.074	-0.084	38.963	-0.003	-0.003	0.000	0.000	0.000	0.000
113	A	901	ALA	0	-0.083	0.103	38.478	0.001	0.001	0.000	0.000	0.000	0.000
114	A	902	GLN	0	0.066	-0.124	36.420	0.000	0.000	0.000	0.000	0.000	0.000
115	A	902	GLN	0	-0.120	0.104	34.880	-0.003	-0.003	0.000	0.000	0.000	0.000
116	A	903	GLN	0	0.111	-0.116	36.700	0.003	0.003	0.000	0.000	0.000	0.000
117	A	903	GLN	0	-0.119	0.094	39.064	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	904	VAL	0	0.008	-0.090	33.550	-0.004	-0.004	0.000	0.000	0.000	0.000
119	A	904	VAL	0	-0.096	0.084	32.543	0.000	0.000	0.000	0.000	0.000	0.000
120	A	905	SER	0	0.025	-0.134	33.107	0.002	0.002	0.000	0.000	0.000	0.000
121	A	905	SER	0	0.013	0.104	33.551	0.000	0.000	0.000	0.000	0.000	0.000
122	A	906	PRO	0	0.057	-0.079	30.624	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	907	GLU	0	0.065	-0.029	29.269	0.005	0.005	0.000	0.000	0.000	0.000
124	A	907	GLU	-1	-0.916	-0.806	31.647	0.034	0.034	0.000	0.000	0.000	0.000
125	A	908	TRP	0	0.082	-0.104	29.065	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	908	TRP	0	-0.093	0.084	29.391	0.003	0.003	0.000	0.000	0.000	0.000
127	A	909	ILE	0	0.116	-0.071	27.212	-0.010	-0.010	0.000	0.000	0.000	0.000
128	A	909	ILE	0	-0.074	0.112	25.637	0.001	0.001	0.000	0.000	0.000	0.000
129	A	910	TRP	0	0.071	-0.102	24.646	-0.002	-0.002	0.000	0.000	0.000	0.000
130	A	910	TRP	0	-0.078	0.087	22.494	0.003	0.003	0.000	0.000	0.000	0.000
131	A	911	ALA	0	0.060	-0.108	24.078	0.002	0.002	0.000	0.000	0.000	0.000
132	A	911	ALA	0	-0.053	0.103	27.468	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	912	CYS	0	0.084	-0.135	24.439	-0.012	-0.012	0.000	0.000	0.000	0.000
134	A	912	CYS	0	-0.082	0.142	24.404	-0.003	-0.003	0.000	0.000	0.000	0.000
135	A	913	ILE	0	0.071	-0.072	20.851	-0.022	-0.022	0.000	0.000	0.000	0.000
136	A	913	ILE	0	-0.097	0.098	19.386	0.005	0.005	0.000	0.000	0.000	0.000
137	A	914	ARG	0	0.078	-0.105	19.658	-0.006	-0.006	0.000	0.000	0.000	0.000
138	A	914	ARG	1	0.811	1.046	21.880	-0.018	-0.018	0.000	0.000	0.000	0.000
139	A	915	LYS	0	-0.029	-0.135	20.088	-0.015	-0.015	0.000	0.000	0.000	0.000
140	A	915	LYS	1	0.906	1.088	23.115	0.072	0.072	0.000	0.000	0.000	0.000
141	A	916	ARG	0	0.054	-0.064	18.159	-0.018	-0.018	0.000	0.000	0.000	0.000
142	A	916	ARG	1	0.858	1.050	12.419	0.189	0.189	0.000	0.000	0.000	0.000
143	A	917	ARG	0	0.133	-0.077	19.403	-0.019	-0.019	0.000	0.000	0.000	0.000
144	A	917	ARG	1	0.848	1.048	20.952	0.139	0.139	0.000	0.000	0.000	0.000
145	A	918	LEU	0	0.129	-0.118	22.548	0.010	0.010	0.000	0.000	0.000	0.000
146	A	918	LEU	0	-0.024	0.154	25.792	0.000	0.000	0.000	0.000	0.000	0.000
147	A	919	VAL	0	0.002	-0.099	26.139	-0.012	-0.012	0.000	0.000	0.000	0.000
148	A	919	VAL	0	-0.090	0.068	25.986	-0.001	-0.001	0.000	0.000	0.000	0.000
149	A	920	ALA	0	0.151	-0.113	28.325	0.005	0.005	0.000	0.000	0.000	0.000
150	A	920	ALA	0	-0.068	0.132	32.831	0.000	0.000	0.000	0.000	0.000	0.000
151	A	921	PRO	0	-0.049	-0.115	32.101	0.003	0.003	0.000	0.000	0.000	0.000
152	A	922	SER	0	-0.025	-0.029	33.620	0.000	0.000	0.000	0.000	0.000	0.000
153	A	922	SER	0	0.070	0.062	32.285	0.002	0.002	0.000	0.000	0.000	0.000

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