FMO DATABASE

FMODB ID: 2N4KR

Calculation Name: 3VNN-A-Xray372

Preferred Name: LIG4/XRCC4

Target Type: PROTEIN COMPLEX

Ligand Name:

ligand 3-letter code:

PDB ID: 3VNN

Chain ID: A

ChEMBL ID: CHEMBL4296097

UniProt ID: P49917

Base Structure: X-ray

Registration Date: 2023-09-22

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	126
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1133525.122002
FMO2-HF: Nuclear repulsion	1080661.880855
FMO2-HF: Total energy	-52863.241146
FMO2-MP2: Total energy	-53012.521158

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:268:PHE)

Summations of interaction energy for fragment #1(A:268:PHE)

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.
-6.856	-1.699	1.3	-2.703	-3.754	-0.009

Interaction energy analysis for fragmet #1(A:268:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : 0.003

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	270	ILE	0	0.008	-0.002	2.339	-6.423	-1.329	1.301	-2.697	-3.698	-0.009
4	A	271	GLU	-1	-0.899	-0.932	5.034	-0.440	-0.377	-0.001	-0.006	-0.056	0.000
5	A	272	THR	0	-0.048	-0.051	8.724	-0.024	-0.024	0.000	0.000	0.000	0.000
6	A	273	LYS	1	0.807	0.900	11.449	0.394	0.394	0.000	0.000	0.000	0.000
7	A	274	LEU	0	-0.005	-0.002	14.808	-0.002	-0.002	0.000	0.000	0.000	0.000
8	A	275	ASP	-1	-0.850	-0.919	17.445	-0.289	-0.289	0.000	0.000	0.000	0.000
9	A	276	GLY	0	0.052	0.010	21.277	-0.007	-0.007	0.000	0.000	0.000	0.000
10	A	277	GLU	-1	-0.920	-0.957	24.139	-0.156	-0.156	0.000	0.000	0.000	0.000
11	A	278	ARG	1	0.719	0.839	25.660	0.203	0.203	0.000	0.000	0.000	0.000
12	A	279	MET	0	-0.046	-0.008	28.387	0.020	0.020	0.000	0.000	0.000	0.000
13	A	280	GLN	0	0.015	0.009	29.388	0.000	0.000	0.000	0.000	0.000	0.000
14	A	281	MET	0	0.004	0.009	31.071	0.003	0.003	0.000	0.000	0.000	0.000
15	A	282	HIS	0	-0.032	-0.037	32.816	0.004	0.004	0.000	0.000	0.000	0.000
16	A	283	LYS	1	0.898	0.958	32.957	0.123	0.123	0.000	0.000	0.000	0.000
17	A	284	ASP	-1	-0.824	-0.933	35.817	-0.084	-0.084	0.000	0.000	0.000	0.000
18	A	285	GLY	0	0.034	0.012	38.977	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	286	ASP	-1	-0.866	-0.932	38.480	-0.099	-0.099	0.000	0.000	0.000	0.000
20	A	287	VAL	0	0.015	0.038	39.534	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	288	TYR	0	-0.056	-0.035	33.906	0.000	0.000	0.000	0.000	0.000	0.000
22	A	289	LYS	1	0.823	0.891	37.292	0.101	0.101	0.000	0.000	0.000	0.000
23	A	290	TYR	0	0.017	0.010	31.242	-0.011	-0.011	0.000	0.000	0.000	0.000
24	A	291	PHE	0	-0.033	-0.019	34.724	0.007	0.007	0.000	0.000	0.000	0.000
25	A	292	SER	0	0.086	0.034	33.352	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	293	ARG	1	0.935	0.973	30.371	0.144	0.144	0.000	0.000	0.000	0.000
27	A	294	ASN	0	-0.027	-0.019	33.258	0.000	0.000	0.000	0.000	0.000	0.000
28	A	295	GLY	0	0.008	0.013	36.554	0.007	0.007	0.000	0.000	0.000	0.000
29	A	296	TYR	0	-0.038	-0.012	37.695	0.007	0.007	0.000	0.000	0.000	0.000
30	A	297	ASN	0	0.045	0.019	37.731	-0.011	-0.011	0.000	0.000	0.000	0.000
31	A	298	TYR	0	0.053	0.015	34.339	0.006	0.006	0.000	0.000	0.000	0.000
32	A	299	THR	0	-0.010	-0.012	36.733	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	300	ASP	-1	-0.914	-0.946	38.165	-0.107	-0.107	0.000	0.000	0.000	0.000
34	A	301	GLN	0	-0.006	0.011	33.982	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	302	PHE	0	-0.021	-0.027	31.058	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	303	GLY	0	0.084	0.042	34.638	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	304	ALA	0	-0.033	-0.023	37.351	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	305	SER	0	-0.003	-0.021	39.539	0.005	0.005	0.000	0.000	0.000	0.000
39	A	306	PRO	0	-0.025	-0.012	37.039	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	307	THR	0	-0.091	-0.055	38.010	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	308	GLU	-1	-0.829	-0.903	39.541	-0.101	-0.101	0.000	0.000	0.000	0.000
42	A	309	GLY	0	0.017	-0.008	36.206	-0.006	-0.006	0.000	0.000	0.000	0.000
43	A	310	SER	0	-0.062	-0.050	36.673	0.003	0.003	0.000	0.000	0.000	0.000
44	A	311	LEU	0	-0.023	0.002	31.293	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	312	THR	0	-0.076	-0.042	29.878	-0.018	-0.018	0.000	0.000	0.000	0.000
46	A	313	PRO	0	0.081	0.067	31.778	0.001	0.001	0.000	0.000	0.000	0.000
47	A	314	PHE	0	-0.028	-0.043	29.415	0.000	0.000	0.000	0.000	0.000	0.000
48	A	315	ILE	0	-0.001	0.008	27.633	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	316	HIS	0	0.012	0.040	29.806	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	317	ASN	0	-0.046	-0.026	30.816	0.008	0.008	0.000	0.000	0.000	0.000
51	A	318	ALA	0	0.024	0.013	26.600	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	319	PHE	0	0.003	-0.013	27.487	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	320	LYS	1	0.903	0.957	26.584	0.134	0.134	0.000	0.000	0.000	0.000
54	A	321	ALA	0	-0.001	-0.020	29.833	0.008	0.008	0.000	0.000	0.000	0.000
55	A	322	ASP	-1	-0.869	-0.924	33.386	-0.079	-0.079	0.000	0.000	0.000	0.000
56	A	323	ILE	0	-0.065	-0.014	30.847	0.003	0.003	0.000	0.000	0.000	0.000
57	A	324	GLN	0	0.006	0.010	33.904	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	325	ILE	0	0.014	-0.001	36.734	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	326	CYS	0	-0.044	-0.021	32.182	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	327	ILE	0	-0.050	0.010	33.047	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	328	LEU	0	0.026	0.001	27.969	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	329	ASP	-1	-0.775	-0.862	27.606	-0.181	-0.181	0.000	0.000	0.000	0.000
63	A	330	GLY	0	0.082	0.019	24.655	-0.015	-0.015	0.000	0.000	0.000	0.000
64	A	331	GLU	-1	-0.788	-0.890	22.924	-0.234	-0.234	0.000	0.000	0.000	0.000
65	A	332	MET	0	-0.063	-0.016	23.880	-0.018	-0.018	0.000	0.000	0.000	0.000
66	A	333	MET	0	-0.036	-0.003	19.095	0.005	0.005	0.000	0.000	0.000	0.000
67	A	334	ALA	0	0.038	0.018	22.568	0.015	0.015	0.000	0.000	0.000	0.000
68	A	335	TYR	0	-0.002	-0.001	18.473	-0.014	-0.014	0.000	0.000	0.000	0.000
69	A	336	ASN	0	0.023	-0.015	20.039	0.054	0.054	0.000	0.000	0.000	0.000
70	A	337	PRO	0	0.020	0.007	19.833	-0.026	-0.026	0.000	0.000	0.000	0.000
71	A	338	ASN	0	-0.022	-0.001	19.863	-0.028	-0.028	0.000	0.000	0.000	0.000
72	A	339	THR	0	0.010	0.011	16.608	0.012	0.012	0.000	0.000	0.000	0.000
73	A	340	GLN	0	0.007	0.024	15.271	-0.054	-0.054	0.000	0.000	0.000	0.000
74	A	341	THR	0	0.018	0.001	13.404	-0.041	-0.041	0.000	0.000	0.000	0.000
75	A	342	PHE	0	0.031	0.002	15.708	0.052	0.052	0.000	0.000	0.000	0.000
76	A	343	MET	0	-0.029	-0.009	17.484	-0.026	-0.026	0.000	0.000	0.000	0.000
77	A	344	GLN	0	0.038	0.037	18.147	0.016	0.016	0.000	0.000	0.000	0.000
78	A	345	LYS	1	0.946	0.972	20.193	0.241	0.241	0.000	0.000	0.000	0.000
79	A	359	ASP	-1	-0.911	-0.957	28.615	-0.178	-0.178	0.000	0.000	0.000	0.000
80	A	360	LEU	0	-0.082	-0.036	23.811	-0.012	-0.012	0.000	0.000	0.000	0.000
81	A	361	GLN	0	-0.017	-0.004	25.062	0.018	0.018	0.000	0.000	0.000	0.000
82	A	362	THR	0	0.027	0.014	24.891	-0.019	-0.019	0.000	0.000	0.000	0.000
83	A	363	CYS	0	-0.070	0.001	20.976	0.005	0.005	0.000	0.000	0.000	0.000
84	A	364	TYR	0	-0.001	-0.007	24.416	0.008	0.008	0.000	0.000	0.000	0.000
85	A	365	CYS	0	0.004	0.012	19.924	-0.012	-0.012	0.000	0.000	0.000	0.000
86	A	366	VAL	0	0.003	0.008	22.012	0.012	0.012	0.000	0.000	0.000	0.000
87	A	367	PHE	0	-0.012	-0.002	20.589	-0.020	-0.020	0.000	0.000	0.000	0.000
88	A	368	ASP	-1	-0.802	-0.873	22.432	-0.163	-0.163	0.000	0.000	0.000	0.000
89	A	369	VAL	0	0.011	0.011	25.523	0.002	0.002	0.000	0.000	0.000	0.000
90	A	370	LEU	0	-0.034	-0.016	28.587	0.009	0.009	0.000	0.000	0.000	0.000
91	A	371	MET	0	-0.040	-0.035	32.061	0.012	0.012	0.000	0.000	0.000	0.000
92	A	372	VAL	0	0.030	0.026	31.044	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	373	ASN	0	0.022	-0.003	34.002	0.002	0.002	0.000	0.000	0.000	0.000
94	A	374	ASN	0	0.006	-0.002	36.888	0.005	0.005	0.000	0.000	0.000	0.000
95	A	375	LYS	1	0.925	0.973	34.061	0.082	0.082	0.000	0.000	0.000	0.000
96	A	376	LYS	1	0.984	0.989	34.965	0.087	0.087	0.000	0.000	0.000	0.000
97	A	377	LEU	0	-0.026	-0.017	32.127	0.007	0.007	0.000	0.000	0.000	0.000
98	A	378	GLY	0	0.024	0.007	31.736	-0.005	-0.005	0.000	0.000	0.000	0.000
99	A	379	HIS	0	0.010	0.000	32.025	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	380	GLU	-1	-0.832	-0.888	28.734	-0.079	-0.079	0.000	0.000	0.000	0.000
101	A	381	THR	0	0.036	0.005	25.141	-0.007	-0.007	0.000	0.000	0.000	0.000
102	A	382	LEU	0	0.019	0.013	22.548	0.000	0.000	0.000	0.000	0.000	0.000
103	A	383	ARG	1	0.823	0.883	18.263	0.193	0.193	0.000	0.000	0.000	0.000
104	A	384	LYS	1	0.900	0.931	21.838	0.071	0.071	0.000	0.000	0.000	0.000
105	A	385	ARG	1	0.773	0.873	24.515	0.136	0.136	0.000	0.000	0.000	0.000
106	A	386	TYR	0	0.045	0.016	15.718	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	387	GLU	-1	-0.756	-0.846	19.266	-0.212	-0.212	0.000	0.000	0.000	0.000
108	A	388	ILE	0	-0.055	-0.017	22.050	0.001	0.001	0.000	0.000	0.000	0.000
109	A	389	LEU	0	0.006	0.015	22.027	0.007	0.007	0.000	0.000	0.000	0.000
110	A	390	SER	0	-0.036	-0.028	20.577	0.003	0.003	0.000	0.000	0.000	0.000
111	A	391	SER	0	-0.037	-0.024	22.304	0.013	0.013	0.000	0.000	0.000	0.000
112	A	392	ILE	0	-0.023	-0.008	25.800	0.016	0.016	0.000	0.000	0.000	0.000
113	A	393	PHE	0	-0.016	-0.013	23.589	0.012	0.012	0.000	0.000	0.000	0.000
114	A	394	THR	0	-0.016	-0.003	21.853	0.001	0.001	0.000	0.000	0.000	0.000
115	A	395	PRO	0	0.000	0.012	18.890	0.012	0.012	0.000	0.000	0.000	0.000
116	A	396	ILE	0	0.011	0.008	21.548	0.003	0.003	0.000	0.000	0.000	0.000
117	A	397	PRO	0	-0.014	-0.020	18.270	-0.006	-0.006	0.000	0.000	0.000	0.000
118	A	398	GLY	0	0.007	-0.014	19.546	0.028	0.028	0.000	0.000	0.000	0.000
119	A	399	ARG	1	0.815	0.882	21.041	0.230	0.230	0.000	0.000	0.000	0.000
120	A	400	ILE	0	0.009	0.010	22.669	0.023	0.023	0.000	0.000	0.000	0.000
121	A	401	GLU	-1	-0.740	-0.887	17.088	-0.426	-0.426	0.000	0.000	0.000	0.000
122	A	402	ILE	0	-0.025	-0.002	18.659	0.033	0.033	0.000	0.000	0.000	0.000
123	A	403	VAL	0	0.002	-0.002	16.452	-0.062	-0.062	0.000	0.000	0.000	0.000
124	A	404	GLN	0	-0.038	-0.028	14.961	0.083	0.083	0.000	0.000	0.000	0.000
125	A	405	LYS	1	0.802	0.896	17.808	0.189	0.189	0.000	0.000	0.000	0.000
126	A	406	THR	0	-0.024	0.005	14.906	0.053	0.053	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:268:PHE)