FMO DATABASE

FMODB ID: 76YJK

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:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
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
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1134784.545527
FMO2-HF: Nuclear repulsion	1081923.090436
FMO2-HF: Total energy	-52861.45509
FMO2-MP2: Total energy	-53010.927883

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.
-5.834	-0.63	0.9	-2.608	-3.495	-0.004

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 : 0.002 / q_NPA : 0.005

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	0.002	0.002	2.444	-5.383	-0.257	0.901	-2.601	-3.426	-0.004
4	A	271	GLU	-1	-0.930	-0.949	4.939	-0.451	-0.373	-0.001	-0.007	-0.069	0.000
5	A	272	THR	0	-0.046	-0.042	8.537	0.010	0.010	0.000	0.000	0.000	0.000
6	A	273	LYS	1	0.784	0.891	11.418	0.396	0.396	0.000	0.000	0.000	0.000
7	A	274	LEU	0	-0.010	-0.016	14.768	-0.001	-0.001	0.000	0.000	0.000	0.000
8	A	275	ASP	-1	-0.838	-0.902	17.468	-0.280	-0.280	0.000	0.000	0.000	0.000
9	A	276	GLY	0	0.059	0.017	21.272	-0.009	-0.009	0.000	0.000	0.000	0.000
10	A	277	GLU	-1	-0.936	-0.960	24.003	-0.159	-0.159	0.000	0.000	0.000	0.000
11	A	278	ARG	1	0.707	0.842	26.091	0.190	0.190	0.000	0.000	0.000	0.000
12	A	279	MET	0	-0.034	0.002	28.379	0.018	0.018	0.000	0.000	0.000	0.000
13	A	280	GLN	0	0.004	0.003	29.524	0.001	0.001	0.000	0.000	0.000	0.000
14	A	281	MET	0	0.021	0.014	31.243	0.002	0.002	0.000	0.000	0.000	0.000
15	A	282	HIS	0	-0.031	-0.031	32.899	0.006	0.006	0.000	0.000	0.000	0.000
16	A	283	LYS	1	0.889	0.937	32.661	0.114	0.114	0.000	0.000	0.000	0.000
17	A	284	ASP	-1	-0.896	-0.952	35.908	-0.076	-0.076	0.000	0.000	0.000	0.000
18	A	285	GLY	0	0.004	0.007	38.142	0.000	0.000	0.000	0.000	0.000	0.000
19	A	286	ASP	-1	-0.880	-0.931	37.833	-0.090	-0.090	0.000	0.000	0.000	0.000
20	A	287	VAL	0	0.053	0.042	39.019	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	288	TYR	0	-0.121	-0.074	34.169	0.000	0.000	0.000	0.000	0.000	0.000
22	A	289	LYS	1	0.872	0.924	37.303	0.096	0.096	0.000	0.000	0.000	0.000
23	A	290	TYR	0	0.053	0.022	31.209	-0.009	-0.009	0.000	0.000	0.000	0.000
24	A	291	PHE	0	-0.040	-0.007	34.854	0.005	0.005	0.000	0.000	0.000	0.000
25	A	292	SER	0	0.078	0.029	33.455	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	293	ARG	1	0.960	0.986	30.530	0.137	0.137	0.000	0.000	0.000	0.000
27	A	294	ASN	0	-0.036	-0.030	33.603	0.001	0.001	0.000	0.000	0.000	0.000
28	A	295	GLY	0	0.024	0.045	36.587	0.006	0.006	0.000	0.000	0.000	0.000
29	A	296	TYR	0	-0.005	-0.026	37.817	0.005	0.005	0.000	0.000	0.000	0.000
30	A	297	ASN	0	0.023	0.025	38.324	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	298	TYR	0	0.087	0.018	34.983	0.004	0.004	0.000	0.000	0.000	0.000
32	A	299	THR	0	-0.064	-0.049	36.517	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	300	ASP	-1	-0.906	-0.949	38.370	-0.100	-0.100	0.000	0.000	0.000	0.000
34	A	301	GLN	0	-0.061	-0.016	33.671	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	302	PHE	0	0.002	-0.007	30.577	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	303	GLY	0	0.114	0.043	34.386	0.000	0.000	0.000	0.000	0.000	0.000
37	A	304	ALA	0	-0.010	-0.014	36.924	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	305	SER	0	0.006	-0.003	39.223	0.005	0.005	0.000	0.000	0.000	0.000
39	A	306	PRO	0	0.009	0.003	36.429	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	307	THR	0	-0.094	-0.063	37.406	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	308	GLU	-1	-0.845	-0.850	38.784	-0.101	-0.101	0.000	0.000	0.000	0.000
42	A	309	GLY	0	-0.053	-0.094	35.777	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	310	SER	0	0.022	-0.016	36.749	0.004	0.004	0.000	0.000	0.000	0.000
44	A	311	LEU	0	0.008	0.011	31.385	-0.007	-0.007	0.000	0.000	0.000	0.000
45	A	312	THR	0	-0.115	-0.075	29.795	-0.018	-0.018	0.000	0.000	0.000	0.000
46	A	313	PRO	0	0.080	0.113	31.829	0.001	0.001	0.000	0.000	0.000	0.000
47	A	314	PHE	0	-0.027	-0.042	29.499	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	315	ILE	0	-0.014	-0.007	27.311	0.002	0.002	0.000	0.000	0.000	0.000
49	A	316	HIS	0	0.012	0.051	29.489	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	317	ASN	0	-0.058	-0.039	30.634	0.010	0.010	0.000	0.000	0.000	0.000
51	A	318	ALA	0	0.039	0.023	26.036	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	319	PHE	0	0.037	-0.008	27.939	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	320	LYS	1	0.918	0.982	26.628	0.112	0.112	0.000	0.000	0.000	0.000
54	A	321	ALA	0	0.013	-0.008	29.726	0.006	0.006	0.000	0.000	0.000	0.000
55	A	322	ASP	-1	-0.912	-0.957	33.207	-0.068	-0.068	0.000	0.000	0.000	0.000
56	A	323	ILE	0	-0.097	-0.032	30.465	0.002	0.002	0.000	0.000	0.000	0.000
57	A	324	GLN	0	0.005	0.006	33.668	0.000	0.000	0.000	0.000	0.000	0.000
58	A	325	ILE	0	0.031	0.006	36.724	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	326	CYS	0	-0.048	-0.023	31.978	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	327	ILE	0	-0.041	-0.006	32.800	0.000	0.000	0.000	0.000	0.000	0.000
61	A	328	LEU	0	0.014	-0.004	27.459	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	329	ASP	-1	-0.804	-0.873	27.881	-0.173	-0.173	0.000	0.000	0.000	0.000
63	A	330	GLY	0	0.054	0.008	24.904	-0.012	-0.012	0.000	0.000	0.000	0.000
64	A	331	GLU	-1	-0.836	-0.928	23.068	-0.225	-0.225	0.000	0.000	0.000	0.000
65	A	332	MET	0	-0.063	-0.026	23.820	-0.021	-0.021	0.000	0.000	0.000	0.000
66	A	333	MET	0	-0.002	0.020	19.221	0.011	0.011	0.000	0.000	0.000	0.000
67	A	334	ALA	0	0.052	0.032	22.669	0.013	0.013	0.000	0.000	0.000	0.000
68	A	335	TYR	0	-0.004	0.008	18.294	-0.013	-0.013	0.000	0.000	0.000	0.000
69	A	336	ASN	0	0.002	-0.028	19.655	0.056	0.056	0.000	0.000	0.000	0.000
70	A	337	PRO	0	0.033	0.015	19.418	-0.030	-0.030	0.000	0.000	0.000	0.000
71	A	338	ASN	0	-0.017	-0.005	19.809	-0.030	-0.030	0.000	0.000	0.000	0.000
72	A	339	THR	0	0.010	-0.010	16.677	0.006	0.006	0.000	0.000	0.000	0.000
73	A	340	GLN	0	-0.042	-0.006	15.137	-0.049	-0.049	0.000	0.000	0.000	0.000
74	A	341	THR	0	0.052	0.042	13.135	-0.049	-0.049	0.000	0.000	0.000	0.000
75	A	342	PHE	0	0.015	-0.009	15.572	0.056	0.056	0.000	0.000	0.000	0.000
76	A	343	MET	0	-0.087	-0.033	17.473	-0.026	-0.026	0.000	0.000	0.000	0.000
77	A	344	GLN	0	0.088	0.035	17.440	0.014	0.014	0.000	0.000	0.000	0.000
78	A	345	LYS	1	0.975	1.008	20.249	0.269	0.269	0.000	0.000	0.000	0.000
79	A	359	ASP	-1	-0.937	-0.979	28.452	-0.178	-0.178	0.000	0.000	0.000	0.000
80	A	360	LEU	0	-0.088	-0.038	23.563	-0.010	-0.010	0.000	0.000	0.000	0.000
81	A	361	GLN	0	0.014	0.011	25.043	0.020	0.020	0.000	0.000	0.000	0.000
82	A	362	THR	0	0.024	0.009	24.866	-0.022	-0.022	0.000	0.000	0.000	0.000
83	A	363	CYS	0	-0.065	0.000	20.639	0.011	0.011	0.000	0.000	0.000	0.000
84	A	364	TYR	0	-0.020	-0.020	23.976	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	365	CYS	0	0.020	0.024	19.735	-0.009	-0.009	0.000	0.000	0.000	0.000
86	A	366	VAL	0	0.028	0.012	22.004	0.012	0.012	0.000	0.000	0.000	0.000
87	A	367	PHE	0	0.007	0.006	20.829	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	368	ASP	-1	-0.811	-0.897	22.436	-0.147	-0.147	0.000	0.000	0.000	0.000
89	A	369	VAL	0	0.040	0.027	25.517	0.001	0.001	0.000	0.000	0.000	0.000
90	A	370	LEU	0	-0.058	-0.019	28.500	0.009	0.009	0.000	0.000	0.000	0.000
91	A	371	MET	0	0.003	-0.012	31.867	0.010	0.010	0.000	0.000	0.000	0.000
92	A	372	VAL	0	0.030	0.011	30.776	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	373	ASN	0	0.071	0.051	33.913	0.003	0.003	0.000	0.000	0.000	0.000
94	A	374	ASN	0	-0.003	-0.014	36.434	0.005	0.005	0.000	0.000	0.000	0.000
95	A	375	LYS	1	0.897	0.960	34.253	0.067	0.067	0.000	0.000	0.000	0.000
96	A	376	LYS	1	0.997	0.999	34.879	0.078	0.078	0.000	0.000	0.000	0.000
97	A	377	LEU	0	-0.054	-0.024	32.044	0.007	0.007	0.000	0.000	0.000	0.000
98	A	378	GLY	0	0.040	0.013	31.701	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	379	HIS	0	-0.019	-0.013	32.301	0.000	0.000	0.000	0.000	0.000	0.000
100	A	380	GLU	-1	-0.828	-0.902	28.730	-0.060	-0.060	0.000	0.000	0.000	0.000
101	A	381	THR	0	0.020	0.006	25.229	-0.006	-0.006	0.000	0.000	0.000	0.000
102	A	382	LEU	0	0.032	0.010	22.569	0.001	0.001	0.000	0.000	0.000	0.000
103	A	383	ARG	1	0.831	0.886	18.415	0.148	0.148	0.000	0.000	0.000	0.000
104	A	384	LYS	1	0.897	0.931	22.348	0.051	0.051	0.000	0.000	0.000	0.000
105	A	385	ARG	1	0.819	0.904	24.967	0.123	0.123	0.000	0.000	0.000	0.000
106	A	386	TYR	0	0.059	0.032	15.587	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	387	GLU	-1	-0.789	-0.859	19.096	-0.171	-0.171	0.000	0.000	0.000	0.000
108	A	388	ILE	0	-0.057	-0.026	21.746	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	389	LEU	0	0.013	0.024	21.825	0.007	0.007	0.000	0.000	0.000	0.000
110	A	390	SER	0	-0.043	-0.026	20.193	0.002	0.002	0.000	0.000	0.000	0.000
111	A	391	SER	0	-0.067	-0.053	22.010	0.011	0.011	0.000	0.000	0.000	0.000
112	A	392	ILE	0	-0.048	-0.023	25.495	0.010	0.010	0.000	0.000	0.000	0.000
113	A	393	PHE	0	-0.003	-0.008	23.236	0.008	0.008	0.000	0.000	0.000	0.000
114	A	394	THR	0	0.023	0.028	21.425	0.010	0.010	0.000	0.000	0.000	0.000
115	A	395	PRO	0	-0.007	-0.004	18.678	0.012	0.012	0.000	0.000	0.000	0.000
116	A	396	ILE	0	-0.004	0.016	21.593	0.008	0.008	0.000	0.000	0.000	0.000
117	A	397	PRO	0	0.027	0.003	18.048	-0.010	-0.010	0.000	0.000	0.000	0.000
118	A	398	GLY	0	0.004	-0.010	19.431	0.027	0.027	0.000	0.000	0.000	0.000
119	A	399	ARG	1	0.870	0.893	20.793	0.237	0.237	0.000	0.000	0.000	0.000
120	A	400	ILE	0	-0.031	-0.005	23.650	0.006	0.006	0.000	0.000	0.000	0.000
121	A	401	GLU	-1	-0.782	-0.887	17.345	-0.446	-0.446	0.000	0.000	0.000	0.000
122	A	402	ILE	0	-0.021	-0.015	18.421	0.036	0.036	0.000	0.000	0.000	0.000
123	A	403	VAL	0	0.003	0.005	16.681	-0.061	-0.061	0.000	0.000	0.000	0.000
124	A	404	GLN	0	-0.038	-0.021	15.036	0.073	0.073	0.000	0.000	0.000	0.000
125	A	405	LYS	1	0.842	0.916	17.803	0.173	0.173	0.000	0.000	0.000	0.000
126	A	406	THR	0	-0.019	0.000	15.429	0.045	0.045	0.000	0.000	0.000	0.000

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