FMO DATABASE

FMODB ID: MNRMZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1135624.467719
FMO2-HF: Nuclear repulsion	1082765.078285
FMO2-HF: Total energy	-52859.389434
FMO2-MP2: Total energy	-53009.145117

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.
-4.759	-0.298	0.343	-1.815	-2.99	-0.005

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 : 0.011 / q_NPA : 0.010

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	0.000	0.004	2.773	-4.213	0.157	0.344	-1.804	-2.911	-0.005
4	A	271	GLU	-1	-0.940	-0.957	4.732	-0.439	-0.348	-0.001	-0.011	-0.079	0.000
5	A	272	THR	0	-0.040	-0.038	8.369	0.011	0.011	0.000	0.000	0.000	0.000
6	A	273	LYS	1	0.775	0.896	11.227	0.444	0.444	0.000	0.000	0.000	0.000
7	A	274	LEU	0	-0.028	-0.034	14.381	0.010	0.010	0.000	0.000	0.000	0.000
8	A	275	ASP	-1	-0.831	-0.899	17.254	-0.312	-0.312	0.000	0.000	0.000	0.000
9	A	276	GLY	0	0.044	0.008	21.046	-0.012	-0.012	0.000	0.000	0.000	0.000
10	A	277	GLU	-1	-0.927	-0.955	23.712	-0.177	-0.177	0.000	0.000	0.000	0.000
11	A	278	ARG	1	0.721	0.832	26.627	0.193	0.193	0.000	0.000	0.000	0.000
12	A	279	MET	0	-0.050	-0.001	28.046	0.020	0.020	0.000	0.000	0.000	0.000
13	A	280	GLN	0	0.034	0.029	29.203	0.000	0.000	0.000	0.000	0.000	0.000
14	A	281	MET	0	0.017	0.008	30.843	0.000	0.000	0.000	0.000	0.000	0.000
15	A	282	HIS	0	-0.056	-0.045	32.518	0.007	0.007	0.000	0.000	0.000	0.000
16	A	283	LYS	1	0.898	0.939	32.772	0.117	0.117	0.000	0.000	0.000	0.000
17	A	284	ASP	-1	-0.904	-0.954	35.875	-0.077	-0.077	0.000	0.000	0.000	0.000
18	A	285	GLY	0	-0.011	-0.003	38.174	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	286	ASP	-1	-0.901	-0.934	37.826	-0.091	-0.091	0.000	0.000	0.000	0.000
20	A	287	VAL	0	0.055	0.035	38.982	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	288	TYR	0	-0.092	-0.035	34.302	0.002	0.002	0.000	0.000	0.000	0.000
22	A	289	LYS	1	0.853	0.918	36.803	0.101	0.101	0.000	0.000	0.000	0.000
23	A	290	TYR	0	0.063	0.028	30.856	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	291	PHE	0	-0.022	0.001	34.433	0.005	0.005	0.000	0.000	0.000	0.000
25	A	292	SER	0	0.079	0.021	33.085	-0.008	-0.008	0.000	0.000	0.000	0.000
26	A	293	ARG	1	0.957	0.985	30.695	0.149	0.149	0.000	0.000	0.000	0.000
27	A	294	ASN	0	-0.030	-0.026	33.362	0.004	0.004	0.000	0.000	0.000	0.000
28	A	295	GLY	0	0.016	0.042	36.286	0.007	0.007	0.000	0.000	0.000	0.000
29	A	296	TYR	0	-0.010	-0.033	37.459	0.004	0.004	0.000	0.000	0.000	0.000
30	A	297	ASN	0	0.027	0.006	37.925	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	298	TYR	0	0.055	0.003	34.801	0.002	0.002	0.000	0.000	0.000	0.000
32	A	299	THR	0	-0.063	-0.025	36.055	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	300	ASP	-1	-0.885	-0.942	37.884	-0.108	-0.108	0.000	0.000	0.000	0.000
34	A	301	GLN	0	-0.025	0.007	33.065	-0.009	-0.009	0.000	0.000	0.000	0.000
35	A	302	PHE	0	-0.022	-0.009	30.432	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	303	GLY	0	0.121	0.047	33.877	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	304	ALA	0	0.008	-0.011	36.374	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	305	SER	0	0.001	0.009	38.901	0.006	0.006	0.000	0.000	0.000	0.000
39	A	306	PRO	0	-0.003	-0.003	36.119	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	307	THR	0	-0.084	-0.057	36.784	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	308	GLU	-1	-0.786	-0.784	38.202	-0.111	-0.111	0.000	0.000	0.000	0.000
42	A	309	GLY	0	-0.099	-0.151	35.375	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	310	SER	0	0.003	-0.043	36.022	0.009	0.009	0.000	0.000	0.000	0.000
44	A	311	LEU	0	-0.001	-0.001	30.336	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	312	THR	0	-0.175	-0.159	29.002	-0.015	-0.015	0.000	0.000	0.000	0.000
46	A	313	PRO	0	0.081	0.175	31.260	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	314	PHE	0	-0.024	-0.032	28.830	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	315	ILE	0	0.015	-0.002	26.914	0.001	0.001	0.000	0.000	0.000	0.000
49	A	316	HIS	0	0.024	0.030	29.163	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	317	ASN	0	-0.044	-0.027	31.375	0.000	0.000	0.000	0.000	0.000	0.000
51	A	318	ALA	0	0.049	0.029	25.999	-0.007	-0.007	0.000	0.000	0.000	0.000
52	A	319	PHE	0	0.011	-0.024	27.906	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	320	LYS	1	0.933	0.986	26.613	0.105	0.105	0.000	0.000	0.000	0.000
54	A	321	ALA	0	0.009	-0.007	29.707	0.006	0.006	0.000	0.000	0.000	0.000
55	A	322	ASP	-1	-0.899	-0.960	33.191	-0.066	-0.066	0.000	0.000	0.000	0.000
56	A	323	ILE	0	-0.089	-0.021	30.335	0.002	0.002	0.000	0.000	0.000	0.000
57	A	324	GLN	0	-0.016	-0.005	33.650	0.001	0.001	0.000	0.000	0.000	0.000
58	A	325	ILE	0	0.043	0.013	36.702	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	326	CYS	0	-0.058	-0.027	30.780	0.000	0.000	0.000	0.000	0.000	0.000
60	A	327	ILE	0	-0.015	0.004	32.403	0.000	0.000	0.000	0.000	0.000	0.000
61	A	328	LEU	0	0.002	-0.012	27.329	0.000	0.000	0.000	0.000	0.000	0.000
62	A	329	ASP	-1	-0.817	-0.875	27.169	-0.179	-0.179	0.000	0.000	0.000	0.000
63	A	330	GLY	0	0.063	0.019	24.603	-0.013	-0.013	0.000	0.000	0.000	0.000
64	A	331	GLU	-1	-0.882	-0.937	22.673	-0.260	-0.260	0.000	0.000	0.000	0.000
65	A	332	MET	0	-0.059	-0.038	23.393	-0.023	-0.023	0.000	0.000	0.000	0.000
66	A	333	MET	0	-0.007	0.018	19.658	0.006	0.006	0.000	0.000	0.000	0.000
67	A	334	ALA	0	0.055	0.036	22.280	0.016	0.016	0.000	0.000	0.000	0.000
68	A	335	TYR	0	-0.030	0.016	18.071	-0.033	-0.033	0.000	0.000	0.000	0.000
69	A	336	ASN	0	0.020	-0.014	19.221	0.054	0.054	0.000	0.000	0.000	0.000
70	A	337	PRO	0	0.040	0.011	18.951	-0.036	-0.036	0.000	0.000	0.000	0.000
71	A	338	ASN	0	-0.015	-0.005	19.491	-0.034	-0.034	0.000	0.000	0.000	0.000
72	A	339	THR	0	0.005	0.005	16.629	-0.022	-0.022	0.000	0.000	0.000	0.000
73	A	340	GLN	0	-0.022	-0.001	14.680	-0.036	-0.036	0.000	0.000	0.000	0.000
74	A	341	THR	0	-0.001	0.010	13.090	-0.052	-0.052	0.000	0.000	0.000	0.000
75	A	342	PHE	0	0.046	-0.003	15.436	0.069	0.069	0.000	0.000	0.000	0.000
76	A	343	MET	0	-0.078	-0.031	17.174	-0.027	-0.027	0.000	0.000	0.000	0.000
77	A	344	GLN	0	0.098	0.041	16.877	0.039	0.039	0.000	0.000	0.000	0.000
78	A	345	LYS	1	0.969	1.010	20.095	0.305	0.305	0.000	0.000	0.000	0.000
79	A	359	ASP	-1	-0.938	-0.978	28.072	-0.199	-0.199	0.000	0.000	0.000	0.000
80	A	360	LEU	0	-0.091	-0.038	22.981	-0.012	-0.012	0.000	0.000	0.000	0.000
81	A	361	GLN	0	-0.003	-0.002	24.535	0.026	0.026	0.000	0.000	0.000	0.000
82	A	362	THR	0	0.024	0.010	24.388	-0.026	-0.026	0.000	0.000	0.000	0.000
83	A	363	CYS	0	-0.066	-0.013	19.974	0.010	0.010	0.000	0.000	0.000	0.000
84	A	364	TYR	0	-0.019	-0.008	23.490	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	365	CYS	0	-0.003	0.013	19.639	-0.018	-0.018	0.000	0.000	0.000	0.000
86	A	366	VAL	0	0.026	0.013	21.507	0.013	0.013	0.000	0.000	0.000	0.000
87	A	367	PHE	0	0.002	-0.013	20.571	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	368	ASP	-1	-0.861	-0.936	22.101	-0.150	-0.150	0.000	0.000	0.000	0.000
89	A	369	VAL	0	-0.069	-0.065	25.328	-0.017	-0.017	0.000	0.000	0.000	0.000
90	A	370	LEU	0	-0.054	-0.011	28.514	0.011	0.011	0.000	0.000	0.000	0.000
91	A	371	MET	0	0.006	-0.013	31.880	0.012	0.012	0.000	0.000	0.000	0.000
92	A	372	VAL	0	0.007	0.001	30.866	-0.009	-0.009	0.000	0.000	0.000	0.000
93	A	373	ASN	0	0.077	0.046	33.898	0.002	0.002	0.000	0.000	0.000	0.000
94	A	374	ASN	0	-0.013	-0.014	36.421	0.006	0.006	0.000	0.000	0.000	0.000
95	A	375	LYS	1	0.894	0.956	34.110	0.063	0.063	0.000	0.000	0.000	0.000
96	A	376	LYS	1	0.998	1.003	34.897	0.080	0.080	0.000	0.000	0.000	0.000
97	A	377	LEU	0	-0.057	-0.026	32.006	0.008	0.008	0.000	0.000	0.000	0.000
98	A	378	GLY	0	0.042	0.015	31.713	-0.008	-0.008	0.000	0.000	0.000	0.000
99	A	379	HIS	0	-0.019	-0.015	32.307	0.001	0.001	0.000	0.000	0.000	0.000
100	A	380	GLU	-1	-0.855	-0.931	28.641	-0.049	-0.049	0.000	0.000	0.000	0.000
101	A	381	THR	0	0.016	0.000	24.810	-0.009	-0.009	0.000	0.000	0.000	0.000
102	A	382	LEU	0	0.041	0.013	22.849	0.003	0.003	0.000	0.000	0.000	0.000
103	A	383	ARG	1	0.849	0.904	18.537	0.123	0.123	0.000	0.000	0.000	0.000
104	A	384	LYS	1	0.933	0.969	22.363	0.042	0.042	0.000	0.000	0.000	0.000
105	A	385	ARG	1	0.841	0.928	24.982	0.117	0.117	0.000	0.000	0.000	0.000
106	A	386	TYR	0	0.107	0.060	15.690	-0.008	-0.008	0.000	0.000	0.000	0.000
107	A	387	GLU	-1	-0.850	-0.897	19.312	-0.156	-0.156	0.000	0.000	0.000	0.000
108	A	388	ILE	0	-0.036	-0.028	21.767	0.000	0.000	0.000	0.000	0.000	0.000
109	A	389	LEU	0	0.107	0.072	22.268	0.027	0.027	0.000	0.000	0.000	0.000
110	A	390	SER	0	-0.062	-0.008	20.386	0.000	0.000	0.000	0.000	0.000	0.000
111	A	391	SER	0	-0.082	-0.056	21.999	0.012	0.012	0.000	0.000	0.000	0.000
112	A	392	ILE	0	-0.015	-0.021	25.487	0.009	0.009	0.000	0.000	0.000	0.000
113	A	393	PHE	0	-0.045	-0.017	23.068	0.010	0.010	0.000	0.000	0.000	0.000
114	A	394	THR	0	0.045	0.039	21.416	0.012	0.012	0.000	0.000	0.000	0.000
115	A	395	PRO	0	-0.016	-0.014	18.901	0.012	0.012	0.000	0.000	0.000	0.000
116	A	396	ILE	0	-0.001	0.026	21.550	0.010	0.010	0.000	0.000	0.000	0.000
117	A	397	PRO	0	0.040	-0.013	17.335	-0.007	-0.007	0.000	0.000	0.000	0.000
118	A	398	GLY	0	-0.015	-0.027	18.763	0.032	0.032	0.000	0.000	0.000	0.000
119	A	399	ARG	1	0.885	0.905	20.200	0.267	0.267	0.000	0.000	0.000	0.000
120	A	400	ILE	0	-0.016	0.004	23.087	0.007	0.007	0.000	0.000	0.000	0.000
121	A	401	GLU	-1	-0.789	-0.869	17.079	-0.527	-0.527	0.000	0.000	0.000	0.000
122	A	402	ILE	0	-0.036	-0.028	18.375	0.043	0.043	0.000	0.000	0.000	0.000
123	A	403	VAL	0	0.009	0.012	16.296	-0.067	-0.067	0.000	0.000	0.000	0.000
124	A	404	GLN	0	-0.034	-0.019	15.057	0.079	0.079	0.000	0.000	0.000	0.000
125	A	405	LYS	1	0.962	0.976	17.515	0.177	0.177	0.000	0.000	0.000	0.000
126	A	406	THR	0	0.005	0.026	15.321	0.035	0.035	0.000	0.000	0.000	0.000

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