FMO DATABASE

FMODB ID: 2N5QR

Calculation Name: 2D3E-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D3E

Chain ID: A

ChEMBL ID:

UniProt ID: P03069

Base Structure: X-ray

Registration Date: 2023-09-23

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	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	130
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-679820.000137
FMO2-HF: Nuclear repulsion	626815.657768
FMO2-HF: Total energy	-53004.342369
FMO2-MP2: Total energy	-53159.820933

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:153:ASP)

Summations of interaction energy for fragment #1(A:153:ASP)

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.
21.856	29.53	1.12	-3.937	-4.856	0.034

Interaction energy analysis for fragmet #1(A:153:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.831 / q_NPA : -0.916

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	155	VAL	0	-0.001	-0.003	2.684	-20.004	-15.262	0.453	-2.479	-2.716	0.019
4	A	156	GLU	-1	-0.900	-0.941	2.738	25.484	28.000	0.666	-1.262	-1.919	0.014
5	A	157	GLU	-1	-0.794	-0.847	3.923	29.002	29.418	0.001	-0.196	-0.221	0.001
6	A	158	LEU	0	-0.012	-0.016	5.891	-5.718	-5.718	0.000	0.000	0.000	0.000
7	A	159	LEU	0	-0.001	0.004	6.941	-4.145	-4.145	0.000	0.000	0.000	0.000
8	A	160	SER	0	-0.017	-0.017	7.501	-3.847	-3.847	0.000	0.000	0.000	0.000
9	A	161	LYS	1	0.836	0.897	9.718	-30.794	-30.794	0.000	0.000	0.000	0.000
10	A	162	ASN	0	-0.006	0.002	11.969	-1.866	-1.866	0.000	0.000	0.000	0.000
11	A	163	TYR	0	0.078	0.045	13.192	-1.688	-1.688	0.000	0.000	0.000	0.000
12	A	164	HIS	0	-0.051	-0.026	14.228	-0.979	-0.979	0.000	0.000	0.000	0.000
13	A	165	LEU	0	0.033	0.005	15.872	-1.204	-1.204	0.000	0.000	0.000	0.000
14	A	166	GLU	-1	-0.940	-0.968	16.776	16.265	16.265	0.000	0.000	0.000	0.000
15	A	167	ASN	0	-0.020	-0.013	18.161	-1.785	-1.785	0.000	0.000	0.000	0.000
16	A	168	GLU	-1	-0.909	-0.938	20.216	13.685	13.685	0.000	0.000	0.000	0.000
17	A	169	VAL	0	0.034	0.003	21.867	-0.819	-0.819	0.000	0.000	0.000	0.000
18	A	170	ALA	0	-0.030	-0.011	23.479	-0.642	-0.642	0.000	0.000	0.000	0.000
19	A	171	ARG	1	0.867	0.920	22.522	-13.152	-13.152	0.000	0.000	0.000	0.000
20	A	172	LEU	0	0.007	0.002	24.613	-0.498	-0.498	0.000	0.000	0.000	0.000
21	A	173	LYS	1	0.966	0.989	26.265	-12.026	-12.026	0.000	0.000	0.000	0.000
22	A	174	LYS	1	0.819	0.898	29.391	-9.434	-9.434	0.000	0.000	0.000	0.000
23	A	175	LEU	0	-0.059	-0.022	29.107	-0.337	-0.337	0.000	0.000	0.000	0.000
24	A	176	LEU	0	0.027	0.008	32.014	-0.233	-0.233	0.000	0.000	0.000	0.000
25	A	177	GLU	-1	-0.755	-0.860	33.751	8.686	8.686	0.000	0.000	0.000	0.000
26	A	178	ARG	1	0.924	0.954	33.149	-9.090	-9.090	0.000	0.000	0.000	0.000
27	A	179	ALA	0	-0.094	-0.041	36.503	-0.233	-0.233	0.000	0.000	0.000	0.000
28	A	180	GLU	-1	-0.933	-0.968	37.829	8.244	8.244	0.000	0.000	0.000	0.000
29	A	181	GLU	-1	-0.874	-0.938	39.686	7.572	7.572	0.000	0.000	0.000	0.000
30	A	182	ARG	1	0.916	0.950	40.616	-7.839	-7.839	0.000	0.000	0.000	0.000
31	A	183	ALA	0	-0.030	0.010	42.546	-0.185	-0.185	0.000	0.000	0.000	0.000
32	A	184	GLU	-1	-0.857	-0.929	43.748	7.014	7.014	0.000	0.000	0.000	0.000
33	A	185	LEU	0	-0.033	0.000	45.773	-0.195	-0.195	0.000	0.000	0.000	0.000
34	A	186	SER	0	-0.091	-0.071	46.524	-0.177	-0.177	0.000	0.000	0.000	0.000
35	A	187	GLU	-1	-0.944	-0.968	48.019	6.582	6.582	0.000	0.000	0.000	0.000
36	A	188	GLY	0	0.022	0.004	50.013	-0.146	-0.146	0.000	0.000	0.000	0.000
37	A	189	LYS	1	0.805	0.873	51.697	-5.811	-5.811	0.000	0.000	0.000	0.000
38	A	190	CYS	0	-0.002	0.005	53.003	-0.132	-0.132	0.000	0.000	0.000	0.000
39	A	191	ALA	0	0.051	0.028	54.715	-0.127	-0.127	0.000	0.000	0.000	0.000
40	A	192	GLU	-1	-0.875	-0.915	56.367	5.519	5.519	0.000	0.000	0.000	0.000
41	A	193	LEU	0	-0.013	-0.012	55.949	-0.105	-0.105	0.000	0.000	0.000	0.000
42	A	194	GLU	-1	-0.949	-0.967	58.216	5.420	5.420	0.000	0.000	0.000	0.000
43	A	195	GLU	-1	-0.771	-0.863	60.613	4.908	4.908	0.000	0.000	0.000	0.000
44	A	196	GLU	-1	-0.921	-0.953	61.431	5.040	5.040	0.000	0.000	0.000	0.000
45	A	197	LEU	0	-0.002	-0.008	62.160	-0.119	-0.119	0.000	0.000	0.000	0.000
46	A	198	LYS	1	0.797	0.905	64.709	-5.063	-5.063	0.000	0.000	0.000	0.000
47	A	199	THR	0	-0.035	-0.029	66.551	-0.122	-0.122	0.000	0.000	0.000	0.000
48	A	200	VAL	0	-0.011	-0.016	67.567	-0.101	-0.101	0.000	0.000	0.000	0.000
49	A	201	THR	0	-0.008	-0.015	67.950	-0.092	-0.092	0.000	0.000	0.000	0.000
50	A	202	ASN	0	-0.046	-0.026	70.584	-0.104	-0.104	0.000	0.000	0.000	0.000
51	A	203	ASN	0	0.024	0.008	72.624	-0.094	-0.094	0.000	0.000	0.000	0.000
52	A	204	LEU	0	0.028	0.031	73.087	-0.071	-0.071	0.000	0.000	0.000	0.000
53	A	205	LYS	1	0.884	0.926	73.954	-4.387	-4.387	0.000	0.000	0.000	0.000
54	A	206	SER	0	-0.052	-0.020	76.844	-0.080	-0.080	0.000	0.000	0.000	0.000
55	A	207	LEU	0	0.015	0.010	78.001	-0.059	-0.059	0.000	0.000	0.000	0.000
56	A	208	GLU	-1	-0.871	-0.937	78.545	4.043	4.043	0.000	0.000	0.000	0.000
57	A	209	ALA	0	-0.036	-0.018	80.633	-0.059	-0.059	0.000	0.000	0.000	0.000
58	A	210	GLN	0	-0.104	-0.056	82.259	-0.093	-0.093	0.000	0.000	0.000	0.000
59	A	211	ALA	0	0.030	0.015	83.027	-0.054	-0.054	0.000	0.000	0.000	0.000
60	A	212	GLU	-1	-0.888	-0.932	84.631	3.696	3.696	0.000	0.000	0.000	0.000
61	A	213	LYS	1	0.932	0.957	86.406	-3.800	-3.800	0.000	0.000	0.000	0.000
62	A	214	TYR	0	-0.039	-0.038	86.714	-0.069	-0.069	0.000	0.000	0.000	0.000
63	A	215	SER	0	0.071	0.052	88.305	-0.030	-0.030	0.000	0.000	0.000	0.000
64	A	216	GLN	0	-0.042	-0.015	89.757	-0.067	-0.067	0.000	0.000	0.000	0.000
65	A	217	LYS	1	0.825	0.920	92.476	-3.442	-3.442	0.000	0.000	0.000	0.000
66	A	218	GLU	-1	-0.960	-0.987	91.470	3.488	3.488	0.000	0.000	0.000	0.000
67	A	219	ASP	-1	-0.880	-0.942	93.184	3.447	3.447	0.000	0.000	0.000	0.000
68	A	220	LYS	1	0.784	0.881	96.206	-3.249	-3.249	0.000	0.000	0.000	0.000
69	A	221	TYR	0	-0.015	-0.021	96.485	-0.025	-0.025	0.000	0.000	0.000	0.000
70	A	222	GLU	-1	-0.896	-0.935	98.320	3.241	3.241	0.000	0.000	0.000	0.000
71	A	223	GLU	-1	-0.933	-0.967	100.352	3.168	3.168	0.000	0.000	0.000	0.000
72	A	224	GLU	-1	-0.854	-0.917	102.708	3.118	3.118	0.000	0.000	0.000	0.000
73	A	225	ILE	0	0.036	0.016	101.079	-0.047	-0.047	0.000	0.000	0.000	0.000
74	A	226	LYS	1	0.816	0.904	104.347	-3.053	-3.053	0.000	0.000	0.000	0.000
75	A	227	VAL	0	-0.008	-0.012	106.253	-0.042	-0.042	0.000	0.000	0.000	0.000
76	A	228	LEU	0	-0.045	-0.024	107.290	-0.042	-0.042	0.000	0.000	0.000	0.000
77	A	229	SER	0	-0.022	-0.025	107.813	-0.035	-0.035	0.000	0.000	0.000	0.000
78	A	230	ASP	-1	-0.828	-0.892	110.189	2.945	2.945	0.000	0.000	0.000	0.000
79	A	231	LYS	1	0.969	0.984	111.875	-2.933	-2.933	0.000	0.000	0.000	0.000
80	A	232	LEU	0	-0.026	0.007	112.659	-0.030	-0.030	0.000	0.000	0.000	0.000
81	A	233	LYS	1	0.839	0.898	112.624	-2.875	-2.875	0.000	0.000	0.000	0.000
82	A	234	GLU	-1	-0.940	-0.958	116.494	2.766	2.766	0.000	0.000	0.000	0.000
83	A	235	ALA	0	-0.066	-0.041	118.395	-0.033	-0.033	0.000	0.000	0.000	0.000
84	A	236	GLU	-1	-0.775	-0.867	116.430	2.784	2.784	0.000	0.000	0.000	0.000
85	A	237	THR	0	-0.008	-0.015	119.950	-0.031	-0.031	0.000	0.000	0.000	0.000
86	A	238	ARG	1	0.917	0.961	122.374	-2.664	-2.664	0.000	0.000	0.000	0.000
87	A	239	ALA	0	0.010	0.013	123.893	-0.029	-0.029	0.000	0.000	0.000	0.000
88	A	240	GLU	-1	-0.842	-0.933	122.280	2.635	2.635	0.000	0.000	0.000	0.000
89	A	241	PHE	0	-0.086	-0.041	126.387	-0.029	-0.029	0.000	0.000	0.000	0.000
90	A	242	ALA	0	0.004	0.010	128.386	-0.028	-0.028	0.000	0.000	0.000	0.000
91	A	243	GLU	-1	-0.873	-0.935	128.215	2.520	2.520	0.000	0.000	0.000	0.000
92	A	244	ARG	1	0.926	0.976	130.063	-2.514	-2.514	0.000	0.000	0.000	0.000
93	A	245	SER	0	-0.077	-0.051	132.209	-0.024	-0.024	0.000	0.000	0.000	0.000
94	A	246	VAL	0	-0.012	-0.006	134.039	-0.023	-0.023	0.000	0.000	0.000	0.000
95	A	247	THR	0	0.035	0.014	134.134	-0.019	-0.019	0.000	0.000	0.000	0.000
96	A	248	LYS	1	0.874	0.928	136.248	-2.401	-2.401	0.000	0.000	0.000	0.000
97	A	249	LEU	0	-0.022	0.007	137.625	-0.020	-0.020	0.000	0.000	0.000	0.000
98	A	250	GLU	-1	-0.876	-0.946	137.768	2.355	2.355	0.000	0.000	0.000	0.000
99	A	251	LYS	1	0.811	0.887	141.210	-2.262	-2.262	0.000	0.000	0.000	0.000
100	A	252	SER	0	-0.053	-0.050	142.620	-0.018	-0.018	0.000	0.000	0.000	0.000
101	A	253	ILE	0	-0.029	-0.008	143.172	-0.017	-0.017	0.000	0.000	0.000	0.000
102	A	254	ASP	-1	-0.869	-0.929	144.703	2.238	2.238	0.000	0.000	0.000	0.000
103	A	255	ASP	-1	-0.814	-0.885	147.079	2.207	2.207	0.000	0.000	0.000	0.000
104	A	256	LEU	0	-0.027	-0.014	148.174	-0.020	-0.020	0.000	0.000	0.000	0.000
105	A	257	GLU	-1	-0.960	-0.982	149.363	2.166	2.166	0.000	0.000	0.000	0.000
106	A	258	ASP	-1	-0.881	-0.937	151.903	2.126	2.126	0.000	0.000	0.000	0.000
107	A	259	GLU	-1	-1.011	-0.998	153.641	2.096	2.096	0.000	0.000	0.000	0.000
108	A	260	LEU	0	-0.022	-0.018	154.654	-0.024	-0.024	0.000	0.000	0.000	0.000
109	A	261	TYR	0	-0.013	-0.010	156.180	-0.023	-0.023	0.000	0.000	0.000	0.000
110	A	262	ALA	0	0.037	0.014	157.925	-0.019	-0.019	0.000	0.000	0.000	0.000
111	A	263	GLN	0	-0.022	-0.013	159.066	-0.035	-0.035	0.000	0.000	0.000	0.000
112	A	264	LYS	1	0.933	0.966	156.943	-2.095	-2.095	0.000	0.000	0.000	0.000
113	A	265	LEU	0	0.008	0.008	161.065	-0.017	-0.017	0.000	0.000	0.000	0.000
114	A	266	LYS	1	0.891	0.952	163.480	-2.015	-2.015	0.000	0.000	0.000	0.000
115	A	267	TYR	0	-0.018	-0.012	165.332	-0.014	-0.014	0.000	0.000	0.000	0.000
116	A	268	LYS	1	0.795	0.874	166.128	-1.958	-1.958	0.000	0.000	0.000	0.000
117	A	269	ALA	0	0.036	0.018	168.165	-0.012	-0.012	0.000	0.000	0.000	0.000
118	A	270	ILE	0	-0.025	-0.010	170.047	-0.013	-0.013	0.000	0.000	0.000	0.000
119	A	271	SER	0	-0.006	-0.007	171.070	-0.011	-0.011	0.000	0.000	0.000	0.000
120	A	272	GLU	-1	-0.832	-0.895	170.696	1.914	1.914	0.000	0.000	0.000	0.000
121	A	273	GLU	-1	-0.860	-0.922	174.176	1.832	1.832	0.000	0.000	0.000	0.000
122	A	274	LEU	0	-0.058	-0.019	175.821	-0.013	-0.013	0.000	0.000	0.000	0.000
123	A	275	ASP	-1	-0.896	-0.956	176.852	1.826	1.826	0.000	0.000	0.000	0.000
124	A	276	HIS	0	-0.048	-0.031	178.262	-0.020	-0.020	0.000	0.000	0.000	0.000
125	A	277	ALA	0	0.011	0.001	180.150	-0.012	-0.012	0.000	0.000	0.000	0.000
126	A	278	LEU	0	-0.062	-0.036	180.521	-0.013	-0.013	0.000	0.000	0.000	0.000
127	A	279	ASN	0	-0.079	-0.050	180.683	-0.020	-0.020	0.000	0.000	0.000	0.000
128	A	280	ASP	-1	-0.966	-0.960	184.341	1.748	1.748	0.000	0.000	0.000	0.000
129	A	281	MET	0	-0.059	-0.024	185.999	-0.013	-0.013	0.000	0.000	0.000	0.000
130	A	282	THR	0	-0.097	-0.036	187.907	-0.017	-0.017	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:153:ASP)