FMO DATABASE

FMODB ID: 2K61R

Calculation Name: 2Y0N-A-Xray307

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2Y0N

Chain ID: A

ChEMBL ID:

UniProt ID: Q8N5Y2

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	171
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1773762.397221
FMO2-HF: Nuclear repulsion	1706349.377925
FMO2-HF: Total energy	-67413.019296
FMO2-MP2: Total energy	-67611.479513

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:170:ACE )

Summations of interaction energy for fragment #1(A:170:ACE )

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.
0.678	1.486	-0.005	-0.371	-0.431	0

Interaction energy analysis for fragmet #1(A:170:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : -0.006

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].
3	A	172	ILE	0	0.030	0.026	3.870	0.833	1.641	-0.005	-0.371	-0.431
4	A	173	THR	0	-0.006	-0.008	7.048	0.058	0.058	0.000	0.000	0.000
5	A	174	ILE	0	0.000	-0.003	9.664	0.082	0.082	0.000	0.000	0.000
6	A	175	GLU	-1	-0.937	-0.959	13.426	-0.094	-0.094	0.000	0.000	0.000
7	A	176	ILE	0	-0.002	0.000	15.469	0.013	0.013	0.000	0.000	0.000
8	A	177	PRO	0	-0.005	-0.006	18.845	0.014	0.014	0.000	0.000	0.000
9	A	178	GLU	-1	-0.848	-0.946	21.079	-0.068	-0.068	0.000	0.000	0.000
10	A	179	VAL	0	-0.044	-0.019	23.392	0.000	0.000	0.000	0.000	0.000
11	A	180	LEU	0	0.028	0.000	23.231	0.000	0.000	0.000	0.000	0.000
12	A	181	LYS	1	0.930	0.973	17.137	0.132	0.132	0.000	0.000	0.000
13	A	182	LYS	1	0.992	1.006	23.011	0.054	0.054	0.000	0.000	0.000
14	A	183	GLN	0	0.032	0.041	26.508	-0.006	-0.006	0.000	0.000	0.000
15	A	184	LEU	0	0.002	-0.012	21.406	-0.002	-0.002	0.000	0.000	0.000
16	A	185	GLU	-1	-0.984	-0.983	23.954	-0.099	-0.099	0.000	0.000	0.000
17	A	186	ASP	-1	-0.909	-0.960	26.655	-0.066	-0.066	0.000	0.000	0.000
18	A	187	ASP	-1	-0.825	-0.876	27.656	-0.104	-0.104	0.000	0.000	0.000
19	A	188	CYS	0	-0.046	-0.020	26.572	0.000	0.000	0.000	0.000	0.000
20	A	189	TYR	0	-0.016	-0.013	28.679	0.007	0.007	0.000	0.000	0.000
21	A	190	TYR	0	-0.020	-0.037	31.649	0.008	0.008	0.000	0.000	0.000
22	A	191	ILE	0	-0.014	0.020	30.412	0.004	0.004	0.000	0.000	0.000
23	A	192	ASN	0	-0.082	-0.044	28.747	0.006	0.006	0.000	0.000	0.000
24	A	193	ARG	1	0.920	0.963	30.354	0.076	0.076	0.000	0.000	0.000
25	A	194	ARG	1	0.893	0.956	35.102	0.056	0.056	0.000	0.000	0.000
26	A	195	LYS	1	0.898	0.966	36.611	0.062	0.062	0.000	0.000	0.000
27	A	196	ARG	1	0.955	0.991	36.382	0.056	0.056	0.000	0.000	0.000
28	A	197	LEU	0	-0.008	-0.018	35.087	-0.005	-0.005	0.000	0.000	0.000
29	A	198	VAL	0	0.070	0.049	32.649	0.004	0.004	0.000	0.000	0.000
30	A	199	LYS	1	0.950	0.976	35.905	0.047	0.047	0.000	0.000	0.000
31	A	200	LEU	0	-0.054	0.002	34.580	-0.002	-0.002	0.000	0.000	0.000
32	A	201	PRO	0	0.008	-0.011	37.859	0.002	0.002	0.000	0.000	0.000
33	A	202	CYS	0	-0.026	-0.006	35.138	0.001	0.001	0.000	0.000	0.000
34	A	203	GLN	0	-0.023	-0.015	37.668	0.000	0.000	0.000	0.000	0.000
35	A	204	THR	0	0.026	0.019	35.166	0.002	0.002	0.000	0.000	0.000
36	A	205	ASN	0	-0.011	0.019	34.385	-0.003	-0.003	0.000	0.000	0.000
37	A	206	ILE	0	0.047	0.016	28.039	0.002	0.002	0.000	0.000	0.000
38	A	207	ILE	0	-0.011	0.004	30.943	-0.001	-0.001	0.000	0.000	0.000
39	A	208	THR	0	-0.001	0.000	32.864	0.003	0.003	0.000	0.000	0.000
40	A	209	ILE	0	-0.006	0.004	29.464	0.002	0.002	0.000	0.000	0.000
41	A	210	LEU	0	-0.033	-0.024	26.563	0.002	0.002	0.000	0.000	0.000
42	A	211	GLU	-1	-0.918	-0.964	30.078	-0.049	-0.049	0.000	0.000	0.000
43	A	212	SER	0	-0.055	-0.029	33.111	0.006	0.006	0.000	0.000	0.000
44	A	213	TYR	0	0.049	0.028	24.874	0.004	0.004	0.000	0.000	0.000
45	A	214	VAL	0	0.034	0.018	29.459	0.005	0.005	0.000	0.000	0.000
46	A	215	LYS	1	0.915	0.960	31.167	0.045	0.045	0.000	0.000	0.000
47	A	216	HIS	0	0.010	0.000	32.047	0.006	0.006	0.000	0.000	0.000
48	A	217	PHE	0	-0.016	-0.010	25.443	0.004	0.004	0.000	0.000	0.000
49	A	218	ALA	0	-0.022	-0.020	30.560	0.004	0.004	0.000	0.000	0.000
50	A	219	ILE	0	-0.005	-0.002	33.257	0.004	0.004	0.000	0.000	0.000
51	A	220	ASN	0	0.017	0.005	31.041	0.006	0.006	0.000	0.000	0.000
52	A	221	ALA	0	-0.039	-0.010	30.518	0.004	0.004	0.000	0.000	0.000
53	A	222	ALA	0	-0.069	-0.021	32.045	0.004	0.004	0.000	0.000	0.000
54	A	223	PHE	0	-0.056	-0.022	35.743	0.003	0.003	0.000	0.000	0.000
55	A	224	SER	0	0.042	0.008	32.170	0.000	0.000	0.000	0.000	0.000
56	A	225	ALA	0	-0.065	-0.029	32.686	0.002	0.002	0.000	0.000	0.000
57	A	226	NME	0	0.007	0.021	34.212	0.001	0.001	0.000	0.000	0.000
58	A	246	ACE	0	0.008	-0.006	24.448	0.001	0.001	0.000	0.000	0.000
59	A	247	ALA	0	0.006	-0.019	21.401	-0.002	-0.002	0.000	0.000	0.000
60	A	248	GLU	-1	-0.865	-0.942	21.373	-0.031	-0.031	0.000	0.000	0.000
61	A	249	LYS	1	0.982	0.997	23.935	0.002	0.002	0.000	0.000	0.000
62	A	250	ASN	0	-0.015	-0.001	25.727	0.001	0.001	0.000	0.000	0.000
63	A	251	VAL	0	0.068	0.021	26.819	-0.006	-0.006	0.000	0.000	0.000
64	A	252	ASP	-1	-0.905	-0.953	28.891	-0.038	-0.038	0.000	0.000	0.000
65	A	253	LEU	0	-0.029	-0.014	21.358	-0.003	-0.003	0.000	0.000	0.000
66	A	254	CYS	0	-0.028	0.005	23.973	-0.012	-0.012	0.000	0.000	0.000
67	A	255	LYS	1	0.946	0.965	25.460	0.033	0.033	0.000	0.000	0.000
68	A	256	GLU	-1	-0.903	-0.943	23.535	-0.067	-0.067	0.000	0.000	0.000
69	A	257	MET	0	-0.037	0.017	20.443	-0.014	-0.014	0.000	0.000	0.000
70	A	258	VAL	0	-0.030	-0.019	22.782	-0.012	-0.012	0.000	0.000	0.000
71	A	259	ASP	-1	-0.825	-0.922	25.658	-0.090	-0.090	0.000	0.000	0.000
72	A	260	GLY	0	0.040	0.018	22.320	-0.005	-0.005	0.000	0.000	0.000
73	A	261	LEU	0	-0.028	0.000	21.057	-0.015	-0.015	0.000	0.000	0.000
74	A	262	ARG	1	0.923	0.964	23.324	0.081	0.081	0.000	0.000	0.000
75	A	263	ILE	0	-0.007	0.019	24.379	0.000	0.000	0.000	0.000	0.000
76	A	264	THR	0	-0.018	-0.051	19.382	-0.011	-0.011	0.000	0.000	0.000
77	A	265	PHE	0	-0.027	0.033	22.668	-0.010	-0.010	0.000	0.000	0.000
78	A	266	ASP	-1	-0.837	-0.916	24.786	-0.100	-0.100	0.000	0.000	0.000
79	A	267	TYR	0	-0.044	-0.010	21.457	-0.003	-0.003	0.000	0.000	0.000
80	A	268	THR	0	-0.025	-0.075	20.719	-0.010	-0.010	0.000	0.000	0.000
81	A	269	LEU	0	-0.012	0.000	23.470	-0.002	-0.002	0.000	0.000	0.000
82	A	270	PRO	0	-0.032	-0.018	26.110	-0.001	-0.001	0.000	0.000	0.000
83	A	271	LEU	0	-0.053	-0.018	23.561	0.002	0.002	0.000	0.000	0.000
84	A	272	VAL	0	-0.039	-0.039	19.309	-0.005	-0.005	0.000	0.000	0.000
85	A	273	LEU	0	-0.009	0.007	20.980	-0.010	-0.010	0.000	0.000	0.000
86	A	274	LEU	0	-0.015	0.008	24.151	0.013	0.013	0.000	0.000	0.000
87	A	275	TYR	0	0.042	0.013	25.228	-0.007	-0.007	0.000	0.000	0.000
88	A	276	PRO	0	-0.015	-0.024	28.008	0.007	0.007	0.000	0.000	0.000
89	A	277	TYR	0	0.022	-0.006	30.956	0.007	0.007	0.000	0.000	0.000
90	A	278	GLU	-1	-0.762	-0.868	29.801	-0.102	-0.102	0.000	0.000	0.000
91	A	279	GLN	0	0.022	0.016	29.141	0.005	0.005	0.000	0.000	0.000
92	A	280	ALA	0	-0.023	-0.018	33.726	0.003	0.003	0.000	0.000	0.000
93	A	281	GLN	0	-0.022	-0.014	35.482	0.000	0.000	0.000	0.000	0.000
94	A	282	TYR	0	0.084	0.049	31.759	0.003	0.003	0.000	0.000	0.000
95	A	283	LYS	1	0.970	0.975	35.033	0.074	0.074	0.000	0.000	0.000
96	A	284	LYS	1	0.922	0.956	37.391	0.058	0.058	0.000	0.000	0.000
97	A	285	VAL	0	0.007	0.005	36.375	0.003	0.003	0.000	0.000	0.000
98	A	286	THR	0	-0.037	-0.016	34.622	0.002	0.002	0.000	0.000	0.000
99	A	287	SER	0	-0.051	-0.010	38.025	0.002	0.002	0.000	0.000	0.000
100	A	288	SER	0	-0.021	-0.002	41.252	0.004	0.004	0.000	0.000	0.000
101	A	289	NME	0	0.024	0.019	41.937	-0.002	-0.002	0.000	0.000	0.000
102	A	439	ACE	0	-0.033	-0.028	39.557	-0.001	-0.001	0.000	0.000	0.000
103	A	440	GLU	-1	-0.968	-0.990	39.063	-0.051	-0.051	0.000	0.000	0.000
104	A	441	PHE	0	-0.035	-0.023	41.993	0.002	0.002	0.000	0.000	0.000
105	A	442	ASP	-1	-0.907	-0.934	44.226	-0.042	-0.042	0.000	0.000	0.000
106	A	443	GLN	0	-0.042	-0.018	39.281	0.001	0.001	0.000	0.000	0.000
107	A	444	PRO	0	0.000	0.001	36.135	0.001	0.001	0.000	0.000	0.000
108	A	445	PRO	0	0.008	-0.008	36.723	-0.003	-0.003	0.000	0.000	0.000
109	A	446	PRO	0	0.032	0.026	32.560	-0.003	-0.003	0.000	0.000	0.000
110	A	447	PRO	0	0.005	-0.002	29.650	0.003	0.003	0.000	0.000	0.000
111	A	448	SER	0	0.035	-0.004	29.657	0.000	0.000	0.000	0.000	0.000
112	A	449	TYR	0	-0.002	-0.016	31.366	0.004	0.004	0.000	0.000	0.000
113	A	450	ILE	0	-0.062	-0.014	34.097	0.005	0.005	0.000	0.000	0.000
114	A	451	TYR	0	0.023	-0.011	30.819	0.003	0.003	0.000	0.000	0.000
115	A	452	GLY	0	0.076	0.019	32.122	0.003	0.003	0.000	0.000	0.000
116	A	453	ALA	0	0.052	0.012	29.291	-0.008	-0.008	0.000	0.000	0.000
117	A	454	GLN	0	0.013	0.016	28.028	-0.009	-0.009	0.000	0.000	0.000
118	A	455	HIS	0	-0.004	-0.028	27.060	-0.008	-0.008	0.000	0.000	0.000
119	A	456	LEU	0	0.017	0.013	24.359	-0.014	-0.014	0.000	0.000	0.000
120	A	457	LEU	0	0.029	0.020	22.559	-0.016	-0.016	0.000	0.000	0.000
121	A	458	ARG	1	0.808	0.882	21.859	0.107	0.107	0.000	0.000	0.000
122	A	459	LEU	0	0.001	0.003	19.923	-0.027	-0.027	0.000	0.000	0.000
123	A	460	PHE	0	0.003	-0.013	18.129	-0.034	-0.034	0.000	0.000	0.000
124	A	461	VAL	0	-0.013	0.005	16.618	-0.029	-0.029	0.000	0.000	0.000
125	A	462	LYS	1	0.906	0.955	15.383	0.251	0.251	0.000	0.000	0.000
126	A	463	LEU	0	0.011	0.010	14.876	-0.057	-0.057	0.000	0.000	0.000
127	A	464	PRO	0	0.019	0.018	10.324	-0.035	-0.035	0.000	0.000	0.000
128	A	465	GLU	-1	-0.903	-0.966	10.515	-0.592	-0.592	0.000	0.000	0.000
129	A	466	ILE	0	-0.065	-0.030	11.655	-0.021	-0.021	0.000	0.000	0.000
130	A	467	LEU	0	-0.015	-0.025	11.674	0.024	0.024	0.000	0.000	0.000
131	A	468	GLY	0	-0.006	0.011	8.849	-0.019	-0.019	0.000	0.000	0.000
132	A	469	LYS	1	0.899	0.948	9.573	0.480	0.480	0.000	0.000	0.000
133	A	470	MET	0	-0.010	0.020	12.524	0.090	0.090	0.000	0.000	0.000
134	A	471	SER	0	-0.007	-0.002	11.281	-0.034	-0.034	0.000	0.000	0.000
135	A	472	PHE	0	0.013	0.007	11.444	0.080	0.080	0.000	0.000	0.000
136	A	473	SER	0	0.005	0.002	11.327	0.014	0.014	0.000	0.000	0.000
137	A	474	GLU	-1	-0.865	-0.950	8.873	0.196	0.196	0.000	0.000	0.000
138	A	475	LYS	1	0.893	0.934	11.936	-0.079	-0.079	0.000	0.000	0.000
139	A	476	ASN	0	0.029	0.010	15.369	0.012	0.012	0.000	0.000	0.000
140	A	477	LEU	0	0.072	0.051	8.786	-0.006	-0.006	0.000	0.000	0.000
141	A	478	LYS	1	0.983	0.984	11.215	-0.171	-0.171	0.000	0.000	0.000
142	A	479	ALA	0	-0.022	-0.007	13.613	-0.003	-0.003	0.000	0.000	0.000
143	A	480	LEU	0	0.031	0.025	14.608	0.001	0.001	0.000	0.000	0.000
144	A	481	LEU	0	-0.007	-0.022	10.310	-0.003	-0.003	0.000	0.000	0.000
145	A	482	LYS	1	0.953	0.986	14.950	-0.001	-0.001	0.000	0.000	0.000
146	A	483	HIS	0	0.003	-0.005	17.690	0.002	0.002	0.000	0.000	0.000
147	A	484	PHE	0	0.020	0.005	15.406	-0.001	-0.001	0.000	0.000	0.000
148	A	485	ASP	-1	-0.896	-0.936	16.729	-0.108	-0.108	0.000	0.000	0.000
149	A	486	LEU	0	-0.030	-0.014	19.518	0.007	0.007	0.000	0.000	0.000
150	A	487	PHE	0	0.015	0.015	22.345	0.004	0.004	0.000	0.000	0.000
151	A	488	LEU	0	0.004	-0.004	18.822	0.003	0.003	0.000	0.000	0.000
152	A	489	ARG	1	0.915	0.955	21.382	0.065	0.065	0.000	0.000	0.000
153	A	490	PHE	0	0.039	0.020	24.852	0.004	0.004	0.000	0.000	0.000
154	A	491	LEU	0	0.002	-0.011	24.917	0.002	0.002	0.000	0.000	0.000
155	A	492	ALA	0	-0.072	-0.048	25.534	0.002	0.002	0.000	0.000	0.000
156	A	493	GLU	-1	-0.996	-0.992	27.557	-0.033	-0.033	0.000	0.000	0.000
157	A	494	TYR	0	0.001	0.007	30.385	0.005	0.005	0.000	0.000	0.000
158	A	495	HIS	0	-0.025	-0.016	29.613	-0.006	-0.006	0.000	0.000	0.000
159	A	496	ASP	-1	-0.877	-0.952	31.499	-0.046	-0.046	0.000	0.000	0.000
160	A	497	ASP	-1	-0.953	-0.960	35.120	-0.041	-0.041	0.000	0.000	0.000
161	A	498	PHE	0	-0.062	-0.046	30.977	-0.002	-0.002	0.000	0.000	0.000
162	A	499	PHE	0	-0.089	-0.044	27.683	-0.006	-0.006	0.000	0.000	0.000
163	A	500	PRO	0	0.044	0.051	33.510	0.002	0.002	0.000	0.000	0.000
164	A	501	GLU	-1	-0.794	-0.915	35.668	-0.058	-0.058	0.000	0.000	0.000
165	A	502	SER	0	-0.115	-0.061	37.608	-0.002	-0.002	0.000	0.000	0.000
166	A	503	ALA	0	0.017	0.024	35.887	0.001	0.001	0.000	0.000	0.000
167	A	504	TYR	0	-0.063	-0.064	31.065	-0.001	-0.001	0.000	0.000	0.000
168	A	505	VAL	0	-0.051	-0.040	37.882	0.005	0.005	0.000	0.000	0.000
169	A	506	ALA	0	0.018	-0.007	39.906	-0.002	-0.002	0.000	0.000	0.000
170	A	507	ALA	0	-0.047	-0.011	42.409	0.001	0.001	0.000	0.000	0.000
171	A	508	NME	0	0.030	0.029	44.622	0.002	0.002	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:170:ACE )