FMO DATABASE

FMODB ID: 43YRN

Calculation Name: 2Y0N-A-Xray372

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: 2023-03-14

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	165
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1752423.572953
FMO2-HF: Nuclear repulsion	1685522.127805
FMO2-HF: Total energy	-66901.445148
FMO2-MP2: Total energy	-67098.301199

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:171:THR)

Summations of interaction energy for fragment #1(A:171:THR)

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.
-1.306	1.374	-0.015	-1.341	-1.324	0.005

Interaction energy analysis for fragmet #1(A:171:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / 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

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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	173	THR	0	0.001	0.001	3.740	-1.292	1.388	-0.015	-1.341	-1.324	0.005
4	A	174	ILE	0	-0.016	-0.017	5.968	-0.128	-0.128	0.000	0.000	0.000	0.000
5	A	175	GLU	-1	-0.863	-0.925	9.423	0.108	0.108	0.000	0.000	0.000	0.000
6	A	176	ILE	0	0.007	0.011	11.831	-0.029	-0.029	0.000	0.000	0.000	0.000
7	A	177	PRO	0	0.037	0.012	14.637	0.038	0.038	0.000	0.000	0.000	0.000
8	A	178	GLU	-1	-0.799	-0.906	17.562	0.048	0.048	0.000	0.000	0.000	0.000
9	A	179	VAL	0	-0.054	-0.020	19.538	0.016	0.016	0.000	0.000	0.000	0.000
10	A	180	LEU	0	0.033	0.003	18.814	0.009	0.009	0.000	0.000	0.000	0.000
11	A	181	LYS	1	0.764	0.877	14.189	-0.047	-0.047	0.000	0.000	0.000	0.000
12	A	182	LYS	1	0.995	1.006	18.374	0.005	0.005	0.000	0.000	0.000	0.000
13	A	183	GLN	0	0.026	0.030	21.890	0.012	0.012	0.000	0.000	0.000	0.000
14	A	184	LEU	0	-0.021	-0.019	16.106	0.005	0.005	0.000	0.000	0.000	0.000
15	A	185	GLU	-1	-0.969	-0.979	19.223	0.122	0.122	0.000	0.000	0.000	0.000
16	A	186	ASP	-1	-0.909	-0.965	21.596	0.035	0.035	0.000	0.000	0.000	0.000
17	A	187	ASP	-1	-0.791	-0.867	22.244	0.027	0.027	0.000	0.000	0.000	0.000
18	A	188	CYS	0	-0.047	-0.001	21.200	0.009	0.009	0.000	0.000	0.000	0.000
19	A	189	TYR	0	0.011	-0.006	23.255	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	190	TYR	0	-0.030	-0.062	26.393	0.003	0.003	0.000	0.000	0.000	0.000
21	A	191	ILE	0	-0.030	0.010	24.572	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	192	ASN	0	-0.108	-0.079	23.431	0.003	0.003	0.000	0.000	0.000	0.000
23	A	193	ARG	1	0.930	0.969	25.073	-0.101	-0.101	0.000	0.000	0.000	0.000
24	A	194	ARG	1	0.881	0.957	29.828	-0.038	-0.038	0.000	0.000	0.000	0.000
25	A	195	LYS	1	0.886	0.959	31.180	-0.065	-0.065	0.000	0.000	0.000	0.000
26	A	196	ARG	1	0.959	0.994	30.820	-0.025	-0.025	0.000	0.000	0.000	0.000
27	A	197	LEU	0	-0.009	-0.014	29.395	0.004	0.004	0.000	0.000	0.000	0.000
28	A	198	VAL	0	0.062	0.042	27.135	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	199	LYS	1	0.958	0.989	30.331	0.009	0.009	0.000	0.000	0.000	0.000
30	A	200	LEU	0	-0.036	0.007	29.056	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	201	PRO	0	0.009	-0.010	32.633	0.003	0.003	0.000	0.000	0.000	0.000
32	A	202	CYS	0	-0.041	-0.015	29.943	0.002	0.002	0.000	0.000	0.000	0.000
33	A	203	GLN	0	-0.019	-0.017	32.434	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	204	THR	0	-0.009	0.010	30.914	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	205	ASN	0	0.019	0.013	29.416	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	206	ILE	0	0.052	0.028	23.213	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	207	ILE	0	0.007	0.010	26.671	-0.012	-0.012	0.000	0.000	0.000	0.000
38	A	208	THR	0	-0.011	-0.009	28.726	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	209	ILE	0	-0.007	-0.001	25.097	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	210	LEU	0	-0.018	-0.010	22.319	-0.010	-0.010	0.000	0.000	0.000	0.000
41	A	211	GLU	-1	-0.846	-0.920	26.311	-0.088	-0.088	0.000	0.000	0.000	0.000
42	A	212	SER	0	-0.049	-0.021	29.276	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	213	TYR	0	0.052	0.042	21.982	0.001	0.001	0.000	0.000	0.000	0.000
44	A	214	VAL	0	0.027	0.016	26.683	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	215	LYS	1	0.833	0.908	28.431	0.084	0.084	0.000	0.000	0.000	0.000
46	A	216	HIS	0	0.003	-0.012	28.960	0.004	0.004	0.000	0.000	0.000	0.000
47	A	217	PHE	0	-0.002	-0.007	23.620	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	218	ALA	0	-0.026	-0.020	28.304	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	219	ILE	0	0.000	-0.004	31.230	0.002	0.002	0.000	0.000	0.000	0.000
50	A	220	ASN	0	-0.009	0.005	29.085	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	221	ALA	0	0.007	0.002	28.963	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	222	ALA	0	-0.035	-0.004	30.572	0.000	0.000	0.000	0.000	0.000	0.000
53	A	223	PHE	0	-0.041	-0.013	34.263	0.005	0.005	0.000	0.000	0.000	0.000
54	A	224	SER	0	0.015	0.001	30.153	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	225	ALA	0	-0.016	0.008	31.551	0.003	0.003	0.000	0.000	0.000	0.000
56	A	247	ALA	0	0.029	-0.004	20.434	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	248	GLU	-1	-0.761	-0.871	19.624	-0.369	-0.369	0.000	0.000	0.000	0.000
58	A	249	LYS	1	0.924	0.963	22.755	0.174	0.174	0.000	0.000	0.000	0.000
59	A	250	ASN	0	-0.041	-0.013	24.460	0.031	0.031	0.000	0.000	0.000	0.000
60	A	251	VAL	0	0.082	0.028	25.191	-0.013	-0.013	0.000	0.000	0.000	0.000
61	A	252	ASP	-1	-0.835	-0.911	26.888	-0.154	-0.154	0.000	0.000	0.000	0.000
62	A	253	LEU	0	-0.024	-0.006	19.901	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	254	CYS	0	-0.033	-0.004	21.873	-0.017	-0.017	0.000	0.000	0.000	0.000
64	A	255	LYS	1	0.850	0.907	22.909	0.142	0.142	0.000	0.000	0.000	0.000
65	A	256	GLU	-1	-0.915	-0.947	21.483	-0.238	-0.238	0.000	0.000	0.000	0.000
66	A	257	MET	0	-0.038	0.010	17.601	-0.010	-0.010	0.000	0.000	0.000	0.000
67	A	258	VAL	0	-0.012	-0.010	19.972	0.005	0.005	0.000	0.000	0.000	0.000
68	A	259	ASP	-1	-0.813	-0.908	22.541	-0.126	-0.126	0.000	0.000	0.000	0.000
69	A	260	GLY	0	0.042	0.017	19.156	0.011	0.011	0.000	0.000	0.000	0.000
70	A	261	LEU	0	-0.032	-0.010	16.737	0.010	0.010	0.000	0.000	0.000	0.000
71	A	262	ARG	1	0.862	0.927	19.671	0.125	0.125	0.000	0.000	0.000	0.000
72	A	263	ILE	0	-0.011	0.013	20.828	0.019	0.019	0.000	0.000	0.000	0.000
73	A	264	THR	0	-0.030	-0.042	15.442	0.006	0.006	0.000	0.000	0.000	0.000
74	A	265	PHE	0	-0.028	0.000	18.768	0.025	0.025	0.000	0.000	0.000	0.000
75	A	266	ASP	-1	-0.827	-0.888	20.243	-0.053	-0.053	0.000	0.000	0.000	0.000
76	A	267	TYR	0	-0.025	-0.003	16.958	0.018	0.018	0.000	0.000	0.000	0.000
77	A	268	THR	0	-0.008	-0.039	15.791	0.017	0.017	0.000	0.000	0.000	0.000
78	A	269	LEU	0	-0.006	0.005	18.846	0.024	0.024	0.000	0.000	0.000	0.000
79	A	270	PRO	0	-0.023	-0.020	21.104	0.015	0.015	0.000	0.000	0.000	0.000
80	A	271	LEU	0	-0.062	-0.019	18.867	0.015	0.015	0.000	0.000	0.000	0.000
81	A	272	VAL	0	-0.031	-0.038	14.237	0.021	0.021	0.000	0.000	0.000	0.000
82	A	273	LEU	0	-0.014	0.018	15.850	0.010	0.010	0.000	0.000	0.000	0.000
83	A	274	LEU	0	-0.020	0.016	18.781	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	275	TYR	0	0.063	0.024	19.397	0.016	0.016	0.000	0.000	0.000	0.000
85	A	276	PRO	0	-0.003	-0.021	22.653	-0.009	-0.009	0.000	0.000	0.000	0.000
86	A	277	TYR	0	0.015	-0.007	25.629	-0.007	-0.007	0.000	0.000	0.000	0.000
87	A	278	GLU	-1	-0.756	-0.850	24.134	0.029	0.029	0.000	0.000	0.000	0.000
88	A	279	GLN	0	0.005	0.009	24.294	-0.012	-0.012	0.000	0.000	0.000	0.000
89	A	280	ALA	0	-0.020	-0.016	28.465	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	281	GLN	0	-0.018	-0.022	30.151	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	282	TYR	0	0.090	0.050	27.273	-0.005	-0.005	0.000	0.000	0.000	0.000
92	A	283	LYS	1	0.972	0.982	29.847	-0.042	-0.042	0.000	0.000	0.000	0.000
93	A	284	LYS	1	0.930	0.961	32.364	-0.024	-0.024	0.000	0.000	0.000	0.000
94	A	285	VAL	0	-0.006	-0.002	31.099	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	286	THR	0	-0.023	-0.015	29.902	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	287	SER	0	-0.047	-0.008	33.176	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	288	SER	0	-0.015	0.011	36.431	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	440	GLU	-1	-0.981	-1.000	35.358	-0.046	-0.046	0.000	0.000	0.000	0.000
99	A	441	PHE	0	-0.044	-0.038	38.212	0.001	0.001	0.000	0.000	0.000	0.000
100	A	442	ASP	-1	-0.921	-0.942	39.881	-0.015	-0.015	0.000	0.000	0.000	0.000
101	A	443	GLN	0	-0.032	-0.011	34.966	0.005	0.005	0.000	0.000	0.000	0.000
102	A	444	PRO	0	-0.008	-0.006	31.902	0.000	0.000	0.000	0.000	0.000	0.000
103	A	445	PRO	0	0.003	0.006	32.393	-0.005	-0.005	0.000	0.000	0.000	0.000
104	A	446	PRO	0	0.057	0.026	28.163	0.004	0.004	0.000	0.000	0.000	0.000
105	A	447	PRO	0	0.003	-0.001	24.861	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	448	SER	0	0.026	-0.026	25.311	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	449	TYR	0	-0.001	-0.009	26.792	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	450	ILE	0	-0.058	-0.018	29.223	0.004	0.004	0.000	0.000	0.000	0.000
109	A	451	TYR	0	0.020	-0.006	25.571	0.005	0.005	0.000	0.000	0.000	0.000
110	A	452	GLY	0	0.070	0.020	26.864	-0.007	-0.007	0.000	0.000	0.000	0.000
111	A	453	ALA	0	0.052	0.020	24.219	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	454	GLN	0	0.015	0.014	22.781	-0.009	-0.009	0.000	0.000	0.000	0.000
113	A	455	HIS	0	-0.010	-0.027	21.493	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	456	LEU	0	0.008	0.004	19.849	-0.004	-0.004	0.000	0.000	0.000	0.000
115	A	457	LEU	0	0.028	0.021	17.464	-0.026	-0.026	0.000	0.000	0.000	0.000
116	A	458	ARG	1	0.777	0.851	16.529	-0.037	-0.037	0.000	0.000	0.000	0.000
117	A	459	LEU	0	0.001	0.007	14.707	0.012	0.012	0.000	0.000	0.000	0.000
118	A	460	PHE	0	-0.008	-0.018	13.140	-0.042	-0.042	0.000	0.000	0.000	0.000
119	A	461	VAL	0	-0.005	0.008	11.288	-0.044	-0.044	0.000	0.000	0.000	0.000
120	A	462	LYS	1	0.819	0.893	9.805	-0.187	-0.187	0.000	0.000	0.000	0.000
121	A	463	LEU	0	-0.012	0.002	9.796	-0.033	-0.033	0.000	0.000	0.000	0.000
122	A	464	PRO	0	0.038	0.021	5.069	-0.097	-0.097	0.000	0.000	0.000	0.000
123	A	465	GLU	-1	-0.828	-0.905	5.896	0.055	0.055	0.000	0.000	0.000	0.000
124	A	466	ILE	0	-0.051	-0.031	6.948	0.074	0.074	0.000	0.000	0.000	0.000
125	A	467	LEU	0	-0.015	-0.014	7.918	0.036	0.036	0.000	0.000	0.000	0.000
126	A	468	GLY	0	-0.008	0.004	5.510	-0.133	-0.133	0.000	0.000	0.000	0.000
127	A	469	LYS	1	0.900	0.949	6.166	0.011	0.011	0.000	0.000	0.000	0.000
128	A	470	MET	0	-0.009	0.023	9.430	0.060	0.060	0.000	0.000	0.000	0.000
129	A	471	SER	0	-0.002	-0.008	9.796	-0.088	-0.088	0.000	0.000	0.000	0.000
130	A	472	PHE	0	0.022	0.018	9.794	0.050	0.050	0.000	0.000	0.000	0.000
131	A	473	SER	0	0.003	0.002	10.786	-0.080	-0.080	0.000	0.000	0.000	0.000
132	A	474	GLU	-1	-0.777	-0.903	9.399	-1.352	-1.352	0.000	0.000	0.000	0.000
133	A	475	LYS	1	0.918	0.952	11.733	0.330	0.330	0.000	0.000	0.000	0.000
134	A	476	ASN	0	0.024	0.007	14.789	0.008	0.008	0.000	0.000	0.000	0.000
135	A	477	LEU	0	0.066	0.050	7.247	0.037	0.037	0.000	0.000	0.000	0.000
136	A	478	LYS	1	0.869	0.920	10.057	1.162	1.162	0.000	0.000	0.000	0.000
137	A	479	ALA	0	-0.015	-0.003	12.622	0.052	0.052	0.000	0.000	0.000	0.000
138	A	480	LEU	0	0.026	0.021	12.615	0.056	0.056	0.000	0.000	0.000	0.000
139	A	481	LEU	0	0.000	-0.015	8.534	0.040	0.040	0.000	0.000	0.000	0.000
140	A	482	LYS	1	0.824	0.894	12.917	0.524	0.524	0.000	0.000	0.000	0.000
141	A	483	HIS	0	-0.024	-0.021	16.014	0.067	0.067	0.000	0.000	0.000	0.000
142	A	484	PHE	0	0.043	0.009	12.346	0.048	0.048	0.000	0.000	0.000	0.000
143	A	485	ASP	-1	-0.872	-0.909	15.379	-0.298	-0.298	0.000	0.000	0.000	0.000
144	A	486	LEU	0	0.012	0.002	16.704	0.052	0.052	0.000	0.000	0.000	0.000
145	A	487	PHE	0	0.009	0.014	18.732	0.036	0.036	0.000	0.000	0.000	0.000
146	A	488	LEU	0	-0.003	-0.007	14.481	0.035	0.035	0.000	0.000	0.000	0.000
147	A	489	ARG	1	0.874	0.919	17.544	0.249	0.249	0.000	0.000	0.000	0.000
148	A	490	PHE	0	0.023	0.011	21.439	0.021	0.021	0.000	0.000	0.000	0.000
149	A	491	LEU	0	-0.011	-0.009	20.083	0.017	0.017	0.000	0.000	0.000	0.000
150	A	492	ALA	0	-0.060	-0.043	21.484	0.018	0.018	0.000	0.000	0.000	0.000
151	A	493	GLU	-1	-0.946	-0.948	23.455	-0.103	-0.103	0.000	0.000	0.000	0.000
152	A	494	TYR	0	-0.051	-0.037	26.548	0.009	0.009	0.000	0.000	0.000	0.000
153	A	495	HIS	0	-0.019	-0.017	24.515	0.009	0.009	0.000	0.000	0.000	0.000
154	A	496	ASP	-1	-0.874	-0.943	26.981	-0.028	-0.028	0.000	0.000	0.000	0.000
155	A	497	ASP	-1	-0.938	-0.950	30.540	-0.050	-0.050	0.000	0.000	0.000	0.000
156	A	498	PHE	0	-0.059	-0.045	26.625	0.002	0.002	0.000	0.000	0.000	0.000
157	A	499	PHE	0	-0.074	-0.037	22.527	0.002	0.002	0.000	0.000	0.000	0.000
158	A	500	PRO	0	0.036	0.046	28.435	0.006	0.006	0.000	0.000	0.000	0.000
159	A	501	GLU	-1	-0.778	-0.887	30.822	0.011	0.011	0.000	0.000	0.000	0.000
160	A	502	SER	0	-0.093	-0.056	32.355	0.003	0.003	0.000	0.000	0.000	0.000
161	A	503	ALA	0	0.001	0.018	30.467	0.000	0.000	0.000	0.000	0.000	0.000
162	A	504	TYR	0	-0.070	-0.070	25.564	0.000	0.000	0.000	0.000	0.000	0.000
163	A	505	VAL	0	-0.044	-0.037	32.316	-0.001	-0.001	0.000	0.000	0.000	0.000
164	A	506	ALA	0	0.012	-0.004	34.272	0.004	0.004	0.000	0.000	0.000	0.000
165	A	507	ALA	0	-0.010	0.021	36.768	0.001	0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:171:THR)