FMO DATABASE

FMODB ID: 535ZZ

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:

Apendix: None

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	165
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1759852.277052
FMO2-HF: Nuclear repulsion	1692950.254171
FMO2-HF: Total energy	-66902.022881
FMO2-MP2: Total energy	-67098.842815

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.
-1.648	0.067	0.001	-0.751	-0.965	0.002

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 : -0.024 / q_NPA : -0.023

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	-0.008	-0.002	3.446	-2.201	-0.486	0.001	-0.751	-0.965	0.002
4	A	174	ILE	0	-0.013	-0.015	5.893	0.649	0.649	0.000	0.000	0.000	0.000
5	A	175	GLU	-1	-0.796	-0.876	9.532	-0.819	-0.819	0.000	0.000	0.000	0.000
6	A	176	ILE	0	-0.001	-0.001	11.762	0.099	0.099	0.000	0.000	0.000	0.000
7	A	177	PRO	0	0.013	-0.001	14.727	0.033	0.033	0.000	0.000	0.000	0.000
8	A	178	GLU	-1	-0.826	-0.922	17.364	-0.395	-0.395	0.000	0.000	0.000	0.000
9	A	179	VAL	0	-0.025	0.005	19.556	0.023	0.023	0.000	0.000	0.000	0.000
10	A	180	LEU	0	0.029	0.003	18.713	0.015	0.015	0.000	0.000	0.000	0.000
11	A	181	LYS	1	0.753	0.855	14.184	0.628	0.628	0.000	0.000	0.000	0.000
12	A	182	LYS	1	0.959	0.989	18.127	0.300	0.300	0.000	0.000	0.000	0.000
13	A	183	GLN	0	0.035	0.020	21.705	0.020	0.020	0.000	0.000	0.000	0.000
14	A	184	LEU	0	-0.014	-0.009	15.836	0.014	0.014	0.000	0.000	0.000	0.000
15	A	185	GLU	-1	-0.943	-0.967	19.348	-0.274	-0.274	0.000	0.000	0.000	0.000
16	A	186	ASP	-1	-0.892	-0.950	21.468	-0.169	-0.169	0.000	0.000	0.000	0.000
17	A	187	ASP	-1	-0.775	-0.857	22.230	-0.191	-0.191	0.000	0.000	0.000	0.000
18	A	188	CYS	0	-0.029	0.010	20.785	0.025	0.025	0.000	0.000	0.000	0.000
19	A	189	TYR	0	0.000	-0.006	23.061	0.025	0.025	0.000	0.000	0.000	0.000
20	A	190	TYR	0	-0.047	-0.072	26.232	0.026	0.026	0.000	0.000	0.000	0.000
21	A	191	ILE	0	-0.039	0.006	24.654	0.014	0.014	0.000	0.000	0.000	0.000
22	A	192	ASN	0	-0.124	-0.093	23.063	0.018	0.018	0.000	0.000	0.000	0.000
23	A	193	ARG	1	0.906	0.963	24.449	0.138	0.138	0.000	0.000	0.000	0.000
24	A	194	ARG	1	0.891	0.953	29.585	0.130	0.130	0.000	0.000	0.000	0.000
25	A	195	LYS	1	0.887	0.957	30.947	0.082	0.082	0.000	0.000	0.000	0.000
26	A	196	ARG	1	0.904	0.965	30.879	0.107	0.107	0.000	0.000	0.000	0.000
27	A	197	LEU	0	-0.012	-0.012	29.544	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	198	VAL	0	0.044	0.030	26.905	0.003	0.003	0.000	0.000	0.000	0.000
29	A	199	LYS	1	0.907	0.954	30.112	0.090	0.090	0.000	0.000	0.000	0.000
30	A	200	LEU	0	-0.018	0.008	29.048	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	201	PRO	0	0.003	-0.006	32.812	0.006	0.006	0.000	0.000	0.000	0.000
32	A	202	CYS	0	-0.064	-0.027	29.812	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	203	GLN	0	0.001	-0.010	32.270	0.003	0.003	0.000	0.000	0.000	0.000
34	A	204	THR	0	-0.008	0.016	30.662	0.001	0.001	0.000	0.000	0.000	0.000
35	A	205	ASN	0	0.020	0.005	29.229	-0.010	-0.010	0.000	0.000	0.000	0.000
36	A	206	ILE	0	0.050	0.025	23.221	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	207	ILE	0	0.001	0.013	26.539	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	208	THR	0	0.003	-0.006	28.785	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	209	ILE	0	-0.014	-0.002	25.091	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	210	LEU	0	-0.008	-0.005	22.300	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	211	GLU	-1	-0.859	-0.926	26.291	-0.089	-0.089	0.000	0.000	0.000	0.000
42	A	212	SER	0	-0.024	-0.010	29.123	0.005	0.005	0.000	0.000	0.000	0.000
43	A	213	TYR	0	0.031	0.033	21.392	0.002	0.002	0.000	0.000	0.000	0.000
44	A	214	VAL	0	0.019	0.003	26.617	0.002	0.002	0.000	0.000	0.000	0.000
45	A	215	LYS	1	0.845	0.913	28.355	0.102	0.102	0.000	0.000	0.000	0.000
46	A	216	HIS	0	0.013	-0.003	29.085	0.009	0.009	0.000	0.000	0.000	0.000
47	A	217	PHE	0	-0.005	-0.002	23.389	0.005	0.005	0.000	0.000	0.000	0.000
48	A	218	ALA	0	-0.013	-0.019	28.446	0.005	0.005	0.000	0.000	0.000	0.000
49	A	219	ILE	0	-0.001	0.007	31.369	0.006	0.006	0.000	0.000	0.000	0.000
50	A	220	ASN	0	0.017	0.008	28.635	0.006	0.006	0.000	0.000	0.000	0.000
51	A	221	ALA	0	-0.002	-0.015	29.175	0.002	0.002	0.000	0.000	0.000	0.000
52	A	222	ALA	0	-0.025	-0.003	30.656	0.005	0.005	0.000	0.000	0.000	0.000
53	A	223	PHE	0	-0.057	-0.023	33.984	0.006	0.006	0.000	0.000	0.000	0.000
54	A	224	SER	0	0.018	0.011	29.452	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	225	ALA	0	0.005	0.014	30.779	0.008	0.008	0.000	0.000	0.000	0.000
56	A	247	ALA	0	0.037	0.001	20.654	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	248	GLU	-1	-0.777	-0.874	19.591	-0.290	-0.290	0.000	0.000	0.000	0.000
58	A	249	LYS	1	0.879	0.954	22.969	0.113	0.113	0.000	0.000	0.000	0.000
59	A	250	ASN	0	-0.034	-0.012	24.488	0.013	0.013	0.000	0.000	0.000	0.000
60	A	251	VAL	0	0.081	0.024	25.268	-0.010	-0.010	0.000	0.000	0.000	0.000
61	A	252	ASP	-1	-0.819	-0.899	27.078	-0.069	-0.069	0.000	0.000	0.000	0.000
62	A	253	LEU	0	0.003	0.009	19.650	0.001	0.001	0.000	0.000	0.000	0.000
63	A	254	CYS	0	-0.021	0.008	21.896	-0.013	-0.013	0.000	0.000	0.000	0.000
64	A	255	LYS	1	0.813	0.892	23.256	0.065	0.065	0.000	0.000	0.000	0.000
65	A	256	GLU	-1	-0.927	-0.961	21.435	-0.053	-0.053	0.000	0.000	0.000	0.000
66	A	257	MET	0	-0.055	-0.004	17.711	-0.018	-0.018	0.000	0.000	0.000	0.000
67	A	258	VAL	0	0.004	-0.007	19.832	-0.017	-0.017	0.000	0.000	0.000	0.000
68	A	259	ASP	-1	-0.815	-0.906	22.449	-0.083	-0.083	0.000	0.000	0.000	0.000
69	A	260	GLY	0	0.039	0.023	18.987	0.006	0.006	0.000	0.000	0.000	0.000
70	A	261	LEU	0	-0.033	-0.005	16.726	-0.010	-0.010	0.000	0.000	0.000	0.000
71	A	262	ARG	1	0.821	0.895	19.237	0.082	0.082	0.000	0.000	0.000	0.000
72	A	263	ILE	0	-0.011	0.001	20.323	0.008	0.008	0.000	0.000	0.000	0.000
73	A	264	THR	0	-0.029	-0.026	15.200	0.010	0.010	0.000	0.000	0.000	0.000
74	A	265	PHE	0	-0.037	-0.013	18.480	0.000	0.000	0.000	0.000	0.000	0.000
75	A	266	ASP	-1	-0.800	-0.871	20.407	-0.095	-0.095	0.000	0.000	0.000	0.000
76	A	267	TYR	0	-0.012	0.003	16.880	0.013	0.013	0.000	0.000	0.000	0.000
77	A	268	THR	0	-0.004	-0.038	15.811	0.003	0.003	0.000	0.000	0.000	0.000
78	A	269	LEU	0	-0.007	0.002	18.827	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	270	PRO	0	-0.010	-0.016	21.284	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	271	LEU	0	-0.051	-0.013	18.955	0.009	0.009	0.000	0.000	0.000	0.000
81	A	272	VAL	0	-0.043	-0.028	14.492	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	273	LEU	0	-0.005	0.025	15.913	-0.034	-0.034	0.000	0.000	0.000	0.000
83	A	274	LEU	0	-0.035	0.007	18.996	0.000	0.000	0.000	0.000	0.000	0.000
84	A	275	TYR	0	0.033	0.015	20.149	0.002	0.002	0.000	0.000	0.000	0.000
85	A	276	PRO	0	0.002	-0.022	23.028	0.010	0.010	0.000	0.000	0.000	0.000
86	A	277	TYR	0	0.008	-0.002	25.940	0.012	0.012	0.000	0.000	0.000	0.000
87	A	278	GLU	-1	-0.710	-0.834	24.304	-0.150	-0.150	0.000	0.000	0.000	0.000
88	A	279	GLN	0	-0.001	0.011	24.062	0.012	0.012	0.000	0.000	0.000	0.000
89	A	280	ALA	0	-0.032	-0.019	28.517	0.007	0.007	0.000	0.000	0.000	0.000
90	A	281	GLN	0	-0.041	-0.026	30.478	0.001	0.001	0.000	0.000	0.000	0.000
91	A	282	TYR	0	0.083	0.032	27.278	0.002	0.002	0.000	0.000	0.000	0.000
92	A	283	LYS	1	0.971	0.990	30.066	0.048	0.048	0.000	0.000	0.000	0.000
93	A	284	LYS	1	0.950	0.978	32.539	0.057	0.057	0.000	0.000	0.000	0.000
94	A	285	VAL	0	0.003	0.010	31.556	0.003	0.003	0.000	0.000	0.000	0.000
95	A	286	THR	0	-0.007	-0.015	29.781	0.004	0.004	0.000	0.000	0.000	0.000
96	A	287	SER	0	-0.061	-0.024	33.181	0.005	0.005	0.000	0.000	0.000	0.000
97	A	288	SER	0	-0.030	-0.002	36.369	0.003	0.003	0.000	0.000	0.000	0.000
98	A	440	GLU	-1	-0.976	-1.000	35.052	-0.032	-0.032	0.000	0.000	0.000	0.000
99	A	441	PHE	0	-0.048	-0.038	37.974	0.003	0.003	0.000	0.000	0.000	0.000
100	A	442	ASP	-1	-0.918	-0.950	39.895	-0.027	-0.027	0.000	0.000	0.000	0.000
101	A	443	GLN	0	-0.020	0.001	34.804	0.001	0.001	0.000	0.000	0.000	0.000
102	A	444	PRO	0	-0.013	-0.001	32.298	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	445	PRO	0	0.002	0.005	32.557	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	446	PRO	0	0.044	0.015	27.831	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	447	PRO	0	0.031	0.010	25.010	-0.005	-0.005	0.000	0.000	0.000	0.000
106	A	448	SER	0	0.018	-0.031	24.997	-0.012	-0.012	0.000	0.000	0.000	0.000
107	A	449	TYR	0	-0.003	-0.003	26.761	-0.005	-0.005	0.000	0.000	0.000	0.000
108	A	450	ILE	0	-0.071	-0.020	29.367	0.003	0.003	0.000	0.000	0.000	0.000
109	A	451	TYR	0	0.047	0.006	25.625	0.003	0.003	0.000	0.000	0.000	0.000
110	A	452	GLY	0	0.067	0.024	26.800	0.004	0.004	0.000	0.000	0.000	0.000
111	A	453	ALA	0	0.037	0.019	23.974	-0.012	-0.012	0.000	0.000	0.000	0.000
112	A	454	GLN	0	0.011	0.019	22.424	-0.024	-0.024	0.000	0.000	0.000	0.000
113	A	455	HIS	0	0.015	-0.018	21.362	-0.029	-0.029	0.000	0.000	0.000	0.000
114	A	456	LEU	0	0.010	0.008	19.849	-0.021	-0.021	0.000	0.000	0.000	0.000
115	A	457	LEU	0	0.008	0.009	17.272	-0.043	-0.043	0.000	0.000	0.000	0.000
116	A	458	ARG	1	0.765	0.830	16.495	0.156	0.156	0.000	0.000	0.000	0.000
117	A	459	LEU	0	-0.011	0.001	15.085	-0.037	-0.037	0.000	0.000	0.000	0.000
118	A	460	PHE	0	0.006	-0.016	13.410	-0.056	-0.056	0.000	0.000	0.000	0.000
119	A	461	VAL	0	-0.002	0.011	11.521	-0.160	-0.160	0.000	0.000	0.000	0.000
120	A	462	LYS	1	0.823	0.893	10.015	0.281	0.281	0.000	0.000	0.000	0.000
121	A	463	LEU	0	0.002	0.013	10.138	-0.020	-0.020	0.000	0.000	0.000	0.000
122	A	464	PRO	0	0.032	0.016	5.387	0.113	0.113	0.000	0.000	0.000	0.000
123	A	465	GLU	-1	-0.818	-0.898	5.947	-0.380	-0.380	0.000	0.000	0.000	0.000
124	A	466	ILE	0	-0.045	-0.010	7.329	0.319	0.319	0.000	0.000	0.000	0.000
125	A	467	LEU	0	0.011	-0.002	7.612	0.155	0.155	0.000	0.000	0.000	0.000
126	A	468	GLY	0	-0.011	-0.002	5.239	0.279	0.279	0.000	0.000	0.000	0.000
127	A	469	LYS	1	0.850	0.922	5.961	0.408	0.408	0.000	0.000	0.000	0.000
128	A	470	MET	0	-0.012	0.006	9.373	-0.039	-0.039	0.000	0.000	0.000	0.000
129	A	471	SER	0	0.005	0.006	10.121	0.028	0.028	0.000	0.000	0.000	0.000
130	A	472	PHE	0	0.016	0.006	10.157	-0.108	-0.108	0.000	0.000	0.000	0.000
131	A	473	SER	0	-0.001	-0.007	11.526	0.147	0.147	0.000	0.000	0.000	0.000
132	A	474	GLU	-1	-0.799	-0.895	10.285	0.171	0.171	0.000	0.000	0.000	0.000
133	A	475	LYS	1	0.950	0.973	12.539	-0.190	-0.190	0.000	0.000	0.000	0.000
134	A	476	ASN	0	0.044	0.033	15.509	-0.033	-0.033	0.000	0.000	0.000	0.000
135	A	477	LEU	0	0.057	0.039	7.676	-0.055	-0.055	0.000	0.000	0.000	0.000
136	A	478	LYS	1	0.864	0.902	10.049	-0.130	-0.130	0.000	0.000	0.000	0.000
137	A	479	ALA	0	-0.024	-0.007	13.178	-0.071	-0.071	0.000	0.000	0.000	0.000
138	A	480	LEU	0	0.016	0.012	13.080	-0.026	-0.026	0.000	0.000	0.000	0.000
139	A	481	LEU	0	-0.001	-0.010	8.682	-0.036	-0.036	0.000	0.000	0.000	0.000
140	A	482	LYS	1	0.821	0.898	12.973	0.296	0.296	0.000	0.000	0.000	0.000
141	A	483	HIS	0	-0.010	-0.011	16.190	0.000	0.000	0.000	0.000	0.000	0.000
142	A	484	PHE	0	0.040	-0.002	12.380	0.017	0.017	0.000	0.000	0.000	0.000
143	A	485	ASP	-1	-0.862	-0.902	14.717	-0.583	-0.583	0.000	0.000	0.000	0.000
144	A	486	LEU	0	0.013	-0.006	16.405	0.039	0.039	0.000	0.000	0.000	0.000
145	A	487	PHE	0	-0.006	0.001	18.803	0.031	0.031	0.000	0.000	0.000	0.000
146	A	488	LEU	0	0.010	-0.003	14.456	0.020	0.020	0.000	0.000	0.000	0.000
147	A	489	ARG	1	0.837	0.899	16.683	0.491	0.491	0.000	0.000	0.000	0.000
148	A	490	PHE	0	0.036	0.021	21.329	0.021	0.021	0.000	0.000	0.000	0.000
149	A	491	LEU	0	-0.039	-0.019	19.882	0.016	0.016	0.000	0.000	0.000	0.000
150	A	492	ALA	0	-0.028	-0.029	21.495	0.010	0.010	0.000	0.000	0.000	0.000
151	A	493	GLU	-1	-0.945	-0.946	23.482	-0.181	-0.181	0.000	0.000	0.000	0.000
152	A	494	TYR	0	-0.048	-0.035	26.641	0.019	0.019	0.000	0.000	0.000	0.000
153	A	495	HIS	0	-0.015	-0.014	24.300	-0.008	-0.008	0.000	0.000	0.000	0.000
154	A	496	ASP	-1	-0.872	-0.936	26.909	-0.163	-0.163	0.000	0.000	0.000	0.000
155	A	497	ASP	-1	-0.922	-0.953	30.412	-0.134	-0.134	0.000	0.000	0.000	0.000
156	A	498	PHE	0	-0.058	-0.034	26.254	0.009	0.009	0.000	0.000	0.000	0.000
157	A	499	PHE	0	-0.083	-0.049	22.269	-0.004	-0.004	0.000	0.000	0.000	0.000
158	A	500	PRO	0	0.042	0.043	28.183	0.002	0.002	0.000	0.000	0.000	0.000
159	A	501	GLU	-1	-0.778	-0.886	31.204	-0.136	-0.136	0.000	0.000	0.000	0.000
160	A	502	SER	0	-0.083	-0.047	32.544	0.001	0.001	0.000	0.000	0.000	0.000
161	A	503	ALA	0	-0.007	0.013	30.145	0.006	0.006	0.000	0.000	0.000	0.000
162	A	504	TYR	0	-0.042	-0.048	25.286	0.005	0.005	0.000	0.000	0.000	0.000
163	A	505	VAL	0	0.007	-0.004	32.135	0.006	0.006	0.000	0.000	0.000	0.000
164	A	506	ALA	0	0.019	-0.006	34.099	-0.004	-0.004	0.000	0.000	0.000	0.000
165	A	507	ALA	0	-0.001	0.015	36.603	0.006	0.006	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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