FMO DATABASE

FMODB ID: K3V73

Calculation Name: 2Y0N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422
Remarks

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	-1751399.644021
FMO2-HF: Nuclear repulsion	1684499.445589
FMO2-HF: Total energy	-66900.198432
FMO2-MP2: Total energy	-67097.039474

3D Structure Molmil

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.
-0.51	1.54	-0.008	-0.941	-1.101	0.001

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 : 0.013 / q_NPA : -0.013

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	-0.010	-0.010	3.563	-0.672	1.378	-0.008	-0.941	-1.101	0.001
4	A	174	ILE	0	0.001	-0.001	5.612	0.391	0.391	0.000	0.000	0.000	0.000
5	A	175	GLU	-1	-0.937	-0.959	9.402	-0.770	-0.770	0.000	0.000	0.000	0.000
6	A	176	ILE	0	-0.002	0.001	11.371	0.097	0.097	0.000	0.000	0.000	0.000
7	A	177	PRO	0	-0.004	-0.005	14.523	0.039	0.039	0.000	0.000	0.000	0.000
8	A	178	GLU	-1	-0.849	-0.946	17.194	-0.348	-0.348	0.000	0.000	0.000	0.000
9	A	179	VAL	0	-0.043	-0.019	19.156	0.032	0.032	0.000	0.000	0.000	0.000
10	A	180	LEU	0	0.029	0.001	18.892	0.024	0.024	0.000	0.000	0.000	0.000
11	A	181	LYS	1	0.930	0.973	12.910	0.494	0.494	0.000	0.000	0.000	0.000
12	A	182	LYS	1	0.993	1.007	18.500	0.248	0.248	0.000	0.000	0.000	0.000
13	A	183	GLN	0	0.032	0.041	22.015	0.024	0.024	0.000	0.000	0.000	0.000
14	A	184	LEU	0	-0.001	-0.013	16.172	0.018	0.018	0.000	0.000	0.000	0.000
15	A	185	GLU	-1	-0.984	-0.983	19.609	-0.164	-0.164	0.000	0.000	0.000	0.000
16	A	186	ASP	-1	-0.909	-0.960	21.682	-0.125	-0.125	0.000	0.000	0.000	0.000
17	A	187	ASP	-1	-0.824	-0.876	22.251	-0.134	-0.134	0.000	0.000	0.000	0.000
18	A	188	CYS	0	-0.045	-0.019	21.224	0.023	0.023	0.000	0.000	0.000	0.000
19	A	189	TYR	0	-0.015	-0.012	23.292	0.021	0.021	0.000	0.000	0.000	0.000
20	A	190	TYR	0	-0.021	-0.038	26.445	0.024	0.024	0.000	0.000	0.000	0.000
21	A	191	ILE	0	-0.016	0.018	24.793	0.012	0.012	0.000	0.000	0.000	0.000
22	A	192	ASN	0	-0.085	-0.045	23.283	0.011	0.011	0.000	0.000	0.000	0.000
23	A	193	ARG	1	0.926	0.966	25.582	0.049	0.049	0.000	0.000	0.000	0.000
24	A	194	ARG	1	0.894	0.957	29.855	0.080	0.080	0.000	0.000	0.000	0.000
25	A	195	LYS	1	0.899	0.964	31.192	0.025	0.025	0.000	0.000	0.000	0.000
26	A	196	ARG	1	0.952	0.990	30.830	0.072	0.072	0.000	0.000	0.000	0.000
27	A	197	LEU	0	-0.007	-0.016	29.450	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	198	VAL	0	0.070	0.049	27.107	0.002	0.002	0.000	0.000	0.000	0.000
29	A	199	LYS	1	0.950	0.976	30.327	0.073	0.073	0.000	0.000	0.000	0.000
30	A	200	LEU	0	-0.052	0.003	29.137	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	201	PRO	0	0.010	-0.009	32.596	0.007	0.007	0.000	0.000	0.000	0.000
32	A	202	CYS	0	-0.030	-0.007	29.827	0.000	0.000	0.000	0.000	0.000	0.000
33	A	203	GLN	0	-0.019	-0.015	32.423	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	204	THR	0	0.025	0.018	30.373	0.000	0.000	0.000	0.000	0.000	0.000
35	A	205	ASN	0	-0.010	0.020	29.419	-0.015	-0.015	0.000	0.000	0.000	0.000
36	A	206	ILE	0	0.041	0.014	23.130	-0.008	-0.008	0.000	0.000	0.000	0.000
37	A	207	ILE	0	-0.008	0.005	26.653	-0.013	-0.013	0.000	0.000	0.000	0.000
38	A	208	THR	0	0.001	0.000	28.698	-0.006	-0.006	0.000	0.000	0.000	0.000
39	A	209	ILE	0	-0.004	0.004	25.065	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	210	LEU	0	-0.036	-0.025	22.621	-0.014	-0.014	0.000	0.000	0.000	0.000
41	A	211	GLU	-1	-0.916	-0.963	26.315	-0.130	-0.130	0.000	0.000	0.000	0.000
42	A	212	SER	0	-0.057	-0.029	29.289	0.002	0.002	0.000	0.000	0.000	0.000
43	A	213	TYR	0	0.047	0.028	22.516	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	214	VAL	0	0.038	0.020	26.708	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	215	LYS	1	0.912	0.958	28.458	0.136	0.136	0.000	0.000	0.000	0.000
46	A	216	HIS	0	0.009	-0.001	29.049	0.007	0.007	0.000	0.000	0.000	0.000
47	A	217	PHE	0	-0.014	-0.008	23.541	0.002	0.002	0.000	0.000	0.000	0.000
48	A	218	ALA	0	-0.024	-0.020	28.329	0.000	0.000	0.000	0.000	0.000	0.000
49	A	219	ILE	0	-0.003	-0.001	31.229	0.007	0.007	0.000	0.000	0.000	0.000
50	A	220	ASN	0	0.017	0.004	28.514	0.010	0.010	0.000	0.000	0.000	0.000
51	A	221	ALA	0	-0.033	-0.008	28.994	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	222	ALA	0	-0.073	-0.023	30.509	0.005	0.005	0.000	0.000	0.000	0.000
53	A	223	PHE	0	-0.058	-0.023	34.062	0.009	0.009	0.000	0.000	0.000	0.000
54	A	224	SER	0	0.043	0.015	30.209	-0.011	-0.011	0.000	0.000	0.000	0.000
55	A	225	ALA	0	-0.054	-0.012	31.046	0.011	0.011	0.000	0.000	0.000	0.000
56	A	247	ALA	0	0.020	-0.009	20.409	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	248	GLU	-1	-0.864	-0.950	19.736	-0.475	-0.475	0.000	0.000	0.000	0.000
58	A	249	LYS	1	0.987	0.993	22.571	0.223	0.223	0.000	0.000	0.000	0.000
59	A	250	ASN	0	-0.028	-0.008	24.484	0.031	0.031	0.000	0.000	0.000	0.000
60	A	251	VAL	0	0.071	0.023	25.194	-0.016	-0.016	0.000	0.000	0.000	0.000
61	A	252	ASP	-1	-0.905	-0.953	26.888	-0.153	-0.153	0.000	0.000	0.000	0.000
62	A	253	LEU	0	-0.034	-0.017	20.175	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	254	CYS	0	-0.026	0.007	21.874	-0.022	-0.022	0.000	0.000	0.000	0.000
64	A	255	LYS	1	0.945	0.964	22.906	0.140	0.140	0.000	0.000	0.000	0.000
65	A	256	GLU	-1	-0.903	-0.943	21.224	-0.186	-0.186	0.000	0.000	0.000	0.000
66	A	257	MET	0	-0.037	0.016	17.696	-0.018	-0.018	0.000	0.000	0.000	0.000
67	A	258	VAL	0	-0.029	-0.018	19.964	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	259	ASP	-1	-0.827	-0.922	22.533	-0.135	-0.135	0.000	0.000	0.000	0.000
69	A	260	GLY	0	0.040	0.018	19.150	0.014	0.014	0.000	0.000	0.000	0.000
70	A	261	LEU	0	-0.026	0.001	17.041	0.006	0.006	0.000	0.000	0.000	0.000
71	A	262	ARG	1	0.921	0.964	19.620	0.136	0.136	0.000	0.000	0.000	0.000
72	A	263	ILE	0	-0.007	0.019	20.762	0.020	0.020	0.000	0.000	0.000	0.000
73	A	264	THR	0	-0.016	-0.050	15.366	0.012	0.012	0.000	0.000	0.000	0.000
74	A	265	PHE	0	-0.031	0.032	18.712	0.016	0.016	0.000	0.000	0.000	0.000
75	A	266	ASP	-1	-0.839	-0.917	20.161	-0.094	-0.094	0.000	0.000	0.000	0.000
76	A	267	TYR	0	-0.041	-0.009	17.638	0.023	0.023	0.000	0.000	0.000	0.000
77	A	268	THR	0	-0.023	-0.073	15.747	0.012	0.012	0.000	0.000	0.000	0.000
78	A	269	LEU	0	-0.010	0.001	18.727	0.015	0.015	0.000	0.000	0.000	0.000
79	A	270	PRO	0	-0.031	-0.019	21.011	0.006	0.006	0.000	0.000	0.000	0.000
80	A	271	LEU	0	-0.054	-0.018	19.111	0.019	0.019	0.000	0.000	0.000	0.000
81	A	272	VAL	0	-0.037	-0.039	14.287	0.014	0.014	0.000	0.000	0.000	0.000
82	A	273	LEU	0	-0.007	0.008	15.629	-0.017	-0.017	0.000	0.000	0.000	0.000
83	A	274	LEU	0	-0.017	0.007	18.711	-0.006	-0.006	0.000	0.000	0.000	0.000
84	A	275	TYR	0	0.038	0.013	19.762	0.009	0.009	0.000	0.000	0.000	0.000
85	A	276	PRO	0	-0.015	-0.024	22.609	0.003	0.003	0.000	0.000	0.000	0.000
86	A	277	TYR	0	0.021	-0.007	25.585	0.004	0.004	0.000	0.000	0.000	0.000
87	A	278	GLU	-1	-0.761	-0.868	24.191	-0.095	-0.095	0.000	0.000	0.000	0.000
88	A	279	GLN	0	0.022	0.016	23.912	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	280	ALA	0	-0.024	-0.018	28.380	0.001	0.001	0.000	0.000	0.000	0.000
90	A	281	GLN	0	-0.020	-0.014	29.928	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	282	TYR	0	0.084	0.049	26.816	0.003	0.003	0.000	0.000	0.000	0.000
92	A	283	LYS	1	0.971	0.975	29.759	0.004	0.004	0.000	0.000	0.000	0.000
93	A	284	LYS	1	0.921	0.956	32.269	0.028	0.028	0.000	0.000	0.000	0.000
94	A	285	VAL	0	0.010	0.006	31.144	0.001	0.001	0.000	0.000	0.000	0.000
95	A	286	THR	0	-0.037	-0.016	29.728	0.002	0.002	0.000	0.000	0.000	0.000
96	A	287	SER	0	-0.052	-0.010	33.072	0.003	0.003	0.000	0.000	0.000	0.000
97	A	288	SER	0	0.002	0.018	36.340	0.001	0.001	0.000	0.000	0.000	0.000
98	A	440	GLU	-1	-0.983	-1.000	35.415	-0.050	-0.050	0.000	0.000	0.000	0.000
99	A	441	PHE	0	-0.049	-0.038	38.300	0.002	0.002	0.000	0.000	0.000	0.000
100	A	442	ASP	-1	-0.914	-0.939	39.861	-0.027	-0.027	0.000	0.000	0.000	0.000
101	A	443	GLN	0	-0.028	-0.012	35.179	0.004	0.004	0.000	0.000	0.000	0.000
102	A	444	PRO	0	-0.011	-0.003	31.776	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	445	PRO	0	0.004	-0.007	32.276	-0.004	-0.004	0.000	0.000	0.000	0.000
104	A	446	PRO	0	0.039	0.027	28.302	0.001	0.001	0.000	0.000	0.000	0.000
105	A	447	PRO	0	0.005	-0.003	24.826	-0.005	-0.005	0.000	0.000	0.000	0.000
106	A	448	SER	0	0.033	-0.005	25.281	-0.013	-0.013	0.000	0.000	0.000	0.000
107	A	449	TYR	0	-0.003	-0.016	26.728	-0.007	-0.007	0.000	0.000	0.000	0.000
108	A	450	ILE	0	-0.062	-0.015	29.167	0.005	0.005	0.000	0.000	0.000	0.000
109	A	451	TYR	0	0.020	-0.011	25.550	0.006	0.006	0.000	0.000	0.000	0.000
110	A	452	GLY	0	0.073	0.018	26.866	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	453	ALA	0	0.056	0.014	24.236	-0.011	-0.011	0.000	0.000	0.000	0.000
112	A	454	GLN	0	0.012	0.015	22.809	-0.021	-0.021	0.000	0.000	0.000	0.000
113	A	455	HIS	0	-0.004	-0.027	21.583	-0.021	-0.021	0.000	0.000	0.000	0.000
114	A	456	LEU	0	0.018	0.013	19.589	-0.017	-0.017	0.000	0.000	0.000	0.000
115	A	457	LEU	0	0.028	0.020	17.544	-0.044	-0.044	0.000	0.000	0.000	0.000
116	A	458	ARG	1	0.807	0.882	16.559	0.099	0.099	0.000	0.000	0.000	0.000
117	A	459	LEU	0	0.002	0.003	14.878	-0.026	-0.026	0.000	0.000	0.000	0.000
118	A	460	PHE	0	0.003	-0.013	13.157	-0.054	-0.054	0.000	0.000	0.000	0.000
119	A	461	VAL	0	-0.011	0.006	11.324	-0.144	-0.144	0.000	0.000	0.000	0.000
120	A	462	LYS	1	0.903	0.954	9.803	0.053	0.053	0.000	0.000	0.000	0.000
121	A	463	LEU	0	0.015	0.012	9.709	-0.019	-0.019	0.000	0.000	0.000	0.000
122	A	464	PRO	0	0.017	0.017	5.096	0.011	0.011	0.000	0.000	0.000	0.000
123	A	465	GLU	-1	-0.905	-0.966	6.005	-0.143	-0.143	0.000	0.000	0.000	0.000
124	A	466	ILE	0	-0.064	-0.030	6.898	0.268	0.268	0.000	0.000	0.000	0.000
125	A	467	LEU	0	-0.013	-0.024	7.983	0.138	0.138	0.000	0.000	0.000	0.000
126	A	468	GLY	0	-0.011	0.009	5.501	0.089	0.089	0.000	0.000	0.000	0.000
127	A	469	LYS	1	0.903	0.948	6.161	0.140	0.140	0.000	0.000	0.000	0.000
128	A	470	MET	0	-0.010	0.020	9.447	0.033	0.033	0.000	0.000	0.000	0.000
129	A	471	SER	0	-0.006	-0.002	9.809	-0.034	-0.034	0.000	0.000	0.000	0.000
130	A	472	PHE	0	0.013	0.007	9.914	-0.070	-0.070	0.000	0.000	0.000	0.000
131	A	473	SER	0	0.006	0.003	10.950	0.065	0.065	0.000	0.000	0.000	0.000
132	A	474	GLU	-1	-0.863	-0.949	9.315	-0.389	-0.389	0.000	0.000	0.000	0.000
133	A	475	LYS	1	0.894	0.934	12.175	0.025	0.025	0.000	0.000	0.000	0.000
134	A	476	ASN	0	0.026	0.009	15.153	-0.030	-0.030	0.000	0.000	0.000	0.000
135	A	477	LEU	0	0.075	0.053	7.278	-0.030	-0.030	0.000	0.000	0.000	0.000
136	A	478	LYS	1	0.982	0.984	10.811	0.695	0.695	0.000	0.000	0.000	0.000
137	A	479	ALA	0	-0.025	-0.008	12.619	-0.031	-0.031	0.000	0.000	0.000	0.000
138	A	480	LEU	0	0.029	0.024	12.145	0.023	0.023	0.000	0.000	0.000	0.000
139	A	481	LEU	0	-0.005	-0.022	8.594	0.003	0.003	0.000	0.000	0.000	0.000
140	A	482	LYS	1	0.956	0.987	12.917	0.636	0.636	0.000	0.000	0.000	0.000
141	A	483	HIS	0	-0.003	-0.008	15.937	0.051	0.051	0.000	0.000	0.000	0.000
142	A	484	PHE	0	0.023	0.006	12.382	0.062	0.062	0.000	0.000	0.000	0.000
143	A	485	ASP	-1	-0.897	-0.936	13.694	-0.959	-0.959	0.000	0.000	0.000	0.000
144	A	486	LEU	0	-0.030	-0.015	16.435	0.069	0.069	0.000	0.000	0.000	0.000
145	A	487	PHE	0	0.017	0.016	18.836	0.049	0.049	0.000	0.000	0.000	0.000
146	A	488	LEU	0	0.001	-0.005	14.607	0.041	0.041	0.000	0.000	0.000	0.000
147	A	489	ARG	1	0.921	0.957	17.699	0.525	0.525	0.000	0.000	0.000	0.000
148	A	490	PHE	0	0.035	0.019	21.180	0.034	0.034	0.000	0.000	0.000	0.000
149	A	491	LEU	0	0.006	-0.010	20.279	0.026	0.026	0.000	0.000	0.000	0.000
150	A	492	ALA	0	-0.076	-0.049	21.389	0.021	0.021	0.000	0.000	0.000	0.000
151	A	493	GLU	-1	-0.995	-0.992	23.406	-0.227	-0.227	0.000	0.000	0.000	0.000
152	A	494	TYR	0	0.001	0.008	26.425	0.023	0.023	0.000	0.000	0.000	0.000
153	A	495	HIS	0	-0.025	-0.016	25.157	0.007	0.007	0.000	0.000	0.000	0.000
154	A	496	ASP	-1	-0.878	-0.953	27.084	-0.152	-0.152	0.000	0.000	0.000	0.000
155	A	497	ASP	-1	-0.954	-0.960	30.642	-0.140	-0.140	0.000	0.000	0.000	0.000
156	A	498	PHE	0	-0.065	-0.047	26.553	0.009	0.009	0.000	0.000	0.000	0.000
157	A	499	PHE	0	-0.085	-0.043	22.705	-0.002	-0.002	0.000	0.000	0.000	0.000
158	A	500	PRO	0	0.043	0.051	28.503	0.006	0.006	0.000	0.000	0.000	0.000
159	A	501	GLU	-1	-0.795	-0.915	30.630	-0.119	-0.119	0.000	0.000	0.000	0.000
160	A	502	SER	0	-0.113	-0.061	32.420	0.004	0.004	0.000	0.000	0.000	0.000
161	A	503	ALA	0	0.016	0.023	30.489	0.006	0.006	0.000	0.000	0.000	0.000
162	A	504	TYR	0	-0.061	-0.063	25.576	0.005	0.005	0.000	0.000	0.000	0.000
163	A	505	VAL	0	-0.050	-0.039	32.339	0.006	0.006	0.000	0.000	0.000	0.000
164	A	506	ALA	0	0.020	-0.002	34.279	0.000	0.000	0.000	0.000	0.000	0.000
165	A	507	ALA	0	-0.020	0.013	36.770	0.005	0.005	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)