FMO DATABASE

FMODB ID: ZYR8N

Calculation Name: 2VY1-A-Xray319

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VY1

Chain ID: A

ChEMBL ID:

UniProt ID: Q00958

Base Structure: X-ray

Registration Date: 2021-09-07

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	164
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1668695.372133
FMO2-HF: Nuclear repulsion	1602243.597825
FMO2-HF: Total energy	-66451.774308
FMO2-MP2: Total energy	-66643.996637

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:236:ACE )

Summations of interaction energy for fragment #1(A:236: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.
1.876	2.818	-0.006	-0.39	-0.545	0

Interaction energy analysis for fragmet #1(A:236:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.055 / q_NPA : 0.019

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	238	GLU	-1	-0.877	-0.923	3.828	0.243	1.185	-0.006	-0.390	-0.545
4	A	239	HIS	0	0.051	0.028	6.852	-0.166	-0.166	0.000	0.000	0.000
5	A	240	PRO	0	-0.034	-0.009	9.581	0.002	0.002	0.000	0.000	0.000
6	A	241	PHE	0	0.008	-0.002	12.366	0.040	0.040	0.000	0.000	0.000
7	A	242	ILE	0	-0.019	-0.029	15.596	-0.004	-0.004	0.000	0.000	0.000
8	A	243	VAL	0	0.025	0.001	18.800	0.001	0.001	0.000	0.000	0.000
9	A	244	THR	0	0.016	0.035	20.681	0.001	0.001	0.000	0.000	0.000
10	A	245	GLU	-1	-0.846	-0.914	23.422	-0.060	-0.060	0.000	0.000	0.000
11	A	246	PRO	0	-0.027	-0.034	25.442	-0.002	-0.002	0.000	0.000	0.000
12	A	247	GLY	0	0.016	0.013	25.336	0.006	0.006	0.000	0.000	0.000
13	A	248	GLU	-1	-0.861	-0.906	23.051	-0.075	-0.075	0.000	0.000	0.000
14	A	249	VAL	0	-0.012	-0.006	19.305	-0.012	-0.012	0.000	0.000	0.000
15	A	250	ALA	0	-0.025	-0.015	17.289	0.001	0.001	0.000	0.000	0.000
16	A	251	ARG	1	1.005	1.001	18.242	0.058	0.058	0.000	0.000	0.000
17	A	252	GLY	0	0.020	0.008	16.443	-0.017	-0.017	0.000	0.000	0.000
18	A	253	LYS	1	0.943	0.972	10.048	-0.025	-0.025	0.000	0.000	0.000
19	A	254	LYS	1	0.921	0.960	12.385	0.154	0.154	0.000	0.000	0.000
20	A	255	ASN	0	0.033	0.030	10.660	0.090	0.090	0.000	0.000	0.000
21	A	256	GLY	0	0.078	0.021	14.813	-0.008	-0.008	0.000	0.000	0.000
22	A	257	LEU	0	-0.034	-0.031	17.729	-0.022	-0.022	0.000	0.000	0.000
23	A	258	ASP	-1	-0.718	-0.847	20.230	-0.088	-0.088	0.000	0.000	0.000
24	A	259	TYR	0	-0.037	-0.021	10.848	0.025	0.025	0.000	0.000	0.000
25	A	260	LEU	0	-0.028	-0.017	16.504	-0.013	-0.013	0.000	0.000	0.000
26	A	261	PHE	0	0.011	-0.013	17.498	-0.006	-0.006	0.000	0.000	0.000
27	A	262	HIS	0	0.107	0.069	17.704	-0.009	-0.009	0.000	0.000	0.000
28	A	263	LEU	0	-0.022	-0.016	13.076	-0.002	-0.002	0.000	0.000	0.000
29	A	264	TYR	0	-0.045	-0.073	16.978	-0.004	-0.004	0.000	0.000	0.000
30	A	265	GLU	-1	-0.914	-0.956	20.063	-0.061	-0.061	0.000	0.000	0.000
31	A	266	GLN	0	0.063	0.045	15.142	0.018	0.018	0.000	0.000	0.000
32	A	267	CYS	0	-0.056	-0.022	17.114	0.001	0.001	0.000	0.000	0.000
33	A	268	ARG	1	0.961	0.984	19.520	0.060	0.060	0.000	0.000	0.000
34	A	269	GLU	-1	-0.905	-0.947	21.537	-0.026	-0.026	0.000	0.000	0.000
35	A	270	PHE	0	-0.001	-0.014	16.156	0.007	0.007	0.000	0.000	0.000
36	A	271	LEU	0	-0.054	-0.028	21.345	0.005	0.005	0.000	0.000	0.000
37	A	272	LEU	0	0.009	0.012	24.090	0.006	0.006	0.000	0.000	0.000
38	A	273	GLN	0	0.049	0.030	21.286	0.012	0.012	0.000	0.000	0.000
39	A	274	VAL	0	-0.030	-0.017	22.834	0.003	0.003	0.000	0.000	0.000
40	A	275	GLN	0	-0.061	-0.062	25.578	0.005	0.005	0.000	0.000	0.000
41	A	276	THR	0	-0.025	-0.009	28.683	0.003	0.003	0.000	0.000	0.000
42	A	277	ILE	0	0.012	0.012	26.858	0.003	0.003	0.000	0.000	0.000
43	A	278	ALA	0	0.000	0.003	29.330	0.001	0.001	0.000	0.000	0.000
44	A	279	LYS	1	0.917	0.946	30.917	0.024	0.024	0.000	0.000	0.000
45	A	280	ASP	-1	-0.927	-0.946	32.878	-0.001	-0.001	0.000	0.000	0.000
46	A	281	ARG	1	0.921	0.959	27.419	0.006	0.006	0.000	0.000	0.000
47	A	282	GLY	0	0.019	0.028	34.317	0.000	0.000	0.000	0.000	0.000
48	A	283	GLU	-1	-0.970	-0.979	30.420	-0.019	-0.019	0.000	0.000	0.000
49	A	284	LYS	1	0.939	0.961	31.152	0.040	0.040	0.000	0.000	0.000
50	A	285	CYS	0	0.022	0.011	31.197	-0.001	-0.001	0.000	0.000	0.000
51	A	286	PRO	0	-0.071	-0.017	26.939	-0.003	-0.003	0.000	0.000	0.000
52	A	287	THR	0	0.092	0.036	29.580	0.000	0.000	0.000	0.000	0.000
53	A	288	LYS	1	0.911	0.968	26.993	0.065	0.065	0.000	0.000	0.000
54	A	289	VAL	0	0.040	0.033	20.594	0.002	0.002	0.000	0.000	0.000
55	A	290	THR	0	0.032	0.011	22.902	-0.006	-0.006	0.000	0.000	0.000
56	A	291	ASN	0	0.048	0.001	19.933	-0.021	-0.021	0.000	0.000	0.000
57	A	292	GLN	0	-0.001	0.003	19.565	0.002	0.002	0.000	0.000	0.000
58	A	293	VAL	0	0.051	0.041	19.715	0.005	0.005	0.000	0.000	0.000
59	A	294	PHE	0	0.035	0.008	15.820	-0.003	-0.003	0.000	0.000	0.000
60	A	295	ARG	1	0.949	0.971	15.512	0.065	0.065	0.000	0.000	0.000
61	A	296	TYR	0	-0.012	-0.009	16.465	0.019	0.019	0.000	0.000	0.000
62	A	297	ALA	0	0.043	0.022	14.760	0.016	0.016	0.000	0.000	0.000
63	A	298	LYS	1	0.945	0.970	9.474	0.111	0.111	0.000	0.000	0.000
64	A	299	LYS	1	0.896	0.954	12.841	0.033	0.033	0.000	0.000	0.000
65	A	300	SER	0	-0.041	-0.014	15.519	0.029	0.029	0.000	0.000	0.000
66	A	301	GLY	0	0.061	0.040	11.935	0.011	0.011	0.000	0.000	0.000
67	A	302	ALA	0	0.024	0.025	11.083	0.016	0.016	0.000	0.000	0.000
68	A	303	SER	0	-0.032	-0.029	6.744	-0.111	-0.111	0.000	0.000	0.000
69	A	304	TYR	0	-0.028	-0.019	7.644	-0.186	-0.186	0.000	0.000	0.000
70	A	305	ILE	0	-0.009	0.007	8.523	-0.067	-0.067	0.000	0.000	0.000
71	A	306	ASN	0	0.001	-0.018	9.447	0.048	0.048	0.000	0.000	0.000
72	A	307	LYS	1	0.921	0.955	12.452	0.202	0.202	0.000	0.000	0.000
73	A	308	PRO	0	0.016	0.003	13.178	0.034	0.034	0.000	0.000	0.000
74	A	309	LYS	1	0.948	0.985	9.756	0.666	0.666	0.000	0.000	0.000
75	A	310	MET	0	0.004	0.014	14.797	0.022	0.022	0.000	0.000	0.000
76	A	311	ARG	1	0.894	0.959	17.163	0.182	0.182	0.000	0.000	0.000
77	A	312	HIS	0	-0.023	0.002	17.583	0.033	0.033	0.000	0.000	0.000
78	A	313	TYR	0	0.047	0.012	15.567	0.002	0.002	0.000	0.000	0.000
79	A	314	VAL	0	0.057	0.047	20.431	0.017	0.017	0.000	0.000	0.000
80	A	315	HIS	0	-0.012	-0.023	22.804	0.009	0.009	0.000	0.000	0.000
81	A	316	CYS	0	-0.038	-0.012	22.570	0.004	0.004	0.000	0.000	0.000
82	A	317	TYR	0	0.031	0.016	22.385	0.010	0.010	0.000	0.000	0.000
83	A	318	ALA	0	0.009	-0.012	24.361	0.011	0.011	0.000	0.000	0.000
84	A	319	LEU	0	0.013	0.004	27.748	0.008	0.008	0.000	0.000	0.000
85	A	320	HIS	0	0.010	-0.001	25.984	0.003	0.003	0.000	0.000	0.000
86	A	321	CYS	0	-0.075	-0.028	26.879	0.007	0.007	0.000	0.000	0.000
87	A	322	LEU	0	-0.063	-0.043	29.645	0.006	0.006	0.000	0.000	0.000
88	A	323	ASP	-1	-0.878	-0.942	32.130	-0.051	-0.051	0.000	0.000	0.000
89	A	324	GLU	-1	-0.885	-0.934	29.788	-0.062	-0.062	0.000	0.000	0.000
90	A	325	GLU	-1	-0.888	-0.939	31.661	-0.050	-0.050	0.000	0.000	0.000
91	A	326	ALA	0	0.005	0.006	33.803	-0.002	-0.002	0.000	0.000	0.000
92	A	327	SER	0	-0.090	-0.036	27.679	-0.007	-0.007	0.000	0.000	0.000
93	A	328	ASN	0	0.022	-0.013	29.331	-0.010	-0.010	0.000	0.000	0.000
94	A	329	ALA	0	0.001	0.005	30.413	-0.001	-0.001	0.000	0.000	0.000
95	A	330	LEU	0	-0.017	-0.009	29.172	-0.001	-0.001	0.000	0.000	0.000
96	A	331	ARG	1	0.774	0.880	24.097	0.090	0.090	0.000	0.000	0.000
97	A	332	ARG	1	1.005	0.997	27.972	0.052	0.052	0.000	0.000	0.000
98	A	333	ALA	0	0.044	0.034	30.342	0.000	0.000	0.000	0.000	0.000
99	A	334	PHE	0	-0.040	-0.041	27.034	-0.001	-0.001	0.000	0.000	0.000
100	A	335	LYS	1	0.798	0.883	25.992	0.065	0.065	0.000	0.000	0.000
101	A	336	GLU	-1	-0.953	-0.962	27.463	-0.054	-0.054	0.000	0.000	0.000
102	A	337	ARG	1	0.873	0.946	30.400	0.081	0.081	0.000	0.000	0.000
103	A	338	GLY	0	-0.003	0.012	26.702	-0.001	-0.001	0.000	0.000	0.000
104	A	339	GLU	-1	-0.900	-0.948	26.085	-0.109	-0.109	0.000	0.000	0.000
105	A	340	ASN	0	-0.008	-0.004	20.921	-0.011	-0.011	0.000	0.000	0.000
106	A	341	VAL	0	0.036	-0.001	18.245	0.005	0.005	0.000	0.000	0.000
107	A	342	GLY	0	-0.031	-0.013	20.886	0.003	0.003	0.000	0.000	0.000
108	A	343	SER	0	0.052	0.018	21.950	0.010	0.010	0.000	0.000	0.000
109	A	344	TRP	0	0.064	0.025	21.261	0.000	0.000	0.000	0.000	0.000
110	A	345	ARG	1	0.850	0.916	20.946	0.199	0.199	0.000	0.000	0.000
111	A	346	GLN	0	-0.039	-0.016	24.373	0.016	0.016	0.000	0.000	0.000
112	A	347	ALA	0	0.038	0.024	27.182	0.009	0.009	0.000	0.000	0.000
113	A	348	CYS	0	-0.007	0.007	26.771	0.007	0.007	0.000	0.000	0.000
114	A	349	TYR	0	-0.036	-0.020	26.132	0.001	0.001	0.000	0.000	0.000
115	A	350	LYS	1	1.017	1.017	30.773	0.068	0.068	0.000	0.000	0.000
116	A	351	PRO	0	0.028	0.012	32.088	0.005	0.005	0.000	0.000	0.000
117	A	352	LEU	0	0.013	0.009	28.999	0.003	0.003	0.000	0.000	0.000
118	A	353	VAL	0	0.011	0.000	33.600	0.003	0.003	0.000	0.000	0.000
119	A	354	ASN	0	-0.003	-0.003	36.135	0.004	0.004	0.000	0.000	0.000
120	A	355	ILE	0	-0.003	0.002	34.310	0.004	0.004	0.000	0.000	0.000
121	A	356	ALA	0	0.014	0.001	36.526	0.003	0.003	0.000	0.000	0.000
122	A	357	CYS	0	-0.037	0.001	38.380	0.004	0.004	0.000	0.000	0.000
123	A	358	ARG	1	0.920	0.960	38.829	0.052	0.052	0.000	0.000	0.000
124	A	359	HIS	0	-0.032	-0.015	40.118	0.003	0.003	0.000	0.000	0.000
125	A	360	GLY	0	0.048	0.029	42.306	0.000	0.000	0.000	0.000	0.000
126	A	361	TRP	0	-0.020	-0.025	39.655	-0.002	-0.002	0.000	0.000	0.000
127	A	362	ASP	-1	-0.843	-0.915	39.289	-0.054	-0.054	0.000	0.000	0.000
128	A	363	ILE	0	0.005	-0.018	33.110	-0.001	-0.001	0.000	0.000	0.000
129	A	364	ASP	-1	-0.802	-0.881	34.065	-0.071	-0.071	0.000	0.000	0.000
130	A	365	ALA	0	-0.009	0.009	35.211	0.000	0.000	0.000	0.000	0.000
131	A	366	VAL	0	-0.008	0.003	34.050	0.001	0.001	0.000	0.000	0.000
132	A	367	PHE	0	-0.016	-0.035	27.666	-0.004	-0.004	0.000	0.000	0.000
133	A	368	ASN	0	-0.042	-0.045	32.629	-0.002	-0.002	0.000	0.000	0.000
134	A	369	ALA	0	0.032	0.041	34.550	0.003	0.003	0.000	0.000	0.000
135	A	370	HIS	0	0.050	0.037	30.178	0.001	0.001	0.000	0.000	0.000
136	A	371	PRO	0	0.052	0.013	32.117	-0.004	-0.004	0.000	0.000	0.000
137	A	372	ARG	1	0.908	0.952	26.709	0.051	0.051	0.000	0.000	0.000
138	A	373	LEU	0	0.012	0.014	27.023	-0.008	-0.008	0.000	0.000	0.000
139	A	374	SER	0	0.025	0.037	28.676	-0.005	-0.005	0.000	0.000	0.000
140	A	375	ILE	0	-0.031	-0.011	24.555	-0.001	-0.001	0.000	0.000	0.000
141	A	376	TRP	0	-0.051	-0.035	19.626	-0.018	-0.018	0.000	0.000	0.000
142	A	377	TYR	0	-0.029	-0.028	25.104	0.003	0.003	0.000	0.000	0.000
143	A	378	VAL	0	0.058	0.038	26.724	-0.009	-0.009	0.000	0.000	0.000
144	A	379	PRO	0	-0.030	-0.007	25.329	-0.003	-0.003	0.000	0.000	0.000
145	A	380	THR	0	0.033	0.002	27.138	0.007	0.007	0.000	0.000	0.000
146	A	381	LYS	1	0.976	1.000	27.699	0.111	0.111	0.000	0.000	0.000
147	A	382	LEU	0	0.035	0.018	29.060	0.005	0.005	0.000	0.000	0.000
148	A	383	ARG	1	0.855	0.898	30.816	0.083	0.083	0.000	0.000	0.000
149	A	384	GLN	0	0.002	-0.014	31.673	0.002	0.002	0.000	0.000	0.000
150	A	385	LEU	0	-0.008	0.001	31.443	0.003	0.003	0.000	0.000	0.000
151	A	386	CYS	0	0.004	0.010	34.452	0.004	0.004	0.000	0.000	0.000
152	A	387	HIS	0	-0.013	0.003	37.010	0.004	0.004	0.000	0.000	0.000
153	A	388	LEU	0	-0.015	-0.026	36.474	0.002	0.002	0.000	0.000	0.000
154	A	389	GLU	-1	-0.930	-0.957	39.008	-0.055	-0.055	0.000	0.000	0.000
155	A	390	ARG	1	1.009	1.003	40.851	0.052	0.052	0.000	0.000	0.000
156	A	391	ASN	0	-0.031	-0.018	42.785	0.004	0.004	0.000	0.000	0.000
157	A	392	ASN	0	0.027	0.010	42.216	0.003	0.003	0.000	0.000	0.000
158	A	393	ALA	0	-0.027	-0.007	44.968	0.002	0.002	0.000	0.000	0.000
159	A	394	VAL	0	-0.034	-0.026	46.765	0.002	0.002	0.000	0.000	0.000
160	A	395	ALA	0	-0.025	-0.002	48.358	0.002	0.002	0.000	0.000	0.000
161	A	396	ALA	0	-0.005	-0.008	48.906	0.002	0.002	0.000	0.000	0.000
162	A	397	ALA	0	-0.068	-0.030	50.354	0.002	0.002	0.000	0.000	0.000
163	A	398	ALA	0	0.002	0.010	52.082	0.001	0.001	0.000	0.000	0.000
164	A	399	NME	0	-0.049	-0.008	54.579	0.001	0.001	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:236:ACE )