FMO DATABASE

FMODB ID: 66M9Z

Calculation Name: 2VY1-A-Xray372

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: 2023-06-20

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	OptH
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	162
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1661960.82033
FMO2-HF: Nuclear repulsion	1595679.96457
FMO2-HF: Total energy	-66280.85576
FMO2-MP2: Total energy	-66472.552792

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:237:ARG)

Summations of interaction energy for fragment #1(A:237:ARG)

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.
191.209	194.293	0.491	-1.616	-1.959	-0.013

Interaction energy analysis for fragmet #1(A:237:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.972 / q_NPA : 0.965

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	239	HIS	0	0.054	0.029	2.680	-14.020	-10.936	0.491	-1.616	-1.959	-0.013
4	A	240	PRO	0	-0.035	-0.009	4.975	1.625	1.625	0.000	0.000	0.000	0.000
5	A	241	PHE	0	0.008	-0.002	6.424	1.982	1.982	0.000	0.000	0.000	0.000
6	A	242	ILE	0	-0.019	-0.028	9.861	-0.884	-0.884	0.000	0.000	0.000	0.000
7	A	243	VAL	0	0.034	0.005	13.048	0.176	0.176	0.000	0.000	0.000	0.000
8	A	244	THR	0	0.006	0.031	15.753	-0.105	-0.105	0.000	0.000	0.000	0.000
9	A	245	GLU	-1	-0.847	-0.914	18.372	-11.902	-11.902	0.000	0.000	0.000	0.000
10	A	246	PRO	0	-0.025	-0.034	21.161	-0.396	-0.396	0.000	0.000	0.000	0.000
11	A	247	GLY	0	0.012	0.012	21.748	0.415	0.415	0.000	0.000	0.000	0.000
12	A	248	GLU	-1	-0.860	-0.906	19.059	-14.684	-14.684	0.000	0.000	0.000	0.000
13	A	249	VAL	0	-0.010	-0.005	16.987	-0.778	-0.778	0.000	0.000	0.000	0.000
14	A	250	ALA	0	-0.024	-0.015	13.537	0.133	0.133	0.000	0.000	0.000	0.000
15	A	251	ARG	1	1.005	1.001	15.211	13.908	13.908	0.000	0.000	0.000	0.000
16	A	252	GLY	0	0.019	0.008	13.999	-0.793	-0.793	0.000	0.000	0.000	0.000
17	A	253	LYS	1	0.943	0.972	8.239	24.228	24.228	0.000	0.000	0.000	0.000
18	A	254	LYS	1	0.921	0.959	8.666	23.815	23.815	0.000	0.000	0.000	0.000
19	A	255	ASN	0	0.033	0.030	7.475	2.793	2.793	0.000	0.000	0.000	0.000
20	A	256	GLY	0	0.076	0.021	10.774	-0.159	-0.159	0.000	0.000	0.000	0.000
21	A	257	LEU	0	-0.032	-0.031	13.535	-0.878	-0.878	0.000	0.000	0.000	0.000
22	A	258	ASP	-1	-0.717	-0.847	15.660	-13.927	-13.927	0.000	0.000	0.000	0.000
23	A	259	TYR	0	-0.037	-0.021	9.068	0.765	0.765	0.000	0.000	0.000	0.000
24	A	260	LEU	0	-0.031	-0.018	12.000	-0.336	-0.336	0.000	0.000	0.000	0.000
25	A	261	PHE	0	0.014	-0.012	13.810	-0.063	-0.063	0.000	0.000	0.000	0.000
26	A	262	HIS	0	0.104	0.068	16.207	-0.364	-0.364	0.000	0.000	0.000	0.000
27	A	263	LEU	0	-0.018	-0.015	10.339	0.068	0.068	0.000	0.000	0.000	0.000
28	A	264	TYR	0	-0.048	-0.073	14.641	-0.106	-0.106	0.000	0.000	0.000	0.000
29	A	265	GLU	-1	-0.918	-0.958	17.465	-12.545	-12.545	0.000	0.000	0.000	0.000
30	A	266	GLN	0	0.065	0.046	13.870	0.310	0.310	0.000	0.000	0.000	0.000
31	A	267	CYS	0	-0.052	-0.021	15.008	0.042	0.042	0.000	0.000	0.000	0.000
32	A	268	ARG	1	0.961	0.984	17.730	11.572	11.572	0.000	0.000	0.000	0.000
33	A	269	GLU	-1	-0.910	-0.948	20.514	-11.740	-11.740	0.000	0.000	0.000	0.000
34	A	270	PHE	0	0.005	-0.012	15.363	0.349	0.349	0.000	0.000	0.000	0.000
35	A	271	LEU	0	-0.062	-0.031	20.437	0.239	0.239	0.000	0.000	0.000	0.000
36	A	272	LEU	0	0.013	0.013	22.784	0.399	0.399	0.000	0.000	0.000	0.000
37	A	273	GLN	0	0.048	0.030	21.022	0.435	0.435	0.000	0.000	0.000	0.000
38	A	274	VAL	0	-0.030	-0.017	22.014	0.205	0.205	0.000	0.000	0.000	0.000
39	A	275	GLN	0	-0.057	-0.060	24.975	0.349	0.349	0.000	0.000	0.000	0.000
40	A	276	THR	0	-0.026	-0.010	28.047	0.398	0.398	0.000	0.000	0.000	0.000
41	A	277	ILE	0	0.013	0.013	27.105	0.247	0.247	0.000	0.000	0.000	0.000
42	A	278	ALA	0	-0.002	0.003	28.822	0.200	0.200	0.000	0.000	0.000	0.000
43	A	279	LYS	1	0.924	0.948	30.458	9.087	9.087	0.000	0.000	0.000	0.000
44	A	280	ASP	-1	-0.933	-0.948	32.838	-8.070	-8.070	0.000	0.000	0.000	0.000
45	A	281	ARG	1	0.923	0.959	28.014	9.851	9.851	0.000	0.000	0.000	0.000
46	A	282	GLY	0	0.017	0.027	34.351	0.114	0.114	0.000	0.000	0.000	0.000
47	A	283	GLU	-1	-0.970	-0.979	30.183	-9.620	-9.620	0.000	0.000	0.000	0.000
48	A	284	LYS	1	0.941	0.961	29.918	9.844	9.844	0.000	0.000	0.000	0.000
49	A	285	CYS	0	0.024	0.012	30.105	-0.330	-0.330	0.000	0.000	0.000	0.000
50	A	286	PRO	0	-0.073	-0.017	25.717	0.024	0.024	0.000	0.000	0.000	0.000
51	A	287	THR	0	0.091	0.035	28.018	-0.078	-0.078	0.000	0.000	0.000	0.000
52	A	288	LYS	1	0.911	0.969	24.425	10.719	10.719	0.000	0.000	0.000	0.000
53	A	289	VAL	0	0.040	0.032	18.247	-0.042	-0.042	0.000	0.000	0.000	0.000
54	A	290	THR	0	0.033	0.012	21.061	-0.268	-0.268	0.000	0.000	0.000	0.000
55	A	291	ASN	0	0.045	0.000	18.227	-1.005	-1.005	0.000	0.000	0.000	0.000
56	A	292	GLN	0	0.002	0.004	18.371	-0.359	-0.359	0.000	0.000	0.000	0.000
57	A	293	VAL	0	0.048	0.040	18.244	-0.130	-0.130	0.000	0.000	0.000	0.000
58	A	294	PHE	0	0.038	0.009	13.965	-0.380	-0.380	0.000	0.000	0.000	0.000
59	A	295	ARG	1	0.946	0.970	14.705	13.498	13.498	0.000	0.000	0.000	0.000
60	A	296	TYR	0	-0.010	-0.008	16.512	-0.146	-0.146	0.000	0.000	0.000	0.000
61	A	297	ALA	0	0.044	0.022	13.927	0.119	0.119	0.000	0.000	0.000	0.000
62	A	298	LYS	1	0.948	0.971	10.154	21.175	21.175	0.000	0.000	0.000	0.000
63	A	299	LYS	1	0.891	0.951	13.261	13.044	13.044	0.000	0.000	0.000	0.000
64	A	300	SER	0	-0.037	-0.014	16.339	0.592	0.592	0.000	0.000	0.000	0.000
65	A	301	GLY	0	0.058	0.040	13.365	0.243	0.243	0.000	0.000	0.000	0.000
66	A	302	ALA	0	0.025	0.026	11.845	-0.733	-0.733	0.000	0.000	0.000	0.000
67	A	303	SER	0	-0.028	-0.027	7.648	-0.620	-0.620	0.000	0.000	0.000	0.000
68	A	304	TYR	0	-0.033	-0.021	6.094	-1.867	-1.867	0.000	0.000	0.000	0.000
69	A	305	ILE	0	-0.007	0.007	7.161	-1.344	-1.344	0.000	0.000	0.000	0.000
70	A	306	ASN	0	0.003	-0.018	6.301	0.015	0.015	0.000	0.000	0.000	0.000
71	A	307	LYS	1	0.918	0.954	10.021	18.186	18.186	0.000	0.000	0.000	0.000
72	A	308	PRO	0	0.016	0.003	9.276	1.247	1.247	0.000	0.000	0.000	0.000
73	A	309	LYS	1	0.946	0.984	6.243	31.862	31.862	0.000	0.000	0.000	0.000
74	A	310	MET	0	0.010	0.017	10.044	0.526	0.526	0.000	0.000	0.000	0.000
75	A	311	ARG	1	0.890	0.958	13.245	16.999	16.999	0.000	0.000	0.000	0.000
76	A	312	HIS	0	-0.027	0.000	12.031	1.409	1.409	0.000	0.000	0.000	0.000
77	A	313	TYR	0	0.050	0.012	10.062	-0.233	-0.233	0.000	0.000	0.000	0.000
78	A	314	VAL	0	0.058	0.048	15.345	0.781	0.781	0.000	0.000	0.000	0.000
79	A	315	HIS	0	-0.015	-0.024	18.239	0.502	0.502	0.000	0.000	0.000	0.000
80	A	316	CYS	0	-0.032	-0.009	17.533	0.226	0.226	0.000	0.000	0.000	0.000
81	A	317	TYR	0	0.027	0.015	18.468	0.570	0.570	0.000	0.000	0.000	0.000
82	A	318	ALA	0	0.012	-0.010	20.173	0.578	0.578	0.000	0.000	0.000	0.000
83	A	319	LEU	0	0.011	0.004	23.072	0.485	0.485	0.000	0.000	0.000	0.000
84	A	320	HIS	0	0.010	-0.001	21.855	0.249	0.249	0.000	0.000	0.000	0.000
85	A	321	CYS	0	-0.072	-0.027	23.384	0.372	0.372	0.000	0.000	0.000	0.000
86	A	322	LEU	0	-0.066	-0.044	25.939	0.419	0.419	0.000	0.000	0.000	0.000
87	A	323	ASP	-1	-0.878	-0.941	27.735	-9.446	-9.446	0.000	0.000	0.000	0.000
88	A	324	GLU	-1	-0.887	-0.935	25.768	-11.327	-11.327	0.000	0.000	0.000	0.000
89	A	325	GLU	-1	-0.888	-0.939	27.121	-10.116	-10.116	0.000	0.000	0.000	0.000
90	A	326	ALA	0	0.004	0.006	28.848	-0.174	-0.174	0.000	0.000	0.000	0.000
91	A	327	SER	0	-0.080	-0.033	23.037	-0.541	-0.541	0.000	0.000	0.000	0.000
92	A	328	ASN	0	0.015	-0.015	24.093	-0.890	-0.890	0.000	0.000	0.000	0.000
93	A	329	ALA	0	0.002	0.005	25.372	-0.222	-0.222	0.000	0.000	0.000	0.000
94	A	330	LEU	0	-0.020	-0.009	23.356	-0.121	-0.121	0.000	0.000	0.000	0.000
95	A	331	ARG	1	0.775	0.881	19.520	13.729	13.729	0.000	0.000	0.000	0.000
96	A	332	ARG	1	1.006	0.997	22.324	10.569	10.569	0.000	0.000	0.000	0.000
97	A	333	ALA	0	0.045	0.034	24.816	-0.062	-0.062	0.000	0.000	0.000	0.000
98	A	334	PHE	0	-0.042	-0.042	20.392	-0.052	-0.052	0.000	0.000	0.000	0.000
99	A	335	LYS	1	0.806	0.886	20.583	12.944	12.944	0.000	0.000	0.000	0.000
100	A	336	GLU	-1	-0.957	-0.964	21.684	-10.867	-10.867	0.000	0.000	0.000	0.000
101	A	337	ARG	1	0.872	0.946	23.843	12.404	12.404	0.000	0.000	0.000	0.000
102	A	338	GLY	0	-0.003	0.012	20.673	-0.101	-0.101	0.000	0.000	0.000	0.000
103	A	339	GLU	-1	-0.900	-0.948	19.467	-14.960	-14.960	0.000	0.000	0.000	0.000
104	A	340	ASN	0	-0.008	-0.003	13.802	-0.548	-0.548	0.000	0.000	0.000	0.000
105	A	341	VAL	0	0.038	-0.001	12.096	0.607	0.607	0.000	0.000	0.000	0.000
106	A	342	GLY	0	-0.034	-0.014	13.662	0.552	0.552	0.000	0.000	0.000	0.000
107	A	343	SER	0	0.050	0.017	14.715	0.883	0.883	0.000	0.000	0.000	0.000
108	A	344	TRP	0	0.068	0.028	15.559	0.213	0.213	0.000	0.000	0.000	0.000
109	A	345	ARG	1	0.850	0.916	14.720	19.482	19.482	0.000	0.000	0.000	0.000
110	A	346	GLN	0	-0.041	-0.017	17.933	1.288	1.288	0.000	0.000	0.000	0.000
111	A	347	ALA	0	0.035	0.023	20.340	0.679	0.679	0.000	0.000	0.000	0.000
112	A	348	CYS	0	0.005	0.012	20.776	0.553	0.553	0.000	0.000	0.000	0.000
113	A	349	TYR	0	-0.041	-0.021	20.147	0.099	0.099	0.000	0.000	0.000	0.000
114	A	350	LYS	1	1.014	1.016	24.691	10.409	10.409	0.000	0.000	0.000	0.000
115	A	351	PRO	0	0.025	0.011	26.437	0.415	0.415	0.000	0.000	0.000	0.000
116	A	352	LEU	0	0.012	0.008	23.874	0.289	0.289	0.000	0.000	0.000	0.000
117	A	353	VAL	0	0.013	0.002	28.189	0.261	0.261	0.000	0.000	0.000	0.000
118	A	354	ASN	0	-0.004	-0.003	30.455	0.387	0.387	0.000	0.000	0.000	0.000
119	A	355	ILE	0	-0.004	0.002	29.448	0.331	0.331	0.000	0.000	0.000	0.000
120	A	356	ALA	0	0.016	0.001	31.468	0.237	0.237	0.000	0.000	0.000	0.000
121	A	357	CYS	0	-0.035	0.002	33.389	0.310	0.310	0.000	0.000	0.000	0.000
122	A	358	ARG	1	0.917	0.959	33.849	9.119	9.119	0.000	0.000	0.000	0.000
123	A	359	HIS	0	-0.031	-0.015	35.516	0.244	0.244	0.000	0.000	0.000	0.000
124	A	360	GLY	0	0.048	0.029	37.689	-0.030	-0.030	0.000	0.000	0.000	0.000
125	A	361	TRP	0	-0.022	-0.026	33.899	-0.119	-0.119	0.000	0.000	0.000	0.000
126	A	362	ASP	-1	-0.841	-0.915	34.750	-9.107	-9.107	0.000	0.000	0.000	0.000
127	A	363	ILE	0	0.004	-0.017	28.281	-0.137	-0.137	0.000	0.000	0.000	0.000
128	A	364	ASP	-1	-0.799	-0.880	29.893	-10.607	-10.607	0.000	0.000	0.000	0.000
129	A	365	ALA	0	-0.012	0.007	31.199	-0.117	-0.117	0.000	0.000	0.000	0.000
130	A	366	VAL	0	-0.003	0.005	29.780	-0.012	-0.012	0.000	0.000	0.000	0.000
131	A	367	PHE	0	-0.017	-0.036	23.465	-0.301	-0.301	0.000	0.000	0.000	0.000
132	A	368	ASN	0	-0.044	-0.046	28.911	-0.320	-0.320	0.000	0.000	0.000	0.000
133	A	369	ALA	0	0.033	0.041	31.220	0.118	0.118	0.000	0.000	0.000	0.000
134	A	370	HIS	0	0.049	0.037	27.391	0.038	0.038	0.000	0.000	0.000	0.000
135	A	371	PRO	0	0.053	0.013	29.191	-0.311	-0.311	0.000	0.000	0.000	0.000
136	A	372	ARG	1	0.908	0.952	24.555	10.911	10.911	0.000	0.000	0.000	0.000
137	A	373	LEU	0	0.011	0.014	23.423	-0.521	-0.521	0.000	0.000	0.000	0.000
138	A	374	SER	0	0.026	0.036	25.387	-0.289	-0.289	0.000	0.000	0.000	0.000
139	A	375	ILE	0	-0.034	-0.013	22.344	-0.017	-0.017	0.000	0.000	0.000	0.000
140	A	376	TRP	0	-0.050	-0.033	16.989	-0.995	-0.995	0.000	0.000	0.000	0.000
141	A	377	TYR	0	-0.031	-0.028	21.691	0.172	0.172	0.000	0.000	0.000	0.000
142	A	378	VAL	0	0.063	0.040	22.592	-0.542	-0.542	0.000	0.000	0.000	0.000
143	A	379	PRO	0	-0.032	-0.008	20.258	-0.170	-0.170	0.000	0.000	0.000	0.000
144	A	380	THR	0	0.033	0.003	22.164	0.464	0.464	0.000	0.000	0.000	0.000
145	A	381	LYS	1	0.975	0.999	21.816	13.704	13.704	0.000	0.000	0.000	0.000
146	A	382	LEU	0	0.036	0.018	23.648	0.302	0.302	0.000	0.000	0.000	0.000
147	A	383	ARG	1	0.854	0.898	25.332	11.346	11.346	0.000	0.000	0.000	0.000
148	A	384	GLN	0	-0.001	-0.015	25.256	0.112	0.112	0.000	0.000	0.000	0.000
149	A	385	LEU	0	-0.005	0.002	25.024	0.262	0.262	0.000	0.000	0.000	0.000
150	A	386	CYS	0	0.006	0.011	29.030	0.328	0.328	0.000	0.000	0.000	0.000
151	A	387	HIS	0	-0.016	0.002	31.398	0.327	0.327	0.000	0.000	0.000	0.000
152	A	388	LEU	0	-0.017	-0.026	29.876	0.210	0.210	0.000	0.000	0.000	0.000
153	A	389	GLU	-1	-0.926	-0.955	32.852	-9.073	-9.073	0.000	0.000	0.000	0.000
154	A	390	ARG	1	1.009	1.003	34.711	8.748	8.748	0.000	0.000	0.000	0.000
155	A	391	ASN	0	-0.030	-0.018	36.835	0.386	0.386	0.000	0.000	0.000	0.000
156	A	392	ASN	0	0.023	0.009	35.237	0.339	0.339	0.000	0.000	0.000	0.000
157	A	393	ALA	0	-0.027	-0.007	38.837	0.202	0.202	0.000	0.000	0.000	0.000
158	A	394	VAL	0	-0.037	-0.027	40.655	0.188	0.188	0.000	0.000	0.000	0.000
159	A	395	ALA	0	-0.033	-0.006	41.774	0.183	0.183	0.000	0.000	0.000	0.000
160	A	396	ALA	0	-0.014	-0.010	42.177	0.163	0.163	0.000	0.000	0.000	0.000
161	A	397	ALA	0	-0.066	-0.023	44.053	0.153	0.153	0.000	0.000	0.000	0.000
162	A	398	ALA	0	-0.023	0.008	45.846	0.160	0.160	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:237:ARG)