FMO DATABASE

FMODB ID: R5ZR8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1667202.678194
FMO2-HF: Nuclear repulsion	1600920.85238
FMO2-HF: Total energy	-66281.825814
FMO2-MP2: Total energy	-66473.546972

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.
189.744	193.604	1.002	-2.287	-2.575	-0.017

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 : 0.976 / q_NPA : 0.986

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	0.063	0.042	2.511	-15.292	-11.432	1.002	-2.287	-2.575	-0.017
4	A	240	PRO	0	-0.032	-0.010	4.855	1.650	1.650	0.000	0.000	0.000	0.000
5	A	241	PHE	0	0.016	-0.005	6.429	2.139	2.139	0.000	0.000	0.000	0.000
6	A	242	ILE	0	-0.003	-0.009	9.878	-0.613	-0.613	0.000	0.000	0.000	0.000
7	A	243	VAL	0	0.024	0.004	13.275	0.084	0.084	0.000	0.000	0.000	0.000
8	A	244	THR	0	0.000	0.024	15.405	0.307	0.307	0.000	0.000	0.000	0.000
9	A	245	GLU	-1	-0.768	-0.861	18.065	-11.783	-11.783	0.000	0.000	0.000	0.000
10	A	246	PRO	0	-0.017	-0.024	20.858	-0.433	-0.433	0.000	0.000	0.000	0.000
11	A	247	GLY	0	0.026	0.022	21.199	0.511	0.511	0.000	0.000	0.000	0.000
12	A	248	GLU	-1	-0.864	-0.909	18.943	-14.186	-14.186	0.000	0.000	0.000	0.000
13	A	249	VAL	0	0.003	-0.008	16.391	-0.910	-0.910	0.000	0.000	0.000	0.000
14	A	250	ALA	0	-0.013	-0.006	13.050	0.186	0.186	0.000	0.000	0.000	0.000
15	A	251	ARG	1	1.003	0.999	15.024	14.293	14.293	0.000	0.000	0.000	0.000
16	A	252	GLY	0	0.036	0.015	13.651	-0.824	-0.824	0.000	0.000	0.000	0.000
17	A	253	LYS	1	0.951	0.978	7.973	25.231	25.231	0.000	0.000	0.000	0.000
18	A	254	LYS	1	0.919	0.952	8.691	25.353	25.353	0.000	0.000	0.000	0.000
19	A	255	ASN	0	0.004	-0.003	6.936	2.889	2.889	0.000	0.000	0.000	0.000
20	A	256	GLY	0	0.061	0.019	10.299	0.360	0.360	0.000	0.000	0.000	0.000
21	A	257	LEU	0	-0.044	-0.018	13.469	-0.824	-0.824	0.000	0.000	0.000	0.000
22	A	258	ASP	-1	-0.700	-0.812	15.520	-14.256	-14.256	0.000	0.000	0.000	0.000
23	A	259	TYR	0	-0.044	-0.037	8.801	1.105	1.105	0.000	0.000	0.000	0.000
24	A	260	LEU	0	-0.033	-0.015	11.575	-0.373	-0.373	0.000	0.000	0.000	0.000
25	A	261	PHE	0	0.020	-0.009	13.471	-0.089	-0.089	0.000	0.000	0.000	0.000
26	A	262	HIS	0	0.085	0.047	15.933	-0.264	-0.264	0.000	0.000	0.000	0.000
27	A	263	LEU	0	0.017	0.002	9.957	0.058	0.058	0.000	0.000	0.000	0.000
28	A	264	TYR	0	-0.037	-0.044	14.235	-0.104	-0.104	0.000	0.000	0.000	0.000
29	A	265	GLU	-1	-0.786	-0.865	17.265	-12.068	-12.068	0.000	0.000	0.000	0.000
30	A	266	GLN	0	0.060	0.036	13.777	0.042	0.042	0.000	0.000	0.000	0.000
31	A	267	CYS	0	-0.090	-0.040	14.977	0.063	0.063	0.000	0.000	0.000	0.000
32	A	268	ARG	1	0.906	0.936	17.532	11.965	11.965	0.000	0.000	0.000	0.000
33	A	269	GLU	-1	-0.819	-0.890	20.568	-11.748	-11.748	0.000	0.000	0.000	0.000
34	A	270	PHE	0	0.004	-0.007	15.031	0.318	0.318	0.000	0.000	0.000	0.000
35	A	271	LEU	0	-0.031	-0.023	20.123	0.266	0.266	0.000	0.000	0.000	0.000
36	A	272	LEU	0	0.028	0.017	22.369	0.392	0.392	0.000	0.000	0.000	0.000
37	A	273	GLN	0	0.040	0.036	20.694	0.382	0.382	0.000	0.000	0.000	0.000
38	A	274	VAL	0	-0.031	-0.019	21.559	0.274	0.274	0.000	0.000	0.000	0.000
39	A	275	GLN	0	-0.063	-0.053	24.603	0.476	0.476	0.000	0.000	0.000	0.000
40	A	276	THR	0	-0.023	-0.018	27.623	0.418	0.418	0.000	0.000	0.000	0.000
41	A	277	ILE	0	0.025	0.012	26.012	0.227	0.227	0.000	0.000	0.000	0.000
42	A	278	ALA	0	-0.019	-0.010	28.514	0.203	0.203	0.000	0.000	0.000	0.000
43	A	279	LYS	1	0.907	0.938	30.154	9.518	9.518	0.000	0.000	0.000	0.000
44	A	280	ASP	-1	-0.936	-0.951	32.157	-8.284	-8.284	0.000	0.000	0.000	0.000
45	A	281	ARG	1	0.855	0.910	27.042	10.028	10.028	0.000	0.000	0.000	0.000
46	A	282	GLY	0	0.030	0.036	34.135	0.160	0.160	0.000	0.000	0.000	0.000
47	A	283	GLU	-1	-0.899	-0.925	29.556	-9.804	-9.804	0.000	0.000	0.000	0.000
48	A	284	LYS	1	0.956	0.964	29.753	9.825	9.825	0.000	0.000	0.000	0.000
49	A	285	CYS	0	0.005	0.005	29.930	-0.404	-0.404	0.000	0.000	0.000	0.000
50	A	286	PRO	0	-0.050	-0.002	25.536	0.035	0.035	0.000	0.000	0.000	0.000
51	A	287	THR	0	0.062	0.016	27.944	-0.097	-0.097	0.000	0.000	0.000	0.000
52	A	288	LYS	1	0.861	0.932	24.351	10.695	10.695	0.000	0.000	0.000	0.000
53	A	289	VAL	0	0.025	0.029	18.091	-0.085	-0.085	0.000	0.000	0.000	0.000
54	A	290	THR	0	0.037	0.013	20.846	-0.471	-0.471	0.000	0.000	0.000	0.000
55	A	291	ASN	0	0.038	-0.004	17.932	-1.242	-1.242	0.000	0.000	0.000	0.000
56	A	292	GLN	0	0.054	0.037	18.027	-0.682	-0.682	0.000	0.000	0.000	0.000
57	A	293	VAL	0	0.051	0.042	17.742	-0.050	-0.050	0.000	0.000	0.000	0.000
58	A	294	PHE	0	0.027	0.005	13.582	-0.390	-0.390	0.000	0.000	0.000	0.000
59	A	295	ARG	1	0.909	0.954	14.287	12.881	12.881	0.000	0.000	0.000	0.000
60	A	296	TYR	0	0.029	0.007	16.130	-0.274	-0.274	0.000	0.000	0.000	0.000
61	A	297	ALA	0	0.059	0.028	13.949	0.119	0.119	0.000	0.000	0.000	0.000
62	A	298	LYS	1	0.938	0.967	9.159	22.535	22.535	0.000	0.000	0.000	0.000
63	A	299	LYS	1	0.838	0.918	12.670	13.540	13.540	0.000	0.000	0.000	0.000
64	A	300	SER	0	-0.028	-0.009	15.422	0.759	0.759	0.000	0.000	0.000	0.000
65	A	301	GLY	0	0.063	0.048	12.126	0.253	0.253	0.000	0.000	0.000	0.000
66	A	302	ALA	0	0.025	0.030	10.623	-1.148	-1.148	0.000	0.000	0.000	0.000
67	A	303	SER	0	-0.067	-0.050	7.236	-1.083	-1.083	0.000	0.000	0.000	0.000
68	A	304	TYR	0	0.034	0.011	5.774	-2.271	-2.271	0.000	0.000	0.000	0.000
69	A	305	ILE	0	-0.023	0.000	6.828	-1.541	-1.541	0.000	0.000	0.000	0.000
70	A	306	ASN	0	-0.010	-0.016	6.608	0.404	0.404	0.000	0.000	0.000	0.000
71	A	307	LYS	1	0.941	0.969	9.911	17.613	17.613	0.000	0.000	0.000	0.000
72	A	308	PRO	0	0.012	-0.003	9.427	1.078	1.078	0.000	0.000	0.000	0.000
73	A	309	LYS	1	0.868	0.939	6.564	30.764	30.764	0.000	0.000	0.000	0.000
74	A	310	MET	0	-0.002	0.007	10.076	0.456	0.456	0.000	0.000	0.000	0.000
75	A	311	ARG	1	0.858	0.932	13.322	16.715	16.715	0.000	0.000	0.000	0.000
76	A	312	HIS	0	-0.037	-0.008	11.950	1.232	1.232	0.000	0.000	0.000	0.000
77	A	313	TYR	0	0.073	0.027	10.308	-0.312	-0.312	0.000	0.000	0.000	0.000
78	A	314	VAL	0	0.027	0.024	15.330	0.738	0.738	0.000	0.000	0.000	0.000
79	A	315	HIS	0	-0.005	-0.016	18.098	0.512	0.512	0.000	0.000	0.000	0.000
80	A	316	CYS	0	-0.052	-0.029	17.549	0.298	0.298	0.000	0.000	0.000	0.000
81	A	317	TYR	0	-0.017	-0.017	18.472	0.449	0.449	0.000	0.000	0.000	0.000
82	A	318	ALA	0	0.018	0.003	20.218	0.573	0.573	0.000	0.000	0.000	0.000
83	A	319	LEU	0	-0.004	-0.006	22.978	0.489	0.489	0.000	0.000	0.000	0.000
84	A	320	HIS	0	-0.008	-0.005	21.845	-0.012	-0.012	0.000	0.000	0.000	0.000
85	A	321	CYS	0	-0.085	-0.034	23.359	0.363	0.363	0.000	0.000	0.000	0.000
86	A	322	LEU	0	-0.057	-0.036	25.969	0.435	0.435	0.000	0.000	0.000	0.000
87	A	323	ASP	-1	-0.884	-0.946	27.686	-9.500	-9.500	0.000	0.000	0.000	0.000
88	A	324	GLU	-1	-0.841	-0.894	26.155	-11.399	-11.399	0.000	0.000	0.000	0.000
89	A	325	GLU	-1	-0.820	-0.904	26.870	-10.359	-10.359	0.000	0.000	0.000	0.000
90	A	326	ALA	0	-0.002	0.005	28.539	-0.141	-0.141	0.000	0.000	0.000	0.000
91	A	327	SER	0	-0.089	-0.059	22.765	-0.527	-0.527	0.000	0.000	0.000	0.000
92	A	328	ASN	0	-0.030	-0.050	23.964	-0.944	-0.944	0.000	0.000	0.000	0.000
93	A	329	ALA	0	0.006	0.007	25.534	-0.172	-0.172	0.000	0.000	0.000	0.000
94	A	330	LEU	0	-0.023	-0.013	23.211	-0.170	-0.170	0.000	0.000	0.000	0.000
95	A	331	ARG	1	0.734	0.825	19.150	13.910	13.910	0.000	0.000	0.000	0.000
96	A	332	ARG	1	0.925	0.947	22.200	10.814	10.814	0.000	0.000	0.000	0.000
97	A	333	ALA	0	0.074	0.042	24.688	-0.132	-0.132	0.000	0.000	0.000	0.000
98	A	334	PHE	0	-0.064	-0.044	20.557	-0.089	-0.089	0.000	0.000	0.000	0.000
99	A	335	LYS	1	0.805	0.878	20.652	12.958	12.958	0.000	0.000	0.000	0.000
100	A	336	GLU	-1	-0.957	-0.972	21.642	-10.887	-10.887	0.000	0.000	0.000	0.000
101	A	337	ARG	1	0.803	0.892	23.500	12.849	12.849	0.000	0.000	0.000	0.000
102	A	338	GLY	0	0.000	0.011	20.499	-0.134	-0.134	0.000	0.000	0.000	0.000
103	A	339	GLU	-1	-0.823	-0.876	19.111	-15.305	-15.305	0.000	0.000	0.000	0.000
104	A	340	ASN	0	-0.004	0.003	13.852	-1.559	-1.559	0.000	0.000	0.000	0.000
105	A	341	VAL	0	0.031	-0.012	12.400	0.662	0.662	0.000	0.000	0.000	0.000
106	A	342	GLY	0	-0.010	-0.001	14.149	0.402	0.402	0.000	0.000	0.000	0.000
107	A	343	SER	0	-0.002	-0.018	15.082	0.530	0.530	0.000	0.000	0.000	0.000
108	A	344	TRP	0	0.061	0.031	16.127	0.131	0.131	0.000	0.000	0.000	0.000
109	A	345	ARG	1	0.858	0.926	14.474	19.094	19.094	0.000	0.000	0.000	0.000
110	A	346	GLN	0	-0.028	-0.012	18.005	0.814	0.814	0.000	0.000	0.000	0.000
111	A	347	ALA	0	0.034	0.020	20.437	0.660	0.660	0.000	0.000	0.000	0.000
112	A	348	CYS	0	0.024	0.028	20.785	0.514	0.514	0.000	0.000	0.000	0.000
113	A	349	TYR	0	-0.051	-0.030	19.785	0.103	0.103	0.000	0.000	0.000	0.000
114	A	350	LYS	1	1.005	1.014	24.656	10.313	10.313	0.000	0.000	0.000	0.000
115	A	351	PRO	0	0.027	0.016	26.169	0.414	0.414	0.000	0.000	0.000	0.000
116	A	352	LEU	0	0.013	0.008	23.836	0.278	0.278	0.000	0.000	0.000	0.000
117	A	353	VAL	0	0.017	0.008	28.323	0.272	0.272	0.000	0.000	0.000	0.000
118	A	354	ASN	0	0.002	-0.003	30.617	0.246	0.246	0.000	0.000	0.000	0.000
119	A	355	ILE	0	-0.007	0.000	29.264	0.326	0.326	0.000	0.000	0.000	0.000
120	A	356	ALA	0	0.016	0.005	31.383	0.246	0.246	0.000	0.000	0.000	0.000
121	A	357	CYS	0	-0.053	-0.011	33.280	0.318	0.318	0.000	0.000	0.000	0.000
122	A	358	ARG	1	0.912	0.955	33.612	9.163	9.163	0.000	0.000	0.000	0.000
123	A	359	HIS	0	-0.037	-0.022	34.855	0.235	0.235	0.000	0.000	0.000	0.000
124	A	360	GLY	0	0.040	0.025	37.603	-0.019	-0.019	0.000	0.000	0.000	0.000
125	A	361	TRP	0	0.004	-0.021	34.411	-0.074	-0.074	0.000	0.000	0.000	0.000
126	A	362	ASP	-1	-0.820	-0.891	34.425	-9.206	-9.206	0.000	0.000	0.000	0.000
127	A	363	ILE	0	0.009	-0.020	27.865	-0.143	-0.143	0.000	0.000	0.000	0.000
128	A	364	ASP	-1	-0.812	-0.871	29.721	-10.705	-10.705	0.000	0.000	0.000	0.000
129	A	365	ALA	0	0.010	0.021	31.200	-0.115	-0.115	0.000	0.000	0.000	0.000
130	A	366	VAL	0	-0.003	-0.002	29.632	-0.059	-0.059	0.000	0.000	0.000	0.000
131	A	367	PHE	0	-0.003	-0.028	23.336	-0.356	-0.356	0.000	0.000	0.000	0.000
132	A	368	ASN	0	-0.061	-0.059	28.809	-0.228	-0.228	0.000	0.000	0.000	0.000
133	A	369	ALA	0	0.031	0.035	30.960	0.103	0.103	0.000	0.000	0.000	0.000
134	A	370	HIS	0	0.046	0.031	27.771	0.088	0.088	0.000	0.000	0.000	0.000
135	A	371	PRO	0	0.046	0.011	28.932	-0.387	-0.387	0.000	0.000	0.000	0.000
136	A	372	ARG	1	0.851	0.927	24.008	11.260	11.260	0.000	0.000	0.000	0.000
137	A	373	LEU	0	0.007	0.017	23.782	-0.618	-0.618	0.000	0.000	0.000	0.000
138	A	374	SER	0	0.007	0.004	25.393	-0.280	-0.280	0.000	0.000	0.000	0.000
139	A	375	ILE	0	-0.005	0.015	21.853	0.035	0.035	0.000	0.000	0.000	0.000
140	A	376	TRP	0	-0.049	-0.029	16.964	-1.077	-1.077	0.000	0.000	0.000	0.000
141	A	377	TYR	0	-0.007	-0.017	22.189	0.318	0.318	0.000	0.000	0.000	0.000
142	A	378	VAL	0	0.050	0.038	22.660	-0.568	-0.568	0.000	0.000	0.000	0.000
143	A	379	PRO	0	-0.035	-0.004	20.210	-0.063	-0.063	0.000	0.000	0.000	0.000
144	A	380	THR	0	0.032	-0.008	22.220	0.327	0.327	0.000	0.000	0.000	0.000
145	A	381	LYS	1	0.979	1.006	21.945	13.302	13.302	0.000	0.000	0.000	0.000
146	A	382	LEU	0	0.049	0.026	23.810	0.303	0.303	0.000	0.000	0.000	0.000
147	A	383	ARG	1	0.851	0.888	25.534	11.242	11.242	0.000	0.000	0.000	0.000
148	A	384	GLN	0	-0.008	-0.014	25.329	0.133	0.133	0.000	0.000	0.000	0.000
149	A	385	LEU	0	0.002	0.003	25.468	0.291	0.291	0.000	0.000	0.000	0.000
150	A	386	CYS	0	0.002	0.006	28.951	0.308	0.308	0.000	0.000	0.000	0.000
151	A	387	HIS	0	-0.001	0.024	31.537	0.359	0.359	0.000	0.000	0.000	0.000
152	A	388	LEU	0	-0.027	-0.024	29.935	0.235	0.235	0.000	0.000	0.000	0.000
153	A	389	GLU	-1	-0.854	-0.915	32.835	-9.124	-9.124	0.000	0.000	0.000	0.000
154	A	390	ARG	1	0.910	0.948	34.747	8.864	8.864	0.000	0.000	0.000	0.000
155	A	391	ASN	0	-0.012	-0.007	36.401	0.393	0.393	0.000	0.000	0.000	0.000
156	A	392	ASN	0	-0.024	-0.025	34.953	0.317	0.317	0.000	0.000	0.000	0.000
157	A	393	ALA	0	-0.015	0.000	38.728	0.209	0.209	0.000	0.000	0.000	0.000
158	A	394	VAL	0	-0.024	-0.020	40.562	0.192	0.192	0.000	0.000	0.000	0.000
159	A	395	ALA	0	-0.016	-0.001	42.023	0.187	0.187	0.000	0.000	0.000	0.000
160	A	396	ALA	0	-0.010	-0.004	42.636	0.155	0.155	0.000	0.000	0.000	0.000
161	A	397	ALA	0	-0.037	-0.022	44.326	0.162	0.162	0.000	0.000	0.000	0.000
162	A	398	ALA	0	-0.066	-0.011	46.212	0.307	0.307	0.000	0.000	0.000	0.000

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