FMO DATABASE

FMODB ID: R8NR8

Calculation Name: 2VJW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VJW

Chain ID: A

ChEMBL ID:

UniProt ID: A0R2U9

Base Structure: X-ray

Registration Date: 2023-09-20

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	142
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1120340.426017
FMO2-HF: Nuclear repulsion	1069842.472649
FMO2-HF: Total energy	-50497.953368
FMO2-MP2: Total energy	-50645.995912

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:232:ASP)

Summations of interaction energy for fragment #1(A:232:ASP)

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.
29.239	37.949	2.734	-4.878	-6.566	0.045

Interaction energy analysis for fragmet #1(A:232:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.901 / q_NPA : -0.973

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	234	ALA	0	0.056	0.042	2.276	-24.658	-19.212	2.393	-3.605	-4.234	0.044
4	A	235	THR	0	-0.003	-0.007	2.426	-15.464	-13.209	0.251	-1.006	-1.500	0.000
5	A	236	VAL	0	-0.039	-0.026	4.605	-6.335	-6.131	-0.001	-0.024	-0.179	0.000
6	A	237	PHE	0	0.055	0.019	6.894	-4.096	-4.096	0.000	0.000	0.000	0.000
7	A	238	ARG	1	1.021	1.027	7.234	-35.301	-35.301	0.000	0.000	0.000	0.000
8	A	239	LEU	0	-0.054	-0.031	7.704	-2.763	-2.763	0.000	0.000	0.000	0.000
9	A	240	VAL	0	-0.013	0.000	11.185	-2.158	-2.158	0.000	0.000	0.000	0.000
10	A	241	ALA	0	0.057	0.029	12.797	-1.778	-1.778	0.000	0.000	0.000	0.000
11	A	242	ALA	0	0.004	0.011	13.769	-1.593	-1.593	0.000	0.000	0.000	0.000
12	A	243	GLU	-1	-0.929	-0.979	14.585	15.769	15.769	0.000	0.000	0.000	0.000
13	A	244	ALA	0	0.002	0.006	16.937	-1.200	-1.200	0.000	0.000	0.000	0.000
14	A	245	LEU	0	-0.009	0.022	18.468	-0.918	-0.918	0.000	0.000	0.000	0.000
15	A	246	THR	0	-0.038	-0.017	19.191	-1.039	-1.039	0.000	0.000	0.000	0.000
16	A	247	LEU	0	-0.060	-0.035	19.742	-0.811	-0.811	0.000	0.000	0.000	0.000
17	A	248	THR	0	-0.084	-0.057	22.612	-0.715	-0.715	0.000	0.000	0.000	0.000
18	A	249	GLY	0	-0.033	-0.010	24.150	-0.585	-0.585	0.000	0.000	0.000	0.000
19	A	250	ALA	0	-0.087	-0.036	23.887	-0.472	-0.472	0.000	0.000	0.000	0.000
20	A	251	ASP	-1	-0.810	-0.911	24.692	11.375	11.375	0.000	0.000	0.000	0.000
21	A	252	GLY	0	0.004	0.004	21.895	0.276	0.276	0.000	0.000	0.000	0.000
22	A	253	THR	0	-0.080	-0.041	17.612	-0.222	-0.222	0.000	0.000	0.000	0.000
23	A	254	LEU	0	0.026	0.018	16.305	0.313	0.313	0.000	0.000	0.000	0.000
24	A	255	VAL	0	-0.009	-0.013	11.840	-0.724	-0.724	0.000	0.000	0.000	0.000
25	A	256	ALA	0	-0.011	0.003	13.409	0.954	0.954	0.000	0.000	0.000	0.000
26	A	257	VAL	0	0.011	-0.004	8.801	-0.636	-0.636	0.000	0.000	0.000	0.000
27	A	258	PRO	0	0.006	0.020	12.114	-0.891	-0.891	0.000	0.000	0.000	0.000
28	A	259	ALA	0	0.010	-0.001	11.215	1.956	1.956	0.000	0.000	0.000	0.000
29	A	260	ASP	-1	-0.923	-0.946	10.545	28.672	28.672	0.000	0.000	0.000	0.000
30	A	261	PRO	0	-0.061	-0.035	12.326	1.054	1.054	0.000	0.000	0.000	0.000
31	A	262	ASP	-1	-0.847	-0.941	14.751	16.726	16.726	0.000	0.000	0.000	0.000
32	A	263	ALA	0	-0.107	-0.058	15.151	1.102	1.102	0.000	0.000	0.000	0.000
33	A	264	SER	0	-0.033	-0.003	16.785	-0.737	-0.737	0.000	0.000	0.000	0.000
34	A	265	ALA	0	-0.029	-0.019	18.448	0.592	0.592	0.000	0.000	0.000	0.000
35	A	266	ALA	0	0.034	0.033	17.365	0.069	0.069	0.000	0.000	0.000	0.000
36	A	267	GLU	-1	-0.959	-0.994	19.412	12.839	12.839	0.000	0.000	0.000	0.000
37	A	268	GLU	-1	-0.940	-0.984	18.313	15.795	15.795	0.000	0.000	0.000	0.000
38	A	269	LEU	0	-0.075	-0.045	15.642	0.817	0.817	0.000	0.000	0.000	0.000
39	A	270	VAL	0	0.019	0.018	12.578	-1.008	-1.008	0.000	0.000	0.000	0.000
40	A	271	ILE	0	-0.037	-0.013	13.164	1.322	1.322	0.000	0.000	0.000	0.000
41	A	272	VAL	0	-0.019	0.001	8.708	0.263	0.263	0.000	0.000	0.000	0.000
42	A	273	GLU	-1	-0.864	-0.938	8.368	34.195	34.195	0.000	0.000	0.000	0.000
43	A	274	VAL	0	-0.014	-0.008	12.123	-1.525	-1.525	0.000	0.000	0.000	0.000
44	A	275	ALA	0	-0.010	-0.002	15.344	0.567	0.567	0.000	0.000	0.000	0.000
45	A	276	GLY	0	0.003	-0.001	17.681	-0.628	-0.628	0.000	0.000	0.000	0.000
46	A	277	ALA	0	-0.025	-0.040	21.318	0.105	0.105	0.000	0.000	0.000	0.000
47	A	278	VAL	0	-0.043	-0.005	19.449	-0.481	-0.481	0.000	0.000	0.000	0.000
48	A	279	PRO	0	0.014	0.003	20.035	0.528	0.528	0.000	0.000	0.000	0.000
49	A	280	ALA	0	0.094	0.036	17.076	0.554	0.554	0.000	0.000	0.000	0.000
50	A	281	GLU	-1	-0.959	-0.984	16.787	15.636	15.636	0.000	0.000	0.000	0.000
51	A	282	VAL	0	-0.064	-0.027	18.226	-0.142	-0.142	0.000	0.000	0.000	0.000
52	A	283	GLU	-1	-0.958	-0.978	10.948	26.388	26.388	0.000	0.000	0.000	0.000
53	A	284	ALA	0	-0.035	-0.033	13.284	-0.527	-0.527	0.000	0.000	0.000	0.000
54	A	285	SER	0	-0.069	-0.015	14.283	-0.839	-0.839	0.000	0.000	0.000	0.000
55	A	286	ALA	0	0.045	0.027	16.763	1.056	1.056	0.000	0.000	0.000	0.000
56	A	287	ILE	0	-0.023	-0.022	18.290	-1.089	-1.089	0.000	0.000	0.000	0.000
57	A	288	PRO	0	0.058	0.041	19.950	0.476	0.476	0.000	0.000	0.000	0.000
58	A	289	VAL	0	-0.011	0.005	19.825	-0.154	-0.154	0.000	0.000	0.000	0.000
59	A	290	GLN	0	-0.036	-0.038	22.363	-0.667	-0.667	0.000	0.000	0.000	0.000
60	A	291	ASP	-1	-0.908	-0.954	26.200	10.703	10.703	0.000	0.000	0.000	0.000
61	A	292	ASN	0	-0.007	-0.017	23.723	0.150	0.150	0.000	0.000	0.000	0.000
62	A	293	ALA	0	0.007	-0.010	25.737	0.227	0.227	0.000	0.000	0.000	0.000
63	A	294	ILE	0	0.045	0.029	19.596	0.081	0.081	0.000	0.000	0.000	0.000
64	A	295	GLY	0	0.075	0.038	21.161	0.549	0.549	0.000	0.000	0.000	0.000
65	A	296	GLN	0	-0.092	-0.058	22.204	-0.131	-0.131	0.000	0.000	0.000	0.000
66	A	297	ALA	0	0.015	0.021	21.903	-0.051	-0.051	0.000	0.000	0.000	0.000
67	A	298	PHE	0	-0.017	-0.014	15.638	0.006	0.006	0.000	0.000	0.000	0.000
68	A	299	ARG	1	0.862	0.952	20.214	-12.465	-12.465	0.000	0.000	0.000	0.000
69	A	300	ASP	-1	-0.852	-0.938	23.041	12.014	12.014	0.000	0.000	0.000	0.000
70	A	301	ARG	1	0.842	0.933	19.516	-15.473	-15.473	0.000	0.000	0.000	0.000
71	A	302	ALA	0	0.011	0.003	23.241	-0.126	-0.126	0.000	0.000	0.000	0.000
72	A	303	PRO	0	-0.026	-0.011	23.566	0.150	0.150	0.000	0.000	0.000	0.000
73	A	304	ARG	1	0.935	0.980	25.115	-11.515	-11.515	0.000	0.000	0.000	0.000
74	A	305	ARG	1	0.929	0.978	26.572	-9.299	-9.299	0.000	0.000	0.000	0.000
75	A	306	LEU	0	-0.068	-0.035	27.182	-0.318	-0.318	0.000	0.000	0.000	0.000
76	A	307	ASP	-1	-0.868	-0.939	30.594	9.224	9.224	0.000	0.000	0.000	0.000
77	A	308	VAL	0	-0.032	-0.020	31.953	-0.038	-0.038	0.000	0.000	0.000	0.000
78	A	309	LEU	0	-0.038	-0.008	24.269	0.096	0.096	0.000	0.000	0.000	0.000
79	A	310	ASP	-1	-0.879	-0.937	28.527	10.281	10.281	0.000	0.000	0.000	0.000
80	A	311	GLY	0	-0.004	0.023	25.905	0.434	0.434	0.000	0.000	0.000	0.000
81	A	312	PRO	0	-0.027	-0.036	21.178	-0.172	-0.172	0.000	0.000	0.000	0.000
82	A	313	GLY	0	-0.021	-0.017	23.272	0.368	0.368	0.000	0.000	0.000	0.000
83	A	314	LEU	0	-0.020	-0.023	24.572	-0.097	-0.097	0.000	0.000	0.000	0.000
84	A	315	GLY	0	0.046	0.019	27.735	-0.351	-0.351	0.000	0.000	0.000	0.000
85	A	316	GLY	0	-0.059	-0.015	30.028	-0.427	-0.427	0.000	0.000	0.000	0.000
86	A	317	PRO	0	-0.032	-0.011	30.164	0.222	0.222	0.000	0.000	0.000	0.000
87	A	318	ALA	0	-0.009	-0.009	25.349	0.357	0.357	0.000	0.000	0.000	0.000
88	A	319	LEU	0	-0.048	-0.021	24.148	-0.480	-0.480	0.000	0.000	0.000	0.000
89	A	320	VAL	0	0.002	-0.002	22.175	0.643	0.643	0.000	0.000	0.000	0.000
90	A	321	LEU	0	0.004	-0.012	19.848	-0.642	-0.642	0.000	0.000	0.000	0.000
91	A	322	PRO	0	0.030	0.034	18.504	1.035	1.035	0.000	0.000	0.000	0.000
92	A	323	LEU	0	0.008	-0.003	12.830	-0.335	-0.335	0.000	0.000	0.000	0.000
93	A	324	ARG	1	0.799	0.894	15.798	-13.313	-13.313	0.000	0.000	0.000	0.000
94	A	325	ALA	0	0.081	0.039	14.861	-0.090	-0.090	0.000	0.000	0.000	0.000
95	A	326	THR	0	-0.042	-0.031	16.942	-1.008	-1.008	0.000	0.000	0.000	0.000
96	A	327	ASP	-1	-0.938	-0.973	18.126	14.955	14.955	0.000	0.000	0.000	0.000
97	A	328	THR	0	-0.012	0.003	14.125	0.054	0.054	0.000	0.000	0.000	0.000
98	A	329	VAL	0	-0.041	-0.017	16.251	-0.317	-0.317	0.000	0.000	0.000	0.000
99	A	330	ALA	0	0.001	0.000	10.985	0.492	0.492	0.000	0.000	0.000	0.000
100	A	331	GLY	0	0.072	0.027	11.666	1.984	1.984	0.000	0.000	0.000	0.000
101	A	332	VAL	0	-0.081	-0.036	13.953	-1.339	-1.339	0.000	0.000	0.000	0.000
102	A	333	LEU	0	0.005	0.020	16.020	0.714	0.714	0.000	0.000	0.000	0.000
103	A	334	VAL	0	-0.032	-0.025	17.198	-1.161	-1.161	0.000	0.000	0.000	0.000
104	A	335	ALA	0	0.017	0.017	20.050	0.469	0.469	0.000	0.000	0.000	0.000
105	A	336	VAL	0	-0.016	-0.020	22.465	-0.606	-0.606	0.000	0.000	0.000	0.000
106	A	337	GLN	0	0.058	0.030	25.022	0.167	0.167	0.000	0.000	0.000	0.000
107	A	338	GLY	0	0.054	0.036	28.423	-0.009	-0.009	0.000	0.000	0.000	0.000
108	A	339	SER	0	-0.014	-0.032	30.610	-0.166	-0.166	0.000	0.000	0.000	0.000
109	A	340	GLY	0	-0.028	-0.015	34.015	-0.103	-0.103	0.000	0.000	0.000	0.000
110	A	341	ALA	0	0.003	0.028	32.324	-0.184	-0.184	0.000	0.000	0.000	0.000
111	A	342	ARG	1	0.922	0.949	32.812	-9.544	-9.544	0.000	0.000	0.000	0.000
112	A	343	PRO	0	0.071	0.025	33.108	0.289	0.289	0.000	0.000	0.000	0.000
113	A	344	PHE	0	-0.013	0.019	26.689	-0.091	-0.091	0.000	0.000	0.000	0.000
114	A	345	THR	0	-0.002	-0.015	31.363	-0.115	-0.115	0.000	0.000	0.000	0.000
115	A	346	ALA	0	0.001	-0.006	31.287	0.342	0.342	0.000	0.000	0.000	0.000
116	A	347	GLU	-1	-0.810	-0.919	31.213	9.440	9.440	0.000	0.000	0.000	0.000
117	A	348	GLN	0	-0.002	0.009	28.243	0.104	0.104	0.000	0.000	0.000	0.000
118	A	349	LEU	0	0.013	0.001	26.170	0.438	0.438	0.000	0.000	0.000	0.000
119	A	350	GLU	-1	-0.958	-0.963	26.434	10.612	10.612	0.000	0.000	0.000	0.000
120	A	351	MET	0	-0.019	-0.013	24.240	0.256	0.256	0.000	0.000	0.000	0.000
121	A	352	MET	0	-0.017	-0.015	20.307	0.452	0.452	0.000	0.000	0.000	0.000
122	A	353	THR	0	-0.016	-0.013	21.666	0.772	0.772	0.000	0.000	0.000	0.000
123	A	354	GLY	0	0.028	0.022	21.975	0.442	0.442	0.000	0.000	0.000	0.000
124	A	355	PHE	0	-0.015	-0.004	15.628	0.568	0.568	0.000	0.000	0.000	0.000
125	A	356	ALA	0	0.013	0.002	17.616	1.042	1.042	0.000	0.000	0.000	0.000
126	A	357	ASP	-1	-0.850	-0.923	17.145	15.532	15.532	0.000	0.000	0.000	0.000
127	A	358	GLN	0	-0.053	-0.037	16.937	1.044	1.044	0.000	0.000	0.000	0.000
128	A	359	ALA	0	0.012	0.009	13.514	1.094	1.094	0.000	0.000	0.000	0.000
129	A	360	ALA	0	0.015	0.013	12.460	2.296	2.296	0.000	0.000	0.000	0.000
130	A	361	VAL	0	0.012	0.006	13.324	1.235	1.235	0.000	0.000	0.000	0.000
131	A	362	ALA	0	-0.023	-0.004	10.335	0.971	0.971	0.000	0.000	0.000	0.000
132	A	363	TRP	0	0.034	0.014	6.918	-0.685	-0.685	0.000	0.000	0.000	0.000
133	A	364	GLN	0	0.032	0.005	8.812	1.985	1.985	0.000	0.000	0.000	0.000
134	A	365	LEU	0	-0.026	-0.017	10.585	0.511	0.511	0.000	0.000	0.000	0.000
135	A	366	ALA	0	0.011	0.013	5.367	0.359	0.359	0.000	0.000	0.000	0.000
136	A	367	SER	0	0.000	-0.005	6.162	5.279	5.279	0.000	0.000	0.000	0.000
137	A	368	SER	0	-0.081	-0.045	7.468	-0.533	-0.533	0.000	0.000	0.000	0.000
138	A	369	GLN	0	0.002	0.011	6.910	1.330	1.330	0.000	0.000	0.000	0.000
139	A	370	ARG	1	0.967	0.987	2.809	-59.853	-59.048	0.091	-0.243	-0.653	0.001
140	A	371	ARG	1	0.955	0.959	6.833	-27.633	-27.633	0.000	0.000	0.000	0.000
141	A	372	MET	0	-0.074	-0.011	10.088	-2.197	-2.197	0.000	0.000	0.000	0.000
142	A	373	SER	0	-0.033	-0.004	9.201	-0.905	-0.905	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:232:ASP)