FMO DATABASE

FMODB ID: ZV8KN

Calculation Name: 3V46-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3V46

Chain ID: A

ChEMBL ID:

UniProt ID: Q06697

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptHSide
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	160
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1777156.324102
FMO2-HF: Nuclear repulsion	1711516.772125
FMO2-HF: Total energy	-65639.551977
FMO2-MP2: Total energy	-65835.84598

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:234:PRO)

Summations of interaction energy for fragment #1(A:234:PRO)

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.
-14.322	-4.439	2.957	-4.663	-8.173	-0.024

Interaction energy analysis for fragmet #1(A:234:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.069 / q_NPA : 0.027

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	236	LYS	1	0.893	0.965	3.814	-4.834	-1.224	-0.037	-1.859	-1.713	0.000
4	A	237	ASP	-1	-0.854	-0.927	4.447	-1.181	-1.148	-0.001	-0.016	-0.016	0.000
5	A	238	PRO	0	-0.002	0.018	5.407	0.199	0.199	0.000	0.000	0.000	0.000
6	A	239	ILE	0	-0.025	-0.020	6.450	0.284	0.284	0.000	0.000	0.000	0.000
7	A	240	ILE	0	-0.012	0.000	9.697	-0.134	-0.134	0.000	0.000	0.000	0.000
8	A	241	LEU	0	-0.014	0.001	12.695	0.092	0.092	0.000	0.000	0.000	0.000
9	A	242	ILE	0	-0.012	-0.015	15.554	-0.019	-0.019	0.000	0.000	0.000	0.000
10	A	243	PRO	0	0.004	0.019	18.993	0.032	0.032	0.000	0.000	0.000	0.000
11	A	244	SER	0	-0.035	-0.024	21.727	-0.006	-0.006	0.000	0.000	0.000	0.000
12	A	245	ALA	0	0.030	0.010	25.156	0.013	0.013	0.000	0.000	0.000	0.000
13	A	246	ALA	0	0.014	-0.002	28.506	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	247	SER	0	-0.005	-0.005	30.516	0.002	0.002	0.000	0.000	0.000	0.000
15	A	248	SER	0	-0.009	0.010	25.539	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	249	ILE	0	0.033	0.034	26.909	0.007	0.007	0.000	0.000	0.000	0.000
17	A	250	LEU	0	-0.015	0.010	22.435	0.003	0.003	0.000	0.000	0.000	0.000
18	A	251	THR	0	0.034	0.005	23.215	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	252	VAL	0	0.042	0.009	19.621	-0.012	-0.012	0.000	0.000	0.000	0.000
20	A	253	ALA	0	-0.008	0.003	22.139	0.002	0.002	0.000	0.000	0.000	0.000
21	A	254	ASN	0	-0.005	-0.018	24.924	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	255	ILE	0	0.019	0.022	19.012	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	256	LYS	1	0.933	0.968	19.806	0.230	0.230	0.000	0.000	0.000	0.000
24	A	257	GLN	0	0.007	-0.008	21.946	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	258	PHE	0	0.031	0.017	22.127	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	259	LEU	0	0.016	-0.004	17.307	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	260	LEU	0	-0.028	-0.014	18.952	-0.019	-0.019	0.000	0.000	0.000	0.000
28	A	261	GLU	-1	-0.854	-0.902	22.180	-0.174	-0.174	0.000	0.000	0.000	0.000
29	A	262	SER	0	-0.049	-0.014	24.640	0.008	0.008	0.000	0.000	0.000	0.000
30	A	263	LYS	1	0.846	0.913	25.983	0.198	0.198	0.000	0.000	0.000	0.000
31	A	264	TYR	0	-0.047	-0.034	27.284	0.000	0.000	0.000	0.000	0.000	0.000
32	A	265	VAL	0	0.002	0.002	28.938	0.015	0.015	0.000	0.000	0.000	0.000
33	A	266	ASN	0	0.026	0.014	29.702	-0.011	-0.011	0.000	0.000	0.000	0.000
34	A	267	PRO	0	0.049	0.019	27.814	0.007	0.007	0.000	0.000	0.000	0.000
35	A	268	ARG	1	0.942	0.980	29.820	0.112	0.112	0.000	0.000	0.000	0.000
36	A	269	ASN	0	-0.059	-0.033	32.887	0.011	0.011	0.000	0.000	0.000	0.000
37	A	270	LEU	0	0.010	0.017	28.446	0.002	0.002	0.000	0.000	0.000	0.000
38	A	271	PRO	0	0.006	0.002	29.759	0.003	0.003	0.000	0.000	0.000	0.000
39	A	272	SER	0	0.020	0.016	28.610	-0.011	-0.011	0.000	0.000	0.000	0.000
40	A	273	VAL	0	0.024	0.007	22.539	0.006	0.006	0.000	0.000	0.000	0.000
41	A	274	PRO	0	-0.001	0.005	25.314	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	275	ASN	0	0.023	0.003	21.589	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	276	GLY	0	0.025	0.012	21.825	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	277	LEU	0	-0.059	-0.018	15.825	-0.030	-0.030	0.000	0.000	0.000	0.000
45	A	278	VAL	0	-0.009	-0.007	17.938	0.020	0.020	0.000	0.000	0.000	0.000
46	A	279	ASN	0	0.003	0.000	14.058	0.001	0.001	0.000	0.000	0.000	0.000
47	A	280	ILE	0	0.003	-0.009	14.797	0.045	0.045	0.000	0.000	0.000	0.000
48	A	281	GLU	-1	-0.821	-0.879	13.867	-0.374	-0.374	0.000	0.000	0.000	0.000
49	A	282	LYS	1	0.886	0.961	13.190	0.589	0.589	0.000	0.000	0.000	0.000
50	A	283	ASN	0	0.020	0.011	13.421	-0.061	-0.061	0.000	0.000	0.000	0.000
51	A	284	PHE	0	-0.033	-0.031	10.666	0.013	0.013	0.000	0.000	0.000	0.000
52	A	285	GLU	-1	-0.844	-0.908	14.252	-0.405	-0.405	0.000	0.000	0.000	0.000
53	A	286	ARG	1	0.833	0.910	13.602	0.536	0.536	0.000	0.000	0.000	0.000
54	A	287	ILE	0	-0.052	-0.020	7.800	-0.130	-0.130	0.000	0.000	0.000	0.000
55	A	288	SER	0	-0.028	0.005	10.855	0.111	0.111	0.000	0.000	0.000	0.000
56	A	289	ARG	1	0.898	0.953	4.050	2.274	2.558	-0.001	-0.105	-0.177	0.000
57	A	290	PRO	0	0.062	0.025	11.103	-0.164	-0.164	0.000	0.000	0.000	0.000
58	A	291	ILE	0	-0.039	-0.014	6.967	-0.106	-0.106	0.000	0.000	0.000	0.000
59	A	292	ARG	1	0.872	0.918	9.639	0.347	0.347	0.000	0.000	0.000	0.000
60	A	293	PHE	0	0.023	-0.002	9.521	-0.106	-0.106	0.000	0.000	0.000	0.000
61	A	294	ILE	0	-0.012	-0.012	10.249	0.145	0.145	0.000	0.000	0.000	0.000
62	A	295	ILE	0	-0.005	-0.002	12.392	-0.072	-0.072	0.000	0.000	0.000	0.000
63	A	296	VAL	0	0.038	0.007	14.566	0.060	0.060	0.000	0.000	0.000	0.000
64	A	297	ASP	-1	-0.838	-0.899	17.117	-0.219	-0.219	0.000	0.000	0.000	0.000
65	A	298	ASN	0	-0.067	-0.058	18.890	0.035	0.035	0.000	0.000	0.000	0.000
66	A	299	THR	0	0.036	-0.005	16.846	-0.024	-0.024	0.000	0.000	0.000	0.000
67	A	300	ARG	1	0.965	0.989	18.162	0.135	0.135	0.000	0.000	0.000	0.000
68	A	301	MET	0	-0.026	0.001	11.885	0.008	0.008	0.000	0.000	0.000	0.000
69	A	302	PHE	0	-0.032	-0.007	11.583	0.038	0.038	0.000	0.000	0.000	0.000
70	A	303	THR	0	0.014	0.006	15.327	0.017	0.017	0.000	0.000	0.000	0.000
71	A	304	LYS	1	0.880	0.918	12.200	-0.466	-0.466	0.000	0.000	0.000	0.000
72	A	305	PRO	0	0.102	0.039	12.941	-0.025	-0.025	0.000	0.000	0.000	0.000
73	A	306	GLU	-1	-0.777	-0.865	8.364	0.714	0.714	0.000	0.000	0.000	0.000
74	A	307	TYR	0	-0.078	-0.040	7.841	0.003	0.003	0.000	0.000	0.000	0.000
75	A	308	TRP	0	0.049	0.015	9.104	-0.184	-0.184	0.000	0.000	0.000	0.000
76	A	309	ASP	-1	-0.894	-0.935	5.651	-0.348	-0.348	0.000	0.000	0.000	0.000
77	A	310	ARG	1	0.774	0.883	4.783	-0.569	-0.396	-0.001	-0.007	-0.164	0.000
78	A	311	VAL	0	-0.008	0.010	6.057	-0.228	-0.228	0.000	0.000	0.000	0.000
79	A	312	VAL	0	-0.010	-0.008	5.901	-0.202	-0.202	0.000	0.000	0.000	0.000
80	A	313	ALA	0	0.001	0.002	8.586	0.057	0.057	0.000	0.000	0.000	0.000
81	A	314	ILE	0	-0.006	0.000	12.371	0.069	0.069	0.000	0.000	0.000	0.000
82	A	315	PHE	0	0.000	0.004	15.541	0.011	0.011	0.000	0.000	0.000	0.000
83	A	316	THR	0	-0.045	-0.032	18.976	0.037	0.037	0.000	0.000	0.000	0.000
84	A	317	THR	0	0.002	-0.015	21.653	0.016	0.016	0.000	0.000	0.000	0.000
85	A	318	GLY	0	0.015	0.009	24.760	0.013	0.013	0.000	0.000	0.000	0.000
86	A	319	HIS	0	0.004	0.016	26.310	0.016	0.016	0.000	0.000	0.000	0.000
87	A	320	THR	0	0.056	0.002	25.223	-0.017	-0.017	0.000	0.000	0.000	0.000
88	A	321	TRP	0	0.014	0.008	24.873	-0.009	-0.009	0.000	0.000	0.000	0.000
89	A	322	GLN	0	-0.007	0.011	19.728	0.023	0.023	0.000	0.000	0.000	0.000
90	A	323	PHE	0	0.003	-0.012	19.350	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	324	ASN	0	-0.014	0.007	21.060	0.009	0.009	0.000	0.000	0.000	0.000
92	A	325	ASN	0	0.015	-0.007	20.741	0.000	0.000	0.000	0.000	0.000	0.000
93	A	326	TYR	0	0.020	0.005	16.681	-0.013	-0.013	0.000	0.000	0.000	0.000
94	A	327	GLN	0	-0.028	-0.002	13.596	0.053	0.053	0.000	0.000	0.000	0.000
95	A	328	TRP	0	0.032	0.003	9.964	-0.015	-0.015	0.000	0.000	0.000	0.000
96	A	329	ASN	0	0.000	0.000	17.056	-0.037	-0.037	0.000	0.000	0.000	0.000
97	A	330	SER	0	0.010	0.014	20.089	0.008	0.008	0.000	0.000	0.000	0.000
98	A	331	PRO	0	0.032	-0.007	19.570	-0.025	-0.025	0.000	0.000	0.000	0.000
99	A	332	GLN	0	-0.022	0.002	19.160	-0.037	-0.037	0.000	0.000	0.000	0.000
100	A	333	GLU	-1	-0.806	-0.899	15.611	-0.327	-0.327	0.000	0.000	0.000	0.000
101	A	334	LEU	0	-0.027	-0.007	14.238	-0.067	-0.067	0.000	0.000	0.000	0.000
102	A	335	PHE	0	-0.017	-0.031	14.228	-0.071	-0.071	0.000	0.000	0.000	0.000
103	A	336	GLN	0	-0.023	0.002	15.308	-0.008	-0.008	0.000	0.000	0.000	0.000
104	A	337	ARG	1	0.882	0.944	10.209	0.435	0.435	0.000	0.000	0.000	0.000
105	A	338	CYS	0	-0.072	-0.015	9.697	-0.250	-0.250	0.000	0.000	0.000	0.000
106	A	339	LYS	1	0.908	0.964	11.136	0.871	0.871	0.000	0.000	0.000	0.000
107	A	340	GLY	0	0.033	0.013	13.130	0.014	0.014	0.000	0.000	0.000	0.000
108	A	341	TYR	0	-0.030	-0.029	14.530	-0.026	-0.026	0.000	0.000	0.000	0.000
109	A	342	TYR	0	-0.001	0.000	19.233	0.024	0.024	0.000	0.000	0.000	0.000
110	A	343	PHE	0	0.042	0.014	20.066	0.003	0.003	0.000	0.000	0.000	0.000
111	A	344	HIS	0	-0.027	-0.014	24.939	0.002	0.002	0.000	0.000	0.000	0.000
112	A	345	PHE	0	0.007	-0.012	28.715	-0.005	-0.005	0.000	0.000	0.000	0.000
113	A	346	ALA	0	0.062	0.038	31.892	0.004	0.004	0.000	0.000	0.000	0.000
114	A	347	GLY	0	-0.029	-0.022	33.561	0.009	0.009	0.000	0.000	0.000	0.000
115	A	348	ASP	-1	-0.859	-0.906	33.359	-0.148	-0.148	0.000	0.000	0.000	0.000
116	A	349	SER	0	-0.002	-0.009	33.183	-0.007	-0.007	0.000	0.000	0.000	0.000
117	A	350	VAL	0	-0.005	0.009	28.083	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	351	PRO	0	0.012	0.006	29.342	0.009	0.009	0.000	0.000	0.000	0.000
119	A	352	GLN	0	0.071	0.031	30.114	-0.020	-0.020	0.000	0.000	0.000	0.000
120	A	353	HIS	0	-0.005	-0.021	27.614	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	354	VAL	0	0.011	0.009	24.852	-0.014	-0.014	0.000	0.000	0.000	0.000
122	A	355	GLN	0	-0.001	-0.017	25.483	-0.038	-0.038	0.000	0.000	0.000	0.000
123	A	356	GLN	0	-0.033	-0.022	26.526	-0.016	-0.016	0.000	0.000	0.000	0.000
124	A	357	TRP	0	0.001	0.009	21.832	-0.017	-0.017	0.000	0.000	0.000	0.000
125	A	358	ASN	0	-0.006	0.002	17.124	0.028	0.028	0.000	0.000	0.000	0.000
126	A	359	VAL	0	-0.035	-0.019	18.463	-0.051	-0.051	0.000	0.000	0.000	0.000
127	A	360	GLU	-1	-0.759	-0.849	18.666	-0.531	-0.531	0.000	0.000	0.000	0.000
128	A	361	LYS	1	0.849	0.951	20.817	0.305	0.305	0.000	0.000	0.000	0.000
129	A	362	VAL	0	-0.027	-0.015	21.541	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	363	GLU	-1	-0.856	-0.930	24.863	-0.200	-0.200	0.000	0.000	0.000	0.000
131	A	364	LEU	0	-0.044	-0.019	26.191	-0.007	-0.007	0.000	0.000	0.000	0.000
132	A	365	ASP	-1	-0.799	-0.876	29.644	-0.168	-0.168	0.000	0.000	0.000	0.000
133	A	366	LYS	1	0.847	0.915	33.114	0.147	0.147	0.000	0.000	0.000	0.000
134	A	367	ASN	0	0.003	-0.009	35.217	0.000	0.000	0.000	0.000	0.000	0.000
135	A	368	LYS	1	0.899	0.960	35.796	0.133	0.133	0.000	0.000	0.000	0.000
136	A	369	ARG	1	0.851	0.877	30.747	0.185	0.185	0.000	0.000	0.000	0.000
137	A	370	PHE	0	0.010	0.006	31.928	-0.008	-0.008	0.000	0.000	0.000	0.000
138	A	371	LYS	1	0.903	0.934	30.263	0.181	0.181	0.000	0.000	0.000	0.000
139	A	372	ASP	-1	-0.749	-0.850	27.780	-0.233	-0.233	0.000	0.000	0.000	0.000
140	A	373	VAL	0	0.025	0.005	26.109	-0.022	-0.022	0.000	0.000	0.000	0.000
141	A	374	GLU	-1	-0.868	-0.910	25.108	-0.317	-0.317	0.000	0.000	0.000	0.000
142	A	375	VAL	0	0.020	0.009	23.874	-0.028	-0.028	0.000	0.000	0.000	0.000
143	A	376	VAL	0	0.001	0.003	21.011	-0.041	-0.041	0.000	0.000	0.000	0.000
144	A	377	ARG	1	0.876	0.932	20.275	0.242	0.242	0.000	0.000	0.000	0.000
145	A	378	TYR	0	-0.028	-0.032	19.724	-0.047	-0.047	0.000	0.000	0.000	0.000
146	A	379	PHE	0	0.015	0.005	15.748	-0.059	-0.059	0.000	0.000	0.000	0.000
147	A	380	TRP	0	-0.014	-0.034	13.629	-0.100	-0.100	0.000	0.000	0.000	0.000
148	A	381	HIS	0	0.056	0.041	14.719	-0.085	-0.085	0.000	0.000	0.000	0.000
149	A	382	SER	0	-0.047	-0.036	14.968	-0.108	-0.108	0.000	0.000	0.000	0.000
150	A	383	LEU	0	0.006	0.001	10.735	-0.094	-0.094	0.000	0.000	0.000	0.000
151	A	384	GLU	-1	-0.837	-0.937	10.522	-0.985	-0.985	0.000	0.000	0.000	0.000
152	A	385	LYS	1	0.893	0.942	10.212	0.422	0.422	0.000	0.000	0.000	0.000
153	A	386	GLU	-1	-0.838	-0.911	8.759	-1.677	-1.677	0.000	0.000	0.000	0.000
154	A	387	LEU	0	-0.028	-0.014	5.668	-0.418	-0.418	0.000	0.000	0.000	0.000
155	A	388	ILE	0	-0.009	-0.010	5.608	-0.903	-0.903	0.000	0.000	0.000	0.000
156	A	389	SER	0	-0.076	-0.034	7.182	-0.088	-0.088	0.000	0.000	0.000	0.000
157	A	390	ARG	1	0.855	0.931	3.964	2.191	2.376	0.000	-0.023	-0.162	0.000
158	A	391	GLY	0	0.006	0.004	2.867	-4.942	-2.940	0.290	-0.951	-1.340	-0.008
159	A	392	TYR	0	-0.058	-0.031	2.826	-4.608	-1.300	2.705	-1.670	-4.343	-0.016
160	A	393	ARG	1	0.978	0.991	4.034	0.906	1.194	0.002	-0.032	-0.258	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:234:PRO)