FMO DATABASE

FMODB ID: 6Y2KZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1776267.028335
FMO2-HF: Nuclear repulsion	1710628.325342
FMO2-HF: Total energy	-65638.702994
FMO2-MP2: Total energy	-65834.969278

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.
-13.092	-2.814	4.819	-5.258	-9.838	-0.033

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 : 0.064 / q_NPA : 0.031

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	0.952	0.995	3.809	-4.452	-0.646	-0.035	-1.974	-1.796	0.002
4	A	237	ASP	-1	-0.862	-0.928	4.453	-1.305	-1.277	-0.001	-0.016	-0.012	0.000
5	A	238	PRO	0	-0.011	0.013	5.429	0.239	0.239	0.000	0.000	0.000	0.000
6	A	239	ILE	0	-0.018	-0.017	6.463	0.241	0.241	0.000	0.000	0.000	0.000
7	A	240	ILE	0	-0.006	0.002	9.696	-0.108	-0.108	0.000	0.000	0.000	0.000
8	A	241	LEU	0	-0.024	-0.007	12.705	0.080	0.080	0.000	0.000	0.000	0.000
9	A	242	ILE	0	-0.014	-0.011	15.550	-0.019	-0.019	0.000	0.000	0.000	0.000
10	A	243	PRO	0	0.005	0.018	19.004	0.026	0.026	0.000	0.000	0.000	0.000
11	A	244	SER	0	-0.036	-0.023	21.720	-0.008	-0.008	0.000	0.000	0.000	0.000
12	A	245	ALA	0	0.028	0.004	25.154	0.014	0.014	0.000	0.000	0.000	0.000
13	A	246	ALA	0	0.009	-0.004	28.502	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	247	SER	0	-0.012	-0.007	30.311	0.000	0.000	0.000	0.000	0.000	0.000
15	A	248	SER	0	0.001	0.017	25.767	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	249	ILE	0	0.039	0.041	26.960	0.005	0.005	0.000	0.000	0.000	0.000
17	A	250	LEU	0	-0.014	0.003	22.159	0.000	0.000	0.000	0.000	0.000	0.000
18	A	251	THR	0	0.024	0.004	23.260	0.003	0.003	0.000	0.000	0.000	0.000
19	A	252	VAL	0	0.050	0.009	19.656	-0.014	-0.014	0.000	0.000	0.000	0.000
20	A	253	ALA	0	0.007	0.007	22.152	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	254	ASN	0	-0.022	-0.029	24.935	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	255	ILE	0	0.021	0.022	19.028	-0.009	-0.009	0.000	0.000	0.000	0.000
23	A	256	LYS	1	0.985	0.994	20.543	0.229	0.229	0.000	0.000	0.000	0.000
24	A	257	GLN	0	0.051	0.023	21.982	-0.011	-0.011	0.000	0.000	0.000	0.000
25	A	258	PHE	0	0.032	0.017	21.989	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	259	LEU	0	0.008	-0.008	17.081	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	260	LEU	0	-0.024	-0.013	18.874	-0.024	-0.024	0.000	0.000	0.000	0.000
28	A	261	GLU	-1	-0.958	-0.974	21.873	-0.197	-0.197	0.000	0.000	0.000	0.000
29	A	262	SER	0	-0.061	-0.023	24.328	0.011	0.011	0.000	0.000	0.000	0.000
30	A	263	LYS	1	0.906	0.957	25.685	0.219	0.219	0.000	0.000	0.000	0.000
31	A	264	TYR	0	-0.033	-0.020	27.164	0.000	0.000	0.000	0.000	0.000	0.000
32	A	265	VAL	0	0.008	0.004	28.892	0.015	0.015	0.000	0.000	0.000	0.000
33	A	266	ASN	0	0.018	0.009	29.732	-0.011	-0.011	0.000	0.000	0.000	0.000
34	A	267	PRO	0	0.043	0.018	27.900	0.005	0.005	0.000	0.000	0.000	0.000
35	A	268	ARG	1	0.956	0.982	29.840	0.103	0.103	0.000	0.000	0.000	0.000
36	A	269	ASN	0	-0.051	-0.024	32.902	0.012	0.012	0.000	0.000	0.000	0.000
37	A	270	LEU	0	0.003	0.009	28.287	0.000	0.000	0.000	0.000	0.000	0.000
38	A	271	PRO	0	0.003	0.001	29.690	0.005	0.005	0.000	0.000	0.000	0.000
39	A	272	SER	0	0.021	0.017	28.619	-0.011	-0.011	0.000	0.000	0.000	0.000
40	A	273	VAL	0	0.024	0.008	22.552	0.004	0.004	0.000	0.000	0.000	0.000
41	A	274	PRO	0	-0.002	0.003	25.309	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	275	ASN	0	0.026	0.005	21.789	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	276	GLY	0	0.019	0.014	21.808	0.001	0.001	0.000	0.000	0.000	0.000
44	A	277	LEU	0	-0.070	-0.016	15.719	-0.025	-0.025	0.000	0.000	0.000	0.000
45	A	278	VAL	0	-0.011	-0.016	17.925	0.015	0.015	0.000	0.000	0.000	0.000
46	A	279	ASN	0	-0.010	-0.013	14.369	0.007	0.007	0.000	0.000	0.000	0.000
47	A	280	ILE	0	-0.007	-0.006	14.828	0.040	0.040	0.000	0.000	0.000	0.000
48	A	281	GLU	-1	-0.853	-0.905	13.933	-0.513	-0.513	0.000	0.000	0.000	0.000
49	A	282	LYS	1	0.900	0.965	12.792	0.632	0.632	0.000	0.000	0.000	0.000
50	A	283	ASN	0	0.025	0.010	12.965	-0.117	-0.117	0.000	0.000	0.000	0.000
51	A	284	PHE	0	-0.045	-0.033	10.229	0.031	0.031	0.000	0.000	0.000	0.000
52	A	285	GLU	-1	-0.912	-0.952	13.890	-0.469	-0.469	0.000	0.000	0.000	0.000
53	A	286	ARG	1	0.913	0.958	13.224	0.598	0.598	0.000	0.000	0.000	0.000
54	A	287	ILE	0	-0.044	-0.020	7.519	-0.170	-0.170	0.000	0.000	0.000	0.000
55	A	288	SER	0	-0.040	-0.005	10.900	0.114	0.114	0.000	0.000	0.000	0.000
56	A	289	ARG	1	0.917	0.966	4.218	2.842	3.006	-0.001	-0.031	-0.131	0.000
57	A	290	PRO	0	0.076	0.035	10.776	-0.162	-0.162	0.000	0.000	0.000	0.000
58	A	291	ILE	0	-0.044	-0.015	6.651	-0.167	-0.167	0.000	0.000	0.000	0.000
59	A	292	ARG	1	0.905	0.939	9.682	0.508	0.508	0.000	0.000	0.000	0.000
60	A	293	PHE	0	0.024	0.001	9.181	-0.113	-0.113	0.000	0.000	0.000	0.000
61	A	294	ILE	0	-0.018	-0.015	10.203	0.140	0.140	0.000	0.000	0.000	0.000
62	A	295	ILE	0	-0.002	0.002	12.397	-0.052	-0.052	0.000	0.000	0.000	0.000
63	A	296	VAL	0	0.035	0.006	14.526	0.052	0.052	0.000	0.000	0.000	0.000
64	A	297	ASP	-1	-0.849	-0.910	17.110	-0.185	-0.185	0.000	0.000	0.000	0.000
65	A	298	ASN	0	-0.053	-0.046	18.879	0.039	0.039	0.000	0.000	0.000	0.000
66	A	299	THR	0	0.033	-0.007	16.747	-0.024	-0.024	0.000	0.000	0.000	0.000
67	A	300	ARG	1	0.978	0.993	18.125	0.107	0.107	0.000	0.000	0.000	0.000
68	A	301	MET	0	-0.030	0.001	11.680	0.005	0.005	0.000	0.000	0.000	0.000
69	A	302	PHE	0	-0.049	-0.009	11.597	0.035	0.035	0.000	0.000	0.000	0.000
70	A	303	THR	0	0.008	0.004	15.394	0.029	0.029	0.000	0.000	0.000	0.000
71	A	304	LYS	1	0.915	0.966	12.466	-0.447	-0.447	0.000	0.000	0.000	0.000
72	A	305	PRO	0	0.106	0.033	13.209	-0.022	-0.022	0.000	0.000	0.000	0.000
73	A	306	GLU	-1	-0.842	-0.922	8.559	0.868	0.868	0.000	0.000	0.000	0.000
74	A	307	TYR	0	-0.102	-0.054	8.094	0.031	0.031	0.000	0.000	0.000	0.000
75	A	308	TRP	0	0.053	0.017	9.190	-0.180	-0.180	0.000	0.000	0.000	0.000
76	A	309	ASP	-1	-0.896	-0.935	5.669	0.239	0.239	0.000	0.000	0.000	0.000
77	A	310	ARG	1	0.765	0.879	4.754	-0.460	-0.302	-0.001	-0.006	-0.150	0.000
78	A	311	VAL	0	-0.012	0.008	6.019	-0.292	-0.292	0.000	0.000	0.000	0.000
79	A	312	VAL	0	-0.015	-0.009	5.809	-0.139	-0.139	0.000	0.000	0.000	0.000
80	A	313	ALA	0	0.001	-0.001	8.501	0.038	0.038	0.000	0.000	0.000	0.000
81	A	314	ILE	0	-0.006	0.000	12.264	0.062	0.062	0.000	0.000	0.000	0.000
82	A	315	PHE	0	-0.006	-0.002	15.513	0.008	0.008	0.000	0.000	0.000	0.000
83	A	316	THR	0	-0.032	-0.032	18.894	0.036	0.036	0.000	0.000	0.000	0.000
84	A	317	THR	0	0.004	-0.001	21.637	0.010	0.010	0.000	0.000	0.000	0.000
85	A	318	GLY	0	0.032	0.014	24.793	0.009	0.009	0.000	0.000	0.000	0.000
86	A	319	HIS	0	0.010	0.018	26.397	0.014	0.014	0.000	0.000	0.000	0.000
87	A	320	THR	0	0.059	0.003	25.298	-0.014	-0.014	0.000	0.000	0.000	0.000
88	A	321	TRP	0	0.005	0.004	25.069	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	322	GLN	0	-0.020	-0.001	19.654	0.015	0.015	0.000	0.000	0.000	0.000
90	A	323	PHE	0	-0.004	-0.013	19.557	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	324	ASN	0	-0.010	0.008	21.239	0.016	0.016	0.000	0.000	0.000	0.000
92	A	325	ASN	0	-0.006	-0.020	20.582	0.001	0.001	0.000	0.000	0.000	0.000
93	A	326	TYR	0	0.035	0.012	17.022	-0.012	-0.012	0.000	0.000	0.000	0.000
94	A	327	GLN	0	0.002	0.015	13.656	0.026	0.026	0.000	0.000	0.000	0.000
95	A	328	TRP	0	0.028	0.003	10.233	-0.018	-0.018	0.000	0.000	0.000	0.000
96	A	329	ASN	0	0.001	0.001	17.327	-0.039	-0.039	0.000	0.000	0.000	0.000
97	A	330	SER	0	0.017	0.014	20.406	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	331	PRO	0	0.030	-0.006	19.836	-0.016	-0.016	0.000	0.000	0.000	0.000
99	A	332	GLN	0	-0.022	0.001	19.350	-0.036	-0.036	0.000	0.000	0.000	0.000
100	A	333	GLU	-1	-0.870	-0.932	16.419	-0.117	-0.117	0.000	0.000	0.000	0.000
101	A	334	LEU	0	-0.028	-0.013	14.443	-0.047	-0.047	0.000	0.000	0.000	0.000
102	A	335	PHE	0	-0.023	-0.035	14.420	-0.058	-0.058	0.000	0.000	0.000	0.000
103	A	336	GLN	0	-0.026	0.004	15.484	-0.015	-0.015	0.000	0.000	0.000	0.000
104	A	337	ARG	1	0.932	0.976	9.812	0.190	0.190	0.000	0.000	0.000	0.000
105	A	338	CYS	0	-0.063	-0.016	9.870	-0.194	-0.194	0.000	0.000	0.000	0.000
106	A	339	LYS	1	0.957	1.001	11.110	0.745	0.745	0.000	0.000	0.000	0.000
107	A	340	GLY	0	0.026	0.012	13.072	0.010	0.010	0.000	0.000	0.000	0.000
108	A	341	TYR	0	-0.023	-0.027	14.350	-0.032	-0.032	0.000	0.000	0.000	0.000
109	A	342	TYR	0	-0.005	0.002	19.104	0.024	0.024	0.000	0.000	0.000	0.000
110	A	343	PHE	0	0.040	0.015	19.868	0.000	0.000	0.000	0.000	0.000	0.000
111	A	344	HIS	0	-0.030	-0.018	24.760	0.005	0.005	0.000	0.000	0.000	0.000
112	A	345	PHE	0	0.016	-0.008	28.540	-0.006	-0.006	0.000	0.000	0.000	0.000
113	A	346	ALA	0	0.061	0.032	31.700	0.005	0.005	0.000	0.000	0.000	0.000
114	A	347	GLY	0	-0.042	-0.030	33.373	0.008	0.008	0.000	0.000	0.000	0.000
115	A	348	ASP	-1	-0.871	-0.927	33.087	-0.134	-0.134	0.000	0.000	0.000	0.000
116	A	349	SER	0	-0.009	-0.018	33.043	-0.009	-0.009	0.000	0.000	0.000	0.000
117	A	350	VAL	0	0.003	0.014	27.992	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	351	PRO	0	0.008	0.004	29.324	0.009	0.009	0.000	0.000	0.000	0.000
119	A	352	GLN	0	0.073	0.027	30.118	-0.016	-0.016	0.000	0.000	0.000	0.000
120	A	353	HIS	0	-0.013	-0.029	27.569	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	354	VAL	0	0.011	0.011	24.870	-0.010	-0.010	0.000	0.000	0.000	0.000
122	A	355	GLN	0	-0.017	-0.021	25.487	-0.034	-0.034	0.000	0.000	0.000	0.000
123	A	356	GLN	0	-0.034	-0.019	26.522	-0.013	-0.013	0.000	0.000	0.000	0.000
124	A	357	TRP	0	0.002	0.012	21.869	-0.012	-0.012	0.000	0.000	0.000	0.000
125	A	358	ASN	0	-0.010	-0.003	17.195	0.012	0.012	0.000	0.000	0.000	0.000
126	A	359	VAL	0	-0.038	-0.016	18.470	-0.042	-0.042	0.000	0.000	0.000	0.000
127	A	360	GLU	-1	-0.809	-0.905	18.590	-0.458	-0.458	0.000	0.000	0.000	0.000
128	A	361	LYS	1	0.843	0.940	20.669	0.258	0.258	0.000	0.000	0.000	0.000
129	A	362	VAL	0	-0.019	-0.008	21.436	-0.003	-0.003	0.000	0.000	0.000	0.000
130	A	363	GLU	-1	-0.876	-0.937	24.653	-0.184	-0.184	0.000	0.000	0.000	0.000
131	A	364	LEU	0	-0.043	-0.020	26.058	-0.010	-0.010	0.000	0.000	0.000	0.000
132	A	365	ASP	-1	-0.810	-0.904	29.536	-0.161	-0.161	0.000	0.000	0.000	0.000
133	A	366	LYS	1	0.877	0.938	32.968	0.132	0.132	0.000	0.000	0.000	0.000
134	A	367	ASN	0	-0.010	-0.012	35.087	0.001	0.001	0.000	0.000	0.000	0.000
135	A	368	LYS	1	0.902	0.965	35.613	0.132	0.132	0.000	0.000	0.000	0.000
136	A	369	ARG	1	0.862	0.893	30.503	0.181	0.181	0.000	0.000	0.000	0.000
137	A	370	PHE	0	0.010	0.007	31.696	-0.009	-0.009	0.000	0.000	0.000	0.000
138	A	371	LYS	1	0.934	0.970	30.085	0.175	0.175	0.000	0.000	0.000	0.000
139	A	372	ASP	-1	-0.742	-0.851	27.527	-0.233	-0.233	0.000	0.000	0.000	0.000
140	A	373	VAL	0	0.021	0.006	25.888	-0.022	-0.022	0.000	0.000	0.000	0.000
141	A	374	GLU	-1	-0.913	-0.952	24.872	-0.320	-0.320	0.000	0.000	0.000	0.000
142	A	375	VAL	0	0.010	0.010	23.705	-0.026	-0.026	0.000	0.000	0.000	0.000
143	A	376	VAL	0	0.000	0.002	20.708	-0.038	-0.038	0.000	0.000	0.000	0.000
144	A	377	ARG	1	0.912	0.964	20.056	0.262	0.262	0.000	0.000	0.000	0.000
145	A	378	TYR	0	-0.035	-0.032	19.534	-0.057	-0.057	0.000	0.000	0.000	0.000
146	A	379	PHE	0	0.017	0.007	15.480	-0.054	-0.054	0.000	0.000	0.000	0.000
147	A	380	TRP	0	-0.024	-0.040	13.146	-0.100	-0.100	0.000	0.000	0.000	0.000
148	A	381	HIS	0	0.033	0.023	14.531	-0.096	-0.096	0.000	0.000	0.000	0.000
149	A	382	SER	0	-0.029	-0.004	14.882	-0.106	-0.106	0.000	0.000	0.000	0.000
150	A	383	LEU	0	0.012	0.001	10.692	-0.084	-0.084	0.000	0.000	0.000	0.000
151	A	384	GLU	-1	-0.842	-0.935	10.433	-1.063	-1.063	0.000	0.000	0.000	0.000
152	A	385	LYS	1	0.921	0.964	10.129	0.406	0.406	0.000	0.000	0.000	0.000
153	A	386	GLU	-1	-0.883	-0.937	8.651	-1.330	-1.330	0.000	0.000	0.000	0.000
154	A	387	LEU	0	-0.029	-0.017	5.600	-0.392	-0.392	0.000	0.000	0.000	0.000
155	A	388	ILE	0	-0.010	-0.010	5.663	-0.931	-0.931	0.000	0.000	0.000	0.000
156	A	389	SER	0	-0.066	-0.029	6.888	-0.092	-0.092	0.000	0.000	0.000	0.000
157	A	390	ARG	1	0.889	0.953	3.882	1.821	2.022	0.000	-0.025	-0.176	0.000
158	A	391	GLY	0	0.013	0.008	2.966	-4.544	-2.492	0.339	-0.984	-1.407	-0.009
159	A	392	TYR	0	-0.052	-0.028	2.755	-6.130	-2.540	4.511	-2.238	-5.864	-0.026
160	A	393	ARG	1	0.989	0.992	3.745	1.827	2.106	0.007	0.016	-0.302	0.000

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