FMO DATABASE

FMODB ID: 5J27Z

Calculation Name: 3GRC-A-Xray372

Preferred Name:
Warning: Undefined array key "pref_name" in /home/FMODBwui_src/fmodbwui/detail.php on line 446

Target Type:
Warning: Undefined array key "target_type" in /home/FMODBwui_src/fmodbwui/detail.php on line 447

Ligand Name:
Warning: Undefined variable $Ligand in /home/FMODBwui_src/fmodbwui/detail.php on line 448

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 448

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 448

ligand 3-letter code:
Warning: Undefined variable $Ligand in /home/FMODBwui_src/fmodbwui/detail.php on line 449

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 449

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 449

PDB ID: 3GRC

Chain ID: A

ChEMBL ID:
Warning: Undefined array key "chembl_id" in /home/FMODBwui_src/fmodbwui/detail.php on line 452

Warning: Undefined array key "chembl_id" in /home/FMODBwui_src/fmodbwui/detail.php on line 452

UniProt ID: Q121U0

Base Structure: X-ray

Registration Date: 2023-09-21

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	125
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1091395.642682
FMO2-HF: Nuclear repulsion	1042114.679612
FMO2-HF: Total energy	-49280.96307
FMO2-MP2: Total energy	-49423.529233

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:546:PRO)

Summations of interaction energy for fragment #1(A:546: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.
-15.985	-8.869	10.703	-7.168	-10.651	-0.052

Interaction energy analysis for fragmet #1(A:546:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : -0.007

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	548	PRO	0	0.007	0.023	3.587	-4.433	-0.778	-0.028	-1.979	-1.648	0.001
4	A	549	ARG	1	0.806	0.874	4.888	1.941	1.941	0.000	0.000	0.000	0.000
5	A	550	ILE	0	-0.005	-0.001	6.483	-0.147	-0.147	0.000	0.000	0.000	0.000
6	A	551	LEU	0	-0.028	-0.011	8.942	-0.175	-0.175	0.000	0.000	0.000	0.000
7	A	552	ILE	0	-0.019	-0.005	9.826	0.030	0.030	0.000	0.000	0.000	0.000
8	A	553	CYS	0	-0.039	-0.013	13.499	-0.027	-0.027	0.000	0.000	0.000	0.000
9	A	554	GLU	-1	-0.810	-0.907	16.921	-0.041	-0.041	0.000	0.000	0.000	0.000
10	A	555	ASP	-1	-0.887	-0.940	18.747	-0.074	-0.074	0.000	0.000	0.000	0.000
11	A	556	ASP	-1	-0.830	-0.904	20.343	-0.112	-0.112	0.000	0.000	0.000	0.000
12	A	557	PRO	0	0.007	-0.020	18.816	-0.014	-0.014	0.000	0.000	0.000	0.000
13	A	558	ASP	-1	-0.904	-0.937	17.349	-0.182	-0.182	0.000	0.000	0.000	0.000
14	A	559	ILE	0	-0.049	-0.037	16.482	-0.025	-0.025	0.000	0.000	0.000	0.000
15	A	560	ALA	0	0.025	0.023	14.877	-0.012	-0.012	0.000	0.000	0.000	0.000
16	A	561	ARG	1	0.914	0.934	8.942	0.554	0.554	0.000	0.000	0.000	0.000
17	A	562	LEU	0	-0.022	-0.005	11.777	-0.075	-0.075	0.000	0.000	0.000	0.000
18	A	563	LEU	0	0.043	0.017	11.398	-0.032	-0.032	0.000	0.000	0.000	0.000
19	A	564	ASN	0	0.007	-0.004	7.589	0.019	0.019	0.000	0.000	0.000	0.000
20	A	565	LEU	0	-0.062	-0.028	7.009	-0.230	-0.230	0.000	0.000	0.000	0.000
21	A	566	MET	0	0.002	0.004	7.570	-0.103	-0.103	0.000	0.000	0.000	0.000
22	A	567	LEU	0	-0.024	-0.012	5.793	0.045	0.045	0.000	0.000	0.000	0.000
23	A	568	GLU	-1	-0.882	-0.921	3.039	-1.770	-1.276	0.056	-0.169	-0.381	0.000
24	A	569	LYS	1	0.800	0.882	3.678	-0.298	0.289	0.010	-0.188	-0.409	-0.001
25	A	570	GLY	0	0.006	0.008	6.009	0.140	0.140	0.000	0.000	0.000	0.000
26	A	571	GLY	0	-0.039	-0.015	2.320	-0.255	0.138	0.936	-0.596	-0.733	-0.002
27	A	572	PHE	0	-0.045	-0.033	3.019	2.195	3.641	0.488	-0.417	-1.517	-0.006
28	A	573	ASP	-1	-0.777	-0.865	1.965	-13.798	-12.988	9.098	-4.280	-5.628	-0.045
29	A	574	SER	0	0.016	0.000	2.995	0.854	0.585	0.143	0.461	-0.335	0.001
30	A	575	ASP	-1	-0.820	-0.865	6.695	-0.548	-0.548	0.000	0.000	0.000	0.000
31	A	576	MET	0	-0.012	-0.001	10.104	0.060	0.060	0.000	0.000	0.000	0.000
32	A	577	VAL	0	-0.043	-0.018	13.366	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	578	HIS	0	0.055	0.019	16.979	0.012	0.012	0.000	0.000	0.000	0.000
34	A	579	SER	0	-0.025	-0.027	20.258	0.008	0.008	0.000	0.000	0.000	0.000
35	A	580	ALA	0	0.062	0.012	21.185	0.001	0.001	0.000	0.000	0.000	0.000
36	A	581	ALA	0	0.001	-0.004	22.573	0.006	0.006	0.000	0.000	0.000	0.000
37	A	582	GLN	0	0.007	-0.002	19.585	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	583	ALA	0	0.021	0.009	18.014	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	584	LEU	0	-0.026	-0.023	18.711	0.013	0.013	0.000	0.000	0.000	0.000
40	A	585	GLU	-1	-0.912	-0.928	20.406	-0.061	-0.061	0.000	0.000	0.000	0.000
41	A	586	GLN	0	-0.007	-0.030	13.189	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	587	VAL	0	-0.027	-0.022	15.650	0.007	0.007	0.000	0.000	0.000	0.000
43	A	588	ALA	0	-0.033	-0.007	16.727	0.021	0.021	0.000	0.000	0.000	0.000
44	A	589	ARG	1	0.824	0.910	16.782	0.097	0.097	0.000	0.000	0.000	0.000
45	A	590	ARG	1	0.819	0.914	9.126	0.242	0.242	0.000	0.000	0.000	0.000
46	A	591	PRO	0	0.000	-0.002	12.233	0.012	0.012	0.000	0.000	0.000	0.000
47	A	592	TYR	0	-0.038	-0.033	9.878	-0.013	-0.013	0.000	0.000	0.000	0.000
48	A	593	ALA	0	-0.024	-0.004	9.592	-0.016	-0.016	0.000	0.000	0.000	0.000
49	A	594	ALA	0	0.029	0.001	11.173	-0.048	-0.048	0.000	0.000	0.000	0.000
50	A	595	MET	0	-0.043	-0.012	12.015	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	596	THR	0	-0.012	0.004	12.534	0.003	0.003	0.000	0.000	0.000	0.000
52	A	597	VAL	0	-0.001	-0.003	15.029	-0.028	-0.028	0.000	0.000	0.000	0.000
53	A	598	ASP	-1	-0.699	-0.814	18.551	-0.015	-0.015	0.000	0.000	0.000	0.000
54	A	599	LEU	0	-0.039	-0.034	20.788	0.005	0.005	0.000	0.000	0.000	0.000
55	A	600	ASN	0	-0.053	-0.033	24.420	0.007	0.007	0.000	0.000	0.000	0.000
56	A	601	LEU	0	-0.006	0.000	20.925	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	602	PRO	0	0.020	0.022	24.508	0.005	0.005	0.000	0.000	0.000	0.000
58	A	603	ASP	-1	-0.819	-0.867	25.561	-0.027	-0.027	0.000	0.000	0.000	0.000
59	A	604	GLN	0	-0.089	-0.067	26.575	0.003	0.003	0.000	0.000	0.000	0.000
60	A	605	ASP	-1	-0.757	-0.862	26.215	0.009	0.009	0.000	0.000	0.000	0.000
61	A	606	GLY	0	0.036	-0.001	23.854	0.003	0.003	0.000	0.000	0.000	0.000
62	A	607	VAL	0	-0.010	-0.004	24.433	0.011	0.011	0.000	0.000	0.000	0.000
63	A	608	SER	0	-0.032	-0.010	27.039	0.007	0.007	0.000	0.000	0.000	0.000
64	A	609	LEU	0	0.009	0.013	20.372	0.003	0.003	0.000	0.000	0.000	0.000
65	A	610	ILE	0	0.026	0.009	21.516	0.007	0.007	0.000	0.000	0.000	0.000
66	A	611	ARG	1	0.861	0.927	23.869	-0.033	-0.033	0.000	0.000	0.000	0.000
67	A	612	ALA	0	-0.056	-0.020	25.517	0.001	0.001	0.000	0.000	0.000	0.000
68	A	613	LEU	0	0.037	0.018	19.644	0.003	0.003	0.000	0.000	0.000	0.000
69	A	614	ARG	1	0.761	0.873	20.151	-0.123	-0.123	0.000	0.000	0.000	0.000
70	A	615	ARG	1	0.889	0.944	25.347	-0.034	-0.034	0.000	0.000	0.000	0.000
71	A	616	ASP	-1	-0.791	-0.865	24.402	0.047	0.047	0.000	0.000	0.000	0.000
72	A	617	SER	0	-0.042	-0.027	24.575	0.009	0.009	0.000	0.000	0.000	0.000
73	A	618	ARG	1	0.847	0.903	20.768	-0.034	-0.034	0.000	0.000	0.000	0.000
74	A	619	THR	0	-0.007	-0.023	18.806	0.010	0.010	0.000	0.000	0.000	0.000
75	A	620	ARG	1	0.763	0.859	20.899	-0.101	-0.101	0.000	0.000	0.000	0.000
76	A	621	ASP	-1	-0.776	-0.858	20.832	0.135	0.135	0.000	0.000	0.000	0.000
77	A	622	LEU	0	-0.032	0.008	14.323	0.027	0.027	0.000	0.000	0.000	0.000
78	A	623	ALA	0	0.063	0.040	15.038	-0.028	-0.028	0.000	0.000	0.000	0.000
79	A	624	ILE	0	0.014	-0.007	15.925	0.005	0.005	0.000	0.000	0.000	0.000
80	A	625	VAL	0	-0.028	-0.009	15.487	0.002	0.002	0.000	0.000	0.000	0.000
81	A	626	VAL	0	0.018	0.020	17.373	-0.013	-0.013	0.000	0.000	0.000	0.000
82	A	627	VAL	0	-0.012	-0.018	15.412	0.006	0.006	0.000	0.000	0.000	0.000
83	A	628	SER	0	-0.032	-0.048	18.832	-0.014	-0.014	0.000	0.000	0.000	0.000
84	A	629	ALA	0	-0.007	-0.003	21.999	0.005	0.005	0.000	0.000	0.000	0.000
85	A	630	ASN	0	-0.012	-0.003	24.953	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	631	ALA	0	0.023	0.010	23.125	0.004	0.004	0.000	0.000	0.000	0.000
87	A	632	ARG	1	0.879	0.942	25.165	-0.015	-0.015	0.000	0.000	0.000	0.000
88	A	633	GLU	-1	-0.830	-0.915	27.857	0.012	0.012	0.000	0.000	0.000	0.000
89	A	634	GLY	0	0.049	0.016	27.778	0.001	0.001	0.000	0.000	0.000	0.000
90	A	635	GLU	-1	-0.898	-0.948	26.509	0.068	0.068	0.000	0.000	0.000	0.000
91	A	636	LEU	0	-0.054	-0.036	28.359	0.002	0.002	0.000	0.000	0.000	0.000
92	A	637	GLU	-1	-0.962	-0.967	31.839	0.014	0.014	0.000	0.000	0.000	0.000
93	A	638	PHE	0	-0.021	-0.014	29.518	0.001	0.001	0.000	0.000	0.000	0.000
94	A	639	ASN	0	-0.010	-0.010	26.259	0.006	0.006	0.000	0.000	0.000	0.000
95	A	640	SER	0	-0.039	-0.034	28.714	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	641	GLN	0	0.026	0.011	28.482	0.008	0.008	0.000	0.000	0.000	0.000
97	A	642	PRO	0	-0.035	-0.026	28.014	0.006	0.006	0.000	0.000	0.000	0.000
98	A	643	LEU	0	0.002	0.009	25.411	0.001	0.001	0.000	0.000	0.000	0.000
99	A	644	ALA	0	-0.004	0.008	23.854	0.005	0.005	0.000	0.000	0.000	0.000
100	A	645	VAL	0	0.019	0.037	20.800	0.016	0.016	0.000	0.000	0.000	0.000
101	A	646	SER	0	-0.010	-0.007	18.632	0.000	0.000	0.000	0.000	0.000	0.000
102	A	647	THR	0	-0.002	-0.025	18.390	0.002	0.002	0.000	0.000	0.000	0.000
103	A	648	TRP	0	0.005	0.013	20.401	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	649	LEU	0	-0.051	-0.023	16.558	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	650	GLU	-1	-0.809	-0.902	20.721	0.011	0.011	0.000	0.000	0.000	0.000
106	A	651	LYS	1	0.756	0.860	18.947	0.041	0.041	0.000	0.000	0.000	0.000
107	A	652	PRO	0	-0.019	-0.019	21.072	0.000	0.000	0.000	0.000	0.000	0.000
108	A	653	ILE	0	0.025	0.011	15.150	0.011	0.011	0.000	0.000	0.000	0.000
109	A	654	ASP	-1	-0.791	-0.884	17.436	0.018	0.018	0.000	0.000	0.000	0.000
110	A	655	GLU	-1	-0.863	-0.951	10.755	-0.162	-0.162	0.000	0.000	0.000	0.000
111	A	656	ASN	0	-0.079	-0.052	12.982	0.037	0.037	0.000	0.000	0.000	0.000
112	A	657	LEU	0	0.007	-0.005	14.668	0.040	0.040	0.000	0.000	0.000	0.000
113	A	658	LEU	0	0.026	0.031	11.433	0.029	0.029	0.000	0.000	0.000	0.000
114	A	659	ILE	0	0.002	0.005	8.010	0.072	0.072	0.000	0.000	0.000	0.000
115	A	660	LEU	0	-0.035	-0.015	11.224	0.090	0.090	0.000	0.000	0.000	0.000
116	A	661	SER	0	-0.039	-0.036	14.254	0.019	0.019	0.000	0.000	0.000	0.000
117	A	662	LEU	0	-0.004	0.003	9.981	0.007	0.007	0.000	0.000	0.000	0.000
118	A	663	HIS	0	0.011	0.012	7.736	0.034	0.034	0.000	0.000	0.000	0.000
119	A	664	ARG	1	0.949	0.974	12.614	-0.231	-0.231	0.000	0.000	0.000	0.000
120	A	665	ALA	0	0.007	0.011	15.191	-0.019	-0.019	0.000	0.000	0.000	0.000
121	A	666	ILE	0	-0.028	-0.019	10.463	0.003	0.003	0.000	0.000	0.000	0.000
122	A	667	ASP	-1	-0.908	-0.949	14.660	0.405	0.405	0.000	0.000	0.000	0.000
123	A	668	ASN	0	-0.133	-0.058	16.466	-0.043	-0.043	0.000	0.000	0.000	0.000
124	A	669	MET	0	-0.008	0.001	18.230	-0.034	-0.034	0.000	0.000	0.000	0.000
125	A	670	ALA	0	-0.117	-0.051	16.401	-0.040	-0.040	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:546:PRO)