FMO DATABASE

FMODB ID: GNLR1

Calculation Name: 3W6K-B-Xray318

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3W6K

Chain ID: B

ChEMBL ID:
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UniProt ID: A0A0E0

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	84
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-483980.453748
FMO2-HF: Nuclear repulsion	453310.168298
FMO2-HF: Total energy	-30670.28545
FMO2-MP2: Total energy	-30761.461575

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(B:11:ACE )

Summations of interaction energy for fragment #1(B:11:ACE )

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.
3.028	3.948	-0.006	-0.397	-0.517	-0.001

Interaction energy analysis for fragmet #1(B:11:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.046 / q_NPA : 0.013

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

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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	B	13	ALA	0	0.008	0.000	3.794	0.689	1.609	-0.006	-0.397	-0.517	-0.001
4	B	14	LEU	0	0.108	0.064	6.324	0.224	0.224	0.000	0.000	0.000	0.000
5	B	15	LYS	1	0.910	0.971	5.520	2.160	2.160	0.000	0.000	0.000	0.000
6	B	16	PRO	0	0.038	0.024	7.537	0.117	0.117	0.000	0.000	0.000	0.000
7	B	17	ALA	0	0.077	0.034	10.558	0.080	0.080	0.000	0.000	0.000	0.000
8	B	18	LYS	1	0.909	0.939	11.598	0.690	0.690	0.000	0.000	0.000	0.000
9	B	19	ALA	0	-0.023	-0.009	12.834	0.049	0.049	0.000	0.000	0.000	0.000
10	B	20	ILE	0	-0.004	0.005	14.472	0.046	0.046	0.000	0.000	0.000	0.000
11	B	21	VAL	0	0.030	0.009	16.603	0.030	0.030	0.000	0.000	0.000	0.000
12	B	22	GLU	-1	-0.910	-0.954	17.508	-0.230	-0.230	0.000	0.000	0.000	0.000
13	B	23	ALA	0	-0.024	-0.017	18.653	0.025	0.025	0.000	0.000	0.000	0.000
14	B	24	LEU	0	-0.005	-0.008	20.490	0.020	0.020	0.000	0.000	0.000	0.000
15	B	25	LEU	0	-0.011	-0.013	22.184	0.013	0.013	0.000	0.000	0.000	0.000
16	B	26	PHE	0	-0.065	-0.037	23.271	0.012	0.012	0.000	0.000	0.000	0.000
17	B	27	ALA	0	-0.040	-0.025	24.796	0.010	0.010	0.000	0.000	0.000	0.000
18	B	28	ALA	0	-0.034	0.001	26.707	0.008	0.008	0.000	0.000	0.000	0.000
19	B	29	GLY	0	-0.002	0.014	28.571	0.007	0.007	0.000	0.000	0.000	0.000
20	B	30	ASP	-1	-0.957	-0.989	30.147	-0.075	-0.075	0.000	0.000	0.000	0.000
21	B	31	GLU	-1	-0.935	-0.978	32.716	-0.058	-0.058	0.000	0.000	0.000	0.000
22	B	32	GLY	0	-0.072	-0.013	28.923	-0.001	-0.001	0.000	0.000	0.000	0.000
23	B	33	LEU	0	0.004	-0.008	25.002	0.004	0.004	0.000	0.000	0.000	0.000
24	B	34	SER	0	0.039	0.025	27.720	-0.008	-0.008	0.000	0.000	0.000	0.000
25	B	35	LEU	0	0.015	-0.008	23.483	-0.006	-0.006	0.000	0.000	0.000	0.000
26	B	36	SER	0	-0.002	-0.015	25.118	-0.003	-0.003	0.000	0.000	0.000	0.000
27	B	37	GLN	0	0.014	0.021	26.345	-0.002	-0.002	0.000	0.000	0.000	0.000
28	B	38	ILE	0	0.011	0.016	20.958	-0.002	-0.002	0.000	0.000	0.000	0.000
29	B	39	ALA	0	0.000	-0.010	21.600	-0.006	-0.006	0.000	0.000	0.000	0.000
30	B	40	ALA	0	-0.017	-0.006	22.214	0.003	0.003	0.000	0.000	0.000	0.000
31	B	41	VAL	0	-0.043	-0.023	21.089	0.005	0.005	0.000	0.000	0.000	0.000
32	B	42	LEU	0	-0.087	-0.051	17.168	-0.002	-0.002	0.000	0.000	0.000	0.000
33	B	43	GLU	-1	-0.972	-0.961	18.466	-0.045	-0.045	0.000	0.000	0.000	0.000
34	B	44	VAL	0	-0.060	-0.020	16.633	-0.002	-0.002	0.000	0.000	0.000	0.000
35	B	45	SER	0	-0.029	-0.042	19.820	0.007	0.007	0.000	0.000	0.000	0.000
36	B	46	GLU	-1	-0.808	-0.920	21.375	-0.100	-0.100	0.000	0.000	0.000	0.000
37	B	47	LEU	0	-0.021	-0.010	20.889	-0.012	-0.012	0.000	0.000	0.000	0.000
38	B	48	GLU	-1	-0.846	-0.907	16.898	-0.157	-0.157	0.000	0.000	0.000	0.000
39	B	49	ALA	0	0.042	0.023	17.871	-0.033	-0.033	0.000	0.000	0.000	0.000
40	B	50	LYS	1	0.915	0.971	19.545	0.120	0.120	0.000	0.000	0.000	0.000
41	B	51	ALA	0	0.019	0.013	16.708	-0.011	-0.011	0.000	0.000	0.000	0.000
42	B	52	VAL	0	-0.026	-0.009	14.276	-0.042	-0.042	0.000	0.000	0.000	0.000
43	B	53	ILE	0	-0.010	-0.013	16.471	-0.018	-0.018	0.000	0.000	0.000	0.000
44	B	54	GLU	-1	-0.906	-0.970	19.713	-0.179	-0.179	0.000	0.000	0.000	0.000
45	B	55	GLU	-1	-0.962	-0.966	13.380	-0.467	-0.467	0.000	0.000	0.000	0.000
46	B	56	LEU	0	-0.010	-0.008	16.818	-0.012	-0.012	0.000	0.000	0.000	0.000
47	B	57	GLN	0	-0.035	-0.012	17.591	0.017	0.017	0.000	0.000	0.000	0.000
48	B	58	GLN	0	0.034	0.028	18.035	0.032	0.032	0.000	0.000	0.000	0.000
49	B	59	ASP	-1	-0.855	-0.933	14.803	-0.457	-0.457	0.000	0.000	0.000	0.000
50	B	60	CYS	0	-0.048	-0.019	18.086	0.023	0.023	0.000	0.000	0.000	0.000
51	B	61	ARG	1	0.857	0.922	21.328	0.205	0.205	0.000	0.000	0.000	0.000
52	B	62	ARG	1	0.944	0.983	17.201	0.317	0.317	0.000	0.000	0.000	0.000
53	B	63	GLU	-1	-0.926	-0.975	22.210	-0.109	-0.109	0.000	0.000	0.000	0.000
54	B	64	GLU	-1	-0.944	-0.960	19.224	-0.214	-0.214	0.000	0.000	0.000	0.000
55	B	65	ARG	1	0.844	0.940	18.513	0.233	0.233	0.000	0.000	0.000	0.000
56	B	66	GLY	0	0.044	0.009	23.387	0.010	0.010	0.000	0.000	0.000	0.000
57	B	67	ILE	0	-0.058	-0.036	22.695	0.012	0.012	0.000	0.000	0.000	0.000
58	B	68	GLN	0	-0.032	-0.027	24.472	-0.016	-0.016	0.000	0.000	0.000	0.000
59	B	69	LEU	0	0.034	0.021	21.612	0.006	0.006	0.000	0.000	0.000	0.000
60	B	70	VAL	0	-0.041	-0.028	25.111	-0.001	-0.001	0.000	0.000	0.000	0.000
61	B	71	GLU	-1	-0.909	-0.961	27.998	-0.112	-0.112	0.000	0.000	0.000	0.000
62	B	72	LEU	0	-0.032	-0.021	29.609	0.006	0.006	0.000	0.000	0.000	0.000
63	B	73	GLY	0	-0.003	-0.001	33.259	0.001	0.001	0.000	0.000	0.000	0.000
64	B	74	GLY	0	-0.004	0.005	32.090	0.002	0.002	0.000	0.000	0.000	0.000
65	B	75	VAL	0	-0.010	0.001	29.900	-0.001	-0.001	0.000	0.000	0.000	0.000
66	B	76	PHE	0	-0.026	-0.030	25.570	-0.005	-0.005	0.000	0.000	0.000	0.000
67	B	77	LEU	0	0.055	0.028	27.436	0.003	0.003	0.000	0.000	0.000	0.000
68	B	78	LEU	0	0.002	0.008	22.697	-0.008	-0.008	0.000	0.000	0.000	0.000
69	B	79	ALA	0	0.022	0.011	26.791	0.012	0.012	0.000	0.000	0.000	0.000
70	B	80	THR	0	0.037	0.014	28.433	-0.007	-0.007	0.000	0.000	0.000	0.000
71	B	81	LYS	1	0.873	0.960	24.612	0.157	0.157	0.000	0.000	0.000	0.000
72	B	82	LYS	1	0.896	0.937	30.707	0.090	0.090	0.000	0.000	0.000	0.000
73	B	83	GLU	-1	-0.876	-0.937	30.221	-0.098	-0.098	0.000	0.000	0.000	0.000
74	B	84	HIS	0	0.030	0.016	28.717	0.005	0.005	0.000	0.000	0.000	0.000
75	B	85	ALA	0	0.017	0.003	34.229	0.003	0.003	0.000	0.000	0.000	0.000
76	B	86	PRO	0	-0.055	-0.042	37.206	0.004	0.004	0.000	0.000	0.000	0.000
77	B	87	TYR	0	0.022	0.005	35.595	0.004	0.004	0.000	0.000	0.000	0.000
78	B	88	LEU	0	0.007	0.007	33.632	0.001	0.001	0.000	0.000	0.000	0.000
79	B	89	LYS	1	0.975	0.987	37.580	0.054	0.054	0.000	0.000	0.000	0.000
80	B	90	LYS	1	0.925	0.978	40.080	0.048	0.048	0.000	0.000	0.000	0.000
81	B	91	LEU	0	-0.034	-0.006	35.905	0.000	0.000	0.000	0.000	0.000	0.000
82	B	92	VAL	0	-0.014	-0.012	40.102	0.002	0.002	0.000	0.000	0.000	0.000
83	B	93	GLU	-1	-0.996	-0.997	42.672	-0.039	-0.039	0.000	0.000	0.000	0.000
84	B	94	NME	0	-0.003	0.015	44.417	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:11:ACE )