FMO DATABASE

FMODB ID: ZVGGN

Calculation Name: 1YA9-A-Xray372

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: 1YA9

Chain ID: A

ChEMBL ID:
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UniProt ID: P08226

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	174
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1737589.186999
FMO2-HF: Nuclear repulsion	1666196.869691
FMO2-HF: Total energy	-71392.317308
FMO2-MP2: Total energy	-71599.786179

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:4:PRO)

Summations of interaction energy for fragment #1(A:4: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.
-2.523	0.591	0.006	-1.381	-1.738	0.002

Interaction energy analysis for fragmet #1(A:4:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.001

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	6	VAL	0	-0.035	-0.017	3.254	-1.188	1.664	0.007	-1.348	-1.510	0.002
4	A	7	THR	0	0.010	0.007	4.273	-0.402	-0.140	-0.001	-0.033	-0.228	0.000
5	A	8	ASP	-1	-0.934	-0.960	6.092	0.501	0.501	0.000	0.000	0.000	0.000
6	A	9	GLN	0	-0.047	-0.031	8.196	0.047	0.047	0.000	0.000	0.000	0.000
7	A	10	LEU	0	0.007	0.012	11.883	0.036	0.036	0.000	0.000	0.000	0.000
8	A	11	GLU	-1	-0.850	-0.917	14.028	-0.112	-0.112	0.000	0.000	0.000	0.000
9	A	12	TRP	0	-0.054	-0.050	15.566	-0.028	-0.028	0.000	0.000	0.000	0.000
10	A	13	GLN	0	0.027	0.009	10.333	-0.047	-0.047	0.000	0.000	0.000	0.000
11	A	14	SER	0	0.073	0.026	11.992	-0.012	-0.012	0.000	0.000	0.000	0.000
12	A	15	ASN	0	-0.101	-0.066	13.099	-0.058	-0.058	0.000	0.000	0.000	0.000
13	A	16	GLN	0	-0.011	0.000	10.008	0.054	0.054	0.000	0.000	0.000	0.000
14	A	17	PRO	0	0.093	0.049	7.415	0.120	0.120	0.000	0.000	0.000	0.000
15	A	18	TRP	0	0.056	0.006	8.770	0.049	0.049	0.000	0.000	0.000	0.000
16	A	19	GLU	-1	-0.853	-0.890	11.776	0.119	0.119	0.000	0.000	0.000	0.000
17	A	20	GLN	0	-0.026	-0.021	7.196	0.073	0.073	0.000	0.000	0.000	0.000
18	A	21	ALA	0	-0.003	0.020	9.464	0.087	0.087	0.000	0.000	0.000	0.000
19	A	22	LEU	0	0.011	0.002	10.453	0.037	0.037	0.000	0.000	0.000	0.000
20	A	23	ASN	0	0.001	-0.010	11.999	-0.037	-0.037	0.000	0.000	0.000	0.000
21	A	24	ARG	1	1.007	1.015	5.814	-0.369	-0.369	0.000	0.000	0.000	0.000
22	A	25	PHE	0	-0.008	-0.002	12.090	-0.011	-0.011	0.000	0.000	0.000	0.000
23	A	26	TRP	0	0.016	-0.012	14.909	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	27	ASP	-1	-0.892	-0.957	14.184	0.374	0.374	0.000	0.000	0.000	0.000
25	A	28	TYR	0	-0.004	-0.004	14.525	-0.022	-0.022	0.000	0.000	0.000	0.000
26	A	29	LEU	0	0.031	0.005	16.729	-0.018	-0.018	0.000	0.000	0.000	0.000
27	A	30	ARG	1	0.766	0.889	18.055	-0.282	-0.282	0.000	0.000	0.000	0.000
28	A	31	TRP	0	0.024	0.029	19.241	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	32	VAL	0	0.073	0.043	20.404	-0.016	-0.016	0.000	0.000	0.000	0.000
30	A	33	GLN	0	-0.090	-0.061	22.865	-0.012	-0.012	0.000	0.000	0.000	0.000
31	A	34	THR	0	-0.070	-0.048	24.703	-0.010	-0.010	0.000	0.000	0.000	0.000
32	A	35	LEU	0	-0.055	-0.028	26.361	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	36	SER	0	0.043	0.026	25.746	-0.011	-0.011	0.000	0.000	0.000	0.000
34	A	37	ASP	-1	-0.853	-0.926	28.498	0.083	0.083	0.000	0.000	0.000	0.000
35	A	38	GLN	0	-0.064	-0.050	21.378	0.001	0.001	0.000	0.000	0.000	0.000
36	A	39	VAL	0	-0.053	-0.014	23.140	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	40	GLN	0	-0.047	-0.041	25.127	-0.017	-0.017	0.000	0.000	0.000	0.000
38	A	41	GLU	-1	-0.857	-0.924	27.351	0.049	0.049	0.000	0.000	0.000	0.000
39	A	42	GLU	-1	-0.825	-0.919	21.124	0.123	0.123	0.000	0.000	0.000	0.000
40	A	43	LEU	0	-0.077	-0.034	23.753	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	44	GLN	0	-0.086	-0.035	25.474	-0.018	-0.018	0.000	0.000	0.000	0.000
42	A	45	SER	0	0.070	0.048	23.607	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	46	SER	0	-0.140	-0.091	23.647	-0.011	-0.011	0.000	0.000	0.000	0.000
44	A	47	GLN	0	0.090	0.071	17.838	-0.029	-0.029	0.000	0.000	0.000	0.000
45	A	48	VAL	0	0.036	0.024	18.629	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	49	THR	0	0.001	-0.016	19.047	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	50	GLN	0	-0.037	0.001	17.946	-0.008	-0.008	0.000	0.000	0.000	0.000
48	A	51	GLU	-1	-0.801	-0.901	14.724	0.092	0.092	0.000	0.000	0.000	0.000
49	A	52	LEU	0	-0.043	-0.026	14.615	-0.010	-0.010	0.000	0.000	0.000	0.000
50	A	53	THR	0	0.007	-0.019	16.371	-0.012	-0.012	0.000	0.000	0.000	0.000
51	A	54	ALA	0	0.036	0.030	12.103	-0.026	-0.026	0.000	0.000	0.000	0.000
52	A	55	LEU	0	0.002	0.011	10.527	-0.033	-0.033	0.000	0.000	0.000	0.000
53	A	56	MET	0	-0.055	-0.029	12.873	-0.009	-0.009	0.000	0.000	0.000	0.000
54	A	57	GLU	-1	-0.947	-0.978	14.287	-0.239	-0.239	0.000	0.000	0.000	0.000
55	A	58	ASP	-1	-0.891	-0.941	8.177	-0.598	-0.598	0.000	0.000	0.000	0.000
56	A	59	THR	0	-0.032	-0.019	11.492	-0.017	-0.017	0.000	0.000	0.000	0.000
57	A	60	MET	0	-0.061	-0.034	13.189	-0.014	-0.014	0.000	0.000	0.000	0.000
58	A	61	THR	0	-0.018	-0.008	11.241	0.014	0.014	0.000	0.000	0.000	0.000
59	A	62	GLU	-1	-0.834	-0.911	7.734	-0.865	-0.865	0.000	0.000	0.000	0.000
60	A	63	VAL	0	-0.101	-0.049	11.727	0.032	0.032	0.000	0.000	0.000	0.000
61	A	64	LYS	1	0.837	0.919	15.307	0.235	0.235	0.000	0.000	0.000	0.000
62	A	65	ALA	0	0.045	0.026	12.316	0.021	0.021	0.000	0.000	0.000	0.000
63	A	66	TYR	0	0.092	0.050	13.881	0.038	0.038	0.000	0.000	0.000	0.000
64	A	67	LYS	1	0.790	0.895	15.257	0.205	0.205	0.000	0.000	0.000	0.000
65	A	68	LYS	1	0.909	0.938	17.690	0.277	0.277	0.000	0.000	0.000	0.000
66	A	69	GLU	-1	-0.806	-0.887	14.120	-0.310	-0.310	0.000	0.000	0.000	0.000
67	A	70	LEU	0	-0.031	-0.033	17.792	0.027	0.027	0.000	0.000	0.000	0.000
68	A	71	GLU	-1	-0.958	-0.985	20.359	-0.149	-0.149	0.000	0.000	0.000	0.000
69	A	72	GLU	-1	-0.984	-0.993	19.257	-0.278	-0.278	0.000	0.000	0.000	0.000
70	A	73	GLN	0	-0.055	-0.010	17.597	0.034	0.034	0.000	0.000	0.000	0.000
71	A	74	LEU	0	-0.039	0.017	22.853	0.019	0.019	0.000	0.000	0.000	0.000
72	A	75	GLY	0	-0.058	-0.018	25.795	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	76	PRO	0	0.033	-0.004	28.993	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	77	VAL	0	-0.007	-0.013	30.007	0.006	0.006	0.000	0.000	0.000	0.000
75	A	78	ALA	0	0.026	0.014	32.873	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	79	GLU	-1	-0.896	-0.950	33.302	-0.083	-0.083	0.000	0.000	0.000	0.000
77	A	80	GLU	-1	-0.851	-0.936	33.188	-0.063	-0.063	0.000	0.000	0.000	0.000
78	A	81	THR	0	-0.043	-0.042	31.665	0.004	0.004	0.000	0.000	0.000	0.000
79	A	82	ARG	1	0.999	1.023	27.626	0.116	0.116	0.000	0.000	0.000	0.000
80	A	83	ALA	0	-0.001	0.005	28.873	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	84	ARG	1	0.898	0.939	30.457	0.044	0.044	0.000	0.000	0.000	0.000
82	A	85	LEU	0	0.071	0.036	27.369	0.003	0.003	0.000	0.000	0.000	0.000
83	A	86	GLY	0	0.017	0.022	25.721	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	87	LYS	1	0.899	0.939	26.167	0.072	0.072	0.000	0.000	0.000	0.000
85	A	88	GLU	-1	-0.942	-0.976	28.242	-0.042	-0.042	0.000	0.000	0.000	0.000
86	A	89	VAL	0	0.043	0.030	21.693	0.005	0.005	0.000	0.000	0.000	0.000
87	A	90	GLN	0	-0.060	-0.013	23.721	0.005	0.005	0.000	0.000	0.000	0.000
88	A	91	ALA	0	0.029	-0.002	25.018	0.001	0.001	0.000	0.000	0.000	0.000
89	A	92	ALA	0	-0.042	-0.025	24.237	0.006	0.006	0.000	0.000	0.000	0.000
90	A	93	GLN	0	0.064	0.020	19.136	-0.009	-0.009	0.000	0.000	0.000	0.000
91	A	94	ALA	0	-0.012	0.012	22.162	0.002	0.002	0.000	0.000	0.000	0.000
92	A	95	ARG	1	0.925	0.960	24.704	0.031	0.031	0.000	0.000	0.000	0.000
93	A	96	LEU	0	0.041	0.024	18.285	0.008	0.008	0.000	0.000	0.000	0.000
94	A	97	GLY	0	0.040	0.017	21.252	0.007	0.007	0.000	0.000	0.000	0.000
95	A	98	ALA	0	0.046	0.017	22.161	0.005	0.005	0.000	0.000	0.000	0.000
96	A	99	ASH	0	-0.109	-0.108	23.731	0.008	0.008	0.000	0.000	0.000	0.000
97	A	100	MET	0	-0.045	-0.020	16.752	0.005	0.005	0.000	0.000	0.000	0.000
98	A	101	GLU	-1	-0.934	-0.966	21.935	-0.055	-0.055	0.000	0.000	0.000	0.000
99	A	102	ASP	-1	-0.952	-0.968	24.066	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	103	LEU	0	-0.030	-0.025	22.090	0.008	0.008	0.000	0.000	0.000	0.000
101	A	104	ARG	1	0.950	0.957	20.683	0.066	0.066	0.000	0.000	0.000	0.000
102	A	105	ASN	0	0.028	0.012	23.494	0.000	0.000	0.000	0.000	0.000	0.000
103	A	106	ARG	1	0.866	0.938	27.005	-0.022	-0.022	0.000	0.000	0.000	0.000
104	A	107	LEU	0	-0.007	-0.014	23.069	0.003	0.003	0.000	0.000	0.000	0.000
105	A	108	GLY	0	0.037	0.034	26.849	0.002	0.002	0.000	0.000	0.000	0.000
106	A	109	GLN	0	-0.059	-0.035	27.966	0.002	0.002	0.000	0.000	0.000	0.000
107	A	110	TYR	0	0.019	0.017	29.289	0.001	0.001	0.000	0.000	0.000	0.000
108	A	111	ARG	1	0.952	0.988	24.541	0.000	0.000	0.000	0.000	0.000	0.000
109	A	112	ASN	0	0.007	-0.020	30.331	0.000	0.000	0.000	0.000	0.000	0.000
110	A	113	GLU	-1	-0.876	-0.944	33.127	0.020	0.020	0.000	0.000	0.000	0.000
111	A	114	VAL	0	0.020	0.021	32.642	0.000	0.000	0.000	0.000	0.000	0.000
112	A	115	HIS	0	0.023	0.015	30.510	0.001	0.001	0.000	0.000	0.000	0.000
113	A	116	THR	0	-0.095	-0.046	35.417	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	117	MET	0	-0.058	-0.019	37.981	0.000	0.000	0.000	0.000	0.000	0.000
115	A	118	LEU	0	-0.052	-0.027	38.064	0.002	0.002	0.000	0.000	0.000	0.000
116	A	119	GLY	0	0.029	0.009	34.769	0.001	0.001	0.000	0.000	0.000	0.000
117	A	120	GLN	0	-0.021	0.004	35.433	0.008	0.008	0.000	0.000	0.000	0.000
118	A	121	SER	0	0.028	0.007	33.942	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	122	THR	0	0.021	-0.008	36.276	0.001	0.001	0.000	0.000	0.000	0.000
120	A	123	GLU	-1	-0.884	-0.960	36.901	0.051	0.051	0.000	0.000	0.000	0.000
121	A	124	GLU	-1	-0.943	-0.960	37.812	0.028	0.028	0.000	0.000	0.000	0.000
122	A	125	ILE	0	-0.008	-0.016	35.202	0.001	0.001	0.000	0.000	0.000	0.000
123	A	126	ARG	1	0.977	1.015	32.619	-0.055	-0.055	0.000	0.000	0.000	0.000
124	A	127	ALA	0	0.015	0.026	33.167	0.004	0.004	0.000	0.000	0.000	0.000
125	A	128	ARG	1	0.930	0.952	34.899	-0.021	-0.021	0.000	0.000	0.000	0.000
126	A	129	LEU	0	-0.020	0.000	28.331	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	130	SER	0	0.028	0.016	30.072	0.002	0.002	0.000	0.000	0.000	0.000
128	A	131	THR	0	-0.031	-0.030	30.504	0.005	0.005	0.000	0.000	0.000	0.000
129	A	132	HIS	0	-0.027	-0.018	30.987	0.001	0.001	0.000	0.000	0.000	0.000
130	A	133	LEU	0	0.076	0.025	25.443	-0.003	-0.003	0.000	0.000	0.000	0.000
131	A	134	ARG	1	0.957	1.010	26.997	-0.075	-0.075	0.000	0.000	0.000	0.000
132	A	135	LYS	1	0.917	0.942	28.450	-0.024	-0.024	0.000	0.000	0.000	0.000
133	A	136	MET	0	-0.047	-0.013	26.528	-0.003	-0.003	0.000	0.000	0.000	0.000
134	A	137	ARG	1	0.955	0.994	22.732	-0.117	-0.117	0.000	0.000	0.000	0.000
135	A	138	LYS	1	0.946	0.968	24.433	-0.076	-0.076	0.000	0.000	0.000	0.000
136	A	139	ARG	1	0.889	0.951	26.778	-0.013	-0.013	0.000	0.000	0.000	0.000
137	A	140	LEU	0	0.059	0.026	19.641	-0.004	-0.004	0.000	0.000	0.000	0.000
138	A	141	MET	0	-0.047	-0.012	22.235	-0.003	-0.003	0.000	0.000	0.000	0.000
139	A	142	ARG	1	1.010	1.019	23.374	-0.029	-0.029	0.000	0.000	0.000	0.000
140	A	143	ASP	-1	-0.808	-0.859	24.565	-0.002	-0.002	0.000	0.000	0.000	0.000
141	A	144	ALA	0	0.033	0.014	19.643	-0.014	-0.014	0.000	0.000	0.000	0.000
142	A	145	GLU	-1	-0.944	-0.961	21.048	0.063	0.063	0.000	0.000	0.000	0.000
143	A	146	ASP	-1	-0.966	-0.994	23.236	-0.002	-0.002	0.000	0.000	0.000	0.000
144	A	147	LEU	0	-0.056	-0.037	18.568	-0.009	-0.009	0.000	0.000	0.000	0.000
145	A	148	GLN	0	-0.016	-0.015	18.361	-0.017	-0.017	0.000	0.000	0.000	0.000
146	A	149	LYS	1	0.959	0.982	20.859	0.000	0.000	0.000	0.000	0.000	0.000
147	A	150	ARG	1	0.856	0.925	24.037	0.028	0.028	0.000	0.000	0.000	0.000
148	A	151	LEU	0	0.060	0.029	17.872	-0.008	-0.008	0.000	0.000	0.000	0.000
149	A	152	ALA	0	0.001	0.004	21.792	-0.009	-0.009	0.000	0.000	0.000	0.000
150	A	153	VAL	0	-0.078	-0.036	23.085	-0.003	-0.003	0.000	0.000	0.000	0.000
151	A	154	TYR	0	-0.038	-0.022	23.099	-0.004	-0.004	0.000	0.000	0.000	0.000
152	A	155	LYS	1	0.886	0.963	17.931	0.084	0.084	0.000	0.000	0.000	0.000
153	A	156	ALA	0	0.035	0.013	23.289	0.014	0.014	0.000	0.000	0.000	0.000
154	A	157	GLY	0	-0.039	-0.027	26.427	-0.009	-0.009	0.000	0.000	0.000	0.000
155	A	158	ALA	0	0.024	0.026	28.401	0.007	0.007	0.000	0.000	0.000	0.000
156	A	159	ARG	1	0.866	0.906	29.703	0.055	0.055	0.000	0.000	0.000	0.000
157	A	160	GLU	-1	-0.846	-0.898	31.993	-0.029	-0.029	0.000	0.000	0.000	0.000
158	A	161	GLY	0	0.002	0.001	34.973	0.003	0.003	0.000	0.000	0.000	0.000
159	A	162	ALA	0	-0.006	0.001	35.484	0.000	0.000	0.000	0.000	0.000	0.000
160	A	163	GLU	-1	-0.839	-0.900	34.748	-0.049	-0.049	0.000	0.000	0.000	0.000
161	A	164	ARG	1	0.826	0.861	29.072	0.037	0.037	0.000	0.000	0.000	0.000
162	A	165	GLY	0	0.015	0.030	28.818	-0.002	-0.002	0.000	0.000	0.000	0.000
163	A	166	VAL	0	0.043	0.009	29.002	-0.003	-0.003	0.000	0.000	0.000	0.000
164	A	167	SER	0	-0.003	-0.008	30.852	0.001	0.001	0.000	0.000	0.000	0.000
165	A	168	ALA	0	0.053	0.042	28.631	-0.001	-0.001	0.000	0.000	0.000	0.000
166	A	169	ILE	0	0.005	-0.001	25.713	-0.003	-0.003	0.000	0.000	0.000	0.000
167	A	170	ARG	1	0.918	0.942	28.901	0.030	0.030	0.000	0.000	0.000	0.000
168	A	171	GLU	-1	-0.913	-0.948	32.426	-0.067	-0.067	0.000	0.000	0.000	0.000
169	A	172	ARG	1	0.895	0.951	23.440	0.125	0.125	0.000	0.000	0.000	0.000
170	A	173	LEU	0	-0.049	-0.024	28.337	-0.001	-0.001	0.000	0.000	0.000	0.000
171	A	174	GLY	0	-0.004	0.026	31.389	0.002	0.002	0.000	0.000	0.000	0.000
172	A	175	PRO	0	-0.013	-0.051	34.835	0.003	0.003	0.000	0.000	0.000	0.000
173	A	176	LEU	0	0.011	0.031	35.261	0.002	0.002	0.000	0.000	0.000	0.000
174	A	177	VAL	0	-0.031	-0.003	38.256	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:PRO)