PDB Chemical Component PY5

The following tables include covalent bond distance, bond angle and torsion angle values for the experimental model and ideal geometries stored in the definition for this chemical component.

Bond Distances for PY5

Atom I	Atom J	Distance (Experimental Model)	Distance (Ideal Model)
N1	C2	1.374	1.317
N1	C6	1.359	1.318
C2	C2A	1.514	1.507
C2	C3	1.449	1.386
C2A	H2A1	1.115	1.089
C2A	H2A2	1.115	1.089
C2A	H2A3	1.115	1.091
C3	O3	1.355	1.359
C3	C4	1.402	1.392
O3	HO3	0.949	0.966
C4	C4A	1.539	1.507
C4	C5	1.445	1.384
C4A	N	1.538	1.468
C4A	H4A1	1.116	1.090
C4A	H4A2	1.116	1.090
C5	C6	1.390	1.382
C5	C5A	1.534	1.507
C6	H6	1.103	1.080
C5A	O4P	1.371	1.429
C5A	H5A1	1.115	1.090
C5A	H5A2	1.115	1.089
O4P	P	1.571	1.610
P	O1P	1.422	1.480
P	O2P	1.507	1.610
P	O3P	1.501	1.609
O2P	HOP2	0.951	0.967
O3P	HOP3	0.951	0.967
N	CA	1.519	1.469
N	HN2	1.020	1.010
CA	C	1.529	1.507
CA	CB	1.524	1.529
CA	HA	1.115	1.089
C	O	1.348	1.208
C	OXT	1.300	1.342
CB	CG	1.521	1.530
CB	HB1	1.115	1.091
CB	HB2	1.116	1.090
CG	CD	1.517	1.530
CG	HG1	1.115	1.090
CG	HG2	1.114	1.089
CD	HD1	1.115	1.089
CD	HD2	1.115	1.091
CD	HD3	1.116	1.089
OXT	HXT	0.949	0.966

Bond Angles for PY5

Atom I	Atom J	Atom K	Angle (Experimental Model)	Angle (Ideal Model)
C2	N1	C6	121.9	121.8
N1	C2	C2A	109.4	119.6
N1	C2	C3	118.6	120.7
N1	C6	C5	118.1	120.9
N1	C6	H6	119.9	119.6
C2A	C2	C3	132.0	119.7
C2	C2A	H2A1	109.4	109.5
C2	C2A	H2A2	112.2	109.5
C2	C2A	H2A3	112.2	109.4
C2	C3	O3	111.1	120.5
C2	C3	C4	123.7	119.0
H2A1	C2A	H2A2	112.3	109.5
H2A1	C2A	H2A3	112.2	109.5
H2A2	C2A	H2A3	98.2	109.5
O3	C3	C4	125.2	120.5
C3	O3	HO3	111.0	106.8
C3	C4	C4A	122.2	120.8
C3	C4	C5	111.6	118.4
C4A	C4	C5	126.2	120.8
C4	C4A	N	104.8	109.5
C4	C4A	H4A1	114.0	109.5
C4	C4A	H4A2	114.0	109.5
C4	C5	C6	126.2	119.2
C4	C5	C5A	123.0	120.4
N	C4A	H4A1	114.0	109.4
N	C4A	H4A2	114.0	109.5
C4A	N	CA	111.1	106.7
C4A	N	HN2	111.6	106.7
H4A1	C4A	H4A2	96.4	109.5
C6	C5	C5A	110.8	120.4
C5	C6	H6	122.0	119.5
C5	C5A	O4P	117.6	109.4
C5	C5A	H5A1	109.3	109.4
C5	C5A	H5A2	109.3	109.5
O4P	C5A	H5A1	109.2	109.4
O4P	C5A	H5A2	109.3	109.5
C5A	O4P	P	124.1	106.8
H5A1	C5A	H5A2	100.8	109.5
O4P	P	O1P	111.6	109.4
O4P	P	O2P	104.5	109.5
O4P	P	O3P	104.4	109.5
O1P	P	O2P	122.2	109.4
O1P	P	O3P	103.8	109.5
O2P	P	O3P	109.1	109.5
P	O2P	HOP2	104.5	106.8
P	O3P	HOP3	104.4	106.8
CA	N	HN2	111.7	106.7
N	CA	C	110.0	109.4
N	CA	CB	110.6	109.5
N	CA	HA	108.7	109.4
C	CA	CB	110.6	109.5
C	CA	HA	108.8	109.5
CA	C	O	111.4	120.0
CA	C	OXT	124.4	120.1
CB	CA	HA	108.0	109.5
CA	CB	CG	114.8	109.5
CA	CB	HB1	110.3	109.5
CA	CB	HB2	110.3	109.5
O	C	OXT	124.2	120.0
C	OXT	HXT	124.4	120.0
CG	CB	HB1	110.3	109.5
CG	CB	HB2	110.2	109.5
CB	CG	CD	112.9	109.5
CB	CG	HG1	110.9	109.4
CB	CG	HG2	111.0	109.4
HB1	CB	HB2	99.9	109.4
CD	CG	HG1	110.9	109.5
CD	CG	HG2	110.9	109.5
CG	CD	HD1	112.9	109.5
CG	CD	HD2	111.0	109.4
CG	CD	HD3	111.0	109.5
HG1	CG	HG2	99.4	109.5
HD1	CD	HD2	111.0	109.5
HD1	CD	HD3	110.9	109.5
HD2	CD	HD3	99.3	109.5

Torsion Angles for PY5

Atom I	Atom J	Atom K	Atom L	Angle (Experimental Model)	Angle (Ideal Model)
C2	N1	C6	C5	358.9	359.7
C2	N1	C6	H6	178.9	180.0
C2A	C2	N1	C3	179.6	180.0
N1	C2	C2A	H2A1	180.0	270.0
N1	C2	C2A	H2A2	305.3	30.1
N1	C2	C2A	H2A3	54.8	150.0
N1	C2	C3	O3	180.2	179.9
N1	C2	C3	C4	359.3	0.0
C6	N1	C2	C2A	180.4	180.0
C6	N1	C2	C3	0.8	0.0
C4	C5	C6	N1	1.3	0.5
N1	C6	C5	C5A	179.8	180.0
C5	C6	N1	H6	180.0	179.7
C2A	C2	N1	C6	180.4	180.0
N1	C2	C2A	C3	180.5	180.0
C2A	C2	C3	O3	0.7	359.9
C2A	C2	C3	C4	179.8	180.0
H2A1	C2A	C2	H2A2	234.7	240.0
H2A1	C2A	C2	H2A3	125.2	120.0
H2A2	C2A	C2	H2A3	250.5	240.0
C3	C2	N1	C6	0.8	0.0
N1	C2	C3	C2A	179.5	180.0
C3	C2	C2A	H2A1	359.5	90.0
C3	C2	C2A	H2A2	124.8	210.1
C3	C2	C2A	H2A3	234.3	330.0
O3	C3	C2	C4	180.9	179.9
C2	C3	O3	HO3	180.0	270.1
C2	C3	C4	C4A	179.9	180.0
C2	C3	C4	C5	0.8	0.2
H2A1	C2A	C2	C3	359.5	90.0
C2	C2A	H2A1	H2A2	125.3	120.0
C2	C2A	H2A1	H2A3	234.8	240.1
H2A2	C2A	H2A1	H2A3	109.5	120.0
H2A2	C2A	C2	C3	124.8	210.1
C2	C2A	H2A2	H2A1	236.3	240.0
C2	C2A	H2A2	H2A3	118.1	119.9
H2A1	C2A	H2A2	H2A3	241.8	239.9
H2A3	C2A	C2	C3	234.3	330.0
C2	C2A	H2A3	H2A1	123.6	120.0
C2	C2A	H2A3	H2A2	241.9	240.0
H2A1	C2A	H2A3	H2A2	118.2	120.0
C2	C3	O3	C4	179.1	180.1
O3	C3	C4	C4A	358.9	0.1
O3	C3	C4	C5	179.8	180.3
C2	C3	C4	O3	181.1	179.9
C4	C3	O3	HO3	0.9	89.9
C4A	C4	C3	C5	179.1	179.8
C3	C4	C4A	N	332.3	89.9
C3	C4	C4A	H4A1	97.6	330.0
C3	C4	C4A	H4A2	207.0	210.0
C3	C4	C5	C6	358.9	359.5
C3	C4	C5	C5A	180.5	180.1
HO3	O3	C3	C4	0.9	89.9
C3	C4	C4A	C5	181.0	180.2
C4A	C4	C5	C6	179.8	179.8
C4A	C4	C5	C5A	1.4	0.3
N	C4A	C4	H4A1	234.7	119.9
N	C4A	C4	H4A2	125.3	240.0
C4	C4A	N	CA	159.8	180.0
C4	C4A	N	HN2	34.5	66.2
H4A1	C4A	C4	H4A2	250.6	120.0
N1	C6	C5	C4	1.3	0.5
C3	C4	C5	C4A	179.1	179.8
C5	C4	C4A	N	151.3	269.7
C5	C4	C4A	H4A1	276.5	149.7
C5	C4	C4A	H4A2	25.9	29.7
C6	C5	C4	C5A	178.4	179.5
C4	C5	C6	H6	181.3	180.2
C4	C5	C5A	O4P	26.2	179.5
C4	C5	C5A	H5A1	151.5	299.4
C4	C5	C5A	H5A2	260.9	59.4
N	C4A	C4	C5	151.3	269.7
C4	C4A	N	H4A1	125.3	240.0
C4	C4A	N	H4A2	234.7	120.0
H4A1	C4A	N	H4A2	109.4	240.0
CA	N	C4A	HN2	125.3	113.8
C4A	N	CA	C	180.1	270.0
C4A	N	CA	CB	57.7	150.0
C4A	N	CA	HA	299.2	30.0
H4A1	C4A	C4	C5	276.5	149.7
C4	C4A	H4A1	N	239.8	120.0
C4	C4A	H4A1	H4A2	119.9	240.0
N	C4A	H4A1	H4A2	240.1	120.0
H4A1	C4A	N	CA	34.5	300.0
H4A1	C4A	N	HN2	269.2	186.2
H4A2	C4A	C4	C5	25.9	29.7
C4	C4A	H4A2	N	120.3	240.0
C4	C4A	H4A2	H4A1	240.1	120.0
N	C4A	H4A2	H4A1	119.9	240.0
H4A2	C4A	N	CA	285.1	60.0
H4A2	C4A	N	HN2	159.8	306.2
N1	C6	C5	H6	180.0	180.3
C4	C5	C6	C5A	181.4	180.5
C6	C5	C5A	O4P	207.6	0.1
C6	C5	C5A	H5A1	332.8	120.0
C6	C5	C5A	H5A2	82.3	240.0
C4	C5	C5A	C6	178.6	179.4
C5A	C5	C6	H6	359.9	359.7
O4P	C5A	C5	H5A1	234.8	240.1
O4P	C5A	C5	H5A2	125.3	120.1
C5	C5A	O4P	P	156.9	179.9
H5A1	C5A	C5	H5A2	250.5	240.0
N1	C6	H6	C5	180.0	179.7
H6	C6	C5	C5A	359.9	359.7
C5	C5A	O4P	H5A1	125.3	119.9
C5	C5A	O4P	H5A2	234.7	240.0
H5A1	C5A	O4P	H5A2	109.4	120.1
C5A	O4P	P	O1P	295.1	60.0
C5A	O4P	P	O2P	161.1	179.9
C5A	O4P	P	O3P	46.6	300.0
C5	C5A	H5A1	O4P	230.1	240.1
C5	C5A	H5A1	H5A2	115.1	120.0
O4P	C5A	H5A1	H5A2	245.0	239.9
H5A1	C5A	O4P	P	31.6	60.1
C5	C5A	H5A2	O4P	130.0	120.0
C5	C5A	H5A2	H5A1	244.9	240.1
O4P	C5A	H5A2	H5A1	114.9	120.0
H5A2	C5A	O4P	P	282.2	300.0
P	O4P	C5A	H5A1	31.6	60.1
P	O4P	C5A	H5A2	282.2	300.0
O1P	P	O4P	O2P	134.0	240.1
O1P	P	O4P	O3P	248.5	120.0
O2P	P	O4P	O3P	114.5	239.9
O4P	P	O2P	HOP2	180.0	180.1
O4P	P	O3P	HOP3	180.0	300.0
O4P	P	O1P	O2P	235.4	120.0
O4P	P	O1P	O3P	111.8	240.0
O2P	P	O1P	O3P	236.5	120.0
O1P	P	O2P	HOP2	52.2	300.0
O1P	P	O3P	HOP3	297.0	180.0
O4P	P	O2P	O1P	127.8	240.1
O4P	P	O2P	O3P	248.9	120.1
O1P	P	O2P	O3P	121.1	240.0
O2P	P	O3P	HOP3	68.8	60.0
O4P	P	O3P	O1P	243.0	120.0
O4P	P	O3P	O2P	111.2	239.9
O1P	P	O3P	O2P	228.3	120.0
O3P	P	O2P	HOP2	291.2	60.0
HOP2	O2P	P	O3P	291.2	60.0
CA	N	C4A	H4A1	34.5	300.0
CA	N	C4A	H4A2	285.1	60.0
C4A	N	CA	HN2	234.8	246.2
C	CA	N	CB	122.5	120.0
C	CA	N	HA	240.9	240.0
N	CA	C	O	42.7	149.9
N	CA	C	OXT	222.7	330.0
CB	CA	N	HA	118.5	120.0
N	CA	CB	CG	59.9	300.0
N	CA	CB	HB1	185.2	180.0
N	CA	CB	HB2	294.6	60.0
HN2	N	C4A	H4A1	269.2	186.2
HN2	N	C4A	H4A2	159.8	306.2
C4A	N	HN2	CA	125.0	113.8
HN2	N	CA	C	305.3	23.8
HN2	N	CA	CB	182.9	263.8
HN2	N	CA	HA	64.4	143.8
C	CA	N	HN2	305.3	23.8
N	CA	C	CB	237.5	240.0
N	CA	C	HA	119.0	119.9
CB	CA	C	HA	241.5	240.0
C	CA	CB	CG	297.8	180.0
C	CA	CB	HB1	63.1	60.0
C	CA	CB	HB2	172.5	300.0
O	C	CA	OXT	180.0	179.9
CA	C	OXT	HXT	180.0	180.0
CB	CA	N	HN2	182.9	263.8
N	CA	CB	C	122.1	120.0
N	CA	CB	HA	241.1	240.1
C	CA	CB	HA	119.0	120.1
CB	CA	C	O	165.2	270.0
CB	CA	C	OXT	345.2	90.0
CG	CB	CA	HB1	234.7	120.0
CG	CB	CA	HB2	125.3	240.0
CA	CB	CG	CD	195.0	180.0
CA	CB	CG	HG1	320.2	60.0
CA	CB	CG	HG2	69.7	300.0
HB1	CB	CA	HB2	250.6	120.0
HA	CA	N	HN2	64.4	143.8
N	CA	HA	C	240.2	240.0
N	CA	HA	CB	120.1	120.0
C	CA	HA	CB	239.9	240.0
HA	CA	C	O	283.7	30.0
HA	CA	C	OXT	103.7	210.1
HA	CA	CB	CG	178.8	60.0
HA	CA	CB	HB1	304.1	299.9
HA	CA	CB	HB2	53.5	180.0
O	C	CA	CB	165.2	270.0
O	C	CA	HA	283.7	30.0
CA	C	O	OXT	180.0	180.1
O	C	OXT	HXT	0.0	0.1
OXT	C	CA	CB	345.2	90.0
OXT	C	CA	HA	103.7	210.1
CA	C	OXT	O	180.0	179.9
CG	CB	CA	HA	178.8	60.0
CA	CB	CG	HB1	125.3	239.9
CA	CB	CG	HB2	234.7	120.0
HB1	CB	CG	HB2	109.4	240.1
CD	CG	CB	HG1	234.8	120.0
CD	CG	CB	HG2	125.2	240.0
CB	CG	CD	HD1	180.0	180.0
CB	CG	CD	HD2	305.3	300.0
CB	CG	CD	HD3	54.7	60.0
HG1	CG	CB	HG2	250.5	120.0
HB1	CB	CA	HA	304.1	299.9
CA	CB	HB1	CG	232.1	120.1
CA	CB	HB1	HB2	116.1	240.0
CG	CB	HB1	HB2	244.0	119.9
HB1	CB	CG	CD	69.6	300.1
HB1	CB	CG	HG1	194.9	180.1
HB1	CB	CG	HG2	304.4	60.0
HB2	CB	CA	HA	53.5	180.0
CA	CB	HB2	CG	127.9	240.0
CA	CB	HB2	HB1	243.9	120.0
CG	CB	HB2	HB1	116.0	240.1
HB2	CB	CG	CD	320.3	60.0
HB2	CB	CG	HG1	85.5	300.0
HB2	CB	CG	HG2	195.1	180.0
CD	CG	CB	HB1	69.6	300.1
CD	CG	CB	HB2	320.3	60.0
CB	CG	CD	HG1	125.2	240.0
CB	CG	CD	HG2	234.7	120.0
HG1	CG	CD	HG2	109.5	239.9
HD1	CD	CG	HD2	234.7	240.0
HD1	CD	CG	HD3	125.3	120.0
HD2	CD	CG	HD3	250.6	240.0
HG1	CG	CB	HB1	194.9	180.1
HG1	CG	CB	HB2	85.5	300.0
CB	CG	HG1	CD	233.7	120.0
CB	CG	HG1	HG2	116.9	240.0
CD	CG	HG1	HG2	243.2	120.0
HG1	CG	CD	HD1	54.8	300.0
HG1	CG	CD	HD2	180.1	60.0
HG1	CG	CD	HD3	289.5	179.9
HG2	CG	CB	HB1	304.4	60.0
HG2	CG	CB	HB2	195.1	180.0
CB	CG	HG2	CD	126.3	240.0
CB	CG	HG2	HG1	243.2	120.0
CD	CG	HG2	HG1	116.8	240.0
HG2	CG	CD	HD1	305.2	60.1
HG2	CG	CD	HD2	70.6	180.0
HG2	CG	CD	HD3	180.0	300.0
HD1	CD	CG	HG1	54.8	300.0
HD1	CD	CG	HG2	305.2	60.1
CG	CD	HD1	HD2	125.3	120.0
CG	CD	HD1	HD3	234.7	240.0
HD2	CD	HD1	HD3	109.4	120.0
HD2	CD	CG	HG1	180.1	60.0
HD2	CD	CG	HG2	70.6	180.0
CG	CD	HD2	HD1	233.6	240.0
CG	CD	HD2	HD3	116.8	120.0
HD1	CD	HD2	HD3	243.2	239.9
HD3	CD	CG	HG1	289.5	179.9
HD3	CD	CG	HG2	180.0	300.0
CG	CD	HD3	HD1	126.4	120.0
CG	CD	HD3	HD2	243.1	240.1
HD1	CD	HD3	HD2	116.8	120.0