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Summary Geometry Related PDB entries

2E5

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C3	C4	doub	1.38Å	1.39Å	Aromatic
C3	N2	sing	1.32Å	1.35Å	Aromatic
C4	C5	sing	1.39Å	1.39Å	Aromatic
N2	C1	doub	1.32Å	1.35Å	Aromatic
C1	C6	sing	1.38Å	1.39Å	Aromatic
C5	C7	sing	1.51Å	1.52Å
C5	C6	doub	1.39Å	1.40Å	Aromatic
C7	O8	sing	1.43Å	1.42Å
O8	P9	sing	1.61Å	1.60Å
O14	P13	doub	1.48Å	1.47Å
P9	O12	sing	1.61Å	1.58Å
P9	O11	doub	1.48Å	1.55Å
P9	O10	sing	1.61Å	1.49Å
O16	P13	sing	1.61Å	1.57Å
O12	P13	sing	1.61Å	1.58Å
P13	O15	sing	1.61Å	1.60Å
C1	H1	sing	1.08Å	1.08Å
C3	H2	sing	1.08Å	1.08Å
O15	H3	sing	0.97Å	0.95Å
O16	H4	sing	0.97Å	0.95Å
O10	H5	sing	0.97Å	0.95Å
C7	H6	sing	1.09Å	1.10Å
C7	H7	sing	1.09Å	1.10Å
C6	H8	sing	1.08Å	1.08Å
C4	H9	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C4	C3	N2	120.8°	120.8°
C3	C4	C5	119.3°	119.2°
C4	C3	H2	119.6°	119.6°
C3	C4	H9	120.4°	120.5°
C3	N2	C1	121.2°	121.7°
N2	C3	H2	119.6°	119.6°
C4	C5	C7	119.7°	120.8°
C4	C5	C6	118.9°	118.4°
C5	C4	H9	120.4°	120.4°
N2	C1	C6	120.1°	120.7°
N2	C1	H1	120.0°	119.6°
C1	C6	C5	119.7°	119.2°
C6	C1	H1	119.9°	119.7°
C1	C6	H8	120.2°	120.4°
C7	C5	C6	121.3°	120.8°
C5	C7	O8	111.6°	109.5°
C5	C7	H6	108.9°	109.5°
C5	C7	H7	108.9°	109.5°
C5	C6	H8	120.1°	120.4°
C7	O8	P9	120.1°	123.0°
O8	C7	H6	108.9°	109.5°
O8	C7	H7	108.9°	109.5°
O8	P9	O12	105.7°	109.4°
O8	P9	O11	105.9°	109.5°
O8	P9	O10	107.2°	109.4°
O14	P13	O16	110.6°	109.4°
O14	P13	O12	114.6°	109.5°
O14	P13	O15	109.4°	109.5°
O12	P9	O11	116.6°	109.5°
O12	P9	O10	106.2°	109.5°
P9	O12	P13	127.2°	133.9°
O11	P9	O10	114.5°	109.5°
P9	O10	H5	109.5°	114.0°
O16	P13	O12	106.0°	109.4°
O16	P13	O15	106.3°	109.5°
P13	O16	H4	109.5°	114.0°
O12	P13	O15	109.6°	109.5°
P13	O15	H3	109.5°	114.1°
H6	C7	H7	109.5°	109.4°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C4	C3	N2	H2	180.0°	179.7°
C3	C4	C5	H9	180.0°	179.8°
C4	C3	N2	C1	0.9°	0.0°
C3	C4	C5	C7	178.4°	180.0°
C3	C4	C5	C6	0.8°	0.5°
N2	C3	C4	C5	0.0°	0.2°
C3	N2	C1	C6	1.0°	0.0°
C3	N2	C1	H1	179.0°	179.7°
N2	C3	C4	H9	180.0°	180.0°
C4	C5	C6	C1	0.8°	0.5°
C4	C5	C7	C6	177.5°	179.6°
C4	C5	C7	O8	48.0°	89.5°
C5	C4	C3	H2	180.0°	180.0°
C4	C5	C7	H6	72.3°	150.4°
C4	C5	C7	H7	168.3°	30.5°
C4	C5	C6	H8	179.2°	179.6°
N2	C1	C6	H1	180.0°	179.7°
N2	C1	C6	C5	0.1°	0.3°
C1	N2	C3	H2	179.1°	179.7°
N2	C1	C6	H8	179.9°	179.8°
C1	C6	C5	C7	178.3°	180.0°
C1	C6	C5	H8	180.0°	179.9°
C5	C7	O8	H6	120.3°	120.0°
C5	C7	O8	H7	120.3°	120.0°
C5	C7	O8	P9	82.7°	180.0°
C5	C7	H6	H7	119.0°	120.0°
C7	C5	C6	H8	1.7°	0.0°
C7	C5	C4	H9	1.6°	0.2°
C6	C5	C7	O8	134.4°	90.0°
C5	C6	C1	H1	179.9°	180.0°
C6	C5	C7	H6	105.2°	30.0°
C6	C5	C7	H7	14.1°	150.0°
C6	C5	C4	H9	179.2°	179.7°
C7	O8	P9	O12	72.8°	175.0°
C7	O8	P9	O11	162.9°	55.0°
C7	O8	P9	O10	40.2°	65.0°
O8	C7	H6	H7	119.0°	120.0°
O8	P9	O12	O11	117.3°	120.0°
O8	P9	O12	O10	113.7°	119.9°
O8	P9	O11	O10	117.9°	120.0°
O8	P9	O12	P13	99.4°	165.0°
O8	P9	O10	H5	117.2°	60.0°
P9	O8	C7	H6	157.0°	60.0°
P9	O8	C7	H7	37.7°	60.0°
O14	P13	O12	P9	37.7°	39.9°
O14	P13	O16	O12	124.8°	120.0°
O14	P13	O16	O15	118.7°	120.0°
O14	P13	O12	O15	123.4°	120.0°
O14	P13	O15	H3	0.0°	60.0°
O14	P13	O16	H4	0.0°	180.0°
O12	P9	O11	O10	124.9°	120.1°
P9	O12	P13	O16	160.0°	80.0°
P9	O12	P13	O15	85.7°	160.0°
O12	P9	O10	H5	130.2°	59.9°
O11	P9	O12	P13	18.0°	45.0°
O11	P9	O10	H5	0.0°	180.0°
O10	P9	O12	P13	146.9°	75.1°
O16	P13	O12	O15	114.3°	120.0°
O16	P13	O15	H3	119.4°	60.0°
O12	P13	O15	H3	126.5°	180.0°
O12	P13	O16	H4	124.8°	60.0°
O15	P13	O16	H4	118.7°	60.0°
H1	C1	C6	H8	0.1°	0.1°
H2	C3	C4	H9	0.0°	0.2°

223532

PDB entries from 2024-08-07

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