Summary Geometry PCM/PTM Related PDB entries

A1IQW

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O8	C5	doub	1.28Å	1.52Å
C12	C13	doub	1.38Å	1.36Å	Aromatic
C12	C11	sing	1.36Å	1.40Å	Aromatic
C5	O5	sing	1.28Å	1.27Å
C5	O6	sing	1.27Å	1.28Å
C13	C8	sing	1.39Å	1.43Å	Aromatic
O5	RU1	sing	2.24Å	2.04Å
C17	C16	doub	1.38Å	1.36Å	Aromatic
C17	C18	sing	1.36Å	1.38Å	Aromatic
F2	C11	sing	1.36Å	1.42Å
C16	C15	sing	1.39Å	1.39Å	Aromatic
C11	C10	doub	1.36Å	1.38Å	Aromatic
O6	RU2	sing	2.07Å	2.03Å
F1	C18	sing	1.36Å	1.44Å
C18	C19	doub	1.36Å	1.38Å	Aromatic
C8	N1	sing	1.43Å	1.45Å
C8	C9	doub	1.39Å	1.35Å	Aromatic
C7	N1	doub	1.33Å	1.31Å
C7	N2	sing	1.35Å	1.33Å
N1	RU1	sing	1.85Å	2.05Å
C15	N2	sing	1.43Å	1.40Å
C15	C20	doub	1.39Å	1.39Å	Aromatic
N2	RU2	sing	2.71Å	2.03Å
RU1	RU2	sing	2.54Å	2.31Å
RU1	O3	sing	2.07Å	2.05Å
RU1	O1	sing	2.50Å	2.04Å
C10	C9	sing	1.38Å	1.37Å	Aromatic
C19	C20	sing	1.38Å	1.41Å	Aromatic
RU2	O4	sing	2.33Å	2.05Å
RU2	O2	sing	1.90Å	2.04Å
O3	C3	doub	1.24Å	1.25Å
C3	O4	sing	1.25Å	1.26Å
C3	C4	sing	1.50Å	1.49Å
C12	H1	sing	0.94Å	1.08Å
C10	H2	sing	0.94Å	1.08Å
C13	H3	sing	0.94Å	1.08Å
C7	H4	sing	0.94Å	1.08Å
C4	H7	sing	0.97Å	1.10Å
C4	H8	sing	0.97Å	1.10Å
C4	H9	sing	0.97Å	1.10Å
C9	H10	sing	0.94Å	1.08Å
C20	H13	sing	0.94Å	1.08Å
C16	H14	sing	0.94Å	1.08Å
C17	H15	sing	0.94Å	1.08Å
C19	H16	sing	0.94Å	1.08Å
O1	C1	sing	1.26Å	49.20Å
C1	O2	doub	1.25Å	48.00Å
C1	C2	sing	1.50Å	0.00Å
C2	H12	sing	0.97Å	0.00Å
C2	H6	sing	0.97Å	0.00Å
C2	H11	sing	0.97Å	0.00Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O8	C5	O5	124.2°	120.9°
O8	C5	O6	116.0°	120.9°
C13	C12	C11	120.7°	118.7°
C12	C13	C8	119.1°	120.7°
C13	C12	H1	119.6°	120.6°
C12	C13	H3	120.4°	119.4°
C12	C11	F2	119.9°	118.6°
C12	C11	C10	119.1°	122.6°
C11	C12	H1	119.6°	120.7°
O5	C5	O6	119.9°	118.2°
C5	O5	RU1	119.1°	116.2°
C5	O6	RU2	119.4°	92.8°
C13	C8	N1	120.0°	124.4°
C13	C8	C9	118.9°	118.5°
C8	C13	H3	120.4°	119.9°
O5	RU1	N1	94.6°	109.2°
O5	RU1	RU2	89.0°	55.3°
O5	RU1	O3	91.5°	120.3°
O5	RU1	O1	174.9°	111.9°
C16	C17	C18	119.4°	118.7°
C17	C16	C15	120.2°	120.8°
C17	C16	H14	119.9°	119.2°
C16	C17	H15	120.3°	120.6°
C17	C18	F1	120.5°	118.7°
C17	C18	C19	121.5°	122.6°
C18	C17	H15	120.3°	120.7°
F2	C11	C10	121.0°	118.7°
C16	C15	N2	116.1°	125.4°
C16	C15	C20	121.7°	118.3°
C15	C16	H14	119.9°	120.0°
C11	C10	C9	120.2°	118.7°
C11	C10	H2	119.9°	120.7°
O6	RU2	N2	86.4°	127.0°
O6	RU2	RU1	87.8°	101.3°
O6	RU2	O4	88.2°	86.5°
O6	RU2	O2	178.9°	126.4°
F1	C18	C19	117.9°	118.8°
C18	C19	C20	120.2°	118.7°
C18	C19	H16	119.9°	120.7°
N1	C8	C9	121.1°	117.0°
C8	N1	C7	113.4°	131.1°
C8	N1	RU1	127.9°	120.9°
C8	C9	C10	121.8°	120.8°
C8	C9	H10	119.1°	119.6°
N1	C7	N2	121.3°	121.9°
C7	N1	RU1	118.7°	108.0°
N1	C7	H4	119.4°	118.9°
C7	N2	C15	117.3°	128.1°
C7	N2	RU2	118.3°	126.3°
N2	C7	H4	119.3°	119.2°
N1	RU1	RU2	89.3°	120.4°
N1	RU1	O3	173.7°	126.6°
N1	RU1	O1	84.0°	88.0°
N2	C15	C20	122.2°	116.3°
C15	N2	RU2	123.4°	104.8°
C15	C20	C19	117.0°	120.9°
C15	C20	H13	121.5°	119.6°
N2	RU2	RU1	89.1°	61.6°
N2	RU2	O4	173.8°	122.8°
N2	RU2	O2	93.8°	104.6°
RU2	RU1	O3	89.5°	104.1°
RU2	RU1	O1	86.1°	59.2°
RU1	RU2	O4	87.6°	67.8°
RU1	RU2	O2	91.1°	116.6°
O3	RU1	O1	89.8°	90.9°
RU1	O3	C3	118.4°	98.6°
RU1	O1	C1	74.3°	128.6°
C9	C10	H2	119.9°	120.6°
C10	C9	H10	119.1°	119.6°
C19	C20	H13	121.5°	119.5°
C20	C19	H16	119.9°	120.6°
O4	RU2	O2	91.5°	75.5°
RU2	O4	C3	120.0°	121.6°
RU2	O2	C1	69.3°	93.0°
O3	C3	O4	123.3°	122.5°
O3	C3	C4	120.2°	118.8°
O4	C3	C4	116.5°	118.6°
C3	C4	H7	109.5°	109.7°
C3	C4	H8	109.5°	109.6°
C3	C4	H9	109.5°	109.6°
H7	C4	H8	109.5°	109.3°
H7	C4	H9	109.4°	109.3°
H8	C4	H9	109.5°	109.3°
O1	C1	O2	2.2°	125.0°
O1	C1	C2	90.0°	118.2°
O2	C1	C2	90.0°	116.8°
C1	C2	H12	90.0°	109.8°
C1	C2	H6	90.0°	109.6°
C1	C2	H11	90.0°	109.6°
H12	C2	H6	90.0°	109.2°
H12	C2	H11	90.0°	109.3°
H6	C2	H11	90.0°	109.3°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O8	C5	O5	O6	179.3°	179.9°
O8	C5	O5	RU1	158.3°	99.1°
O8	C5	O6	RU2	152.1°	161.5°
C13	C12	C11	H1	180.0°	179.9°
C12	C13	C8	H3	180.0°	179.1°
C13	C12	C11	F2	179.5°	179.8°
C13	C12	C11	C10	0.2°	0.1°
C12	C13	C8	N1	179.0°	179.6°
C12	C13	C8	C9	1.1°	1.0°
C11	C12	C13	C8	0.4°	0.6°
C12	C11	F2	C10	179.8°	179.9°
C12	C11	C10	C9	0.1°	0.0°
C12	C11	C10	H2	179.9°	180.0°
C11	C12	C13	H3	179.6°	179.7°
O5	C5	O6	RU2	27.3°	18.4°
C5	O5	RU1	N1	83.4°	172.8°
C5	O5	RU1	RU2	5.7°	73.0°
C5	O5	RU1	O3	95.2°	13.4°
C5	O5	RU1	O1	9.9°	91.4°
O6	C5	O5	RU1	21.0°	80.8°
C5	O6	RU2	N2	71.3°	33.9°
C5	O6	RU2	RU1	17.9°	28.9°
C5	O6	RU2	O4	105.6°	95.4°
C5	O6	RU2	O2	30.9°	164.5°
C13	C8	N1	C9	177.9°	178.6°
C13	C8	N1	C7	76.2°	4.3°
C13	C8	N1	RU1	103.2°	174.6°
C13	C8	C9	C10	1.2°	0.9°
C8	C13	C12	H1	179.6°	179.5°
C13	C8	C9	H10	178.8°	179.3°
O5	RU1	RU2	O6	5.0°	42.2°
O5	RU1	N1	C8	103.1°	128.6°
O5	RU1	N1	C7	76.2°	52.3°
O5	RU1	N1	RU2	88.9°	60.4°
O5	RU1	N1	O3	167.6°	157.8°
O5	RU1	N1	O1	175.1°	112.6°
O5	RU1	RU2	N2	81.4°	83.9°
O5	RU1	RU2	O3	91.5°	117.4°
O5	RU1	RU2	O1	178.6°	160.1°
O5	RU1	O3	O1	175.1°	116.2°
O5	RU1	RU2	O4	93.3°	123.6°
O5	RU1	RU2	O2	175.2°	176.8°
O5	RU1	O3	C3	85.5°	42.4°
O5	RU1	O1	C1	65.5°	12.5°
C16	C17	C18	H15	180.0°	179.9°
C17	C16	C15	H14	180.0°	179.5°
C16	C17	C18	F1	180.0°	179.9°
C16	C17	C18	C19	1.2°	0.1°
C17	C16	C15	N2	178.5°	180.0°
C17	C16	C15	C20	0.6°	0.4°
C18	C17	C16	C15	0.2°	0.3°
C17	C18	F1	C19	178.8°	180.0°
C17	C18	C19	C20	1.5°	0.0°
C18	C17	C16	H14	179.8°	179.8°
C17	C18	C19	H16	178.4°	180.0°
F2	C11	C10	C9	179.6°	180.0°
F2	C11	C12	H1	0.4°	0.1°
F2	C11	C10	H2	0.3°	0.1°
C16	C15	N2	C7	117.8°	3.0°
C16	C15	N2	C20	177.9°	179.5°
C16	C15	N2	RU2	74.0°	167.4°
C16	C15	C20	C19	0.3°	0.3°
C16	C15	C20	H13	179.7°	179.7°
C15	C16	C17	H15	179.9°	179.8°
C11	C10	C9	C8	0.6°	0.3°
C11	C10	C9	H2	180.0°	179.9°
C10	C11	C12	H1	179.8°	180.0°
C11	C10	C9	H10	179.4°	179.8°
O6	RU2	N2	C7	105.9°	95.7°
O6	RU2	RU1	N1	99.7°	135.6°
O6	RU2	N2	C15	86.0°	93.6°
O6	RU2	N2	RU1	87.9°	82.6°
O6	RU2	N2	O4	29.7°	113.2°
O6	RU2	N2	O2	178.9°	164.8°
O6	RU2	RU1	O4	88.3°	81.4°
O6	RU2	RU1	O2	179.7°	141.0°
O6	RU2	RU1	O3	86.5°	75.2°
O6	RU2	RU1	O1	176.3°	157.7°
O6	RU2	O4	O2	178.9°	129.0°
O6	RU2	O4	C3	80.0°	69.8°
O6	RU2	O2	C1	115.1°	166.8°
F1	C18	C19	C20	179.6°	180.0°
F1	C18	C17	H15	0.0°	0.0°
F1	C18	C19	H16	0.4°	0.1°
C18	C19	C20	C15	0.7°	0.1°
C18	C19	C20	H16	180.0°	179.9°
C18	C19	C20	H13	179.2°	179.9°
C19	C18	C17	H15	178.8°	180.0°
C8	N1	C7	RU1	179.4°	178.9°
C8	N1	C7	N2	178.5°	177.8°
C8	N1	RU1	RU2	168.0°	171.0°
C8	N1	RU1	O3	89.3°	29.1°
C8	N1	RU1	O1	81.8°	118.8°
N1	C8	C9	C10	179.1°	179.6°
N1	C8	C13	H3	1.0°	1.3°
C8	N1	C7	H4	1.5°	2.1°
N1	C8	C9	H10	0.9°	0.6°
C9	C8	N1	C7	101.7°	174.4°
C9	C8	N1	RU1	78.9°	6.8°
C8	C9	C10	H10	180.0°	179.8°
C8	C9	C10	H2	179.4°	179.6°
C9	C8	C13	H3	178.9°	179.9°
N1	C7	N2	H4	180.0°	179.9°
N1	C7	N2	C15	178.2°	177.7°
N1	C7	N2	RU2	13.0°	13.8°
C7	N1	RU1	RU2	12.7°	8.1°
C7	N1	RU1	O3	91.4°	150.0°
C7	N1	RU1	O1	98.9°	60.3°
N2	C7	N1	RU1	2.1°	3.3°
C7	N2	C15	RU2	168.2°	170.4°
C7	N2	C15	C20	64.3°	176.5°
C7	N2	RU2	RU1	18.0°	13.1°
C7	N2	RU2	O4	76.1°	17.5°
C7	N2	RU2	O2	73.0°	99.5°
N1	RU1	RU2	N2	13.2°	9.4°
N1	RU1	RU2	O3	173.9°	149.2°
N1	RU1	RU2	O1	84.0°	66.7°
N1	RU1	O3	O1	7.5°	88.2°
N1	RU1	RU2	O4	172.1°	143.0°
N1	RU1	RU2	O2	80.6°	83.4°
N1	RU1	O3	C3	82.1°	162.0°
RU1	N1	C7	H4	177.9°	176.8°
N1	RU1	O1	C1	139.5°	122.5°
C15	N2	RU2	RU1	173.9°	176.2°
N2	C15	C20	C19	178.1°	179.9°
C15	N2	RU2	O4	115.8°	153.1°
C15	N2	RU2	O2	95.1°	71.1°
C15	N2	C7	H4	1.8°	2.2°
N2	C15	C20	H13	1.9°	0.1°
N2	C15	C16	H14	1.5°	0.5°
C20	C15	N2	RU2	103.9°	13.0°
C15	C20	C19	H13	180.0°	180.0°
C20	C15	C16	H14	179.4°	179.9°
C15	C20	C19	H16	179.2°	179.9°
N2	RU2	RU1	O4	174.7°	152.4°
N2	RU2	RU1	O2	93.8°	92.9°
N2	RU2	RU1	O3	172.9°	158.7°
N2	RU2	RU1	O1	97.2°	76.2°
N2	RU2	O4	O2	149.2°	98.3°
N2	RU2	O4	C3	50.3°	62.9°
RU2	N2	C7	H4	167.0°	166.3°
N2	RU2	O2	C1	142.8°	28.3°
RU2	RU1	O3	O1	86.1°	58.4°
RU1	RU2	O4	O2	91.0°	127.2°
RU2	RU1	O3	C3	3.5°	15.4°
RU1	RU2	O4	C3	7.9°	34.0°
RU2	RU1	O1	C1	49.9°	5.0°
RU1	RU2	O2	C1	128.1°	36.9°
O3	RU1	RU2	O4	1.8°	6.3°
O3	RU1	RU2	O2	93.3°	65.8°
RU1	O3	C3	O4	10.8°	48.8°
RU1	O3	C3	C4	169.0°	131.4°
O3	RU1	O1	C1	39.6°	110.9°
O1	RU1	RU2	O4	88.1°	76.3°
O1	RU1	RU2	O2	3.4°	16.7°
O1	RU1	O3	C3	89.6°	73.8°
RU1	O1	C1	O2	105.9°	40.6°
RU1	O1	C1	C2	90.0°	139.6°
RU2	O4	C3	O3	13.2°	68.2°
RU2	O4	C3	C4	166.6°	112.1°
O4	RU2	O2	C1	40.4°	92.4°
O2	RU2	O4	C3	98.9°	161.2°
RU2	O2	C1	O1	74.8°	45.4°
RU2	O2	C1	C2	90.0°	134.8°
O3	C3	O4	C4	179.8°	179.8°
O3	C3	C4	H7	0.0°	1.8°
O3	C3	C4	H8	120.0°	118.2°
O3	C3	C4	H9	120.0°	121.8°
O4	C3	C4	H7	179.8°	178.0°
O4	C3	C4	H8	59.8°	62.0°
O4	C3	C4	H9	60.2°	57.9°
C3	C4	H7	H8	120.0°	120.2°
C3	C4	H7	H9	120.0°	120.2°
C3	C4	H8	H9	120.0°	120.1°
H1	C12	C13	H3	0.4°	0.4°
H2	C10	C9	H10	0.6°	0.2°
H7	C4	H8	H9	119.9°	119.6°
H13	C20	C19	H16	0.8°	0.1°
H14	C16	C17	H15	0.1°	0.3°
O1	C1	O2	C2	90.0°	179.8°
O1	C1	C2	H12	90.0°	1.1°
O1	C1	C2	H6	90.0°	121.0°
O1	C1	C2	H11	90.0°	119.0°
O2	C1	C2	H12	90.0°	178.7°
O2	C1	C2	H6	90.0°	58.8°
O2	C1	C2	H11	90.0°	61.1°
C1	C2	H12	H6	90.0°	120.2°
C1	C2	H12	H11	90.0°	120.3°
C1	C2	H6	H11	90.0°	120.1°
H12	C2	H6	H11	90.0°	119.5°

Release date:	2024-12-11
Definition date:	2024-10-02
Last modified:	2026-07-31
Release status:	REL
Processing site:	PDBE
Derived from:	9GYS