ZMatrixFormat
Example molecule, Z-4-methoxybenzaldoxime, CSD reference code AANHOX:
There are two variable torsion angles about bonds C2-O16 and C1-C11.
EXAMPLE MOL2 file
# File Created by: PC Spartan Pro Export
#
@\<TRIPOS>MOLECULE
C:\\motherwell\\samoxime.mo2
20 20
SMALL
NO_CHARGES
@\<TRIPOS>ATOM
1 C1 0.293217313 0.250035865 1.069792204 C.ar 1 Molecule001
2 C2 -0.008979730 0.027063995 3.852291799 C.ar 1 Molecule001
3 C3 0.488999937 -0.978777859 1.703096616 C.ar 1 Molecule001
4 C4 -0.080645376 1.364432686 1.825562143 C.ar 1 Molecule001
5 C5 -0.223538726 1.250142376 3.211062816 C.ar 1 Molecule001
6 C6 0.344323476 -1.088558606 3.092210833 C.ar 1 Molecule001
7 H7 0.737253557 -1.865934089 1.127281963 H 1 Molecule001
8 H8 -0.252034022 2.327749313 1.352239204 H 1 Molecule001
9 H9 -0.504578299 2.121804863 3.797847048 H 1 Molecule001
10 H10 0.508767609 -2.061069866 3.544242324 H 1 Molecule001
11 C11 0.389641286 0.420855758 -0.395989867 C.2 1 Molecule001
12 H12 -0.290524363 1.180800541 -0.819438688 H 1 Molecule001
13 N13 1.166972637 -0.174090243 -1.259879230 N.2 1 Molecule001
14 O14 2.081028705 -1.042636861 -0.672914357 O.3 1 Molecule001
15 H15 2.599746303 -1.348446047 -1.440188292 H 1 Molecule001
16 O16 -0.183225243 0.055644157 5.208123004 O.3 1 Molecule001
17 C17 0.050187143 -1.157264365 5.913234641 C.3 1 Molecule001
18 H18 1.085947683 -1.491802143 5.793237167 H 1 Molecule001
19 H19 -0.655864517 -1.935183860 5.604477331 H 1 Molecule001
20 H20 -0.114861688 -0.961941388 6.977167021 H 1 Molecule001
@\<TRIPOS>BOND
1 1 4 ar
2 4 5 ar
3 2 5 ar
4 2 6 ar
5 3 6 ar
6 1 3 ar
7 5 9 1
8 6 10 1
9 3 7 1
10 4 8 1
11 11 12 1
12 1 11 1
13 11 13 2
14 14 15 1
15 13 14 1
16 2 16 1
17 17 18 1
18 17 19 1
19 17 20 1
20 16 17 1
Z-Matrix file created by DASH from the input MOL2 file
Zmatrix generated by Mercury
1.0 1.0 1.0 90.0 90.0 90.0
20 0
C 0.0000000 0 0.0000000 0 0.0000000 0 0 0 0 3.0 1.0 3 C3
C 1.3962050 0 0.0000000 0 0.0000000 0 1 0 0 3.0 1.0 1 C1 C3
C 1.4009359 0 120.2814856 0 0.0000000 0 1 2 0 3.0 1.0 6 C6 C3 C1
H 1.0863878 0 120.6861954 0 178.8814973 0 1 2 3 6.0 1.0 7 H7 C3 C1 C6
C 1.3974412 0 119.6071742 0 -1.5745262 0 2 1 3 3.0 1.0 4 C4 C1 C3 C6
C 1.4788489 0 122.8266674 0 -176.4571818 0 2 1 5 3.0 1.0 11 C11 C1 C3 C4
C 1.3954068 0 120.2386237 0 0.6027188 0 3 1 2 3.0 1.0 2 C2 C6 C3 C1
H 1.0849666 0 117.8853515 0 179.6006996 0 3 1 7 6.0 1.0 10 H10 C6 C3 C2
C 1.3975310 0 119.8880618 0 1.5806770 0 5 2 1 3.0 1.0 5 C5 C4 C1 C3
H 1.0869166 0 120.8934394 0 179.2769860 0 5 2 9 6.0 1.0 8 H8 C4 C1 C5
H 1.1042872 0 114.7967855 0 146.8411988 1 6 2 1 6.0 1.0 12 H12 C11 C1 C3
N 1.3055687 0 129.9435928 0 178.8979722 0 6 2 11 3.0 1.0 13 N13 C11 C1
H12
O 1.3672807 0 126.0945149 0 179.9304618 0 7 3 1 3.0 1.0 16 O16 C2 C6 C3
H 1.0877015 0 119.7165368 0 179.3664126 0 9 5 2 6.0 1.0 9 H9 C5 C4 C1
O 1.3908269 0 113.3670309 0 -3.8330576 0 12 6 2 3.0 1.0 14 O14 N13 C11
C1
C 1.4222555 0 116.9284636 0 1.6874795 1 13 7 3 3.0 1.0 17 C17 O16 C2 C6
H 0.9753443 0 102.3173121 0 -176.8034053 0 15 12 6 6.0 1.0 15 H15 O14
N13 C11
H 1.0950410 0 111.1884452 0 61.2946259 0 16 13 7 6.0 1.0 18 H18 C17 O16
C2
H 1.0949880 0 111.1155213 0 -124.4607417 0 16 13 18 6.0 1.0 19 H19 C17
O16 H18
H 1.0942323 0 107.7617586 0 117.7913565 0 16 13 18 6.0 1.0 20 H20 C17
O16 H18
The Z-Matrix format is commonly used in molecular modelling (see Appendix I: References ). In this format we describe the molecular co-ordinates in terms of internal co-ordinates, namely the bond-lengths, bond-angles, and torsion angles. The molecule is assembled by building up the molecule atom-by-atom, and placing each atom at a given bond-length, bond angle and torsion angle with reference to the earlier atoms. Each atom-line effectively gives the “instructions” for adding another atom to the molecule. The atoms in this Z-matrix file are referred to by their sequence numbers, I, J, K, L in this list. In the example above there are 20 atoms, which is specified as the first item on line 2 of the file, NAT. (Note that the atoms are presented in a different order from the input Cartesian co-ordinate file in mol2 or pdb format).
Line 1 Title line
Line 2 Is ignored
Line 3 NAT = the number of atoms following in the atom-list
IAT = the atom number to use as origin for DASH rotation parameters
= 0 is taken as using centre of mass as origin
Line 4 Atom-lines. These atoms are given sequence number I = 1 to NAT
Item 1 EL Element type
Item 2 BL Bond length in Angstroms to connect this atom to atom J (item 8 on line)
Item 3 FB Flag to signal fixed (=0) or variable (=1)
Item 4 BA Bond angle in degrees for angle I-J-K, where K is item 9 on line
Item 5 FA Flag to signal bond angle fixed/variable
Item 6 BT Torsion angle I-J-K-L, where atom L is item 10 on line
Item 7 FT Flag to signal torsion angle fixed/variable
Item 8 J atom number for bond I-J
Item 9 K atom number for angle I-J-K
Item 10 L atom number for torsion angle I-J-K-L
Item 11 Temperature factor to be used in DASH structure factor calculation
Item 12 Occupancy factor of atom, in range 0.0 to 1.0
Item 13 Original number
Item 14 Label of atom I in input Cartesian file
Item 15 Label of atom J in input Cartesian file
Item 16 Label of atom K in input Cartesian file
Item 17 Label of atom L in input Cartesian file
Notes:
-
The flags FT for torsion angles are set as fixed or variable by the Z-Matrix generation program, using the chemical knowledge of the bond type and hybridisation state. It is possible to over-ride these settings, by locating the torsion angle with the help of the input atom labels e.g. O14-C11-N13-C1. There may be a case where one wishes to make this a variable torsion angle, although described as a double bond, by setting FT=1 and thus effectively allowing exploration of cis- and trans-isomers in the search.
-
Only those torsion angles flagged with FT=1 are displayed as parameters in the Simulated annealing parameter setup window (see Checking and Setting Parameter Ranges).