The 2D and 3D domain are connected by matching numbers. These indicate which atom in the 3D domain maps to which atom in the 2D domain. For some entries, this mapping is not possible. Such an entry is said to be unmatched. When an entry is unmatched it is impossible to relate the bond types stored in the 2D domain to the crystal connectivity and coordinates stored in the 3D domain.
If an entry is matched then atom-typing is done predominantly from the 2D element and bond types. Only one 3D test is used in order to distinguish planar and pyramidal nitrogen.
If an entry is unmatched then the atom-typing can only be done using the 3D crystal connectivity and the geometry of the structure. Because there is no information about bond types and hydrogen atoms by be missing from the 3D domain, atom-typing will be less accurate.
Some entries are partially matched. In these entries, if an atom is matched then the 2D atom-type is used; otherwise, the 3D atom-type is used.
Some entries have coordinates but no crystal connectivity (they will as a consequence be unmatched). For these entries, it is only possible to make a wild guess at the atom-types.
Clark, M., Cramer, R.D. III, Van Opdenbosch, N., J. Comp. Chem., 10, 982-1012 (1989).
Carbon sp3 (C.3) 1.6.1, 2.5.1, 2.5.2, 2.5.3, 3.5 Carbon sp2 (C.2) 1.6.5, 2.5.2, 2.5.3 Carbon sp (C.1) 1.6.4, 2.5.2, 2.5.3 Carbon aromatic (C.ar) 1.6.3 Carbocation (guanadinium) (C.cat) 1.6.2 Nitrogen sp3 (N.3) 1.8.6, 2.7.2, 2.7.4, 3.7 Nitrogen sp2 (N.2) 1.8.7, 2.7.5 Nitrogen sp (N.1) 1.8.3, 1.8.4, 2.7.2, 2.7.5 Nitrogen aromatic (N.ar) 1.8.2 Nitrogen amide (N.am) 1.8.5, 2.7.3 Nitrogen trigonal planar (N.pl3) 1.8.6, 2.7.4 Nitrogen sp3 positively charged (N.4) 1.8.1, 2.7.1 Oxygen sp3 (O.3) 1.7.2, 2.6.2, 2.6.3, 3.6 Oxygen sp2 (O.2) 1.7.3, 2.6.4 Oxygen in carboxylates and phosphates (O.co2) 1.7.1, 2.6.1 Sulphur sp3 (S.3) 1.9.3, 2.8.3, 3.8 Sulphur sp2 (S.2) 1.9.4, 2.8.4 Sulphoxide sulphur (S.o) 1.9.1, 2.8.1 Sulphone sulphur (S.o2) 1.9.2, 2.8.2 Phosphorus sp3 (P.3) 1.4, 2.3, 3.3 Titanium (Ti.th, Ti.oh) 1.10, 2.9, 3.4 Chromium (Cr.th, Cr.oh) 1.10, 2.9, 3.4 Cobalt (Co.oh) 1.5, 2.4, 3.4 Ruthenium (Ru.oh) 1.5, 2.4, 3.4 Deuterium 1.3, 2.2, 3.2 Polymeric atoms 1.2 Suppressed atoms 1.1, 2.1, 3.1 Other atoms 1.11, 2.10, 3.9 Matched entries 1 Unmatched entries 2 Entries with no crystal connectivity 3
A non-metal bond is a bond to one of
H D B C N O F Si P S Cl As Se Br Te I At He Ne Ar Kr Xe RnDefault atom-type is dummy (Du).
The order of the rules is important.
1. If entry is matched then for each atom 1.1 If atom is suppressed then atom_type is Du 1.2 If atom is at the end of a polymeric bond then atom_type is Du 1.3 If element_symbol is D then atom_type is H 1.4 If element_symbol is P then atom_type is P.3 1.5 If element_symbol is Co .OR. element_symbol is Ru then atom_type is Co.oh or Ru.oh 1.6 If element_symbol is C then 1.6.1 If num_bond .ge. 4 .AND. all bonds are single then atom_type is C.3 1.6.2 If num_bond .eq. 3 .AND. all bonds are acyclic .AND. all bonds are to nitrogen .AND. each nitrogen forms bonds to 2 other atoms both of which are not oxygen then atom_type is C.cat 1.6.3 If num_bond .ge. 2 .AND. 2 bonds are aromatic then atom_type is C.ar 1.6.4 If ( num_bond .eq. 1 .OR. num_bond .eq. 2 ) .AND. one bond is triple then atom_type is C.1 1.6.5 If element_symbol is C and none of the above then atom_type is C.2 1.7 If element_symbol is O then 1.7.1 If num_nonmet .eq. 1 then 1.7.1.1 If bond is to carbon .AND. carbon forms a total of 3 bonds, 2 of which are to an oxygen forming only 1 non-metal bond then atom_type is O.co2 1.7.1.2 If bond is to phosphorus .AND. phosphorus forms at least 2 bonds to an oxygen forming only 1 non-metal bond then atom_type is O.co2 1.7.2 If num_bond .ge. 2 .AND. all bonds are single then atom_type is O.3 1.7.3 If element_symbol is O and none of the above then atom_type is O.2 1.8 If element_symbol is N then 1.8.1 If num_nonmet .eq. 4 .AND. all bonds are single then atom_type is N.4 1.8.2 If num_bond .ge. 2 .AND. 2 bonds are aromatic then atom_type is N.ar 1.8.3 If num_nonmet .eq. 1 .AND. bond is triple then atom_type is N.1 1.8.4 If num_nonmet .eq. 2 .AND. ( bonds are double, double .OR. bonds are single, triple ) then atom_type is N.1 1.8.5 If num_nonmet .eq. 3 .AND. one bond is to C=O or C=S then atom_type is N.am 1.8.6 If num_nonmet .eq. 3 then 1.8.6.1 If one bond is not single then atom_type is N.pl3 1.8.6.2 If all bonds are single then 1.8.6.2.1 If one single bond is to an atom that forms a bond of type double, triple, aromatic or delocalised .AND. one other single bond is to H then atom_type is N.pl3 1.8.6.2.2 If one single bond is to an atom that forms a bond of type double, triple, aromatic or delocalised .AND. neither of the other single bonds are to H .AND. sum_of_angles around N .ge. 350 deg then atom_type is N.pl3 1.8.6.3 If num_nonmet .eq. 3 otherwise then atom_type is N.3 1.8.7 If element_symbol is N and none of the above then atom_type is N.2 1.9 If element_symbol is S then 1.9.1 If num_nonmet .eq. 3 .AND. 1 bond is to an oxygen with only one non-metal bond then atom_type is S.o 1.9.2 If num_nonmet .eq. 4 .AND. 2 bonds are to an oxygen with only one non-metal bond then atom_type is S.o2 1.9.3 If num_bond .ge. 2 .AND. all bonds are single then atom_type is S.3 1.9.4 If element_symbol is S and none of the above then atom_type is S.2 1.10 If element_symbol is Ti .OR. element_symbol is Cr then 1.10.1 If num_bond .le. 4 then atom_type is Ti.th or Cr.th 1.10.2 If num_bond .gt. 4 then atom_type is Ti.oh or Cr.oh 1.11 If element_symbol is none of the above then atom_type is element_symbol 2. If entry is not matched then for each atom 2.1 If atom is suppressed then atom_type is Du 2.2 If element_symbol is D then atom_type is H 2.3 If element_symbol is P then atom_type is P.3 2.4 If element_symbol is Co .OR. element_symbol is Ru then atom_type is Co.oh or Ru.oh 2.5 If element_symbol is C then 2.5.1 If num_bond .ge. 4 then atom_type is C.3 2.5.2 If num_bond .eq. 1 then calculate bond_distance 2.5.2.1 If bond_distance .gt. 1.41A then atom_type is C.3 2.5.2.2 If bond_distance .le. 1.22A then atom_type is C.1 2.5.2.3 If bond_distance is none of the above then atom_type is C.2 2.5.3 If element_symbol is C and none of the above then calculate average_angle about C 2.5.3.1 If average_angle .le. 115 deg then atom_type is C.3 2.5.3.2 If average_angle .gt. 160 deg then atom_type is C.1 2.5.3.3 If average_angle is none of the above then atom_type is C.2 2.6 If element_symbol is O then 2.6.1 If num_nonmet .eq. 1 then 2.6.1.1 If bond is to carbon .AND. carbon forms a total of 3 bonds, 2 of which are to an oxygen forming only 1 non-metal bond then atom_type is O.co2 2.6.1.2 If bond is to phosphorus .AND. phosphorus forms at least 2 bonds to an oxygen forming only 1 non-metal bond then atom_type is O.co2 2.6.2 If num_nonmet .eq. 0 then atom_type is O.3 2.6.3 If num_bond .ge. 2 then atom_type is O.3 2.6.4 If element_symbol is O and none of the above then atom_type is O.2 2.7 If element_symbol is N then 2.7.1 If num_nonmet .eq. 4 then atom_type is N.4 2.7.2 If num_nonmet .eq. 1 then calculate bond_distance 2.7.2.1 If bond_distance .le. 1.2A then atom_type is N.1 2.7.2.2 If bond_distance .gt. 1.2A then atom_type is N.3 2.7.3 If num_nonmet .eq. 3 .AND. one bond is to C--O or C--S then atom_type is N.am 2.7.4 If num_nonmet .eq. 3 otherwise then calculate sum_of_angles around N 2.7.4.1 If sum_of_angles .ge. 350 deg then atom_type is N.pl3 2.7.4.2 If sum_of_angles .lt. 350 deg then atom_type is N.3 2.7.5 If element_symbol is N and none of the above then calculate average_angle about N 2.7.5.1 If average_angle .gt. 160 deg then atom_type is N.1 2.7.5.2 If average_angle .le. 160 deg then atom_type is N.2 2.8 If element_symbol is S then 2.8.1 If num_nonmet .eq. 3 .AND. 1 bond is to an oxygen with only one non-metal bond then atom_type is S.o 2.8.2 If num_nonmet .eq. 4 .AND. 2 bonds are to an oxygen with only one non-metal bond then atom_type is S.o2 2.8.3 If num_bond .ge. 2 then atom_type is S.3 2.8.4 If element_symbol is S and none of the above then atom_type is S.2 2.9 If element_symbol is Ti .OR. element_symbol is Cr then 2.9.1 If num_bond .le. 4 then atom_type is Ti.th or Cr.th 2.9.2 If num_bond .gt. 4 then atom_type is Ti.oh or Cr.oh 2.10 If element_symbol is none of the above then atom_type is element_symbol 3. If entry has no crystal connectivity then for each atom 3.1 If atom is suppressed then atom_type is Du 3.2 If element_symbol is D then atom_type is H 3.3 If element_symbol is P then atom_type is P.3 3.4 If element_symbol is Co .OR. element_symbol is Ru .OR. element_symbol is Ti .OR. element_symbol is Cr then atom_type is Co.oh or Ru.oh or Ti.oh or Cr.oh 3.5 If element_symbol is C then atom_type is C.3 3.6 If element_symbol is O then atom_type is O.3 3.7 If element_symbol is N then atom_type is N.3 3.8 If element_symbol is S then atom_type is S.3 3.9 If element_symbol is none of the above then atom_type is element_symbol
CSD bond type SYBYL bond type 1 (single) 1 2 (double) 2 3 (triple) 3 4 (quadruple) un 5 (aromatic) ar 6 (polymeric) un 7 (delocalised double) un 9 (pi) unIn addition, the SYBYL bond type amide (am) is assigned to a bond from an amide nitrogen (N.am) to a carbon atom connected to oxygen with a double bond.
For unmatched entries, bond types are assigned as follows.
Any bond from the following SYBYL atom types is single (1): H F Cl Br I C.3 S.3 N.3 N.4 A bond between SYBYL atom types O.2 and C.2 is double (2). A bond between N.am and C--O or C--S is amide (am) All other bond types are unspecified (un)No bond record is written for entries with no crystal connectivity.