Atom numbering refers to the order of real atoms in the data set. This order is also used in the working within MOPAC. This means that dummy atoms are not counted, and that the number in an atom label, if present, is ignored.
For proteins, individual atom numbers can be defined using the PDB or Jmol labels of the atoms. When the job starts to run, the labels will be replaced by the atom number. This is particularly useful when the positions of one or two atoms in a protein need to be defined using internal coordinates.
Here is a part of a data-set where all the atoms are defined using Cartesian coordinates:
N(ATOM 238 N ILE A 34) 0.51224417 +1 6.53818990 +1 -1.04530637 +1 C(ATOM 239 CA ILE A 34) -0.16583088 +1 5.27003704 +1 -0.80703857 +1 C(ATOM 240 C ILE A 34) -0.68714875 +1 4.80818590 +1 -2.17651227 +1 O(ATOM 241 O ILE A 34) -1.39480687 +1 5.59251124 +1 -2.84577137 +1 C(ATOM 242 CB ILE A 34) -1.34157959 +1 5.35970563 +1 0.16960032 +1 C(ATOM 243 CG1 ILE A 34) -0.88698566 +1 5.93876778 +1 1.50252957 +1 C(ATOM 244 CG2 ILE A 34) -1.97622375 +1 3.98432823 +1 0.34729045 +1 C(ATOM 245 CD1 ILE A 34) -2.11986936 +1 6.24297761 +1 2.36481093 +1 N(ATOM 246 N ILE A 35) -0.41349112 +1 3.53815368 +1 -2.52406899 +1 C(ATOM 247 CA ILE A 35) -0.96588627 +1 2.96694653 +1 -3.72618837 +1 C(ATOM 248 C ILE A 35) -1.70739788 +1 1.68320195 +1 -3.38891197 +1 O(ATOM 249 O ILE A 35) -1.36948744 +1 1.03220215 +1 -2.40835407 +1 C(ATOM 250 CB ILE A 35) 0.14480897 +1 2.67981879 +1 -4.80718686 +1 C(ATOM 251 CG1 ILE A 35) 1.17485652 +1 1.69119218 +1 -4.29719814 +1 C(ATOM 252 CG2 ILE A 35) 0.75772955 +1 4.00257136 +1 -5.26108111 +1 C(ATOM 253 CD1 ILE A 35) 2.13561476 +1 1.20998426 +1 -5.39083727 +1
If CB on Ile 35 needed to be defined in internal coordinates, the data set fragment would look like this:
N(ATOM 238 N ILE A 34) 0.51224417 +1 6.53818990 +1 -1.04530637 +1 C(ATOM 239 CA ILE A 34) -0.16583088 +1 5.27003704 +1 -0.80703857 +1 C(ATOM 240 C ILE A 34) -0.68714875 +1 4.80818590 +1 -2.17651227 +1 O(ATOM 241 O ILE A 34) -1.39480687 +1 5.59251124 +1 -2.84577137 +1 C(ATOM 242 CB ILE A 34) -1.34157959 +1 5.35970563 +1 0.16960032 +1 C(ATOM 243 CG1 ILE A 34) -0.88698566 +1 5.93876778 +1 1.50252957 +1 C(ATOM 244 CG2 ILE A 34) -1.97622375 +1 3.98432823 +1 0.34729045 +1 C(ATOM 245 CD1 ILE A 34) -2.11986936 +1 6.24297761 +1 2.36481093 +1 N(ATOM 246 N ILE A 35) -0.41349112 +1 3.53815368 +1 -2.52406899 +1 C(ATOM 247 CA ILE A 35) -0.96588627 +1 2.96694653 +1 -3.72618837 +1 C(ATOM 248 C ILE A 35) -1.70739788 +1 1.68320195 +1 -3.38891197 +1 O(ATOM 249 O ILE A 35) -1.36948744 +1 1.03220215 +1 -2.40835407 +1 C(ATOM 250 CB ILE A 35) 1.57627536 +1 111.9745394 +1 112.2059245 +1 247 246 240 C(ATOM 251 CG1 ILE A 35) 1.17485652 +1 1.69119218 +1 -4.29719814 +1 C(ATOM 252 CG2 ILE A 35) 0.75772955 +1 4.00257136 +1 -5.26108111 +1 C(ATOM 253 CD1 ILE A 35) 2.13561476 +1 1.20998426 +1 -5.39083727 +1
In this specific case the atom number in the label is the same as the actual atom number. This is normally not the case,
When PDB atom labels are used, the format for specifying an atom is "text", where the quotation marks are part of the specification. Only part of the PDB label is used; text starts at the first character of the atom name and ends with the last character of the residue number. If the atom name is preceded by a number, that number must be included, thus if an atom name is 3HB, the text would start with "3". Here is an example of an atom in a protein being defined using PDB atom labels:
N(ATOM 238 N ILE A 34) 0.51224417 +1 6.53818990 +1 -1.04530637 +1 C(ATOM 239 CA ILE A 34) -0.16583088 +1 5.27003704 +1 -0.80703857 +1 C(ATOM 240 C ILE A 34) -0.68714875 +1 4.80818590 +1 -2.17651227 +1 O(ATOM 241 O ILE A 34) -1.39480687 +1 5.59251124 +1 -2.84577137 +1 C(ATOM 242 CB ILE A 34) -1.34157959 +1 5.35970563 +1 0.16960032 +1 C(ATOM 243 CG1 ILE A 34) -0.88698566 +1 5.93876778 +1 1.50252957 +1 C(ATOM 244 CG2 ILE A 34) -1.97622375 +1 3.98432823 +1 0.34729045 +1 C(ATOM 245 CD1 ILE A 34) -2.11986936 +1 6.24297761 +1 2.36481093 +1 N(ATOM 246 N ILE A 35) -0.41349112 +1 3.53815368 +1 -2.52406899 +1 C(ATOM 247 CA ILE A 35) -0.96588627 +1 2.96694653 +1 -3.72618837 +1 C(ATOM 248 C ILE A 35) -1.70739788 +1 1.68320195 +1 -3.38891197 +1 O(ATOM 249 O ILE A 35) -1.36948744 +1 1.03220215 +1 -2.40835407 +1 C(ATOM 250 CB ILE A 35) 1.57627536 +1 111.9745394 +1 112.2059245 +1 "CA ILE A 35" "N ILE A 35" "C ILE A 34" C(ATOM 251 CG1 ILE A 35) 1.17485652 +1 1.69119218 +1 -4.29719814 +1 C(ATOM 252 CG2 ILE A 35) 0.75772955 +1 4.00257136 +1 -5.26108111 +1 C(ATOM 253 CD1 ILE A 35) 2.13561476 +1 1.20998426 +1 -5.39083727 +1
When Jmol (JSmol) atom labels are used, the format is similar to the PDB format, except the text is now in JSmol style. To use this style, open a PDB file using JSMOL, and identify the atom of interest. Hover the cursor over the atom, and a small pop-up window containing the JSmol atom label will appear. All the text in this label, up to but not including the hash (#) sign, should be used. Example of an atom in a protein being defined using Jmol atom labels:
N(ATOM 238 N ILE A 34) 0.51224417 +1 6.53818990 +1 -1.04530637 +1 C(ATOM 239 CA ILE A 34) -0.16583088 +1 5.27003704 +1 -0.80703857 +1 C(ATOM 240 C ILE A 34) -0.68714875 +1 4.80818590 +1 -2.17651227 +1 O(ATOM 241 O ILE A 34) -1.39480687 +1 5.59251124 +1 -2.84577137 +1 C(ATOM 242 CB ILE A 34) -1.34157959 +1 5.35970563 +1 0.16960032 +1 C(ATOM 243 CG1 ILE A 34) -0.88698566 +1 5.93876778 +1 1.50252957 +1 C(ATOM 244 CG2 ILE A 34) -1.97622375 +1 3.98432823 +1 0.34729045 +1 C(ATOM 245 CD1 ILE A 34) -2.11986936 +1 6.24297761 +1 2.36481093 +1 N(ATOM 246 N ILE A 35) -0.41349112 +1 3.53815368 +1 -2.52406899 +1 C(ATOM 247 CA ILE A 35) -0.96588627 +1 2.96694653 +1 -3.72618837 +1 C(ATOM 248 C ILE A 35) -1.70739788 +1 1.68320195 +1 -3.38891197 +1 O(ATOM 249 O ILE A 35) -1.36948744 +1 1.03220215 +1 -2.40835407 +1 C(ATOM 250 CB ILE A 35) 1.57627536 +1 111.9745394 +1 112.2059245 +1 "[ILE]34:A.CA" "[ILE]34:A.N" "[ILE]34:A.C" C(ATOM 251 CG1 ILE A 35) 1.17485652 +1 1.69119218 +1 -4.29719814 +1 C(ATOM 252 CG2 ILE A 35) 0.75772955 +1 4.00257136 +1 -5.26108111 +1 C(ATOM 253 CD1 ILE A 35) 2.13561476 +1 1.20998426 +1 -5.39083727 +1
Using Jmol or PDB labels is particularly useful when defining a reaction path. All three ways of defining connectivity can be used for any atom, but don't - it would make the data set unnecessary complicated.
In the following example, the geometry of nitrogen trifluoride, a molecule with C3v symmetry, is defined using two geometric variables, the N-F distance, and the angle between a fluorine atom, the nitrogen, and the C3 axis. The atom numbering is thus: N(1), F(2), F(3), F(4), with the atom numbers in parenthesis.
SYMMETRY Nitrogen trifluoride Using dummy atoms to allow C3v symmetry to be imposed. N 0.00000000 +0 0.0000000 +0 0.0000000 +0 XX 1.36495796 +1 0.0000000 +0 0.0000000 +0 1 0 0 XX 1.00000000 +0 120.0000000 +0 0.0000000 +0 2 1 0 F 1.36495796 +0 117.0472386 +1 180.0000000 +0 1 2 3 F 1.36495796 +0 117.0472386 +0 60.0000000 +0 1 2 3 F 1.36495796 +0 117.0472386 +0 -60.0000000 +0 1 2 3 2 1 4 5 6 4 2 5 6
Files that use Protein Data Bank format label atoms with a word, either "ATOM " or "HETATM", an atom serial number, an atom name, and a description of the atom. First, be aware that the atom serial number refers to the line in the coordinate definition, not to the atom. The first number is normally 1, the next atom is 2, etc. If a line does not define an atom, for example a line that indicates the end of a chain, then that line is also given a number. Thus, in 8GCH, chymotrypsin, there is a gap between residues 11 and 16, this is indicated by a line that starts with the word "TER" followed by a number. Up to the first occurrence of a line starting with "TER" the atom serial numbers correspond to the order in which the atom occurs, but because the "TER" line uses a number, the next atom has an atom serial number that is one larger than the number of the atom. This can be seen in the following snippet of 8GCH:
ATOM 70 CD2 LEU E 10 9.438 14.352 39.180 1.00 15.69 C ATOM 71 N SER E 11 6.843 10.440 42.087 1.00 15.10 N TER 72 SER E 11 ATOM 73 N ILE F 16 18.164 1.430 39.984 1.00 5.77 N ATOM 74 CA ILE F 16 17.888 2.418 41.019 1.00 5.90 CResidue serine 11 in chain E consists of a nitrogen atom only, the rest of the residue and everything up to the start of isoleucine 16 is missing. This gap is indicated by the word "TER" on the line with serial number 72. Up to this line each atom serial number corresponds to the order of occurrence of each atom, so the serine 11 nitrogen atom is the 70th atom defined, and has the serial number "70". The "TER" uses up a number, so the next atom, the nitrogen of isoleucine 16, has an atom serial number that is two, not one, higher than the previous atom. That is, there is a gap of size one in the atom serial numbers. When a PDB file is read in, atoms are given atom numbers, and in the snippet above, the atom numbers would be C(70), N(71), N(72), C(73). So after N(71) the atom numbers used in MOPAC do not agree with the atom serial numbers used in the PDB format.
When MOPAC writes a PDB file, it switches from MOPAC numbering to the numbering convention defined by the PDB format.