APPENDIX D - PDB ATDL 1.1
The PDB ATDL (PDBA) File Format is another special version of the standard PDB. This format was created in order to include extra information keeping the compatibility with the Brookhaven National Library specifications. For this reason, REMARK records (one for each atom) were added at the beginning of file to store the non-standard data. The REMARK type is the user defined REMARK 78 (see PDB specifications). This rule was introduced to recognize custom records from standatd REMARKs. In each custom REMARK, some information are included as: atom number, atomic charge, atom type (that is force field-dependent) and ATDL atom description. This last item isn't fully exhaustive, because it ends at second level of the ATDL description.
1 2 3 4 1234567890123456789012345678901234567890 REMARK 78 NNNNN CCC.CCCC FFFFFFFF ATDL NNNNN <- Atom number (C: %5d, Fortran: i5) CC.CCCC <- Atom charge (C: %8.4f, Fortran: f8.4) FFFF <- Atom type (C: %-4.4s, Fortran: a4) ATDL <- ATDL description (free format, see ATDL specifications)
Warning:
Starting from 1.1 specifications, introduced in VEGA 1.5.0, the atom type
format is changed in order to support atom types with more than four
characters (the limit is now eight characters). The old 1.0
specifications are supported by VEGA in read mode for backward compatibility.
Example:
A3 molecule with TRIPOS atom types and Mopac atom charges.
REMARK 4 REMARK 4 File converted by VEGA V1.4.0 REMARK 4 REMARK 78 1 -0.1342 C.ar C-361 (C-361 C-361 H-100) REMARK 78 2 -0.1211 C.ar C-361 (C-361 C-361 H-100) REMARK 78 3 0.0103 C.ar C-361 (C-361 C-361 O-260) REMARK 78 4 0.0127 C.ar C-361 (C-361 C-361 O-260) REMARK 78 5 -0.1224 C.ar C-361 (C-361 C-361 H-100) REMARK 78 6 -0.1317 C.ar C-361 (C-361 C-361 H-100) REMARK 78 7 0.1346 H H-100 (C-361) REMARK 78 8 0.1490 H H-100 (C-361) REMARK 78 9 0.1495 H H-100 (C-361) REMARK 78 10 0.1351 H H-100 (C-361) REMARK 78 11 -0.2053 O.3 O-260 (C-361 C-460) REMARK 78 12 -0.0061 C.3 C-460 (O-260 C-460 C-400 H-100) REMARK 78 13 -0.0495 C.3 C-460 (C-460 O-260 H-100 H-100) REMARK 78 14 -0.2028 O.3 O-260 (C-361 C-460) REMARK 78 15 0.0983 H H-100 (C-460) REMARK 78 16 0.1358 H H-100 (C-460) REMARK 78 17 -0.0742 C.3 C-400 (C-460 N-300 H-100 H-100) REMARK 78 18 0.1037 H H-100 (C-460) REMARK 78 19 -0.3024 N.3 N-300 (C-400 C-400 H-100) REMARK 78 20 0.1057 H H-100 (C-400) REMARK 78 21 0.0759 H H-100 (C-400) REMARK 78 22 -0.0813 C.3 C-400 (N-300 C-400 H-100 H-100) REMARK 78 23 -0.0242 C.3 C-400 (C-400 O-200 H-100 H-100) REMARK 78 24 0.1049 H H-100 (C-400) REMARK 78 25 0.0725 H H-100 (C-400) REMARK 78 26 -0.1971 O.3 O-200 (C-400 C-361) REMARK 78 27 0.0840 H H-100 (C-400) REMARK 78 28 0.0887 H H-100 (C-400) REMARK 78 29 -0.0066 C.ar C-361 (O-200 C-361 C-361) REMARK 78 30 0.1008 C.ar C-361 (C-361 C-361 O-200) REMARK 78 31 -0.2280 C.ar C-361 (C-361 C-361 H-100) REMARK 78 32 -0.0676 C.ar C-361 (C-361 C-361 H-100) REMARK 78 33 -0.2270 C.ar C-361 (C-361 C-361 H-100) REMARK 78 34 0.0895 C.ar C-361 (C-361 C-361 O-200) REMARK 78 35 0.1412 H H-100 (C-361) REMARK 78 36 0.1345 H H-100 (C-361) REMARK 78 37 0.1406 H H-100 (C-361) REMARK 78 38 -0.2037 O.3 O-200 (C-361 C-400) REMARK 78 39 -0.0770 C.3 C-400 (O-200 H-100 H-100 H-100) REMARK 78 40 0.1068 H H-100 (C-400) REMARK 78 41 0.0717 H H-100 (C-400) REMARK 78 42 0.0779 H H-100 (C-400) REMARK 78 43 -0.1905 O.3 O-200 (C-361 C-400) REMARK 78 44 -0.0788 C.3 C-400 (O-200 H-100 H-100 H-100) REMARK 78 45 0.1089 H H-100 (C-400) REMARK 78 46 0.0758 H H-100 (C-400) REMARK 78 47 0.0713 H H-100 (C-400) REMARK 78 48 0.1521 H H-100 (N-300) ATOM 1 C1 A3 1 -0.167 0.519 -0.316 1.00 0.00 ATOM 2 C2 A3 1 1.205 0.304 -0.310 1.00 0.00 ATOM 3 C3 A3 1 2.080 1.373 -0.177 1.00 0.00 ATOM 4 C4 A3 1 1.577 2.671 -0.061 1.00 0.00 ATOM 5 C5 A3 1 0.206 2.881 -0.062 1.00 0.00 ATOM 6 C6 A3 1 -0.667 1.809 -0.189 1.00 0.00 ATOM 7 H7 A3 1 -0.841 -0.318 -0.417 1.00 0.00 ATOM 8 H8 A3 1 1.601 -0.695 -0.405 1.00 0.00 ATOM 9 H9 A3 1 -0.173 3.887 0.035 1.00 0.00 ATOM 10 H10 A3 1 -1.733 1.980 -0.190 1.00 0.00 ATOM 11 O11 A3 1 3.444 1.107 -0.166 1.00 0.00 ATOM 12 C12 A3 1 4.203 2.182 0.346 1.00 0.00 ATOM 13 C13 A3 1 3.744 3.489 -0.311 1.00 0.00 ATOM 14 O14 A3 1 2.411 3.776 0.059 1.00 0.00 ATOM 15 H15 A3 1 3.813 3.412 -1.397 1.00 0.00 ATOM 16 H16 A3 1 4.382 4.319 -0.007 1.00 0.00 ATOM 17 C17 A3 1 5.678 1.886 0.076 1.00 0.00 ATOM 18 H18 A3 1 4.039 2.246 1.423 1.00 0.00 ATOM 19 N19 A3 1 6.547 2.933 0.612 1.00 0.00 ATOM 20 H20 A3 1 5.855 1.798 -0.997 1.00 0.00 ATOM 21 H21 A3 1 5.961 0.938 0.536 1.00 0.00 ATOM 22 C22 A3 1 7.967 2.742 0.320 1.00 0.00 ATOM 23 C23 A3 1 8.807 3.913 0.821 1.00 0.00 ATOM 24 H24 A3 1 8.092 2.633 -0.758 1.00 0.00 ATOM 25 H25 A3 1 8.294 1.815 0.791 1.00 0.00 ATOM 26 O26 A3 1 10.161 3.658 0.516 1.00 0.00 ATOM 27 H27 A3 1 8.681 4.035 1.898 1.00 0.00 ATOM 28 H28 A3 1 8.484 4.839 0.341 1.00 0.00 ATOM 29 C29 A3 1 10.955 4.719 0.921 1.00 0.00 ATOM 30 C30 A3 1 11.271 5.713 0.003 1.00 0.00 ATOM 31 C31 A3 1 12.069 6.782 0.410 1.00 0.00 ATOM 32 C32 A3 1 12.536 6.846 1.716 1.00 0.00 ATOM 33 C33 A3 1 12.215 5.847 2.625 1.00 0.00 ATOM 34 C34 A3 1 11.418 4.771 2.231 1.00 0.00 ATOM 35 H35 A3 1 12.341 7.576 -0.267 1.00 0.00 ATOM 36 H36 A3 1 13.151 7.677 2.027 1.00 0.00 ATOM 37 H37 A3 1 12.597 5.930 3.630 1.00 0.00 ATOM 38 O38 A3 1 11.039 3.720 3.067 1.00 0.00 ATOM 39 C39 A3 1 11.482 3.798 4.406 1.00 0.00 ATOM 40 H40 A3 1 11.115 2.931 4.956 1.00 0.00 ATOM 41 H41 A3 1 11.092 4.691 4.895 1.00 0.00 ATOM 42 H42 A3 1 12.572 3.787 4.458 1.00 0.00 ATOM 43 O43 A3 1 10.748 5.558 -1.281 1.00 0.00 ATOM 44 C44 A3 1 11.069 6.573 -2.210 1.00 0.00 ATOM 45 H45 A3 1 10.609 6.340 -3.170 1.00 0.00 ATOM 46 H46 A3 1 12.147 6.634 -2.365 1.00 0.00 ATOM 47 H47 A3 1 10.682 7.538 -1.882 1.00 0.00 ATOM 48 H48 A3 1 6.406 3.027 1.611 1.00 0.00 TER 49 A3 1 CONECT 1 2 6 7 CONECT 2 1 3 8 CONECT 3 2 4 11 CONECT 4 3 5 14 CONECT 5 4 6 9 CONECT 6 1 5 10 CONECT 7 1 CONECT 8 2 CONECT 9 5 CONECT 10 6 CONECT 11 3 12 CONECT 12 11 13 17 18 CONECT 13 12 14 15 16 CONECT 14 4 13 CONECT 15 13 CONECT 16 13 CONECT 17 12 19 20 21 CONECT 18 12 CONECT 19 17 22 48 CONECT 20 17 CONECT 21 17 CONECT 22 19 23 24 25 CONECT 23 22 26 27 28 CONECT 24 22 CONECT 25 22 CONECT 26 23 29 CONECT 27 23 CONECT 28 23 CONECT 29 26 30 34 CONECT 30 29 31 43 CONECT 31 30 32 35 CONECT 32 31 33 36 CONECT 33 32 34 37 CONECT 34 29 33 38 CONECT 35 31 CONECT 36 32 CONECT 37 33 CONECT 38 34 39 CONECT 39 38 40 41 42 CONECT 40 39 CONECT 41 39 CONECT 42 39 CONECT 43 30 44 CONECT 44 43 45 46 47 CONECT 45 44 CONECT 46 44 CONECT 47 44 CONECT 48 19 MASTER 51 0 0 0 0 0 0 0 48 1 48 0 END