LIGPLOT Operating Manual
Appendix B - LIGPLOT file formats
a. Hydrogen-bonds file, .hhb
The table below shows the LIGPLOT file format for the .hhb file containing the listing of hydrogen bonds to be plotted.Line 1: 'ligplot.hhb'
Line 2: (blank)
Line 3:
' Donor Acceptor Distance'
Lines 4 to end:-
--------------------------------------------------------------------------- Field | Column | FORTRAN | No. | range | format | Description --------------------------------------------------------------------------- 1. | 1 - 3 | A3 | Donor residue standard 3 letter code - | 4 - 4 | 1X | Blank 2. | 5 - 5 | A1 | Donor chain identifier - | 6 - 6 | 1X | Blank 3. | 7 - 11 | A5 | Donor residue sequence number - | 12 - 13 | 2X | Blank 4. | 14 - 16 | A3 | Donor residue atom name (eg CA or ND1) - | 17 - 21 | 5X | Blank 5. | 22 - 24 | A3 | Acceptor residue standard 3 letter code - | 25 - 25 | 1X | Blank 6. | 26 - 26 | A1 | Acceptor chain identifier - | 27 - 27 | 1X | Blank 7. | 28 - 32 | A5 | Acceptor residue sequence number - | 33 - 34 | 2X | Blank 8. | 35 - 37 | A3 | Acceptor residue atom name (eg CA or ND1) - | 38 - 41 | 4X | Blank 9. | 42 - 45 | F4.2 | Hydrogen bond distance ---------------------------------------------------------------------------
Example of .hhb file
A sample ligplot.hhb file is given below:-
1 2 3 4
123456789012345678901234567890123456789012345
---------------------------------------------
ligplot.hhb output:
Donor Acceptor Distance
HIS 57 NE2 TRP C 252 OXT 3.13
GLY 193 N TRP C 252 O 3.03
SER 195 N TRP C 252 O 2.69
TRP C 252 N SER 214 O 3.00
GLY 216 N GLY C 250 O 3.15
GLY C 250 N GLY 216 O 2.92
TRP C 252 NE1 SER 217 O 3.12
b. Non-bonded contacts file, .nnb
The table below shows the LIGPLOT file format for the .nnb file containing the listing of non-bonded contacts to be plotted.Line 1: 'ligplot.nnb'
Line 2: (blank)
Line 3:
' Atom 1 Atom 2 Distance'
Lines 4 to end:-
--------------------------------------------------------------------------- Field | Column | FORTRAN | No. | range | format | Description --------------------------------------------------------------------------- 1. | 1 - 3 | A3 | Atom 1: standard 3 letter code - | 4 - 4 | 1X | Blank 2. | 5 - 5 | A1 | Atom 1: chain identifier - | 6 - 6 | 1X | Blank 3. | 7 - 11 | A5 | Atom 1: residue sequence number - | 12 - 13 | 2X | Blank 4. | 14 - 16 | A3 | Atom 1: residue atom name (eg CA or ND1) - | 17 - 21 | 5X | Blank 5. | 22 - 24 | A3 | Atom 2: residue standard 3 letter code - | 25 - 25 | 1X | Blank 6. | 26 - 26 | A1 | Atom 2: chain identifier - | 27 - 27 | 1X | Blank 7. | 28 - 32 | A5 | Atom 2: residue sequence number - | 33 - 34 | 2X | Blank 8. | 35 - 37 | A3 | Atom 2: residue atom name (eg CA or ND1) - | 38 - 41 | 4X | Blank 9. | 42 - 45 | F4.2 | Contact distance ---------------------------------------------------------------------------
Example of .nnb file
A sample ligplot.nnb file is given below:-
1 2 3 4
123456789012345678901234567890123456789012345
---------------------------------------------
ligplot.nnb output
Atom 1 Atom 2 Distance
ALA C 251 CB HIS 57 CD2 3.67
TRP C 252 CE3 SER 190 CB 3.52
TRP C 252 CZ3 SER 190 CB 3.58
TRP C 252 CG CYS 191 C 3.83
TRP C 252 CD1 CYS 191 C 3.77
TRP C 252 C SER 195 CA 3.79
TRP C 252 C SER 195 CB 2.86
TRP C 252 CD2 TRP 215 C 3.62
TRP C 252 CE3 TRP 215 C 3.54
TRP C 252 CZ3 TRP 215 C 3.81
GLY C 250 C TRP 215 CB 3.89
TRP C 252 CE2 GLY 216 CA 3.65
TRP C 252 CZ2 GLY 216 CA 3.29
TRP C 252 CH2 GLY 216 CA 3.48
TRP C 252 CZ2 GLY 216 C 3.60
TRP C 252 CZ3 GLY 226 CA 3.38
TRP C 252 CH2 GLY 226 CA 3.43
c. Residue centres-of-mass file, .rcm
The table below shows the file format for the .rcm file containing the centres of mass (x-y coordinates) of the residues on the plot.Line 1:
' Res. Res Flattened'
Line 2:
' Atom Name Num coordinates'
Line 3:
' ---- --- ----- ----------------'
Lines 4 onwards, defining residue centres of mass:-
--------------------------------------------------------------------------- Field | Column | FORTRAN | No. | range | format | Description --------------------------------------------------------------------------- 1. | 1 - 6 | A6 | RESDUE keyword - | 7 - 12 | 6X | Blank 2. | 13 - 16 | A4 | Centre of Mass indicator: "CofM" - | 17 - 17 | 1X | Blank 3. | 18 - 20 | A3 | Standard 3-letter amino acid code for residue - | 21 - 21 | 1X | Blank 4. | 22 - 22 | A1 | Chain identifier code 5. | 23 - 26 | I4 | Residue sequence number 6. | 27 - 27 | A1 | Insertion code (if any) - | 28 - 30 | 3X | Blank 7. | 31 - 38 | F8.3 | x-coordinate of residue's centre of mass 8. | 39 - 46 | F8.3 | y-coordinate of residue's centre of mass ---------------------------------------------------------------------------
Example of a .rcm file as output by LIGPLOT
A sample ligplot.rcm file, as generated by LIGPLOT for PDB code 8gch, is given below:-
1 2 3 4 5 6 7
1234567890123456789012345678901234567890123456789012345678901234567890
----------------------------------------------------------------------
Res. Res Flattened
Atom Name Num coordinates
---- --- ----- ----------------
RESDUE CofM GLY C 250 -0.696 3.692
RESDUE CofM ALA C 251 0.805 0.245
RESDUE CofM TRP C 252 -3.097 -1.856
RESDUE CofM HIS - 57 6.414 -3.497
RESDUE CofM GLY - 216 -4.914 3.844
RESDUE CofM ASP - 102 6.205 -8.482
RESDUE CofM SER - 195 -1.501 -8.050
RESDUE CofM SER - 214 5.391 0.946
RESDUE CofM TRP - 215 -9.097 1.708
RESDUE CofM SER - 217 -9.342 -2.440
RESDUE CofM GLY - 193 -5.669 -6.010
RESDUE CofM SER - 190 -13.399 0.649
RESDUE CofM CYS - 191 -8.321 -9.347
RESDUE CofM GLY - 226 -7.737 6.593
RESDUE CofM MET - 192 -11.215 -5.617
Addition of ATOM records to the .rcm file
In addition to these residue centre-of-mass records, the file can also contain ATOM records in standard PDB format (see Appendix A - Brookhaven file format). These can be taken from, say, a ligplot.pdb file of flattened coordinates generated by a prior run of LIGPLOT. The ATOM records can be used as positional restraints on a subsequent run by following the procedure described in section 6c - Same protein, different ligands.
Example of a .rcm file with ATOM records added
An example of the above ligplot.rcm file, with the His57 and Asp102 centre-of-mass records replaced by the flattened coordinates of these residues as taken from the ligplot.pdb file:-
1 2 3 4 5 6 7
1234567890123456789012345678901234567890123456789012345678901234567890
----------------------------------------------------------------------
Res. Res Flattened
Atom Name Num coordinates
---- --- ----- ----------------
RESDUE CofM GLY C 250 -0.696 3.692
RESDUE CofM ALA C 251 0.805 0.245
RESDUE CofM TRP C 252 -3.097 -1.856
ATOM 385 N HIS 57 7.920 -4.629 0.000 1.00 6.92 6.920
ATOM 386 CA HIS 57 8.002 -3.175 0.000 1.00 7.11 7.110
ATOM 387 C HIS 57 9.316 -2.413 0.000 1.00 7.57 7.570
ATOM 388 O HIS 57 9.345 -1.154 0.000 1.00 8.14 8.140
ATOM 389 CB HIS 57 6.615 -2.482 0.000 1.00 7.18 7.180
ATOM 390 CG HIS 57 5.474 -3.458 0.000 1.00 7.22 7.220
ATOM 391 ND1 HIS 57 5.557 -4.819 0.000 1.00 6.95 6.950
ATOM 392 CD2 HIS 57 4.134 -3.163 0.000 1.00 6.92 6.920
ATOM 393 CE1 HIS 57 4.330 -5.324 0.000 1.00 7.49 7.490
ATOM 394 NE2 HIS 57 3.448 -4.350 0.000 1.00 7.23 7.230
ATOM 729 N ASP 102 3.849 -9.704 0.000 1.00 7.78 7.780
ATOM 730 CA ASP 102 5.273 -9.283 0.000 1.00 6.95 6.950
ATOM 731 C ASP 102 6.476 -10.179 0.000 1.00 7.25 7.250
ATOM 732 O ASP 102 7.641 -9.702 0.000 1.00 7.16 7.160
ATOM 733 CB ASP 102 5.268 -7.731 0.000 1.00 7.18 7.180
ATOM 734 CG ASP 102 6.683 -7.212 0.000 1.00 6.68 6.680
ATOM 735 OD1 ASP 102 7.611 -8.064 0.000 1.00 7.10 7.100
ATOM 736 OD2 ASP 102 6.838 -5.976 0.000 1.00 7.75 7.750
RESDUE CofM GLY - 216 -4.914 3.844
RESDUE CofM SER - 195 -1.501 -8.050
RESDUE CofM SER - 214 5.391 0.946
RESDUE CofM TRP - 215 -9.097 1.708
RESDUE CofM SER - 217 -9.342 -2.440
RESDUE CofM GLY - 193 -5.669 -6.010
RESDUE CofM SER - 190 -13.399 0.649
RESDUE CofM CYS - 191 -8.321 -9.347
RESDUE CofM GLY - 226 -7.737 6.593
RESDUE CofM MET - 192 -11.215 -5.617