Program parameters : Bond tolerance (A) : ( 0.350) Bond deviation tolerance (A) : ( 0.050) Large range for bond lengths (A) : ( 0.070) Large range for bond angles (d) : ( 8.000) Large range for dihedrals (d) : ( 15.000) Large range for impropers (d) : ( 8.000) Improper deviation tolerance (d) : ( 8.000) Flat improper cut-off (d) : ( 15.000) Max distance to a flat plane (A) : ( 0.050) Reading PDB file ... > (COMPND CPZ 4-(4-CHLOROPHENYL)IMIDAZOLE) > (REMARK CPZ Part of HIC-Up: http://xray.bmc.uu.se/hicup) > (REMARK CPZ Extracted from PDB file pdb1suo.ent) > (REMARK CPZ Formula C9 H7 CL N2) Formula : (CPZ C9 H7 CL N2) > (REMARK CPZ Nr of non-hydrogen atoms 12) > (REMARK CPZ Eigen-values covariance X/Y/Z 73.7 8.6 0.3) > (REMARK CPZ Residue type CPZ) > (REMARK CPZ Residue name 2654) > (REMARK CPZ Original residue name (for O) $600) > (REMARK CPZ RESOLUTION. 1.90 ANGSTROMS.) > (REMARK CPZ occurs in 0 other PDB entries) > (REMARK CPZ) Using residue : (CPZ) Identifier : ( 2654) Segment ID : ( ) Using formula : ( C9 H7 CL N2) Element ? | C| Carbon | 6 9 Element ? | H| Hydrogen | 1 7 Element ? |CL| Chlorine | 17 1 Element ? | N| Nitrogen | 7 2 Atom # 1 = C11 @ 0.807 -0.463 0.561 1.00 20.00 Atom # 2 = C10 @ 0.764 -0.484 1.955 1.00 20.00 Atom # 3 = C9 @ 1.800 -1.079 2.676 1.00 20.00 Atom # 4 = C8 @ 2.878 -1.652 2.002 1.00 20.00 Atom # 5 = C7 @ 2.921 -1.631 0.608 1.00 20.00 Atom # 6 = C6 @ 1.885 -1.036 -0.112 1.00 20.00 Atom # 7 = C4 @ 1.928 -1.014 -1.554 1.00 20.00 Atom # 8 = C2 @ 1.425 -0.120 -2.466 1.00 20.00 Atom # 9 = N1 @ 1.711 -0.512 -3.750 1.00 20.00 Atom # 10 = C5 @ 2.383 -1.634 -3.616 1.00 20.00 Atom # 11 = N3 @ 2.539 -1.978 -2.302 1.00 20.00 Atom # 12 = CL @ 1.748 -1.103 4.396 1.00 20.00 > (REMARK CPZ ENDHET) Nr of atoms read : ( 12) Nr of extra examples : ( 0) Expected formula : ( C9 H7 CL N2) Observed formula : (C9 N2 CL1) Element | H| Expected 7 | Observed 0 Element | C| Expected 9 | Observed 9 Element | N| Expected 2 | Observed 2 Element |CL| Expected 1 | Observed 1 Expected and observed formulae agree (ignoring any hydrogens) ! Looking for bonded atoms ... Bond C11 - C10 = 1.395 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.39 (devn. 0.00) For: C-C aromatic or near two triple bonds; range 1.373-1.395 Bond C11 - C6 = 1.394 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.39 (devn. 0.00) For: C-C aromatic or near two triple bonds; range 1.373-1.395 Bond C10 - C9 = 1.395 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.39 (devn. 0.01) For: C-C aromatic or near two triple bonds; range 1.373-1.395 Bond C9 - C8 = 1.395 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.39 (devn. 0.00) For: C-C aromatic or near two triple bonds; range 1.373-1.395 Bond C9 - CL = 1.721 A (cutoff : 2.020) Nr of entries in library : ( 3) Closest to 1.71 (devn. 0.01) For: C-Cl CH2=CH-Cl or C6H5-Cl type; range 1.70-1.72 Bond C8 - C7 = 1.395 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.39 (devn. 0.00) For: C-C aromatic or near two triple bonds; range 1.373-1.395 Bond C7 - C6 = 1.395 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.39 (devn. 0.00) For: C-C aromatic or near two triple bonds; range 1.373-1.395 Bond C6 - C4 = 1.443 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.44 (devn. 0.00) For: C-C single shortened; range 1.421-1.46 Bond C4 - C2 = 1.373 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.39 (devn. 0.02) For: C-C aromatic or near two triple bonds; range 1.373-1.395 Bond C4 - N3 = 1.365 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.34 (devn. 0.02) For: C-N partial double; range 1.322-1.352 Bond C2 - N1 = 1.373 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.34 (devn. 0.03) For: C-N partial double; range 1.322-1.352 Bond N1 - C5 = 1.315 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.34 (devn. 0.03) For: C-N partial double; range 1.322-1.352 Bond C5 - N3 = 1.367 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.34 (devn. 0.03) For: C-N partial double; range 1.322-1.352 Nr of bonds found : ( 13) Generating neighbour lists ... Trying to guess number of hydrogens ... Minimum C-C single bond (A) : ( 1.480) Minimum C-C double bond (A) : ( 1.280) Minimum C-N single bond (A) : ( 1.400) Minimum C-N double bond (A) : ( 1.200) Minimum C-O single bond (A) : ( 1.300) Minimum C-S single bond (A) : ( 1.770) Carbon C11 Nbrs: 2 ~Hs: 1 Carbon C10 Nbrs: 2 ~Hs: 1 Carbon C9 Nbrs: 3 ~Hs: 0 Carbon C8 Nbrs: 2 ~Hs: 1 Carbon C7 Nbrs: 2 ~Hs: 1 Carbon C6 Nbrs: 3 ~Hs: 0 Carbon C4 Nbrs: 3 ~Hs: 0 Carbon C2 Nbrs: 2 ~Hs: 1 Nitrogen N1 Nbrs: 2 ~Hs: 1 Carbon C5 Nbrs: 2 ~Hs: 1 Nitrogen N3 Nbrs: 2 ~Hs: 1 Est. total nr of hydrogens : ( 8) Looking for angles ... AtmJ AtmI AtmK Angle ---- ---- ---- ----- C10 C11 C6 120.01 C11 C10 C9 119.99 C10 C9 C8 119.96 C10 C9 CL 119.99 C8 C9 CL 120.04 C9 C8 C7 120.05 C8 C7 C6 119.96 C11 C6 C7 120.03 C11 C6 C4 119.95 C7 C6 C4 120.02 C6 C4 C2 131.53 C6 C4 N3 123.40 C2 C4 N3 105.07 C4 C2 N1 111.05 C2 N1 C5 104.77 N1 C5 N3 111.78 C4 N3 C5 107.34 Looking for dihedrals (and planes) ... AtmK AtmI AtmJ AtmL Dihedral ---- ---- ---- ---- ------- C6 C11 C10 C9 -0.02 Flat ? C10 C11 C6 C7 0.02 Flat ? C10 C11 C6 C4 179.98 Flat ? C11 C10 C9 C8 0.02 Flat ? C11 C10 C9 CL 179.92 Flat ? C10 C9 C8 C7 -0.02 Flat ? CL C9 C8 C7 -179.92 Flat ? C9 C8 C7 C6 0.02 Flat ? C8 C7 C6 C11 -0.02 Flat ? C8 C7 C6 C4 -179.98 Flat ? C11 C6 C4 C2 30.05 C11 C6 C4 N3 -149.99 C7 C6 C4 C2 -149.99 C7 C6 C4 N3 29.96 C6 C4 C2 N1 -179.99 Flat ? N3 C4 C2 N1 0.05 Flat ? C6 C4 N3 C5 -179.99 Flat ? C2 C4 N3 C5 -0.02 Flat ? C4 C2 N1 C5 -0.06 Flat ? C2 N1 C5 N3 0.04 Flat ? N1 C5 N3 C4 -0.01 Flat ? Looking for impropers (and planes) ... Atm* Nbr1 Nbr2 Nbr3 Improper ---- ---- ---- ---- -------- C9 C10 C8 CL -0.06 C6 C11 C7 C4 -0.02 C4 C6 C2 N3 -0.03 Number of possible flat planes : ( 20) Looking for more planes ... Number of possible flat planes : ( 28) Expanding planes ... WARNING - Reset negative RMSD in LSQGJK : ( -1.638E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.357E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.537E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.010E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.593E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.062E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.757E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.202E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.118E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.118E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.029E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.368E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.065E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.446E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.768E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.022E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.095E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.029E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.357E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.885E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.543E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.446E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.836E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.023E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.095E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.014E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.827E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.834E-08) WARNING - Reset negative RMSD in LSQGJK : ( -8.464E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.092E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.794E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.535E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.897E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.917E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.616E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.743E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.076E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.467E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.455E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.748E-09) WARNING - Reset negative RMSD in LSQGJK : ( -3.905E-10) WARNING - Reset negative RMSD in LSQGJK : ( -3.743E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.351E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.160E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.322E-09) WARNING - Reset negative RMSD in LSQGJK : ( -3.748E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.455E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.100E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.095E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.446E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.029E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.537E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.827E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.828E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.757E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.010E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.505E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.577E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.577E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.019E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.021E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.095E-08) WARNING - Reset negative RMSD in LSQGJK : ( -8.828E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.834E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.424E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.110E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.743E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.743E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.253E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.351E-09) WARNING - Reset negative RMSD in LSQGJK : ( -3.905E-10) WARNING - Reset negative RMSD in LSQGJK : ( -2.790E-07) Removing non-unique planes ... Plane nr : ( 24) Nr of atoms : ( 8) WARNING - Reset negative RMSD in LSQGJK : ( -9.834E-08) RMSD to least-squares plane (A): ( 0.001) Atom Dist (A) C7 0.000 C8 0.000 C6 0.000 C9 -0.001 C11 0.000 C4 0.000 C10 0.000 CL 0.001 Plane nr : ( 28) Nr of atoms : ( 6) WARNING - Reset negative RMSD in LSQGJK : ( -2.160E-08) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) N3 0.000 C4 0.000 C5 0.000 C6 0.000 C2 0.000 N1 0.000 ------------------- ----- SUMMARY ----- ------------------- Residue type : (CPZ) Identifier : ( 2654) Segment ID : ( ) Nr of atoms : ( 12) List of elements (from file) : ( C9 H7 CL N2) Deduced formula : (C9 N2 CL1) Guestimated total nr of Hs : ( 8) Nr of extra examples : ( 0) Nr of distances < 0.8 A : ( 0) Nr of bond angles < 80 degrees : ( 0) Nr of bonds found : ( 13) ... bonds without ideal value : ( 0) ... bonds near ideal value : ( 13) ... bonds far from ideal value : ( 0) -"- % : ( 0.000) Nr of angles found : ( 17) Nr of dihedrals found : ( 21) Nr of atoms with impropers : ( 3) ... imprs far from ideal value : ( 0) -"- % : ( 0.000) Nr of flat planes : ( 2)