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 2CM 2-CHLORO-6-METHYL-ANILINE) > (REMARK 2CM Part of HIC-Up: http://xray.bmc.uu.se/hicup) > (REMARK 2CM Extracted from PDB file pdb1ovh.ent) > (REMARK 2CM Formula C7 H8 CL N) Formula : (2CM C7 H8 CL N) > (REMARK 2CM Nr of non-hydrogen atoms 9) > (REMARK 2CM Eigen-values covariance X/Y/Z 18.6 14.5 0.0) > (REMARK 2CM Residue type 2CM) > (REMARK 2CM Residue name 477) > (REMARK 2CM Original residue name (for O) $404) > (REMARK 2CM RESOLUTION. 1.95 ANGSTROMS.) > (REMARK 2CM occurs in 0 other PDB entries) > (REMARK 2CM) Using residue : (2CM) Identifier : ( 477) Segment ID : ( ) Using formula : ( C7 H8 CL N) Element ? | C| Carbon | 6 7 Element ? | H| Hydrogen | 1 8 Element ? |CL| Chlorine | 17 1 Element ? | N| Nitrogen | 7 1 Atom # 1 = C1 @ 0.273 -0.629 -0.004 1.00 20.00 Atom # 2 = C2 @ 1.598 -0.217 0.001 1.00 20.00 Atom # 3 = C3 @ -0.746 0.317 0.001 1.00 20.00 Atom # 4 = N4 @ -0.037 -1.992 -0.003 1.00 20.00 Atom # 5 = C5 @ 1.901 1.131 0.000 1.00 20.00 Atom # 6 = C6 @ 2.706 -1.239 0.003 1.00 20.00 Atom # 7 = C7 @ -0.436 1.663 0.000 1.00 20.00 Atom # 8 = CL8 @ -2.406 -0.193 0.001 1.00 20.00 Atom # 9 = C9 @ 0.886 2.070 -0.001 1.00 20.00 > (REMARK 2CM ENDHET) Nr of atoms read : ( 9) Nr of extra examples : ( 0) Expected formula : ( C7 H8 CL N) Observed formula : (C7 N1 CL1) Element | H| Expected 8 | Observed 0 Element | C| Expected 7 | Observed 7 Element | N| Expected 1 | Observed 1 Element |CL| Expected 1 | Observed 1 Expected and observed formulae agree (ignoring any hydrogens) ! Looking for bonded atoms ... Bond C1 - C2 = 1.388 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 C1 - C3 = 1.390 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 C1 - N4 = 1.398 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.43 (devn. 0.03) For: C-N aromatic Bond C2 - C5 = 1.382 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 C2 - C6 = 1.507 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.53 (devn. 0.02) For: C-C single; range 1.49-1.54 Bond C3 - C7 = 1.381 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 C3 - CL8 = 1.737 A (cutoff : 2.020) Nr of entries in library : ( 3) Closest to 1.71 (devn. 0.03) For: C-Cl CH2=CH-Cl or C6H5-Cl type; range 1.70-1.72 Bond C5 - C9 = 1.383 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 C7 - C9 = 1.383 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 Nr of bonds found : ( 9) 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 C1 Nbrs: 3 ~Hs: 0 Carbon C2 Nbrs: 3 ~Hs: 0 Carbon C3 Nbrs: 3 ~Hs: 0 Nitrogen N4 Nbrs: 1 ~Hs: 0 Carbon C5 Nbrs: 2 ~Hs: 1 Carbon C6 Nbrs: 1 ~Hs: 3 Carbon C7 Nbrs: 2 ~Hs: 1 Carbon C9 Nbrs: 2 ~Hs: 1 Est. total nr of hydrogens : ( 6) Looking for angles ... AtmJ AtmI AtmK Angle ---- ---- ---- ----- C2 C1 C3 119.85 C2 C1 N4 120.09 C3 C1 N4 120.06 C1 C2 C5 119.94 C1 C2 C6 120.04 C5 C2 C6 120.02 C1 C3 C7 119.90 C1 C3 CL8 120.05 C7 C3 CL8 120.05 C2 C5 C9 120.10 C3 C7 C9 120.08 C5 C9 C7 120.12 Looking for dihedrals (and planes) ... AtmK AtmI AtmJ AtmL Dihedral ---- ---- ---- ---- ------- C3 C1 C2 C5 -0.52 Flat ? C3 C1 C2 C6 179.68 Flat ? N4 C1 C2 C5 -180.00 Flat ? N4 C1 C2 C6 0.20 Flat ? C2 C1 C3 C7 0.52 Flat ? C2 C1 C3 CL8 -179.76 Flat ? N4 C1 C3 C7 180.00 Flat ? N4 C1 C3 CL8 -0.29 Flat ? C1 C2 C5 C9 0.24 Flat ? C6 C2 C5 C9 -179.96 Flat ? C1 C3 C7 C9 -0.24 Flat ? CL8 C3 C7 C9 -179.95 Flat ? C2 C5 C9 C7 0.05 Flat ? C3 C7 C9 C5 -0.05 Flat ? Looking for impropers (and planes) ... Atm* Nbr1 Nbr2 Nbr3 Improper ---- ---- ---- ---- -------- C1 C2 C3 N4 0.30 C2 C1 C5 C6 0.12 C3 C1 C7 CL8 -0.18 Number of possible flat planes : ( 17) Looking for more planes ... Number of possible flat planes : ( 20) Expanding planes ... WARNING - Reset negative RMSD in LSQGJK : ( -3.769E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.308E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.662E-11) WARNING - Reset negative RMSD in LSQGJK : ( -9.478E-10) WARNING - Reset negative RMSD in LSQGJK : ( -4.474E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.277E-12) WARNING - Reset negative RMSD in LSQGJK : ( -1.060E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.547E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.547E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.977E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.211E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.662E-11) WARNING - Reset negative RMSD in LSQGJK : ( -5.217E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.662E-11) WARNING - Reset negative RMSD in LSQGJK : ( -1.905E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.918E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.736E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.296E-09) WARNING - Reset negative RMSD in LSQGJK : ( -3.075E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.214E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.662E-11) WARNING - Reset negative RMSD in LSQGJK : ( -1.713E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.736E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.026E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.281E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.254E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.296E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.713E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.547E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.296E-09) WARNING - Reset negative RMSD in LSQGJK : ( -5.918E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.736E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.150E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.434E-09) WARNING - Reset negative RMSD in LSQGJK : ( -4.693E-08) Removing non-unique planes ... Plane nr : ( 20) Nr of atoms : ( 9) WARNING - Reset negative RMSD in LSQGJK : ( -9.679E-10) RMSD to least-squares plane (A): ( 0.002) Atom Dist (A) C9 -0.001 C5 0.000 C7 0.000 C2 0.001 C3 0.002 C1 -0.004 C6 0.003 CL8 0.002 N4 -0.002 ------------------- ----- SUMMARY ----- ------------------- Residue type : (2CM) Identifier : ( 477) Segment ID : ( ) Nr of atoms : ( 9) List of elements (from file) : ( C7 H8 CL N) Deduced formula : (C7 N1 CL1) Guestimated total nr of Hs : ( 6) Nr of extra examples : ( 0) Nr of distances < 0.8 A : ( 0) Nr of bond angles < 80 degrees : ( 0) Nr of bonds found : ( 9) ... bonds without ideal value : ( 0) ... bonds near ideal value : ( 9) ... bonds far from ideal value : ( 0) -"- % : ( 0.000) Nr of angles found : ( 12) Nr of dihedrals found : ( 14) Nr of atoms with impropers : ( 3) ... imprs far from ideal value : ( 0) -"- % : ( 0.000) Nr of flat planes : ( 1)