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 CP6 5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMIDINE-2,4-DIAMINE; PYRIMETHAMINE) > (REMARK CP6 Part of HIC-Up: http://xray.bmc.uu.se/hicup) > (REMARK CP6 Extracted from PDB file pdb2bl9.ent) > (REMARK CP6 Formula C12 H13 CL N4) Formula : (CP6 C12 H13 CL N4) > (REMARK CP6 Nr of non-hydrogen atoms 17) > (REMARK CP6 Eigen-values covariance X/Y/Z 128.0 30.3 6.6) > (REMARK CP6 Residue type CP6) > (REMARK CP6 Residue name 2627) > (REMARK CP6 Original residue name (for O) $A1240) > (REMARK CP6 RESOLUTION. 1.90 ANGSTROMS.) > (REMARK CP6 occurs in 2 other PDB entries) > (REMARK CP6 Also in 2.0-2.5A : 1J3J 2BLA) > (REMARK CP6 Resolution (A) : 2.30 2.50) > (REMARK CP6) Using residue : (CP6) Identifier : ( 2627) Segment ID : ( ) Using formula : ( C12 H13 CL N4) Element ? | C| Carbon | 6 12 Element ? | H| Hydrogen | 1 13 Element ? |CL| Chlorine | 17 1 Element ? | N| Nitrogen | 7 4 Atom # 1 = N1 @ -1.390 -0.026 -3.071 1.00 20.00 Atom # 2 = C2 @ -0.246 0.096 -3.729 1.00 20.00 Atom # 3 = C3 @ -1.411 -0.039 -1.744 1.00 20.00 Atom # 4 = C4 @ -0.195 0.074 -1.043 1.00 20.00 Atom # 5 = C5 @ 0.979 0.206 -1.779 1.00 20.00 Atom # 6 = N6 @ 0.914 0.210 -3.101 1.00 20.00 Atom # 7 = C7 @ -0.167 0.064 0.438 1.00 20.00 Atom # 8 = C8 @ -0.481 -1.100 1.136 1.00 20.00 Atom # 9 = C9 @ -0.453 -1.104 2.516 1.00 20.00 Atom # 10 = C10 @ -0.114 0.045 3.207 1.00 20.00 Atom # 11 = C11 @ 0.198 1.205 2.519 1.00 20.00 Atom # 12 = C12 @ 0.178 1.219 1.139 1.00 20.00 Atom # 13 = N13 @ -2.607 -0.168 -1.060 1.00 20.00 Atom # 14 = N14 @ -0.265 0.105 -5.112 1.00 20.00 Atom # 15 = C15 @ 2.308 0.336 -1.080 1.00 20.00 Atom # 16 = C16 @ 2.942 -1.047 -0.930 1.00 20.00 Atom # 17 = CL1 @ -0.080 0.034 4.942 1.00 20.00 > (REMARK CP6 ENDHET) Nr of atoms read : ( 17) Nr of extra examples : ( 0) Expected formula : ( C12 H13 CL N4) Observed formula : (C12 N4 CL1) Element | H| Expected 13 | Observed 0 Element | C| Expected 12 | Observed 12 Element | N| Expected 4 | Observed 4 Element |CL| Expected 1 | Observed 1 Expected and observed formulae agree (ignoring any hydrogens) ! Looking for bonded atoms ... Bond N1 - C2 = 1.325 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.34 (devn. 0.01) For: C-N partial double; range 1.322-1.352 Bond N1 - C3 = 1.327 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.34 (devn. 0.01) For: C-N partial double; range 1.322-1.352 Bond C2 - N6 = 1.324 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 - N14 = 1.383 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.34 (devn. 0.04) For: C-N partial double; range 1.322-1.352 Bond C3 - C4 = 1.408 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 C3 - N13 = 1.384 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.34 (devn. 0.04) For: C-N partial double; range 1.322-1.352 Bond C4 - C5 = 1.392 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 C4 - C7 = 1.481 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.44 (devn. 0.04) For: C-C single shortened; range 1.421-1.46 Bond C5 - N6 = 1.324 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 C5 - C15 = 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 C7 - C8 = 1.393 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 - C12 = 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 C8 - C9 = 1.380 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 - C10 = 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 C10 - C11 = 1.384 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 C10 - CL1 = 1.735 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 C11 - C12 = 1.380 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 C15 - C16 = 1.529 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.53 (devn. 0.00) For: C-C single; range 1.49-1.54 Nr of bonds found : ( 18) 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) Nitrogen N1 Nbrs: 2 ~Hs: 1 Carbon C2 Nbrs: 3 ~Hs: 0 Carbon C3 Nbrs: 3 ~Hs: 0 Carbon C4 Nbrs: 3 ~Hs: 0 Carbon C5 Nbrs: 3 ~Hs: 0 Nitrogen N6 Nbrs: 2 ~Hs: 1 Carbon C7 Nbrs: 3 ~Hs: 0 Carbon C8 Nbrs: 2 ~Hs: 1 Carbon C9 Nbrs: 2 ~Hs: 1 Carbon C10 Nbrs: 3 ~Hs: 0 Carbon C11 Nbrs: 2 ~Hs: 1 Carbon C12 Nbrs: 2 ~Hs: 1 Nitrogen N13 Nbrs: 1 ~Hs: 0 Nitrogen N14 Nbrs: 1 ~Hs: 0 Carbon C15 Nbrs: 2 ~Hs: 2 Carbon C16 Nbrs: 1 ~Hs: 3 Est. total nr of hydrogens : ( 11) Looking for angles ... AtmJ AtmI AtmK Angle ---- ---- ---- ----- C2 N1 C3 120.73 N1 C2 N6 121.92 N1 C2 N14 119.02 N6 C2 N14 119.06 N1 C3 C4 118.90 N1 C3 N13 120.58 C4 C3 N13 120.52 C3 C4 C5 118.21 C3 C4 C7 120.90 C5 C4 C7 120.89 C4 C5 N6 119.14 C4 C5 C15 120.44 N6 C5 C15 120.41 C2 N6 C5 121.10 C4 C7 C8 120.15 C4 C7 C12 120.11 C8 C7 C12 119.73 C7 C8 C9 119.92 C8 C9 C10 120.14 C9 C10 C11 120.21 C9 C10 CL1 119.94 C11 C10 CL1 119.85 C10 C11 C12 120.14 C7 C12 C11 119.86 C5 C15 C16 109.46 Looking for dihedrals (and planes) ... AtmK AtmI AtmJ AtmL Dihedral ---- ---- ---- ---- ------- C3 N1 C2 N6 -0.05 Flat ? C3 N1 C2 N14 179.98 Flat ? C2 N1 C3 C4 -0.24 Flat ? C2 N1 C3 N13 -179.93 Flat ? N1 C2 N6 C5 0.04 Flat ? N14 C2 N6 C5 -179.99 Flat ? N1 C3 C4 C5 0.52 Flat ? N1 C3 C4 C7 -179.98 Flat ? N13 C3 C4 C5 -179.79 Flat ? N13 C3 C4 C7 -0.29 Flat ? C3 C4 C5 N6 -0.53 Flat ? C3 C4 C5 C15 179.76 Flat ? C7 C4 C5 N6 179.97 Flat ? C7 C4 C5 C15 0.26 Flat ? C3 C4 C7 C8 68.64 C3 C4 C7 C12 -111.56 C5 C4 C7 C8 -111.87 C5 C4 C7 C12 67.93 C4 C5 N6 C2 0.26 Flat ? C15 C5 N6 C2 179.97 Flat ? C4 C5 C15 C16 93.05 N6 C5 C15 C16 -86.65 C4 C7 C8 C9 179.98 Flat ? C12 C7 C8 C9 0.18 Flat ? C4 C7 C12 C11 179.78 Flat ? C8 C7 C12 C11 -0.42 Flat ? C7 C8 C9 C10 0.00 Flat ? C8 C9 C10 C11 0.05 Flat ? C8 C9 C10 CL1 -179.98 Flat ? C9 C10 C11 C12 -0.29 Flat ? CL1 C10 C11 C12 179.74 Flat ? C10 C11 C12 C7 0.47 Flat ? Looking for impropers (and planes) ... Atm* Nbr1 Nbr2 Nbr3 Improper ---- ---- ---- ---- -------- C2 N1 N6 N14 0.02 C3 N1 C4 N13 0.18 C4 C3 C5 C7 -0.29 C5 C4 N6 C15 0.17 C7 C4 C8 C12 -0.12 C10 C9 C11 CL1 -0.02 Number of possible flat planes : ( 32) Looking for more planes ... Number of possible flat planes : ( 38) Expanding planes ... WARNING - Reset negative RMSD in LSQGJK : ( -3.949E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.921E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.357E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.504E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.605E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.097E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.810E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.060E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.667E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.861E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.144E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.567E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.605E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.097E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.183E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.537E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.164E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.197E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.976E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.355E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.295E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.959E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.289E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.080E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.705E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.854E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.708E-08) WARNING - Reset negative RMSD in LSQGJK : ( -8.522E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.785E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.332E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.962E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.597E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.137E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.052E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.563E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.970E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.332E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.342E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.636E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.810E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.563E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.123E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.123E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.782E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.308E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.567E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.164E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.120E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.197E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.220E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.810E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.053E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.652E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.457E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.370E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.248E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.053E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.671E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.172E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.248E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.176E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.647E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.311E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.068E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.914E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.514E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.977E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.049E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.311E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.986E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.024E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.719E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.504E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.976E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.000E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.403E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.453E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.583E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.854E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.597E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.563E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.748E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.332E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.715E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.123E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.053E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.172E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.514E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.990E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.068E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.504E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.067E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.462E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.847E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.164E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.197E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.537E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.016E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.648E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.337E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.647E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.777E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.386E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.949E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.565E-07) Removing non-unique planes ... Plane nr : ( 34) Nr of atoms : ( 10) WARNING - Reset negative RMSD in LSQGJK : ( -4.567E-07) RMSD to least-squares plane (A): ( 0.002) Atom Dist (A) N6 0.000 C2 0.000 C5 0.002 N1 0.001 N14 -0.002 C4 -0.003 C15 0.002 C3 0.002 C7 -0.003 N13 0.002 Plane nr : ( 38) Nr of atoms : ( 8) RMSD to least-squares plane (A): ( 0.001) Atom Dist (A) C12 -0.003 C7 0.001 C11 0.002 C4 0.000 C8 0.000 C10 0.000 C9 0.000 CL1 0.000 ------------------- ----- SUMMARY ----- ------------------- Residue type : (CP6) Identifier : ( 2627) Segment ID : ( ) Nr of atoms : ( 17) List of elements (from file) : ( C12 H13 CL N4) Deduced formula : (C12 N4 CL1) Guestimated total nr of Hs : ( 11) Nr of extra examples : ( 0) Nr of distances < 0.8 A : ( 0) Nr of bond angles < 80 degrees : ( 0) Nr of bonds found : ( 18) ... bonds without ideal value : ( 0) ... bonds near ideal value : ( 18) ... bonds far from ideal value : ( 0) -"- % : ( 0.000) Nr of angles found : ( 25) Nr of dihedrals found : ( 32) Nr of atoms with impropers : ( 6) ... imprs far from ideal value : ( 0) -"- % : ( 0.000) Nr of flat planes : ( 2)