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 CBT N,N-BIS(4-CHLOROBENZYL)-1H-1,2,3,4-TETRAAZOL-5-AMINE) > (REMARK CBT Part of HIC-Up: http://xray.bmc.uu.se/hicup) > (REMARK CBT Extracted from PDB file pdb1pzo.ent) > (REMARK CBT Formula C15 H13 CL2 N5) Formula : (CBT C15 H13 CL2 N5) > (REMARK CBT Nr of non-hydrogen atoms 22) > (REMARK CBT Eigen-values covariance X/Y/Z 222.5 83.0 11.6) > (REMARK CBT Residue type CBT) > (REMARK CBT Residue name 2369) > (REMARK CBT Original residue name (for O) $300) > (REMARK CBT RESOLUTION. 1.90 ANGSTROMS.) > (REMARK CBT occurs in 0 other PDB entries) > (REMARK CBT) Using residue : (CBT) Identifier : ( 2369) Segment ID : ( ) Using formula : ( C15 H13 CL2 N5) Element ? | C| Carbon | 6 15 Element ? | H| Hydrogen | 1 13 Element ? |CL| Chlorine | 17 2 Element ? | N| Nitrogen | 7 5 Atom # 1 = CL3 @ -1.288 0.446 -6.394 1.00 20.00 Atom # 2 = C29 @ -0.997 0.006 -4.740 1.00 20.00 Atom # 3 = C28 @ 0.157 -0.674 -4.397 1.00 20.00 Atom # 4 = C26 @ 0.388 -1.023 -3.080 1.00 20.00 Atom # 5 = C27 @ -1.917 0.342 -3.762 1.00 20.00 Atom # 6 = C25 @ -1.687 -0.012 -2.446 1.00 20.00 Atom # 7 = C22 @ -0.533 -0.693 -2.105 1.00 20.00 Atom # 8 = C17 @ -0.281 -1.074 -0.669 1.00 20.00 Atom # 9 = N13 @ 0.448 0.003 0.001 1.00 20.00 Atom # 10 = C16 @ 1.845 0.007 0.000 1.00 20.00 Atom # 11 = N18 @ 2.621 0.910 0.562 1.00 20.00 Atom # 12 = N20 @ 3.939 0.499 0.303 1.00 20.00 Atom # 13 = N21 @ 3.868 -0.593 -0.377 1.00 20.00 Atom # 14 = N19 @ 2.635 -0.907 -0.563 1.00 20.00 Atom # 15 = C1 @ -0.286 1.078 0.672 1.00 20.00 Atom # 16 = C2 @ -0.536 0.695 2.108 1.00 20.00 Atom # 17 = C3 @ 0.385 1.030 3.083 1.00 20.00 Atom # 18 = C5 @ 0.156 0.679 4.400 1.00 20.00 Atom # 19 = C7 @ -0.994 -0.007 4.743 1.00 20.00 Atom # 20 = CL8 @ -1.282 -0.448 6.397 1.00 20.00 Atom # 21 = C6 @ -1.916 -0.342 3.767 1.00 20.00 Atom # 22 = C4 @ -1.689 0.014 2.451 1.00 20.00 > (REMARK CBT ENDHET) Nr of atoms read : ( 22) Nr of extra examples : ( 0) Expected formula : ( C15 H13 CL2 N5) Observed formula : (C15 N5 CL2) Element | H| Expected 13 | Observed 0 Element | C| Expected 15 | Observed 15 Element | N| Expected 5 | Observed 5 Element |CL| Expected 2 | Observed 2 Expected and observed formulae agree (ignoring any hydrogens) ! Looking for bonded atoms ... Bond CL3 - C29 = 1.736 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 C29 - C28 = 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 C29 - C27 = 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 C28 - C26 = 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 C26 - C22 = 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 C27 - C25 = 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 C25 - C22 = 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 C22 - C17 = 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 C17 - N13 = 1.463 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.48 (devn. 0.02) For: C-N single; range 1.472-1.479 Bond N13 - C16 = 1.397 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.43 (devn. 0.03) For: C-N aromatic Bond N13 - C1 = 1.464 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.48 (devn. 0.02) For: C-N single; range 1.472-1.479 Bond C16 - N18 = 1.317 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 C16 - N19 = 1.333 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 N18 - N20 = 1.405 A (cutoff : 1.710) Nr of entries in library : ( 0) Bond N20 - N21 = 1.288 A (cutoff : 1.710) Nr of entries in library : ( 0) Bond N21 - N19 = 1.286 A (cutoff : 1.710) Nr of entries in library : ( 0) Bond C1 - C2 = 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 C2 - C3 = 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 - C4 = 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 C3 - 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 C5 - C7 = 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 C7 - CL8 = 1.736 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 C7 - C6 = 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 C6 - C4 = 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 Nr of bonds found : ( 24) 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 C29 Nbrs: 3 ~Hs: 0 Carbon C28 Nbrs: 2 ~Hs: 1 Carbon C26 Nbrs: 2 ~Hs: 1 Carbon C27 Nbrs: 2 ~Hs: 1 Carbon C25 Nbrs: 2 ~Hs: 1 Carbon C22 Nbrs: 3 ~Hs: 0 Carbon C17 Nbrs: 2 ~Hs: 2 Nitrogen N13 Nbrs: 3 ~Hs: 0 Carbon C16 Nbrs: 3 ~Hs: 0 Nitrogen N18 Nbrs: 2 ~Hs: 1 Nitrogen N20 Nbrs: 2 ~Hs: 1 Nitrogen N21 Nbrs: 2 ~Hs: 1 Nitrogen N19 Nbrs: 2 ~Hs: 1 Carbon C1 Nbrs: 2 ~Hs: 2 Carbon C2 Nbrs: 3 ~Hs: 0 Carbon C3 Nbrs: 2 ~Hs: 1 Carbon C5 Nbrs: 2 ~Hs: 1 Carbon C7 Nbrs: 3 ~Hs: 0 Carbon C6 Nbrs: 2 ~Hs: 1 Carbon C4 Nbrs: 2 ~Hs: 1 Est. total nr of hydrogens : ( 16) Looking for angles ... AtmJ AtmI AtmK Angle ---- ---- ---- ----- CL3 C29 C28 120.06 CL3 C29 C27 120.02 C28 C29 C27 119.92 C29 C28 C26 120.01 C28 C26 C22 120.06 C29 C27 C25 120.00 C27 C25 C22 119.99 C26 C22 C25 120.01 C26 C22 C17 120.05 C25 C22 C17 119.94 C22 C17 N13 109.49 C17 N13 C16 120.01 C17 N13 C1 120.03 C16 N13 C1 119.96 N13 C16 N18 126.23 N13 C16 N19 126.23 N18 C16 N19 107.54 C16 N18 N20 105.88 N18 N20 N21 107.07 N20 N21 N19 109.64 C16 N19 N21 109.86 N13 C1 C2 109.46 C1 C2 C3 119.99 C1 C2 C4 120.00 C3 C2 C4 120.01 C2 C3 C5 120.01 C3 C5 C7 120.02 C5 C7 CL8 120.04 C5 C7 C6 119.96 CL8 C7 C6 120.00 C7 C6 C4 119.99 C2 C4 C6 120.01 Looking for dihedrals (and planes) ... AtmK AtmI AtmJ AtmL Dihedral ---- ---- ---- ---- ------- CL3 C29 C28 C26 179.96 Flat ? C27 C29 C28 C26 0.30 Flat ? CL3 C29 C27 C25 179.80 Flat ? C28 C29 C27 C25 -0.54 Flat ? C29 C28 C26 C22 -0.01 Flat ? C28 C26 C22 C25 -0.05 Flat ? C28 C26 C22 C17 179.98 Flat ? C29 C27 C25 C22 0.49 Flat ? C27 C25 C22 C26 -0.19 Flat ? C27 C25 C22 C17 179.78 Flat ? C26 C22 C17 N13 89.99 C25 C22 C17 N13 -89.98 C22 C17 N13 C16 -89.93 C22 C17 N13 C1 90.02 C17 N13 C16 N18 -179.97 Flat ? C17 N13 C16 N19 -0.41 Flat ? C1 N13 C16 N18 0.08 Flat ? C1 N13 C16 N19 179.64 Flat ? C17 N13 C1 C2 89.99 C16 N13 C1 C2 -90.06 N13 C16 N18 N20 179.96 Flat ? N19 C16 N18 N20 0.34 Flat ? N13 C16 N19 N21 179.85 Flat ? N18 C16 N19 N21 -0.52 Flat ? C16 N18 N20 N21 -0.05 Flat ? N18 N20 N21 N19 -0.27 Flat ? N20 N21 N19 C16 0.50 Flat ? N13 C1 C2 C3 90.04 N13 C1 C2 C4 -90.25 C1 C2 C3 C5 180.00 Flat ? C4 C2 C3 C5 0.28 Flat ? C1 C2 C4 C6 179.74 Flat ? C3 C2 C4 C6 -0.54 Flat ? C2 C3 C5 C7 -0.01 Flat ? C3 C5 C7 CL8 -180.00 Flat ? C3 C5 C7 C6 -0.01 Flat ? C5 C7 C6 C4 -0.25 Flat ? CL8 C7 C6 C4 179.74 Flat ? C7 C6 C4 C2 0.53 Flat ? Looking for impropers (and planes) ... Atm* Nbr1 Nbr2 Nbr3 Improper ---- ---- ---- ---- -------- C29 CL3 C28 C27 -0.19 C22 C26 C25 C17 0.02 N13 C17 C16 C1 -0.03 C16 N13 N18 N19 -0.25 C2 C1 C3 C4 -0.16 C7 C5 CL8 C6 -0.01 Number of possible flat planes : ( 37) Looking for more planes ... Number of possible flat planes : ( 49) Expanding planes ... WARNING - Reset negative RMSD in LSQGJK : ( -1.960E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.265E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.203E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.992E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.632E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.836E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.908E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.159E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.180E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.018E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.104E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.573E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.450E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.444E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.480E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.875E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.795E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.202E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.716E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.774E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.319E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.780E-08) WARNING - Reset negative RMSD in LSQGJK : ( -8.043E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.870E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.652E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.795E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.418E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.276E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.620E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.276E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.652E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.870E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.379E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.652E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.379E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.219E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.838E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.732E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.628E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.838E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.608E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.285E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.098E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.516E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.897E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.256E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.979E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.394E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.610E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.240E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.177E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.798E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.256E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.240E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.078E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.682E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.211E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.682E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.569E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.054E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.772E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.880E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.180E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.358E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.798E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.265E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.285E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.679E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.720E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.496E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.573E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.875E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.950E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.276E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.285E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.256E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.066E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.772E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.256E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.959E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.554E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.992E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.528E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.870E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.319E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.780E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.732E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.870E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.838E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.732E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.652E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.017E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.620E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.795E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.500E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.240E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.285E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.369E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.211E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.240E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.417E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.772E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.979E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.610E-08) Removing non-unique planes ... Plane nr : ( 41) Nr of atoms : ( 8) RMSD to least-squares plane (A): ( 0.001) Atom Dist (A) C25 -0.001 C27 0.003 C22 -0.001 C29 -0.001 C26 0.001 C17 0.000 CL3 -0.001 C28 0.001 Plane nr : ( 45) Nr of atoms : ( 8) RMSD to least-squares plane (A): ( 0.002) Atom Dist (A) N19 0.004 C16 -0.001 N21 -0.002 N13 0.000 N18 0.000 N20 -0.001 C17 -0.002 C1 0.001 Plane nr : ( 49) Nr of atoms : ( 8) WARNING - Reset negative RMSD in LSQGJK : ( -2.256E-07) RMSD to least-squares plane (A): ( 0.002) Atom Dist (A) C4 0.003 C2 -0.001 C6 -0.002 C1 -0.001 C3 0.001 C7 -0.001 C5 0.001 CL8 0.000 ------------------- ----- SUMMARY ----- ------------------- Residue type : (CBT) Identifier : ( 2369) Segment ID : ( ) Nr of atoms : ( 22) List of elements (from file) : ( C15 H13 CL2 N5) Deduced formula : (C15 N5 CL2) Guestimated total nr of Hs : ( 16) Nr of extra examples : ( 0) Nr of distances < 0.8 A : ( 0) Nr of bond angles < 80 degrees : ( 0) Nr of bonds found : ( 24) ... bonds without ideal value : ( 3) ... bonds near ideal value : ( 21) ... bonds far from ideal value : ( 0) -"- % : ( 0.000) Nr of angles found : ( 32) Nr of dihedrals found : ( 39) Nr of atoms with impropers : ( 6) ... imprs far from ideal value : ( 0) -"- % : ( 0.000) Nr of flat planes : ( 3)