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 1CI 1-(4-CHLOROPHENYL)-1H-IMIDAZOLE) > (REMARK 1CI Part of HIC-Up: http://xray.bmc.uu.se/hicup) > (REMARK 1CI Extracted from PDB file pdb2q6n.ent) > (REMARK 1CI Formula C9 H7 CL N2) Formula : (1CI C9 H7 CL N2) > (REMARK 1CI Nr of non-hydrogen atoms 12) > (REMARK 1CI Eigen-values covariance X/Y/Z 71.2 7.7 1.3) > (REMARK 1CI Residue type 1CI) > (REMARK 1CI Residue name 300) > (REMARK 1CI Original residue name (for O) $A501) > (REMARK 1CI RESOLUTION. 3.20 ANGSTROMS.) > (REMARK 1CI occurs in 0 other PDB entries) > (REMARK 1CI) Using residue : (1CI) Identifier : ( 300) 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 @ -0.170 -1.199 -0.002 1.00 20.00 Atom # 2 = C10 @ -1.551 -1.197 -0.002 1.00 20.00 Atom # 3 = C9 @ -2.242 0.002 0.000 1.00 20.00 Atom # 4 = CL @ -3.978 0.001 0.001 1.00 20.00 Atom # 5 = C8 @ -1.552 1.201 0.001 1.00 20.00 Atom # 6 = C7 @ -0.171 1.204 0.000 1.00 20.00 Atom # 7 = C6 @ 0.525 0.003 -0.001 1.00 20.00 Atom # 8 = N1 @ 1.928 0.003 -0.001 1.00 20.00 Atom # 9 = C5 @ 2.742 1.106 0.000 1.00 20.00 Atom # 10 = C4 @ 4.010 0.654 0.000 1.00 20.00 Atom # 11 = N3 @ 3.977 -0.687 -0.001 1.00 20.00 Atom # 12 = C2 @ 2.735 -1.089 0.004 1.00 20.00 > (REMARK 1CI 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 = 1.381 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 C11 - C6 = 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 C10 - C9 = 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 C9 - CL = 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 C9 - C8 = 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 C8 - 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 C7 - C6 = 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 C6 - N1 = 1.403 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.43 (devn. 0.03) For: C-N aromatic Bond N1 - C5 = 1.371 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 - C2 = 1.358 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 - C4 = 1.346 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.34 (devn. 0.01) For: C-C double or partial triple; range 1.309-1.337 Bond C4 - N3 = 1.341 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.34 (devn. 0.00) For: C-N partial double; range 1.322-1.352 Bond N3 - C2 = 1.305 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 Nitrogen N1 Nbrs: 3 ~Hs: 0 Carbon C5 Nbrs: 2 ~Hs: 1 Carbon C4 Nbrs: 2 ~Hs: 1 Nitrogen N3 Nbrs: 2 ~Hs: 1 Carbon C2 Nbrs: 2 ~Hs: 1 Est. total nr of hydrogens : ( 8) Looking for angles ... AtmJ AtmI AtmK Angle ---- ---- ---- ----- C10 C11 C6 119.95 C11 C10 C9 120.04 C10 C9 CL 119.92 C10 C9 C8 120.13 CL C9 C8 119.95 C9 C8 C7 120.04 C8 C7 C6 119.97 C11 C6 C7 119.87 C11 C6 N1 120.04 C7 C6 N1 120.09 C6 N1 C5 126.43 C6 N1 C2 126.46 C5 N1 C2 107.11 N1 C5 C4 106.81 C5 C4 N3 108.21 C4 N3 C2 109.34 N1 C2 N3 108.53 Looking for dihedrals (and planes) ... AtmK AtmI AtmJ AtmL Dihedral ---- ---- ---- ---- ------- C6 C11 C10 C9 -0.05 Flat ? C10 C11 C6 C7 0.00 Flat ? C10 C11 C6 N1 -180.00 Flat ? C11 C10 C9 CL -179.96 Flat ? C11 C10 C9 C8 0.05 Flat ? C10 C9 C8 C7 0.00 Flat ? CL C9 C8 C7 -179.99 Flat ? C9 C8 C7 C6 -0.05 Flat ? C8 C7 C6 C11 0.05 Flat ? C8 C7 C6 N1 -179.95 Flat ? C11 C6 N1 C5 -180.00 Flat ? C11 C6 N1 C2 -0.31 Flat ? C7 C6 N1 C5 0.00 Flat ? C7 C6 N1 C2 179.69 Flat ? C6 N1 C5 C4 179.98 Flat ? C2 N1 C5 C4 0.25 Flat ? C6 N1 C2 N3 179.85 Flat ? C5 N1 C2 N3 -0.41 Flat ? N1 C5 C4 N3 0.00 Flat ? C5 C4 N3 C2 -0.26 Flat ? C4 N3 C2 N1 0.42 Flat ? Looking for impropers (and planes) ... Atm* Nbr1 Nbr2 Nbr3 Improper ---- ---- ---- ---- -------- C9 C10 CL C8 0.01 C6 C11 C7 N1 0.00 N1 C6 C5 C2 -0.17 Number of possible flat planes : ( 24) Looking for more planes ... Number of possible flat planes : ( 32) Expanding planes ... WARNING - Reset negative RMSD in LSQGJK : ( -2.854E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.433E-09) WARNING - Reset negative RMSD in LSQGJK : ( -5.151E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.884E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.174E-10) WARNING - Reset negative RMSD in LSQGJK : ( -4.125E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.698E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.086E-21) WARNING - Reset negative RMSD in LSQGJK : ( -5.969E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.174E-10) WARNING - Reset negative RMSD in LSQGJK : ( -2.854E-09) WARNING - Reset negative RMSD in LSQGJK : ( -4.125E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.832E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.508E-10) WARNING - Reset negative RMSD in LSQGJK : ( -1.562E-09) WARNING - Reset negative RMSD in LSQGJK : ( -4.270E-21) WARNING - Reset negative RMSD in LSQGJK : ( -2.717E-10) WARNING - Reset negative RMSD in LSQGJK : ( -3.754E-09) WARNING - Reset negative RMSD in LSQGJK : ( -4.870E-10) WARNING - Reset negative RMSD in LSQGJK : ( -2.172E-10) WARNING - Reset negative RMSD in LSQGJK : ( -1.610E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.274E-13) WARNING - Reset negative RMSD in LSQGJK : ( -3.754E-09) WARNING - Reset negative RMSD in LSQGJK : ( -4.870E-10) WARNING - Reset negative RMSD in LSQGJK : ( -2.172E-10) WARNING - Reset negative RMSD in LSQGJK : ( -1.610E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.355E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.691E-09) WARNING - Reset negative RMSD in LSQGJK : ( -5.151E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.174E-10) WARNING - Reset negative RMSD in LSQGJK : ( -1.355E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.470E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.274E-13) WARNING - Reset negative RMSD in LSQGJK : ( -3.754E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.174E-10) WARNING - Reset negative RMSD in LSQGJK : ( -4.691E-09) WARNING - Reset negative RMSD in LSQGJK : ( -4.470E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.618E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.754E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.174E-10) WARNING - Reset negative RMSD in LSQGJK : ( -1.055E-10) WARNING - Reset negative RMSD in LSQGJK : ( -3.714E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.698E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.172E-10) WARNING - Reset negative RMSD in LSQGJK : ( -3.714E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.686E-09) WARNING - Reset negative RMSD in LSQGJK : ( -4.547E-13) WARNING - Reset negative RMSD in LSQGJK : ( -2.667E-11) WARNING - Reset negative RMSD in LSQGJK : ( -1.467E-10) WARNING - Reset negative RMSD in LSQGJK : ( -2.832E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.581E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.209E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.515E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.686E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.111E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.455E-11) WARNING - Reset negative RMSD in LSQGJK : ( -5.433E-10) WARNING - Reset negative RMSD in LSQGJK : ( -1.701E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.433E-10) WARNING - Reset negative RMSD in LSQGJK : ( -1.455E-11) WARNING - Reset negative RMSD in LSQGJK : ( -5.433E-10) WARNING - Reset negative RMSD in LSQGJK : ( -4.547E-13) WARNING - Reset negative RMSD in LSQGJK : ( -5.476E-21) WARNING - Reset negative RMSD in LSQGJK : ( -5.074E-09) WARNING - Reset negative RMSD in LSQGJK : ( -5.433E-10) WARNING - Reset negative RMSD in LSQGJK : ( -2.274E-13) WARNING - Reset negative RMSD in LSQGJK : ( -2.918E-11) WARNING - Reset negative RMSD in LSQGJK : ( -2.239E-09) WARNING - Reset negative RMSD in LSQGJK : ( -6.276E-11) WARNING - Reset negative RMSD in LSQGJK : ( -5.433E-10) WARNING - Reset negative RMSD in LSQGJK : ( -4.977E-20) WARNING - Reset negative RMSD in LSQGJK : ( -5.476E-21) WARNING - Reset negative RMSD in LSQGJK : ( -3.740E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.308E-09) WARNING - Reset negative RMSD in LSQGJK : ( -5.074E-09) WARNING - Reset negative RMSD in LSQGJK : ( -5.433E-10) WARNING - Reset negative RMSD in LSQGJK : ( -2.274E-13) WARNING - Reset negative RMSD in LSQGJK : ( -1.137E-13) WARNING - Reset negative RMSD in LSQGJK : ( -1.913E-14) WARNING - Reset negative RMSD in LSQGJK : ( -3.211E-09) WARNING - Reset negative RMSD in LSQGJK : ( -5.433E-10) WARNING - Reset negative RMSD in LSQGJK : ( -2.274E-13) WARNING - Reset negative RMSD in LSQGJK : ( -1.137E-13) WARNING - Reset negative RMSD in LSQGJK : ( -5.074E-09) WARNING - Reset negative RMSD in LSQGJK : ( -8.080E-11) WARNING - Reset negative RMSD in LSQGJK : ( -5.433E-10) WARNING - Reset negative RMSD in LSQGJK : ( -1.137E-13) WARNING - Reset negative RMSD in LSQGJK : ( -9.095E-12) WARNING - Reset negative RMSD in LSQGJK : ( -5.074E-09) WARNING - Reset negative RMSD in LSQGJK : ( -5.433E-10) WARNING - Reset negative RMSD in LSQGJK : ( -1.137E-13) WARNING - Reset negative RMSD in LSQGJK : ( -1.355E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.547E-13) WARNING - Reset negative RMSD in LSQGJK : ( -4.547E-13) WARNING - Reset negative RMSD in LSQGJK : ( -3.754E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.172E-10) WARNING - Reset negative RMSD in LSQGJK : ( -4.125E-09) WARNING - Reset negative RMSD in LSQGJK : ( -3.714E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.618E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.547E-13) WARNING - Reset negative RMSD in LSQGJK : ( -9.322E-10) WARNING - Reset negative RMSD in LSQGJK : ( -5.477E-21) WARNING - Reset negative RMSD in LSQGJK : ( -2.209E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.482E-10) WARNING - Reset negative RMSD in LSQGJK : ( -1.308E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.475E-09) WARNING - Reset negative RMSD in LSQGJK : ( -4.251E-09) WARNING - Reset negative RMSD in LSQGJK : ( -5.151E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.174E-10) WARNING - Reset negative RMSD in LSQGJK : ( -4.251E-09) WARNING - Reset negative RMSD in LSQGJK : ( -3.754E-09) WARNING - Reset negative RMSD in LSQGJK : ( -4.870E-10) WARNING - Reset negative RMSD in LSQGJK : ( -2.172E-10) WARNING - Reset negative RMSD in LSQGJK : ( -1.355E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.214E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.274E-13) WARNING - Reset negative RMSD in LSQGJK : ( -3.754E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.172E-10) WARNING - Reset negative RMSD in LSQGJK : ( -2.618E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.684E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.470E-09) WARNING - Reset negative RMSD in LSQGJK : ( -5.151E-09) WARNING - Reset negative RMSD in LSQGJK : ( -3.281E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.172E-10) WARNING - Reset negative RMSD in LSQGJK : ( -1.455E-11) WARNING - Reset negative RMSD in LSQGJK : ( -5.433E-10) WARNING - Reset negative RMSD in LSQGJK : ( -1.137E-13) WARNING - Reset negative RMSD in LSQGJK : ( -1.827E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.913E-14) WARNING - Reset negative RMSD in LSQGJK : ( -3.211E-09) WARNING - Reset negative RMSD in LSQGJK : ( -5.433E-10) WARNING - Reset negative RMSD in LSQGJK : ( -2.274E-13) WARNING - Reset negative RMSD in LSQGJK : ( -5.477E-21) WARNING - Reset negative RMSD in LSQGJK : ( -1.819E-12) WARNING - Reset negative RMSD in LSQGJK : ( -5.074E-09) WARNING - Reset negative RMSD in LSQGJK : ( -5.433E-10) WARNING - Reset negative RMSD in LSQGJK : ( -1.137E-13) WARNING - Reset negative RMSD in LSQGJK : ( -6.821E-12) WARNING - Reset negative RMSD in LSQGJK : ( -2.918E-11) WARNING - Reset negative RMSD in LSQGJK : ( -5.433E-10) Removing non-unique planes ... Plane nr : ( 32) Nr of atoms : ( 12) RMSD to least-squares plane (A): ( 0.002) Atom Dist (A) C2 0.004 N1 -0.001 N3 -0.001 C6 -0.001 C5 0.000 C4 0.000 C11 -0.002 C7 0.000 C10 -0.002 C8 0.001 C9 0.000 CL 0.001 ------------------- ----- SUMMARY ----- ------------------- Residue type : (1CI) Identifier : ( 300) 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 : ( 1)