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 GVO (2S)-2-(4-CHLOROPHENYL)-2-(4-(1H-PYRAZOL-4-YL) PHENYL) ETHANAMINE) > (REMARK GVO Part of HIC-Up: http://xray.bmc.uu.se/hicup) > (REMARK GVO Extracted from PDB file pdb2uw6.ent) > (REMARK GVO Formula C17 H16 CL N3) Formula : (GVO C17 H16 CL N3) > (REMARK GVO Nr of non-hydrogen atoms 21) > (REMARK GVO Eigen-values covariance X/Y/Z 300.2 33.8 9.1) > (REMARK GVO Residue type GVO) > (REMARK GVO Residue name 4068) > (REMARK GVO Original residue name (for O) $A1351) > (REMARK GVO RESOLUTION. 2.23 ANGSTROMS.) > (REMARK GVO occurs in 0 other PDB entries) > (REMARK GVO) Using residue : (GVO) Identifier : ( 4068) Segment ID : ( ) Using formula : ( C17 H16 CL N3) Element ? | C| Carbon | 6 17 Element ? | H| Hydrogen | 1 16 Element ? |CL| Chlorine | 17 1 Element ? | N| Nitrogen | 7 3 Atom # 1 = N1 @ 0.604 -3.294 4.369 1.00 20.00 Atom # 2 = C2 @ 0.562 -1.904 4.769 1.00 20.00 Atom # 3 = C3 @ 1.754 -1.101 4.166 1.00 20.00 Atom # 4 = C4 @ 1.827 0.306 4.782 1.00 20.00 Atom # 5 = C5 @ 3.056 0.908 4.888 1.00 20.00 Atom # 6 = C6 @ 3.122 2.184 5.446 1.00 20.00 Atom # 7 = C7 @ 1.957 2.817 5.880 1.00 20.00 Atom # 8 = CL8 @ 2.039 4.392 6.569 1.00 20.00 Atom # 9 = C9 @ 0.726 2.173 5.756 1.00 20.00 Atom # 10 = C10 @ 0.660 0.896 5.198 1.00 20.00 Atom # 11 = C11 @ 1.800 -1.079 2.676 1.00 20.00 Atom # 12 = C12 @ 2.862 -1.681 2.001 1.00 20.00 Atom # 13 = C13 @ 2.904 -1.661 0.607 1.00 20.00 Atom # 14 = C14 @ 1.885 -1.037 -0.112 1.00 20.00 Atom # 15 = C15 @ 0.823 -0.435 0.562 1.00 20.00 Atom # 16 = C16 @ 0.780 -0.455 1.956 1.00 20.00 Atom # 17 = C17 @ 1.929 -1.016 -1.548 1.00 20.00 Atom # 18 = C18 @ 3.014 -1.012 -2.439 1.00 20.00 Atom # 19 = N19 @ 2.626 -0.990 -3.717 1.00 20.00 Atom # 20 = N20 @ 1.285 -0.981 -3.628 1.00 20.00 Atom # 21 = C21 @ 0.817 -0.995 -2.347 1.00 20.00 > (REMARK GVO ENDHET) Nr of atoms read : ( 21) Nr of extra examples : ( 0) Expected formula : ( C17 H16 CL N3) Observed formula : (C17 N3 CL1) Element | H| Expected 16 | Observed 0 Element | C| Expected 17 | Observed 17 Element | N| Expected 3 | Observed 3 Element |CL| Expected 1 | Observed 1 Expected and observed formulae agree (ignoring any hydrogens) ! Looking for bonded atoms ... Bond N1 - C2 = 1.447 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.43 (devn. 0.02) For: C-N aromatic Bond C2 - C3 = 1.559 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.53 (devn. 0.03) For: C-C single; range 1.49-1.54 Bond C3 - C4 = 1.538 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.53 (devn. 0.01) For: C-C single; range 1.49-1.54 Bond C3 - C11 = 1.491 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.53 (devn. 0.04) For: C-C single; range 1.49-1.54 Bond C4 - C5 = 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 - C10 = 1.372 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 C5 - 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 C6 - C7 = 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 C7 - CL8 = 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 C7 - C9 = 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 - C10 = 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 C11 - C12 = 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 - C16 = 1.396 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 C12 - C13 = 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 C13 - C14 = 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 C14 - C15 = 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 C14 - C17 = 1.437 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 C15 - C16 = 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 C17 - C18 = 1.404 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 C17 - C21 = 1.369 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 C18 - N19 = 1.336 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 N19 - N20 = 1.344 A (cutoff : 1.710) Nr of entries in library : ( 0) Bond N20 - C21 = 1.364 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 Nr of bonds found : ( 23) 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: 1 ~Hs: 1 Carbon C2 Nbrs: 2 ~Hs: 2 Carbon C3 Nbrs: 3 ~Hs: 1 Carbon C4 Nbrs: 3 ~Hs: 0 Carbon C5 Nbrs: 2 ~Hs: 1 Carbon C6 Nbrs: 2 ~Hs: 1 Carbon C7 Nbrs: 3 ~Hs: 0 Carbon C9 Nbrs: 2 ~Hs: 1 Carbon C10 Nbrs: 2 ~Hs: 1 Carbon C11 Nbrs: 3 ~Hs: 0 Carbon C12 Nbrs: 2 ~Hs: 1 Carbon C13 Nbrs: 2 ~Hs: 1 Carbon C14 Nbrs: 3 ~Hs: 0 Carbon C15 Nbrs: 2 ~Hs: 1 Carbon C16 Nbrs: 2 ~Hs: 1 Carbon C17 Nbrs: 3 ~Hs: 0 Carbon C18 Nbrs: 2 ~Hs: 1 Nitrogen N19 Nbrs: 2 ~Hs: 1 Nitrogen N20 Nbrs: 2 ~Hs: 1 Carbon C21 Nbrs: 2 ~Hs: 1 Est. total nr of hydrogens : ( 16) Looking for angles ... AtmJ AtmI AtmK Angle ---- ---- ---- ----- N1 C2 C3 111.45 C2 C3 C4 110.65 C2 C3 C11 114.70 C4 C3 C11 112.67 C3 C4 C5 118.34 C3 C4 C10 118.33 C5 C4 C10 123.33 C4 C5 C6 118.34 C5 C6 C7 120.02 C6 C7 CL8 120.00 C6 C7 C9 119.99 CL8 C7 C9 120.01 C7 C9 C10 119.99 C4 C10 C9 118.33 C3 C11 C12 120.05 C3 C11 C16 119.97 C12 C11 C16 119.98 C11 C12 C13 120.02 C12 C13 C14 119.98 C13 C14 C15 120.03 C13 C14 C17 119.96 C15 C14 C17 120.00 C14 C15 C16 120.02 C11 C16 C15 119.96 C14 C17 C18 131.15 C14 C17 C21 123.95 C18 C17 C21 104.90 C17 C18 N19 112.50 C18 N19 N20 103.10 N19 N20 C21 113.86 C17 C21 N20 105.64 Looking for dihedrals (and planes) ... AtmK AtmI AtmJ AtmL Dihedral ---- ---- ---- ---- ------- N1 C2 C3 C4 -170.65 Flat ? N1 C2 C3 C11 60.54 C2 C3 C4 C5 150.02 C2 C3 C4 C10 -29.97 C11 C3 C4 C5 -80.08 C11 C3 C4 C10 99.93 C2 C3 C11 C12 -115.45 C2 C3 C11 C16 64.59 C4 C3 C11 C12 116.76 C4 C3 C11 C16 -63.21 C3 C4 C5 C6 179.97 Flat ? C10 C4 C5 C6 -0.04 Flat ? C3 C4 C10 C9 -179.95 Flat ? C5 C4 C10 C9 0.05 Flat ? C4 C5 C6 C7 0.00 Flat ? C5 C6 C7 CL8 179.99 Flat ? C5 C6 C7 C9 0.02 Flat ? C6 C7 C9 C10 0.00 Flat ? CL8 C7 C9 C10 -179.97 Flat ? C7 C9 C10 C4 -0.04 Flat ? C3 C11 C12 C13 179.95 Flat ? C16 C11 C12 C13 -0.08 Flat ? C3 C11 C16 C15 -179.98 Flat ? C12 C11 C16 C15 0.06 Flat ? C11 C12 C13 C14 0.11 Flat ? C12 C13 C14 C15 -0.11 Flat ? C12 C13 C14 C17 179.97 Flat ? C13 C14 C15 C16 0.08 Flat ? C17 C14 C15 C16 -179.99 Flat ? C13 C14 C17 C18 -30.02 C13 C14 C17 C21 149.96 C15 C14 C17 C18 150.05 C15 C14 C17 C21 -29.97 C14 C15 C16 C11 -0.06 Flat ? C14 C17 C18 N19 179.98 Flat ? C21 C17 C18 N19 0.00 Flat ? C14 C17 C21 N20 -179.95 Flat ? C18 C17 C21 N20 0.04 Flat ? C17 C18 N19 N20 -0.04 Flat ? C18 N19 N20 C21 0.07 Flat ? N19 N20 C21 C17 -0.07 Flat ? Looking for impropers (and planes) ... Atm* Nbr1 Nbr2 Nbr3 Improper ---- ---- ---- ---- -------- C3 C2 C4 C11 28.63 C4 C3 C5 C10 0.00 C7 C6 CL8 C9 0.02 C11 C3 C12 C16 0.02 C14 C13 C15 C17 0.04 C17 C14 C18 C21 -0.01 Number of possible flat planes : ( 33) Looking for more planes ... Number of possible flat planes : ( 46) Expanding planes ... WARNING - Reset negative RMSD in LSQGJK : ( -2.672E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.500E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.944E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.023E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.430E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.330E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.944E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.755E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.820E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.755E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.517E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.080E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.626E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.192E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.095E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.833E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.277E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.247E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.547E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.294E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.429E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.724E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.864E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.116E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.724E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.555E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.352E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.429E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.724E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.864E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.555E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.422E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.116E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.724E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.753E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.581E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.724E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.197E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.850E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.541E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.581E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.818E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.898E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.871E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.116E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.203E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.178E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.174E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.920E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.557E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.331E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.583E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.770E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.845E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.226E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.067E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.770E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.583E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.067E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.993E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.519E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.768E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.516E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.929E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.555E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.294E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.116E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.429E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.724E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.191E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.877E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.449E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.817E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.116E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.672E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.617E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.755E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.704E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.973E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.626E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.023E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.970E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.933E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.547E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.291E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.189E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.724E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.581E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.547E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.691E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.178E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.898E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.116E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.555E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.352E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.429E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.726E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.066E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.845E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.226E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.066E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.845E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.331E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.583E-07) Removing non-unique planes ... Plane nr : ( 34) Nr of atoms : ( 4) RMSD to least-squares plane (A): ( 0.057) Atom Dist (A) C2 0.059 N1 -0.059 C3 0.054 C4 -0.055 Plane nr : ( 38) Nr of atoms : ( 8) WARNING - Reset negative RMSD in LSQGJK : ( -3.732E-07) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) C10 0.000 C4 0.000 C9 0.000 C3 0.000 C5 0.000 C7 0.000 C6 0.000 CL8 0.000 Plane nr : ( 42) Nr of atoms : ( 8) WARNING - Reset negative RMSD in LSQGJK : ( -1.116E-07) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) C16 0.000 C11 0.000 C15 0.000 C3 0.000 C12 0.000 C14 0.000 C13 0.000 C17 0.000 Plane nr : ( 46) Nr of atoms : ( 6) WARNING - Reset negative RMSD in LSQGJK : ( -4.226E-08) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) C21 0.000 C17 0.000 N20 0.000 C14 0.000 C18 0.000 N19 0.000 ------------------- ----- SUMMARY ----- ------------------- Residue type : (GVO) Identifier : ( 4068) Segment ID : ( ) Nr of atoms : ( 21) List of elements (from file) : ( C17 H16 CL N3) Deduced formula : (C17 N3 CL1) 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 : ( 23) ... bonds without ideal value : ( 1) ... bonds near ideal value : ( 22) ... bonds far from ideal value : ( 0) -"- % : ( 0.000) Nr of angles found : ( 31) Nr of dihedrals found : ( 41) Nr of atoms with impropers : ( 6) ... imprs far from ideal value : ( 0) -"- % : ( 0.000) Nr of flat planes : ( 4)