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 2BL (3S, 4R)-1-TOLUENESULPHONYL-3-ETHYL-AZETIDIN-2-ONE-4- CARBOXYLIC ACID) > (REMARK 2BL Part of HIC-Up: http://xray.bmc.uu.se/hicup) > (REMARK 2BL Extracted from PDB file pdb1btu.ent) > (REMARK 2BL Formula C13 H15 N O5 S) Formula : (2BL C13 H15 N O5 S) > (REMARK 2BL Nr of non-hydrogen atoms 20) > (REMARK 2BL Eigen-values covariance X/Y/Z 167.0 31.2 23.1) > (REMARK 2BL Residue type 2BL) > (REMARK 2BL Residue name 464) > (REMARK 2BL Original residue name (for O) $7) > (REMARK 2BL RESOLUTION. 1.60 ANGSTROMS.) > (REMARK 2BL occurs in 0 other PDB entries) > (REMARK 2BL) Using residue : (2BL) Identifier : ( 464) Segment ID : ( ) Using formula : ( C13 H15 N O5 S) Element ? | C| Carbon | 6 13 Element ? | H| Hydrogen | 1 15 Element ? | N| Nitrogen | 7 1 Element ? | O| Oxygen | 8 5 Element ? | S| Sulfur | 16 1 Atom # 1 = C @ -0.854 -0.718 1.867 1.00 20.00 Atom # 2 = CA @ 0.399 -0.697 2.717 1.00 20.00 Atom # 3 = CB @ 0.851 0.499 1.864 1.00 20.00 Atom # 4 = CC @ 2.071 0.219 1.026 1.00 20.00 Atom # 5 = CD @ 0.142 -0.344 4.184 1.00 20.00 Atom # 6 = CE @ -0.342 -1.588 4.930 1.00 20.00 Atom # 7 = CF @ -0.552 0.384 -1.616 1.00 20.00 Atom # 8 = CG1 @ -1.300 -0.642 -2.162 1.00 20.00 Atom # 9 = CG2 @ 0.612 0.796 -2.236 1.00 20.00 Atom # 10 = CH1 @ -0.880 -1.260 -3.325 1.00 20.00 Atom # 11 = CH2 @ 1.034 0.175 -3.397 1.00 20.00 Atom # 12 = CI @ 0.286 -0.851 -3.942 1.00 20.00 Atom # 13 = CJ @ 0.744 -1.525 -5.210 1.00 20.00 Atom # 14 = O @ -1.852 -1.407 1.847 1.00 20.00 Atom # 15 = OA @ 1.947 -0.220 -0.092 1.00 20.00 Atom # 16 = OB @ 3.295 0.457 1.522 1.00 20.00 Atom # 17 = OC @ -2.486 0.937 -0.055 1.00 20.00 Atom # 18 = OD @ -0.466 2.450 -0.130 1.00 20.00 Atom # 19 = S @ -1.087 1.172 -0.133 1.00 20.00 Atom # 20 = N @ -0.420 0.343 1.135 1.00 20.00 > (REMARK 2BL ENDHET) Nr of atoms read : ( 20) Nr of extra examples : ( 0) Expected formula : ( C13 H15 N O5 S) Observed formula : (C13 N1 O5 S1) Element | H| Expected 15 | Observed 0 Element | C| Expected 13 | Observed 13 Element | N| Expected 1 | Observed 1 Element | O| Expected 5 | Observed 5 Element | S| Expected 1 | Observed 1 Expected and observed formulae agree (ignoring any hydrogens) ! Looking for bonded atoms ... Bond C - CA = 1.514 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 C - O = 1.213 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.19 (devn. 0.02) For: C-O shortened double; range 1.17-1.207 Bond C - N = 1.360 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 CA - CB = 1.537 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 CA - CD = 1.531 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 Bond CB - CC = 1.506 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 CB - N = 1.474 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.48 (devn. 0.01) For: C-N single; range 1.472-1.479 Bond CC - OA = 1.207 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.19 (devn. 0.02) For: C-O shortened double; range 1.17-1.207 Bond CC - OB = 1.342 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.36 (devn. 0.02) For: C-O partial double Bond CD - CE = 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 Bond CF - CG1 = 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 CF - CG2 = 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 CF - S = 1.763 A (cutoff : 2.050) Nr of entries in library : ( 3) Closest to 1.72 (devn. 0.04) For: C-S (partial) double; range 1.71-1.73 Bond CG1 - CH1 = 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 CG2 - CH2 = 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 CH1 - CI = 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 CH2 - CI = 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 CI - CJ = 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 OC - S = 1.421 A (cutoff : 2.050) Nr of entries in library : ( 1) Closest to 1.43 (devn. 0.01) For: O-S double Bond OD - S = 1.421 A (cutoff : 2.050) Nr of entries in library : ( 1) Closest to 1.43 (devn. 0.01) For: O-S double Bond S - N = 1.655 A (cutoff : 2.050) Nr of entries in library : ( 0) Nr of bonds found : ( 21) 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 C Nbrs: 3 ~Hs: 0 Carbon CA Nbrs: 3 ~Hs: 1 Carbon CB Nbrs: 3 ~Hs: 1 Carbon CC Nbrs: 3 ~Hs: 0 Carbon CD Nbrs: 2 ~Hs: 2 Carbon CE Nbrs: 1 ~Hs: 3 Carbon CF Nbrs: 3 ~Hs: 0 Carbon CG1 Nbrs: 2 ~Hs: 1 Carbon CG2 Nbrs: 2 ~Hs: 1 Carbon CH1 Nbrs: 2 ~Hs: 1 Carbon CH2 Nbrs: 2 ~Hs: 1 Carbon CI Nbrs: 3 ~Hs: 0 Carbon CJ Nbrs: 1 ~Hs: 3 Oxygen O Nbrs: 1 ~Hs: 0 Oxygen OA Nbrs: 1 ~Hs: 0 Oxygen OB Nbrs: 1 ~Hs: 1 Oxygen OC Nbrs: 1 ~Hs: 1 Oxygen OD Nbrs: 1 ~Hs: 1 Sulphur S Nbrs: 4 ~Hs: 0 Nitrogen N Nbrs: 3 ~Hs: 0 Est. total nr of hydrogens : ( 17) Looking for angles ... AtmJ AtmI AtmK Angle ---- ---- ---- ----- CA C O 134.27 CA C N 91.56 O C N 134.17 C CA CB 86.71 C CA CD 113.72 CB CA CD 113.69 CA CB CC 113.72 CA CB N 86.48 CC CB N 113.81 CB CC OA 119.97 CB CC OB 120.01 OA CC OB 120.02 CA CD CE 109.46 CG1 CF CG2 120.00 CG1 CF S 120.00 CG2 CF S 120.00 CF CG1 CH1 119.99 CF CG2 CH2 120.00 CG1 CH1 CI 120.00 CG2 CH2 CI 119.97 CH1 CI CH2 120.05 CH1 CI CJ 120.00 CH2 CI CJ 119.96 CF S OC 105.73 CF S OD 105.74 CF S N 107.36 OC S OD 125.38 OC S N 105.78 OD S N 105.83 C N CB 95.25 C N S 132.41 CB N S 132.34 Looking for dihedrals (and planes) ... AtmK AtmI AtmJ AtmL Dihedral ---- ---- ---- ---- ------- O C CA CB -179.96 Flat ? O C CA CD -65.48 N C CA CB -0.05 Flat ? N C CA CD 114.43 CA C N CB 0.05 Flat ? CA C N S -179.91 Flat ? O C N CB 179.96 Flat ? O C N S -0.01 Flat ? C CA CB CC -114.46 C CA CB N 0.04 Flat ? CD CA CB CC 131.04 CD CA CB N -114.46 C CA CD CE 81.11 CB CA CD CE 178.26 Flat ? CA CB CC OA 89.99 CA CB CC OB -89.99 N CB CC OA -6.93 Flat ? N CB CC OB 173.09 Flat ? CA CB N C -0.05 Flat ? CA CB N S 179.91 Flat ? CC CB N C 114.37 CC CB N S -65.67 CG2 CF CG1 CH1 0.30 Flat ? S CF CG1 CH1 -179.99 Flat ? CG1 CF CG2 CH2 -0.50 Flat ? S CF CG2 CH2 179.79 Flat ? CG1 CF S OC -22.60 CG1 CF S OD -157.38 CG1 CF S N 89.98 CG2 CF S OC 157.11 CG2 CF S OD 22.33 CG2 CF S N -90.31 CF CG1 CH1 CI -0.08 Flat ? CF CG2 CH2 CI 0.47 Flat ? CG1 CH1 CI CH2 0.06 Flat ? CG1 CH1 CI CJ 179.99 Flat ? CG2 CH2 CI CH1 -0.25 Flat ? CG2 CH2 CI CJ 179.81 Flat ? CF S N C -89.98 CF S N CB 90.07 OC S N C 22.57 OC S N CB -157.38 OD S N C 157.44 OD S N CB -22.51 Looking for impropers (and planes) ... Atm* Nbr1 Nbr2 Nbr3 Improper ---- ---- ---- ---- -------- C CA O N -0.07 CA C CB CD -33.11 CB CA CC N -45.93 >>> WARNING - previous improper not near 0 or +/-35 ! CC CB OA OB 0.01 CF CG1 CG2 S -0.18 CI CH1 CH2 CJ -0.04 --- Atom with 4 or more non-H neighbours --- S CF OC OD 26.28 >>> WARNING - previous improper not near 0 or +/-35 ! S OC OD N -39.18 S OD N CF 41.59 S N CF OC -37.22 N C CB S 0.02 Number of possible flat planes : ( 27) Looking for more planes ... Number of possible flat planes : ( 32) Expanding planes ... WARNING - Reset negative RMSD in LSQGJK : ( -2.073E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.071E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.838E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.838E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.860E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.740E-08) WARNING - Reset negative RMSD in LSQGJK : ( -8.662E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.520E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.073E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.085E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.500E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.813E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.856E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.838E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.051E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.161E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.367E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.798E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.308E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.801E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.419E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.553E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.890E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.544E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.348E-10) WARNING - Reset negative RMSD in LSQGJK : ( -3.025E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.419E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.658E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.184E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.503E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.127E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.288E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.162E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.249E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.239E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.703E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.030E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.320E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.415E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.629E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.703E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.416E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.475E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.001E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.171E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.426E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.398E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.073E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.523E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.494E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.838E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.591E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.348E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.675E-08) WARNING - Reset negative RMSD in LSQGJK : ( -8.085E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.469E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.110E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.323E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.367E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.290E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.320E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.710E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.043E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.544E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.184E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.503E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.593E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.162E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.119E-08) Removing non-unique planes ... Plane nr : ( 9) Nr of atoms : ( 4) WARNING - Reset negative RMSD in LSQGJK : ( -7.914E-08) RMSD to least-squares plane (A): ( 0.024) Atom Dist (A) N -0.015 CB 0.028 CC -0.032 OA 0.019 Plane nr : ( 10) Nr of atoms : ( 4) WARNING - Reset negative RMSD in LSQGJK : ( -1.228E-07) RMSD to least-squares plane (A): ( 0.037) Atom Dist (A) N -0.034 CB 0.030 CC 0.044 OB -0.040 Plane nr : ( 24) Nr of atoms : ( 4) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) CC 0.000 CB 0.000 OA 0.000 OB 0.000 Plane nr : ( 27) Nr of atoms : ( 6) WARNING - Reset negative RMSD in LSQGJK : ( -1.794E-08) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) N 0.000 C -0.001 CB 0.000 S 0.000 CA 0.001 O 0.000 Plane nr : ( 28) Nr of atoms : ( 4) WARNING - Reset negative RMSD in LSQGJK : ( -4.937E-08) RMSD to least-squares plane (A): ( 0.011) Atom Dist (A) CD -0.010 CA -0.012 CE 0.011 CB 0.011 Plane nr : ( 32) Nr of atoms : ( 8) RMSD to least-squares plane (A): ( 0.001) Atom Dist (A) CH2 -0.002 CG2 0.003 CI 0.000 CF -0.001 CH1 0.001 CJ -0.001 CG1 0.001 S -0.001 ------------------- ----- SUMMARY ----- ------------------- Residue type : (2BL) Identifier : ( 464) Segment ID : ( ) Nr of atoms : ( 20) List of elements (from file) : ( C13 H15 N O5 S) Deduced formula : (C13 N1 O5 S1) Guestimated total nr of Hs : ( 17) Nr of extra examples : ( 0) Nr of distances < 0.8 A : ( 0) Nr of bond angles < 80 degrees : ( 0) Nr of bonds found : ( 21) ... bonds without ideal value : ( 1) ... bonds near ideal value : ( 20) ... bonds far from ideal value : ( 0) -"- % : ( 0.000) Nr of angles found : ( 32) Nr of dihedrals found : ( 44) Nr of atoms with impropers : ( 8) ... imprs far from ideal value : ( 2) -"- % : ( 25.000) Nr of flat planes : ( 6)