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 U73 N-(5-ISOPROPYL-THIAZOL-2-YL)-2-PYRIDIN-3-YL-ACETAMIDE) > (REMARK U73 Part of HIC-Up: http://xray.bmc.uu.se/hicup) > (REMARK U73 Extracted from PDB file pdb2btr.ent) > (REMARK U73 Formula C13 H15 N3 O S) Formula : (U73 C13 H15 N3 O S) > (REMARK U73 Nr of non-hydrogen atoms 18) > (REMARK U73 Eigen-values covariance X/Y/Z 230.1 19.5 12.2) > (REMARK U73 Residue type U73) > (REMARK U73 Residue name 7487) > (REMARK U73 Original residue name (for O) $A300) > (REMARK U73 RESOLUTION. 1.85 ANGSTROMS.) > (REMARK U73 occurs in 0 other PDB entries) > (REMARK U73) Using residue : (U73) Identifier : ( 7487) Segment ID : ( ) Using formula : ( C13 H15 N3 O S) Element ? | C| Carbon | 6 13 Element ? | H| Hydrogen | 1 15 Element ? | N| Nitrogen | 7 3 Element ? | O| Oxygen | 8 1 Element ? | S| Sulfur | 16 1 Atom # 1 = O11 @ 0.160 -0.011 -0.840 1.00 20.00 Atom # 2 = C10 @ -1.043 -0.008 -1.018 1.00 20.00 Atom # 3 = N9 @ -1.867 -0.002 0.020 1.00 20.00 Atom # 4 = C3 @ -1.376 0.000 1.261 1.00 20.00 Atom # 5 = N4 @ -2.048 0.005 2.447 1.00 20.00 Atom # 6 = C5 @ -1.338 0.006 3.605 1.00 20.00 Atom # 7 = S2 @ 0.279 0.003 1.778 1.00 20.00 Atom # 8 = C1 @ -0.003 0.001 3.540 1.00 20.00 Atom # 9 = C6 @ 1.002 0.001 4.662 1.00 20.00 Atom # 10 = C8 @ 1.875 -1.251 4.565 1.00 20.00 Atom # 11 = C7 @ 1.884 1.247 4.558 1.00 20.00 Atom # 12 = C12 @ -1.597 -0.010 -2.420 1.00 20.00 Atom # 13 = C13 @ -0.460 -0.016 -3.409 1.00 20.00 Atom # 14 = C14 @ 0.065 -1.215 -3.867 1.00 20.00 Atom # 15 = C15 @ 1.110 -1.173 -4.777 1.00 20.00 Atom # 16 = C16 @ 1.590 0.053 -5.195 1.00 20.00 Atom # 17 = N17 @ 1.065 1.174 -4.738 1.00 20.00 Atom # 18 = C18 @ 0.067 1.171 -3.877 1.00 20.00 > (REMARK U73 ENDHET) Nr of atoms read : ( 18) Nr of extra examples : ( 0) Expected formula : ( C13 H15 N3 O S) Observed formula : (C13 N3 O1 S1) Element | H| Expected 15 | Observed 0 Element | C| Expected 13 | Observed 13 Element | N| Expected 3 | Observed 3 Element | O| Expected 1 | Observed 1 Element | S| Expected 1 | Observed 1 Expected and observed formulae agree (ignoring any hydrogens) ! Looking for bonded atoms ... Bond O11 - C10 = 1.216 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.24 (devn. 0.02) For: C-O double; range 1.23-1.26 Bond C10 - N9 = 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 C10 - C12 = 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 N9 - C3 = 1.335 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 C3 - N4 = 1.363 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 C3 - S2 = 1.734 A (cutoff : 2.050) Nr of entries in library : ( 3) Closest to 1.72 (devn. 0.01) For: C-S (partial) double; range 1.71-1.73 Bond N4 - C5 = 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 - C1 = 1.337 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.34 (devn. 0.00) For: C-C double or partial triple; range 1.309-1.337 Bond S2 - C1 = 1.784 A (cutoff : 2.050) Nr of entries in library : ( 3) Closest to 1.82 (devn. 0.04) For: C-S single Bond C1 - C6 = 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 C6 - C8 = 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 C6 - C7 = 1.530 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 C12 - C13 = 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 C13 - C14 = 1.387 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 - C18 = 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 C14 - C15 = 1.386 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 C15 - C16 = 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 C16 - N17 = 1.320 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 N17 - C18 = 1.318 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 : ( 19) 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) Oxygen O11 Nbrs: 1 ~Hs: 0 Carbon C10 Nbrs: 3 ~Hs: 0 Nitrogen N9 Nbrs: 2 ~Hs: 1 Carbon C3 Nbrs: 3 ~Hs: 0 Nitrogen N4 Nbrs: 2 ~Hs: 1 Carbon C5 Nbrs: 2 ~Hs: 1 Sulphur S2 Nbrs: 2 ~Hs: 0 Carbon C1 Nbrs: 3 ~Hs: 0 Carbon C6 Nbrs: 3 ~Hs: 1 Carbon C8 Nbrs: 1 ~Hs: 3 Carbon C7 Nbrs: 1 ~Hs: 3 Carbon C12 Nbrs: 2 ~Hs: 2 Carbon C13 Nbrs: 3 ~Hs: 0 Carbon C14 Nbrs: 2 ~Hs: 1 Carbon C15 Nbrs: 2 ~Hs: 1 Carbon C16 Nbrs: 2 ~Hs: 1 Nitrogen N17 Nbrs: 2 ~Hs: 1 Carbon C18 Nbrs: 2 ~Hs: 1 Est. total nr of hydrogens : ( 17) Looking for angles ... AtmJ AtmI AtmK Angle ---- ---- ---- ----- O11 C10 N9 120.03 O11 C10 C12 119.98 N9 C10 C12 119.99 C10 N9 C3 119.97 N9 C3 N4 128.88 N9 C3 S2 128.93 N4 C3 S2 102.19 C3 N4 C5 118.95 N4 C5 C1 118.73 C3 S2 C1 98.26 C5 C1 S2 101.88 C5 C1 C6 129.06 S2 C1 C6 129.06 C1 C6 C8 109.49 C1 C6 C7 109.51 C8 C6 C7 109.47 C10 C12 C13 109.46 C12 C13 C14 120.39 C12 C13 C18 120.47 C14 C13 C18 119.14 C13 C14 C15 118.42 C14 C15 C16 119.17 C15 C16 N17 120.73 C16 N17 C18 121.71 C13 C18 N17 120.83 Looking for dihedrals (and planes) ... AtmK AtmI AtmJ AtmL Dihedral ---- ---- ---- ---- ------- O11 C10 N9 C3 -0.04 Flat ? C12 C10 N9 C3 -179.99 Flat ? O11 C10 C12 C13 0.01 Flat ? N9 C10 C12 C13 179.96 Flat ? C10 N9 C3 N4 -179.95 Flat ? C10 N9 C3 S2 0.31 Flat ? N9 C3 N4 C5 179.99 Flat ? S2 C3 N4 C5 -0.21 Flat ? N9 C3 S2 C1 -179.89 Flat ? N4 C3 S2 C1 0.32 Flat ? C3 N4 C5 C1 -0.05 Flat ? N4 C5 C1 S2 0.28 Flat ? N4 C5 C1 C6 179.99 Flat ? C3 S2 C1 C5 -0.34 Flat ? C3 S2 C1 C6 179.94 Flat ? C5 C1 C6 C8 120.01 C5 C1 C6 C7 -119.96 S2 C1 C6 C8 -60.35 S2 C1 C6 C7 59.68 C10 C12 C13 C14 90.05 C10 C12 C13 C18 -90.35 C12 C13 C14 C15 179.96 Flat ? C18 C13 C14 C15 0.35 Flat ? C12 C13 C18 N17 179.73 Flat ? C14 C13 C18 N17 -0.67 Flat ? C13 C14 C15 C16 -0.03 Flat ? C14 C15 C16 N17 -0.01 Flat ? C15 C16 N17 C18 -0.30 Flat ? C16 N17 C18 C13 0.65 Flat ? Looking for impropers (and planes) ... Atm* Nbr1 Nbr2 Nbr3 Improper ---- ---- ---- ---- -------- C10 O11 N9 C12 -0.03 C3 N9 N4 S2 0.15 C1 C5 S2 C6 -0.14 C6 C1 C8 C7 -35.35 C13 C12 C14 C18 -0.23 Number of possible flat planes : ( 27) Looking for more planes ... Number of possible flat planes : ( 37) Expanding planes ... WARNING - Reset negative RMSD in LSQGJK : ( -1.420E-09) WARNING - Reset negative RMSD in LSQGJK : ( -7.700E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.483E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.383E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.998E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.984E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.420E-09) WARNING - Reset negative RMSD in LSQGJK : ( -5.106E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.481E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.998E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.713E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.160E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.984E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.647E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.505E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.234E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.700E-09) WARNING - Reset negative RMSD in LSQGJK : ( -5.106E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.015E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.797E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.711E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.015E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.631E-08) WARNING - Reset negative RMSD in LSQGJK : ( -8.690E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.299E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.631E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.302E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.859E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.173E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.570E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.368E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.173E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.139E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.238E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.570E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.859E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.711E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.139E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.238E-08) WARNING - Reset negative RMSD in LSQGJK : ( -8.690E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.859E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.173E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.202E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.139E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.238E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.859E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.173E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.139E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.238E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.368E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.173E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.139E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.238E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.247E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.951E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.971E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.368E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.173E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.711E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.951E-09) WARNING - Reset negative RMSD in LSQGJK : ( -4.859E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.711E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.095E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.095E-08) WARNING - Reset negative RMSD in LSQGJK : ( -8.861E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.602E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.480E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.754E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.734E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.470E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.420E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.647E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.713E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.234E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.998E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.631E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.570E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.971E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.951E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.971E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.368E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.780E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.420E-09) WARNING - Reset negative RMSD in LSQGJK : ( -7.700E-09) WARNING - Reset negative RMSD in LSQGJK : ( -3.970E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.483E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.383E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.711E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.973E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.690E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.015E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.971E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.110E-08) WARNING - Reset negative RMSD in LSQGJK : ( -8.690E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.368E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.173E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.139E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.238E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.570E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.247E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.368E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.173E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.713E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.234E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.095E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.143E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.381E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.347E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.274E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.498E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.848E-09) Removing non-unique planes ... Plane nr : ( 32) Nr of atoms : ( 11) RMSD to least-squares plane (A): ( 0.002) Atom Dist (A) C12 0.000 C10 -0.001 C13 -0.001 O11 -0.001 N9 0.000 C3 0.000 N4 0.000 S2 0.006 C5 0.000 C1 -0.002 C6 -0.002 Plane nr : ( 37) Nr of atoms : ( 7) RMSD to least-squares plane (A): ( 0.002) Atom Dist (A) C18 -0.004 C13 0.002 N17 0.002 C12 0.001 C14 -0.001 C16 0.001 C15 -0.001 ------------------- ----- SUMMARY ----- ------------------- Residue type : (U73) Identifier : ( 7487) Segment ID : ( ) Nr of atoms : ( 18) List of elements (from file) : ( C13 H15 N3 O S) Deduced formula : (C13 N3 O1 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 : ( 19) ... bonds without ideal value : ( 0) ... bonds near ideal value : ( 19) ... bonds far from ideal value : ( 0) -"- % : ( 0.000) Nr of angles found : ( 25) Nr of dihedrals found : ( 29) Nr of atoms with impropers : ( 5) ... imprs far from ideal value : ( 0) -"- % : ( 0.000) Nr of flat planes : ( 2)