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 977 2-AMINO-5-BROMO-6-PHENYLPYRIMIDIN-4-OL) > (REMARK 977 Part of HIC-Up: http://xray.bmc.uu.se/hicup) > (REMARK 977 Extracted from PDB file pdb1rsi.ent) > (REMARK 977 Formula C10 H8 BR N3 O) Formula : (977 C10 H8 BR N3 O) > (REMARK 977 Nr of non-hydrogen atoms 15) > (REMARK 977 Eigen-values covariance X/Y/Z 88.6 25.9 5.3) > (REMARK 977 Residue type 977) > (REMARK 977 Residue name 1245) > (REMARK 977 Original residue name (for O) $1001) > (REMARK 977 RESOLUTION. 2.20 ANGSTROMS.) > (REMARK 977 occurs in 0 other PDB entries) > (REMARK 977) Using residue : (977) Identifier : ( 1245) Segment ID : ( ) Using formula : ( C10 H8 BR N3 O) Element ? | C| Carbon | 6 10 Element ? | H| Hydrogen | 1 8 Element ? |BR| Bromine | 35 1 Element ? | N| Nitrogen | 7 3 Element ? | O| Oxygen | 8 1 Atom # 1 = N1 @ 3.198 -0.193 2.848 1.00 20.00 Atom # 2 = C2 @ 1.991 -0.123 2.173 1.00 20.00 Atom # 3 = N3 @ 1.992 -0.114 0.850 1.00 20.00 Atom # 4 = C4 @ 0.849 -0.052 0.168 1.00 20.00 Atom # 5 = C5 @ -0.354 0.013 0.868 1.00 20.00 Atom # 6 = BR6 @ -2.004 0.111 -0.049 1.00 20.00 Atom # 7 = C7 @ -0.311 0.007 2.260 1.00 20.00 Atom # 8 = O8 @ -1.456 0.070 2.982 1.00 20.00 Atom # 9 = N9 @ 0.865 -0.061 2.871 1.00 20.00 Atom # 10 = C10 @ 0.858 -0.048 -1.315 1.00 20.00 Atom # 11 = C11 @ -0.103 -0.767 -2.022 1.00 20.00 Atom # 12 = C12 @ -0.093 -0.756 -3.402 1.00 20.00 Atom # 13 = C13 @ 0.874 -0.042 -4.083 1.00 20.00 Atom # 14 = C14 @ 1.835 0.669 -3.387 1.00 20.00 Atom # 15 = C15 @ 1.831 0.669 -2.006 1.00 20.00 > (REMARK 977 ENDHET) Nr of atoms read : ( 15) Nr of extra examples : ( 0) Expected formula : ( C10 H8 BR N3 O) Observed formula : (C10 N3 O1 BR1) Element | H| Expected 8 | Observed 0 Element | C| Expected 10 | Observed 10 Element | N| Expected 3 | Observed 3 Element | O| Expected 1 | Observed 1 Element |BR| Expected 1 | Observed 1 Expected and observed formulae agree (ignoring any hydrogens) ! Looking for bonded atoms ... Bond N1 - C2 = 1.385 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.34 (devn. 0.04) For: C-N partial double; range 1.322-1.352 Bond C2 - N3 = 1.323 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 C2 - N9 = 1.326 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 N3 - C4 = 1.332 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 C4 - C5 = 1.393 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 C4 - C10 = 1.483 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.44 (devn. 0.04) For: C-C single shortened; range 1.421-1.46 Bond C5 - BR6 = 1.890 A (cutoff : 2.240) Nr of entries in library : ( 3) Closest to 1.87 (devn. 0.02) For: C-Br CH2=CH-Br or C6H5-Br type; range 1.85-1.89 Bond C5 - C7 = 1.393 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 C7 - O8 = 1.355 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.36 (devn. 0.00) For: C-O partial double Bond C7 - N9 = 1.327 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 - C11 = 1.393 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 - C15 = 1.392 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 - C12 = 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 C12 - C13 = 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 C13 - C14 = 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 C14 - C15 = 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 Nr of bonds found : ( 16) 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: 0 Carbon C2 Nbrs: 3 ~Hs: 0 Nitrogen N3 Nbrs: 2 ~Hs: 1 Carbon C4 Nbrs: 3 ~Hs: 0 Carbon C5 Nbrs: 3 ~Hs: 0 Carbon C7 Nbrs: 3 ~Hs: 0 Oxygen O8 Nbrs: 1 ~Hs: 1 Nitrogen N9 Nbrs: 2 ~Hs: 1 Carbon C10 Nbrs: 3 ~Hs: 0 Carbon C11 Nbrs: 2 ~Hs: 1 Carbon C12 Nbrs: 2 ~Hs: 1 Carbon C13 Nbrs: 2 ~Hs: 1 Carbon C14 Nbrs: 2 ~Hs: 1 Carbon C15 Nbrs: 2 ~Hs: 1 Est. total nr of hydrogens : ( 8) Looking for angles ... AtmJ AtmI AtmK Angle ---- ---- ---- ----- N1 C2 N3 119.15 N1 C2 N9 119.07 N3 C2 N9 121.78 C2 N3 C4 120.76 N3 C4 C5 119.06 N3 C4 C10 120.45 C5 C4 C10 120.50 C4 C5 BR6 120.82 C4 C5 C7 118.38 BR6 C5 C7 120.80 C5 C7 O8 120.41 C5 C7 N9 119.20 O8 C7 N9 120.39 C2 N9 C7 120.83 C4 C10 C11 120.13 C4 C10 C15 120.13 C11 C10 C15 119.74 C10 C11 C12 119.89 C11 C12 C13 120.14 C12 C13 C14 120.26 C13 C14 C15 120.08 C10 C15 C14 119.89 Looking for dihedrals (and planes) ... AtmK AtmI AtmJ AtmL Dihedral ---- ---- ---- ---- ------- N1 C2 N3 C4 179.77 Flat ? N9 C2 N3 C4 -0.52 Flat ? N1 C2 N9 C7 -180.00 Flat ? N3 C2 N9 C7 0.30 Flat ? C2 N3 C4 C5 0.44 Flat ? C2 N3 C4 C10 -179.75 Flat ? N3 C4 C5 BR6 179.70 Flat ? N3 C4 C5 C7 -0.16 Flat ? C10 C4 C5 BR6 -0.11 Flat ? C10 C4 C5 C7 -179.97 Flat ? N3 C4 C10 C11 140.24 N3 C4 C10 C15 -39.44 C5 C4 C10 C11 -39.95 C5 C4 C10 C15 140.37 C4 C5 C7 O8 179.94 Flat ? C4 C5 C7 N9 -0.05 Flat ? BR6 C5 C7 O8 0.08 Flat ? BR6 C5 C7 N9 -179.91 Flat ? C5 C7 N9 C2 -0.01 Flat ? O8 C7 N9 C2 180.00 Flat ? C4 C10 C11 C12 179.77 Flat ? C15 C10 C11 C12 -0.55 Flat ? C4 C10 C15 C14 179.98 Flat ? C11 C10 C15 C14 0.30 Flat ? C10 C11 C12 C13 0.50 Flat ? C11 C12 C13 C14 -0.19 Flat ? C12 C13 C14 C15 -0.06 Flat ? C13 C14 C15 C10 0.00 Flat ? Looking for impropers (and planes) ... Atm* Nbr1 Nbr2 Nbr3 Improper ---- ---- ---- ---- -------- C2 N1 N3 N9 0.16 C4 N3 C5 C10 -0.11 C5 C4 BR6 C7 0.08 C7 C5 O8 N9 0.00 C10 C4 C11 C15 0.18 Number of possible flat planes : ( 29) Looking for more planes ... Number of possible flat planes : ( 36) Expanding planes ... WARNING - Reset negative RMSD in LSQGJK : ( -1.238E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.489E-09) WARNING - Reset negative RMSD in LSQGJK : ( -5.563E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.262E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.602E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.297E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.585E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.563E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.655E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.861E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.435E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.713E-08) WARNING - Reset negative RMSD in LSQGJK : ( -8.037E-09) WARNING - Reset negative RMSD in LSQGJK : ( -5.124E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.489E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.605E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.419E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.238E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.489E-09) WARNING - Reset negative RMSD in LSQGJK : ( -8.037E-09) WARNING - Reset negative RMSD in LSQGJK : ( -4.559E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.365E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.843E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.997E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.213E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.241E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.856E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.365E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.027E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.489E-09) WARNING - Reset negative RMSD in LSQGJK : ( -4.550E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.127E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.411E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.585E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.856E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.529E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.143E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.489E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.195E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.866E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.143E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.489E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.529E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.348E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.866E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.561E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.489E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.195E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.622E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.524E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.218E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.070E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.635E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.070E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.602E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.655E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.713E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.266E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.297E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.861E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.087E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.488E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.839E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.547E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.609E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.839E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.867E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.622E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.488E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.785E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.203E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.437E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.355E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.252E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.275E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.437E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.355E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.872E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.609E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.228E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.509E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.609E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.559E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.856E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.843E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.997E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.213E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.365E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.189E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.143E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.192E-08) WARNING - Reset negative RMSD in LSQGJK : ( -8.547E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.605E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.238E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.107E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.297E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.585E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.488E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.033E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.488E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.437E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.430E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.057E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.274E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.355E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.547E-08) Removing non-unique planes ... Plane nr : ( 31) Nr of atoms : ( 10) WARNING - Reset negative RMSD in LSQGJK : ( -2.585E-07) RMSD to least-squares plane (A): ( 0.001) Atom Dist (A) N9 0.000 C2 0.001 C7 0.000 N1 0.001 N3 -0.004 C5 0.001 O8 -0.001 C4 0.001 BR6 -0.001 C10 0.001 Plane nr : ( 36) Nr of atoms : ( 7) RMSD to least-squares plane (A): ( 0.002) Atom Dist (A) C15 -0.001 C10 0.001 C14 -0.001 C4 0.001 C11 -0.003 C13 0.001 C12 0.002 ------------------- ----- SUMMARY ----- ------------------- Residue type : (977) Identifier : ( 1245) Segment ID : ( ) Nr of atoms : ( 15) List of elements (from file) : ( C10 H8 BR N3 O) Deduced formula : (C10 N3 O1 BR1) 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 : ( 16) ... bonds without ideal value : ( 0) ... bonds near ideal value : ( 16) ... bonds far from ideal value : ( 0) -"- % : ( 0.000) Nr of angles found : ( 22) Nr of dihedrals found : ( 28) Nr of atoms with impropers : ( 5) ... imprs far from ideal value : ( 0) -"- % : ( 0.000) Nr of flat planes : ( 2)