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 HMD 4-(5-AMINO-4-OXO-4H-PYRAZOL-3-YL)-2-BROMO-4,5,6,7- TETRAHYDRO-3AH-PYRROLO(2,3-C)AZEPIN-8-ONE; HYMENIALDISINE) > (REMARK HMD Part of HIC-Up: http://xray.bmc.uu.se/hicup) > (REMARK HMD Extracted from PDB file pdb1dm2.ent) > (REMARK HMD Formula C11 H10 BR N5 O2) Formula : (HMD C11 H10 BR N5 O2) > (REMARK HMD Nr of non-hydrogen atoms 19) > (REMARK HMD Eigen-values covariance X/Y/Z 130.4 59.0 1.2) > (REMARK HMD Residue type HMD) > (REMARK HMD Residue name 4246) > (REMARK HMD Original residue name (for O) $400) > (REMARK HMD RESOLUTION. 2.10 ANGSTROMS.) > (REMARK HMD occurs in 1 other PDB entries) > (REMARK HMD Also in 2.5-3.0A : 2PMO) > (REMARK HMD Resolution (A) : 2.90) > (REMARK HMD) Using residue : (HMD) Identifier : ( 4246) Segment ID : ( ) Using formula : ( C11 H10 BR N5 O2) Element ? | C| Carbon | 6 11 Element ? | H| Hydrogen | 1 10 Element ? |BR| Bromine | 35 1 Element ? | N| Nitrogen | 7 5 Element ? | O| Oxygen | 8 2 Atom # 1 = BR1 @ 2.503 0.121 -2.247 1.00 20.00 Atom # 2 = O1 @ -3.306 -0.781 -2.746 1.00 20.00 Atom # 3 = O2 @ -0.436 -2.354 2.873 1.00 20.00 Atom # 4 = N1 @ -0.350 -0.099 -2.191 1.00 20.00 Atom # 5 = N2 @ -3.550 0.669 -1.079 1.00 20.00 Atom # 6 = N3 @ 0.836 -0.724 3.874 1.00 20.00 Atom # 7 = N4 @ 0.181 0.991 2.629 1.00 20.00 Atom # 8 = N5 @ 1.798 1.385 4.378 1.00 20.00 Atom # 9 = C1 @ 0.798 -0.245 -1.515 1.00 20.00 Atom # 10 = C2 @ 0.603 -0.681 -0.263 1.00 20.00 Atom # 11 = C3 @ -0.895 -0.856 -0.151 1.00 20.00 Atom # 12 = C4 @ -1.398 -0.352 -1.469 1.00 20.00 Atom # 13 = C5 @ -2.813 -0.175 -1.814 1.00 20.00 Atom # 14 = C6 @ -3.007 1.595 -0.170 1.00 20.00 Atom # 15 = C7 @ -1.690 1.429 0.544 1.00 20.00 Atom # 16 = C8 @ -1.457 -0.019 1.012 1.00 20.00 Atom # 17 = C9 @ -0.474 -0.025 2.154 1.00 20.00 Atom # 18 = C10 @ -0.054 -1.207 2.983 1.00 20.00 Atom # 19 = C11 @ 0.976 0.573 3.662 1.00 20.00 > (REMARK HMD ENDHET) Nr of atoms read : ( 19) Nr of extra examples : ( 0) Expected formula : ( C11 H10 BR N5 O2) Observed formula : (C11 N5 O2 BR1) Element | H| Expected 10 | Observed 0 Element | C| Expected 11 | Observed 11 Element | N| Expected 5 | Observed 5 Element | O| Expected 2 | Observed 2 Element |BR| Expected 1 | Observed 1 Expected and observed formulae agree (ignoring any hydrogens) ! Looking for bonded atoms ... Bond BR1 - C1 = 1.891 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 O1 - C5 = 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 O2 - C10 = 1.214 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 N1 - C1 = 1.340 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 N1 - C4 = 1.298 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 N2 - C5 = 1.340 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 N2 - C6 = 1.407 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.43 (devn. 0.02) For: C-N aromatic Bond N3 - C10 = 1.349 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 - C11 = 1.322 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 N4 - C9 = 1.299 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 N4 - C11 = 1.369 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 N5 - C11 = 1.359 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 C1 - C2 = 1.340 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 C2 - C3 = 1.512 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 C3 - C4 = 1.498 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 - C8 = 1.539 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 C4 - C5 = 1.467 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.44 (devn. 0.03) For: C-C single shortened; range 1.421-1.46 Bond C6 - C7 = 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 C7 - C8 = 1.539 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 C8 - C9 = 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 C9 - C10 = 1.504 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 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) Oxygen O1 Nbrs: 1 ~Hs: 0 Oxygen O2 Nbrs: 1 ~Hs: 0 Nitrogen N1 Nbrs: 2 ~Hs: 1 Nitrogen N2 Nbrs: 2 ~Hs: 1 Nitrogen N3 Nbrs: 2 ~Hs: 1 Nitrogen N4 Nbrs: 2 ~Hs: 1 Nitrogen N5 Nbrs: 1 ~Hs: 0 Carbon C1 Nbrs: 3 ~Hs: 0 Carbon C2 Nbrs: 2 ~Hs: 1 Carbon C3 Nbrs: 3 ~Hs: 1 Carbon C4 Nbrs: 3 ~Hs: 0 Carbon C5 Nbrs: 3 ~Hs: 0 Carbon C6 Nbrs: 2 ~Hs: 2 Carbon C7 Nbrs: 2 ~Hs: 2 Carbon C8 Nbrs: 3 ~Hs: 1 Carbon C9 Nbrs: 3 ~Hs: 0 Carbon C10 Nbrs: 3 ~Hs: 0 Carbon C11 Nbrs: 3 ~Hs: 0 Est. total nr of hydrogens : ( 11) Looking for angles ... AtmJ AtmI AtmK Angle ---- ---- ---- ----- C1 N1 C4 112.95 C5 N2 C6 123.83 C10 N3 C11 108.38 C9 N4 C11 109.27 BR1 C1 N1 123.77 BR1 C1 C2 123.76 N1 C1 C2 112.46 C1 C2 C3 104.54 C2 C3 C4 103.21 C2 C3 C8 110.78 C4 C3 C8 111.05 N1 C4 C3 106.50 N1 C4 C5 128.65 C3 C4 C5 124.84 O1 C5 N2 120.75 O1 C5 C4 120.74 N2 C5 C4 118.52 N2 C6 C7 124.81 C6 C7 C8 112.32 C3 C8 C7 109.70 C3 C8 C9 109.41 C7 C8 C9 109.44 N4 C9 C8 127.09 N4 C9 C10 105.81 C8 C9 C10 127.10 O2 C10 N3 127.29 O2 C10 C9 127.22 N3 C10 C9 105.49 N3 C11 N4 111.05 N3 C11 N5 124.46 N4 C11 N5 124.49 Looking for dihedrals (and planes) ... AtmK AtmI AtmJ AtmL Dihedral ---- ---- ---- ---- ------- C4 N1 C1 BR1 -177.13 Flat ? C4 N1 C1 C2 2.96 Flat ? C1 N1 C4 C3 -5.57 Flat ? C1 N1 C4 C5 173.37 Flat ? C6 N2 C5 O1 -166.84 Flat ? C6 N2 C5 C4 13.18 Flat ? C5 N2 C6 C7 -26.94 C11 N3 C10 O2 -179.95 Flat ? C11 N3 C10 C9 0.05 Flat ? C10 N3 C11 N4 0.23 Flat ? C10 N3 C11 N5 -179.95 Flat ? C11 N4 C9 C8 -179.82 Flat ? C11 N4 C9 C10 0.45 Flat ? C9 N4 C11 N3 -0.45 Flat ? C9 N4 C11 N5 179.73 Flat ? BR1 C1 C2 C3 -178.79 Flat ? N1 C1 C2 C3 1.12 Flat ? C1 C2 C3 C4 -4.09 Flat ? C1 C2 C3 C8 -123.02 C2 C3 C4 N1 5.80 Flat ? C2 C3 C4 C5 -173.19 Flat ? C8 C3 C4 N1 124.54 C8 C3 C4 C5 -54.45 C2 C3 C8 C7 83.41 C2 C3 C8 C9 -36.65 C4 C3 C8 C7 -30.66 C4 C3 C8 C9 -150.73 N1 C4 C5 O1 61.42 N1 C4 C5 N2 -118.59 C3 C4 C5 O1 -119.82 C3 C4 C5 N2 60.17 N2 C6 C7 C8 -40.07 C6 C7 C8 C3 82.94 C6 C7 C8 C9 -157.01 C3 C8 C9 N4 114.94 C3 C8 C9 C10 -65.38 C7 C8 C9 N4 -5.29 Flat ? C7 C8 C9 C10 174.39 Flat ? N4 C9 C10 O2 179.68 Flat ? N4 C9 C10 N3 -0.31 Flat ? C8 C9 C10 O2 -0.05 Flat ? C8 C9 C10 N3 179.95 Flat ? Looking for impropers (and planes) ... Atm* Nbr1 Nbr2 Nbr3 Improper ---- ---- ---- ---- -------- C1 BR1 N1 C2 -0.05 C3 C2 C4 C8 34.69 C4 N1 C3 C5 -0.53 C5 O1 N2 C4 -0.01 C8 C3 C7 C9 35.00 C9 N4 C8 C10 0.18 C10 O2 N3 C9 0.00 C11 N3 N4 N5 -0.10 Number of possible flat planes : ( 31) Looking for more planes ... Number of possible flat planes : ( 36) Expanding planes ... WARNING - Reset negative RMSD in LSQGJK : ( -6.433E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.883E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.589E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.433E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.290E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.195E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.883E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.624E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.089E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.122E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.066E-09) WARNING - Reset negative RMSD in LSQGJK : ( -8.960E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.771E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.083E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.193E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.281E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.845E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.275E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.844E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.768E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.819E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.124E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.053E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.405E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.474E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.417E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.705E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.085E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.657E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.544E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.339E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.787E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.545E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.440E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.904E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.334E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.087E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.532E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.087E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.197E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.094E-09) WARNING - Reset negative RMSD in LSQGJK : ( -5.031E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.385E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.911E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.264E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.644E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.287E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.041E-08) WARNING - Reset negative RMSD in LSQGJK : ( -8.194E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.732E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.416E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.002E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.041E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.235E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.175E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.589E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.787E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.094E-09) WARNING - Reset negative RMSD in LSQGJK : ( -5.732E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.001E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.752E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.590E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.433E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.066E-09) WARNING - Reset negative RMSD in LSQGJK : ( -9.771E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.098E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.173E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.819E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.124E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.034E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.830E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.286E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.542E-07) Removing non-unique planes ... Plane nr : ( 5) Nr of atoms : ( 4) RMSD to least-squares plane (A): ( 0.063) Atom Dist (A) C6 0.060 N2 -0.063 C5 -0.063 O1 0.067 Plane nr : ( 17) Nr of atoms : ( 7) WARNING - Reset negative RMSD in LSQGJK : ( -1.542E-07) RMSD to least-squares plane (A): ( 0.044) Atom Dist (A) C1 0.003 C2 -0.040 C3 0.039 C4 0.020 BR1 -0.029 N1 0.072 C5 -0.065 Plane nr : ( 28) Nr of atoms : ( 4) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) C5 0.000 O1 0.000 N2 0.000 C4 0.000 Plane nr : ( 29) Nr of atoms : ( 8) WARNING - Reset negative RMSD in LSQGJK : ( -1.598E-07) RMSD to least-squares plane (A): ( 0.032) Atom Dist (A) C9 -0.027 N4 -0.022 C8 -0.053 C10 0.006 C11 0.000 C7 0.059 O2 0.018 N3 0.019 Plane nr : ( 33) Nr of atoms : ( 4) WARNING - Reset negative RMSD in LSQGJK : ( -1.182E-07) RMSD to least-squares plane (A): ( 0.042) Atom Dist (A) N2 0.056 C5 -0.053 C6 -0.027 C4 0.024 Plane nr : ( 34) Nr of atoms : ( 8) RMSD to least-squares plane (A): ( 0.002) Atom Dist (A) N3 0.000 C10 0.000 C11 0.001 O2 -0.001 C9 0.001 N4 -0.005 N5 0.002 C8 0.002 Plane nr : ( 35) Nr of atoms : ( 8) RMSD to least-squares plane (A): ( 0.031) Atom Dist (A) N4 -0.026 C9 -0.022 C11 -0.002 C8 -0.047 C10 0.020 N3 0.028 N5 -0.005 C7 0.054 ------------------- ----- SUMMARY ----- ------------------- Residue type : (HMD) Identifier : ( 4246) Segment ID : ( ) Nr of atoms : ( 19) List of elements (from file) : ( C11 H10 BR N5 O2) Deduced formula : (C11 N5 O2 BR1) Guestimated total nr of Hs : ( 11) 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 : ( 0) ... bonds near ideal value : ( 21) ... bonds far from ideal value : ( 0) -"- % : ( 0.000) Nr of angles found : ( 31) Nr of dihedrals found : ( 42) Nr of atoms with impropers : ( 8) ... imprs far from ideal value : ( 0) -"- % : ( 0.000) Nr of flat planes : ( 7)