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 D6G 2-DEOXY-GLUCOSE-6-PHOSPHATE) > (REMARK D6G Part of HIC-Up: http://xray.bmc.uu.se/hicup) > (REMARK D6G Extracted from PDB file pdb2pri.ent) > (REMARK D6G Formula C6 H13 O8 P) Formula : (D6G C6 H13 O8 P) > (REMARK D6G Nr of non-hydrogen atoms 15) > (REMARK D6G Eigen-values covariance X/Y/Z 111.4 23.4 5.8) > (REMARK D6G Residue type D6G) > (REMARK D6G Residue name 2844) > (REMARK D6G Original residue name (for O) $930) > (REMARK D6G RESOLUTION. 2.30 ANGSTROMS.) > (REMARK D6G occurs in 0 other PDB entries) > (REMARK D6G) Using residue : (D6G) Identifier : ( 2844) Segment ID : ( ) Using formula : ( C6 H13 O8 P) Element ? | C| Carbon | 6 6 Element ? | H| Hydrogen | 1 13 Element ? | O| Oxygen | 8 8 Element ? | P| Phosphorous | 15 1 Atom # 1 = C1 @ -1.786 0.234 -2.269 1.00 20.00 Atom # 2 = C2 @ -0.833 0.614 -3.404 1.00 20.00 Atom # 3 = C3 @ 0.497 -0.119 -3.205 1.00 20.00 Atom # 4 = C4 @ 1.014 0.177 -1.792 1.00 20.00 Atom # 5 = C5 @ -0.078 -0.169 -0.779 1.00 20.00 Atom # 6 = C6 @ 0.438 0.092 0.636 1.00 20.00 Atom # 7 = O1 @ -1.985 -1.180 -2.268 1.00 20.00 Atom # 8 = O3 @ 1.446 0.337 -4.171 1.00 20.00 Atom # 9 = O4 @ 2.176 -0.611 -1.533 1.00 20.00 Atom # 10 = O5 @ -1.230 0.635 -1.018 1.00 20.00 Atom # 11 = O6 @ -0.581 -0.230 1.583 1.00 20.00 Atom # 12 = P @ 0.028 0.067 3.043 1.00 20.00 Atom # 13 = O1P @ 0.400 1.496 3.140 1.00 20.00 Atom # 14 = O2P @ -1.073 -0.276 4.166 1.00 20.00 Atom # 15 = O3P @ 1.334 -0.844 3.276 1.00 20.00 > (REMARK D6G ENDHET) Nr of atoms read : ( 15) Nr of extra examples : ( 0) Expected formula : ( C6 H13 O8 P) Observed formula : (C6 O8 P1) Element | H| Expected 13 | Observed 0 Element | C| Expected 6 | Observed 6 Element | O| Expected 8 | Observed 8 Element | P| Expected 1 | Observed 1 Expected and observed formulae agree (ignoring any hydrogens) ! Looking for bonded atoms ... Bond C1 - C2 = 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 C1 - O1 = 1.428 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.43 (devn. 0.00) For: C-O single Bond C1 - O5 = 1.427 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.43 (devn. 0.00) For: C-O single Bond C2 - C3 = 1.532 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 C3 - C4 = 1.533 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 C3 - O3 = 1.429 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.43 (devn. 0.00) For: C-O single Bond C4 - C5 = 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 C4 - O4 = 1.428 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.43 (devn. 0.00) For: C-O single Bond C5 - C6 = 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 C5 - O5 = 1.425 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.43 (devn. 0.00) For: C-O single Bond C6 - O6 = 1.428 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.43 (devn. 0.00) For: C-O single Bond O6 - P = 1.610 A (cutoff : 2.080) Nr of entries in library : ( 2) Closest to 1.63 (devn. 0.02) For: O-P single Bond P - O1P = 1.480 A (cutoff : 2.080) Nr of entries in library : ( 2) >>> WARNING - Too far from ideal 1.38 (devn. 0.10) For: O-P double Bond P - O2P = 1.610 A (cutoff : 2.080) Nr of entries in library : ( 2) Closest to 1.63 (devn. 0.02) For: O-P single Bond P - O3P = 1.609 A (cutoff : 2.080) Nr of entries in library : ( 2) Closest to 1.63 (devn. 0.02) For: O-P single Nr of bonds found : ( 15) 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 C1 Nbrs: 3 ~Hs: 1 Carbon C2 Nbrs: 2 ~Hs: 2 Carbon C3 Nbrs: 3 ~Hs: 1 Carbon C4 Nbrs: 3 ~Hs: 1 Carbon C5 Nbrs: 3 ~Hs: 1 Carbon C6 Nbrs: 2 ~Hs: 2 Oxygen O1 Nbrs: 1 ~Hs: 1 Oxygen O3 Nbrs: 1 ~Hs: 1 Oxygen O4 Nbrs: 1 ~Hs: 1 Oxygen O5 Nbrs: 2 ~Hs: 0 Oxygen O6 Nbrs: 2 ~Hs: 0 Oxygen O1P Nbrs: 1 ~Hs: 1 Oxygen O2P Nbrs: 1 ~Hs: 1 Oxygen O3P Nbrs: 1 ~Hs: 1 Est. total nr of hydrogens : ( 14) Looking for angles ... AtmJ AtmI AtmK Angle ---- ---- ---- ----- C2 C1 O1 109.47 C2 C1 O5 109.75 O1 C1 O5 109.39 C1 C2 C3 109.00 C2 C3 C4 108.67 C2 C3 O3 109.64 C4 C3 O3 109.72 C3 C4 C5 109.02 C3 C4 O4 109.57 C5 C4 O4 109.64 C4 C5 C6 109.48 C4 C5 O5 109.79 C6 C5 O5 109.38 C5 C6 O6 109.54 C1 O5 C5 107.67 C6 O6 P 106.86 O6 P O1P 109.44 O6 P O2P 109.56 O6 P O3P 109.51 O1P P O2P 109.39 O1P P O3P 109.46 O2P P O3P 109.48 Looking for dihedrals (and planes) ... AtmK AtmI AtmJ AtmL Dihedral ---- ---- ---- ---- ------- O1 C1 C2 C3 -58.82 O5 C1 C2 C3 61.26 C2 C1 O5 C5 -67.61 O1 C1 O5 C5 52.51 C1 C2 C3 C4 -53.73 C1 C2 C3 O3 -173.65 Flat ? C2 C3 C4 C5 53.71 C2 C3 C4 O4 173.71 Flat ? O3 C3 C4 C5 173.58 Flat ? O3 C3 C4 O4 -66.42 C3 C4 C5 C6 178.71 Flat ? C3 C4 C5 O5 -61.20 O4 C4 C5 C6 58.75 O4 C4 C5 O5 178.84 Flat ? C4 C5 C6 O6 179.97 Flat ? O5 C5 C6 O6 59.63 C4 C5 O5 C1 67.59 C6 C5 O5 C1 -172.26 Flat ? C5 C6 O6 P 179.99 Flat ? C6 O6 P O1P 60.08 C6 O6 P O2P -179.99 Flat ? C6 O6 P O3P -59.91 Looking for impropers (and planes) ... Atm* Nbr1 Nbr2 Nbr3 Improper ---- ---- ---- ---- -------- C1 C2 O1 O5 -34.67 C3 C2 C4 O3 34.16 C4 C3 C5 O4 -34.20 C5 C4 C6 O5 -34.16 --- Atom with 4 or more non-H neighbours --- P O6 O1P O2P -35.86 P O1P O2P O3P 35.87 P O2P O3P O6 -35.18 P O3P O6 O1P 34.14 Number of possible flat planes : ( 9) Looking for more planes ... Number of possible flat planes : ( 13) Expanding planes ... WARNING - Reset negative RMSD in LSQGJK : ( -1.704E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.392E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.704E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.431E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.021E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.745E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.021E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.153E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.745E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.178E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.705E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.246E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.153E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.021E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.745E-08) Removing non-unique planes ... Plane nr : ( 2) Nr of atoms : ( 4) RMSD to least-squares plane (A): ( 0.038) Atom Dist (A) C2 0.037 C3 -0.036 C4 -0.040 O4 0.040 Plane nr : ( 4) Nr of atoms : ( 6) WARNING - Reset negative RMSD in LSQGJK : ( -6.043E-08) RMSD to least-squares plane (A): ( 0.037) Atom Dist (A) C3 -0.045 C4 -0.040 C5 0.010 C6 -0.016 O3 0.059 O6 0.031 Plane nr : ( 5) Nr of atoms : ( 4) WARNING - Reset negative RMSD in LSQGJK : ( -4.436E-08) RMSD to least-squares plane (A): ( 0.007) Atom Dist (A) O4 -0.007 C4 0.007 C5 0.007 O5 -0.007 Plane nr : ( 10) Nr of atoms : ( 4) RMSD to least-squares plane (A): ( 0.039) Atom Dist (A) C2 0.037 C1 -0.037 C3 0.040 O3 -0.040 Plane nr : ( 12) Nr of atoms : ( 4) WARNING - Reset negative RMSD in LSQGJK : ( -8.251E-08) RMSD to least-squares plane (A): ( 0.047) Atom Dist (A) O5 0.047 C1 -0.049 C5 0.047 C6 -0.046 Plane nr : ( 13) Nr of atoms : ( 7) WARNING - Reset negative RMSD in LSQGJK : ( -8.745E-08) RMSD to least-squares plane (A): ( 0.008) Atom Dist (A) O6 0.005 C6 0.001 P -0.007 C5 0.011 O2P -0.003 C4 0.007 C3 -0.015 ------------------- ----- SUMMARY ----- ------------------- Residue type : (D6G) Identifier : ( 2844) Segment ID : ( ) Nr of atoms : ( 15) List of elements (from file) : ( C6 H13 O8 P) Deduced formula : (C6 O8 P1) Guestimated total nr of Hs : ( 14) Nr of extra examples : ( 0) Nr of distances < 0.8 A : ( 0) Nr of bond angles < 80 degrees : ( 0) Nr of bonds found : ( 15) ... bonds without ideal value : ( 0) ... bonds near ideal value : ( 14) ... bonds far from ideal value : ( 1) -"- % : ( 6.667) Nr of angles found : ( 22) Nr of dihedrals found : ( 22) Nr of atoms with impropers : ( 5) ... imprs far from ideal value : ( 0) -"- % : ( 0.000) Nr of flat planes : ( 6)