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 PNP METHYL-PHOSPHONIC ACID MONO-(4-NITRO-PHENYL) ESTER; 4- NITROPHENYL HYDROGEN METHYLPHOSPHONATE) > (REMARK PNP Part of HIC-Up: http://xray.bmc.uu.se/hicup) > (REMARK PNP Extracted from PDB file pdb1zed.ent) > (REMARK PNP Formula C7 H8 N O5 P) Formula : (PNP C7 H8 N O5 P) > (REMARK PNP Nr of non-hydrogen atoms 14) > (REMARK PNP Eigen-values covariance X/Y/Z 119.1 11.5 4.1) > (REMARK PNP Residue type PNP) > (REMARK PNP Residue name 6253) > (REMARK PNP Original residue name (for O) $901) > (REMARK PNP RESOLUTION. 1.57 ANGSTROMS.) > (REMARK PNP occurs in 1 other PDB entries) > (REMARK PNP Also in >3.0A : 1KNO) > (REMARK PNP Resolution (A) : 3.20) > (REMARK PNP) Using residue : (PNP) Identifier : ( 6253) Segment ID : ( ) Using formula : ( C7 H8 N O5 P) Element ? | C| Carbon | 6 7 Element ? | H| Hydrogen | 1 8 Element ? | N| Nitrogen | 7 1 Element ? | O| Oxygen | 8 5 Element ? | P| Phosphorous | 15 1 Atom # 1 = C1 @ -0.048 -0.810 0.464 1.00 20.00 Atom # 2 = C2 @ 1.172 -0.682 -0.194 1.00 20.00 Atom # 3 = C3 @ 1.207 -0.340 -1.514 1.00 20.00 Atom # 4 = C4 @ 0.004 -0.116 -2.211 1.00 20.00 Atom # 5 = C5 @ -1.225 -0.246 -1.538 1.00 20.00 Atom # 6 = C6 @ -1.243 -0.594 -0.219 1.00 20.00 Atom # 7 = CM @ -0.061 -0.152 4.397 1.00 20.00 Atom # 8 = N @ 0.030 0.221 -3.508 1.00 20.00 Atom # 9 = O1N @ -1.011 0.414 -4.107 1.00 20.00 Atom # 10 = O2N @ 1.096 0.333 -4.087 1.00 20.00 Atom # 11 = P @ -0.029 0.222 2.614 1.00 20.00 Atom # 12 = O1P @ -0.074 -1.150 1.775 1.00 20.00 Atom # 13 = O2P @ -1.203 1.053 2.263 1.00 20.00 Atom # 14 = O3P @ 1.320 1.024 2.258 1.00 20.00 > (REMARK PNP ENDHET) Nr of atoms read : ( 14) Nr of extra examples : ( 0) Expected formula : ( C7 H8 N O5 P) Observed formula : (C7 N1 O5 P1) Element | H| Expected 8 | Observed 0 Element | C| Expected 7 | Observed 7 Element | N| Expected 1 | Observed 1 Element | O| Expected 5 | Observed 5 Element | P| Expected 1 | Observed 1 Expected and observed formulae agree (ignoring any hydrogens) ! Looking for bonded atoms ... Bond C1 - C2 = 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 C1 - C6 = 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 C1 - O1P = 1.355 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.36 (devn. 0.01) For: C-O partial double Bond C2 - C3 = 1.364 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.34 (devn. 0.02) For: C-C double or partial triple; range 1.309-1.337 Bond C3 - C4 = 1.408 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.39 (devn. 0.02) For: C-C aromatic or near two triple bonds; range 1.373-1.395 Bond C4 - C5 = 1.407 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.39 (devn. 0.02) For: C-C aromatic or near two triple bonds; range 1.373-1.395 Bond C4 - N = 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 C5 - C6 = 1.364 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.34 (devn. 0.02) For: C-C double or partial triple; range 1.309-1.337 Bond CM - P = 1.822 A (cutoff : 2.080) Nr of entries in library : ( 1) Closest to 1.87 (devn. 0.05) For: C-P Bond N - O1N = 1.216 A (cutoff : 1.710) Nr of entries in library : ( 2) >>> WARNING - Too far from ideal 1.14 (devn. 0.08) For: O-N double Bond N - O2N = 1.218 A (cutoff : 1.710) Nr of entries in library : ( 2) >>> WARNING - Too far from ideal 1.14 (devn. 0.08) For: O-N double Bond P - O1P = 1.609 A (cutoff : 2.080) Nr of entries in library : ( 2) Closest to 1.63 (devn. 0.02) For: O-P single Bond P - O2P = 1.481 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 - 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 : ( 14) 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: 0 Carbon C2 Nbrs: 2 ~Hs: 1 Carbon C3 Nbrs: 2 ~Hs: 1 Carbon C4 Nbrs: 3 ~Hs: 0 Carbon C5 Nbrs: 2 ~Hs: 1 Carbon C6 Nbrs: 2 ~Hs: 1 Carbon CM Nbrs: 1 ~Hs: 3 Nitrogen N Nbrs: 3 ~Hs: 0 Oxygen O1N Nbrs: 1 ~Hs: 1 Oxygen O2N Nbrs: 1 ~Hs: 1 Oxygen O1P Nbrs: 2 ~Hs: 0 Oxygen O2P Nbrs: 1 ~Hs: 1 Oxygen O3P Nbrs: 1 ~Hs: 1 Est. total nr of hydrogens : ( 11) Looking for angles ... AtmJ AtmI AtmK Angle ---- ---- ---- ----- C2 C1 C6 120.38 C2 C1 O1P 119.83 C6 C1 O1P 119.79 C1 C2 C3 120.20 C2 C3 C4 119.80 C3 C4 C5 119.65 C3 C4 N 120.16 C5 C4 N 120.20 C4 C5 C6 119.83 C1 C6 C5 120.14 C4 N O1N 119.99 C4 N O2N 120.00 O1N N O2N 120.01 CM P O1P 109.56 CM P O2P 109.47 CM P O3P 109.48 O1P P O2P 109.44 O1P P O3P 109.46 O2P P O3P 109.42 C1 O1P P 106.87 Looking for dihedrals (and planes) ... AtmK AtmI AtmJ AtmL Dihedral ---- ---- ---- ---- ------- C6 C1 C2 C3 0.18 Flat ? O1P C1 C2 C3 180.00 Flat ? C2 C1 C6 C5 -0.44 Flat ? O1P C1 C6 C5 179.73 Flat ? C2 C1 O1P P 89.95 C6 C1 O1P P -90.23 C1 C2 C3 C4 0.01 Flat ? C2 C3 C4 C5 0.06 Flat ? C2 C3 C4 N 179.97 Flat ? C3 C4 C5 C6 -0.32 Flat ? N C4 C5 C6 179.77 Flat ? C3 C4 N O1N -179.99 Flat ? C3 C4 N O2N 0.07 Flat ? C5 C4 N O1N -0.08 Flat ? C5 C4 N O2N 179.97 Flat ? C4 C5 C6 C1 0.51 Flat ? CM P O1P C1 180.00 Flat ? O2P P O1P C1 59.97 O3P P O1P C1 -59.95 Looking for impropers (and planes) ... Atm* Nbr1 Nbr2 Nbr3 Improper ---- ---- ---- ---- -------- C1 C2 C6 O1P -0.10 C4 C3 C5 N -0.05 N C4 O1N O2N 0.03 --- Atom with 4 or more non-H neighbours --- P CM O1P O2P -33.32 P O1P O2P O3P 35.90 P O2P O3P CM -37.47 P O3P CM O1P 34.42 Number of possible flat planes : ( 18) Looking for more planes ... Number of possible flat planes : ( 23) Expanding planes ... WARNING - Reset negative RMSD in LSQGJK : ( -3.862E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.619E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.728E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.444E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.869E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.069E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.728E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.242E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.723E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.862E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.995E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.728E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.619E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.728E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.312E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.730E-08) WARNING - Reset negative RMSD in LSQGJK : ( -8.010E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.619E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.728E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.344E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.010E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.862E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.846E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.370E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.468E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.356E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.862E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.468E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.026E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.021E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.981E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.174E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.021E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.588E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.021E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.246E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.637E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.107E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.862E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.107E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.344E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.468E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.174E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.753E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.519E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.242E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.862E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.619E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.850E-09) WARNING - Reset negative RMSD in LSQGJK : ( -7.265E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.070E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.468E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.246E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.010E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.356E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.862E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.637E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.862E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.107E-08) Removing non-unique planes ... Plane nr : ( 22) Nr of atoms : ( 10) RMSD to least-squares plane (A): ( 0.001) Atom Dist (A) C6 -0.003 C1 0.001 C5 0.002 C2 0.000 O1P 0.001 C4 0.000 C3 0.000 N 0.000 O1N 0.001 O2N -0.001 Plane nr : ( 23) Nr of atoms : ( 4) WARNING - Reset negative RMSD in LSQGJK : ( -7.645E-08) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) O1P 0.000 C1 0.000 P 0.000 CM 0.000 ------------------- ----- SUMMARY ----- ------------------- Residue type : (PNP) Identifier : ( 6253) Segment ID : ( ) Nr of atoms : ( 14) List of elements (from file) : ( C7 H8 N O5 P) Deduced formula : (C7 N1 O5 P1) 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 : ( 14) ... bonds without ideal value : ( 0) ... bonds near ideal value : ( 11) ... bonds far from ideal value : ( 3) -"- % : ( 21.429) Nr of angles found : ( 20) Nr of dihedrals found : ( 19) Nr of atoms with impropers : ( 4) ... imprs far from ideal value : ( 0) -"- % : ( 0.000) Nr of flat planes : ( 2)