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 IHP INOSITOL HEXAKISPHOSPHATE; MYO-INOSITOL HEXAKISPHOSPHATE) > (REMARK IHP Part of HIC-Up: http://xray.bmc.uu.se/hicup) > (REMARK IHP Extracted from PDB file pdb2fvv.ent) > (REMARK IHP Formula C6 H18 O24 P6) Formula : (IHP C6 H18 O24 P6) > (REMARK IHP Nr of non-hydrogen atoms 36) > (REMARK IHP Eigen-values covariance X/Y/Z 256.9 241.0 51.2) > (REMARK IHP Residue type IHP) > (REMARK IHP Residue name 4464) > (REMARK IHP Original residue name (for O) $2360) > (REMARK IHP RESOLUTION. 1.25 ANGSTROMS.) > (REMARK IHP occurs in 15 other PDB entries) > (REMARK IHP Also in <1.5A : 1THB) > (REMARK IHP Resolution (A) : 1.50) > (REMARK IHP Also in 1.5-2.0A : 2Q9P 1ZY7 2P1M 2P1O 2P1Q 1HG5) > (REMARK IHP Resolution (A) : 1.65 1.70 1.80 1.90 1.91 2.00) > (REMARK IHP Also in 2.0-2.5A : 1DKQ 2P1P 1DKP 2P1N) > (REMARK IHP Resolution (A) : 2.05 2.21 2.28 2.50) > (REMARK IHP Also in 2.5-3.0A : 1NIH 2VGL 1BQ3 1ZSH) > (REMARK IHP Resolution (A) : 2.60 2.59 2.70 2.90) > (REMARK IHP) Using residue : (IHP) Identifier : ( 4464) Segment ID : ( ) Using formula : ( C6 H18 O24 P6) Element ? | C| Carbon | 6 6 Element ? | H| Hydrogen | 1 18 Element ? | O| Oxygen | 8 24 Element ? | P| Phosphorous | 15 6 Atom # 1 = C1 @ 1.028 -0.224 -1.011 1.00 20.00 Atom # 2 = C2 @ 1.403 -0.728 0.383 1.00 20.00 Atom # 3 = C3 @ 0.382 -0.218 1.402 1.00 20.00 Atom # 4 = C4 @ -1.009 -0.734 1.030 1.00 20.00 Atom # 5 = C5 @ -1.384 -0.229 -0.364 1.00 20.00 Atom # 6 = C6 @ -0.363 -0.739 -1.382 1.00 20.00 Atom # 7 = O11 @ 1.024 1.204 -1.015 1.00 20.00 Atom # 8 = P1 @ 2.112 1.670 -2.107 1.00 20.00 Atom # 9 = O21 @ 3.444 1.150 -1.728 1.00 20.00 Atom # 10 = O31 @ 2.160 3.278 -2.165 1.00 20.00 Atom # 11 = O41 @ 1.702 1.093 -3.553 1.00 20.00 Atom # 12 = O12 @ 2.703 -0.247 0.729 1.00 20.00 Atom # 13 = P2 @ 3.628 -1.541 0.979 1.00 20.00 Atom # 14 = O22 @ 3.681 -2.355 -0.255 1.00 20.00 Atom # 15 = O32 @ 5.115 -1.070 1.376 1.00 20.00 Atom # 16 = O42 @ 3.006 -2.421 2.176 1.00 20.00 Atom # 17 = O13 @ 0.378 1.210 1.397 1.00 20.00 Atom # 18 = P3 @ 0.776 1.681 2.884 1.00 20.00 Atom # 19 = O23 @ 2.119 1.160 3.224 1.00 20.00 Atom # 20 = O33 @ 0.790 3.289 2.952 1.00 20.00 Atom # 21 = O43 @ -0.301 1.109 3.935 1.00 20.00 Atom # 22 = O14 @ -1.962 -0.258 1.982 1.00 20.00 Atom # 23 = P4 @ -2.632 -1.556 2.660 1.00 20.00 Atom # 24 = O24 @ -1.583 -2.361 3.325 1.00 20.00 Atom # 25 = O34 @ -3.723 -1.090 3.748 1.00 20.00 Atom # 26 = O44 @ -3.351 -2.443 1.525 1.00 20.00 Atom # 27 = O15 @ -1.389 1.199 -0.368 1.00 20.00 Atom # 28 = P5 @ -2.879 1.659 -0.767 1.00 20.00 Atom # 29 = O25 @ -3.841 1.133 0.226 1.00 20.00 Atom # 30 = O35 @ -2.956 3.266 -0.792 1.00 20.00 Atom # 31 = O45 @ -3.246 1.082 -2.225 1.00 20.00 Atom # 32 = O16 @ -0.714 -0.268 -2.685 1.00 20.00 Atom # 33 = P6 @ -0.957 -1.569 -3.601 1.00 20.00 Atom # 34 = O26 @ -2.051 -2.381 -3.024 1.00 20.00 Atom # 35 = O36 @ -1.358 -1.109 -5.091 1.00 20.00 Atom # 36 = O46 @ 0.391 -2.447 -3.655 1.00 20.00 > (REMARK IHP ENDHET) Nr of atoms read : ( 36) Nr of extra examples : ( 0) Expected formula : ( C6 H18 O24 P6) Observed formula : (C6 O24 P6) Element | H| Expected 18 | Observed 0 Element | C| Expected 6 | Observed 6 Element | O| Expected 24 | Observed 24 Element | P| Expected 6 | Observed 6 Expected and observed formulae agree (ignoring any hydrogens) ! Looking for bonded atoms ... Bond C1 - C2 = 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 C1 - 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 C1 - O11 = 1.428 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.43 (devn. 0.00) For: C-O single Bond C2 - C3 = 1.530 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 C2 - O12 = 1.429 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.43 (devn. 0.00) For: C-O single Bond C3 - C4 = 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 C3 - O13 = 1.428 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 - O14 = 1.429 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 - O15 = 1.428 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.43 (devn. 0.00) For: C-O single Bond C6 - O16 = 1.429 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.43 (devn. 0.00) For: C-O single Bond O11 - P1 = 1.610 A (cutoff : 2.080) Nr of entries in library : ( 2) Closest to 1.63 (devn. 0.02) For: O-P single Bond P1 - O21 = 1.479 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 P1 - O31 = 1.610 A (cutoff : 2.080) Nr of entries in library : ( 2) Closest to 1.63 (devn. 0.02) For: O-P single Bond P1 - O41 = 1.610 A (cutoff : 2.080) Nr of entries in library : ( 2) Closest to 1.63 (devn. 0.02) For: O-P single Bond O12 - P2 = 1.610 A (cutoff : 2.080) Nr of entries in library : ( 2) Closest to 1.63 (devn. 0.02) For: O-P single Bond P2 - O22 = 1.479 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 P2 - O32 = 1.610 A (cutoff : 2.080) Nr of entries in library : ( 2) Closest to 1.63 (devn. 0.02) For: O-P single Bond P2 - O42 = 1.611 A (cutoff : 2.080) Nr of entries in library : ( 2) Closest to 1.63 (devn. 0.02) For: O-P single Bond O13 - P3 = 1.610 A (cutoff : 2.080) Nr of entries in library : ( 2) Closest to 1.63 (devn. 0.02) For: O-P single Bond P3 - O23 = 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 P3 - O33 = 1.609 A (cutoff : 2.080) Nr of entries in library : ( 2) Closest to 1.63 (devn. 0.02) For: O-P single Bond P3 - O43 = 1.610 A (cutoff : 2.080) Nr of entries in library : ( 2) Closest to 1.63 (devn. 0.02) For: O-P single Bond O14 - P4 = 1.610 A (cutoff : 2.080) Nr of entries in library : ( 2) Closest to 1.63 (devn. 0.02) For: O-P single Bond P4 - O24 = 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 P4 - O34 = 1.610 A (cutoff : 2.080) Nr of entries in library : ( 2) Closest to 1.63 (devn. 0.02) For: O-P single Bond P4 - O44 = 1.610 A (cutoff : 2.080) Nr of entries in library : ( 2) Closest to 1.63 (devn. 0.02) For: O-P single Bond O15 - P5 = 1.610 A (cutoff : 2.080) Nr of entries in library : ( 2) Closest to 1.63 (devn. 0.02) For: O-P single Bond P5 - O25 = 1.479 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 P5 - O35 = 1.609 A (cutoff : 2.080) Nr of entries in library : ( 2) Closest to 1.63 (devn. 0.02) For: O-P single Bond P5 - O45 = 1.610 A (cutoff : 2.080) Nr of entries in library : ( 2) Closest to 1.63 (devn. 0.02) For: O-P single Bond O16 - P6 = 1.610 A (cutoff : 2.080) Nr of entries in library : ( 2) Closest to 1.63 (devn. 0.02) For: O-P single Bond P6 - O26 = 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 P6 - O36 = 1.610 A (cutoff : 2.080) Nr of entries in library : ( 2) Closest to 1.63 (devn. 0.02) For: O-P single Bond P6 - O46 = 1.610 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 : ( 36) 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: 3 ~Hs: 1 Carbon C3 Nbrs: 3 ~Hs: 1 Carbon C4 Nbrs: 3 ~Hs: 1 Carbon C5 Nbrs: 3 ~Hs: 1 Carbon C6 Nbrs: 3 ~Hs: 1 Oxygen O11 Nbrs: 2 ~Hs: 0 Oxygen O21 Nbrs: 1 ~Hs: 1 Oxygen O31 Nbrs: 1 ~Hs: 1 Oxygen O41 Nbrs: 1 ~Hs: 1 Oxygen O12 Nbrs: 2 ~Hs: 0 Oxygen O22 Nbrs: 1 ~Hs: 1 Oxygen O32 Nbrs: 1 ~Hs: 1 Oxygen O42 Nbrs: 1 ~Hs: 1 Oxygen O13 Nbrs: 2 ~Hs: 0 Oxygen O23 Nbrs: 1 ~Hs: 1 Oxygen O33 Nbrs: 1 ~Hs: 1 Oxygen O43 Nbrs: 1 ~Hs: 1 Oxygen O14 Nbrs: 2 ~Hs: 0 Oxygen O24 Nbrs: 1 ~Hs: 1 Oxygen O34 Nbrs: 1 ~Hs: 1 Oxygen O44 Nbrs: 1 ~Hs: 1 Oxygen O15 Nbrs: 2 ~Hs: 0 Oxygen O25 Nbrs: 1 ~Hs: 1 Oxygen O35 Nbrs: 1 ~Hs: 1 Oxygen O45 Nbrs: 1 ~Hs: 1 Oxygen O16 Nbrs: 2 ~Hs: 0 Oxygen O26 Nbrs: 1 ~Hs: 1 Oxygen O36 Nbrs: 1 ~Hs: 1 Oxygen O46 Nbrs: 1 ~Hs: 1 Est. total nr of hydrogens : ( 24) Looking for angles ... AtmJ AtmI AtmK Angle ---- ---- ---- ----- C2 C1 C6 109.47 C2 C1 O11 109.44 C6 C1 O11 109.49 C1 C2 C3 109.49 C1 C2 O12 109.45 C3 C2 O12 109.49 C2 C3 C4 109.42 C2 C3 O13 109.44 C4 C3 O13 109.51 C3 C4 C5 109.47 C3 C4 O14 109.40 C5 C4 O14 109.50 C4 C5 C6 109.45 C4 C5 O15 109.49 C6 C5 O15 109.51 C1 C6 C5 109.48 C1 C6 O16 109.49 C5 C6 O16 109.45 C1 O11 P1 106.82 O11 P1 O21 109.44 O11 P1 O31 109.49 O11 P1 O41 109.47 O21 P1 O31 109.48 O21 P1 O41 109.48 O31 P1 O41 109.47 C2 O12 P2 106.84 O12 P2 O22 109.47 O12 P2 O32 109.50 O12 P2 O42 109.43 O22 P2 O32 109.49 O22 P2 O42 109.46 O32 P2 O42 109.47 C3 O13 P3 106.78 O13 P3 O23 109.48 O13 P3 O33 109.48 O13 P3 O43 109.49 O23 P3 O33 109.52 O23 P3 O43 109.39 O33 P3 O43 109.46 C4 O14 P4 106.83 O14 P4 O24 109.43 O14 P4 O34 109.46 O14 P4 O44 109.45 O24 P4 O34 109.52 O24 P4 O44 109.49 O34 P4 O44 109.47 C5 O15 P5 106.84 O15 P5 O25 109.51 O15 P5 O35 109.49 O15 P5 O45 109.45 O25 P5 O35 109.54 O25 P5 O45 109.40 O35 P5 O45 109.44 C6 O16 P6 106.83 O16 P6 O26 109.47 O16 P6 O36 109.47 O16 P6 O46 109.48 O26 P6 O36 109.48 O26 P6 O46 109.45 O36 P6 O46 109.47 Looking for dihedrals (and planes) ... AtmK AtmI AtmJ AtmL Dihedral ---- ---- ---- ---- ------- C6 C1 C2 C3 -60.00 C6 C1 C2 O12 179.98 Flat ? O11 C1 C2 C3 60.01 O11 C1 C2 O12 -60.02 C2 C1 C6 C5 60.00 C2 C1 C6 O16 180.00 Flat ? O11 C1 C6 C5 -59.97 O11 C1 C6 O16 60.02 C2 C1 O11 P1 120.02 C6 C1 O11 P1 -119.99 C1 C2 C3 C4 60.00 C1 C2 C3 O13 -59.99 O12 C2 C3 C4 -180.00 Flat ? O12 C2 C3 O13 60.01 C1 C2 O12 P2 -119.97 C3 C2 O12 P2 120.00 C2 C3 C4 C5 -60.03 C2 C3 C4 O14 179.98 Flat ? O13 C3 C4 C5 59.92 O13 C3 C4 O14 -60.07 C2 C3 O13 P3 -120.02 C4 C3 O13 P3 120.04 C3 C4 C5 C6 60.06 C3 C4 C5 O15 -59.98 O14 C4 C5 C6 179.99 Flat ? O14 C4 C5 O15 59.95 C3 C4 O14 P4 -120.02 C5 C4 O14 P4 120.01 C4 C5 C6 C1 -60.03 C4 C5 C6 O16 179.95 Flat ? O15 C5 C6 C1 60.00 O15 C5 C6 O16 -60.02 C4 C5 O15 P5 -119.96 C6 C5 O15 P5 120.03 C1 C6 O16 P6 120.00 C5 C6 O16 P6 -119.99 C1 O11 P1 O21 -60.02 C1 O11 P1 O31 179.98 Flat ? C1 O11 P1 O41 59.97 C2 O12 P2 O22 59.99 C2 O12 P2 O32 -179.96 Flat ? C2 O12 P2 O42 -59.97 C3 O13 P3 O23 59.98 C3 O13 P3 O33 -179.95 Flat ? C3 O13 P3 O43 -59.94 C4 O14 P4 O24 60.03 C4 O14 P4 O34 -179.94 Flat ? C4 O14 P4 O44 -59.96 C5 O15 P5 O25 59.94 C5 O15 P5 O35 -179.95 Flat ? C5 O15 P5 O45 -59.99 C6 O16 P6 O26 59.99 C6 O16 P6 O36 -179.99 Flat ? C6 O16 P6 O46 -59.98 Looking for impropers (and planes) ... Atm* Nbr1 Nbr2 Nbr3 Improper ---- ---- ---- ---- -------- C1 C2 C6 O11 -34.34 C2 C1 C3 O12 34.33 C3 C2 C4 O13 34.33 C4 C3 C5 O14 34.36 C5 C4 C6 O15 34.30 C6 C1 C5 O16 -34.34 --- Atom with 4 or more non-H neighbours --- P1 O11 O21 O31 35.84 P1 O21 O31 O41 -35.85 P1 O31 O41 O11 35.26 P1 O41 O11 O21 -34.12 --- Atom with 4 or more non-H neighbours --- P2 O12 O22 O32 -35.82 P2 O22 O32 O42 35.87 P2 O32 O42 O12 -35.27 P2 O42 O12 O22 34.12 --- Atom with 4 or more non-H neighbours --- P3 O13 O23 O33 -35.81 P3 O23 O33 O43 35.91 P3 O33 O43 O13 -35.25 P3 O43 O13 O23 34.16 --- Atom with 4 or more non-H neighbours --- P4 O14 O24 O34 -35.83 P4 O24 O34 O44 35.83 P4 O34 O44 O14 -35.29 P4 O44 O14 O24 34.13 --- Atom with 4 or more non-H neighbours --- P5 O15 O25 O35 -35.79 P5 O25 O35 O45 35.92 P5 O35 O45 O15 -35.27 P5 O45 O15 O25 34.13 --- Atom with 4 or more non-H neighbours --- P6 O16 O26 O36 -35.85 P6 O26 O36 O46 35.86 P6 O36 O46 O16 -35.25 P6 O46 O16 O26 34.13 Number of possible flat planes : ( 12) Looking for more planes ... Number of possible flat planes : ( 18) Expanding planes ... WARNING - Reset negative RMSD in LSQGJK : ( -2.309E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.426E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.333E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.439E-07) Removing non-unique planes ... Plane nr : ( 2) Nr of atoms : ( 5) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) C2 0.000 C1 0.000 C6 0.000 O16 0.000 O12 0.000 Plane nr : ( 4) Nr of atoms : ( 5) WARNING - Reset negative RMSD in LSQGJK : ( -3.333E-08) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) C2 0.000 C3 0.000 C4 0.000 O14 0.000 O12 0.000 Plane nr : ( 6) Nr of atoms : ( 5) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) C4 0.000 C5 0.000 C6 0.000 O16 0.000 O14 0.000 Plane nr : ( 13) Nr of atoms : ( 4) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) O11 0.000 C1 0.000 P1 0.000 O31 0.000 Plane nr : ( 14) Nr of atoms : ( 4) WARNING - Reset negative RMSD in LSQGJK : ( -8.584E-09) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) O12 0.000 C2 0.000 P2 0.000 O32 0.000 Plane nr : ( 15) Nr of atoms : ( 4) WARNING - Reset negative RMSD in LSQGJK : ( -1.011E-07) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) O13 0.000 C3 0.000 P3 0.000 O33 0.000 Plane nr : ( 16) Nr of atoms : ( 4) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) O14 0.000 C4 0.000 P4 0.000 O34 0.000 Plane nr : ( 17) Nr of atoms : ( 4) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) O15 0.000 C5 0.000 P5 0.000 O35 0.000 Plane nr : ( 18) Nr of atoms : ( 4) WARNING - Reset negative RMSD in LSQGJK : ( -1.011E-07) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) O16 0.000 C6 0.000 P6 0.000 O36 0.000 ------------------- ----- SUMMARY ----- ------------------- Residue type : (IHP) Identifier : ( 4464) Segment ID : ( ) Nr of atoms : ( 36) List of elements (from file) : ( C6 H18 O24 P6) Deduced formula : (C6 O24 P6) Guestimated total nr of Hs : ( 24) Nr of extra examples : ( 0) Nr of distances < 0.8 A : ( 0) Nr of bond angles < 80 degrees : ( 0) Nr of bonds found : ( 36) ... bonds without ideal value : ( 0) ... bonds near ideal value : ( 30) ... bonds far from ideal value : ( 6) -"- % : ( 16.667) Nr of angles found : ( 60) Nr of dihedrals found : ( 54) Nr of atoms with impropers : ( 12) ... imprs far from ideal value : ( 0) -"- % : ( 0.000) Nr of flat planes : ( 9)