-------------------------------------------------------------------------------- input 5 input 5 input 5 input 5 input 5 input 5 input 5 input 5 input 5 input 5 -------------------------------------------------------------------------------- MOGUL MOLECULE FILE MOGUL OUTPUT FILE MOGUL EDIT BOND_TYPES GUESS UNKNOWN_3D MOGUL EDIT BOND_TYPES STANDARDISE ALL ON MOGUL EDIT HYDROGENS GENERATE NONE MOGUL OUTPUT DISTRIBUTION ALL ON CONFIG SEARCH ALL GENERALISATION OFF CONFIG SEARCH BOND MIN_OBSERVATIONS EXACT 20 CONFIG SEARCH ANGLE MIN_OBSERVATIONS EXACT 20 CONFIG SEARCH TORSION MIN_OBSERVATIONS EXACT 40 CONFIG SEARCH RING MIN_OBSERVATIONS EXACT 20 CONFIG SEARCH BOND SELECT BEST CONFIG SEARCH ANGLE SELECT BEST CONFIG SEARCH TORSION SELECT BEST CONFIG SEARCH RING SELECT BEST CONFIG SEARCH ALL FILTER RFACTOR 0.05 CONFIG SEARCH ALL FILTER EXCLUDE_ORGANOMETALLICS CONFIG SEARCH ALL FILTER EXCLUDE_SOLVENTS CONFIG OUTPUT INVALID_FRAGMENTS EXCLUDE CONFIG CLASSIFICATION BOND UNUSUAL z-score 2 CONFIG CLASSIFICATION ANGLE UNUSUAL z-score 2 CONFIG CLASSIFICATION TORSION UNUSUAL local_density 5 WITHIN 10 CONFIG CLASSIFICATION RING UNUSUAL local_density 5 WITHIN 10 CONFIG OUTPUT FORMAT TSV CONFIG OUTPUT HEADER ON CONFIG DISTRIBUTION BOND BIN_WIDTH 0.01 CONFIG DISTRIBUTION ANGLE BIN_WIDTH 2.0 BOND ALL ANGLE ALL TORSION ALL RING ALL -------------------------------------------------------------------------------- result 5 result 5 result 5 result 5 result 5 result 5 result 5 result 5 result 5 -------------------------------------------------------------------------------- Mogul validation Mogul results Input file : data_RUZ.cif_mogul.pdb BOND C1 C2 1.40 1.39 0.009 1.48 BOND C3 C2 1.38 1.39 0.009 1.06 BOND C3 C4 1.40 1.39 0.010 0.18 BOND C5 C4 1.40 1.40 0.011 0.06 BOND C1 C6 1.39 1.40 0.012 0.57 BOND C6 C5 1.40 1.41 0.002 0.96 BOND CA N 1.44 1.47 0.018 1.90 BOND CB CA 1.52 BOND OG CB 1.41 1.42 0.017 0.79 BOND CA C 1.53 1.52 0.017 0.79 BOND O C 1.20 1.23 0.013 1.74 BOND C N3S 1.38 1.37 0.016 1.08 BOND S N3S 1.66 1.64 0.007 3.37 BOND O1S S 1.44 1.42 0.008 2.64 BOND O2S S 1.44 1.42 0.008 2.06 BOND O5' S 1.58 1.59 0.013 0.68 BOND O4' C4' 1.43 1.44 0.011 1.63 BOND O4' C1' 1.41 1.42 0.011 0.81 BOND C2' C1' 1.53 1.53 0.014 0.12 BOND O2' C2' 1.39 1.42 0.012 2.40 BOND C3' C4' 1.55 1.53 0.013 1.54 BOND C3' C2' 1.54 1.53 0.013 0.46 BOND O3' C3' 1.40 1.42 0.012 1.69 BOND C5 N7 1.39 1.38 0.007 1.78 BOND C8 N7 1.36 1.37 0.008 0.92 BOND C1' N7 1.43 1.46 0.012 2.43 BOND C4 N9 1.38 1.40 0.013 1.54 BOND C8 N9 1.29 1.31 0.008 1.90 BOND C6 N6 1.38 1.38 0.022 0.15 BOND C2M C2 1.51 1.51 0.014 0.12 BOND O2M C2M 1.41 1.42 0.019 0.70 BOND O5' C5' 1.44 1.46 0.018 0.97 BOND C5' C4' 1.50 1.51 0.011 0.37 ANGLE C6 C1 C2 123.56 122.39 0.272 4.28 ANGLE C3 C2 C1 120.35 119.03 0.960 1.38 ANGLE C2M C2 C1 117.59 120.27 1.170 2.29 ANGLE C2M C2 C3 122.06 120.27 1.170 1.52 ANGLE C4 C3 C2 117.35 119.76 1.220 1.98 ANGLE C3 C4 C5 122.00 122.31 1.130 0.27 ANGLE C3 C4 N9 127.73 130.32 1.284 2.02 ANGLE C5 C4 N9 110.28 109.74 0.701 0.76 ANGLE C6 C5 C4 121.18 ANGLE C4 C5 N7 104.64 106.48 1.262 1.46 ANGLE C6 C5 N7 134.14 ANGLE C1 C6 C5 115.53 ANGLE C1 C6 N6 121.24 120.09 1.603 0.72 ANGLE C5 C6 N6 123.19 123.73 0.153 3.54 ANGLE N7 C8 N9 114.25 114.10 0.653 0.23 ANGLE CB CA N 111.00 ANGLE C CA N 113.30 111.24 1.846 1.11 ANGLE CB CA C 109.19 ANGLE OG CB CA 107.78 ANGLE O C CA 124.19 121.07 1.131 2.76 ANGLE CA C N3S 113.95 ANGLE O C N3S 121.85 123.34 2.554 0.58 ANGLE C N3S S 124.27 ANGLE O1S S N3S 104.95 108.07 2.963 1.05 ANGLE O2S S N3S 111.28 108.07 2.963 1.08 ANGLE O5' S N3S 103.17 ANGLE O2S S O1S 121.16 121.11 0.915 0.06 ANGLE O5' S O1S 110.56 105.60 2.968 1.67 ANGLE O5' S O2S 104.39 105.60 2.968 0.41 ANGLE C5' O5' S 120.20 ANGLE O4' C4' C3' 107.03 105.21 1.302 1.40 ANGLE O4' C4' C5' 110.44 109.53 1.426 0.63 ANGLE C5' C4' C3' 115.77 115.17 1.752 0.34 ANGLE C4' O4' C1' 106.20 109.34 1.653 1.90 ANGLE O4' C1' C2' 103.41 106.51 1.186 2.61 ANGLE O4' C1' N7 111.55 108.37 1.247 2.55 ANGLE C2' C1' N7 117.54 114.10 1.519 2.26 ANGLE O2' C2' C1' 113.55 110.58 2.814 1.06 ANGLE C3' C2' C1' 100.41 101.56 1.203 0.96 ANGLE O2' C2' C3' 111.73 111.82 2.668 0.03 ANGLE C2' C3' C4' 102.69 102.48 0.969 0.21 ANGLE O3' C3' C4' 107.73 111.09 2.496 1.35 ANGLE O3' C3' C2' 112.12 111.82 2.668 0.11 ANGLE C5 N7 C8 105.83 105.49 0.542 0.61 ANGLE C5 N7 C1' 132.53 126.54 1.952 3.07 ANGLE C1' N7 C8 121.18 126.78 1.928 2.91 ANGLE C4 N9 C8 105.01 104.42 0.584 1.01 ANGLE O2M C2M C2 110.42 112.24 1.986 0.91 ANGLE O5' C5' C4' 107.94 107.32 1.455 0.43 TORSION OG CB CA N 71.19 TORSION OG CB CA C -54.42 TORSION O C CA N -5.95 TORSION N CA C N3S 174.66 TORSION O C CA CB 118.32 TORSION CB CA C N3S -61.08 TORSION CA C N3S S 177.93 TORSION O C N3S S -1.49 TORSION O1S S N3S C -175.42 TORSION O2S S N3S C 51.83 TORSION O5' S N3S C -59.58 TORSION C5' O5' S N3S -59.64 TORSION C5' O5' S O1S 52.13 TORSION C5' O5' S O2S -176.05 TORSION O4' C1' N7 C5 63.94 TORSION O4' C1' N7 C8 -125.14 TORSION C2' C1' N7 C5 -55.22 TORSION C2' C1' N7 C8 115.70 TORSION O2M C2M C2 C1 -163.50 TORSION O2M C2M C2 C3 17.35 TORSION S O5' C5' C4' -170.96 TORSION O4' C4' C5' O5' -65.42 TORSION O5' C5' C4' C3' 56.39 ring etc C1 C2 C3 C4 C5 C6 ring etc C4 C5 N7 C8 N9 ring etc C4' O4' C1' C2' C3' Mogul RMSD for data_RUZ.cif BOND : 0.016085967681491852 ANGLE : 2.4426269066577078