http://viper.lbl.gov:8080/cctbx.xfel/index.php?action=history&feed=atom&title=DO3.cif
DO3.cif - Revision history
2026-04-18T11:46:51Z
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Tara: Created page with "<pre># electronic Ligand Builder and Optimisation Workbench (eLBOW) # - a module of PHENIX version 1.9-1692 # - file written: Mon Oct 6 11:54:24 2014 # # Input file: /U..."
2014-10-06T19:59:40Z
<p>Created page with "<pre># electronic Ligand Builder and Optimisation Workbench (eLBOW) # - a module of PHENIX version 1.9-1692 # - file written: Mon Oct 6 11:54:24 2014 # # Input file: /U..."</p>
<p><b>New page</b></p><div><pre># electronic Ligand Builder and Optimisation Workbench (eLBOW)<br />
# - a module of PHENIX version 1.9-1692<br />
# - file written: Mon Oct 6 11:54:24 2014<br />
#<br />
# Input file: /Users/Tara/projects/Gd-Lysozyme_mark0/.phenix/tmp/libtbx_run_29.eff<br />
# Inital geometry file: a 136 line input string<br />
# Ligand name: 2,2',2''-{10-[(2R)-2-hydroxypropyl]-1,4,7,10-tetraazacyclododecane-1,4,7-triyl}triacetic acid<br />
# Quantum optimisation: True<br />
# Method: uhf<br />
# Random seed: 3628800<br />
# SMILES string: C[C@@H](O)CN1CCN(CCN(CCN(CC1)CC(O)=O)CC(O)=O)CC(O)=O<br />
#<br />
data_comp_list<br />
loop_<br />
_chem_comp.id<br />
_chem_comp.three_letter_code<br />
_chem_comp.name<br />
_chem_comp.group<br />
_chem_comp.number_atoms_all<br />
_chem_comp.number_atoms_nh<br />
_chem_comp.desc_level<br />
DO3 DO3 '2,2',2''-{10-[(2R)-2-hydroxypropyl]-1,4,7,10-tetraazacyclododecane-1,4,7-triyl}triacetic acid' ligand 57 28 .<br />
#<br />
data_comp_DO3<br />
#<br />
loop_<br />
_chem_comp_atom.comp_id<br />
_chem_comp_atom.atom_id<br />
_chem_comp_atom.type_symbol<br />
_chem_comp_atom.type_energy<br />
_chem_comp_atom.partial_charge<br />
_chem_comp_atom.x<br />
_chem_comp_atom.y<br />
_chem_comp_atom.z<br />
DO3 N1 N NT -0.274 0.0291 -0.0438 -0.0784<br />
DO3 N2 N NT -0.287 2.3565 1.3262 1.9879<br />
DO3 N3 N NT -0.269 -0.1370 3.4156 3.6905<br />
DO3 N4 N NT -0.260 -0.8446 3.2869 0.2136<br />
DO3 O1 O OC -0.631 0.0334 -3.5820 -0.9372<br />
DO3 O3 O OC -0.632 3.0340 3.1965 -1.0894<br />
DO3 O5 O OC -0.631 0.2762 4.5054 7.1382<br />
DO3 O7 O OH1 -0.265 0.3395 4.5422 -2.1839<br />
DO3 C1 C CH2 -0.025 1.5395 -0.0869 0.0002<br />
DO3 C2 C CH2 0.028 2.0489 -0.0357 1.4352<br />
DO3 C3 C CH2 -0.020 1.2796 1.4994 3.0164<br />
DO3 C4 C CH2 -0.014 1.2692 2.8979 3.5879<br />
DO3 C5 C CH2 -0.034 -0.3902 4.2232 2.4544<br />
DO3 C6 C CH2 -0.018 -1.3942 3.5027 1.5872<br />
DO3 C7 C CH2 -0.013 -1.3922 1.9560 -0.2163<br />
DO3 C8 C CH2 -0.045 -0.3510 1.1278 -0.9364<br />
DO3 C9 C C 0.388 0.1544 -2.5465 -0.2939<br />
DO3 C10 C CH2 -0.103 -0.2942 -1.2312 -0.9132<br />
DO3 C11 C C 0.388 3.1731 2.4289 -0.1301<br />
DO3 C12 C CH2 -0.130 2.1016 2.3468 0.9335<br />
DO3 C13 C C 0.390 0.1454 3.7752 6.1594<br />
DO3 C14 C CH2 -0.106 -0.0717 4.4077 4.7918<br />
DO3 C15 C CH1 0.091 -1.0025 4.2200 -2.0754<br />
DO3 C16 C CH2 -0.067 -1.5194 4.2965 -0.6404<br />
DO3 C17 C CH3 -0.219 -1.8633 5.1850 -2.8964<br />
DO3 O2 O O -0.599 0.6617 -2.5116 0.8698<br />
DO3 O4 O O -0.634 4.1827 1.6692 0.0066<br />
DO3 O6 O O -0.594 0.1878 2.5084 6.2117<br />
DO3 HO7 H HOH1 0.185 0.4659 5.3919 -1.7532<br />
DO3 HC11 H HCH2 0.074 1.9670 0.6504 -0.7133<br />
DO3 HC12 H HCH2 0.056 1.9139 -1.0302 -0.4344<br />
DO3 HC21 H HCH2 0.054 2.9516 -0.6701 1.5056<br />
DO3 HC22 H HCH2 0.078 1.2788 -0.5225 2.0859<br />
DO3 HC31 H HCH2 0.060 1.4674 0.7746 3.8353<br />
DO3 HC32 H HCH2 0.058 0.2938 1.2326 2.5621<br />
DO3 HC41 H HCH2 0.039 1.8720 3.6327 2.9847<br />
DO3 HC42 H HCH2 0.079 1.7730 2.8815 4.5685<br />
DO3 HC51 H HCH2 0.086 0.5682 4.4283 1.9107<br />
DO3 HC52 H HCH2 0.013 -0.8165 5.2100 2.7397<br />
DO3 HC61 H HCH2 -0.005 -2.3393 4.0905 1.5177<br />
DO3 HC62 H HCH2 0.104 -1.6842 2.5191 2.0268<br />
DO3 HC71 H HCH2 0.089 -1.7857 1.4137 0.6757<br />
DO3 HC72 H HCH2 -0.006 -2.2754 2.1262 -0.8766<br />
DO3 HC81 H HCH2 0.122 0.5492 1.7322 -1.2170<br />
DO3 HC82 H HCH2 0.010 -0.7937 0.7730 -1.8940<br />
DO3 H101 H HCH2 0.027 -1.3784 -1.2676 -1.1327<br />
DO3 H102 H HCH2 0.011 0.2276 -1.1068 -1.9061<br />
DO3 H121 H HCH2 0.067 1.1271 2.1425 0.4430<br />
DO3 H122 H HCH2 0.050 1.9327 3.3594 1.3624<br />
DO3 H141 H HCH2 0.010 0.7691 5.1234 4.5843<br />
DO3 H142 H HCH2 0.029 -1.0033 5.0084 4.8005<br />
DO3 HA H HCH1 0.100 -1.1591 3.1718 -2.4402<br />
DO3 H161 H HCH2 0.052 -1.3924 5.3154 -0.2260<br />
DO3 H162 H HCH2 0.013 -2.6229 4.0763 -0.6347<br />
DO3 H171 H HCH3 0.051 -1.5772 5.1968 -3.9526<br />
DO3 H172 H HCH3 0.038 -2.9157 4.8898 -2.8349<br />
DO3 H173 H HCH3 0.039 -1.8312 6.1936 -2.4665<br />
#<br />
loop_<br />
_chem_comp_bond.comp_id<br />
_chem_comp_bond.atom_id_1<br />
_chem_comp_bond.atom_id_2<br />
_chem_comp_bond.type<br />
_chem_comp_bond.value_dist<br />
_chem_comp_bond.value_dist_esd<br />
DO3 N1 C1 single 1.513 0.038<br />
DO3 N1 C8 single 1.501 0.038<br />
DO3 N1 C10 single 1.487 0.038<br />
DO3 N2 C2 single 1.502 0.037<br />
DO3 N2 C3 single 1.499 0.038<br />
DO3 N2 C12 single 1.489 0.038<br />
DO3 N3 C4 single 1.502 0.037<br />
DO3 N3 C5 single 1.498 0.038<br />
DO3 N3 C14 single 1.484 0.037<br />
DO3 N4 C6 single 1.495 0.037<br />
DO3 N4 C7 single 1.502 0.037<br />
DO3 N4 C16 single 1.485 0.036<br />
DO3 O1 C9 deloc 1.225 0.021<br />
DO3 O3 C11 deloc 1.236 0.023<br />
DO3 O5 C13 deloc 1.228 0.022<br />
DO3 O7 C15 single 1.384 0.032<br />
DO3 O7 HO7 single 0.961 0.036<br />
DO3 C1 C2 single 1.524 0.034<br />
DO3 C1 HC11 single 1.111 0.039<br />
DO3 C1 HC12 single 1.104 0.037<br />
DO3 C2 HC21 single 1.106 0.038<br />
DO3 C2 HC22 single 1.120 0.039<br />
DO3 C3 C4 single 1.511 0.033<br />
DO3 C3 HC31 single 1.110 0.038<br />
DO3 C3 HC32 single 1.118 0.039<br />
DO3 C4 HC41 single 1.126 0.040<br />
DO3 C4 HC42 single 1.103 0.037<br />
DO3 C5 C6 single 1.510 0.033<br />
DO3 C5 HC51 single 1.121 0.039<br />
DO3 C5 HC52 single 1.112 0.038<br />
DO3 C6 HC61 single 1.115 0.039<br />
DO3 C6 HC62 single 1.116 0.039<br />
DO3 C7 C8 single 1.513 0.033<br />
DO3 C7 HC71 single 1.116 0.039<br />
DO3 C7 HC72 single 1.116 0.039<br />
DO3 C8 HC81 single 1.120 0.039<br />
DO3 C8 HC82 single 1.113 0.038<br />
DO3 C9 C10 single 1.521 0.035<br />
DO3 C9 O2 deloc 1.270 0.015<br />
DO3 C10 H101 single 1.107 0.037<br />
DO3 C10 H102 single 1.129 0.039<br />
DO3 C11 C12 single 1.512 0.034<br />
DO3 C11 O4 deloc 1.271 0.017<br />
DO3 C12 H121 single 1.110 0.038<br />
DO3 C12 H122 single 1.113 0.038<br />
DO3 C13 C14 single 1.522 0.035<br />
DO3 C13 O6 deloc 1.269 0.016<br />
DO3 C14 H141 single 1.124 0.039<br />
DO3 C14 H142 single 1.109 0.037<br />
DO3 C15 C16 single 1.527 0.034<br />
DO3 C15 C17 single 1.532 0.035<br />
DO3 C15 HA single 1.121 0.039<br />
DO3 C16 H161 single 1.107 0.038<br />
DO3 C16 H162 single 1.125 0.039<br />
DO3 C17 H171 single 1.094 0.037<br />
DO3 C17 H172 single 1.095 0.037<br />
DO3 C17 H173 single 1.097 0.037<br />
#<br />
loop_<br />
_chem_comp_angle.comp_id<br />
_chem_comp_angle.atom_id_1<br />
_chem_comp_angle.atom_id_2<br />
_chem_comp_angle.atom_id_3<br />
_chem_comp_angle.value_angle<br />
_chem_comp_angle.value_angle_esd<br />
DO3 C10 N1 C8 104.32 2.582<br />
DO3 C10 N1 C1 102.91 2.657<br />
DO3 C8 N1 C1 107.74 2.670<br />
DO3 C12 N2 C3 106.48 2.561<br />
DO3 C12 N2 C2 109.02 2.744<br />
DO3 C3 N2 C2 102.13 2.649<br />
DO3 C14 N3 C5 105.04 2.585<br />
DO3 C14 N3 C4 103.89 2.174<br />
DO3 C5 N3 C4 106.72 2.368<br />
DO3 C16 N4 C7 105.80 2.579<br />
DO3 C16 N4 C6 105.27 2.444<br />
DO3 C7 N4 C6 104.88 2.581<br />
DO3 HO7 O7 C15 107.35 2.565<br />
DO3 HC12 C1 HC11 100.58 2.873<br />
DO3 HC12 C1 C2 106.62 2.586<br />
DO3 HC11 C1 C2 116.99 2.658<br />
DO3 HC12 C1 N1 110.02 2.443<br />
DO3 HC11 C1 N1 109.37 2.377<br />
DO3 C2 C1 N1 112.44 2.382<br />
DO3 HC22 C2 HC21 105.97 2.878<br />
DO3 HC22 C2 C1 107.63 2.663<br />
DO3 HC21 C2 C1 108.28 2.655<br />
DO3 HC22 C2 N2 108.75 2.445<br />
DO3 HC21 C2 N2 109.25 2.451<br />
DO3 C1 C2 N2 116.46 2.449<br />
DO3 HC32 C3 HC31 107.06 2.882<br />
DO3 HC32 C3 C4 111.64 2.177<br />
DO3 HC31 C3 C4 109.07 2.183<br />
DO3 HC32 C3 N2 109.09 2.238<br />
DO3 HC31 C3 N2 108.01 2.424<br />
DO3 C4 C3 N2 111.80 2.440<br />
DO3 HC42 C4 HC41 103.98 2.884<br />
DO3 HC42 C4 C3 108.63 2.370<br />
DO3 HC41 C4 C3 113.45 2.590<br />
DO3 HC42 C4 N3 111.85 2.690<br />
DO3 HC41 C4 N3 108.23 2.347<br />
DO3 HC41 C4 N3 108.23 2.347<br />
DO3 C3 C4 N3 110.57 2.361<br />
DO3 HC52 C5 HC51 106.85 2.885<br />
DO3 HC52 C5 C6 108.41 2.570<br />
DO3 HC51 C5 C6 112.17 2.595<br />
DO3 HC52 C5 N3 109.36 2.028<br />
DO3 HC51 C5 N3 110.76 2.080<br />
DO3 C6 C5 N3 109.21 2.002<br />
DO3 HC62 C6 HC61 105.60 2.886<br />
DO3 HC62 C6 C5 111.55 2.596<br />
DO3 HC61 C6 C5 110.35 2.598<br />
DO3 HC62 C6 N4 109.29 2.650<br />
DO3 HC61 C6 N4 109.29 2.667<br />
DO3 C5 C6 N4 110.62 2.662<br />
DO3 HC72 C7 HC71 105.55 2.886<br />
DO3 HC72 C7 C8 110.28 2.588<br />
DO3 HC71 C7 C8 110.93 2.581<br />
DO3 HC72 C7 N4 108.83 2.657<br />
DO3 HC71 C7 N4 109.29 2.664<br />
DO3 C8 C7 N4 111.75 2.649<br />
DO3 HC82 C8 HC81 106.03 2.885<br />
DO3 HC82 C8 C7 108.08 2.443<br />
DO3 HC81 C8 C7 112.15 2.585<br />
DO3 HC82 C8 N1 110.10 2.440<br />
DO3 HC81 C8 N1 111.15 2.364<br />
DO3 C7 C8 N1 109.24 2.368<br />
DO3 O2 C9 C10 117.84 2.590<br />
DO3 O2 C9 O1 122.95 2.656<br />
DO3 C10 C9 O1 119.20 2.669<br />
DO3 H102 C10 H101 106.38 2.860<br />
DO3 H102 C10 C9 108.49 2.426<br />
DO3 H101 C10 C9 109.95 2.574<br />
DO3 H102 C10 N1 107.78 2.433<br />
DO3 H101 C10 N1 110.52 2.360<br />
DO3 C9 C10 N1 113.44 2.367<br />
DO3 O4 C11 C12 117.06 2.583<br />
DO3 O4 C11 O3 122.94 2.653<br />
DO3 C12 C11 O3 119.99 2.657<br />
DO3 H122 C12 H121 101.80 2.859<br />
DO3 H122 C12 C11 109.23 2.447<br />
DO3 H121 C12 C11 108.75 2.577<br />
DO3 H122 C12 N2 112.14 2.403<br />
DO3 H121 C12 N2 109.69 2.253<br />
DO3 C11 C12 N2 114.46 2.283<br />
DO3 O6 C13 C14 117.17 2.581<br />
DO3 O6 C13 O5 123.87 2.663<br />
DO3 C14 C13 O5 118.96 2.662<br />
DO3 H142 C14 H141 106.56 2.860<br />
DO3 H142 C14 C13 109.75 2.563<br />
DO3 H141 C14 C13 108.90 2.584<br />
DO3 H142 C14 N3 109.34 2.025<br />
DO3 H141 C14 N3 108.77 2.080<br />
DO3 C13 C14 N3 113.29 1.989<br />
DO3 HA C15 C17 109.64 2.718<br />
DO3 HA C15 C16 107.78 2.607<br />
DO3 C17 C15 C16 106.37 2.350<br />
DO3 HA C15 O7 109.12 2.651<br />
DO3 C17 C15 O7 110.87 2.658<br />
DO3 C16 C15 O7 112.96 2.669<br />
DO3 H162 C16 H161 106.90 3.000<br />
DO3 H162 C16 C15 109.08 2.582<br />
DO3 H161 C16 C15 111.04 2.562<br />
DO3 H162 C16 N4 108.04 2.644<br />
DO3 H161 C16 N4 111.00 2.670<br />
DO3 C15 C16 N4 110.65 2.665<br />
DO3 H173 C17 H172 104.72 2.854<br />
DO3 H173 C17 H171 111.14 2.826<br />
DO3 H172 C17 H171 107.96 2.851<br />
DO3 H173 C17 C15 110.66 2.632<br />
DO3 H172 C17 C15 109.89 2.609<br />
DO3 H171 C17 C15 112.16 2.564<br />
#<br />
loop_<br />
_chem_comp_tor.comp_id<br />
_chem_comp_tor.id<br />
_chem_comp_tor.atom_id_1<br />
_chem_comp_tor.atom_id_2<br />
_chem_comp_tor.atom_id_3<br />
_chem_comp_tor.atom_id_4<br />
_chem_comp_tor.value_angle<br />
_chem_comp_tor.value_angle_esd<br />
_chem_comp_tor.period<br />
DO3 Var_01 N2 C2 C1 N1 -91.92 30.0 1<br />
DO3 Var_02 N4 C7 C8 N1 110.95 30.0 1<br />
DO3 Var_03 N3 C4 C3 N2 136.32 30.0 1<br />
DO3 Var_04 N4 C6 C5 N3 -124.63 30.0 1<br />
DO3 Var_05 C7 C8 N1 C1 -129.96 30.0 1<br />
DO3 Var_06 C3 N2 C2 C1 111.18 30.0 1<br />
DO3 Var_07 C4 C3 N2 C2 -172.19 30.0 1<br />
DO3 Var_08 C8 N1 C1 C2 123.08 30.0 1<br />
DO3 Var_09 C5 N3 C4 C3 -95.57 30.0 1<br />
DO3 Var_10 C6 C5 N3 C4 111.01 30.0 1<br />
DO3 Var_11 C8 C7 N4 C6 -138.68 30.0 1<br />
DO3 Var_12 C9 C10 N1 C1 61.34 30.0 3<br />
DO3 Var_13 C11 C12 N2 C2 -76.60 30.0 3<br />
DO3 Var_14 C13 C14 N3 C4 -69.64 30.0 3<br />
DO3 Var_15 C15 C16 N4 C6 177.79 30.0 3<br />
DO3 Var_16 O1 C9 C10 N1 -174.46 30.0 2<br />
DO3 Var_17 O3 C11 C12 N2 176.53 30.0 2<br />
DO3 Var_18 O5 C13 C14 N3 176.74 30.0 2<br />
#<br />
loop_<br />
_chem_comp_chir.comp_id<br />
_chem_comp_chir.id<br />
_chem_comp_chir.atom_id_centre<br />
_chem_comp_chir.atom_id_1<br />
_chem_comp_chir.atom_id_2<br />
_chem_comp_chir.atom_id_3<br />
_chem_comp_chir.volume_sign<br />
DO3 chir_01 C15 O7 C16 C17 negativ<br />
#<br />
loop_<br />
_chem_comp_plane_atom.comp_id<br />
_chem_comp_plane_atom.plane_id<br />
_chem_comp_plane_atom.atom_id<br />
_chem_comp_plane_atom.dist_esd<br />
DO3 plan-1 O1 0.020<br />
DO3 plan-1 C9 0.020<br />
DO3 plan-1 C10 0.020<br />
DO3 plan-1 O2 0.020<br />
DO3 plan-2 O3 0.020<br />
DO3 plan-2 C11 0.020<br />
DO3 plan-2 C12 0.020<br />
DO3 plan-2 O4 0.020<br />
DO3 plan-3 O5 0.020<br />
DO3 plan-3 C13 0.020<br />
DO3 plan-3 C14 0.020<br />
DO3 plan-3 O6 0.020<br />
</pre></div>
Tara