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