# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 04:40:57 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 2',5'-dideoxy-5'-[(diphenylmethyl)amino]uridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1C[C@@H](O[C@@H]1CNC(c2ccccc2)c3ccccc3)N4C=CC(=O)NC4=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
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 DU3  DU3  2',5'-dideoxy-5'-[(diphenylmethyl)amino]uridine  ligand  52  29  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DU3
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 DU3  N1    N  NR6   0  -0.564   3.0274  -0.2206  -0.2794
 DU3  C2    C  CR6   0   0.736   4.3629  -0.0510  -0.5703
 DU3  O2    O  O     0  -0.483   5.0574  -0.9519  -0.9973
 DU3  N3    N  NR16  0  -0.731   4.8515   1.2068  -0.3397
 DU3  C4    C  CR6   0   0.565   4.1658   2.3104   0.1475
 DU3  O4    O  O     0  -0.468   4.7395   3.3724   0.3092
 DU3  C5    C  CR16  0  -0.508   2.7761   2.0431   0.4127
 DU3  C6    C  CR16  0   0.093   2.2784   0.8136   0.1891
 DU3  C1'   C  CH1   0   0.199   2.4668  -1.5785  -0.5158
 DU3  C17   C  CH1   0  -0.194  -2.7474  -0.3798   0.6446
 DU3  C18   C  CR6   0   0.133  -2.2007   1.0325   0.5320
 DU3  C19   C  CR16  0  -0.311  -2.5994   2.0077   1.4394
 DU3  C2'   C  CH2   0  -0.542   2.8514  -2.5601   0.5841
 DU3  C20   C  CR16  0  -0.242  -2.1369   3.3129   1.3288
 DU3  C21   C  CR16  0  -0.268  -1.2601   3.6562   0.3087
 DU3  C22   C  CR16  0  -0.235  -0.8531   2.6855  -0.5988
 DU3  C23   C  CR16  0  -0.305  -1.3217   1.3834  -0.4893
 DU3  C24   C  CR6   0   0.133  -3.9846  -0.5069  -0.2201
 DU3  C25   C  CR16  0  -0.309  -3.8887  -0.7690  -1.5850
 DU3  C26   C  CR16  0  -0.236  -5.0309  -0.8396  -2.3708
 DU3  C27   C  CR16  0  -0.271  -6.2850  -0.6472  -1.8049
 DU3  C28   C  CR16  0  -0.239  -6.3886  -0.3891  -0.4448
 DU3  C29   C  CR16  0  -0.316  -5.2448  -0.3233   0.3401
 DU3  C3'   C  CH1   0   0.018   1.6707  -2.4554   1.5424
 DU3  O3'   O  OH1   0  -0.662   1.4210  -3.5954   2.3158
 DU3  C4'   C  CH1   0   0.016   0.5123  -2.2297   0.5765
 DU3  O4'   O  O2    0  -0.490   1.0765  -1.5041  -0.5188
 DU3  C5'   C  CH2   0  -0.283  -0.6498  -1.4722   1.1788
 DU3  N5'   N  NH1   0  -0.606  -1.7490  -1.3495   0.2430
 DU3  H5    H  HCR6  0   0.284   2.1391   2.8325   0.7808
 DU3  H6    H  HCR6  0   0.321   1.2351   0.6044   0.3655
 DU3  H1'   H  HCH1  0   0.279   2.8225  -1.8881  -1.4988
 DU3  H17   H  HCH1  0   0.239  -3.0648  -0.5226   1.6910
 DU3  H19   H  HCR6  0   0.245  -3.2742   1.7448   2.2466
 DU3  H2'   H  HCH2  0   0.265   2.8902  -3.5681   0.1642
 DU3  H2'A  H  HCH2  0   0.280   3.8155  -2.3451   1.0408
 DU3  H20   H  HCR6  0   0.254  -2.4551   4.0589   2.0459
 DU3  H21   H  HCR6  0   0.254  -0.8918   4.6704   0.2241
 DU3  H22   H  HCR6  0   0.253  -0.1635   2.9410  -1.3936
 DU3  H23   H  HCR6  0   0.261  -0.9843   0.6251  -1.1841
 DU3  H25   H  HCR6  0   0.254  -2.9176  -0.9263  -2.0367
 DU3  H26   H  HCR6  0   0.254  -4.9406  -1.0441  -3.4301
 DU3  H27   H  HCR6  0   0.255  -7.1742  -0.7038  -2.4193
 DU3  H28   H  HCR6  0   0.255  -7.3607  -0.2436   0.0086
 DU3  H29   H  HCR6  0   0.247  -5.3366  -0.1321   1.4032
 DU3  H3'   H  HCH1  0   0.220   1.7887  -1.5675   2.1814
 DU3  HO3'  H  HOH1  0   0.461   2.0735  -3.6378   3.0211
 DU3  H4'   H  HCH1  0   0.240   0.1671  -3.2062   0.2092
 DU3  H5'   H  HCH2  0   0.233  -0.9374  -1.9775   2.1126
 DU3  H5'A  H  HCH2  0   0.233  -0.3129  -0.4735   1.4687
 DU3  HN5'  H  HNH1  0   0.356  -2.1908  -2.2539   0.1264
 DU3  HN3   H  HNR6  0   0.426   5.8346   1.3328  -0.5476

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
_chem_comp_bond.value_dist_neutron
 DU3  C2   N1    single    1.377  0.020  1.377
 DU3  C6   N1    single    1.360  0.020  1.360
 DU3  N1   C1'   single    1.488  0.020  1.488
 DU3  N3   C2    single    1.369  0.020  1.369
 DU3  O2   C2    double    1.215  0.020  1.215
 DU3  C4   N3    single    1.388  0.020  1.388
 DU3  O4   C4    double    1.218  0.020  1.218
 DU3  C4   C5    single    1.440  0.020  1.440
 DU3  C5   C6    double    1.345  0.020  1.345
 DU3  C5   H5    single    0.930  0.020  1.080
 DU3  C6   H6    single    0.930  0.020  1.080
 DU3  O4'  C1'   single    1.392  0.020  1.392
 DU3  C1'  C2'   single    1.524  0.020  1.524
 DU3  C1'  H1'   single    0.970  0.020  1.090
 DU3  C18  C17   single    1.519  0.020  1.519
 DU3  C24  C17   single    1.515  0.020  1.515
 DU3  C17  N5'   single    1.449  0.020  1.449
 DU3  C17  H17   single    0.970  0.020  1.090
 DU3  C19  C18   aromatic  1.391  0.020  1.391
 DU3  C23  C18   aromatic  1.392  0.020  1.392
 DU3  C20  C19   aromatic  1.389  0.020  1.389
 DU3  C19  H19   single    0.930  0.020  1.080
 DU3  C3'  C2'   single    1.524  0.020  1.524
 DU3  C2'  H2'   single    0.970  0.020  1.090
 DU3  C2'  H2'A  single    0.970  0.020  1.090
 DU3  C21  C20   aromatic  1.388  0.020  1.388
 DU3  C20  H20   single    0.930  0.020  1.080
 DU3  C21  C22   aromatic  1.390  0.020  1.390
 DU3  C21  H21   single    0.930  0.020  1.080
 DU3  C22  C23   aromatic  1.388  0.020  1.388
 DU3  C22  H22   single    0.930  0.020  1.080
 DU3  C23  H23   single    0.930  0.020  1.080
 DU3  C25  C24   aromatic  1.393  0.020  1.393
 DU3  C24  C29   aromatic  1.391  0.020  1.391
 DU3  C26  C25   aromatic  1.388  0.020  1.388
 DU3  C25  H25   single    0.930  0.020  1.080
 DU3  C26  C27   aromatic  1.389  0.020  1.389
 DU3  C26  H26   single    0.930  0.020  1.080
 DU3  C27  C28   aromatic  1.388  0.020  1.388
 DU3  C27  H27   single    0.930  0.020  1.080
 DU3  C28  C29   aromatic  1.389  0.020  1.389
 DU3  C28  H28   single    0.930  0.020  1.080
 DU3  C29  H29   single    0.930  0.020  1.080
 DU3  C4'  C3'   single    1.525  0.020  1.525
 DU3  C3'  O3'   single    1.400  0.020  1.400
 DU3  C3'  H3'   single    0.970  0.020  1.090
 DU3  O3'  HO3'  single    0.850  0.020  0.980
 DU3  C5'  C4'   single    1.512  0.020  1.512
 DU3  O4'  C4'   single    1.430  0.020  1.430
 DU3  C4'  H4'   single    0.970  0.020  1.090
 DU3  N5'  C5'   single    1.449  0.020  1.449
 DU3  C5'  H5'   single    0.970  0.020  1.090
 DU3  C5'  H5'A  single    0.970  0.020  1.090
 DU3  N5'  HN5'  single    0.890  0.020  1.040
 DU3  N3   HN3   single    0.860  0.020  1.020

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
 DU3  C1'   N1   C6   122.76  3.000
 DU3  C1'   N1   C2   116.37  3.000
 DU3  C6    N1   C2   120.87  3.000
 DU3  N3    C2   O2   122.45  3.000
 DU3  O2    C2   N1   122.49  3.000
 DU3  N3    C2   N1   115.06  3.000
 DU3  HN3   N3   C4   116.92  3.000
 DU3  HN3   N3   C2   115.22  3.000
 DU3  C4    N3   C2   127.85  3.000
 DU3  C5    C4   O4   126.30  3.000
 DU3  C5    C4   N3   113.20  3.000
 DU3  O4    C4   N3   120.50  3.000
 DU3  H5    C5   C6   120.46  3.000
 DU3  H5    C5   C4   119.79  3.000
 DU3  C6    C5   C4   119.75  3.000
 DU3  H6    C6   C5   120.54  3.000
 DU3  H6    C6   N1   116.19  3.000
 DU3  C5    C6   N1   123.26  3.000
 DU3  H1'   C1'  O4'  109.82  3.000
 DU3  H1'   C1'  C2'  112.68  3.000
 DU3  O4'   C1'  C2'  106.74  3.000
 DU3  H1'   C1'  N1   106.23  3.000
 DU3  C2'   C1'  N1   112.22  3.000
 DU3  O4'   C1'  N1   109.13  3.000
 DU3  H17   C17  N5'  112.01  3.000
 DU3  H17   C17  C24  107.20  3.000
 DU3  N5'   C17  C24  110.40  3.000
 DU3  H17   C17  C18  107.12  3.000
 DU3  N5'   C17  C18  110.73  3.000
 DU3  C24   C17  C18  109.25  3.000
 DU3  C23   C18  C19  118.88  3.000
 DU3  C23   C18  C17  121.07  3.000
 DU3  C19   C18  C17  120.04  3.000
 DU3  H19   C19  C20  119.62  3.000
 DU3  H19   C19  C18  119.61  3.000
 DU3  C20   C19  C18  120.77  3.000
 DU3  H2'A  C2'  H2'  108.18  3.000
 DU3  H2'A  C2'  C3'  114.13  3.000
 DU3  H2'   C2'  C3'  109.42  3.000
 DU3  H2'A  C2'  C1'  113.53  3.000
 DU3  H2'   C2'  C1'  109.02  3.000
 DU3  C3'   C2'  C1'  102.36  3.000
 DU3  H20   C20  C21  120.13  3.000
 DU3  H20   C20  C19  119.79  3.000
 DU3  C21   C20  C19  120.07  3.000
 DU3  H21   C21  C22  120.25  3.000
 DU3  H21   C21  C20  120.27  3.000
 DU3  C22   C21  C20  119.48  3.000
 DU3  H22   C22  C23  119.62  3.000
 DU3  H22   C22  C21  120.07  3.000
 DU3  C23   C22  C21  120.32  3.000
 DU3  H23   C23  C22  120.08  3.000
 DU3  H23   C23  C18  119.41  3.000
 DU3  C22   C23  C18  120.49  3.000
 DU3  C29   C24  C25  118.79  3.000
 DU3  C29   C24  C17  119.93  3.000
 DU3  C25   C24  C17  121.26  3.000
 DU3  H25   C25  C26  119.64  3.000
 DU3  H25   C25  C24  119.86  3.000
 DU3  C26   C25  C24  120.50  3.000
 DU3  H26   C26  C27  120.00  3.000
 DU3  H26   C26  C25  119.66  3.000
 DU3  C27   C26  C25  120.34  3.000
 DU3  H27   C27  C28  120.30  3.000
 DU3  H27   C27  C26  120.21  3.000
 DU3  C28   C27  C26  119.49  3.000
 DU3  H28   C28  C29  119.77  3.000
 DU3  H28   C28  C27  120.16  3.000
 DU3  C29   C28  C27  120.07  3.000
 DU3  H29   C29  C28  119.53  3.000
 DU3  H29   C29  C24  119.66  3.000
 DU3  C28   C29  C24  120.81  3.000
 DU3  H3'   C3'  C4'  109.26  3.000
 DU3  H3'   C3'  O3'  110.82  3.000
 DU3  C4'   C3'  O3'  109.56  3.000
 DU3  H3'   C3'  C2'  109.73  3.000
 DU3  O3'   C3'  C2'  115.44  3.000
 DU3  C4'   C3'  C2'  101.56  3.000
 DU3  HO3'  O3'  C3'  108.66  3.000
 DU3  H4'   C4'  C5'  109.68  3.000
 DU3  H4'   C4'  O4'  108.60  3.000
 DU3  C5'   C4'  O4'  110.73  3.000
 DU3  H4'   C4'  C3'  108.59  3.000
 DU3  O4'   C4'  C3'  105.10  3.000
 DU3  C5'   C4'  C3'  113.93  3.000
 DU3  C4'   O4'  C1'  111.42  3.000
 DU3  H5'A  C5'  H5'  105.96  3.000
 DU3  H5'A  C5'  N5'  109.14  3.000
 DU3  H5'   C5'  N5'  112.88  3.000
 DU3  H5'A  C5'  C4'  109.05  3.000
 DU3  H5'   C5'  C4'  107.99  3.000
 DU3  N5'   C5'  C4'  111.60  3.000
 DU3  HN5'  N5'  C5'  109.24  3.000
 DU3  HN5'  N5'  C17  109.20  3.000
 DU3  C5'   N5'  C17  113.61  3.000

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
 DU3  CONST_01  C21  C20  C19  C18     0.00   0.0  0
 DU3  CONST_02  C21  C22  C23  C18     0.00   0.0  0
 DU3  CONST_03  C22  C23  C18  C19     0.00   0.0  0
 DU3  CONST_04  C22  C21  C20  C19     0.00   0.0  0
 DU3  CONST_05  C23  C18  C19  C20     0.00   0.0  0
 DU3  CONST_06  C23  C22  C21  C20     0.00   0.0  0
 DU3  CONST_07  C27  C26  C25  C24     0.00   0.0  0
 DU3  CONST_08  C27  C28  C29  C24     0.00   0.0  0
 DU3  CONST_09  C28  C29  C24  C25     0.00   0.0  0
 DU3  CONST_10  C28  C27  C26  C25     0.00   0.0  0
 DU3  CONST_11  C29  C24  C25  C26     0.00   0.0  0
 DU3  CONST_12  C29  C28  C27  C26     0.00   0.0  0
 DU3  CONST_13  C4   N3   C2   N1      0.00   0.0  0
 DU3  CONST_14  C5   C4   N3   C2      0.00   0.0  0
 DU3  CONST_15  C6   N1   C2   N3      0.00   0.0  0
 DU3  CONST_16  C1'  N1   C2   N3    180.00   0.0  0
 DU3  CONST_17  C20  C19  C18  C17   180.00   0.0  0
 DU3  CONST_18  C22  C23  C18  C17   180.00   0.0  0
 DU3  CONST_19  C26  C25  C24  C17   180.00   0.0  0
 DU3  CONST_20  C28  C29  C24  C17   180.00   0.0  0
 DU3  CONST_21  O4   C4   N3   C2    180.00   0.0  0
 DU3  CONST_22  C6   N1   C2   O2    180.00   0.0  0
 DU3  CONST_23  C1'  N1   C2   O2      0.00   0.0  0
 DU3  CONST_24  C4   N3   C2   O2    180.00   0.0  0
 DU3  CONST_25  H20  C20  C19  C18   180.00   0.0  0
 DU3  CONST_26  H22  C22  C23  C18   180.00   0.0  0
 DU3  CONST_27  H23  C23  C18  C19   180.00   0.0  0
 DU3  CONST_28  H21  C21  C20  C19   180.00   0.0  0
 DU3  CONST_29  H19  C19  C20  C21   180.00   0.0  0
 DU3  CONST_30  H26  C26  C25  C24   180.00   0.0  0
 DU3  CONST_31  H28  C28  C29  C24   180.00   0.0  0
 DU3  CONST_32  H29  C29  C24  C25   180.00   0.0  0
 DU3  CONST_33  H27  C27  C26  C25   180.00   0.0  0
 DU3  CONST_34  H25  C25  C26  C27   180.00   0.0  0
 DU3  CONST_35  HN3  N3   C2   N1    180.00   0.0  0
 DU3  Var_01    C25  C24  C17  C18    83.35  30.0  2
 DU3  Var_02    C24  C17  C18  C19    92.25  30.0  2
 DU3  Var_03    C4'  C5'  N5'  C17  -166.36  30.0  3
 DU3  Var_04    C5'  N5'  C17  C18    70.34  30.0  3

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
 DU3  chir_01  C1'  N1   O4'  C2'  positiv
 DU3  chir_02  C3'  O3'  C4'  C2'  positiv
 DU3  chir_03  C4'  O4'  C3'  C5'  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
 DU3  plan-1  N1   0.020
 DU3  plan-1  C2   0.020
 DU3  plan-1  O2   0.020
 DU3  plan-1  N3   0.020
 DU3  plan-1  C4   0.020
 DU3  plan-1  O4   0.020
 DU3  plan-1  C5   0.020
 DU3  plan-1  C6   0.020
 DU3  plan-1  C1'  0.020
 DU3  plan-1  H5   0.020
 DU3  plan-1  H6   0.020
 DU3  plan-1  HN3  0.020
 DU3  plan-2  C17  0.020
 DU3  plan-2  C18  0.020
 DU3  plan-2  C19  0.020
 DU3  plan-2  C20  0.020
 DU3  plan-2  C21  0.020
 DU3  plan-2  C22  0.020
 DU3  plan-2  C23  0.020
 DU3  plan-2  H19  0.020
 DU3  plan-2  H20  0.020
 DU3  plan-2  H21  0.020
 DU3  plan-2  H22  0.020
 DU3  plan-2  H23  0.020
 DU3  plan-3  C17  0.020
 DU3  plan-3  C24  0.020
 DU3  plan-3  C25  0.020
 DU3  plan-3  C26  0.020
 DU3  plan-3  C27  0.020
 DU3  plan-3  C28  0.020
 DU3  plan-3  C29  0.020
 DU3  plan-3  H25  0.020
 DU3  plan-3  H26  0.020
 DU3  plan-3  H27  0.020
 DU3  plan-3  H28  0.020
 DU3  plan-3  H29  0.020

