# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 05:27:30 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 2',5'-dideoxy-5'-[(diphenylmethyl)(methyl)amino]uridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C[C@H]1O[C@H](C[C@@H]1O)N2C=CC(=O)NC2=O)C(c3ccccc3)c4ccccc4
#
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
 DU4  DU4  2',5'-dideoxy-5'-[(diphenylmethyl)(methyl)amino]uridine  ligand  55  30  .  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_DU4
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
 DU4  N1    N  NR6   0  -0.562   3.1064  -0.1663  -0.1620
 DU4  C2    C  CR6   0   0.736   4.4356   0.0172  -0.4737
 DU4  O2    O  O     0  -0.483   5.1056  -0.8441  -1.0081
 DU4  N3    N  NR16  0  -0.731   4.9459   1.2412  -0.1349
 DU4  C4    C  CR6   0   0.566   4.2928   2.2914   0.4946
 DU4  O4    O  O     0  -0.468   4.8835   3.3281   0.7390
 DU4  C5    C  CR16  0  -0.509   2.9144   2.0044   0.7952
 DU4  C6    C  CR16  0   0.096   2.3924   0.8120   0.4573
 DU4  C1'   C  CH1   0   0.198   2.5192  -1.4844  -0.5138
 DU4  C17   C  CH1   0  -0.166  -2.7002  -0.3396   0.5391
 DU4  C18   C  CR6   0   0.102  -2.0119   1.0089   0.6345
 DU4  C19   C  CR16  0  -0.307  -2.3424   1.8778   1.6686
 DU4  C2'   C  CH2   0  -0.543   2.8595  -2.5600   0.5117
 DU4  C20   C  CR16  0  -0.241  -1.7749   3.1439   1.7434
 DU4  C21   C  CR16  0  -0.268  -0.8629   3.5551   0.7818
 DU4  C22   C  CR16  0  -0.235  -0.5247   2.6909  -0.2529
 DU4  C23   C  CR16  0  -0.300  -1.0943   1.4278  -0.3265
 DU4  C24   C  CR6   0   0.117  -3.8589  -0.1917  -0.4300
 DU4  C25   C  CR16  0  -0.317  -5.1495  -0.0124   0.0530
 DU4  C26   C  CR16  0  -0.240  -6.2143   0.1837  -0.8192
 DU4  C27   C  CR16  0  -0.270  -5.9969   0.1963  -2.1892
 DU4  C28   C  CR16  0  -0.241  -4.7090   0.0116  -2.6804
 DU4  C29   C  CR16  0  -0.286  -3.6487  -0.1778  -1.8076
 DU4  C3'   C  CH1   0   0.023   1.6478  -2.5230   1.4374
 DU4  O3'   O  OH1   0  -0.661   1.3693  -3.7167   2.1122
 DU4  C4'   C  CH1   0   0.016   0.5296  -2.2206   0.4460
 DU4  O4'   O  O2    0  -0.490   1.1292  -1.3710  -0.5335
 DU4  C41   C  CH3   0  -0.540  -2.4835  -2.6663  -0.0194
 DU4  C5'   C  CH2   0  -0.300  -0.6779  -1.5492   1.0653
 DU4  N5'   N  NT    0  -0.422  -1.7871  -1.3997   0.1327
 DU4  HN3   H  HNR6  0   0.426   5.9221   1.3817  -0.3659
 DU4  H5    H  HCR6  0   0.285   2.3049   2.7506   1.2809
 DU4  H6    H  HCR6  0   0.323   1.3569   0.5872   0.6578
 DU4  H1'   H  HCH1  0   0.278   2.8880  -1.7237  -1.5110
 DU4  H17   H  HCH1  0   0.234  -3.1285  -0.5638   1.5323
 DU4  H19   H  HCR6  0   0.247  -3.0509   1.5636   2.4267
 DU4  H2'   H  HCH2  0   0.266   2.9041  -3.5309   0.0128
 DU4  H2'A  H  HCH2  0   0.280   3.8108  -2.3917   1.0137
 DU4  H20   H  HCR6  0   0.255  -2.0440   3.8064   2.5560
 DU4  H21   H  HCR6  0   0.255  -0.4172   4.5398   0.8379
 DU4  H22   H  HCR6  0   0.254   0.1918   2.9988  -1.0038
 DU4  H23   H  HCR6  0   0.259  -0.8061   0.7574  -1.1257
 DU4  H25   H  HCR6  0   0.247  -5.3265  -0.0252   1.1223
 DU4  H26   H  HCR6  0   0.254  -7.2135   0.3221  -0.4262
 DU4  H27   H  HCR6  0   0.255  -6.8237   0.3446  -2.8718
 DU4  H28   H  HCR6  0   0.254  -4.5318   0.0141  -3.7484
 DU4  H29   H  HCR6  0   0.253  -2.6512  -0.3325  -2.1996
 DU4  H3'   H  HCH1  0   0.219   1.7471  -1.6866   2.1458
 DU4  HO3'  H  HOH1  0   0.462   1.9976  -3.8157   2.8336
 DU4  H4'   H  HCH1  0   0.243   0.2428  -3.1637  -0.0373
 DU4  H41   H  HCH3  0   0.249  -3.2267  -2.6135  -0.8115
 DU4  H41A  H  HCH3  0   0.242  -1.7802  -3.4511  -0.2938
 DU4  H41B  H  HCH3  0   0.203  -2.9892  -2.9850   0.9048
 DU4  H5'   H  HCH2  0   0.231  -0.9755  -2.1288   1.9544
 DU4  H5'A  H  HCH2  0   0.255  -0.3690  -0.5696   1.4356

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
 DU4  N1   C2    single    1.377  0.020  1.377
 DU4  N1   C6    single    1.360  0.020  1.360
 DU4  N1   C1'   single    1.485  0.020  1.485
 DU4  C2   O2    double    1.215  0.020  1.215
 DU4  C2   N3    single    1.369  0.020  1.369
 DU4  N3   C4    single    1.388  0.020  1.388
 DU4  C4   O4    double    1.218  0.020  1.218
 DU4  C4   C5    single    1.440  0.020  1.440
 DU4  C5   C6    double    1.345  0.020  1.345
 DU4  C1'  C2'   single    1.525  0.020  1.525
 DU4  C1'  O4'   single    1.395  0.020  1.395
 DU4  C17  C18   single    1.517  0.020  1.517
 DU4  C17  C24   single    1.518  0.020  1.518
 DU4  C17  N5'   single    1.457  0.020  1.457
 DU4  C18  C19   aromatic  1.390  0.020  1.390
 DU4  C18  C23   aromatic  1.393  0.020  1.393
 DU4  C19  C20   aromatic  1.389  0.020  1.389
 DU4  C2'  C3'   single    1.525  0.020  1.525
 DU4  C20  C21   aromatic  1.388  0.020  1.388
 DU4  C21  C22   aromatic  1.390  0.020  1.390
 DU4  C22  C23   aromatic  1.388  0.020  1.388
 DU4  C24  C25   aromatic  1.390  0.020  1.390
 DU4  C24  C29   aromatic  1.394  0.020  1.394
 DU4  C25  C26   aromatic  1.390  0.020  1.390
 DU4  C26  C27   aromatic  1.387  0.020  1.387
 DU4  C27  C28   aromatic  1.391  0.020  1.391
 DU4  C28  C29   aromatic  1.386  0.020  1.386
 DU4  C3'  O3'   single    1.399  0.020  1.399
 DU4  C3'  C4'   single    1.525  0.020  1.525
 DU4  C4'  O4'   single    1.429  0.020  1.429
 DU4  C4'  C5'   single    1.514  0.020  1.514
 DU4  C41  N5'   single    1.453  0.020  1.453
 DU4  C5'  N5'   single    1.457  0.020  1.457
 DU4  N3   HN3   single    0.860  0.020  1.020
 DU4  C5   H5    single    0.930  0.020  1.080
 DU4  C6   H6    single    0.930  0.020  1.080
 DU4  C1'  H1'   single    0.970  0.020  1.090
 DU4  C17  H17   single    0.970  0.020  1.090
 DU4  C19  H19   single    0.930  0.020  1.080
 DU4  C2'  H2'   single    0.970  0.020  1.090
 DU4  C2'  H2'A  single    0.970  0.020  1.090
 DU4  C20  H20   single    0.930  0.020  1.080
 DU4  C21  H21   single    0.930  0.020  1.080
 DU4  C22  H22   single    0.930  0.020  1.080
 DU4  C23  H23   single    0.930  0.020  1.080
 DU4  C25  H25   single    0.930  0.020  1.080
 DU4  C26  H26   single    0.930  0.020  1.080
 DU4  C27  H27   single    0.930  0.020  1.080
 DU4  C28  H28   single    0.930  0.020  1.080
 DU4  C29  H29   single    0.930  0.020  1.080
 DU4  C3'  H3'   single    0.970  0.020  1.090
 DU4  O3'  HO3'  single    0.850  0.020  0.980
 DU4  C4'  H4'   single    0.970  0.020  1.090
 DU4  C41  H41   single    0.970  0.020  1.090
 DU4  C41  H41A  single    0.970  0.020  1.090
 DU4  C41  H41B  single    0.970  0.020  1.090
 DU4  C5'  H5'   single    0.970  0.020  1.090
 DU4  C5'  H5'A  single    0.970  0.020  1.090

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
 DU4  C1'   N1   C6    122.59  3.000
 DU4  C1'   N1   C2    116.49  3.000
 DU4  C6    N1   C2    120.91  3.000
 DU4  N3    C2   O2    122.49  3.000
 DU4  N3    C2   N1    115.02  3.000
 DU4  O2    C2   N1    122.50  3.000
 DU4  HN3   N3   C4    116.88  3.000
 DU4  HN3   N3   C2    115.27  3.000
 DU4  C4    N3   C2    127.85  3.000
 DU4  C5    C4   O4    126.31  3.000
 DU4  C5    C4   N3    113.23  3.000
 DU4  O4    C4   N3    120.46  3.000
 DU4  H5    C5   C6    120.47  3.000
 DU4  H5    C5   C4    119.80  3.000
 DU4  C6    C5   C4    119.73  3.000
 DU4  H6    C6   C5    120.72  3.000
 DU4  H6    C6   N1    116.02  3.000
 DU4  C5    C6   N1    123.25  3.000
 DU4  H1'   C1'  O4'   110.01  3.000
 DU4  H1'   C1'  C2'   112.65  3.000
 DU4  O4'   C1'  C2'   106.82  3.000
 DU4  H1'   C1'  N1    106.13  3.000
 DU4  O4'   C1'  N1    108.98  3.000
 DU4  C2'   C1'  N1    112.24  3.000
 DU4  H17   C17  N5'   110.25  3.000
 DU4  H17   C17  C24   107.33  3.000
 DU4  N5'   C17  C24   111.79  3.000
 DU4  H17   C17  C18   107.45  3.000
 DU4  N5'   C17  C18   112.33  3.000
 DU4  C24   C17  C18   107.45  3.000
 DU4  C23   C18  C19   118.79  3.000
 DU4  C23   C18  C17   121.51  3.000
 DU4  C19   C18  C17   119.63  3.000
 DU4  H19   C19  C20   119.56  3.000
 DU4  H19   C19  C18   119.62  3.000
 DU4  C20   C19  C18   120.82  3.000
 DU4  H2'A  C2'  H2'   108.20  3.000
 DU4  H2'A  C2'  C3'   114.24  3.000
 DU4  H2'   C2'  C3'   109.33  3.000
 DU4  H2'A  C2'  C1'   113.34  3.000
 DU4  H2'   C2'  C1'   109.20  3.000
 DU4  C3'   C2'  C1'   102.35  3.000
 DU4  H20   C20  C21   120.15  3.000
 DU4  H20   C20  C19   119.77  3.000
 DU4  C21   C20  C19   120.08  3.000
 DU4  H21   C21  C22   120.27  3.000
 DU4  H21   C21  C20   120.29  3.000
 DU4  C22   C21  C20   119.44  3.000
 DU4  H22   C22  C23   119.59  3.000
 DU4  H22   C22  C21   120.04  3.000
 DU4  C23   C22  C21   120.37  3.000
 DU4  H23   C23  C22   119.58  3.000
 DU4  H23   C23  C18   119.91  3.000
 DU4  C22   C23  C18   120.50  3.000
 DU4  C29   C24  C25   118.84  3.000
 DU4  C29   C24  C17   121.13  3.000
 DU4  C25   C24  C17   119.98  3.000
 DU4  H25   C25  C26   119.70  3.000
 DU4  H25   C25  C24   119.54  3.000
 DU4  C26   C25  C24   120.76  3.000
 DU4  H26   C26  C27   120.14  3.000
 DU4  H26   C26  C25   119.81  3.000
 DU4  C27   C26  C25   120.05  3.000
 DU4  H27   C27  C28   120.19  3.000
 DU4  H27   C27  C26   120.29  3.000
 DU4  C28   C27  C26   119.52  3.000
 DU4  H28   C28  C29   119.75  3.000
 DU4  H28   C28  C27   119.98  3.000
 DU4  C29   C28  C27   120.27  3.000
 DU4  H29   C29  C28   119.75  3.000
 DU4  H29   C29  C24   119.70  3.000
 DU4  C28   C29  C24   120.55  3.000
 DU4  H3'   C3'  C4'   109.51  3.000
 DU4  H3'   C3'  O3'   110.85  3.000
 DU4  C4'   C3'  O3'   109.68  3.000
 DU4  H3'   C3'  C2'   109.72  3.000
 DU4  C4'   C3'  C2'   101.12  3.000
 DU4  O3'   C3'  C2'   115.48  3.000
 DU4  HO3'  O3'  C3'   108.63  3.000
 DU4  H4'   C4'  C5'   110.66  3.000
 DU4  H4'   C4'  O4'   108.58  3.000
 DU4  C5'   C4'  O4'   110.58  3.000
 DU4  H4'   C4'  C3'   107.91  3.000
 DU4  C5'   C4'  C3'   114.01  3.000
 DU4  O4'   C4'  C3'   104.83  3.000
 DU4  C4'   O4'  C1'   111.12  3.000
 DU4  H41B  C41  H41A  107.44  3.000
 DU4  H41B  C41  H41   108.16  3.000
 DU4  H41A  C41  H41   107.03  3.000
 DU4  H41B  C41  N5'   112.62  3.000
 DU4  H41A  C41  N5'   110.18  3.000
 DU4  H41   C41  N5'   111.19  3.000
 DU4  H5'A  C5'  H5'   105.94  3.000
 DU4  H5'A  C5'  N5'   109.91  3.000
 DU4  H5'   C5'  N5'   111.39  3.000
 DU4  H5'A  C5'  C4'   108.12  3.000
 DU4  H5'   C5'  C4'   108.18  3.000
 DU4  N5'   C5'  C4'   113.00  3.000
 DU4  C5'   N5'  C41   110.02  3.000
 DU4  C5'   N5'  C17   111.91  3.000
 DU4  C41   N5'  C17   111.28  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
 DU4  CONST_01  C21  C20  C19  C18     0.00   0.0  0
 DU4  CONST_02  C21  C22  C23  C18     0.00   0.0  0
 DU4  CONST_03  C22  C23  C18  C19     0.00   0.0  0
 DU4  CONST_04  C22  C21  C20  C19     0.00   0.0  0
 DU4  CONST_05  C23  C18  C19  C20     0.00   0.0  0
 DU4  CONST_06  C23  C22  C21  C20     0.00   0.0  0
 DU4  CONST_07  C27  C26  C25  C24     0.00   0.0  0
 DU4  CONST_08  C27  C28  C29  C24     0.00   0.0  0
 DU4  CONST_09  C28  C29  C24  C25     0.00   0.0  0
 DU4  CONST_10  C28  C27  C26  C25     0.00   0.0  0
 DU4  CONST_11  C29  C24  C25  C26     0.00   0.0  0
 DU4  CONST_12  C29  C28  C27  C26     0.00   0.0  0
 DU4  CONST_13  C4   N3   C2   N1      0.00   0.0  0
 DU4  CONST_14  C5   C4   N3   C2      0.00   0.0  0
 DU4  CONST_15  C6   N1   C2   N3      0.00   0.0  0
 DU4  CONST_16  C1'  N1   C2   N3    180.00   0.0  0
 DU4  CONST_17  C20  C19  C18  C17   180.00   0.0  0
 DU4  CONST_18  C22  C23  C18  C17   180.00   0.0  0
 DU4  CONST_19  C26  C25  C24  C17   180.00   0.0  0
 DU4  CONST_20  C28  C29  C24  C17   180.00   0.0  0
 DU4  CONST_21  O4   C4   N3   C2    180.00   0.0  0
 DU4  CONST_22  C6   N1   C2   O2    180.00   0.0  0
 DU4  CONST_23  C1'  N1   C2   O2      0.00   0.0  0
 DU4  CONST_24  C4   N3   C2   O2    180.00   0.0  0
 DU4  CONST_25  H20  C20  C19  C18   180.00   0.0  0
 DU4  CONST_26  H22  C22  C23  C18   180.00   0.0  0
 DU4  CONST_27  H23  C23  C18  C19   180.00   0.0  0
 DU4  CONST_28  H21  C21  C20  C19   180.00   0.0  0
 DU4  CONST_29  H19  C19  C20  C21   180.00   0.0  0
 DU4  CONST_30  H26  C26  C25  C24   180.00   0.0  0
 DU4  CONST_31  H28  C28  C29  C24   180.00   0.0  0
 DU4  CONST_32  H29  C29  C24  C25   180.00   0.0  0
 DU4  CONST_33  H27  C27  C26  C25   180.00   0.0  0
 DU4  CONST_34  H25  C25  C26  C27   180.00   0.0  0
 DU4  CONST_35  HN3  N3   C2   N1    180.00   0.0  0
 DU4  Var_01    C25  C24  C17  C18   -99.40  30.0  2
 DU4  Var_02    C24  C17  C18  C19    95.83  30.0  2
 DU4  Var_03    C4'  C5'  N5'  C17  -157.81  30.0  2
 DU4  Var_04    C41  N5'  C17  C18  -177.00  30.0  3
 DU4  Var_05    H41  C41  N5'  C17    63.21  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
 DU4  chir_01  C1'  N1   C2'  O4'  negativ
 DU4  chir_02  C3'  O3'  C4'  C2'  positiv
 DU4  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
 DU4  plan-1  N1   0.020
 DU4  plan-1  C2   0.020
 DU4  plan-1  O2   0.020
 DU4  plan-1  N3   0.020
 DU4  plan-1  C4   0.020
 DU4  plan-1  O4   0.020
 DU4  plan-1  C5   0.020
 DU4  plan-1  C6   0.020
 DU4  plan-1  C1'  0.020
 DU4  plan-1  HN3  0.020
 DU4  plan-1  H5   0.020
 DU4  plan-1  H6   0.020
 DU4  plan-2  C17  0.020
 DU4  plan-2  C18  0.020
 DU4  plan-2  C19  0.020
 DU4  plan-2  C20  0.020
 DU4  plan-2  C21  0.020
 DU4  plan-2  C22  0.020
 DU4  plan-2  C23  0.020
 DU4  plan-2  H19  0.020
 DU4  plan-2  H20  0.020
 DU4  plan-2  H21  0.020
 DU4  plan-2  H22  0.020
 DU4  plan-2  H23  0.020
 DU4  plan-3  C17  0.020
 DU4  plan-3  C24  0.020
 DU4  plan-3  C25  0.020
 DU4  plan-3  C26  0.020
 DU4  plan-3  C27  0.020
 DU4  plan-3  C28  0.020
 DU4  plan-3  C29  0.020
 DU4  plan-3  H25  0.020
 DU4  plan-3  H26  0.020
 DU4  plan-3  H27  0.020
 DU4  plan-3  H28  0.020
 DU4  plan-3  H29  0.020

