# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:04:12 2022
#   Inital geometry file: a 90 line input string
#   Ligand name: 3'-(acetylamino)-3'-deoxyuridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO)N2C=CC(=O)NC2=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
 ADU  ADU  3'-(acetylamino)-3'-deoxyuridine  ligand  35  20  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ADU
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
 ADU  N1    N  NR6   0  -0.565  -1.1421  -2.0144   1.1643
 ADU  C2    C  CR6   0   0.739  -2.1607  -2.1686   2.0859
 ADU  O2    O  O     0  -0.474  -3.3247  -1.9346   1.8409
 ADU  N3    N  NR16  0  -0.734  -1.7509  -2.6100   3.3163
 ADU  C4    C  CR6   0   0.571  -0.4644  -2.9154   3.7331
 ADU  O4    O  O     0  -0.460  -0.2554  -3.2979   4.8685
 ADU  C5    C  CR16  0  -0.513   0.5304  -2.7321   2.7040
 ADU  C6    C  CR16  0   0.104   0.1542  -2.3017   1.4911
 ADU  C1'   C  CH1   0   0.200  -1.4598  -1.5520  -0.1785
 ADU  O4'   O  O2    0  -0.488  -0.8912  -2.4203  -1.1097
 ADU  C4'   C  CH1   0  -0.003  -0.3635  -1.6985  -2.2294
 ADU  C5'   C  CH2   0  -0.154   1.1373  -1.8731  -2.3211
 ADU  O5'   O  OH1   0  -0.667   1.4251  -3.2428  -2.4265
 ADU  C3'   C  CH1   0  -0.168  -0.7487  -0.2275  -2.0196
 ADU  N3'   N  NH1   0  -0.641  -1.9935   0.1275  -2.6532
 ADU  C8'   C  C     0   0.528  -2.0924   0.2658  -3.9894
 ADU  O8'   O  O     0  -0.500  -1.1694  -0.0131  -4.7423
 ADU  C9'   C  CH3   0  -0.776  -3.4150   0.7826  -4.4933
 ADU  C2'   C  CH1   0  -0.033  -0.8992  -0.1669  -0.4933
 ADU  O2'   O  OH1   0  -0.646  -1.7660   0.8030   0.0046
 ADU  HN3   H  HNR6  0   0.428  -2.4905  -2.7255   3.9987
 ADU  H5    H  HCR6  0   0.295   1.5660  -2.9472   2.9162
 ADU  H6    H  HCR6  0   0.327   0.8821  -2.1719   0.7030
 ADU  H1'   H  HCH1  0   0.279  -2.5500  -1.5408  -0.2525
 ADU  H4'   H  HCH1  0   0.263  -0.8234  -2.1020  -3.1340
 ADU  H5'1  H  HCH2  0   0.197   1.6249  -1.4184  -1.4466
 ADU  H5'2  H  HCH2  0   0.217   1.4755  -1.3083  -3.2000
 ADU  HO5'  H  HOH1  0   0.459   2.3802  -3.3495  -2.4481
 ADU  H3'   H  HCH1  0   0.292   0.0513   0.4356  -2.3625
 ADU  HN3'  H  HNH1  0   0.402  -2.7253   0.5091  -2.0735
 ADU  H9'1  H  HCH3  0   0.268  -3.2600   1.7361  -4.9986
 ADU  H9'2  H  HCH3  0   0.267  -3.8216   0.0884  -5.2281
 ADU  H9'3  H  HCH3  0   0.250  -4.1528   0.9260  -3.7062
 ADU  H2'   H  HCH1  0   0.267   0.1065  -0.0628  -0.0644
 ADU  HO2'  H  HOH1  0   0.472  -1.3206   1.6568  -0.0050

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
 ADU  N1   C2    single  1.382  0.020  1.382
 ADU  N1   C6    single  1.367  0.020  1.367
 ADU  N1   C1'   single  1.455  0.020  1.455
 ADU  C2   O2    double  1.212  0.020  1.212
 ADU  C2   N3    single  1.370  0.020  1.370
 ADU  N3   C4    single  1.386  0.020  1.386
 ADU  N3   HN3   single  0.860  0.020  1.020
 ADU  C4   O4    double  1.216  0.020  1.216
 ADU  C4   C5    single  1.443  0.020  1.443
 ADU  C5   C6    double  1.341  0.020  1.341
 ADU  C5   H5    single  0.930  0.020  1.080
 ADU  C6   H6    single  0.930  0.020  1.080
 ADU  C1'  O4'   single  1.394  0.020  1.394
 ADU  C1'  C2'   single  1.527  0.020  1.527
 ADU  C1'  H1'   single  0.970  0.020  1.090
 ADU  O4'  C4'   single  1.433  0.020  1.433
 ADU  C4'  C5'   single  1.514  0.020  1.514
 ADU  C4'  C3'   single  1.535  0.020  1.535
 ADU  C4'  H4'   single  0.970  0.020  1.090
 ADU  C5'  O5'   single  1.404  0.020  1.404
 ADU  C5'  H5'1  single  0.970  0.020  1.090
 ADU  C5'  H5'2  single  0.970  0.020  1.090
 ADU  O5'  HO5'  single  0.850  0.020  0.980
 ADU  C3'  N3'   single  1.441  0.020  1.441
 ADU  C3'  C2'   single  1.535  0.020  1.535
 ADU  C3'  H3'   single  0.970  0.020  1.090
 ADU  N3'  C8'   single  1.347  0.020  1.347
 ADU  N3'  HN3'  single  0.860  0.020  1.020
 ADU  C8'  O8'   double  1.223  0.020  1.223
 ADU  C8'  C9'   single  1.507  0.020  1.507
 ADU  C9'  H9'1  single  0.970  0.020  1.090
 ADU  C9'  H9'2  single  0.970  0.020  1.090
 ADU  C9'  H9'3  single  0.970  0.020  1.090
 ADU  C2'  O2'   single  1.393  0.020  1.393
 ADU  C2'  H2'   single  0.970  0.020  1.090
 ADU  O2'  HO2'  single  0.850  0.020  0.980

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
 ADU  C1'   N1   C6    119.62  3.000
 ADU  C1'   N1   C2    119.33  3.000
 ADU  C6    N1   C2    121.05  3.000
 ADU  N3    C2   O2    122.07  3.000
 ADU  N3    C2   N1    114.48  3.000
 ADU  O2    C2   N1    123.45  3.000
 ADU  HN3   N3   C4    116.74  3.000
 ADU  HN3   N3   C2    115.05  3.000
 ADU  C4    N3   C2    128.21  3.000
 ADU  C5    C4   O4    125.96  3.000
 ADU  C5    C4   N3    113.42  3.000
 ADU  O4    C4   N3    120.62  3.000
 ADU  H5    C5   C6    120.75  3.000
 ADU  H5    C5   C4    119.76  3.000
 ADU  C6    C5   C4    119.50  3.000
 ADU  H6    C6   C5    120.61  3.000
 ADU  H6    C6   N1    116.04  3.000
 ADU  C5    C6   N1    123.34  3.000
 ADU  H1'   C1'  C2'   110.06  3.000
 ADU  H1'   C1'  O4'   111.59  3.000
 ADU  C2'   C1'  O4'   106.11  3.000
 ADU  H1'   C1'  N1    106.47  3.000
 ADU  C2'   C1'  N1    113.47  3.000
 ADU  O4'   C1'  N1    109.23  3.000
 ADU  C4'   O4'  C1'   110.99  3.000
 ADU  H4'   C4'  C3'   111.20  3.000
 ADU  H4'   C4'  C5'   108.95  3.000
 ADU  C3'   C4'  C5'   111.57  3.000
 ADU  H4'   C4'  O4'   107.82  3.000
 ADU  C3'   C4'  O4'   106.47  3.000
 ADU  C5'   C4'  O4'   110.76  3.000
 ADU  H5'2  C5'  H5'1  106.69  3.000
 ADU  H5'2  C5'  O5'   112.25  3.000
 ADU  H5'1  C5'  O5'   111.85  3.000
 ADU  H5'2  C5'  C4'   107.13  3.000
 ADU  H5'1  C5'  C4'   110.10  3.000
 ADU  O5'   C5'  C4'   108.69  3.000
 ADU  HO5'  O5'  C5'   108.29  3.000
 ADU  H3'   C3'  C2'   111.07  3.000
 ADU  H3'   C3'  N3'   110.14  3.000
 ADU  C2'   C3'  N3'   110.04  3.000
 ADU  H3'   C3'  C4'   110.76  3.000
 ADU  C2'   C3'  C4'   101.44  3.000
 ADU  N3'   C3'  C4'   113.12  3.000
 ADU  HN3'  N3'  C8'   118.56  3.000
 ADU  HN3'  N3'  C3'   117.85  3.000
 ADU  C8'   N3'  C3'   121.66  3.000
 ADU  C9'   C8'  O8'   122.32  3.000
 ADU  C9'   C8'  N3'   115.56  3.000
 ADU  O8'   C8'  N3'   122.12  3.000
 ADU  H9'3  C9'  H9'2  108.58  3.000
 ADU  H9'3  C9'  H9'1  108.44  3.000
 ADU  H9'2  C9'  H9'1  107.32  3.000
 ADU  H9'3  C9'  C8'   113.48  3.000
 ADU  H9'2  C9'  C8'   109.55  3.000
 ADU  H9'1  C9'  C8'   109.29  3.000
 ADU  H2'   C2'  O2'   111.36  3.000
 ADU  H2'   C2'  C3'   107.60  3.000
 ADU  O2'   C2'  C3'   116.36  3.000
 ADU  H2'   C2'  C1'   109.97  3.000
 ADU  O2'   C2'  C1'   109.24  3.000
 ADU  C3'   C2'  C1'   101.84  3.000
 ADU  HO2'  O2'  C2'   109.03  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
 ADU  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 ADU  CONST_02  C5    C4   N3   C2     0.00   0.0  0
 ADU  CONST_03  C6    N1   C2   N3     0.00   0.0  0
 ADU  CONST_04  C1'   N1   C2   N3   180.00   0.0  0
 ADU  CONST_05  O4    C4   N3   C2   180.00   0.0  0
 ADU  CONST_06  C6    N1   C2   O2   180.00   0.0  0
 ADU  CONST_07  C1'   N1   C2   O2     0.00   0.0  0
 ADU  CONST_08  C4    N3   C2   O2   180.00   0.0  0
 ADU  CONST_09  HN3   N3   C2   N1   180.00   0.0  0
 ADU  CONST_10  O8'   C8'  N3'  C3'    0.00   0.0  0
 ADU  CONST_11  C9'   C8'  N3'  C3'  180.00   0.0  0
 ADU  CONST_12  HN3'  N3'  C8'  O8'  180.00   0.0  0
 ADU  Var_01    H9'1  C9'  C8'  N3'  117.77  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
 ADU  chir_01  C1'  N1   O4'  C2'  positiv
 ADU  chir_02  C4'  O4'  C3'  C5'  negativ
 ADU  chir_03  C3'  N3'  C2'  C4'  negativ
 ADU  chir_04  C2'  O2'  C1'  C3'  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
 ADU  plan-1  N1    0.020
 ADU  plan-1  C2    0.020
 ADU  plan-1  O2    0.020
 ADU  plan-1  N3    0.020
 ADU  plan-1  C4    0.020
 ADU  plan-1  O4    0.020
 ADU  plan-1  C5    0.020
 ADU  plan-1  C6    0.020
 ADU  plan-1  C1'   0.020
 ADU  plan-1  HN3   0.020
 ADU  plan-1  H5    0.020
 ADU  plan-1  H6    0.020
 ADU  plan-2  C3'   0.020
 ADU  plan-2  N3'   0.020
 ADU  plan-2  C8'   0.020
 ADU  plan-2  O8'   0.020
 ADU  plan-2  C9'   0.020
 ADU  plan-2  HN3'  0.020

