# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 12:09:28 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 5-(5-bromothiophen-2-yl)-2'-deoxyuridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](C[C@@H]1O)N2C=C(C(=O)NC2=O)c3sc(Br)cc3
#
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
 BTD  BTD  5-(5-bromothiophen-2-yl)-2'-deoxyuridine  ligand  35  22  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BTD
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
 BTD  O5'   O   OH1   0  -0.671   0.7726  -2.5441   6.0275
 BTD  C5'   C   CH2   0  -0.163   0.3976  -1.1889   6.0923
 BTD  C4'   C   CH1   0   0.018   1.1985  -0.3988   5.0881
 BTD  O4'   O   O2    0  -0.488   0.8524  -0.7958   3.7710
 BTD  C1'   C   CH1   0   0.219   0.9583   0.2786   2.8851
 BTD  N1    N   NR6   0  -0.568  -0.1937   0.2636   1.9792
 BTD  C6    C   CR16  0   0.075   0.0037  -0.0271   0.6647
 BTD  C2    C   CR6   0   0.749  -1.4658   0.4627   2.4767
 BTD  O2    O   O     0  -0.460  -1.6976   0.6994   3.6407
 BTD  N3    N   NR16  0  -0.734  -2.4606   0.3747   1.5384
 BTD  C4    C   CR6   0   0.556  -2.3511   0.1069   0.1872
 BTD  O4    O   O     0  -0.438  -3.3405   0.0616  -0.5154
 BTD  C5    C   CR6   0  -0.191  -0.9816  -0.1015  -0.2578
 BTD  C55   C   CR5   0  -0.201  -0.7051  -0.3739  -1.6620
 BTD  C44   C   CR15  0  -0.210  -1.4081  -1.1366  -2.5511
 BTD  C33   C   CR15  0  -0.138  -0.8169  -1.1927  -3.8397
 BTD  C22   C   CR5   0  -0.354   0.3256  -0.4586  -3.9056
 BTD  S11   S   S2    0   0.280   0.6886   0.3190  -2.4196
 BTD  BR    BR  BR    0   0.022   1.4443  -0.2445  -5.3733
 BTD  C2'   C   CH2   0  -0.562   1.1447   1.5514   3.7160
 BTD  C3'   C   CH1   0   0.025   0.9341   1.1052   5.1636
 BTD  O3'   O   OH1   0  -0.668   1.8212   1.6772   6.0907
 BTD  HO5'  H   HOH1  0   0.457   0.2877  -3.0220   6.7061
 BTD  H5'1  H   HCH2  0   0.200  -0.6711  -1.0456   5.8842
 BTD  H5'2  H   HCH2  0   0.205   0.5962  -0.7588   7.0823
 BTD  H4'   H   HCH1  0   0.229   2.2720  -0.5710   5.2570
 BTD  H1'   H   HCH1  0   0.257   1.8168   0.1430   2.2226
 BTD  H6    H   HCR6  0   0.327   1.0357  -0.2048   0.3916
 BTD  HN3   H   HNR6  0   0.431  -3.3981   0.5270   1.8911
 BTD  H44   H   HCR5  0   0.271  -2.3165  -1.6610  -2.2972
 BTD  H33   H   HCR5  0   0.289  -1.2220  -1.7568  -4.6670
 BTD  H2'1  H   HCH2  0   0.270   2.1740   1.8931   3.5949
 BTD  H2'2  H   HCH2  0   0.278   0.4921   2.3667   3.4079
 BTD  H3'   H   HCH1  0   0.232  -0.1030   1.2838   5.4622
 BTD  HO3'  H   HOH1  0   0.458   1.5140   2.5655   6.2940

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
 BTD  O5'  C5'   single    1.408  0.020  1.408
 BTD  O5'  HO5'  single    0.850  0.020  0.980
 BTD  C5'  C4'   single    1.508  0.020  1.508
 BTD  C5'  H5'1  single    0.970  0.020  1.090
 BTD  C5'  H5'2  single    0.970  0.020  1.090
 BTD  C4'  O4'   single    1.418  0.020  1.418
 BTD  C4'  C3'   single    1.529  0.020  1.529
 BTD  C4'  H4'   single    0.970  0.020  1.090
 BTD  O4'  C1'   single    1.397  0.020  1.397
 BTD  C1'  N1    single    1.466  0.020  1.466
 BTD  C1'  C2'   single    1.531  0.020  1.531
 BTD  C1'  H1'   single    0.970  0.020  1.090
 BTD  N1   C6    single    1.361  0.020  1.361
 BTD  N1   C2    single    1.380  0.020  1.380
 BTD  C6   C5    double    1.352  0.020  1.352
 BTD  C6   H6    single    0.930  0.020  1.080
 BTD  C2   O2    double    1.210  0.020  1.210
 BTD  C2   N3    single    1.370  0.020  1.370
 BTD  N3   C4    single    1.382  0.020  1.382
 BTD  N3   HN3   single    0.860  0.020  1.020
 BTD  C4   O4    double    1.214  0.020  1.214
 BTD  C4   C5    single    1.455  0.020  1.455
 BTD  C5   C55   single    1.457  0.020  1.457
 BTD  C55  C44   aromatic  1.366  0.020  1.366
 BTD  C55  S11   aromatic  1.731  0.020  1.731
 BTD  C44  C33   aromatic  1.419  0.020  1.419
 BTD  C44  H44   single    0.930  0.020  1.080
 BTD  C33  C22   aromatic  1.360  0.020  1.360
 BTD  C33  H33   single    0.930  0.020  1.080
 BTD  C22  S11   aromatic  1.716  0.020  1.716
 BTD  C22  BR    single    1.858  0.020  1.858
 BTD  C2'  C3'   single    1.529  0.020  1.529
 BTD  C2'  H2'1  single    0.970  0.020  1.090
 BTD  C2'  H2'2  single    0.970  0.020  1.090
 BTD  C3'  O3'   single    1.405  0.020  1.405
 BTD  C3'  H3'   single    0.970  0.020  1.090
 BTD  O3'  HO3'  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
 BTD  HO5'  O5'  C5'   108.16  3.000
 BTD  H5'2  C5'  H5'1  107.21  3.000
 BTD  H5'2  C5'  C4'   107.41  3.000
 BTD  H5'1  C5'  C4'   108.81  3.000
 BTD  H5'2  C5'  O5'   111.75  3.000
 BTD  H5'1  C5'  O5'   112.10  3.000
 BTD  C4'   C5'  O5'   109.41  3.000
 BTD  H4'   C4'  C3'   108.36  3.000
 BTD  H4'   C4'  O4'   109.69  3.000
 BTD  C3'   C4'  O4'   106.20  3.000
 BTD  H4'   C4'  C5'   109.51  3.000
 BTD  C3'   C4'  C5'   112.99  3.000
 BTD  O4'   C4'  C5'   110.00  3.000
 BTD  C1'   O4'  C4'   110.81  3.000
 BTD  H1'   C1'  C2'   109.65  3.000
 BTD  H1'   C1'  N1    103.98  3.000
 BTD  C2'   C1'  N1    116.08  3.000
 BTD  H1'   C1'  O4'   110.40  3.000
 BTD  C2'   C1'  O4'   107.73  3.000
 BTD  N1    C1'  O4'   108.94  3.000
 BTD  C2    N1   C6    120.85  3.000
 BTD  C2    N1   C1'   120.01  3.000
 BTD  C6    N1   C1'   119.03  3.000
 BTD  H6    C6   C5    120.91  3.000
 BTD  H6    C6   N1    114.66  3.000
 BTD  C5    C6   N1    124.42  3.000
 BTD  N3    C2   O2    122.15  3.000
 BTD  N3    C2   N1    114.39  3.000
 BTD  O2    C2   N1    123.46  3.000
 BTD  HN3   N3   C4    116.29  3.000
 BTD  HN3   N3   C2    115.07  3.000
 BTD  C4    N3   C2    128.64  3.000
 BTD  C5    C4   O4    125.77  3.000
 BTD  C5    C4   N3    113.67  3.000
 BTD  O4    C4   N3    120.56  3.000
 BTD  C55   C5   C4    120.01  3.000
 BTD  C55   C5   C6    121.99  3.000
 BTD  C4    C5   C6    118.00  3.000
 BTD  S11   C55  C44   110.67  3.000
 BTD  S11   C55  C5    119.99  3.000
 BTD  C44   C55  C5    129.35  3.000
 BTD  H44   C44  C33   123.04  3.000
 BTD  H44   C44  C55   123.46  3.000
 BTD  C33   C44  C55   113.50  3.000
 BTD  H33   C33  C22   124.05  3.000
 BTD  H33   C33  C44   124.05  3.000
 BTD  C22   C33  C44   111.89  3.000
 BTD  BR    C22  S11   120.30  3.000
 BTD  BR    C22  C33   127.34  3.000
 BTD  S11   C22  C33   112.36  3.000
 BTD  C22   S11  C55    91.56  3.000
 BTD  H2'2  C2'  H2'1  107.43  3.000
 BTD  H2'2  C2'  C3'   113.81  3.000
 BTD  H2'1  C2'  C3'   109.04  3.000
 BTD  H2'2  C2'  C1'   113.32  3.000
 BTD  H2'1  C2'  C1'   108.35  3.000
 BTD  C3'   C2'  C1'   104.73  3.000
 BTD  H3'   C3'  O3'   110.62  3.000
 BTD  H3'   C3'  C2'   109.95  3.000
 BTD  O3'   C3'  C2'   114.77  3.000
 BTD  H3'   C3'  C4'   109.76  3.000
 BTD  O3'   C3'  C4'   108.90  3.000
 BTD  C2'   C3'  C4'   102.50  3.000
 BTD  HO3'  O3'  C3'   108.30  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
 BTD  CONST_01  C22  C33  C44  C55    0.00   0.0  0
 BTD  CONST_02  C33  C22  S11  C55    0.00   0.0  0
 BTD  CONST_03  C22  S11  C55  C44    0.00   0.0  0
 BTD  CONST_04  S11  C22  C33  C44    0.00   0.0  0
 BTD  CONST_05  S11  C55  C44  C33    0.00   0.0  0
 BTD  CONST_06  C33  C44  C55  C5   180.00   0.0  0
 BTD  CONST_07  C22  S11  C55  C5   180.00   0.0  0
 BTD  CONST_08  N3   C2   N1   C1'  180.00   0.0  0
 BTD  CONST_09  C4   N3   C2   N1     0.00   0.0  0
 BTD  CONST_10  N3   C2   N1   C6     0.00   0.0  0
 BTD  CONST_11  C5   C4   N3   C2     0.00   0.0  0
 BTD  CONST_12  BR   C22  S11  C55  180.00   0.0  0
 BTD  CONST_13  BR   C22  C33  C44  180.00   0.0  0
 BTD  CONST_14  O2   C2   N1   C1'    0.00   0.0  0
 BTD  CONST_15  O2   C2   N1   C6   180.00   0.0  0
 BTD  CONST_16  O4   C4   N3   C2   180.00   0.0  0
 BTD  CONST_17  C4   N3   C2   O2   180.00   0.0  0
 BTD  CONST_18  H44  C44  C55  C5     0.00   0.0  0
 BTD  CONST_19  H33  C33  C44  C55  180.00   0.0  0
 BTD  CONST_20  HN3  N3   C2   N1   180.00   0.0  0
 BTD  Var_01    C44  C55  C5   C6   141.60  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
 BTD  chir_01  C4'  C5'  O4'  C3'  negativ
 BTD  chir_02  C1'  O4'  N1   C2'  negativ
 BTD  chir_03  C3'  O3'  C4'  C2'  positiv

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
 BTD  plan-1  C5   0.020
 BTD  plan-1  C55  0.020
 BTD  plan-1  C44  0.020
 BTD  plan-1  C33  0.020
 BTD  plan-1  C22  0.020
 BTD  plan-1  S11  0.020
 BTD  plan-1  BR   0.020
 BTD  plan-1  H44  0.020
 BTD  plan-1  H33  0.020
 BTD  plan-2  C1'  0.020
 BTD  plan-2  N1   0.020
 BTD  plan-2  C6   0.020
 BTD  plan-2  C2   0.020
 BTD  plan-2  O2   0.020
 BTD  plan-2  N3   0.020
 BTD  plan-2  C4   0.020
 BTD  plan-2  O4   0.020
 BTD  plan-2  C5   0.020
 BTD  plan-2  C55  0.020
 BTD  plan-2  H6   0.020
 BTD  plan-2  HN3  0.020

