# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 13:19:32 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 5-[(E)-2-bromoethenyl]-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=C\Br)C(=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
 BVD  BVD  5-[(E)-2-bromoethenyl]-2'-deoxyuridine  ligand  32  19  .  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_BVD
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
 BVD  O5'   O   OH1   0  -0.672  -1.3599   2.2472   5.1853
 BVD  C5'   C   CH2   0  -0.165  -0.3724   1.2439   5.1971
 BVD  C4'   C   CH1   0   0.020  -0.8835   0.0288   4.4637
 BVD  O4'   O   O2    0  -0.488  -1.0509   0.3259   3.0853
 BVD  C1'   C   CH1   0   0.217  -0.7613  -0.7856   2.2920
 BVD  N1    N   NR6   0  -0.569   0.0710  -0.3620   1.1595
 BVD  C6    C   CR16  0   0.077  -0.4388  -0.4270  -0.0970
 BVD  C2    C   CR6   0   0.748   1.3326   0.1546   1.3824
 BVD  O2    O   O     0  -0.458   1.8344   0.2392   2.4802
 BVD  N3    N   NR16  0  -0.733   1.9833   0.5641   0.2493
 BVD  C4    C   CR6   0   0.560   1.5446   0.5250  -1.0613
 BVD  O4    O   O     0  -0.445   2.2603   0.9327  -1.9559
 BVD  C5    C   CR6   0  -0.160   0.2110  -0.0272  -1.2174
 BVD  C5A   C   C1    0  -0.180  -0.4586  -0.1687  -2.5009
 BVD  C5B   C   C1    0  -0.420   0.0122   0.1822  -3.6963
 BVD  BR    BR  BR    0  -0.066  -1.0107  -0.0868  -5.2603
 BVD  C2'   C   CH2   0  -0.561  -0.1624  -1.8623   3.2006
 BVD  C3'   C   CH1   0   0.022   0.0793  -1.1571   4.5356
 BVD  O3'   O   OH1   0  -0.668  -0.2297  -1.9255   5.6706
 BVD  HO5'  H   HOH1  0   0.457  -1.0221   3.0056   5.6695
 BVD  H5'1  H   HCH2  0   0.203   0.5591   1.5756   4.7212
 BVD  H5'2  H   HCH2  0   0.204  -0.1219   0.9298   6.2186
 BVD  H4'   H   HCH1  0   0.229  -1.8486  -0.2802   4.8920
 BVD  H1'   H   HCH1  0   0.258  -1.6723  -1.1634   1.8220
 BVD  H6    H   HCR6  0   0.331  -1.4371  -0.8391  -0.1646
 BVD  HN3   H   HNR6  0   0.431   2.9086   0.9478   0.4017
 BVD  H5A   H   H     0   0.278  -1.4469  -0.6130  -2.4363
 BVD  H5B   H   H     0   0.311   0.9765   0.6309  -3.8789
 BVD  H2'1  H   HCH2  0   0.270  -0.9103  -2.6440   3.3436
 BVD  H2'2  H   HCH2  0   0.278   0.7274  -2.3319   2.7840
 BVD  H3'   H   HCH1  0   0.234   1.1097  -0.7944   4.5842
 BVD  HO3'  H   HOH1  0   0.457   0.4989  -2.5320   5.8315

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
 BVD  O5'  C5'   single  1.408  0.020  1.408
 BVD  O5'  HO5'  single  0.850  0.020  0.980
 BVD  C5'  C4'   single  1.509  0.020  1.509
 BVD  C5'  H5'1  single  0.970  0.020  1.090
 BVD  C5'  H5'2  single  0.970  0.020  1.090
 BVD  C4'  O4'   single  1.420  0.020  1.420
 BVD  C4'  C3'   single  1.529  0.020  1.529
 BVD  C4'  H4'   single  0.970  0.020  1.090
 BVD  O4'  C1'   single  1.396  0.020  1.396
 BVD  C1'  N1    single  1.468  0.020  1.468
 BVD  C1'  C2'   single  1.531  0.020  1.531
 BVD  C1'  H1'   single  0.970  0.020  1.090
 BVD  N1   C6    single  1.358  0.020  1.358
 BVD  N1   C2    single  1.381  0.020  1.381
 BVD  C6   C5    double  1.355  0.020  1.355
 BVD  C6   H6    single  0.930  0.020  1.080
 BVD  C2   O2    double  1.210  0.020  1.210
 BVD  C2   N3    single  1.369  0.020  1.369
 BVD  N3   C4    single  1.383  0.020  1.383
 BVD  N3   HN3   single  0.860  0.020  1.020
 BVD  C4   O4    double  1.216  0.020  1.216
 BVD  C4   C5    single  1.452  0.020  1.452
 BVD  C5   C5A   single  1.455  0.020  1.455
 BVD  C5A  C5B   double  1.332  0.020  1.332
 BVD  C5A  H5A   single  0.930  0.020  1.080
 BVD  C5B  BR    single  1.888  0.020  1.888
 BVD  C5B  H5B   single  0.930  0.020  1.080
 BVD  C2'  C3'   single  1.529  0.020  1.529
 BVD  C2'  H2'1  single  0.970  0.020  1.090
 BVD  C2'  H2'2  single  0.970  0.020  1.090
 BVD  C3'  O3'   single  1.405  0.020  1.405
 BVD  C3'  H3'   single  0.970  0.020  1.090
 BVD  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
 BVD  HO5'  O5'  C5'   108.16  3.000
 BVD  H5'2  C5'  H5'1  107.24  3.000
 BVD  H5'2  C5'  C4'   107.41  3.000
 BVD  H5'1  C5'  C4'   108.68  3.000
 BVD  H5'2  C5'  O5'   111.82  3.000
 BVD  H5'1  C5'  O5'   112.11  3.000
 BVD  C4'   C5'  O5'   109.41  3.000
 BVD  H4'   C4'  C3'   108.43  3.000
 BVD  H4'   C4'  O4'   109.47  3.000
 BVD  C3'   C4'  O4'   106.39  3.000
 BVD  H4'   C4'  C5'   109.52  3.000
 BVD  C3'   C4'  C5'   112.86  3.000
 BVD  O4'   C4'  C5'   110.08  3.000
 BVD  C1'   O4'  C4'   111.14  3.000
 BVD  H1'   C1'  C2'   109.77  3.000
 BVD  H1'   C1'  N1    103.92  3.000
 BVD  C2'   C1'  N1    116.04  3.000
 BVD  H1'   C1'  O4'   110.30  3.000
 BVD  C2'   C1'  O4'   107.69  3.000
 BVD  N1    C1'  O4'   109.05  3.000
 BVD  C2    N1   C6    120.67  3.000
 BVD  C2    N1   C1'   120.08  3.000
 BVD  C6    N1   C1'   119.17  3.000
 BVD  H6    C6   C5    120.19  3.000
 BVD  H6    C6   N1    114.99  3.000
 BVD  C5    C6   N1    124.82  3.000
 BVD  N3    C2   O2    122.19  3.000
 BVD  N3    C2   N1    114.35  3.000
 BVD  O2    C2   N1    123.45  3.000
 BVD  HN3   N3   C4    116.30  3.000
 BVD  HN3   N3   C2    115.01  3.000
 BVD  C4    N3   C2    128.69  3.000
 BVD  C5    C4   O4    126.09  3.000
 BVD  C5    C4   N3    113.84  3.000
 BVD  O4    C4   N3    120.08  3.000
 BVD  C5A   C5   C4    123.69  3.000
 BVD  C5A   C5   C6    118.69  3.000
 BVD  C4    C5   C6    117.62  3.000
 BVD  H5A   C5A  C5B   118.89  3.000
 BVD  H5A   C5A  C5    113.98  3.000
 BVD  C5B   C5A  C5    127.13  3.000
 BVD  H5B   C5B  BR    113.78  3.000
 BVD  H5B   C5B  C5A   125.26  3.000
 BVD  BR    C5B  C5A   120.96  3.000
 BVD  H2'2  C2'  H2'1  107.53  3.000
 BVD  H2'2  C2'  C3'   113.81  3.000
 BVD  H2'1  C2'  C3'   108.92  3.000
 BVD  H2'2  C2'  C1'   113.33  3.000
 BVD  H2'1  C2'  C1'   108.27  3.000
 BVD  C3'   C2'  C1'   104.81  3.000
 BVD  H3'   C3'  O3'   110.65  3.000
 BVD  H3'   C3'  C2'   109.92  3.000
 BVD  O3'   C3'  C2'   114.73  3.000
 BVD  H3'   C3'  C4'   109.76  3.000
 BVD  O3'   C3'  C4'   108.88  3.000
 BVD  C2'   C3'  C4'   102.54  3.000
 BVD  HO3'  O3'  C3'   108.27  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
 BVD  CONST_01  N3   C2   N1   C1'  180.00   0.0  0
 BVD  CONST_02  C4   N3   C2   N1     0.00   0.0  0
 BVD  CONST_03  N3   C2   N1   C6     0.00   0.0  0
 BVD  CONST_04  C5   C4   N3   C2     0.00   0.0  0
 BVD  CONST_05  O2   C2   N1   C1'    0.00   0.0  0
 BVD  CONST_06  O2   C2   N1   C6   180.00   0.0  0
 BVD  CONST_07  O4   C4   N3   C2   180.00   0.0  0
 BVD  CONST_08  C4   N3   C2   O2   180.00   0.0  0
 BVD  CONST_09  HN3  N3   C2   N1   180.00   0.0  0
 BVD  CONST_10  BR   C5B  C5A  C5   180.00   0.0  0
 BVD  CONST_11  H5B  C5B  C5A  C5     0.00   0.0  0
 BVD  CONST_12  H5A  C5A  C5B  BR     0.00   0.0  0
 BVD  Var_01    C5B  C5A  C5   C6   179.07  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
 BVD  chir_01  C4'  C5'  O4'  C3'  negativ
 BVD  chir_02  C1'  O4'  N1   C2'  negativ
 BVD  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
 BVD  plan-1  C1'  0.020
 BVD  plan-1  N1   0.020
 BVD  plan-1  C6   0.020
 BVD  plan-1  C2   0.020
 BVD  plan-1  O2   0.020
 BVD  plan-1  N3   0.020
 BVD  plan-1  C4   0.020
 BVD  plan-1  O4   0.020
 BVD  plan-1  C5   0.020
 BVD  plan-1  C5A  0.020
 BVD  plan-1  H6   0.020
 BVD  plan-1  HN3  0.020
 BVD  plan-2  C5   0.020
 BVD  plan-2  C5A  0.020
 BVD  plan-2  C5B  0.020
 BVD  plan-2  BR   0.020
 BVD  plan-2  H5A  0.020
 BVD  plan-2  H5B  0.020

