# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 23:02:11 2021
#   Inital geometry file: a 114 line input string
#   Ligand name: a 2 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=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
 BUP  BUP  '5-bromouridine 5'-(tetrahydrogen triphosphate)'  ligand  44  30  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_BUP
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
 BUP  BR    BR  BR    0   0.011   0.2103  -48.2025   7.2406
 BUP  C1    C   CR6   0  -0.368   1.5611  -47.0159   6.7442
 BUP  N1    N   NR16  0  -0.734   3.5694  -46.5546   5.6004
 BUP  P1    P   P     0   1.469  -1.7146  -41.3530  10.3983
 BUP  C2    C   CR16  0   0.123   1.5745  -45.7401   7.1696
 BUP  N2    N   NR6   0  -0.572   2.5516  -44.8647   6.8150
 BUP  P2    P   P     0   1.482  -1.3170  -39.0160   8.6189
 BUP  C3    C   CR6   0   0.754   3.6057  -45.2503   6.0114
 BUP  O3    O   O2    0  -0.491   1.6758  -43.3046   8.3347
 BUP  P3    P   P     0   1.483  -3.3125  -37.5739  10.2583
 BUP  C4    C   CR6   0   0.600   2.6171  -47.5164   5.8868
 BUP  O4    O   OH1   0  -0.649   2.7533  -41.2286   6.3850
 BUP  C5    C   CH1   0   0.012   0.6662  -42.3392   6.4671
 BUP  O5    O   OH1   0  -0.683   0.0964  -41.1362   6.0158
 BUP  C6    C   CH1   0  -0.060   2.1608  -42.4755   6.1802
 BUP  O6    O   O2    0  -0.561  -0.8143  -42.5799   9.9346
 BUP  C7    C   CH1   0   0.176   2.5797  -43.4618   7.2859
 BUP  O7    O   O2    0  -0.703  -0.9182  -40.0734   9.7782
 BUP  C8    C   CH1   0  -0.004   0.6332  -42.3992   7.9901
 BUP  O8    O   OH1   0  -0.701  -1.3025  -41.3177  11.9216
 BUP  C9    C   CH2   0  -0.229  -0.6937  -42.8809   8.5403
 BUP  O9    O   O     0  -0.675  -3.1370  -41.3750  10.0301
 BUP  O10   O   O2    0  -0.681  -2.7751  -38.4917   9.0354
 BUP  O11   O   OH1   0  -0.757  -1.7350  -39.8600   7.3649
 BUP  O12   O   O     0  -0.656  -0.2601  -38.0069   8.4999
 BUP  O13   O   OH1   0  -0.723  -2.4453  -36.2469  10.2169
 BUP  O14   O   OH1   0  -0.741  -2.6795  -38.3572  11.4845
 BUP  O15   O   O     0  -0.670  -4.7715  -37.4296  10.1761
 BUP  HN1   H   HNR6  0   0.438   4.3404  -46.8437   5.0094
 BUP  H2    H   HCR6  0   0.326   0.8072  -45.3591   7.8253
 BUP  HO4   H   HOH1  0   0.465   3.6835  -41.2884   6.1442
 BUP  H5    H   HCH1  0   0.276   0.1344  -43.2012   6.0447
 BUP  HO5   H   HOH1  0   0.496  -0.1217  -41.2063   5.0785
 BUP  H6    H   HCH1  0   0.283   2.3547  -42.8698   5.1782
 BUP  H7    H   HCH1  0   0.301   3.5950  -43.2671   7.6358
 BUP  H8    H   HCH1  0   0.271   0.8751  -41.4102   8.3961
 BUP  HO8   H   HOH1  0   0.510  -1.9828  -40.9691  12.5140
 BUP  H9    H   HCH2  0   0.281  -0.7865  -43.9627   8.4391
 BUP  H9A   H   HCH2  0   0.263  -1.5200  -42.4490   7.9700
 BUP  HO11  H   HOH1  0   0.512  -1.0104  -40.2858   6.8208
 BUP  HO13  H   HOH1  0   0.508  -2.7946  -35.5517   9.6419
 BUP  HO14  H   HOH1  0   0.515  -2.9401  -38.0294  12.3575
 BUP  O1    O   O     0  -0.428   2.7033  -48.6417   5.4470
 BUP  O2    O   O     0  -0.469   4.4906  -44.4844   5.6952

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
 BUP  BR   C1    single  1.865  0.020  1.865
 BUP  C1   C2    double  1.345  0.020  1.345
 BUP  C1   C4    single  1.449  0.020  1.449
 BUP  N1   C3    single  1.368  0.020  1.368
 BUP  N1   C4    single  1.383  0.020  1.383
 BUP  O1   C4    double  1.211  0.020  1.211
 BUP  P1   O6    single  1.591  0.020  1.591
 BUP  P1   O7    single  1.630  0.020  1.630
 BUP  P1   O8    single  1.578  0.020  1.578
 BUP  P1   O9    double  1.469  0.020  1.469
 BUP  C2   N2    single  1.359  0.020  1.359
 BUP  N2   C3    single  1.380  0.020  1.380
 BUP  N2   C7    single  1.480  0.020  1.480
 BUP  O2   C3    double  1.212  0.020  1.212
 BUP  P2   O7    single  1.619  0.020  1.619
 BUP  P2   O10   single  1.605  0.020  1.605
 BUP  P2   O11   single  1.568  0.020  1.568
 BUP  P2   O12   double  1.466  0.020  1.466
 BUP  O3   C7    single  1.393  0.020  1.393
 BUP  O3   C8    single  1.423  0.020  1.423
 BUP  P3   O10   single  1.621  0.020  1.621
 BUP  P3   O13   single  1.586  0.020  1.586
 BUP  P3   O14   single  1.587  0.020  1.587
 BUP  P3   O15   double  1.468  0.020  1.468
 BUP  O4   C6    single  1.396  0.020  1.396
 BUP  C5   O5    single  1.406  0.020  1.406
 BUP  C5   C6    single  1.528  0.020  1.528
 BUP  C5   C8    single  1.525  0.020  1.525
 BUP  C6   C7    single  1.540  0.020  1.540
 BUP  O6   C9    single  1.432  0.020  1.432
 BUP  C8   C9    single  1.515  0.020  1.515
 BUP  N1   HN1   single  0.860  0.020  1.020
 BUP  C2   H2    single  0.930  0.020  1.080
 BUP  O4   HO4   single  0.850  0.020  0.980
 BUP  C5   H5    single  0.970  0.020  1.090
 BUP  O5   HO5   single  0.850  0.020  0.980
 BUP  C6   H6    single  0.970  0.020  1.090
 BUP  C7   H7    single  0.970  0.020  1.090
 BUP  C8   H8    single  0.970  0.020  1.090
 BUP  O8   HO8   single  0.850  0.020  0.980
 BUP  C9   H9    single  0.970  0.020  1.090
 BUP  C9   H9A   single  0.970  0.020  1.090
 BUP  O11  HO11  single  0.850  0.020  0.980
 BUP  O13  HO13  single  0.850  0.020  0.980
 BUP  O14  HO14  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
 BUP  C4    C1   C2   120.49  3.000
 BUP  C4    C1   BR   117.74  3.000
 BUP  C2    C1   BR   121.77  3.000
 BUP  HN1   N1   C4   116.49  3.000
 BUP  HN1   N1   C3   115.27  3.000
 BUP  C4    N1   C3   128.24  3.000
 BUP  O9    P1   O8   119.66  3.000
 BUP  O9    P1   O7   112.92  3.000
 BUP  O8    P1   O7   102.83  3.000
 BUP  O9    P1   O6   117.59  3.000
 BUP  O8    P1   O6    98.67  3.000
 BUP  O7    P1   O6   102.59  3.000
 BUP  H2    C2   N2   116.26  3.000
 BUP  H2    C2   C1   121.34  3.000
 BUP  N2    C2   C1   122.39  3.000
 BUP  C7    N2   C3   115.82  3.000
 BUP  C7    N2   C2   122.77  3.000
 BUP  C3    N2   C2   121.40  3.000
 BUP  O12   P2   O11  119.85  3.000
 BUP  O12   P2   O10  116.82  3.000
 BUP  O11   P2   O10   98.12  3.000
 BUP  O12   P2   O7   109.27  3.000
 BUP  O11   P2   O7   106.66  3.000
 BUP  O10   P2   O7   104.56  3.000
 BUP  O2    C3   N2   122.19  3.000
 BUP  O2    C3   N1   122.91  3.000
 BUP  N2    C3   N1   114.89  3.000
 BUP  C8    O3   C7   111.39  3.000
 BUP  O15   P3   O14  119.21  3.000
 BUP  O15   P3   O13  117.37  3.000
 BUP  O14   P3   O13  102.43  3.000
 BUP  O15   P3   O10  110.05  3.000
 BUP  O14   P3   O10   99.86  3.000
 BUP  O13   P3   O10  105.84  3.000
 BUP  O1    C4   N1   121.45  3.000
 BUP  O1    C4   C1   125.98  3.000
 BUP  N1    C4   C1   112.57  3.000
 BUP  HO4   O4   C6   108.54  3.000
 BUP  H5    C5   C8   110.07  3.000
 BUP  H5    C5   C6   109.37  3.000
 BUP  C8    C5   C6   101.84  3.000
 BUP  H5    C5   O5   110.63  3.000
 BUP  C8    C5   O5   110.23  3.000
 BUP  C6    C5   O5   114.37  3.000
 BUP  HO5   O5   C5   109.96  3.000
 BUP  H6    C6   C7   112.25  3.000
 BUP  H6    C6   C5   112.17  3.000
 BUP  C7    C6   C5   100.86  3.000
 BUP  H6    C6   O4   112.41  3.000
 BUP  C7    C6   O4   110.58  3.000
 BUP  C5    C6   O4   107.94  3.000
 BUP  C9    O6   P1   119.59  3.000
 BUP  H7    C7   C6   111.65  3.000
 BUP  H7    C7   O3   110.00  3.000
 BUP  C6    C7   O3   106.96  3.000
 BUP  H7    C7   N2   106.78  3.000
 BUP  C6    C7   N2   111.93  3.000
 BUP  O3    C7   N2   109.52  3.000
 BUP  P2    O7   P1   131.67  3.000
 BUP  H8    C8   C9   110.22  3.000
 BUP  H8    C8   C5   109.25  3.000
 BUP  C9    C8   C5   113.22  3.000
 BUP  H8    C8   O3   108.82  3.000
 BUP  C9    C8   O3   110.57  3.000
 BUP  C5    C8   O3   104.54  3.000
 BUP  HO8   O8   P1   114.55  3.000
 BUP  H9A   C9   H9   106.22  3.000
 BUP  H9A   C9   C8   110.30  3.000
 BUP  H9    C9   C8   110.87  3.000
 BUP  H9A   C9   O6   111.19  3.000
 BUP  H9    C9   O6   106.97  3.000
 BUP  C8    C9   O6   111.14  3.000
 BUP  P3    O10  P2   133.02  3.000
 BUP  HO11  O11  P2   118.07  3.000
 BUP  HO13  O13  P3   114.80  3.000
 BUP  HO14  O14  P3   114.98  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
 BUP  CONST_01  C2   N2  C3   N1    0.00   0.0  0
 BUP  CONST_02  C7   N2  C3   N1  180.00   0.0  0
 BUP  CONST_03  C4   N1  C3   N2    0.00   0.0  0
 BUP  CONST_04  O2   C3  N2   C2  180.00   0.0  0
 BUP  CONST_05  C4   N1  C3   O2  180.00   0.0  0
 BUP  CONST_06  C7   N2  C3   O2    0.00   0.0  0
 BUP  CONST_07  HN1  N1  C3   N2  180.00   0.0  0
 BUP  Var_01    C8   C9  O6   P1  102.70  30.0  3
 BUP  Var_02    O10  P2  O7   P1   51.15  30.0  1
 BUP  Var_03    O6   P1  O7   P2  113.39  30.0  1
 BUP  Var_04    O13  P3  O10  P2   53.69  30.0  1
 BUP  Var_05    O7   P2  O10  P3   68.42  30.0  1

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
 BUP  chir_03  C5  O5   C6   C8  negativ
 BUP  chir_04  C6  O4   C7   C5  negativ
 BUP  chir_05  C7  O3   N2   C6  negativ
 BUP  chir_06  C8  O3   C5   C9  negativ
 BUP  chir_07  P1  O7   O8   O9  both
 BUP  chir_08  P2  O11  O10  O7  both

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
 BUP  plan-1  BR   0.020
 BUP  plan-1  C1   0.020
 BUP  plan-1  N1   0.020
 BUP  plan-1  C2   0.020
 BUP  plan-1  N2   0.020
 BUP  plan-1  C3   0.020
 BUP  plan-1  C4   0.020
 BUP  plan-1  C7   0.020
 BUP  plan-1  HN1  0.020
 BUP  plan-1  H2   0.020
 BUP  plan-1  O1   0.020
 BUP  plan-1  O2   0.020

