# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 23:36:10 2021
#   Inital geometry file: a 112 line input string
#   Ligand name: a 2 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=C(F)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
 B7P  B7P  '2'-deoxy-5-fluorouridine 5'-(tetrahydrogen triphosphate)'  ligand  43  29  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_B7P
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
 B7P  C22  C  CR16  0  -0.165   7.3226   7.2821  11.6584
 B7P  C28  C  CR6   0   0.748   7.6699   7.8037   9.3521
 B7P  O01  O  OH1   0  -0.642   3.7669   4.0921  10.4047
 B7P  C02  C  CH1   0  -0.046   4.5923   5.1678  10.7317
 B7P  C03  C  CH2   0  -0.523   5.0819   5.9226   9.5056
 B7P  C04  C  CH1   0   0.142   5.4037   7.3060  10.0685
 B7P  O05  O  O2    0  -0.505   4.6591   7.4534  11.2418
 B7P  C06  C  CH1   0  -0.013   3.8658   6.2946  11.4728
 B7P  C07  C  CH2   0  -0.213   3.6272   6.1058  12.9466
 B7P  O08  O  O2    0  -0.582   4.8759   5.8253  13.5933
 B7P  P09  P  P     0   1.415   5.0658   5.2930  15.0751
 B7P  O10  O  O     0  -0.664   6.3734   5.6474  15.6339
 B7P  O11  O  OH1   0  -0.627   3.7505   5.6481  15.8838
 B7P  O12  O  O2    0  -0.682   4.9049   3.6805  14.9821
 B7P  P13  P  P     0   1.440   3.9580   2.6477  14.2162
 B7P  O14  O  OH1   0  -0.626   2.5419   3.0007  14.8200
 B7P  O15  O  O     0  -0.733   4.0975   2.6188  12.7518
 B7P  O16  O  O2    0  -0.574   4.4301   1.2693  14.8701
 B7P  P17  P  P     0   1.471   3.9728   0.5509  16.2662
 B7P  O18  O  OH1   0  -0.677   5.1603  -0.4773  16.4624
 B7P  O19  O  O     0  -0.724   2.6044   0.0175  16.2365
 B7P  O20  O  OH1   0  -0.684   4.3111   1.7070  17.2929
 B7P  N21  N  NR6   0  -0.512   6.8389   7.4730  10.3950
 B7P  C23  C  CR6   0   0.402   8.6219   7.4280  11.9392
 B7P  F24  F  F     0  -0.228   9.0877   7.2470  13.1787
 B7P  C25  C  CR6   0   0.441   9.5826   7.8000  10.9280
 B7P  O26  O  O     0  -0.473  10.7719   7.9623  11.1059
 B7P  N27  N  NR16  0  -0.741   8.9921   7.9598   9.6902
 B7P  O29  O  O     0  -0.511   7.2716   7.9465   8.2141
 B7P  H1   H  HCR6  0   0.340   6.6143   7.0200  12.4294
 B7P  H2   H  HOH1  0   0.422   3.7585   3.4914  11.1658
 B7P  H4   H  HCH2  0   0.287   4.2726   6.0113   8.7772
 B7P  H5   H  HCH2  0   0.240   5.9324   5.4553   9.0123
 B7P  H6   H  HCH1  0   0.281   5.1596   8.1038   9.3672
 B7P  H7   H  HCH1  0   0.263   2.8736   6.4275  11.0197
 B7P  H8   H  HCH2  0   0.230   3.1839   7.0027  13.3824
 B7P  H9   H  HCH2  0   0.210   2.9142   5.2884  13.0711
 B7P  H10  H  HOH1  0   0.516   3.7368   6.5344  16.2712
 B7P  H11  H  HOH1  0   0.591   1.7827   2.6595  14.3238
 B7P  H12  H  HOH1  0   0.491   4.9738  -1.3732  16.1480
 B7P  H13  H  HOH1  0   0.523   3.7883   1.6887  18.1069
 B7P  H14  H  HNR6  0   0.441   9.6076   8.2088   8.9245
 B7P  H3   H  HCH1  0   0.253   5.4576   4.8355  11.3203

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
 B7P  O29  C28  double  1.214  0.020  1.214
 B7P  C28  N27  single  1.374  0.020  1.374
 B7P  C28  N21  single  1.374  0.020  1.374
 B7P  N27  C25  single  1.381  0.020  1.381
 B7P  C03  C04  single  1.528  0.020  1.528
 B7P  C03  C02  single  1.521  0.020  1.521
 B7P  C04  N21  single  1.481  0.020  1.481
 B7P  C04  O05  single  1.397  0.020  1.397
 B7P  N21  C22  single  1.366  0.020  1.366
 B7P  O01  C02  single  1.395  0.020  1.395
 B7P  C25  O26  double  1.213  0.020  1.213
 B7P  C25  C23  single  1.443  0.020  1.443
 B7P  C02  C06  single  1.532  0.020  1.532
 B7P  O05  C06  single  1.423  0.020  1.423
 B7P  C22  C23  double  1.337  0.020  1.337
 B7P  C06  C07  single  1.505  0.020  1.505
 B7P  C23  F24  single  1.336  0.020  1.336
 B7P  O15  P13  double  1.471  0.020  1.471
 B7P  C07  O08  single  1.434  0.020  1.434
 B7P  O08  P09  single  1.586  0.020  1.586
 B7P  P13  O12  single  1.597  0.020  1.597
 B7P  P13  O14  single  1.579  0.020  1.579
 B7P  P13  O16  single  1.597  0.020  1.597
 B7P  O12  P09  single  1.623  0.020  1.623
 B7P  O16  P17  single  1.635  0.020  1.635
 B7P  P09  O10  double  1.465  0.020  1.465
 B7P  P09  O11  single  1.584  0.020  1.584
 B7P  P17  O19  double  1.469  0.020  1.469
 B7P  P17  O18  single  1.583  0.020  1.583
 B7P  P17  O20  single  1.583  0.020  1.583
 B7P  C22  H1   single  0.930  0.020  1.080
 B7P  O01  H2   single  0.850  0.020  0.980
 B7P  C02  H3   single  0.970  0.020  1.090
 B7P  C03  H4   single  0.970  0.020  1.090
 B7P  C03  H5   single  0.970  0.020  1.090
 B7P  C04  H6   single  0.970  0.020  1.090
 B7P  C06  H7   single  0.970  0.020  1.090
 B7P  C07  H8   single  0.970  0.020  1.090
 B7P  C07  H9   single  0.970  0.020  1.090
 B7P  O11  H10  single  0.850  0.020  0.980
 B7P  O14  H11  single  0.850  0.020  0.980
 B7P  O18  H12  single  0.850  0.020  0.980
 B7P  O20  H13  single  0.850  0.020  0.980
 B7P  N27  H14  single  0.860  0.020  1.020

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
 B7P  H1   C22  C23  120.94  3.000
 B7P  H1   C22  N21  117.53  3.000
 B7P  C23  C22  N21  121.52  3.000
 B7P  O29  C28  N27  122.22  3.000
 B7P  N27  C28  N21  115.00  3.000
 B7P  O29  C28  N21  122.78  3.000
 B7P  H2   O01  C02  107.39  3.000
 B7P  H3   C02  C06  109.69  3.000
 B7P  H3   C02  C03  109.19  3.000
 B7P  C06  C02  C03  100.23  3.000
 B7P  H3   C02  O01  111.02  3.000
 B7P  C06  C02  O01  113.58  3.000
 B7P  C03  C02  O01  112.60  3.000
 B7P  H5   C03  H4   108.15  3.000
 B7P  H5   C03  C04  113.03  3.000
 B7P  H4   C03  C04  109.16  3.000
 B7P  H5   C03  C02  113.81  3.000
 B7P  H4   C03  C02  109.83  3.000
 B7P  C04  C03  C02  102.72  3.000
 B7P  H6   C04  N21  106.04  3.000
 B7P  H6   C04  O05  110.10  3.000
 B7P  N21  C04  O05  108.62  3.000
 B7P  H6   C04  C03  112.25  3.000
 B7P  O05  C04  C03  107.01  3.000
 B7P  N21  C04  C03  112.79  3.000
 B7P  C06  O05  C04  110.33  3.000
 B7P  H7   C06  C07  106.01  3.000
 B7P  H7   C06  O05  109.75  3.000
 B7P  C07  C06  O05  110.45  3.000
 B7P  H7   C06  C02  108.53  3.000
 B7P  C07  C06  C02  117.17  3.000
 B7P  O05  C06  C02  104.83  3.000
 B7P  H9   C07  H8   107.73  3.000
 B7P  H9   C07  O08  111.77  3.000
 B7P  H8   C07  O08  109.54  3.000
 B7P  H9   C07  C06  108.01  3.000
 B7P  H8   C07  C06  110.63  3.000
 B7P  O08  C07  C06  109.16  3.000
 B7P  P09  O08  C07  126.25  3.000
 B7P  O12  P09  O11   99.77  3.000
 B7P  O11  P09  O10  119.46  3.000
 B7P  O12  P09  O10  110.52  3.000
 B7P  O11  P09  O08  107.59  3.000
 B7P  O10  P09  O08  112.45  3.000
 B7P  O12  P09  O08  105.55  3.000
 B7P  H10  O11  P09  114.93  3.000
 B7P  P13  O12  P09  136.78  3.000
 B7P  O16  P13  O15  111.25  3.000
 B7P  O16  P13  O14  107.54  3.000
 B7P  O15  P13  O14  118.03  3.000
 B7P  O16  P13  O12  100.75  3.000
 B7P  O14  P13  O12  101.76  3.000
 B7P  O15  P13  O12  115.72  3.000
 B7P  H11  O14  P13  115.34  3.000
 B7P  P17  O16  P13  130.24  3.000
 B7P  O20  P17  O19  118.52  3.000
 B7P  O20  P17  O18  103.51  3.000
 B7P  O19  P17  O18  117.74  3.000
 B7P  O20  P17  O16   99.97  3.000
 B7P  O18  P17  O16  100.45  3.000
 B7P  O19  P17  O16  113.75  3.000
 B7P  H12  O18  P17  114.61  3.000
 B7P  H13  O20  P17  114.61  3.000
 B7P  C04  N21  C28  116.48  3.000
 B7P  C04  N21  C22  122.08  3.000
 B7P  C28  N21  C22  121.43  3.000
 B7P  C25  C23  F24  116.91  3.000
 B7P  F24  C23  C22  121.23  3.000
 B7P  C25  C23  C22  121.85  3.000
 B7P  N27  C25  O26  122.35  3.000
 B7P  O26  C25  C23  125.74  3.000
 B7P  N27  C25  C23  111.91  3.000
 B7P  H14  N27  C25  116.48  3.000
 B7P  H14  N27  C28  115.25  3.000
 B7P  C25  N27  C28  128.26  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
 B7P  CONST_01  N27  C28  N21  C22    0.00   0.0  0
 B7P  CONST_02  C23  C25  N27  C28    0.00   0.0  0
 B7P  CONST_03  N27  C28  N21  C04  180.00   0.0  0
 B7P  CONST_04  C25  N27  C28  N21    0.00   0.0  0
 B7P  CONST_05  O29  C28  N21  C22  180.00   0.0  0
 B7P  CONST_06  O26  C25  N27  C28  180.00   0.0  0
 B7P  CONST_07  O29  C28  N21  C04    0.00   0.0  0
 B7P  CONST_08  O29  C28  N27  C25  180.00   0.0  0
 B7P  CONST_09  H14  N27  C28  N21  180.00   0.0  0
 B7P  Var_01    O12  P09  O08  C07   84.36  30.0  3
 B7P  Var_02    O15  P13  O12  P09   66.20  30.0  1
 B7P  Var_03    O19  P17  O16  P13   70.74  30.0  3
 B7P  Var_04    H8   C07  O08  P09   71.09  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
 B7P  chir_01  C02  C03  O01  C06  positiv
 B7P  chir_02  C04  O05  N21  C03  negativ
 B7P  chir_03  C06  O05  C02  C07  negativ
 B7P  chir_04  P09  O12  O10  O11  both
 B7P  chir_05  P13  O14  O12  O15  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
 B7P  plan-1  C22  0.020
 B7P  plan-1  C28  0.020
 B7P  plan-1  C04  0.020
 B7P  plan-1  N21  0.020
 B7P  plan-1  C23  0.020
 B7P  plan-1  F24  0.020
 B7P  plan-1  C25  0.020
 B7P  plan-1  O26  0.020
 B7P  plan-1  N27  0.020
 B7P  plan-1  O29  0.020
 B7P  plan-1  H1   0.020
 B7P  plan-1  H14  0.020

