# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 16:36:07 2022
#   Inital geometry file: a 83 line input string
#   Ligand name: 1-(2-deoxy-2-fluoro-beta-D-arabinofuranosyl)-5-ethynylpyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@@H](F)[C@@H]1O)N2C=C(C#C)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
 FDU  FDU  1-(2-deoxy-2-fluoro-beta-D-arabinofuranosyl)-5-ethynylpyrimidine-2,4(1H,3H)-dione  ligand  30  19  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FDU
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
 FDU  O01  O  OH1   0  -0.670  -3.8050  -2.4146   0.6973
 FDU  C03  C  CH2   0  -0.161  -3.5855  -1.3186  -0.1566
 FDU  C06  C  CH1   0   0.002  -2.8591  -0.2394   0.6049
 FDU  O08  O  O2    0  -0.480  -1.5548  -0.6834   0.9634
 FDU  C09  C  CH1   0  -0.047  -2.6690   1.0423  -0.2050
 FDU  O11  O  OH1   0  -0.663  -3.7959   1.8594  -0.0470
 FDU  C13  C  CH1   0   0.137  -1.3899   1.6042   0.3971
 FDU  F15  F  F     0  -0.354  -0.5947   2.2761  -0.5097
 FDU  C16  C  CH1   0   0.147  -0.6634   0.3816   0.9966
 FDU  N18  N  NR6   0  -0.563   0.5852   0.0387   0.3258
 FDU  C19  C  CR6   0   0.756   0.5785  -0.3393  -1.0089
 FDU  O20  O  O     0  -0.452  -0.4307  -0.4444  -1.6640
 FDU  N21  N  NR16  0  -0.735   1.8184  -0.5942  -1.5331
 FDU  C23  C  CR6   0   0.554   3.0482  -0.5189  -0.9095
 FDU  O24  O  O     0  -0.428   4.0739  -0.7677  -1.5060
 FDU  C25  C  CR6   0  -0.353   2.9635  -0.1254   0.4885
 FDU  C26  C  CR16  0   0.098   1.7473   0.1279   1.0231
 FDU  C28  C  CSP   0   0.319   4.1547  -0.0211   1.2496
 FDU  C29  C  CSP1  0  -0.537   5.1758   0.0703   1.8797
 FDU  H1   H  HOH1  0   0.458  -4.3049  -3.0771   0.2123
 FDU  H2   H  HCH2  0   0.206  -2.9938  -1.5931  -1.0391
 FDU  H3   H  HCH2  0   0.209  -4.5271  -0.8858  -0.5179
 FDU  H4   H  HCH1  0   0.243  -3.4227   0.0071   1.5160
 FDU  H5   H  HCH1  0   0.255  -2.4933   0.8011  -1.2584
 FDU  H6   H  HOH1  0   0.463  -3.8326   2.4821  -0.7785
 FDU  H7   H  HCH1  0   0.257  -1.6319   2.3030   1.2010
 FDU  H8   H  HCH1  0   0.277  -0.3732   0.6029   2.0265
 FDU  H9   H  HNR6  0   0.435   1.8218  -0.8680  -2.5087
 FDU  H10  H  HCR6  0   0.340   1.6502   0.4196   2.0595
 FDU  H11  H  H     0   0.285   6.0789   0.1483   2.4407

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
 FDU  O11  C09  single  1.401  0.020  1.401
 FDU  C13  F15  single  1.381  0.020  1.381
 FDU  C13  C09  single  1.521  0.020  1.521
 FDU  C13  C16  single  1.543  0.020  1.543
 FDU  O20  C19  double  1.208  0.020  1.208
 FDU  C09  C06  single  1.528  0.020  1.528
 FDU  C19  N18  single  1.387  0.020  1.387
 FDU  C19  N21  single  1.370  0.020  1.370
 FDU  C16  N18  single  1.458  0.020  1.458
 FDU  C16  O08  single  1.389  0.020  1.389
 FDU  N18  C26  single  1.358  0.020  1.358
 FDU  N21  C23  single  1.381  0.020  1.381
 FDU  C06  O08  single  1.424  0.020  1.424
 FDU  C06  C03  single  1.507  0.020  1.507
 FDU  C03  O01  single  1.407  0.020  1.407
 FDU  C26  C25  double  1.352  0.020  1.352
 FDU  C23  O24  double  1.212  0.020  1.212
 FDU  C23  C25  single  1.455  0.020  1.455
 FDU  C25  C28  single  1.417  0.020  1.417
 FDU  C28  C29  triple  1.203  0.020  1.203
 FDU  O01  H1   single  0.832  0.020  0.971
 FDU  C03  H2   single  0.939  0.020  1.096
 FDU  C03  H3   single  0.939  0.020  1.096
 FDU  C06  H4   single  0.939  0.020  1.096
 FDU  C09  H5   single  0.939  0.020  1.096
 FDU  O11  H6   single  0.832  0.020  0.971
 FDU  C13  H7   single  0.939  0.020  1.096
 FDU  C16  H8   single  0.939  0.020  1.096
 FDU  N21  H9   single  0.868  0.020  1.013
 FDU  C26  H10  single  0.930  0.020  1.086
 FDU  C29  H11  single  0.913  0.020  1.066

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
 FDU  H1   O01  C03  108.18  3.000
 FDU  H3   C03  H2   107.24  3.000
 FDU  H3   C03  C06  107.30  3.000
 FDU  H2   C03  C06  109.00  3.000
 FDU  H3   C03  O01  111.92  3.000
 FDU  H2   C03  O01  112.18  3.000
 FDU  C06  C03  O01  109.05  3.000
 FDU  H4   C06  C09  108.36  3.000
 FDU  H4   C06  O08  109.32  3.000
 FDU  C09  C06  O08  106.32  3.000
 FDU  H4   C06  C03  109.41  3.000
 FDU  O08  C06  C03  110.21  3.000
 FDU  C09  C06  C03  113.13  3.000
 FDU  C16  O08  C06  110.78  3.000
 FDU  H5   C09  C13  109.10  3.000
 FDU  H5   C09  O11  111.47  3.000
 FDU  C13  C09  O11  114.60  3.000
 FDU  H5   C09  C06  110.19  3.000
 FDU  C13  C09  C06  101.81  3.000
 FDU  O11  C09  C06  109.23  3.000
 FDU  H6   O11  C09  108.83  3.000
 FDU  H7   C13  C16  108.98  3.000
 FDU  H7   C13  F15  107.43  3.000
 FDU  C16  C13  F15  111.69  3.000
 FDU  H7   C13  C09  109.95  3.000
 FDU  C16  C13  C09  104.89  3.000
 FDU  F15  C13  C09  113.83  3.000
 FDU  H8   C16  N18  104.70  3.000
 FDU  H8   C16  C13  109.31  3.000
 FDU  N18  C16  C13  114.24  3.000
 FDU  H8   C16  O08  110.37  3.000
 FDU  N18  C16  O08  110.99  3.000
 FDU  C13  C16  O08  107.22  3.000
 FDU  C26  N18  C19  121.06  3.000
 FDU  C26  N18  C16  118.75  3.000
 FDU  C19  N18  C16  120.17  3.000
 FDU  N21  C19  O20  122.17  3.000
 FDU  N21  C19  N18  114.49  3.000
 FDU  O20  C19  N18  123.34  3.000
 FDU  H9   N21  C23  116.52  3.000
 FDU  H9   N21  C19  114.94  3.000
 FDU  C23  N21  C19  128.54  3.000
 FDU  C25  C23  O24  125.28  3.000
 FDU  C25  C23  N21  113.38  3.000
 FDU  O24  C23  N21  121.34  3.000
 FDU  C28  C25  C26  121.99  3.000
 FDU  C28  C25  C23  119.14  3.000
 FDU  C26  C25  C23  118.87  3.000
 FDU  H10  C26  C25  120.68  3.000
 FDU  H10  C26  N18  115.66  3.000
 FDU  C25  C26  N18  123.66  3.000
 FDU  C29  C28  C25  180.00  3.000
 FDU  H11  C29  C28  180.00  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
 FDU  CONST_01  N21  C19  N18  C16  180.00  0.0  0
 FDU  CONST_02  C23  N21  C19  N18    0.00  0.0  0
 FDU  CONST_03  C25  C23  N21  C19    0.00  0.0  0
 FDU  CONST_04  C26  N18  C19  N21    0.00  0.0  0
 FDU  CONST_05  O20  C19  N18  C16    0.00  0.0  0
 FDU  CONST_06  O24  C23  N21  C19  180.00  0.0  0
 FDU  CONST_07  C26  N18  C19  O20  180.00  0.0  0
 FDU  CONST_08  C23  N21  C19  O20  180.00  0.0  0
 FDU  CONST_09  H9   N21  C19  N18  180.00  0.0  0

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
 FDU  chir_01  C06  C09  O08  C03  positiv
 FDU  chir_02  C09  O11  C13  C06  negativ
 FDU  chir_03  C13  F15  C16  C09  positiv
 FDU  chir_04  C16  O08  N18  C13  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
 FDU  plan-1  C16  0.020
 FDU  plan-1  N18  0.020
 FDU  plan-1  C19  0.020
 FDU  plan-1  O20  0.020
 FDU  plan-1  N21  0.020
 FDU  plan-1  C23  0.020
 FDU  plan-1  O24  0.020
 FDU  plan-1  C25  0.020
 FDU  plan-1  C26  0.020
 FDU  plan-1  C28  0.020
 FDU  plan-1  C29  0.020
 FDU  plan-1  H9   0.020
 FDU  plan-1  H10  0.020

