# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 17 16:56:44 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 5'-deoxy-5'-fluorothymidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@H]2C[C@H](O)[C@@H](CF)O2)C(=O)NC1=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
 0DN  0DN  5'-deoxy-5'-fluorothymidine  ligand  30  17  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0DN
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
 0DN  O4   O  O     0  -0.473  -0.1468  -0.8187  -1.4760
 0DN  C6   C  CR6   0   0.744   0.8057  -0.4578  -0.8170
 0DN  N2   N  NR16  0  -0.733   2.0617  -0.9670  -1.0196
 0DN  C7   C  CR6   0   0.559   3.2290  -0.6532  -0.3473
 0DN  O3   O  O     0  -0.454   4.2796  -1.1917  -0.6448
 0DN  C8   C  CR6   0  -0.184   3.0664   0.3337   0.7005
 0DN  C10  C  CH3   0  -0.707   4.2597   0.7421   1.4997
 0DN  C9   C  CR16  0   0.059   1.8370   0.8369   0.9049
 0DN  N1   N  NR6   0  -0.567   0.7270   0.4875   0.1792
 0DN  C4   C  CH1   0   0.216  -0.5621   1.0910   0.5085
 0DN  C3   C  CH2   0  -0.559  -1.2911   1.7888  -0.6433
 0DN  C2   C  CH1   0   0.014  -2.5441   0.9485  -0.8911
 0DN  O2   O  OH1   0  -0.667  -3.7137   1.6894  -1.1296
 0DN  O1   O  O2    0  -0.491  -1.4186   0.1047   1.0138
 0DN  C1   C  CH1   0  -0.015  -2.7045   0.1922   0.4300
 0DN  C5   C  CH2   0  -0.017  -3.2716  -1.1853   0.2243
 0DN  F1   F  F     0  -0.379  -3.5192  -1.8020   1.4476
 0DN  H1   H  HNR6  0   0.425   2.1314  -1.6600  -1.7549
 0DN  H2   H  HCH3  0   0.248   5.0129   1.2229   0.8733
 0DN  H3   H  HCH3  0   0.247   3.9816   1.4433   2.2848
 0DN  H4   H  HCH3  0   0.247   4.7352  -0.1180   1.9722
 0DN  H5   H  HCR6  0   0.317   1.6634   1.5743   1.6773
 0DN  H6   H  HCH1  0   0.258  -0.3299   1.8176   1.2901
 0DN  H7   H  HCH2  0   0.271  -1.5929   2.7827  -0.3091
 0DN  H8   H  HCH2  0   0.278  -0.6697   1.9137  -1.5282
 0DN  H9   H  HCH1  0   0.237  -2.3646   0.2426  -1.7070
 0DN  H10  H  HOH1  0   0.458  -3.6963   1.9938  -2.0416
 0DN  H11  H  HCH1  0   0.240  -3.3714   0.7719   1.0841
 0DN  H12  H  HCH2  0   0.214  -4.2151  -1.1144  -0.3204
 0DN  H13  H  HCH2  0   0.213  -2.5765  -1.8089  -0.3404

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
 0DN  O3   C7   double  1.217  0.020  1.217
 0DN  N2   C7   single  1.383  0.020  1.383
 0DN  N2   C6   single  1.370  0.020  1.370
 0DN  O4   C6   double  1.213  0.020  1.213
 0DN  C7   C8   single  1.449  0.020  1.449
 0DN  C6   N1   single  1.376  0.020  1.376
 0DN  C8   C9   double  1.344  0.020  1.344
 0DN  C8   C10  single  1.493  0.020  1.493
 0DN  N1   C9   single  1.371  0.020  1.371
 0DN  N1   C4   single  1.461  0.020  1.461
 0DN  C4   O1   single  1.401  0.020  1.401
 0DN  C4   C3   single  1.531  0.020  1.531
 0DN  O1   C1   single  1.415  0.020  1.415
 0DN  C3   C2   single  1.529  0.020  1.529
 0DN  O2   C2   single  1.405  0.020  1.405
 0DN  C1   C2   single  1.531  0.020  1.531
 0DN  C1   C5   single  1.504  0.020  1.504
 0DN  C5   F1   single  1.392  0.020  1.392
 0DN  N2   H1   single  0.860  0.020  1.020
 0DN  C10  H2   single  0.970  0.020  1.090
 0DN  C10  H3   single  0.970  0.020  1.090
 0DN  C10  H4   single  0.970  0.020  1.090
 0DN  C9   H5   single  0.930  0.020  1.080
 0DN  C4   H6   single  0.970  0.020  1.090
 0DN  C3   H7   single  0.970  0.020  1.090
 0DN  C3   H8   single  0.970  0.020  1.090
 0DN  C2   H9   single  0.970  0.020  1.090
 0DN  O2   H10  single  0.850  0.020  0.980
 0DN  C1   H11  single  0.970  0.020  1.090
 0DN  C5   H12  single  0.970  0.020  1.090
 0DN  C5   H13  single  0.970  0.020  1.090

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
 0DN  N1   C6   N2   114.51  3.000
 0DN  N1   C6   O4   123.56  3.000
 0DN  N2   C6   O4   121.92  3.000
 0DN  H1   N2   C7   116.75  3.000
 0DN  H1   N2   C6   115.12  3.000
 0DN  C7   N2   C6   128.13  3.000
 0DN  C8   C7   O3   125.10  3.000
 0DN  C8   C7   N2   114.29  3.000
 0DN  O3   C7   N2   120.61  3.000
 0DN  C9   C8   C10  123.18  3.000
 0DN  C10  C8   C7   118.94  3.000
 0DN  C9   C8   C7   117.89  3.000
 0DN  H4   C10  H3   107.88  3.000
 0DN  H4   C10  H2   107.18  3.000
 0DN  H3   C10  H2   107.85  3.000
 0DN  H4   C10  C8   111.38  3.000
 0DN  H3   C10  C8   110.97  3.000
 0DN  H2   C10  C8   111.40  3.000
 0DN  H5   C9   N1   114.93  3.000
 0DN  H5   C9   C8   120.70  3.000
 0DN  N1   C9   C8   124.37  3.000
 0DN  C4   N1   C9   119.32  3.000
 0DN  C4   N1   C6   119.84  3.000
 0DN  C9   N1   C6   120.79  3.000
 0DN  H6   C4   O1   109.90  3.000
 0DN  H6   C4   C3   109.65  3.000
 0DN  O1   C4   C3   107.52  3.000
 0DN  H6   C4   N1   104.39  3.000
 0DN  C3   C4   N1   116.02  3.000
 0DN  O1   C4   N1   109.27  3.000
 0DN  H8   C3   H7   107.60  3.000
 0DN  H8   C3   C2   113.52  3.000
 0DN  H7   C3   C2   108.87  3.000
 0DN  H8   C3   C4   113.08  3.000
 0DN  H7   C3   C4   108.45  3.000
 0DN  C2   C3   C4   105.17  3.000
 0DN  H9   C2   C1   110.00  3.000
 0DN  H9   C2   O2   110.51  3.000
 0DN  C1   C2   O2   108.65  3.000
 0DN  H9   C2   C3   109.94  3.000
 0DN  C1   C2   C3   102.56  3.000
 0DN  O2   C2   C3   114.84  3.000
 0DN  H10  O2   C2   108.23  3.000
 0DN  C1   O1   C4   111.31  3.000
 0DN  H11  C1   C5   109.62  3.000
 0DN  H11  C1   O1   109.78  3.000
 0DN  C5   C1   O1   110.03  3.000
 0DN  H11  C1   C2   108.45  3.000
 0DN  C5   C1   C2   111.97  3.000
 0DN  O1   C1   C2   106.94  3.000
 0DN  H13  C5   H12  109.23  3.000
 0DN  H13  C5   F1   108.35  3.000
 0DN  H12  C5   F1   108.27  3.000
 0DN  H13  C5   C1   110.73  3.000
 0DN  H12  C5   C1   109.55  3.000
 0DN  F1   C5   C1   110.65  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
 0DN  CONST_01  C9  N1   C6  N2    0.00   0.0  0
 0DN  CONST_02  C4  N1   C6  N2  180.00   0.0  0
 0DN  CONST_03  N1  C6   N2  C7    0.00   0.0  0
 0DN  CONST_04  C7  N2   C6  O4  180.00   0.0  0
 0DN  CONST_05  C9  N1   C6  O4  180.00   0.0  0
 0DN  CONST_06  C4  N1   C6  O4    0.00   0.0  0
 0DN  CONST_07  H1  N2   C6  N1  180.00   0.0  0
 0DN  Var_01    H2  C10  C8  C7   63.06  30.0  3

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
 0DN  chir_01  C4  N1  O1  C3  positiv
 0DN  chir_02  C2  O2  C1  C3  positiv
 0DN  chir_03  C1  O1  C2  C5  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
 0DN  plan-1  O4   0.020
 0DN  plan-1  C6   0.020
 0DN  plan-1  N2   0.020
 0DN  plan-1  C7   0.020
 0DN  plan-1  O3   0.020
 0DN  plan-1  C8   0.020
 0DN  plan-1  C10  0.020
 0DN  plan-1  C9   0.020
 0DN  plan-1  N1   0.020
 0DN  plan-1  C4   0.020
 0DN  plan-1  H1   0.020
 0DN  plan-1  H5   0.020

