# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 08:02:06 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 2'-deoxy-5'-O-[(R)-{[(R)-[(S)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)[C@@H](F)[P](O)(O)=O)O2
#
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
 FF4  FF4  2'-deoxy-5'-O-[(R)-{[(R)-[(S)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine  ligand  42  29  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FF4
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
 FF4  C4   C  CR6    0   0.503  -5.1762  -2.9968   0.1548
 FF4  N4   N  NH2    0  -0.783  -5.4709  -4.1913   0.6663
 FF4  C5   C  CR16   0  -0.443  -5.2300  -2.8015  -1.2590
 FF4  C6   C  CR16   0   0.035  -4.9196  -1.5675  -1.7014
 FF4  N3   N  N      0  -0.524  -4.8395  -2.0276   0.9824
 FF4  C2   C  CR6    0   0.589  -4.5301  -0.7952   0.5285
 FF4  O2   O  O      0  -0.540  -4.2081   0.1158   1.2774
 FF4  N1   N  NR6    0  -0.525  -4.5883  -0.5621  -0.8559
 FF4  C1'  C  CR15   0   0.253  -4.2263   0.7370  -1.4144
 FF4  C2'  C  CH2    0  -0.565  -4.9917   1.9468  -0.8711
 FF4  C3'  C  CR15   0   0.040  -3.9467   2.7691  -0.1167
 FF4  O3'  O  OH1    0  -0.682  -4.0482   4.1609  -0.2993
 FF4  O4'  O  O      0  -0.516  -2.8630   0.9705  -1.2025
 FF4  C4'  C  CR15   0  -0.033  -2.6317   2.2859  -0.7297
 FF4  C5'  C  CH2    0  -0.165  -1.4864   2.2828   0.2538
 FF4  O5'  O  O2     0  -0.579  -0.3047   1.9025  -0.4124
 FF4  PA   P  P      0   1.367   1.1180   2.0168   0.4246
 FF4  O1A  O  OP    -1  -0.890   1.0234   1.1776   1.6641
 FF4  O2A  O  O      0  -0.858   1.4884   3.4659   0.5434
 FF4  O3A  O  O2     0  -0.653   1.9956   1.3090  -0.7412
 FF4  PB   P  P      0   1.205   3.4059   0.4089  -0.5549
 FF4  O1B  O  OP    -1  -0.909   3.9398   0.3354  -1.9575
 FF4  O2B  O  O      0  -0.833   4.2169   1.0354   0.5430
 FF4  C3B  C  CH1    0  -0.316   2.7398  -1.2012  -0.0162
 FF4  F4B  F  F      0  -0.408   1.9720  -1.6926  -1.1062
 FF4  PG   P  P      0   1.117   3.9986  -2.4879   0.5099
 FF4  O1G  O  OP    -1  -0.848   3.2192  -3.8046   0.4347
 FF4  O2G  O  OP    -1  -0.995   5.1541  -2.3938  -0.4892
 FF4  O3G  O  O      0  -0.845   4.3653  -2.0633   1.9325
 FF4  H1   H  HNH2   0   0.412  -5.7257  -4.9662   0.0801
 FF4  H2   H  HNH2   0   0.391  -5.4219  -4.3432   1.6593
 FF4  H3   H  HCR6   0   0.272  -5.4945  -3.5934  -1.9433
 FF4  H4   H  HCR6   0   0.311  -4.9223  -1.3276  -2.7558
 FF4  H5   H  HCR5   0   0.264  -4.4223   0.6330  -2.4854
 FF4  H6   H  HCH2   0   0.260  -5.3599   2.5304  -1.7168
 FF4  H7   H  HCH2   0   0.278  -5.8518   1.6691  -0.2643
 FF4  H8   H  HCR5   0   0.241  -3.9754   2.5177   0.9463
 FF4  H9   H  HOH1   0   0.451  -4.7527   4.4861   0.2682
 FF4  H10  H  HCR5   0   0.268  -2.3809   2.9431  -1.5759
 FF4  H11  H  HCH2   0   0.255  -1.4056   3.2926   0.6771
 FF4  H12  H  HCH2   0   0.211  -1.7213   1.5979   1.0766
 FF4  H15  H  HCH1   0   0.186   2.0396  -1.0290   0.8065

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
 FF4  O2   C2   double  1.222  0.020  1.222
 FF4  C2   N3   single  1.349  0.020  1.349
 FF4  C2   N1   single  1.405  0.020  1.405
 FF4  C2'  C1'  single  1.531  0.020  1.531
 FF4  C2'  C3'  single  1.529  0.020  1.529
 FF4  N3   C4   double  1.318  0.020  1.318
 FF4  C1'  N1   single  1.460  0.020  1.460
 FF4  C1'  O4'  single  1.399  0.020  1.399
 FF4  N1   C6   single  1.355  0.020  1.355
 FF4  O3'  C3'  single  1.407  0.020  1.407
 FF4  C4   N4   single  1.332  0.020  1.332
 FF4  C4   C5   single  1.428  0.020  1.428
 FF4  C3'  C4'  single  1.529  0.020  1.529
 FF4  O4'  C4'  single  1.417  0.020  1.417
 FF4  C4'  C5'  single  1.510  0.020  1.510
 FF4  C6   C5   double  1.347  0.020  1.347
 FF4  O2B  PB   deloc   1.502  0.020  1.502
 FF4  C5'  O5'  single  1.409  0.020  1.409
 FF4  PB   O3A  single  1.683  0.020  1.683
 FF4  PB   O1B  deloc   1.503  0.020  1.503
 FF4  PB   C3B  single  1.824  0.020  1.824
 FF4  O5'  PA   single  1.655  0.020  1.655
 FF4  O3A  PA   single  1.622  0.020  1.622
 FF4  C3B  F4B  single  1.421  0.020  1.421
 FF4  C3B  PG   single  1.875  0.020  1.875
 FF4  PA   O2A  deloc   1.500  0.020  1.500
 FF4  PA   O1A  deloc   1.500  0.020  1.500
 FF4  O3G  PG   deloc   1.529  0.020  1.529
 FF4  PG   O2G  deloc   1.530  0.020  1.530
 FF4  PG   O1G  deloc   1.532  0.020  1.532
 FF4  N4   H1   single  0.860  0.020  1.020
 FF4  N4   H2   single  0.860  0.020  1.020
 FF4  C5   H3   single  0.930  0.020  1.080
 FF4  C6   H4   single  0.930  0.020  1.080
 FF4  C1'  H5   single  0.970  0.020  1.090
 FF4  C2'  H6   single  0.970  0.020  1.090
 FF4  C2'  H7   single  0.970  0.020  1.090
 FF4  C3'  H8   single  0.970  0.020  1.090
 FF4  O3'  H9   single  0.850  0.020  0.980
 FF4  C4'  H10  single  0.970  0.020  1.090
 FF4  C5'  H11  single  0.970  0.020  1.090
 FF4  C5'  H12  single  0.970  0.020  1.090
 FF4  C3B  H15  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
 FF4  N3   C4   C5   122.05  3.000
 FF4  C5   C4   N4   119.62  3.000
 FF4  N3   C4   N4   118.34  3.000
 FF4  H2   N4   H1   118.17  3.000
 FF4  H2   N4   C4   120.24  3.000
 FF4  H1   N4   C4   121.58  3.000
 FF4  H3   C5   C6   121.35  3.000
 FF4  H3   C5   C4   122.44  3.000
 FF4  C6   C5   C4   116.21  3.000
 FF4  H4   C6   N1   116.39  3.000
 FF4  H4   C6   C5   121.53  3.000
 FF4  N1   C6   C5   122.08  3.000
 FF4  C2   N3   C4   121.26  3.000
 FF4  N1   C2   O2   119.40  3.000
 FF4  N1   C2   N3   118.26  3.000
 FF4  O2   C2   N3   122.34  3.000
 FF4  C1'  N1   C2   120.95  3.000
 FF4  C1'  N1   C6   118.84  3.000
 FF4  C2   N1   C6   120.13  3.000
 FF4  H5   C1'  O4'  109.80  3.000
 FF4  H5   C1'  C2'  109.45  3.000
 FF4  O4'  C1'  C2'  107.54  3.000
 FF4  H5   C1'  N1   104.22  3.000
 FF4  O4'  C1'  N1   109.40  3.000
 FF4  C2'  C1'  N1   116.32  3.000
 FF4  H7   C2'  H6   107.56  3.000
 FF4  H7   C2'  C3'  113.72  3.000
 FF4  H6   C2'  C3'  108.98  3.000
 FF4  H7   C2'  C1'  113.03  3.000
 FF4  H6   C2'  C1'  108.43  3.000
 FF4  C3'  C2'  C1'  104.98  3.000
 FF4  H8   C3'  C4'  109.86  3.000
 FF4  H8   C3'  O3'  110.60  3.000
 FF4  C4'  C3'  O3'  108.82  3.000
 FF4  H8   C3'  C2'  109.77  3.000
 FF4  C4'  C3'  C2'  102.71  3.000
 FF4  O3'  C3'  C2'  114.75  3.000
 FF4  H9   O3'  C3'  108.11  3.000
 FF4  C4'  O4'  C1'  111.38  3.000
 FF4  H10  C4'  C5'  109.22  3.000
 FF4  H10  C4'  O4'  109.57  3.000
 FF4  C5'  C4'  O4'  109.84  3.000
 FF4  H10  C4'  C3'  108.39  3.000
 FF4  C5'  C4'  C3'  113.07  3.000
 FF4  O4'  C4'  C3'  106.67  3.000
 FF4  H12  C5'  H11  107.52  3.000
 FF4  H12  C5'  O5'  111.47  3.000
 FF4  H11  C5'  O5'  111.65  3.000
 FF4  H12  C5'  C4'  109.13  3.000
 FF4  H11  C5'  C4'  107.77  3.000
 FF4  O5'  C5'  C4'  109.20  3.000
 FF4  PA   O5'  C5'  117.60  3.000
 FF4  O3A  PA   O2A  110.17  3.000
 FF4  O2A  PA   O1A  119.37  3.000
 FF4  O3A  PA   O1A  112.58  3.000
 FF4  O1A  PA   O5'  108.98  3.000
 FF4  O2A  PA   O5'  108.61  3.000
 FF4  O3A  PA   O5'   94.10  3.000
 FF4  PB   O3A  PA   127.38  3.000
 FF4  C3B  PB   O2B  110.46  3.000
 FF4  C3B  PB   O1B  111.24  3.000
 FF4  O2B  PB   O1B  120.73  3.000
 FF4  C3B  PB   O3A  101.46  3.000
 FF4  O1B  PB   O3A  102.74  3.000
 FF4  O2B  PB   O3A  108.08  3.000
 FF4  H15  C3B  PG   109.06  3.000
 FF4  H15  C3B  F4B  106.59  3.000
 FF4  PG   C3B  F4B  109.91  3.000
 FF4  H15  C3B  PB   108.48  3.000
 FF4  PG   C3B  PB   116.32  3.000
 FF4  F4B  C3B  PB   106.03  3.000
 FF4  O3G  PG   O2G  114.15  3.000
 FF4  O2G  PG   O1G  113.89  3.000
 FF4  O3G  PG   O1G  113.97  3.000
 FF4  O1G  PG   C3B  103.56  3.000
 FF4  O2G  PG   C3B  106.35  3.000
 FF4  O3G  PG   C3B  103.38  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
 FF4  CONST_01  N1   C2   N3   C4     0.00   0.0  0
 FF4  CONST_02  C2   N3   C4   C5     0.00   0.0  0
 FF4  CONST_03  N3   C2   N1   C6     0.00   0.0  0
 FF4  CONST_04  C1'  N1   C2   N3   180.00   0.0  0
 FF4  CONST_05  O2   C2   N3   C4   180.00   0.0  0
 FF4  CONST_06  C2   N3   C4   N4   180.00   0.0  0
 FF4  CONST_07  O2   C2   N1   C6   180.00   0.0  0
 FF4  CONST_08  C1'  N1   C2   O2     0.00   0.0  0
 FF4  CONST_09  H1   N4   C4   C5     0.00   0.0  0
 FF4  CONST_10  H2   N4   C4   C5   180.00   0.0  0
 FF4  Var_01    O3A  PA   O5'  C5'  173.64  30.0  3
 FF4  Var_02    O2B  PB   O3A  PA   -36.95  30.0  2
 FF4  Var_03    H11  C5'  O5'  PA    53.25  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
 FF4  chir_01  C1'  C2'  N1   O4'  positiv
 FF4  chir_02  C3'  O3'  C4'  C2'  positiv
 FF4  chir_03  C4'  O4'  C3'  C5'  negativ
 FF4  chir_06  C3B  PB   F4B  PG   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
 FF4  plan-1  C4   0.020
 FF4  plan-1  N4   0.020
 FF4  plan-1  C5   0.020
 FF4  plan-1  C6   0.020
 FF4  plan-1  N3   0.020
 FF4  plan-1  C2   0.020
 FF4  plan-1  O2   0.020
 FF4  plan-1  N1   0.020
 FF4  plan-1  C1'  0.020
 FF4  plan-1  H1   0.020
 FF4  plan-1  H2   0.020
 FF4  plan-1  H3   0.020
 FF4  plan-1  H4   0.020

