# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 10:00:19 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 2'-deoxy-5'-O-[(R)-{[(R)-[(R)-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
 F3C  F3C  2'-deoxy-5'-O-[(R)-{[(R)-[(R)-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_F3C
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
 F3C  C4   C  CR6    0   0.451  -5.7614  -2.8354   0.1343
 F3C  N4   N  NH2    0  -0.793  -6.2276  -3.9691   0.6570
 F3C  C5   C  CR16   0  -0.344  -5.6557  -2.7041  -1.2841
 F3C  C6   C  CR16   0   0.061  -5.1739  -1.5310  -1.7383
 F3C  N3   N  N      0  -0.558  -5.4104  -1.8656   0.9552
 F3C  C2   C  CR6    0   0.547  -4.9326  -0.6928   0.4895
 F3C  O2   O  O      0  -0.505  -4.6007   0.2197   1.2322
 F3C  N1   N  NR6    0  -0.581  -4.8229  -0.5254  -0.9012
 F3C  C1'  C  CR15   0   0.225  -4.2789   0.7042  -1.4663
 F3C  C2'  C  CH2    0  -0.521  -4.9869   2.0032  -1.0686
 F3C  C3'  C  CR15   0   0.023  -3.9529   2.7815  -0.2556
 F3C  O3'  O  OH1    0  -0.678  -3.9084   4.1621  -0.5237
 F3C  O4'  O  O      0  -0.412  -2.9332   0.8268  -1.1013
 F3C  C4'  C  CR15   0  -0.029  -2.6317   2.1505  -0.6984
 F3C  C5'  C  CH2    0  -0.128  -1.5940   2.1332   0.3975
 F3C  O5'  O  O2     0  -0.646  -0.4008   1.5685  -0.0939
 F3C  PA   P  P      0   1.295   0.9881   1.8259   0.7715
 F3C  O1A  O  OP    -1  -0.924   0.6935   1.5950   2.2239
 F3C  O2A  O  O      0  -0.867   1.5924   3.1265   0.3353
 F3C  O3A  O  O2     0  -0.632   1.7661   0.5599   0.1176
 F3C  PB   P  P      0   1.181   3.4383   0.4228  -0.0128
 F3C  O1B  O  OP    -1  -0.869   3.8258   0.9605  -1.3612
 F3C  O2B  O  O      0  -0.760   4.0350   0.9946   1.2411
 F3C  C3B  C  CH1    0  -0.316   3.5281  -1.4017  -0.0447
 F3C  F4B  F  F      0  -0.368   3.1901  -1.8488   1.2572
 F3C  PG   P  P      0   1.110   5.1734  -2.1314  -0.5761
 F3C  O1G  O  OP    -1  -1.026   5.1144  -3.5750  -0.0671
 F3C  O2G  O  OP    -1  -0.893   5.1368  -2.0118  -2.1006
 F3C  O3G  O  O      0  -0.761   6.2484  -1.2797   0.1021
 F3C  H1   H  HNH2   0   0.424  -6.4930  -4.7453   0.0773
 F3C  H2   H  HNH2   0   0.412  -6.2798  -4.0831   1.6547
 F3C  H3   H  HCR6   0   0.278  -5.9353  -3.4964  -1.9617
 F3C  H4   H  HCR6   0   0.321  -5.0495  -1.3405  -2.7956
 F3C  H5   H  HCR5   0   0.179  -4.3583   0.5636  -2.5482
 F3C  H6   H  HCH2   0   0.267  -5.2243   2.5619  -1.9761
 F3C  H7   H  HCH2   0   0.212  -5.9210   1.8339  -0.5361
 F3C  H8   H  HCR5   0   0.264  -4.1100   2.6006   0.8111
 F3C  H9   H  HOH1   0   0.449  -4.6372   4.5824  -0.0585
 F3C  H10  H  HCR5   0   0.276  -2.2473   2.7213  -1.5575
 F3C  H11  H  HCH2   0   0.242  -1.4525   3.1699   0.7296
 F3C  H12  H  HCH2   0   0.183  -1.9792   1.5651   1.2515
 F3C  H15  H  HCH1   0   0.210   2.7471  -1.7839  -0.7137

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
 F3C  O2   C2   double  1.222  0.020  1.222
 F3C  C2   N3   single  1.349  0.020  1.349
 F3C  C2   N1   single  1.405  0.020  1.405
 F3C  N3   C4   double  1.318  0.020  1.318
 F3C  C2'  C1'  single  1.532  0.020  1.532
 F3C  C2'  C3'  single  1.528  0.020  1.528
 F3C  C1'  N1   single  1.459  0.020  1.459
 F3C  C1'  O4'  single  1.400  0.020  1.400
 F3C  N1   C6   single  1.355  0.020  1.355
 F3C  O3'  C3'  single  1.407  0.020  1.407
 F3C  C4   N4   single  1.333  0.020  1.333
 F3C  C4   C5   single  1.428  0.020  1.428
 F3C  C3'  C4'  single  1.530  0.020  1.530
 F3C  O4'  C4'  single  1.416  0.020  1.416
 F3C  C6   C5   double  1.347  0.020  1.347
 F3C  C4'  C5'  single  1.509  0.020  1.509
 F3C  O2B  PB   deloc   1.502  0.020  1.502
 F3C  C5'  O5'  single  1.409  0.020  1.409
 F3C  PB   O3A  single  1.683  0.020  1.683
 F3C  PB   O1B  deloc   1.502  0.020  1.502
 F3C  PB   C3B  single  1.827  0.020  1.827
 F3C  O5'  PA   single  1.657  0.020  1.657
 F3C  O3A  PA   single  1.623  0.020  1.623
 F3C  F4B  C3B  single  1.417  0.020  1.417
 F3C  C3B  PG   single  1.877  0.020  1.877
 F3C  PA   O2A  deloc   1.499  0.020  1.499
 F3C  PA   O1A  deloc   1.500  0.020  1.500
 F3C  PG   O3G  deloc   1.530  0.020  1.530
 F3C  PG   O1G  deloc   1.532  0.020  1.532
 F3C  PG   O2G  deloc   1.530  0.020  1.530
 F3C  N4   H1   single  0.860  0.020  1.020
 F3C  N4   H2   single  0.860  0.020  1.020
 F3C  C5   H3   single  0.930  0.020  1.080
 F3C  C6   H4   single  0.930  0.020  1.080
 F3C  C1'  H5   single  0.970  0.020  1.090
 F3C  C2'  H6   single  0.970  0.020  1.090
 F3C  C2'  H7   single  0.970  0.020  1.090
 F3C  C3'  H8   single  0.970  0.020  1.090
 F3C  O3'  H9   single  0.850  0.020  0.980
 F3C  C4'  H10  single  0.970  0.020  1.090
 F3C  C5'  H11  single  0.970  0.020  1.090
 F3C  C5'  H12  single  0.970  0.020  1.090
 F3C  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
 F3C  N3   C4   C5   122.08  3.000
 F3C  C5   C4   N4   119.57  3.000
 F3C  N3   C4   N4   118.34  3.000
 F3C  H2   N4   H1   118.12  3.000
 F3C  H2   N4   C4   120.25  3.000
 F3C  H1   N4   C4   121.57  3.000
 F3C  H3   C5   C6   121.34  3.000
 F3C  H3   C5   C4   122.47  3.000
 F3C  C6   C5   C4   116.19  3.000
 F3C  H4   C6   N1   116.33  3.000
 F3C  H4   C6   C5   121.61  3.000
 F3C  N1   C6   C5   122.06  3.000
 F3C  C2   N3   C4   121.25  3.000
 F3C  N1   C2   O2   119.42  3.000
 F3C  N1   C2   N3   118.22  3.000
 F3C  O2   C2   N3   122.36  3.000
 F3C  C1'  N1   C2   120.87  3.000
 F3C  C1'  N1   C6   118.88  3.000
 F3C  C2   N1   C6   120.20  3.000
 F3C  H5   C1'  O4'  109.81  3.000
 F3C  H5   C1'  C2'  109.40  3.000
 F3C  O4'  C1'  C2'  107.60  3.000
 F3C  H5   C1'  N1   104.35  3.000
 F3C  O4'  C1'  N1   109.35  3.000
 F3C  C2'  C1'  N1   116.22  3.000
 F3C  H7   C2'  H6   107.44  3.000
 F3C  H7   C2'  C3'  113.55  3.000
 F3C  H6   C2'  C3'  109.18  3.000
 F3C  H7   C2'  C1'  113.06  3.000
 F3C  H6   C2'  C1'  108.58  3.000
 F3C  C3'  C2'  C1'  104.91  3.000
 F3C  H8   C3'  C4'  109.77  3.000
 F3C  H8   C3'  O3'  110.66  3.000
 F3C  C4'  C3'  O3'  108.80  3.000
 F3C  H8   C3'  C2'  109.72  3.000
 F3C  C4'  C3'  C2'  102.73  3.000
 F3C  O3'  C3'  C2'  114.82  3.000
 F3C  H9   O3'  C3'  108.23  3.000
 F3C  C4'  O4'  C1'  111.15  3.000
 F3C  H10  C4'  C5'  109.43  3.000
 F3C  H10  C4'  O4'  109.70  3.000
 F3C  C5'  C4'  O4'  110.02  3.000
 F3C  H10  C4'  C3'  108.27  3.000
 F3C  C5'  C4'  C3'  112.85  3.000
 F3C  O4'  C4'  C3'  106.50  3.000
 F3C  H12  C5'  H11  107.40  3.000
 F3C  H12  C5'  O5'  111.21  3.000
 F3C  H11  C5'  O5'  112.02  3.000
 F3C  H12  C5'  C4'  109.28  3.000
 F3C  H11  C5'  C4'  107.31  3.000
 F3C  O5'  C5'  C4'  109.49  3.000
 F3C  PA   O5'  C5'  117.75  3.000
 F3C  O3A  PA   O2A  111.48  3.000
 F3C  O2A  PA   O1A  119.64  3.000
 F3C  O3A  PA   O1A  111.36  3.000
 F3C  O1A  PA   O5'  108.50  3.000
 F3C  O2A  PA   O5'  108.71  3.000
 F3C  O3A  PA   O5'   94.02  3.000
 F3C  PB   O3A  PA   124.81  3.000
 F3C  C3B  PB   O2B  112.04  3.000
 F3C  C3B  PB   O1B  109.21  3.000
 F3C  O2B  PB   O1B  120.71  3.000
 F3C  C3B  PB   O3A   97.56  3.000
 F3C  O1B  PB   O3A  107.25  3.000
 F3C  O2B  PB   O3A  107.41  3.000
 F3C  H15  C3B  PG   108.43  3.000
 F3C  H15  C3B  F4B  106.29  3.000
 F3C  PG   C3B  F4B  110.27  3.000
 F3C  H15  C3B  PB   108.88  3.000
 F3C  PG   C3B  PB   115.87  3.000
 F3C  F4B  C3B  PB   106.69  3.000
 F3C  O3G  PG   O2G  114.52  3.000
 F3C  O2G  PG   O1G  113.82  3.000
 F3C  O3G  PG   O1G  113.86  3.000
 F3C  O2G  PG   C3B  103.34  3.000
 F3C  O1G  PG   C3B  103.80  3.000
 F3C  O3G  PG   C3B  105.90  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
 F3C  CONST_01  N1   C2   N3   C4     0.00   0.0  0
 F3C  CONST_02  C2   N3   C4   C5     0.00   0.0  0
 F3C  CONST_03  N3   C2   N1   C6     0.00   0.0  0
 F3C  CONST_04  C1'  N1   C2   N3   180.00   0.0  0
 F3C  CONST_05  O2   C2   N3   C4   180.00   0.0  0
 F3C  CONST_06  C2   N3   C4   N4   180.00   0.0  0
 F3C  CONST_07  O2   C2   N1   C6   180.00   0.0  0
 F3C  CONST_08  C1'  N1   C2   O2     0.00   0.0  0
 F3C  CONST_09  H1   N4   C4   C5     0.00   0.0  0
 F3C  CONST_10  H2   N4   C4   C5   180.00   0.0  0
 F3C  Var_01    O3A  PA   O5'  C5'  159.42  30.0  3
 F3C  Var_02    O2B  PB   O3A  PA    38.44  30.0  2
 F3C  Var_03    H11  C5'  O5'  PA    44.27  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
 F3C  chir_01  C1'  C2'  N1   O4'  positiv
 F3C  chir_02  C3'  O3'  C4'  C2'  positiv
 F3C  chir_03  C4'  O4'  C3'  C5'  negativ
 F3C  chir_06  C3B  PB   F4B  PG   positiv

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
 F3C  plan-1  C4   0.020
 F3C  plan-1  N4   0.020
 F3C  plan-1  C5   0.020
 F3C  plan-1  C6   0.020
 F3C  plan-1  N3   0.020
 F3C  plan-1  C2   0.020
 F3C  plan-1  O2   0.020
 F3C  plan-1  N1   0.020
 F3C  plan-1  C1'  0.020
 F3C  plan-1  H1   0.020
 F3C  plan-1  H2   0.020
 F3C  plan-1  H3   0.020
 F3C  plan-1  H4   0.020

