# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 08:10:46 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 5-fluorocytidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1F)[C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O
#
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
 F01  F01  '5-fluorocytidine         '  ligand  30  18  .  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_F01
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
 F01  O1    O  O     0  -0.504  -0.1332   0.7630   1.6022
 F01  C6    C  CR6   0   0.616   0.8518   0.5171   0.9218
 F01  N1    N  N     0  -0.533   2.0776   0.9978   1.2243
 F01  C7    C  CR6   0   0.405   3.1341   0.7285   0.4903
 F01  N2    N  NH2   0  -0.804   4.3177   1.2264   0.8297
 F01  C8    C  CR6   0   0.309   3.0072  -0.0948  -0.6689
 F01  F1    F  F     0  -0.301   4.0922  -0.3622  -1.4122
 F01  C9    C  CR16  0  -0.061   1.7991  -0.5781  -0.9872
 F01  N3    N  NR6   0  -0.553   0.7192  -0.2975  -0.2104
 F01  C1    C  CH1   0   0.207  -0.5860  -0.7919  -0.6266
 F01  O4    O  O2    0  -0.491  -1.3845   0.2836  -1.0295
 F01  C4    C  CH1   0   0.023  -2.6948   0.1785  -0.4987
 F01  C5    C  CH2   0  -0.164  -3.2369   1.5496  -0.1810
 F01  O5    O  OH1   0  -0.671  -3.4163   2.2720  -1.3759
 F01  C3    C  CH1   0  -0.034  -2.5776  -0.7042   0.7430
 F01  O3    O  OH1   0  -0.665  -3.7662  -1.4347   0.9212
 F01  C2    C  CH1   0  -0.043  -1.3720  -1.6048   0.4164
 F01  O2    O  OH1   0  -0.677  -1.8008  -2.7904  -0.2049
 F01  HN2   H  HNH2  0   0.412   4.3985   1.7994   1.6529
 F01  HN2A  H  HNH2  0   0.421   5.1519   1.0431   0.2999
 F01  H9    H  HCR6  0   0.337   1.6457  -1.2032  -1.8565
 F01  H1    H  HCH1  0   0.254  -0.3800  -1.4518  -1.4751
 F01  H4    H  HCH1  0   0.231  -3.3537  -0.3170  -1.2271
 F01  H5    H  HCH2  0   0.204  -4.1845   1.4139   0.3572
 F01  H5A   H  HCH2  0   0.202  -2.5413   2.0519   0.5041
 F01  HO5   H  HOH1  0   0.457  -3.7817   3.1322  -1.1511
 F01  H3    H  HCH1  0   0.259  -2.3526  -0.0963   1.6196
 F01  HO3   H  HOH1  0   0.469  -3.8776  -1.6224   1.8582
 F01  H2    H  HCH1  0   0.246  -0.7688  -1.8276   1.3033
 F01  HO2   H  HOH1  0   0.447  -2.7065  -2.9495   0.0954

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
 F01  O1  C6    double  1.222  0.020  1.222
 F01  C6  N1    single  1.351  0.020  1.351
 F01  C6  N3    single  1.401  0.020  1.401
 F01  N1  C7    double  1.314  0.020  1.314
 F01  C7  N2    single  1.328  0.020  1.328
 F01  C7  C8    single  1.427  0.020  1.427
 F01  C8  F1    single  1.342  0.020  1.342
 F01  C8  C9    double  1.340  0.020  1.340
 F01  C9  N3    single  1.360  0.020  1.360
 F01  N3  C1    single  1.456  0.020  1.456
 F01  C1  O4    single  1.399  0.020  1.399
 F01  C1  C2    single  1.538  0.020  1.538
 F01  O4  C4    single  1.418  0.020  1.418
 F01  C4  C5    single  1.508  0.020  1.508
 F01  C4  C3    single  1.528  0.020  1.528
 F01  C5  O5    single  1.408  0.020  1.408
 F01  C3  O3    single  1.407  0.020  1.407
 F01  C3  C2    single  1.540  0.020  1.540
 F01  C2  O2    single  1.406  0.020  1.406
 F01  N2  HN2   single  0.860  0.020  1.020
 F01  N2  HN2A  single  0.860  0.020  1.020
 F01  C9  H9    single  0.930  0.020  1.080
 F01  C1  H1    single  0.970  0.020  1.090
 F01  C4  H4    single  0.970  0.020  1.090
 F01  C5  H5    single  0.970  0.020  1.090
 F01  C5  H5A   single  0.970  0.020  1.090
 F01  O5  HO5   single  0.850  0.020  0.980
 F01  C3  H3    single  0.970  0.020  1.090
 F01  O3  HO3   single  0.850  0.020  0.980
 F01  C2  H2    single  0.970  0.020  1.090
 F01  O2  HO2   single  0.850  0.020  0.980

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
 F01  N3    C6  N1   118.28  3.000
 F01  N3    C6  O1   119.38  3.000
 F01  N1    C6  O1   122.35  3.000
 F01  C7    N1  C6   122.10  3.000
 F01  C8    C7  N2   120.20  3.000
 F01  C8    C7  N1   120.01  3.000
 F01  N2    C7  N1   119.79  3.000
 F01  HN2A  N2  HN2  117.94  3.000
 F01  HN2A  N2  C7   122.45  3.000
 F01  HN2   N2  C7   119.61  3.000
 F01  C9    C8  F1   121.71  3.000
 F01  C9    C8  C7   118.77  3.000
 F01  F1    C8  C7   119.52  3.000
 F01  H9    C9  N3   117.77  3.000
 F01  H9    C9  C8   121.83  3.000
 F01  N3    C9  C8   120.40  3.000
 F01  C1    N3  C9   118.58  3.000
 F01  C1    N3  C6   120.88  3.000
 F01  C9    N3  C6   120.43  3.000
 F01  H1    C1  C2   107.65  3.000
 F01  H1    C1  O4   110.35  3.000
 F01  C2    C1  O4   108.05  3.000
 F01  H1    C1  N3   104.93  3.000
 F01  C2    C1  N3   116.33  3.000
 F01  O4    C1  N3   109.44  3.000
 F01  C4    O4  C1   111.27  3.000
 F01  H4    C4  C3   108.89  3.000
 F01  H4    C4  C5   109.49  3.000
 F01  C3    C4  C5   112.43  3.000
 F01  H4    C4  O4   109.83  3.000
 F01  C3    C4  O4   106.04  3.000
 F01  C5    C4  O4   110.10  3.000
 F01  H5A   C5  H5   107.30  3.000
 F01  H5A   C5  O5   112.06  3.000
 F01  H5    C5  O5   111.68  3.000
 F01  H5A   C5  C4   108.64  3.000
 F01  H5    C5  C4   107.52  3.000
 F01  O5    C5  C4   109.48  3.000
 F01  HO5   O5  C5   108.01  3.000
 F01  H3    C3  C2   109.58  3.000
 F01  H3    C3  O3   111.23  3.000
 F01  C2    C3  O3   112.62  3.000
 F01  H3    C3  C4   110.32  3.000
 F01  C2    C3  C4   103.03  3.000
 F01  O3    C3  C4   109.77  3.000
 F01  HO3   O3  C3   108.82  3.000
 F01  H2    C2  O2   110.75  3.000
 F01  H2    C2  C3   112.23  3.000
 F01  O2    C2  C3   110.38  3.000
 F01  H2    C2  C1   112.03  3.000
 F01  O2    C2  C1   107.57  3.000
 F01  C3    C2  C1   103.58  3.000
 F01  HO2   O2  C2   106.68  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
 F01  CONST_01  C8    C7  N1  C6    0.00  0.0  0
 F01  CONST_02  C9    N3  C6  N1    0.00  0.0  0
 F01  CONST_03  C1    N3  C6  N1  180.00  0.0  0
 F01  CONST_04  N3    C6  N1  C7    0.00  0.0  0
 F01  CONST_05  C7    N1  C6  O1  180.00  0.0  0
 F01  CONST_06  C9    N3  C6  O1  180.00  0.0  0
 F01  CONST_07  C1    N3  C6  O1    0.00  0.0  0
 F01  CONST_08  N2    C7  N1  C6  180.00  0.0  0
 F01  CONST_09  HN2   N2  C7  N1    0.00  0.0  0
 F01  CONST_10  HN2A  N2  C7  N1  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
 F01  chir_01  C1  N3  O4  C2  positiv
 F01  chir_02  C4  O4  C5  C3  positiv
 F01  chir_03  C3  O3  C4  C2  positiv
 F01  chir_04  C2  O2  C3  C1  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
 F01  plan-1  O1    0.020
 F01  plan-1  C6    0.020
 F01  plan-1  N1    0.020
 F01  plan-1  C7    0.020
 F01  plan-1  N2    0.020
 F01  plan-1  C8    0.020
 F01  plan-1  F1    0.020
 F01  plan-1  C9    0.020
 F01  plan-1  N3    0.020
 F01  plan-1  C1    0.020
 F01  plan-1  HN2   0.020
 F01  plan-1  HN2A  0.020
 F01  plan-1  H9    0.020

