# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 18:43:03 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 2'-deoxy-5-fluorocytidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1F)[C@H]2C[C@H](O)[C@@H](CO)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
 B86  B86  2'-deoxy-5-fluorocytidine  ligand  29  17  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_B86
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
 B86  C1    C  CR6   0   0.403   3.0622  -0.6647  -0.4063
 B86  N2    N  N     0  -0.533   2.0037  -0.9895  -1.1139
 B86  C3    C  CR6   0   0.614   0.7802  -0.4733  -0.8577
 B86  N4    N  NR6   0  -0.550   0.6573   0.4492   0.1901
 B86  C5    C  CR16  0  -0.064   1.7384   0.7854   0.9406
 B86  C6    C  CR6   0   0.308   2.9417   0.2586   0.6750
 B86  N7    N  NH2   0  -0.805   4.2426  -1.2000  -0.7003
 B86  F8    F  F     0  -0.302   4.0272   0.5789   1.3972
 B86  O9    O  O     0  -0.501  -0.2056  -0.7810  -1.5103
 B86  C10   C  CH1   0   0.223  -0.6391   1.0296   0.5312
 B86  O11   O  O2    0  -0.491  -1.4864   0.0247   1.0105
 B86  C12   C  CH1   0   0.025  -2.7768   0.1190   0.4315
 B86  C13   C  CH1   0   0.022  -2.6203   0.9105  -0.8678
 B86  O13   O  OH1   0  -0.671  -3.7939   1.6550  -1.0877
 B86  C14   C  CH2   0  -0.555  -1.3710   1.7508  -0.6045
 B86  C15   C  CH2   0  -0.166  -3.3469  -1.2593   0.2080
 B86  O16   O  OH1   0  -0.673  -3.5687  -1.8834   1.4511
 B86  H5    H  HCR6  0   0.335   1.5918   1.4915   1.7471
 B86  HN7   H  HNH2  0   0.411   4.3189  -1.8408  -1.4722
 B86  HN7A  H  HNH2  0   0.420   5.0777  -0.9806  -0.1862
 B86  H10   H  HCH1  0   0.248  -0.4187   1.7416   1.3310
 B86  H12   H  HCH1  0   0.223  -3.4396   0.6848   1.1037
 B86  H13   H  HCH1  0   0.231  -2.4393   0.2246  -1.6995
 B86  HO13  H  HOH1  0   0.456  -3.7738   1.9871  -1.9898
 B86  H14   H  HCH2  0   0.262  -1.6757   2.7361  -0.2474
 B86  H14A  H  HCH2  0   0.272  -0.7509   1.8965  -1.4870
 B86  H15   H  HCH2  0   0.201  -4.2797  -1.1436  -0.3600
 B86  H15A  H  HCH2  0   0.202  -2.6510  -1.8297  -0.4204
 B86  HO16  H  HOH1  0   0.456  -3.9522  -2.7490   1.2853

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
 B86  C1   N2    double  1.314  0.020  1.314
 B86  C1   C6    single  1.427  0.020  1.427
 B86  C1   N7    single  1.329  0.020  1.329
 B86  N2   C3    single  1.352  0.020  1.352
 B86  C3   N4    single  1.401  0.020  1.401
 B86  C3   O9    double  1.222  0.020  1.222
 B86  N4   C5    single  1.358  0.020  1.358
 B86  N4   C10   single  1.461  0.020  1.461
 B86  C5   C6    double  1.340  0.020  1.340
 B86  C6   F8    single  1.343  0.020  1.343
 B86  C10  O11   single  1.399  0.020  1.399
 B86  C10  C14   single  1.531  0.020  1.531
 B86  O11  C12   single  1.417  0.020  1.417
 B86  C12  C13   single  1.529  0.020  1.529
 B86  C12  C15   single  1.508  0.020  1.508
 B86  C13  O13   single  1.407  0.020  1.407
 B86  C13  C14   single  1.528  0.020  1.528
 B86  C15  O16   single  1.408  0.020  1.408
 B86  C5   H5    single  0.930  0.020  1.080
 B86  N7   HN7   single  0.860  0.020  1.020
 B86  N7   HN7A  single  0.860  0.020  1.020
 B86  C10  H10   single  0.970  0.020  1.090
 B86  C12  H12   single  0.970  0.020  1.090
 B86  C13  H13   single  0.970  0.020  1.090
 B86  O13  HO13  single  0.850  0.020  0.980
 B86  C14  H14   single  0.970  0.020  1.090
 B86  C14  H14A  single  0.970  0.020  1.090
 B86  C15  H15   single  0.970  0.020  1.090
 B86  C15  H15A  single  0.970  0.020  1.090
 B86  O16  HO16  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
 B86  N7    C1   C6   120.22  3.000
 B86  N7    C1   N2   119.79  3.000
 B86  C6    C1   N2   120.00  3.000
 B86  C3    N2   C1   122.17  3.000
 B86  O9    C3   N4   119.63  3.000
 B86  O9    C3   N2   122.19  3.000
 B86  N4    C3   N2   118.17  3.000
 B86  C10   N4   C5   118.62  3.000
 B86  C10   N4   C3   120.93  3.000
 B86  C5    N4   C3   120.42  3.000
 B86  H5    C5   C6   121.74  3.000
 B86  H5    C5   N4   117.75  3.000
 B86  C6    C5   N4   120.52  3.000
 B86  F8    C6   C5   121.70  3.000
 B86  F8    C6   C1   119.58  3.000
 B86  C5    C6   C1   118.71  3.000
 B86  HN7A  N7   HN7  117.94  3.000
 B86  HN7A  N7   C1   122.48  3.000
 B86  HN7   N7   C1   119.58  3.000
 B86  H10   C10  C14  109.40  3.000
 B86  H10   C10  O11  109.83  3.000
 B86  C14   C10  O11  107.63  3.000
 B86  H10   C10  N4   104.52  3.000
 B86  C14   C10  N4   115.98  3.000
 B86  O11   C10  N4   109.39  3.000
 B86  C12   O11  C10  111.32  3.000
 B86  H12   C12  C15  109.43  3.000
 B86  H12   C12  C13  108.33  3.000
 B86  C15   C12  C13  112.69  3.000
 B86  H12   C12  O11  109.45  3.000
 B86  C15   C12  O11  110.11  3.000
 B86  C13   C12  O11  106.76  3.000
 B86  H13   C13  C14  109.92  3.000
 B86  H13   C13  O13  110.56  3.000
 B86  C14   C13  O13  114.70  3.000
 B86  H13   C13  C12  109.79  3.000
 B86  C14   C13  C12  102.81  3.000
 B86  O13   C13  C12  108.74  3.000
 B86  HO13  O13  C13  108.17  3.000
 B86  H14A  C14  H14  107.67  3.000
 B86  H14A  C14  C13  113.55  3.000
 B86  H14   C14  C13  108.93  3.000
 B86  H14A  C14  C10  113.08  3.000
 B86  H14   C14  C10  108.41  3.000
 B86  C13   C14  C10  105.04  3.000
 B86  H15A  C15  H15  107.29  3.000
 B86  H15A  C15  O16  112.02  3.000
 B86  H15   C15  O16  111.68  3.000
 B86  H15A  C15  C12  108.67  3.000
 B86  H15   C15  C12  107.54  3.000
 B86  O16   C15  C12  109.49  3.000
 B86  HO16  O16  C15  108.04  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
 B86  CONST_01  N4    C3  N2  C1    0.00  0.0  0
 B86  CONST_02  C5    N4  C3  N2    0.00  0.0  0
 B86  CONST_03  C10   N4  C3  N2  180.00  0.0  0
 B86  CONST_04  C6    C1  N2  C3    0.00  0.0  0
 B86  CONST_05  O9    C3  N2  C1  180.00  0.0  0
 B86  CONST_06  N7    C1  N2  C3  180.00  0.0  0
 B86  CONST_07  O9    C3  N4  C5  180.00  0.0  0
 B86  CONST_08  C10   N4  C3  O9    0.00  0.0  0
 B86  CONST_09  HN7   N7  C1  N2    0.00  0.0  0
 B86  CONST_10  HN7A  N7  C1  N2  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
 B86  chir_01  C10  N4   O11  C14  positiv
 B86  chir_02  C12  O11  C13  C15  negativ
 B86  chir_03  C13  O13  C12  C14  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
 B86  plan-1  C1    0.020
 B86  plan-1  N2    0.020
 B86  plan-1  C3    0.020
 B86  plan-1  N4    0.020
 B86  plan-1  C5    0.020
 B86  plan-1  C6    0.020
 B86  plan-1  N7    0.020
 B86  plan-1  F8    0.020
 B86  plan-1  O9    0.020
 B86  plan-1  C10   0.020
 B86  plan-1  H5    0.020
 B86  plan-1  HN7   0.020
 B86  plan-1  HN7A  0.020

