# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 16:37:50 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: 2'-deoxy-2',2'-difluorocytidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO)[C@@H](O)C2(F)F
#
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
 GEO  GEO  2'-deoxy-2',2'-difluorocytidine  ligand  29  18  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_GEO
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
 GEO  O5'   O  OH1   0  -0.670  -3.2150   2.6967  -0.6279
 GEO  C5'   C  CH2   0  -0.159  -2.9175   1.6958   0.3145
 GEO  C4'   C  CR15  0  -0.004  -2.4009   0.4787  -0.4094
 GEO  O4'   O  O     0  -0.483  -1.1399   0.7603  -1.0066
 GEO  C1'   C  CR15  0   0.099  -0.3301  -0.3720  -1.0441
 GEO  N1    N  NR6   0  -0.558   1.0184  -0.0702  -0.6247
 GEO  C6    C  CR16  0   0.105   2.0382  -0.2960  -1.4945
 GEO  C5    C  CR16  0  -0.474   3.3164  -0.0385  -1.1675
 GEO  C4    C  CR6   0   0.519   3.5427   0.4952   0.1405
 GEO  N3    N  N     0  -0.540   2.5556   0.7233   0.9847
 GEO  C2    C  CR6   0   0.612   1.2785   0.4511   0.6579
 GEO  O2    O  OC    0  -0.507   0.3453   0.6357   1.4242
 GEO  N4    N  NH2   0  -0.805   4.7835   0.7774   0.5269
 GEO  C2'   C  CR5   0   0.708  -1.0565  -1.4505  -0.2092
 GEO  F1    F  F     0  -0.323  -0.2201  -2.1386   0.5996
 GEO  F2    F  F     0  -0.338  -1.5824  -2.3660  -1.0668
 GEO  C3'   C  CR15  0  -0.100  -2.1807  -0.7160   0.5177
 GEO  O3'   O  OH1   0  -0.657  -3.3606  -1.4455   0.6464
 GEO  H5'   H  HOH1  0   0.459  -3.5973   3.4452  -0.1610
 GEO  H5'1  H  HCH2  0   0.209  -3.8077   1.3874   0.8774
 GEO  H5'2  H  HCH2  0   0.207  -2.1661   2.0234   1.0438
 GEO  H4'   H  HCR5  0   0.245  -3.1208   0.1890  -1.1884
 GEO  H1'   H  HCR5  0   0.279  -0.2416  -0.7474  -2.0691
 GEO  H6    H  HCR6  0   0.324   1.7654  -0.6919  -2.4628
 GEO  H5    H  HCR6  0   0.292   4.1196  -0.2183  -1.8655
 GEO  HN41  H  HNH2  0   0.405   4.9562   1.1520   1.4444
 GEO  HN42  H  HNH2  0   0.417   5.5731   0.6095  -0.0716
 GEO  H3'   H  HCR5  0   0.272  -1.7963  -0.3755   1.4826
 GEO  H1    H  HOH1  0   0.467  -3.3369  -1.9387   1.4719

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
 GEO  O5'  C5'   single    1.407  0.020  1.407
 GEO  O5'  H5'   single    0.850  0.020  0.980
 GEO  C5'  C4'   single    1.507  0.020  1.507
 GEO  C5'  H5'1  single    0.970  0.020  1.090
 GEO  C5'  H5'2  single    0.970  0.020  1.090
 GEO  C4'  O4'   single    1.423  0.020  1.423
 GEO  C4'  C3'   single    1.528  0.020  1.528
 GEO  C4'  H4'   single    0.970  0.020  1.090
 GEO  O4'  C1'   single    1.393  0.020  1.393
 GEO  C1'  N1    single    1.444  0.020  1.444
 GEO  C1'  C2'   single    1.545  0.020  1.545
 GEO  C1'  H1'   single    0.970  0.020  1.090
 GEO  N1   C6    aromatic  1.359  0.020  1.359
 GEO  N1   C2    aromatic  1.409  0.020  1.409
 GEO  C6   C5    aromatic  1.344  0.020  1.344
 GEO  C6   H6    single    0.930  0.020  1.080
 GEO  C5   C4    aromatic  1.431  0.020  1.431
 GEO  C5   H5    single    0.930  0.020  1.080
 GEO  C4   N3    aromatic  1.319  0.020  1.319
 GEO  C4   N4    single    1.330  0.020  1.330
 GEO  N3   C2    aromatic  1.346  0.020  1.346
 GEO  C2   O2    double    1.222  0.020  1.222
 GEO  N4   HN41  single    0.860  0.020  1.020
 GEO  N4   HN42  single    0.860  0.020  1.020
 GEO  C2'  F1    single    1.352  0.020  1.352
 GEO  C2'  F2    single    1.360  0.020  1.360
 GEO  C2'  C3'   single    1.527  0.020  1.527
 GEO  C3'  O3'   single    1.393  0.020  1.393
 GEO  C3'  H3'   single    0.970  0.020  1.090
 GEO  O3'  H1    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
 GEO  H5'   O5'  C5'   108.22  3.000
 GEO  H5'2  C5'  H5'1  107.37  3.000
 GEO  H5'2  C5'  C4'   109.01  3.000
 GEO  H5'1  C5'  C4'   107.30  3.000
 GEO  H5'2  C5'  O5'   112.19  3.000
 GEO  H5'1  C5'  O5'   111.84  3.000
 GEO  C4'   C5'  O5'   108.98  3.000
 GEO  H4'   C4'  C3'   108.56  3.000
 GEO  H4'   C4'  O4'   109.57  3.000
 GEO  C3'   C4'  O4'   106.36  3.000
 GEO  H4'   C4'  C5'   109.18  3.000
 GEO  C3'   C4'  C5'   112.90  3.000
 GEO  O4'   C4'  C5'   110.20  3.000
 GEO  C1'   O4'  C4'   111.44  3.000
 GEO  H1'   C1'  C2'   107.72  3.000
 GEO  H1'   C1'  N1    105.54  3.000
 GEO  C2'   C1'  N1    115.33  3.000
 GEO  H1'   C1'  O4'   110.55  3.000
 GEO  C2'   C1'  O4'   106.23  3.000
 GEO  N1    C1'  O4'   111.43  3.000
 GEO  C2    N1   C6    120.37  3.000
 GEO  C2    N1   C1'   120.94  3.000
 GEO  C6    N1   C1'   118.69  3.000
 GEO  H6    C6   C5    121.87  3.000
 GEO  H6    C6   N1    116.40  3.000
 GEO  C5    C6   N1    121.73  3.000
 GEO  H5    C5   C4    122.40  3.000
 GEO  H5    C5   C6    121.22  3.000
 GEO  C4    C5   C6    116.37  3.000
 GEO  N4    C4   N3    118.41  3.000
 GEO  N4    C4   C5    119.49  3.000
 GEO  N3    C4   C5    122.10  3.000
 GEO  C2    N3   C4    121.32  3.000
 GEO  O2    C2   N3    122.81  3.000
 GEO  O2    C2   N1    119.08  3.000
 GEO  N3    C2   N1    118.10  3.000
 GEO  HN42  N4   HN41  118.07  3.000
 GEO  HN42  N4   C4    121.64  3.000
 GEO  HN41  N4   C4    120.27  3.000
 GEO  C3'   C2'  F2    109.83  3.000
 GEO  C3'   C2'  F1    114.55  3.000
 GEO  F2    C2'  F1    105.89  3.000
 GEO  C3'   C2'  C1'   105.52  3.000
 GEO  F2    C2'  C1'   108.11  3.000
 GEO  F1    C2'  C1'   112.81  3.000
 GEO  H3'   C3'  O3'   112.30  3.000
 GEO  H3'   C3'  C2'   108.13  3.000
 GEO  O3'   C3'  C2'   114.56  3.000
 GEO  H3'   C3'  C4'   110.05  3.000
 GEO  O3'   C3'  C4'   110.08  3.000
 GEO  C2'   C3'  C4'   101.14  3.000
 GEO  H1    O3'  C3'   109.07  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
 GEO  CONST_01  C4    C5  C6  N1     0.00  0.0  0
 GEO  CONST_02  C4    N3  C2  N1     0.00  0.0  0
 GEO  CONST_03  N3    C2  N1  C6     0.00  0.0  0
 GEO  CONST_04  N3    C4  C5  C6     0.00  0.0  0
 GEO  CONST_05  C2    N1  C6  C5     0.00  0.0  0
 GEO  CONST_06  C2    N3  C4  C5     0.00  0.0  0
 GEO  CONST_07  C5    C6  N1  C1'  180.00  0.0  0
 GEO  CONST_08  N3    C2  N1  C1'  180.00  0.0  0
 GEO  CONST_09  O2    C2  N1  C1'    0.00  0.0  0
 GEO  CONST_10  O2    C2  N1  C6   180.00  0.0  0
 GEO  CONST_11  N4    C4  C5  C6   180.00  0.0  0
 GEO  CONST_12  O2    C2  N3  C4   180.00  0.0  0
 GEO  CONST_13  N4    C4  N3  C2   180.00  0.0  0
 GEO  CONST_14  H6    C6  N1  C1'    0.00  0.0  0
 GEO  CONST_15  H5    C5  C6  N1   180.00  0.0  0
 GEO  CONST_16  HN41  N4  C4  C5   180.00  0.0  0
 GEO  CONST_17  HN42  N4  C4  C5     0.00  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
 GEO  chir_01  C4'  C5'  O4'  C3'  negativ
 GEO  chir_02  C1'  O4'  N1   C2'  negativ
 GEO  chir_03  C3'  O3'  C4'  C2'  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
 GEO  plan-1  C1'   0.020
 GEO  plan-1  N1    0.020
 GEO  plan-1  C6    0.020
 GEO  plan-1  C5    0.020
 GEO  plan-1  C4    0.020
 GEO  plan-1  N3    0.020
 GEO  plan-1  C2    0.020
 GEO  plan-1  O2    0.020
 GEO  plan-1  N4    0.020
 GEO  plan-1  H6    0.020
 GEO  plan-1  H5    0.020
 GEO  plan-2  C4    0.020
 GEO  plan-2  N4    0.020
 GEO  plan-2  HN41  0.020
 GEO  plan-2  HN42  0.020

