# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 16:49:18 2022
#   Inital geometry file: a 74 line input string
#   Ligand name: cytidine
#   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)[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
 CTN  CTN  'cytidine                 '  ligand  30  17  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CTN
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
 CTN  O5'   O  OH1   0  -0.671  -3.1576   2.4344  -1.0691
 CTN  C5'   C  CH2   0  -0.162  -2.9120   1.6269   0.0576
 CTN  C4'   C  CR15  0   0.023  -2.4022   0.2821  -0.3953
 CTN  O4'   O  O     0  -0.492  -1.1286   0.4234  -1.0002
 CTN  C1'   C  CR15  0   0.208  -0.3435  -0.7150  -0.7818
 CTN  N1    N  NR6   0  -0.557   1.0125  -0.3131  -0.4458
 CTN  C6    C  CR16  0   0.102   2.0125  -0.5740  -1.3236
 CTN  C5    C  CR16  0  -0.477   3.2831  -0.1950  -1.0882
 CTN  C4    C  CR6   0   0.515   3.5171   0.5113   0.1319
 CTN  N3    N  N     0  -0.541   2.5467   0.7770   0.9844
 CTN  C2    C  CR6   0   0.603   1.2796   0.3869   0.7428
 CTN  O2    O  OC    0  -0.508   0.3621   0.6141   1.5185
 CTN  N4    N  NH2   0  -0.808   4.7480   0.9241   0.4280
 CTN  C2'   C  CR15  0  -0.046  -1.0693  -1.6006   0.2465
 CTN  O2'   O  OH1   0  -0.678  -1.5979  -2.7059  -0.4433
 CTN  C3'   C  CR15  0  -0.032  -2.2058  -0.6975   0.7601
 CTN  O3'   O  OH1   0  -0.665  -3.3990  -1.4055   0.9923
 CTN  H5'   H  HOH1  0   0.457  -3.5167   3.2725  -0.7646
 CTN  H5'1  H  HCH2  0   0.204  -3.8255   1.4541   0.6416
 CTN  H5'2  H  HCH2  0   0.201  -2.1722   2.0759   0.7337
 CTN  H4'   H  HCR5  0   0.228  -3.1120  -0.1554  -1.1135
 CTN  H1'   H  HCR5  0   0.251  -0.2467  -1.2932  -1.7062
 CTN  H6    H  HCR6  0   0.319   1.7355  -1.1073  -2.2225
 CTN  H5    H  HCR6  0   0.289   4.0719  -0.4111  -1.7924
 CTN  HN41  H  HNH2  0   0.403   4.9236   1.4147   1.2882
 CTN  HN42  H  HNH2  0   0.415   5.5278   0.7333  -0.1759
 CTN  H2'   H  HCR5  0   0.245  -0.4027  -1.9277   1.0521
 CTN  H1    H  HOH1  0   0.447  -2.4753  -2.8738  -0.0727
 CTN  H3'   H  HCR5  0   0.258  -1.8778  -0.1686   1.6553
 CTN  H2    H  HOH1  0   0.468  -3.4159  -1.6900   1.9113

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
 CTN  O5'  C5'   single    1.408  0.020  1.408
 CTN  O5'  H5'   single    0.850  0.020  0.980
 CTN  C5'  C4'   single    1.508  0.020  1.508
 CTN  C5'  H5'1  single    0.970  0.020  1.090
 CTN  C5'  H5'2  single    0.970  0.020  1.090
 CTN  C4'  O4'   single    1.417  0.020  1.417
 CTN  C4'  C3'   single    1.527  0.020  1.527
 CTN  C4'  H4'   single    0.970  0.020  1.090
 CTN  O4'  C1'   single    1.400  0.020  1.400
 CTN  C1'  N1    single    1.454  0.020  1.454
 CTN  C1'  C2'   single    1.539  0.020  1.539
 CTN  C1'  H1'   single    0.970  0.020  1.090
 CTN  N1   C6    aromatic  1.356  0.020  1.356
 CTN  N1   C2    aromatic  1.405  0.020  1.405
 CTN  C6   C5    aromatic  1.347  0.020  1.347
 CTN  C6   H6    single    0.930  0.020  1.080
 CTN  C5   C4    aromatic  1.429  0.020  1.429
 CTN  C5   H5    single    0.930  0.020  1.080
 CTN  C4   N3    aromatic  1.319  0.020  1.319
 CTN  C4   N4    single    1.332  0.020  1.332
 CTN  N3   C2    aromatic  1.348  0.020  1.348
 CTN  C2   O2    double    1.223  0.020  1.223
 CTN  N4   HN41  single    0.860  0.020  1.020
 CTN  N4   HN42  single    0.860  0.020  1.020
 CTN  C2'  O2'   single    1.406  0.020  1.406
 CTN  C2'  C3'   single    1.540  0.020  1.540
 CTN  C2'  H2'   single    0.970  0.020  1.090
 CTN  O2'  H1    single    0.850  0.020  0.980
 CTN  C3'  O3'   single    1.407  0.020  1.407
 CTN  C3'  H3'   single    0.970  0.020  1.090
 CTN  O3'  H2    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
 CTN  H5'   O5'  C5'   108.16  3.000
 CTN  H5'2  C5'  H5'1  107.30  3.000
 CTN  H5'2  C5'  C4'   108.77  3.000
 CTN  H5'1  C5'  C4'   107.50  3.000
 CTN  H5'2  C5'  O5'   112.07  3.000
 CTN  H5'1  C5'  O5'   111.76  3.000
 CTN  C4'   C5'  O5'   109.28  3.000
 CTN  H4'   C4'  C3'   108.76  3.000
 CTN  H4'   C4'  O4'   109.92  3.000
 CTN  C3'   C4'  O4'   105.74  3.000
 CTN  H4'   C4'  C5'   109.42  3.000
 CTN  C3'   C4'  C5'   112.85  3.000
 CTN  O4'   C4'  C5'   110.07  3.000
 CTN  C1'   O4'  C4'   110.87  3.000
 CTN  H1'   C1'  C2'   107.58  3.000
 CTN  H1'   C1'  N1    104.99  3.000
 CTN  C2'   C1'  N1    116.40  3.000
 CTN  H1'   C1'  O4'   110.33  3.000
 CTN  C2'   C1'  O4'   107.92  3.000
 CTN  N1    C1'  O4'   109.53  3.000
 CTN  C2    N1   C6    120.22  3.000
 CTN  C2    N1   C1'   120.70  3.000
 CTN  C6    N1   C1'   119.02  3.000
 CTN  H6    C6   C5    121.73  3.000
 CTN  H6    C6   N1    116.36  3.000
 CTN  C5    C6   N1    121.91  3.000
 CTN  H5    C5   C4    122.43  3.000
 CTN  H5    C5   C6    121.28  3.000
 CTN  C4    C5   C6    116.29  3.000
 CTN  N4    C4   N3    118.29  3.000
 CTN  N4    C4   C5    119.63  3.000
 CTN  N3    C4   C5    122.07  3.000
 CTN  C2    N3   C4    121.18  3.000
 CTN  O2    C2   N3    122.55  3.000
 CTN  O2    C2   N1    119.11  3.000
 CTN  N3    C2   N1    118.33  3.000
 CTN  HN42  N4   HN41  118.11  3.000
 CTN  HN42  N4   C4    121.67  3.000
 CTN  HN41  N4   C4    120.19  3.000
 CTN  H2'   C2'  C3'   112.27  3.000
 CTN  H2'   C2'  O2'   110.78  3.000
 CTN  C3'   C2'  O2'   110.32  3.000
 CTN  H2'   C2'  C1'   112.10  3.000
 CTN  C3'   C2'  C1'   103.50  3.000
 CTN  O2'   C2'  C1'   107.57  3.000
 CTN  H1    O2'  C2'   106.83  3.000
 CTN  H3'   C3'  O3'   111.33  3.000
 CTN  H3'   C3'  C2'   109.66  3.000
 CTN  O3'   C3'  C2'   112.70  3.000
 CTN  H3'   C3'  C4'   110.41  3.000
 CTN  O3'   C3'  C4'   109.79  3.000
 CTN  C2'   C3'  C4'   102.64  3.000
 CTN  H2    O3'  C3'   108.75  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
 CTN  CONST_01  C4    C5  C6  N1     0.00  0.0  0
 CTN  CONST_02  C4    N3  C2  N1     0.00  0.0  0
 CTN  CONST_03  N3    C2  N1  C6     0.00  0.0  0
 CTN  CONST_04  N3    C4  C5  C6     0.00  0.0  0
 CTN  CONST_05  C2    N1  C6  C5     0.00  0.0  0
 CTN  CONST_06  C2    N3  C4  C5     0.00  0.0  0
 CTN  CONST_07  C5    C6  N1  C1'  180.00  0.0  0
 CTN  CONST_08  N3    C2  N1  C1'  180.00  0.0  0
 CTN  CONST_09  O2    C2  N1  C1'    0.00  0.0  0
 CTN  CONST_10  O2    C2  N1  C6   180.00  0.0  0
 CTN  CONST_11  N4    C4  C5  C6   180.00  0.0  0
 CTN  CONST_12  O2    C2  N3  C4   180.00  0.0  0
 CTN  CONST_13  N4    C4  N3  C2   180.00  0.0  0
 CTN  CONST_14  H6    C6  N1  C1'    0.00  0.0  0
 CTN  CONST_15  H5    C5  C6  N1   180.00  0.0  0
 CTN  CONST_16  HN41  N4  C4  C5   180.00  0.0  0
 CTN  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
 CTN  chir_01  C4'  C5'  O4'  C3'  negativ
 CTN  chir_02  C1'  O4'  N1   C2'  negativ
 CTN  chir_03  C2'  O2'  C1'  C3'  negativ
 CTN  chir_04  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
 CTN  plan-1  C1'   0.020
 CTN  plan-1  N1    0.020
 CTN  plan-1  C6    0.020
 CTN  plan-1  C5    0.020
 CTN  plan-1  C4    0.020
 CTN  plan-1  N3    0.020
 CTN  plan-1  C2    0.020
 CTN  plan-1  O2    0.020
 CTN  plan-1  N4    0.020
 CTN  plan-1  H6    0.020
 CTN  plan-1  H5    0.020
 CTN  plan-2  C4    0.020
 CTN  plan-2  N4    0.020
 CTN  plan-2  HN41  0.020
 CTN  plan-2  HN42  0.020

