# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 00:34:59 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 2'-cytidylic acid
#   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[P](O)(O)=O
#
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
 C2P  C2P  '2'-cytidylic acid        '  ligand  35  21  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_C2P
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
 C2P  N1    N  NR6   0  -0.560   0.9672  -0.4186   1.3535
 C2P  C2    C  CR6   0   0.606   1.5443   0.8515   1.5258
 C2P  N3    N  N     0  -0.540   2.0404   1.1674   2.7368
 C2P  C4    C  CR6   0   0.518   1.9731   0.3183   3.7444
 C2P  C5    C  CR16  0  -0.476   1.3810  -0.9759   3.6096
 C2P  C6    C  CR16  0   0.102   0.9062  -1.2915   2.3907
 C2P  O2    O  O     0  -0.509   1.5675   1.6244   0.5780
 C2P  N4    N  NH2   0  -0.806   2.4811   0.6887   4.9172
 C2P  C1'   C  CR15  0   0.222   0.4878  -0.8352   0.0512
 C2P  C2'   C  CR15  0  -0.090  -0.5778   0.0726  -0.5915
 C2P  O2'   O  O2    0  -0.600  -1.6825  -0.7741  -0.9052
 C2P  C3'   C  CR15  0   0.026   0.0949   0.5831  -1.8790
 C2P  C4'   C  CR15  0   0.005   1.1962  -0.4479  -2.1192
 C2P  O4'   O  O     0  -0.488   1.5629  -0.9238  -0.8361
 C2P  O3'   O  OH1   0  -0.654  -0.7374   0.6480  -2.9973
 C2P  C5'   C  CH2   0  -0.161   2.4005   0.1424  -2.8095
 C2P  O5'   O  OH1   0  -0.671   3.3227  -0.8815  -3.0940
 C2P  P     P  P     0   1.456  -3.1385  -0.1696  -1.1642
 C2P  O1P   O  O     0  -0.715  -3.2191   1.2872  -1.3909
 C2P  O2P   O  OH1   0  -0.728  -3.5822  -1.1493  -2.3396
 C2P  O3P   O  OH1   0  -0.731  -4.0115  -0.5528   0.1180
 C2P  H5    H  HCR6  0   0.291   1.3240  -1.6730   4.4312
 C2P  H6    H  HCR6  0   0.322   0.4530  -2.2518   2.1860
 C2P  HN41  H  HNH2  0   0.405   2.9013   1.5966   5.0233
 C2P  HN42  H  HNH2  0   0.415   2.4371   0.0905   5.7233
 C2P  H1'   H  HCR5  0   0.263   0.0386  -1.8209   0.2110
 C2P  H2'   H  HCR5  0   0.290  -0.8929   0.8806   0.0698
 C2P  H3'   H  HCR5  0   0.249   0.5441   1.5534  -1.6529
 C2P  H4'   H  HCR5  0   0.235   0.7882  -1.2707  -2.7256
 C2P  HO3'  H  HOH1  0   0.459  -1.2648   1.4517  -2.9462
 C2P  H5'1  H  HCH2  0   0.206   2.0482   0.6397  -3.7225
 C2P  H5'2  H  HCH2  0   0.202   2.8293   0.9179  -2.1606
 C2P  HO5'  H  HOH1  0   0.458   4.0743  -0.4907  -3.5482
 C2P  HOP2  H  HOH1  0   0.502  -4.5089  -1.0607  -2.6007
 C2P  HOP3  H  HOH1  0   0.496  -4.0381  -1.4923   0.3438

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
 C2P  N1   C2    single  1.406  0.020  1.406
 C2P  N1   C6    single  1.357  0.020  1.357
 C2P  N1   C1'   single  1.449  0.020  1.449
 C2P  C2   N3    single  1.346  0.020  1.346
 C2P  C2   O2    double  1.223  0.020  1.223
 C2P  N3   C4    double  1.319  0.020  1.319
 C2P  C4   C5    single  1.430  0.020  1.430
 C2P  C4   N4    single  1.331  0.020  1.331
 C2P  C5   C6    double  1.346  0.020  1.346
 C2P  C5   H5    single  0.930  0.020  1.080
 C2P  C6   H6    single  0.930  0.020  1.080
 C2P  N4   HN41  single  0.860  0.020  1.020
 C2P  N4   HN42  single  0.860  0.020  1.020
 C2P  C1'  C2'   single  1.540  0.020  1.540
 C2P  C1'  O4'   single  1.397  0.020  1.397
 C2P  C1'  H1'   single  0.970  0.020  1.090
 C2P  C2'  O2'   single  1.427  0.020  1.427
 C2P  C2'  C3'   single  1.540  0.020  1.540
 C2P  C2'  H2'   single  0.970  0.020  1.090
 C2P  O2'  P     single  1.598  0.020  1.598
 C2P  C3'  C4'   single  1.528  0.020  1.528
 C2P  C3'  O3'   single  1.396  0.020  1.396
 C2P  C3'  H3'   single  0.970  0.020  1.090
 C2P  C4'  O4'   single  1.417  0.020  1.417
 C2P  C4'  C5'   single  1.508  0.020  1.508
 C2P  C4'  H4'   single  0.970  0.020  1.090
 C2P  O3'  HO3'  single  0.850  0.020  0.980
 C2P  C5'  O5'   single  1.407  0.020  1.407
 C2P  C5'  H5'1  single  0.970  0.020  1.090
 C2P  C5'  H5'2  single  0.970  0.020  1.090
 C2P  O5'  HO5'  single  0.850  0.020  0.980
 C2P  P    O1P   double  1.476  0.020  1.476
 C2P  P    O2P   single  1.593  0.020  1.593
 C2P  P    O3P   single  1.598  0.020  1.598
 C2P  O2P  HOP2  single  0.850  0.020  0.980
 C2P  O3P  HOP3  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
 C2P  C1'   N1   C6    119.16  3.000
 C2P  C1'   N1   C2    120.38  3.000
 C2P  C6    N1   C2    120.40  3.000
 C2P  O2    C2   N3    122.80  3.000
 C2P  O2    C2   N1    118.93  3.000
 C2P  N3    C2   N1    118.27  3.000
 C2P  C4    N3   C2    121.14  3.000
 C2P  N4    C4   C5    119.55  3.000
 C2P  N4    C4   N3    118.32  3.000
 C2P  C5    C4   N3    122.12  3.000
 C2P  H5    C5   C6    121.31  3.000
 C2P  H5    C5   C4    122.34  3.000
 C2P  C6    C5   C4    116.35  3.000
 C2P  H6    C6   C5    121.84  3.000
 C2P  H6    C6   N1    116.45  3.000
 C2P  C5    C6   N1    121.71  3.000
 C2P  HN42  N4   HN41  118.09  3.000
 C2P  HN42  N4   C4    121.64  3.000
 C2P  HN41  N4   C4    120.24  3.000
 C2P  H1'   C1'  O4'   110.57  3.000
 C2P  H1'   C1'  C2'   107.92  3.000
 C2P  O4'   C1'  C2'   107.75  3.000
 C2P  H1'   C1'  N1    105.27  3.000
 C2P  O4'   C1'  N1    109.55  3.000
 C2P  C2'   C1'  N1    115.75  3.000
 C2P  H2'   C2'  C3'   112.81  3.000
 C2P  H2'   C2'  O2'   110.44  3.000
 C2P  C3'   C2'  O2'   110.56  3.000
 C2P  H2'   C2'  C1'   112.55  3.000
 C2P  C3'   C2'  C1'   104.01  3.000
 C2P  O2'   C2'  C1'   106.12  3.000
 C2P  P     O2'  C2'   121.11  3.000
 C2P  H3'   C3'  O3'   111.69  3.000
 C2P  H3'   C3'  C4'   109.60  3.000
 C2P  O3'   C3'  C4'   109.60  3.000
 C2P  H3'   C3'  C2'   107.51  3.000
 C2P  O3'   C3'  C2'   115.15  3.000
 C2P  C4'   C3'  C2'   102.87  3.000
 C2P  H4'   C4'  C5'   109.66  3.000
 C2P  H4'   C4'  O4'   110.11  3.000
 C2P  C5'   C4'  O4'   109.84  3.000
 C2P  H4'   C4'  C3'   108.90  3.000
 C2P  C5'   C4'  C3'   112.54  3.000
 C2P  O4'   C4'  C3'   105.71  3.000
 C2P  C4'   O4'  C1'   110.78  3.000
 C2P  HO3'  O3'  C3'   108.85  3.000
 C2P  H5'2  C5'  H5'1  107.27  3.000
 C2P  H5'2  C5'  O5'   112.17  3.000
 C2P  H5'1  C5'  O5'   111.83  3.000
 C2P  H5'2  C5'  C4'   108.52  3.000
 C2P  H5'1  C5'  C4'   107.56  3.000
 C2P  O5'   C5'  C4'   109.33  3.000
 C2P  HO5'  O5'  C5'   108.19  3.000
 C2P  O3P   P    O2P   107.00  3.000
 C2P  O3P   P    O1P   109.27  3.000
 C2P  O2P   P    O1P   118.57  3.000
 C2P  O3P   P    O2'   106.08  3.000
 C2P  O2P   P    O2'    98.09  3.000
 C2P  O1P   P    O2'   116.62  3.000
 C2P  HOP2  O2P  P     114.19  3.000
 C2P  HOP3  O3P  P     115.83  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
 C2P  CONST_01  C4    N3  C2   N1     0.00   0.0  0
 C2P  CONST_02  C5    C4  N3   C2     0.00   0.0  0
 C2P  CONST_03  C6    N1  C2   N3     0.00   0.0  0
 C2P  CONST_04  C1'   N1  C2   N3   180.00   0.0  0
 C2P  CONST_05  N4    C4  N3   C2   180.00   0.0  0
 C2P  CONST_06  O2    C2  N3   C4   180.00   0.0  0
 C2P  CONST_07  O2    C2  N1   C6   180.00   0.0  0
 C2P  CONST_08  C1'   N1  C2   O2     0.00   0.0  0
 C2P  CONST_09  HN41  N4  C4   N3     0.00   0.0  0
 C2P  CONST_10  HN42  N4  C4   N3   180.00   0.0  0
 C2P  Var_01    O1P   P   O2'  C2'   14.53  30.0  3

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
 C2P  chir_01  C1'  N1   C2'  O4'  negativ
 C2P  chir_02  C2'  O2'  C3'  C1'  positiv
 C2P  chir_03  C3'  O3'  C2'  C4'  negativ
 C2P  chir_04  C4'  O4'  C3'  C5'  negativ

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
 C2P  plan-1  N1    0.020
 C2P  plan-1  C2    0.020
 C2P  plan-1  N3    0.020
 C2P  plan-1  C4    0.020
 C2P  plan-1  C5    0.020
 C2P  plan-1  C6    0.020
 C2P  plan-1  O2    0.020
 C2P  plan-1  N4    0.020
 C2P  plan-1  C1'   0.020
 C2P  plan-1  H5    0.020
 C2P  plan-1  H6    0.020
 C2P  plan-1  HN41  0.020
 C2P  plan-1  HN42  0.020

