# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 10:31:06 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 5'-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[P](O)(O)=O)[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
 C5P  C5P  '5'-cytidylic acid        '  ligand  33  21  .  2020-10-21  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_C5P
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
 C5P  O3P   O  OP    -1  -0.898  -4.2496   1.8832  -1.5886
 C5P  P     P  P      0   1.223  -3.9033   1.2084  -0.2683
 C5P  O1P   O  O      0  -0.907  -3.4534   2.1510   0.8429
 C5P  O2P   O  OP    -1  -0.905  -4.8857   0.1335   0.1843
 C5P  O5'   O  O2     0  -0.659  -2.4930   0.3504  -0.7121
 C5P  C5'   C  CH2    0  -0.131  -1.8379  -0.3483   0.2997
 C5P  C4'   C  CR15   0   0.015  -0.7983  -1.2745  -0.2864
 C5P  O4'   O  O      0  -0.492   0.2336  -0.5206  -0.9048
 C5P  C3'   C  CR15   0  -0.034  -0.1058  -2.1379   0.7649
 C5P  O3'   O  OH1    0  -0.667  -0.8104  -3.3460   0.9300
 C5P  C2'   C  CR15   0  -0.045   1.2994  -2.3531   0.1721
 C5P  O2'   O  OH1    0  -0.680   1.3297  -3.5323  -0.5938
 C5P  C1'   C  CR15   0   0.208   1.4700  -1.1626  -0.7880
 C5P  N1    N  NT     0  -0.556   2.4892  -0.1843  -0.4380
 C5P  C2    C  C      0   0.602   2.4665   0.4634   0.8084
 C5P  N3    N  N      0  -0.541   3.3890   1.4156   1.0524
 C5P  C4    C  C      0   0.514   4.2875   1.7439   0.1450
 C5P  C5    C  C1     0  -0.478   4.3354   1.1155  -1.1370
 C5P  C6    C  C1     0   0.101   3.4084   0.1670  -1.3706
 C5P  O2    O  O      0  -0.507   1.6221   0.1411   1.6320
 C5P  N4    N  NH2    0  -0.808   5.1733   2.6920   0.4456
 C5P  H5'1  H  HCH2   0   0.174  -2.5330  -0.9686   0.8848
 C5P  H5'2  H  HCH2   0   0.175  -1.3385   0.3240   1.0118
 C5P  H4'   H  HCR5   0   0.215  -1.2730  -1.9334  -1.0292
 C5P  H3'   H  HCR5   0   0.255  -0.0286  -1.5968   1.7084
 C5P  HO3'  H  HOH1   0   0.467  -0.6679  -3.6672   1.8256
 C5P  H2'1  H  HCR5   0   0.242   2.0770  -2.3748   0.9424
 C5P  HO2'  H  HOH1   0   0.446   0.6312  -4.1022  -0.2422
 C5P  H1'   H  HCR5   0   0.247   1.7870  -1.5640  -1.7563
 C5P  H5    H  H      0   0.288   5.0643   1.3837  -1.8864
 C5P  H6    H  H      0   0.319   3.3620  -0.3586  -2.3142
 C5P  HN41  H  HNH2   0   0.403   5.1425   3.1498   1.3406
 C5P  HN42  H  HNH2   0   0.414   5.8652   2.9941  -0.2171

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
 C5P  O3P  P     deloc   1.523  0.020  1.523
 C5P  P    O1P   deloc   1.525  0.020  1.525
 C5P  P    O2P   deloc   1.525  0.020  1.525
 C5P  P    O5'   single  1.709  0.020  1.709
 C5P  O5'  C5'   single  1.393  0.020  1.393
 C5P  C5'  C4'   single  1.511  0.020  1.511
 C5P  C5'  H5'1  single  0.970  0.020  1.090
 C5P  C5'  H5'2  single  0.970  0.020  1.090
 C5P  C4'  O4'   single  1.420  0.020  1.420
 C5P  C4'  C3'   single  1.526  0.020  1.526
 C5P  C4'  H4'   single  0.970  0.020  1.090
 C5P  O4'  C1'   single  1.398  0.020  1.398
 C5P  C3'  O3'   single  1.408  0.020  1.408
 C5P  C3'  C2'   single  1.540  0.020  1.540
 C5P  C3'  H3'   single  0.970  0.020  1.090
 C5P  O3'  HO3'  single  0.850  0.020  0.980
 C5P  C2'  O2'   single  1.406  0.020  1.406
 C5P  C2'  C1'   single  1.539  0.020  1.539
 C5P  C2'  H2'1  single  0.970  0.020  1.090
 C5P  O2'  HO2'  single  0.850  0.020  0.980
 C5P  C1'  N1    single  1.455  0.020  1.455
 C5P  C1'  H1'   single  0.970  0.020  1.090
 C5P  N1   C2    single  1.405  0.020  1.405
 C5P  N1   C6    single  1.356  0.020  1.356
 C5P  C2   N3    single  1.348  0.020  1.348
 C5P  C2   O2    double  1.223  0.020  1.223
 C5P  N3   C4    double  1.319  0.020  1.319
 C5P  C4   C5    single  1.428  0.020  1.428
 C5P  C4   N4    single  1.332  0.020  1.332
 C5P  C5   C6    double  1.347  0.020  1.347
 C5P  C5   H5    single  0.930  0.020  1.080
 C5P  C6   H6    single  0.930  0.020  1.080
 C5P  N4   HN41  single  0.860  0.020  1.020
 C5P  N4   HN42  single  0.860  0.020  1.020

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
 C5P  O5'   P    O2P   104.76  3.000
 C5P  O5'   P    O1P   104.83  3.000
 C5P  O2P   P    O1P   114.17  3.000
 C5P  O5'   P    O3P   100.66  3.000
 C5P  O2P   P    O3P   115.04  3.000
 C5P  O1P   P    O3P   115.15  3.000
 C5P  C5'   O5'  P     116.81  3.000
 C5P  H5'2  C5'  H5'1  106.70  3.000
 C5P  H5'2  C5'  C4'   108.27  3.000
 C5P  H5'1  C5'  C4'   107.18  3.000
 C5P  H5'2  C5'  O5'   112.17  3.000
 C5P  H5'1  C5'  O5'   111.84  3.000
 C5P  C4'   C5'  O5'   110.45  3.000
 C5P  H4'   C4'  C3'   108.77  3.000
 C5P  H4'   C4'  O4'   109.72  3.000
 C5P  C3'   C4'  O4'   105.70  3.000
 C5P  H4'   C4'  C5'   109.40  3.000
 C5P  C3'   C4'  C5'   113.07  3.000
 C5P  O4'   C4'  C5'   110.10  3.000
 C5P  C1'   O4'  C4'   111.26  3.000
 C5P  H3'   C3'  C2'   109.74  3.000
 C5P  H3'   C3'  O3'   111.08  3.000
 C5P  C2'   C3'  O3'   112.44  3.000
 C5P  H3'   C3'  C4'   110.33  3.000
 C5P  C2'   C3'  C4'   103.17  3.000
 C5P  O3'   C3'  C4'   109.81  3.000
 C5P  HO3'  O3'  C3'   108.75  3.000
 C5P  H2'1  C2'  C1'   112.07  3.000
 C5P  H2'1  C2'  O2'   110.56  3.000
 C5P  C1'   C2'  O2'   107.85  3.000
 C5P  H2'1  C2'  C3'   112.33  3.000
 C5P  C1'   C2'  C3'   103.48  3.000
 C5P  O2'   C2'  C3'   110.27  3.000
 C5P  HO2'  O2'  C2'   106.29  3.000
 C5P  H1'   C1'  N1    104.85  3.000
 C5P  H1'   C1'  C2'   107.47  3.000
 C5P  N1    C1'  C2'   116.59  3.000
 C5P  H1'   C1'  O4'   110.52  3.000
 C5P  N1    C1'  O4'   109.32  3.000
 C5P  C2'   C1'  O4'   108.02  3.000
 C5P  C6    N1   C2    120.12  3.000
 C5P  C6    N1   C1'   118.92  3.000
 C5P  C2    N1   C1'   120.79  3.000
 C5P  O2    C2   N3    122.47  3.000
 C5P  O2    C2   N1    119.16  3.000
 C5P  N3    C2   N1    118.37  3.000
 C5P  C4    N3   C2    121.18  3.000
 C5P  N4    C4   C5    119.56  3.000
 C5P  N4    C4   N3    118.37  3.000
 C5P  C5    C4   N3    122.07  3.000
 C5P  H5    C5   C6    121.29  3.000
 C5P  H5    C5   C4    122.45  3.000
 C5P  C6    C5   C4    116.26  3.000
 C5P  H6    C6   C5    121.56  3.000
 C5P  H6    C6   N1    116.44  3.000
 C5P  C5    C6   N1    122.00  3.000
 C5P  HN42  N4   HN41  118.12  3.000
 C5P  HN42  N4   C4    121.55  3.000
 C5P  HN41  N4   C4    120.29  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
 C5P  CONST_01  N3    C2   N1   C1'  180.00   0.0  0
 C5P  CONST_02  C4    N3   C2   N1     0.00   0.0  0
 C5P  CONST_03  C5    C4   N3   C2     0.00   0.0  0
 C5P  CONST_04  C6    N1   C2   N3     0.00   0.0  0
 C5P  CONST_05  O2    C2   N1   C1'    0.00   0.0  0
 C5P  CONST_06  N4    C4   N3   C2   180.00   0.0  0
 C5P  CONST_07  O2    C2   N3   C4   180.00   0.0  0
 C5P  CONST_08  O2    C2   N1   C6   180.00   0.0  0
 C5P  CONST_09  HN41  N4   C4   N3     0.00   0.0  0
 C5P  CONST_10  HN42  N4   C4   N3   180.00   0.0  0
 C5P  Var_01    C4'   C5'  O5'  P    168.22  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
 C5P  chir_01  C4'  C5'  O4'  C3'  negativ
 C5P  chir_02  C3'  O3'  C4'  C2'  positiv
 C5P  chir_03  C2'  O2'  C3'  C1'  positiv
 C5P  chir_04  C1'  O4'  N1   C2'  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
 C5P  plan-1  C1'   0.020
 C5P  plan-1  N1    0.020
 C5P  plan-1  C2    0.020
 C5P  plan-1  N3    0.020
 C5P  plan-1  C4    0.020
 C5P  plan-1  C5    0.020
 C5P  plan-1  C6    0.020
 C5P  plan-1  O2    0.020
 C5P  plan-1  N4    0.020
 C5P  plan-1  H5    0.020
 C5P  plan-1  H6    0.020
 C5P  plan-1  HN41  0.020
 C5P  plan-1  HN42  0.020

