# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 30 18:49:20 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 3'-uridylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)N2C=CC(=O)NC2=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
 U3P  U3P  '3'-uridylic acid         '  ligand  34  21  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_U3P
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
 U3P  N1    N  NR6   0  -0.583  -0.2358   0.4256  -1.9951
 U3P  C2    C  CR6   0   0.753   0.4467  -0.5784  -2.6620
 U3P  N3    N  NR16  0  -0.735   0.2285  -0.6171  -4.0134
 U3P  C4    C  CR6   0   0.569  -0.5704   0.2177  -4.7804
 U3P  C5    C  CR16  0  -0.508  -1.2265   1.2450  -4.0097
 U3P  C6    C  CR16  0   0.100  -1.0271   1.3057  -2.6852
 U3P  O2    O  O     0  -0.465   1.1746  -1.3714  -2.1072
 U3P  O4    O  O     0  -0.460  -0.6647   0.0525  -5.9814
 U3P  O1P   O  OH1   0  -0.729  -2.0884   1.5269   3.7164
 U3P  O2P   O  O     0  -0.702  -0.3293   0.0119   4.8936
 U3P  O3P   O  OH1   0  -0.766  -1.9417  -1.0072   3.2230
 U3P  O5'   O  OH1   0  -0.668   3.8737   0.1073   0.2010
 U3P  C5'   C  CH2   0  -0.151   2.8012  -0.5683   0.8057
 U3P  C4'   C  CH1   0  -0.003   1.6611   0.4156   0.9776
 U3P  O4'   O  O2    0  -0.480   1.2579   0.9653  -0.2772
 U3P  C3'   C  CH1   0  -0.105   0.4208  -0.2437   1.5745
 U3P  O3'   O  O2    0  -0.599  -0.2794   0.7160   2.3631
 U3P  C2'   C  CH1   0  -0.008  -0.3970  -0.5820   0.3289
 U3P  O2'   O  OH1   0  -0.673  -1.7757  -0.6799   0.5856
 U3P  C1'   C  CH1   0   0.223  -0.0615   0.6169  -0.5655
 U3P  HN3   H  HNR6  0   0.428   0.7179  -1.3568  -4.5034
 U3P  H5    H  HCR6  0   0.296  -1.8634   1.9626  -4.5029
 U3P  H6    H  HCR6  0   0.331  -1.4946   2.0729  -2.0849
 U3P  HOP1  H  HOH1  0   0.502  -2.4227   1.7222   4.6020
 U3P  HOP3  H  HOH1  0   0.496  -2.1308  -1.0197   2.2554
 U3P  HO5'  H  HOH1  0   0.459   4.5715  -0.5316   0.0312
 U3P  H5'1  H  HCH2  0   0.213   2.4735  -1.4301   0.2137
 U3P  H5'2  H  HCH2  0   0.207   3.0631  -0.9418   1.8046
 U3P  H4'   H  HCH1  0   0.270   1.9955   1.2342   1.6229
 U3P  H3'   H  HCH1  0   0.306   0.6773  -1.1325   2.1581
 U3P  H2'   H  HCH1  0   0.297  -0.0093  -1.5127  -0.0871
 U3P  HO2'  H  HOH1  0   0.488  -2.1623  -1.3461   0.0074
 U3P  H1'   H  HCH1  0   0.264  -0.7484   1.4315  -0.3068
 U3P  P     P  P     0   1.430  -1.1077   0.2701   3.6678

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
 U3P  N1   C2    single  1.385  0.020  1.385
 U3P  N1   C6    single  1.370  0.020  1.370
 U3P  N1   C1'   single  1.453  0.020  1.453
 U3P  C2   N3    single  1.369  0.020  1.369
 U3P  C2   O2    double  1.211  0.020  1.211
 U3P  N3   C4    single  1.387  0.020  1.387
 U3P  N3   HN3   single  0.860  0.020  1.020
 U3P  C4   C5    single  1.442  0.020  1.442
 U3P  C4   O4    double  1.216  0.020  1.216
 U3P  C5   C6    double  1.341  0.020  1.341
 U3P  C5   H5    single  0.930  0.020  1.080
 U3P  C6   H6    single  0.930  0.020  1.080
 U3P  P    O1P   single  1.595  0.020  1.595
 U3P  P    O2P   double  1.475  0.020  1.475
 U3P  P    O3P   single  1.589  0.020  1.589
 U3P  P    O3'   single  1.608  0.020  1.608
 U3P  O1P  HOP1  single  0.850  0.020  0.980
 U3P  O3P  HOP3  single  0.850  0.020  0.980
 U3P  O5'  C5'   single  1.404  0.020  1.404
 U3P  O5'  HO5'  single  0.850  0.020  0.980
 U3P  C5'  C4'   single  1.516  0.020  1.516
 U3P  C5'  H5'1  single  0.970  0.020  1.090
 U3P  C5'  H5'2  single  0.970  0.020  1.090
 U3P  C4'  O4'   single  1.428  0.020  1.428
 U3P  C4'  C3'   single  1.526  0.020  1.526
 U3P  C4'  H4'   single  0.970  0.020  1.090
 U3P  O4'  C1'   single  1.395  0.020  1.395
 U3P  C3'  O3'   single  1.426  0.020  1.426
 U3P  C3'  C2'   single  1.528  0.020  1.528
 U3P  C3'  H3'   single  0.970  0.020  1.090
 U3P  C2'  O2'   single  1.406  0.020  1.406
 U3P  C2'  C1'   single  1.533  0.020  1.533
 U3P  C2'  H2'   single  0.970  0.020  1.090
 U3P  O2'  HO2'  single  0.850  0.020  0.980
 U3P  C1'  H1'   single  0.970  0.020  1.090

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
 U3P  C1'   N1   C6    118.71  3.000
 U3P  C1'   N1   C2    120.67  3.000
 U3P  C6    N1   C2    120.51  3.000
 U3P  O2    C2   N3    121.96  3.000
 U3P  O2    C2   N1    123.38  3.000
 U3P  N3    C2   N1    114.66  3.000
 U3P  HN3   N3   C4    116.76  3.000
 U3P  HN3   N3   C2    114.89  3.000
 U3P  C4    N3   C2    128.35  3.000
 U3P  O4    C4   C5    126.11  3.000
 U3P  O4    C4   N3    120.60  3.000
 U3P  C5    C4   N3    113.28  3.000
 U3P  H5    C5   C6    120.62  3.000
 U3P  H5    C5   C4    119.87  3.000
 U3P  C6    C5   C4    119.51  3.000
 U3P  H6    C6   C5    121.11  3.000
 U3P  H6    C6   N1    115.22  3.000
 U3P  C5    C6   N1    123.67  3.000
 U3P  HOP1  O1P  P     113.58  3.000
 U3P  HOP3  O3P  P     112.67  3.000
 U3P  HO5'  O5'  C5'   108.09  3.000
 U3P  H5'2  C5'  H5'1  107.18  3.000
 U3P  H5'2  C5'  C4'   107.28  3.000
 U3P  H5'1  C5'  C4'   110.29  3.000
 U3P  H5'2  C5'  O5'   111.91  3.000
 U3P  H5'1  C5'  O5'   111.98  3.000
 U3P  C4'   C5'  O5'   108.11  3.000
 U3P  H4'   C4'  C3'   109.92  3.000
 U3P  H4'   C4'  O4'   108.45  3.000
 U3P  C3'   C4'  O4'   106.29  3.000
 U3P  H4'   C4'  C5'   108.81  3.000
 U3P  C3'   C4'  C5'   112.03  3.000
 U3P  O4'   C4'  C5'   111.26  3.000
 U3P  C1'   O4'  C4'   110.65  3.000
 U3P  H3'   C3'  C2'   112.37  3.000
 U3P  H3'   C3'  O3'   111.53  3.000
 U3P  C2'   C3'  O3'   109.69  3.000
 U3P  H3'   C3'  C4'   111.66  3.000
 U3P  C2'   C3'  C4'   102.23  3.000
 U3P  O3'   C3'  C4'   108.94  3.000
 U3P  C3'   O3'  P     120.99  3.000
 U3P  H2'   C2'  C1'   111.53  3.000
 U3P  H2'   C2'  O2'   111.03  3.000
 U3P  C1'   C2'  O2'   112.06  3.000
 U3P  H2'   C2'  C3'   108.03  3.000
 U3P  C1'   C2'  C3'   100.68  3.000
 U3P  O2'   C2'  C3'   113.05  3.000
 U3P  HO2'  O2'  C2'   109.40  3.000
 U3P  H1'   C1'  C2'   107.83  3.000
 U3P  H1'   C1'  O4'   110.99  3.000
 U3P  C2'   C1'  O4'   106.37  3.000
 U3P  H1'   C1'  N1    104.77  3.000
 U3P  C2'   C1'  N1    116.42  3.000
 U3P  O4'   C1'  N1    110.48  3.000
 U3P  O3'   P    O3P   105.43  3.000
 U3P  O3'   P    O2P   116.80  3.000
 U3P  O3P   P    O2P   111.65  3.000
 U3P  O3'   P    O1P    97.06  3.000
 U3P  O3P   P    O1P   108.62  3.000
 U3P  O2P   P    O1P   115.92  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
 U3P  CONST_01  C4   N3  C2  N1    0.00  0.0  0
 U3P  CONST_02  C5   C4  N3  C2    0.00  0.0  0
 U3P  CONST_03  C6   N1  C2  N3    0.00  0.0  0
 U3P  CONST_04  C1'  N1  C2  N3  180.00  0.0  0
 U3P  CONST_05  O4   C4  N3  C2  180.00  0.0  0
 U3P  CONST_06  O2   C2  N3  C4  180.00  0.0  0
 U3P  CONST_07  O2   C2  N1  C6  180.00  0.0  0
 U3P  CONST_08  C1'  N1  C2  O2    0.00  0.0  0
 U3P  CONST_09  HN3  N3  C2  N1  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
 U3P  chir_01  C4'  C5'  O4'  C3'  negativ
 U3P  chir_02  C3'  O3'  C4'  C2'  positiv
 U3P  chir_03  C2'  O2'  C3'  C1'  positiv
 U3P  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
 U3P  plan-1  N1   0.020
 U3P  plan-1  C2   0.020
 U3P  plan-1  N3   0.020
 U3P  plan-1  C4   0.020
 U3P  plan-1  C5   0.020
 U3P  plan-1  C6   0.020
 U3P  plan-1  O2   0.020
 U3P  plan-1  O4   0.020
 U3P  plan-1  C1'  0.020
 U3P  plan-1  HN3  0.020
 U3P  plan-1  H5   0.020
 U3P  plan-1  H6   0.020

