# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 30 18:01:42 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 5'-uridylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[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
 U5P  U5P  '5'-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 PERFECT
;

data_comp_U5P
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
 U5P  N1    N  NR6   0  -0.568   2.3029   0.0952   0.3756
 U5P  C2    C  CR6   0   0.751   2.2250  -0.4795  -0.8772
 U5P  N3    N  NR16  0  -0.734   3.1279  -1.4820  -1.1075
 U5P  C4    C  CR6   0   0.569   4.0923  -1.9810  -0.2437
 U5P  C5    C  CR16  0  -0.512   4.0954  -1.3322   1.0440
 U5P  C6    C  CR16  0   0.104   3.2154  -0.3498   1.2917
 U5P  O2    O  O     0  -0.469   1.4260  -0.1246  -1.7170
 U5P  O4    O  O     0  -0.461   4.8320  -2.8801  -0.5957
 U5P  C1'   C  CR15  0   0.201   1.3545   1.1322   0.7589
 U5P  C2'   C  CR15  0  -0.047   1.3057   2.3833  -0.1368
 U5P  O2'   O  OH1   0  -0.673   1.3950   3.5050   0.7017
 U5P  C3'   C  CR15  0  -0.033  -0.0889   2.3077  -0.7883
 U5P  C4'   C  CR15  0   0.011  -0.8748   1.4477   0.2012
 U5P  O3'   O  OH1   0  -0.661  -0.7005   3.5652  -0.9116
 U5P  O4'   O  O     0  -0.486   0.0676   0.5848   0.8077
 U5P  C5'   C  CH2   0  -0.182  -1.9447   0.6344  -0.4778
 U5P  O5'   O  O2    0  -0.590  -2.6896  -0.0614   0.5263
 U5P  P     P  P     0   1.458  -3.7939  -1.1262   0.0837
 U5P  O1P   O  O     0  -0.710  -4.7850  -0.6727  -0.9091
 U5P  O2P   O  OH1   0  -0.741  -3.0111  -2.3975  -0.4855
 U5P  O3P   O  OH1   0  -0.731  -4.3093  -1.4821   1.5483
 U5P  HN3   H  HNR6  0   0.428   3.0814  -1.8984  -2.0296
 U5P  H5    H  HCR6  0   0.295   4.7977  -1.6434   1.8013
 U5P  H6    H  HCR6  0   0.330   3.1908   0.1496   2.2498
 U5P  H1'   H  HCR5  0   0.266   1.6751   1.4481   1.7553
 U5P  H2'   H  HCR5  0   0.254   2.1086   2.3868  -0.8815
 U5P  HO2'  H  HOH1  0   0.450   0.7856   4.1683   0.3491
 U5P  H3'   H  HCR5  0   0.265  -0.0138   1.8079  -1.7552
 U5P  H4'   H  HCR5  0   0.249  -1.3341   2.1007   0.9567
 U5P  HO3'  H  HOH1  0   0.472  -0.5189   3.9163  -1.7889
 U5P  H5'1  H  HCH2  0   0.253  -2.6008   1.3046  -1.0382
 U5P  H5'2  H  HCH2  0   0.243  -1.4828  -0.0679  -1.1776
 U5P  HOP2  H  HOH1  0   0.496  -2.3760  -2.8082   0.1166
 U5P  HOP3  H  HOH1  0   0.505  -5.1019  -2.0355   1.5641

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
 U5P  N1   C2    single  1.381  0.020  1.381
 U5P  N1   C6    single  1.367  0.020  1.367
 U5P  N1   C1'   single  1.457  0.020  1.457
 U5P  C2   N3    single  1.369  0.020  1.369
 U5P  C2   O2    double  1.212  0.020  1.212
 U5P  N3   C4    single  1.387  0.020  1.387
 U5P  N3   HN3   single  0.860  0.020  1.020
 U5P  C4   C5    single  1.442  0.020  1.442
 U5P  C4   O4    double  1.216  0.020  1.216
 U5P  C5   C6    double  1.342  0.020  1.342
 U5P  C5   H5    single  0.930  0.020  1.080
 U5P  C6   H6    single  0.930  0.020  1.080
 U5P  C1'  C2'   single  1.539  0.020  1.539
 U5P  C1'  O4'   single  1.399  0.020  1.399
 U5P  C1'  H1'   single  0.970  0.020  1.090
 U5P  C2'  O2'   single  1.403  0.020  1.403
 U5P  C2'  C3'   single  1.541  0.020  1.541
 U5P  C2'  H2'   single  0.970  0.020  1.090
 U5P  O2'  HO2'  single  0.850  0.020  0.980
 U5P  C3'  C4'   single  1.529  0.020  1.529
 U5P  C3'  O3'   single  1.404  0.020  1.404
 U5P  C3'  H3'   single  0.970  0.020  1.090
 U5P  C4'  O4'   single  1.414  0.020  1.414
 U5P  C4'  C5'   single  1.506  0.020  1.506
 U5P  C4'  H4'   single  0.970  0.020  1.090
 U5P  O3'  HO3'  single  0.850  0.020  0.980
 U5P  C5'  O5'   single  1.431  0.020  1.431
 U5P  C5'  H5'1  single  0.970  0.020  1.090
 U5P  C5'  H5'2  single  0.970  0.020  1.090
 U5P  O5'  P     single  1.597  0.020  1.597
 U5P  P    O1P   double  1.474  0.020  1.474
 U5P  P    O2P   single  1.598  0.020  1.598
 U5P  P    O3P   single  1.593  0.020  1.593
 U5P  O2P  HOP2  single  0.850  0.020  0.980
 U5P  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
 U5P  C1'   N1   C6    119.33  3.000
 U5P  C1'   N1   C2    119.90  3.000
 U5P  C6    N1   C2    120.68  3.000
 U5P  O2    C2   N3    122.19  3.000
 U5P  O2    C2   N1    122.96  3.000
 U5P  N3    C2   N1    114.86  3.000
 U5P  HN3   N3   C4    116.80  3.000
 U5P  HN3   N3   C2    115.09  3.000
 U5P  C4    N3   C2    128.11  3.000
 U5P  O4    C4   C5    126.14  3.000
 U5P  O4    C4   N3    120.56  3.000
 U5P  C5    C4   N3    113.31  3.000
 U5P  H5    C5   C6    120.57  3.000
 U5P  H5    C5   C4    119.90  3.000
 U5P  C6    C5   C4    119.52  3.000
 U5P  H6    C6   C5    121.12  3.000
 U5P  H6    C6   N1    115.36  3.000
 U5P  C5    C6   N1    123.51  3.000
 U5P  H1'   C1'  O4'   110.54  3.000
 U5P  H1'   C1'  C2'   107.75  3.000
 U5P  O4'   C1'  C2'   108.00  3.000
 U5P  H1'   C1'  N1    104.75  3.000
 U5P  O4'   C1'  N1    109.24  3.000
 U5P  C2'   C1'  N1    116.49  3.000
 U5P  H2'   C2'  C3'   112.10  3.000
 U5P  H2'   C2'  O2'   110.92  3.000
 U5P  C3'   C2'  O2'   110.45  3.000
 U5P  H2'   C2'  C1'   112.03  3.000
 U5P  C3'   C2'  C1'   103.58  3.000
 U5P  O2'   C2'  C1'   107.45  3.000
 U5P  HO2'  O2'  C2'   106.86  3.000
 U5P  H3'   C3'  O3'   111.25  3.000
 U5P  H3'   C3'  C4'   110.56  3.000
 U5P  O3'   C3'  C4'   109.69  3.000
 U5P  H3'   C3'  C2'   109.56  3.000
 U5P  O3'   C3'  C2'   112.80  3.000
 U5P  C4'   C3'  C2'   102.66  3.000
 U5P  H4'   C4'  C5'   109.50  3.000
 U5P  H4'   C4'  O4'   110.25  3.000
 U5P  C5'   C4'  O4'   109.72  3.000
 U5P  H4'   C4'  C3'   108.99  3.000
 U5P  C5'   C4'  C3'   112.17  3.000
 U5P  O4'   C4'  C3'   106.16  3.000
 U5P  HO3'  O3'  C3'   108.95  3.000
 U5P  C4'   O4'  C1'   111.05  3.000
 U5P  H5'2  C5'  H5'1  108.62  3.000
 U5P  H5'2  C5'  O5'   110.89  3.000
 U5P  H5'1  C5'  O5'   110.22  3.000
 U5P  H5'2  C5'  C4'   109.59  3.000
 U5P  H5'1  C5'  C4'   109.07  3.000
 U5P  O5'   C5'  C4'   108.43  3.000
 U5P  P     O5'  C5'   119.33  3.000
 U5P  O3P   P    O2P   107.95  3.000
 U5P  O3P   P    O1P   118.06  3.000
 U5P  O2P   P    O1P   109.52  3.000
 U5P  O3P   P    O5'    96.78  3.000
 U5P  O2P   P    O5'   106.89  3.000
 U5P  O1P   P    O5'   116.52  3.000
 U5P  HOP2  O2P  P     115.98  3.000
 U5P  HOP3  O3P  P     114.09  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
 U5P  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 U5P  CONST_02  C5    C4   N3   C2     0.00   0.0  0
 U5P  CONST_03  C6    N1   C2   N3     0.00   0.0  0
 U5P  CONST_04  C1'   N1   C2   N3   180.00   0.0  0
 U5P  CONST_05  O4    C4   N3   C2   180.00   0.0  0
 U5P  CONST_06  O2    C2   N3   C4   180.00   0.0  0
 U5P  CONST_07  O2    C2   N1   C6   180.00   0.0  0
 U5P  CONST_08  C1'   N1   C2   O2     0.00   0.0  0
 U5P  CONST_09  HN3   N3   C2   N1   180.00   0.0  0
 U5P  Var_01    O1P   P    O5'  C5'  -51.00  30.0  3
 U5P  Var_02    H5'1  C5'  O5'  P     67.15  30.0  1

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
 U5P  chir_01  C1'  N1   C2'  O4'  negativ
 U5P  chir_02  C2'  O2'  C3'  C1'  positiv
 U5P  chir_03  C3'  O3'  C2'  C4'  negativ
 U5P  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
 U5P  plan-1  N1   0.020
 U5P  plan-1  C2   0.020
 U5P  plan-1  N3   0.020
 U5P  plan-1  C4   0.020
 U5P  plan-1  C5   0.020
 U5P  plan-1  C6   0.020
 U5P  plan-1  O2   0.020
 U5P  plan-1  O4   0.020
 U5P  plan-1  C1'  0.020
 U5P  plan-1  HN3  0.020
 U5P  plan-1  H5   0.020
 U5P  plan-1  H6   0.020

