# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 14:40:03 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  32  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   2.4392   0.1345   0.4028
 U5P  C2    C  CR6    0   0.747   2.3654  -0.5129  -0.8144
 U5P  N3    N  NR16   0  -0.734   3.2958  -1.5014  -0.9972
 U5P  C4    C  CR6    0   0.567   4.2791  -1.9267  -0.1165
 U5P  C5    C  CR16   0  -0.513   4.2739  -1.2081   1.1331
 U5P  C6    C  CR16   0   0.103   3.3697  -0.2361   1.3326
 U5P  O2    O  O      0  -0.467   1.5508  -0.2303  -1.6658
 U5P  O4    O  O      0  -0.464   5.0401  -2.8244  -0.4256
 U5P  C1'   C  CH1    0   0.206   1.4590   1.1607   0.7417
 U5P  C2'   C  CH1    0  -0.047   1.3433   2.3433  -0.2382
 U5P  O2'   O  OH1    0  -0.676   1.4432   3.5313   0.5042
 U5P  C3'   C  CH1    0  -0.032  -0.0767   2.1871  -0.8152
 U5P  C4'   C  CH1    0   0.010  -0.8002   1.3782   0.2576
 U5P  O3'   O  OH1    0  -0.665  -0.7215   3.4239  -0.9967
 U5P  O4'   O  O2     0  -0.490   0.2008   0.5690   0.8596
 U5P  C5'   C  CH2    0  -0.130  -1.9068   0.5101  -0.2930
 U5P  O5'   O  O2     0  -0.659  -2.5997  -0.1044   0.7469
 U5P  P     P  P      0   1.223  -3.8994  -1.1292   0.3122
 U5P  O1P   O  O      0  -0.906  -4.8243  -0.2493  -0.5219
 U5P  O2P   O  OP    -1  -0.906  -3.2530  -2.2695  -0.4662
 U5P  O3P   O  OP    -1  -0.897  -4.4292  -1.5070   1.6884
 U5P  HN3   H  HNR6   0   0.427   3.2529  -1.9702  -1.8939
 U5P  H5    H  HCR6   0   0.293   4.9891  -1.4581   1.9009
 U5P  H6    H  HCR6   0   0.328   3.3397   0.3149   2.2620
 U5P  H1'   H  HCH1   0   0.257   1.7969   1.5574   1.7039
 U5P  H2'   H  HCH1   0   0.247   2.1137   2.3089  -1.0155
 U5P  HO2'  H  HOH1   0   0.447   0.7659   4.1287   0.1564
 U5P  H3'   H  HCH1   0   0.255  -0.0355   1.6231  -1.7486
 U5P  H4'   H  HCH1   0   0.220  -1.2193   2.0695   1.0040
 U5P  HO3'  H  HOH1   0   0.469  -0.5715   3.7245  -1.8983
 U5P  H5'1  H  HCH2   0   0.179  -2.5612   1.1561  -0.8959
 U5P  H5'2  H  HCH2   0   0.175  -1.4603  -0.2191  -0.9851

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  1.459  0.020  1.459
 U5P  C2   N3    single  1.370  0.020  1.370
 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  1.441  0.020  1.441
 U5P  C4   O4    double  1.217  0.020  1.217
 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  1.540  0.020  1.540
 U5P  C1'  O4'   single  1.395  0.020  1.395
 U5P  C1'  H1'   single  0.970  0.020  1.090
 U5P  C2'  O2'   single  1.404  0.020  1.404
 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  1.526  0.020  1.526
 U5P  C3'  O3'   single  1.407  0.020  1.407
 U5P  C3'  H3'   single  0.970  0.020  1.090
 U5P  C4'  O4'   single  1.421  0.020  1.421
 U5P  C4'  C5'   single  1.510  0.020  1.510
 U5P  C4'  H4'   single  0.970  0.020  1.090
 U5P  O3'  HO3'  single  0.850  0.020  0.980
 U5P  C5'  O5'   single  1.393  0.020  1.393
 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  1.711  0.020  1.711
 U5P  P    O1P   deloc   1.525  0.020  1.525
 U5P  P    O2P   deloc   1.525  0.020  1.525
 U5P  P    O3P   deloc   1.522  0.020  1.522

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    119.35  3.000
 U5P  C1'   N1   C2    119.91  3.000
 U5P  C6    N1   C2    120.61  3.000
 U5P  O2    C2   N3    122.09  3.000
 U5P  O2    C2   N1    123.09  3.000
 U5P  N3    C2   N1    114.82  3.000
 U5P  HN3   N3   C4    116.76  3.000
 U5P  HN3   N3   C2    115.05  3.000
 U5P  C4    N3   C2    128.18  3.000
 U5P  O4    C4   C5    126.18  3.000
 U5P  O4    C4   N3    120.55  3.000
 U5P  C5    C4   N3    113.27  3.000
 U5P  H5    C5   C6    120.57  3.000
 U5P  H5    C5   C4    119.94  3.000
 U5P  C6    C5   C4    119.49  3.000
 U5P  H6    C6   C5    121.04  3.000
 U5P  H6    C6   N1    115.33  3.000
 U5P  C5    C6   N1    123.63  3.000
 U5P  H1'   C1'  O4'   110.97  3.000
 U5P  H1'   C1'  C2'   107.72  3.000
 U5P  O4'   C1'  C2'   108.15  3.000
 U5P  H1'   C1'  N1    104.59  3.000
 U5P  O4'   C1'  N1    109.09  3.000
 U5P  C2'   C1'  N1    116.28  3.000
 U5P  H2'   C2'  C3'   112.31  3.000
 U5P  H2'   C2'  O2'   110.59  3.000
 U5P  C3'   C2'  O2'   110.45  3.000
 U5P  H2'   C2'  C1'   112.00  3.000
 U5P  C3'   C2'  C1'   103.28  3.000
 U5P  O2'   C2'  C1'   107.93  3.000
 U5P  HO2'  O2'  C2'   106.40  3.000
 U5P  H3'   C3'  O3'   111.19  3.000
 U5P  H3'   C3'  C4'   110.19  3.000
 U5P  O3'   C3'  C4'   109.84  3.000
 U5P  H3'   C3'  C2'   109.75  3.000
 U5P  O3'   C3'  C2'   112.44  3.000
 U5P  C4'   C3'  C2'   103.14  3.000
 U5P  H4'   C4'  C5'   109.23  3.000
 U5P  H4'   C4'  O4'   109.80  3.000
 U5P  C5'   C4'  O4'   110.08  3.000
 U5P  H4'   C4'  C3'   108.93  3.000
 U5P  C5'   C4'  C3'   113.31  3.000
 U5P  O4'   C4'  C3'   105.41  3.000
 U5P  HO3'  O3'  C3'   108.91  3.000
 U5P  C4'   O4'  C1'   110.97  3.000
 U5P  H5'2  C5'  H5'1  106.62  3.000
 U5P  H5'2  C5'  O5'   112.29  3.000
 U5P  H5'1  C5'  O5'   111.87  3.000
 U5P  H5'2  C5'  C4'   108.24  3.000
 U5P  H5'1  C5'  C4'   107.36  3.000
 U5P  O5'   C5'  C4'   110.24  3.000
 U5P  P     O5'  C5'   116.90  3.000
 U5P  O3P   P    O2P   115.05  3.000
 U5P  O3P   P    O1P   115.25  3.000
 U5P  O2P   P    O1P   114.17  3.000
 U5P  O3P   P    O5'   100.57  3.000
 U5P  O2P   P    O5'   104.81  3.000
 U5P  O1P   P    O5'   104.72  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'  -56.49  30.0  3
 U5P  Var_02    H5'1  C5'  O5'  P     60.46  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

