# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 00:41:59 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: uridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)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
 URI  URI  'uridine                  '  ligand  29  17  .  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_URI
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
 URI  N1    N  NR6   0  -0.577  -0.2489   0.3831  -0.8922
 URI  C2    C  CR6   0   0.749   0.7095  -0.5540  -1.2381
 URI  N3    N  NR16  0  -0.734   1.0056  -0.6017  -2.5762
 URI  C4    C  CR6   0   0.567   0.4704   0.1568  -3.6053
 URI  C5    C  CR16  0  -0.511  -0.5140   1.1088  -3.1554
 URI  C6    C  CR16  0   0.098  -0.8153   1.1795  -1.8497
 URI  O2    O  O     0  -0.464   1.2512  -1.2855  -0.4398
 URI  O4    O  O     0  -0.463   0.8376  -0.0090  -4.7533
 URI  C1'   C  CR15  0   0.230  -0.6349   0.5808   0.4990
 URI  C2'   C  CR15  0  -0.021  -1.2313  -0.6297   1.2149
 URI  C3'   C  CR15  0  -0.050  -0.9743  -0.2452   2.6740
 URI  C4'   C  CR15  0  -0.027   0.3933   0.4392   2.5723
 URI  O2'   O  OH1   0  -0.658  -2.5666  -0.7682   0.8377
 URI  O3'   O  OH1   0  -0.669  -1.9885   0.6429   3.0689
 URI  O4'   O  O     0  -0.488   0.4590   0.9965   1.2557
 URI  C5'   C  CH2   0  -0.153   1.5494  -0.5030   2.8340
 URI  O5'   O  OH1   0  -0.672   2.7505   0.2144   2.6828
 URI  H3    H  HNR6  0   0.426   1.7039  -1.2893  -2.8322
 URI  H5    H  HCR6  0   0.294  -0.9950   1.7636  -3.8649
 URI  H6    H  HCR6  0   0.329  -1.5430   1.8908  -1.4858
 URI  H1'   H  HCR5  0   0.252  -1.4018   1.3632   0.4614
 URI  H2'   H  HCR5  0   0.261  -0.6552  -1.5310   0.9908
 URI  H3'   H  HCR5  0   0.249  -0.9356  -1.1249   3.3292
 URI  H4'   H  HCR5  0   0.249   0.4556   1.2654   3.2906
 URI  HO2'  H  HOH1  0   0.462  -2.8856  -1.6226   1.1435
 URI  HO3'  H  HOH1  0   0.456  -1.7948   0.9440   3.9622
 URI  H5'1  H  HCH2  0   0.211   1.5053  -1.3646   2.1593
 URI  H5'2  H  HCH2  0   0.199   1.4308  -0.8859   3.8567
 URI  HO5'  H  HOH1  0   0.456   3.4806  -0.4021   2.7848

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
 URI  N1   C2    single  1.384  0.020  1.384
 URI  N1   C6    single  1.368  0.020  1.368
 URI  N1   C1'   single  1.457  0.020  1.457
 URI  C2   N3    single  1.371  0.020  1.371
 URI  C2   O2    double  1.211  0.020  1.211
 URI  N3   C4    single  1.386  0.020  1.386
 URI  N3   H3    single  0.860  0.020  1.020
 URI  C4   C5    single  1.441  0.020  1.441
 URI  C4   O4    double  1.217  0.020  1.217
 URI  C5   C6    double  1.342  0.020  1.342
 URI  C5   H5    single  0.930  0.020  1.080
 URI  C6   H6    single  0.930  0.020  1.080
 URI  C1'  C2'   single  1.528  0.020  1.528
 URI  C1'  O4'   single  1.394  0.020  1.394
 URI  C1'  H1'   single  0.970  0.020  1.090
 URI  C2'  C3'   single  1.531  0.020  1.531
 URI  C2'  O2'   single  1.394  0.020  1.394
 URI  C2'  H2'   single  0.970  0.020  1.090
 URI  C3'  C4'   single  1.533  0.020  1.533
 URI  C3'  O3'   single  1.405  0.020  1.405
 URI  C3'  H3'   single  0.970  0.020  1.090
 URI  C4'  O4'   single  1.431  0.020  1.431
 URI  C4'  C5'   single  1.514  0.020  1.514
 URI  C4'  H4'   single  0.970  0.020  1.090
 URI  O2'  HO2'  single  0.850  0.020  0.980
 URI  O3'  HO3'  single  0.850  0.020  0.980
 URI  C5'  O5'   single  1.407  0.020  1.407
 URI  C5'  H5'1  single  0.970  0.020  1.090
 URI  C5'  H5'2  single  0.970  0.020  1.090
 URI  O5'  HO5'  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
 URI  C1'   N1   C6    118.66  3.000
 URI  C1'   N1   C2    120.91  3.000
 URI  C6    N1   C2    120.38  3.000
 URI  O2    C2   N3    121.72  3.000
 URI  O2    C2   N1    123.64  3.000
 URI  N3    C2   N1    114.64  3.000
 URI  H3    N3   C4    116.76  3.000
 URI  H3    N3   C2    114.78  3.000
 URI  C4    N3   C2    128.47  3.000
 URI  O4    C4   C5    126.20  3.000
 URI  O4    C4   N3    120.62  3.000
 URI  C5    C4   N3    113.17  3.000
 URI  H5    C5   C6    120.53  3.000
 URI  H5    C5   C4    120.01  3.000
 URI  C6    C5   C4    119.46  3.000
 URI  H6    C6   C5    120.90  3.000
 URI  H6    C6   N1    115.22  3.000
 URI  C5    C6   N1    123.88  3.000
 URI  H1'   C1'  O4'   110.78  3.000
 URI  H1'   C1'  C2'   107.97  3.000
 URI  O4'   C1'  C2'   106.76  3.000
 URI  H1'   C1'  N1    104.44  3.000
 URI  O4'   C1'  N1    110.54  3.000
 URI  C2'   C1'  N1    116.32  3.000
 URI  H2'   C2'  O2'   111.55  3.000
 URI  H2'   C2'  C3'   108.30  3.000
 URI  O2'   C2'  C3'   116.34  3.000
 URI  H2'   C2'  C1'   110.59  3.000
 URI  O2'   C2'  C1'   109.02  3.000
 URI  C3'   C2'  C1'   100.50  3.000
 URI  H3'   C3'  O3'   111.37  3.000
 URI  H3'   C3'  C4'   111.47  3.000
 URI  O3'   C3'  C4'   112.37  3.000
 URI  H3'   C3'  C2'   111.95  3.000
 URI  O3'   C3'  C2'   107.79  3.000
 URI  C4'   C3'  C2'   101.47  3.000
 URI  H4'   C4'  C5'   108.20  3.000
 URI  H4'   C4'  O4'   107.85  3.000
 URI  C5'   C4'  O4'   111.49  3.000
 URI  H4'   C4'  C3'   110.11  3.000
 URI  C5'   C4'  C3'   113.07  3.000
 URI  O4'   C4'  C3'   106.01  3.000
 URI  HO2'  O2'  C2'   108.65  3.000
 URI  HO3'  O3'  C3'   108.27  3.000
 URI  C4'   O4'  C1'   110.33  3.000
 URI  H5'2  C5'  H5'1  107.16  3.000
 URI  H5'2  C5'  O5'   111.71  3.000
 URI  H5'1  C5'  O5'   111.67  3.000
 URI  H5'2  C5'  C4'   107.18  3.000
 URI  H5'1  C5'  C4'   110.63  3.000
 URI  O5'   C5'  C4'   108.41  3.000
 URI  HO5'  O5'  C5'   108.06  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
 URI  CONST_01  C4   N3  C2  N1    0.00  0.0  0
 URI  CONST_02  C5   C4  N3  C2    0.00  0.0  0
 URI  CONST_03  C6   N1  C2  N3    0.00  0.0  0
 URI  CONST_04  C1'  N1  C2  N3  180.00  0.0  0
 URI  CONST_05  O4   C4  N3  C2  180.00  0.0  0
 URI  CONST_06  O2   C2  N3  C4  180.00  0.0  0
 URI  CONST_07  O2   C2  N1  C6  180.00  0.0  0
 URI  CONST_08  C1'  N1  C2  O2    0.00  0.0  0
 URI  CONST_09  H3   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
 URI  chir_01  C1'  N1   C2'  O4'  negativ
 URI  chir_02  C2'  O2'  C3'  C1'  positiv
 URI  chir_03  C3'  O3'  C2'  C4'  negativ
 URI  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
 URI  plan-1  N1   0.020
 URI  plan-1  C2   0.020
 URI  plan-1  N3   0.020
 URI  plan-1  C4   0.020
 URI  plan-1  C5   0.020
 URI  plan-1  C6   0.020
 URI  plan-1  O2   0.020
 URI  plan-1  O4   0.020
 URI  plan-1  C1'  0.020
 URI  plan-1  H3   0.020
 URI  plan-1  H5   0.020
 URI  plan-1  H6   0.020

