# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 02:33:45 2022
#   Inital geometry file: a 53 line input string
#   Ligand name: (3~{a}~{S},6~{S},6~{a}~{S})-3-oxidanylidene-4,5,6,6~{a}-tetrahydro-3~{a}~{H}-pyrrolo[3,4-d][1,2]oxazole-6-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H]1NC[C@H]2[C@@H]1ONC2=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
 UR5  UR5  "(+)-3-Hydroxy-4,5,6,6a-tetrahydro-3aH-pyrrolo[3,4-d]isoxazole-6-carboxylic acid"  ligand  19  12  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_UR5
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
 UR5  N   N  NR15   0  -0.347  109.1699  139.3362   96.5391
 UR5  C   C  CR5    0   0.515  110.1795  139.8201   97.2748
 UR5  O   O  O      0  -0.477  111.1302  140.4527   96.8467
 UR5  C1  C  CR15   0   0.084  108.7501  138.4325   98.5843
 UR5  C2  C  CR15   0  -0.472  109.8711  139.4583   98.7061
 UR5  C3  C  CH2    0  -0.307  109.2301  140.6295   99.5041
 UR5  C4  C  CH1    0  -0.301  107.6741  138.9092   99.5571
 UR5  C5  C  C      0   0.435  107.9041  138.3675  100.9906
 UR5  N1  N  NH1    0  -0.577  107.8006  140.3680   99.5639
 UR5  O1  O  O      0  -0.408  108.2532  138.5703   97.2288
 UR5  O2  O  O      0  -0.600  106.9353  138.4476  101.7659
 UR5  O3  O  OC    -1  -0.592  109.0432  137.9260  101.2477
 UR5  H1  H  HNR5   0   0.417  109.1557  139.2064   95.5374
 UR5  H2  H  HCR5   0   0.249  109.0659  137.3980   98.7264
 UR5  H3  H  HCR5   0   0.297  110.7652  139.0751   99.1939
 UR5  H4  H  HCH2   0   0.242  109.6536  140.6446  100.5089
 UR5  H5  H  HCH2   0   0.249  109.4256  141.6059   99.0595
 UR5  H6  H  HCH1   0   0.245  106.6715  138.6319   99.2211
 UR5  H7  H  HNH1   0   0.350  107.3574  140.7419   98.7331

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
 UR5  N   C   single  1.340  0.020  1.340
 UR5  N   O1  single  1.379  0.020  1.379
 UR5  O   C   double  1.220  0.020  1.220
 UR5  C   C2  single  1.508  0.020  1.508
 UR5  O1  C1  single  1.450  0.020  1.450
 UR5  C2  C1  single  1.524  0.020  1.524
 UR5  C2  C3  single  1.555  0.020  1.555
 UR5  C1  C4  single  1.527  0.020  1.527
 UR5  C4  N1  single  1.464  0.020  1.464
 UR5  C4  C5  single  1.550  0.020  1.550
 UR5  N1  C3  single  1.454  0.020  1.454
 UR5  C5  O2  deloc   1.243  0.020  1.243
 UR5  C5  O3  deloc   1.248  0.020  1.248
 UR5  N   H1  single  0.860  0.020  1.020
 UR5  C1  H2  single  0.970  0.020  1.090
 UR5  C2  H3  single  0.970  0.020  1.090
 UR5  C3  H4  single  0.970  0.020  1.090
 UR5  C3  H5  single  0.970  0.020  1.090
 UR5  C4  H6  single  0.970  0.020  1.090
 UR5  N1  H7  single  0.890  0.020  1.040

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
 UR5  H1  N   O1  114.53  3.000
 UR5  H1  N   C   126.99  3.000
 UR5  O1  N   C   115.27  3.000
 UR5  C2  C   O   128.09  3.000
 UR5  C2  C   N   106.29  3.000
 UR5  O   C   N   125.60  3.000
 UR5  H2  C1  O1  108.12  3.000
 UR5  H2  C1  C4  114.65  3.000
 UR5  O1  C1  C4  108.93  3.000
 UR5  H2  C1  C2  114.51  3.000
 UR5  C4  C1  C2  104.91  3.000
 UR5  O1  C1  C2  105.23  3.000
 UR5  H3  C2  C3  111.95  3.000
 UR5  H3  C2  C1  113.77  3.000
 UR5  C3  C2  C1  104.16  3.000
 UR5  H3  C2  C   109.99  3.000
 UR5  C3  C2  C   112.99  3.000
 UR5  C1  C2  C   103.65  3.000
 UR5  H5  C3  H4  107.08  3.000
 UR5  H5  C3  N1  110.73  3.000
 UR5  H4  C3  N1  110.26  3.000
 UR5  H5  C3  C2  113.02  3.000
 UR5  H4  C3  C2  108.85  3.000
 UR5  N1  C3  C2  106.90  3.000
 UR5  H6  C4  N1  109.47  3.000
 UR5  H6  C4  C5  109.38  3.000
 UR5  N1  C4  C5  109.34  3.000
 UR5  H6  C4  C1  111.80  3.000
 UR5  C5  C4  C1  112.07  3.000
 UR5  N1  C4  C1  104.66  3.000
 UR5  O3  C5  O2  127.25  3.000
 UR5  O3  C5  C4  116.71  3.000
 UR5  O2  C5  C4  116.02  3.000
 UR5  H7  N1  C4  109.03  3.000
 UR5  H7  N1  C3  109.26  3.000
 UR5  C4  N1  C3  105.30  3.000
 UR5  C1  O1  N   107.00  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
 UR5  CONST_01  O1  N   C   C2    0.00   0.0  0
 UR5  CONST_02  O1  N   C   O   180.00   0.0  0
 UR5  Var_01    C1  O1  N   C    -4.65  30.0  1
 UR5  Var_02    C4  N1  C3  C2   30.69  30.0  1
 UR5  Var_03    H1  N   O1  C1  156.53  30.0  1
 UR5  Var_04    H7  N1  C3  C2  -86.29  30.0  1
 UR5  Var_05    H4  C3  N1  C4  -87.48  30.0  1
 UR5  Var_06    H5  C3  N1  C4  154.20  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
 UR5  chir_01  C1  O1  C2  C4  negativ
 UR5  chir_02  C2  C   C1  C3  positiv
 UR5  chir_03  C4  N1  C5  C1  positiv

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
 UR5  plan-1  N   0.020
 UR5  plan-1  C   0.020
 UR5  plan-1  O   0.020
 UR5  plan-1  C2  0.020
 UR5  plan-1  O1  0.020
 UR5  plan-1  H1  0.020
 UR5  plan-2  C4  0.020
 UR5  plan-2  C5  0.020
 UR5  plan-2  O2  0.020
 UR5  plan-2  O3  0.020

