# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 02:10:41 2022
#   Inital geometry file: a 53 line input string
#   Ligand name: (3~{a}~{R},6~{R},6~{a}~{R})-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
 UR8  UR8  "(-)-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 PERFECT
;

data_comp_UR8
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
 UR8  N   N  NR15   0  -0.364  109.5385  138.9008   96.8232
 UR8  C   C  CR5    0   0.545  109.8029  140.0862   97.4035
 UR8  O   O  O      0  -0.469  110.7544  140.8005   97.1504
 UR8  O1  O  O      0  -0.398  108.2961  138.3845   97.1551
 UR8  O2  O  O      0  -0.598  106.3533  137.4940  100.2948
 UR8  O3  O  OC    -1  -0.592  107.7176  138.2639  101.8886
 UR8  C1  C  CR15   0   0.045  107.9801  138.9746   98.4219
 UR8  C2  C  CR15   0  -0.473  108.7291  140.3068   98.4512
 UR8  C3  C  CH2    0  -0.281  109.3163  140.3789   99.8501
 UR8  C4  C  CH1    0  -0.245  108.5230  138.2064   99.6391
 UR8  C5  C  C      0   0.402  107.4205  137.9801  100.7134
 UR8  N1  N  NH1    0  -0.600  109.6660  138.9892  100.0986
 UR8  H1  H  HNR5   0   0.416  109.8667  138.6069   95.9136
 UR8  H3  H  HCR5   0   0.268  106.8955  139.0544   98.4414
 UR8  H4  H  HCR5   0   0.303  108.1284  141.1794   98.1864
 UR8  H5  H  HCH2   0   0.236  110.1876  141.0346   99.9018
 UR8  H6  H  HCH2   0   0.218  108.5610  140.7766  100.5418
 UR8  H7  H  HCH1   0   0.245  108.8505  137.2091   99.3204
 UR8  H8  H  HNH1   0   0.342  109.7800  138.8318  101.0933

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
 UR8  N   O1  single  1.386  0.020  1.386
 UR8  N   C   single  1.346  0.020  1.346
 UR8  O   C   double  1.216  0.020  1.216
 UR8  O1  C1  single  1.433  0.020  1.433
 UR8  C   C2  single  1.516  0.020  1.516
 UR8  C1  C2  single  1.529  0.020  1.529
 UR8  C1  C4  single  1.538  0.020  1.538
 UR8  C2  C3  single  1.519  0.020  1.519
 UR8  C4  N1  single  1.460  0.020  1.460
 UR8  C4  C5  single  1.556  0.020  1.556
 UR8  C3  N1  single  1.454  0.020  1.454
 UR8  O2  C5  deloc   1.245  0.020  1.245
 UR8  C5  O3  deloc   1.245  0.020  1.245
 UR8  N   H1  single  0.890  0.020  1.040
 UR8  C1  H3  single  0.970  0.020  1.090
 UR8  C2  H4  single  0.970  0.020  1.090
 UR8  C3  H5  single  0.970  0.020  1.090
 UR8  C3  H6  single  0.970  0.020  1.090
 UR8  C4  H7  single  0.970  0.020  1.090
 UR8  N1  H8  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
 UR8  H1  N   O1  113.48  3.000
 UR8  H1  N   C   125.47  3.000
 UR8  O1  N   C   113.64  3.000
 UR8  C2  C   O   127.76  3.000
 UR8  C2  C   N   106.67  3.000
 UR8  O   C   N   125.53  3.000
 UR8  C1  O1  N   104.84  3.000
 UR8  H3  C1  C4  111.99  3.000
 UR8  H3  C1  C2  115.11  3.000
 UR8  C4  C1  C2  104.31  3.000
 UR8  H3  C1  O1  105.43  3.000
 UR8  C4  C1  O1  114.59  3.000
 UR8  C2  C1  O1  105.53  3.000
 UR8  H4  C2  C3  113.45  3.000
 UR8  H4  C2  C1  114.97  3.000
 UR8  C3  C2  C1  104.38  3.000
 UR8  H4  C2  C   109.77  3.000
 UR8  C3  C2  C   111.69  3.000
 UR8  C1  C2  C   101.95  3.000
 UR8  H6  C3  H5  107.54  3.000
 UR8  H6  C3  N1  113.80  3.000
 UR8  H5  C3  N1  111.95  3.000
 UR8  H6  C3  C2  109.35  3.000
 UR8  H5  C3  C2  112.38  3.000
 UR8  N1  C3  C2  101.83  3.000
 UR8  H7  C4  N1  110.20  3.000
 UR8  H7  C4  C5  106.25  3.000
 UR8  N1  C4  C5  114.55  3.000
 UR8  H7  C4  C1  109.24  3.000
 UR8  C5  C4  C1  111.65  3.000
 UR8  N1  C4  C1  104.93  3.000
 UR8  C4  C5  O3  116.71  3.000
 UR8  O3  C5  O2  127.65  3.000
 UR8  C4  C5  O2  115.59  3.000
 UR8  H8  N1  C4  108.29  3.000
 UR8  H8  N1  C3  110.07  3.000
 UR8  C4  N1  C3  105.68  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
 UR8  CONST_01  C2  C   N   O1     0.00   0.0  0
 UR8  CONST_02  O1  N   C   O    180.00   0.0  0
 UR8  Var_01    C1  O1  N   C    -24.90  30.0  1
 UR8  Var_02    C4  N1  C3  C2   -44.37  30.0  1
 UR8  Var_03    H1  N   O1  C1  -176.63  30.0  1
 UR8  Var_04    H8  N1  C3  C2  -161.09  30.0  1
 UR8  Var_05    H5  C3  N1  C4  -164.62  30.0  1
 UR8  Var_06    H6  C3  N1  C4    73.17  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
 UR8  chir_01  C1  O1  C2  C4  positiv
 UR8  chir_02  C2  C   C1  C3  negativ
 UR8  chir_03  C4  N1  C5  C1  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
 UR8  plan-1  N   0.020
 UR8  plan-1  C   0.020
 UR8  plan-1  O   0.020
 UR8  plan-1  O1  0.020
 UR8  plan-1  C2  0.020
 UR8  plan-1  H1  0.020
 UR8  plan-2  O2  0.020
 UR8  plan-2  O3  0.020
 UR8  plan-2  C4  0.020
 UR8  plan-2  C5  0.020

