# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 21:49:27 2022
#   Inital geometry file: a 69 line input string
#   Ligand name: 5-amino-2,4,5-trideoxy-2-(2-oxoazetidin-1-yl)-D-threo-pentonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC[C@@H](O)[C@H](N1CCC1=O)C(O)=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
 PCV  PCV  '5-amino-2,4,5-trideoxy-2-(2-oxoazetidin-1-yl)-D-threo-pentonic acid'  ligand  27  14  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PCV
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
 PCV  N1    N  N      0  -0.427  -0.5986   1.0063  -0.6046
 PCV  C8    C  C      0   0.531  -0.7603   1.7323   0.5135
 PCV  O1    O  O      0  -0.507  -0.4306   1.5302   1.6715
 PCV  C9    C  C      0  -0.632  -1.4748   2.8496  -0.2232
 PCV  C7    C  C      0  -0.232  -1.3569   1.9244  -1.4501
 PCV  C1    C  CH1    0  -0.260  -0.3501  -0.3964  -0.8108
 PCV  C2    C  CH1    0   0.023   0.8655  -0.9178  -0.0299
 PCV  C4    C  CH2    0  -0.445   2.1273  -0.1028  -0.3040
 PCV  C5    C  CH2    0  -0.273   3.3793  -0.7296   0.2912
 PCV  N2    N  NH2    0  -0.803   4.5557   0.0719  -0.0257
 PCV  O3    O  OH1    0  -0.696   0.5986  -1.0565   1.3479
 PCV  C3    C  C      0   0.433  -1.6076  -1.2543  -0.4920
 PCV  O2    O  O      0  -0.585  -2.5751  -0.6769   0.0292
 PCV  O4    O  OC    -1  -0.611  -1.5132  -2.4565  -0.8032
 PCV  HC91  H  H      0   0.279  -0.9311   3.7920  -0.2780
 PCV  HC92  H  H      0   0.281  -2.4903   3.0330   0.1256
 PCV  HC71  H  H      0   0.243  -0.7903   2.3115  -2.2969
 PCV  HC72  H  H      0   0.242  -2.3054   1.5112  -1.7932
 PCV  HC1   H  HCH1   0   0.258  -0.1196  -0.5157  -1.8745
 PCV  H22   H  HCH1   0   0.225   1.0325  -1.9331  -0.4017
 PCV  HC41  H  HCH2   0   0.219   2.0128   0.9169   0.0796
 PCV  HC42  H  HCH2   0   0.217   2.2607  -0.0103  -1.3860
 PCV  HC51  H  HCH2   0   0.209   3.5216  -1.7241  -0.1426
 PCV  HC52  H  HCH2   0   0.193   3.2344  -0.8799   1.3684
 PCV  HN21  H  HNH2   0   0.336   4.4988   0.9522   0.4728
 PCV  HN22  H  HNH2   0   0.344   5.3796  -0.3883   0.3405
 PCV  HO3   H  HOH1   0   0.440   0.3154  -0.1889   1.6851

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
 PCV  N1  C8    single  1.343  0.020  1.343
 PCV  N1  C7    single  1.460  0.020  1.460
 PCV  N1  C1    single  1.439  0.020  1.439
 PCV  C8  O1    double  1.221  0.020  1.221
 PCV  C8  C9    single  1.517  0.020  1.517
 PCV  C9  C7    single  1.541  0.020  1.541
 PCV  C9  HC91  single  0.970  0.020  1.090
 PCV  C9  HC92  single  0.970  0.020  1.090
 PCV  C7  HC71  single  0.970  0.020  1.090
 PCV  C7  HC72  single  0.970  0.020  1.090
 PCV  C1  C2    single  1.536  0.020  1.536
 PCV  C1  C3    single  1.555  0.020  1.555
 PCV  C1  HC1   single  0.970  0.020  1.090
 PCV  C2  C4    single  1.527  0.020  1.527
 PCV  C2  O3    single  1.410  0.020  1.410
 PCV  C2  H22   single  0.970  0.020  1.090
 PCV  C4  C5    single  1.521  0.020  1.521
 PCV  C4  HC41  single  0.970  0.020  1.090
 PCV  C4  HC42  single  0.970  0.020  1.090
 PCV  C5  N2    single  1.458  0.020  1.458
 PCV  C5  HC51  single  0.970  0.020  1.090
 PCV  C5  HC52  single  0.970  0.020  1.090
 PCV  N2  HN21  single  0.890  0.020  1.040
 PCV  N2  HN22  single  0.890  0.020  1.040
 PCV  O3  HO3   single  0.850  0.020  0.980
 PCV  C3  O2    deloc   1.241  0.020  1.241
 PCV  C3  O4    deloc   1.245  0.020  1.245

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
 PCV  C1    N1  C7    128.27  3.000
 PCV  C1    N1  C8    131.82  3.000
 PCV  C7    N1  C8     94.57  3.000
 PCV  C9    C8  O1    135.21  3.000
 PCV  C9    C8  N1     92.90  3.000
 PCV  O1    C8  N1    131.89  3.000
 PCV  HC92  C9  HC91  109.62  3.000
 PCV  HC92  C9  C7    115.30  3.000
 PCV  HC91  C9  C7    116.17  3.000
 PCV  HC92  C9  C8    114.05  3.000
 PCV  HC91  C9  C8    115.24  3.000
 PCV  C7    C9  C8     84.74  3.000
 PCV  HC72  C7  HC71  110.02  3.000
 PCV  HC72  C7  C9    114.31  3.000
 PCV  HC71  C7  C9    116.43  3.000
 PCV  HC72  C7  N1    113.31  3.000
 PCV  HC71  C7  N1    113.78  3.000
 PCV  C9    C7  N1     87.49  3.000
 PCV  HC1   C1  C3    108.02  3.000
 PCV  HC1   C1  C2    106.88  3.000
 PCV  C3    C1  C2    110.39  3.000
 PCV  HC1   C1  N1    106.36  3.000
 PCV  C3    C1  N1    111.63  3.000
 PCV  C2    C1  N1    113.24  3.000
 PCV  H22   C2  O3    105.65  3.000
 PCV  H22   C2  C4    107.95  3.000
 PCV  O3    C2  C4    112.60  3.000
 PCV  H22   C2  C1    105.25  3.000
 PCV  O3    C2  C1    112.35  3.000
 PCV  C4    C2  C1    112.43  3.000
 PCV  HC42  C4  HC41  106.28  3.000
 PCV  HC42  C4  C5    108.74  3.000
 PCV  HC41  C4  C5    109.42  3.000
 PCV  HC42  C4  C2    108.87  3.000
 PCV  HC41  C4  C2    110.34  3.000
 PCV  C5    C4  C2    112.95  3.000
 PCV  HC52  C5  HC51  106.37  3.000
 PCV  HC52  C5  N2    113.27  3.000
 PCV  HC51  C5  N2    107.97  3.000
 PCV  HC52  C5  C4    109.38  3.000
 PCV  HC51  C5  C4    109.05  3.000
 PCV  N2    C5  C4    110.63  3.000
 PCV  HN22  N2  HN21  105.23  3.000
 PCV  HN22  N2  C5    109.15  3.000
 PCV  HN21  N2  C5    108.98  3.000
 PCV  HO3   O3  C2    107.82  3.000
 PCV  O4    C3  O2    127.81  3.000
 PCV  O4    C3  C1    114.83  3.000
 PCV  O2    C3  C1    117.36  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
 PCV  CONST_01  C7    C9  C8  N1     0.00   0.0  0
 PCV  CONST_02  C7    N1  C8  O1   180.00   0.0  0
 PCV  CONST_03  C7    C9  C8  O1   180.00   0.0  0
 PCV  Var_01    HC91  C9  C8  N1  -112.39  30.0  1
 PCV  Var_02    HC71  C7  N1  C8   122.15  30.0  1
 PCV  Var_03    N2    C5  C4  C2   178.71  30.0  3
 PCV  Var_04    HN21  N2  C5  C4    68.36  30.0  3

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
 PCV  chir_01  C1  N1  C2  C3  negativ
 PCV  chir_02  C2  O3  C1  C4  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
 PCV  plan-1  N1  0.020
 PCV  plan-1  C8  0.020
 PCV  plan-1  O1  0.020
 PCV  plan-1  C9  0.020
 PCV  plan-1  C7  0.020
 PCV  plan-1  C1  0.020
 PCV  plan-2  C1  0.020
 PCV  plan-2  C3  0.020
 PCV  plan-2  O2  0.020
 PCV  plan-2  O4  0.020

