# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 04:18:34 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: (5R,9R,10S)-10-(acetylamino)-2-amino-4-oxo-9-(pentan-3-yloxy)-1-thia-3-azaspiro[4.5]deca-2,6-diene-7-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(CC)O[C@@H]1CC(=C[C@@]2(SC(=NC2=O)N)[C@H]1NC(C)=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
 27S  27S  '(5R,9R,10S)-10-(acetylamino)-2-amino-4-oxo-9-(pentan-3-yloxy)-1-thia-3-azaspiro[4.5]deca-2,6-diene-7-carboxylic acid'  ligand  48  25  .  2022-07-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_27S
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
 27S  OAG  O  O     0  -0.388  -0.1146  -0.5287   2.5481
 27S  CAT  C  CR5   0   0.542   0.8710  -0.3241   1.8882
 27S  NAM  N  N     0  -0.467   2.0419   0.1796   2.3805
 27S  CAS  C  CR5   0   0.366   3.0483  -0.1126   1.6132
 27S  NAD  N  NH2   0  -0.780   4.2990   0.1866   1.8955
 27S  SAP  S  S2    0   0.135   2.7106  -0.9903   0.1220
 27S  CAY  C  CR5   0  -0.492   0.9324  -0.6443   0.3581
 27S  CAX  C  CH1   0  -0.106   0.5554   0.5793  -0.5265
 27S  NAN  N  NH1   0  -0.632   1.1563   0.4806  -1.8300
 27S  CAQ  C  C     0   0.539   2.1623   1.2817  -2.2474
 27S  OAE  O  O     0  -0.488   2.6230   2.1812  -1.5636
 27S  CAC  C  CH3   0  -0.782   2.6826   0.9796  -3.6284
 27S  CAI  C  C1    0  -0.119   0.1088  -1.8444   0.0541
 27S  CAU  C  C     0  -0.065  -1.0152  -1.8090  -0.6632
 27S  CAR  C  C     0   0.528  -1.7305  -3.1002  -0.8592
 27S  OAH  O  OH1   0  -0.590  -2.8143  -2.9639  -1.6101
 27S  OAF  O  O     0  -0.437  -1.3765  -4.1595  -0.3984
 27S  CAL  C  CH2   0  -0.545  -1.5554  -0.5560  -1.2874
 27S  CAW  C  CH1   0   0.069  -0.9598   0.7153  -0.6868
 27S  OAO  O  O2    0  -0.490  -1.4720   1.0197   0.5786
 27S  CAV  C  CH1   0   0.050  -2.7702   1.5920   0.6315
 27S  CAK  C  CH2   0  -0.414  -3.5686   0.8909   1.7239
 27S  CAB  C  CH3   0  -0.683  -3.7354  -0.6062   1.5166
 27S  CAJ  C  CH2   0  -0.417  -2.6833   3.0925   0.8981
 27S  CAA  C  CH3   0  -0.680  -1.8749   3.8827  -0.1210
 27S  H2   H  HNH2  0   0.426   4.5211   0.6481   2.7634
 27S  H3   H  HCH1  0   0.293   0.9471   1.4851  -0.0617
 27S  H4   H  HNH1  0   0.409   0.8436  -0.2506  -2.4499
 27S  H5   H  HCH3  0   0.251   2.1300   0.1959  -4.1423
 27S  H6   H  HCH3  0   0.268   2.6490   1.8829  -4.2360
 27S  H7   H  HCH3  0   0.269   3.7268   0.6745  -3.5567
 27S  H8   H  H     0   0.290   0.4497  -2.7824   0.4771
 27S  H9   H  HOH1  0   0.487  -3.2567  -3.8200  -1.7123
 27S  H10  H  HCH2  0   0.272  -1.3709  -0.5708  -2.3672
 27S  H11  H  HCH2  0   0.281  -2.6415  -0.5176  -1.1995
 27S  H12  H  HCH1  0   0.249  -1.1354   1.5353  -1.3945
 27S  H13  H  HCH1  0   0.202  -3.2867   1.4393  -0.3282
 27S  H14  H  HCH2  0   0.216  -3.0867   1.0783   2.6884
 27S  H15  H  HCH2  0   0.215  -4.5513   1.3671   1.7761
 27S  H16  H  HCH3  0   0.210  -4.2128  -0.8273   0.5594
 27S  H17  H  HCH3  0   0.241  -2.7726  -1.1155   1.5446
 27S  H18  H  HCH3  0   0.228  -4.3638  -1.0366   2.2974
 27S  H19  H  HCH2  0   0.218  -3.7051   3.4805   0.9281
 27S  H20  H  HCH2  0   0.216  -2.2683   3.2524   1.8984
 27S  H21  H  HCH3  0   0.222  -0.8229   3.5939  -0.1187
 27S  H22  H  HCH3  0   0.218  -2.2599   3.7494  -1.1340
 27S  H23  H  HCH3  0   0.236  -1.9139   4.9492   0.1034
 27S  H1   H  HNH2  0   0.430   5.0597  -0.0360   1.2755

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
 27S  NAD  CAS  single  1.317  0.020  1.317
 27S  CAK  CAV  single  1.524  0.020  1.524
 27S  CAK  CAB  single  1.521  0.020  1.521
 27S  CAC  CAQ  single  1.506  0.020  1.506
 27S  CAJ  CAV  single  1.526  0.020  1.526
 27S  CAJ  CAA  single  1.522  0.020  1.522
 27S  CAV  OAO  single  1.420  0.020  1.420
 27S  SAP  CAS  single  1.763  0.020  1.763
 27S  SAP  CAY  single  1.827  0.020  1.827
 27S  CAS  NAM  double  1.299  0.020  1.299
 27S  NAN  CAQ  single  1.352  0.020  1.352
 27S  NAN  CAX  single  1.439  0.020  1.439
 27S  CAQ  OAE  double  1.220  0.020  1.220
 27S  OAO  CAW  single  1.399  0.020  1.399
 27S  CAW  CAX  single  1.530  0.020  1.530
 27S  CAW  CAL  single  1.527  0.020  1.527
 27S  NAM  CAT  single  1.366  0.020  1.366
 27S  CAX  CAY  single  1.556  0.020  1.556
 27S  CAY  CAT  single  1.564  0.020  1.564
 27S  CAY  CAI  single  1.487  0.020  1.487
 27S  CAL  CAU  single  1.500  0.020  1.500
 27S  CAT  OAG  double  1.204  0.020  1.204
 27S  CAI  CAU  double  1.334  0.020  1.334
 27S  CAU  CAR  single  1.489  0.020  1.489
 27S  CAR  OAF  double  1.208  0.020  1.208
 27S  CAR  OAH  single  1.326  0.020  1.326
 27S  NAD  H2   single  0.860  0.020  1.020
 27S  CAX  H3   single  0.970  0.020  1.090
 27S  NAN  H4   single  0.860  0.020  1.020
 27S  CAC  H5   single  0.970  0.020  1.090
 27S  CAC  H6   single  0.970  0.020  1.090
 27S  CAC  H7   single  0.970  0.020  1.090
 27S  CAI  H8   single  0.930  0.020  1.080
 27S  OAH  H9   single  0.850  0.020  0.980
 27S  CAL  H10  single  0.970  0.020  1.090
 27S  CAL  H11  single  0.970  0.020  1.090
 27S  CAW  H12  single  0.970  0.020  1.090
 27S  CAV  H13  single  0.970  0.020  1.090
 27S  CAK  H14  single  0.970  0.020  1.090
 27S  CAK  H15  single  0.970  0.020  1.090
 27S  CAB  H16  single  0.970  0.020  1.090
 27S  CAB  H17  single  0.970  0.020  1.090
 27S  CAB  H18  single  0.970  0.020  1.090
 27S  CAJ  H19  single  0.970  0.020  1.090
 27S  CAJ  H20  single  0.970  0.020  1.090
 27S  CAA  H21  single  0.970  0.020  1.090
 27S  CAA  H22  single  0.970  0.020  1.090
 27S  CAA  H23  single  0.970  0.020  1.090
 27S  NAD  H1   single  0.860  0.020  1.020

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
 27S  CAY  CAT  NAM  113.22  3.000
 27S  CAY  CAT  OAG  122.25  3.000
 27S  NAM  CAT  OAG  124.53  3.000
 27S  CAS  NAM  CAT  111.60  3.000
 27S  SAP  CAS  NAD  118.45  3.000
 27S  SAP  CAS  NAM  117.60  3.000
 27S  NAD  CAS  NAM  123.94  3.000
 27S  H1   NAD  H2   117.73  3.000
 27S  H1   NAD  CAS  122.39  3.000
 27S  H2   NAD  CAS  119.87  3.000
 27S  CAY  SAP  CAS   89.02  3.000
 27S  CAI  CAY  CAX  112.59  3.000
 27S  CAI  CAY  SAP  111.09  3.000
 27S  CAX  CAY  SAP  108.14  3.000
 27S  CAI  CAY  CAT  110.09  3.000
 27S  CAX  CAY  CAT  112.67  3.000
 27S  SAP  CAY  CAT  101.73  3.000
 27S  H3   CAX  CAW  109.06  3.000
 27S  H3   CAX  NAN  107.04  3.000
 27S  CAW  CAX  NAN  108.96  3.000
 27S  H3   CAX  CAY  108.89  3.000
 27S  CAW  CAX  CAY  111.68  3.000
 27S  NAN  CAX  CAY  111.09  3.000
 27S  H4   NAN  CAQ  118.08  3.000
 27S  H4   NAN  CAX  118.50  3.000
 27S  CAQ  NAN  CAX  123.36  3.000
 27S  CAC  CAQ  OAE  122.08  3.000
 27S  OAE  CAQ  NAN  123.00  3.000
 27S  CAC  CAQ  NAN  114.91  3.000
 27S  H7   CAC  H6   107.36  3.000
 27S  H7   CAC  H5   108.42  3.000
 27S  H6   CAC  H5   108.56  3.000
 27S  H7   CAC  CAQ  109.07  3.000
 27S  H6   CAC  CAQ  109.54  3.000
 27S  H5   CAC  CAQ  113.70  3.000
 27S  H8   CAI  CAU  119.86  3.000
 27S  H8   CAI  CAY  116.38  3.000
 27S  CAU  CAI  CAY  123.73  3.000
 27S  CAL  CAU  CAR  119.76  3.000
 27S  CAR  CAU  CAI  116.91  3.000
 27S  CAL  CAU  CAI  123.31  3.000
 27S  OAF  CAR  OAH  123.08  3.000
 27S  OAH  CAR  CAU  112.22  3.000
 27S  OAF  CAR  CAU  124.70  3.000
 27S  H9   OAH  CAR  110.01  3.000
 27S  H11  CAL  H10  104.34  3.000
 27S  H11  CAL  CAW  109.12  3.000
 27S  H10  CAL  CAW  109.46  3.000
 27S  H11  CAL  CAU  110.77  3.000
 27S  H10  CAL  CAU  109.76  3.000
 27S  CAW  CAL  CAU  113.03  3.000
 27S  H12  CAW  OAO  111.24  3.000
 27S  H12  CAW  CAL  107.82  3.000
 27S  OAO  CAW  CAL  113.21  3.000
 27S  H12  CAW  CAX  107.01  3.000
 27S  CAL  CAW  CAX  110.71  3.000
 27S  OAO  CAW  CAX  106.69  3.000
 27S  CAV  OAO  CAW  117.15  3.000
 27S  H13  CAV  CAJ  108.39  3.000
 27S  H13  CAV  CAK  108.39  3.000
 27S  CAJ  CAV  CAK  110.91  3.000
 27S  H13  CAV  OAO  109.92  3.000
 27S  CAJ  CAV  OAO  110.53  3.000
 27S  CAK  CAV  OAO  108.68  3.000
 27S  H15  CAK  H14  106.22  3.000
 27S  H15  CAK  CAB  109.68  3.000
 27S  H14  CAK  CAB  109.70  3.000
 27S  H15  CAK  CAV  107.74  3.000
 27S  H14  CAK  CAV  108.80  3.000
 27S  CAB  CAK  CAV  114.37  3.000
 27S  H18  CAB  H17  107.83  3.000
 27S  H18  CAB  H16  107.20  3.000
 27S  H17  CAB  H16  108.31  3.000
 27S  H18  CAB  CAK  110.74  3.000
 27S  H17  CAB  CAK  111.09  3.000
 27S  H16  CAB  CAK  111.51  3.000
 27S  H20  CAJ  H19  106.11  3.000
 27S  H20  CAJ  CAA  109.55  3.000
 27S  H19  CAJ  CAA  109.30  3.000
 27S  H20  CAJ  CAV  108.96  3.000
 27S  H19  CAJ  CAV  107.48  3.000
 27S  CAA  CAJ  CAV  115.06  3.000
 27S  H23  CAA  H22  107.32  3.000
 27S  H23  CAA  H21  107.03  3.000
 27S  H22  CAA  H21  108.04  3.000
 27S  H23  CAA  CAJ  110.55  3.000
 27S  H22  CAA  CAJ  111.75  3.000
 27S  H21  CAA  CAJ  111.92  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
 27S  CONST_01  SAP  CAS  NAM  CAT    0.00   0.0  0
 27S  CONST_02  NAD  CAS  NAM  CAT  180.00   0.0  0
 27S  CONST_03  H2   NAD  CAS  NAM    0.00   0.0  0
 27S  CONST_04  H1   NAD  CAS  NAM  180.00   0.0  0
 27S  CONST_05  CAC  CAQ  NAN  CAX  180.00   0.0  0
 27S  CONST_06  OAE  CAQ  NAN  CAX    0.00   0.0  0
 27S  CONST_07  H9   OAH  CAR  CAU  180.00   0.0  0
 27S  CONST_08  H4   NAN  CAQ  OAE  180.00   0.0  0
 27S  Var_01    CAY  CAT  NAM  CAS  -20.68  30.0  1
 27S  Var_02    CAL  CAU  CAI  CAY    2.14  30.0  1
 27S  Var_03    CAW  CAL  CAU  CAI  -17.62  30.0  1
 27S  Var_04    OAF  CAR  CAU  CAI    1.30  30.0  2
 27S  Var_05    CAK  CAV  OAO  CAW  134.82  30.0  2
 27S  Var_06    CAB  CAK  CAV  OAO  -59.82  30.0  1
 27S  Var_07    CAA  CAJ  CAV  OAO   57.97  30.0  1
 27S  Var_08    H5   CAC  CAQ  NAN    4.15  30.0  3
 27S  Var_09    H16  CAB  CAK  CAV  -57.33  30.0  3
 27S  Var_10    H21  CAA  CAJ  CAV  -64.40  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
 27S  chir_01  CAY  CAX  CAT  CAI  negativ
 27S  chir_02  CAX  NAN  CAW  CAY  negativ
 27S  chir_03  CAW  OAO  CAL  CAX  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
 27S  plan-1  CAX  0.020
 27S  plan-1  NAN  0.020
 27S  plan-1  CAQ  0.020
 27S  plan-1  OAE  0.020
 27S  plan-1  CAC  0.020
 27S  plan-1  H4   0.020
 27S  plan-2  OAG  0.020
 27S  plan-2  CAT  0.020
 27S  plan-2  NAM  0.020
 27S  plan-2  CAY  0.020
 27S  plan-3  CAT  0.020
 27S  plan-3  NAM  0.020
 27S  plan-3  CAS  0.020
 27S  plan-3  NAD  0.020
 27S  plan-3  SAP  0.020
 27S  plan-3  H2   0.020
 27S  plan-3  H1   0.020
 27S  plan-4  CAU  0.020
 27S  plan-4  CAR  0.020
 27S  plan-4  OAH  0.020
 27S  plan-4  OAF  0.020
 27S  plan-4  H9   0.020

