# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 10:29:16 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  47  25  .  2022-07-22  2022-07-26
;
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  -0.393  -0.1497  -0.5299   2.5263
 27S  CAT  C  CR5    0   0.536   0.8312  -0.3117   1.8625
 27S  NAM  N  N      0  -0.473   1.9938   0.2096   2.3667
 27S  CAS  C  CR5    0   0.359   3.0095  -0.0808   1.6111
 27S  NAD  N  NH2    0  -0.783   4.2559   0.2323   1.9067
 27S  SAP  S  S2     0   0.113   2.6926  -0.9736   0.1271
 27S  CAY  C  CR5    0  -0.470   0.9036  -0.6308   0.3376
 27S  CAX  C  CH1    0  -0.104   0.5566   0.5987  -0.5503
 27S  NAN  N  NH1    0  -0.628   1.1481   0.4660  -1.8565
 27S  CAQ  C  C      0   0.535   2.1511   1.2476  -2.3092
 27S  OAE  O  O      0  -0.492   2.6181   2.1755  -1.6673
 27S  CAC  C  CH3    0  -0.782   2.6685   0.8850  -3.6776
 27S  CAI  C  C1     0  -0.173   0.0767  -1.8209  -0.0067
 27S  CAU  C  C      0  -0.084  -1.0438  -1.7710  -0.7265
 27S  CAR  C  C      0   0.398  -1.8214  -3.0537  -1.0110
 27S  OAH  O  OC    -1  -0.592  -2.8398  -2.9247  -1.7177
 27S  OAF  O  O      0  -0.594  -1.3793  -4.1145  -0.5287
 27S  CAL  C  CH2    0  -0.550  -1.5730  -0.4935  -1.3047
 27S  CAW  C  CH1    0   0.081  -0.9555   0.7665  -0.7063
 27S  OAO  O  O2     0  -0.494  -1.4426   1.0832   0.5685
 27S  CAV  C  CH1    0   0.058  -2.7543   1.6122   0.6643
 27S  CAK  C  CH2    0  -0.413  -3.4900   0.8668   1.7721
 27S  CAB  C  CH3    0  -0.683  -3.7294  -0.6062   1.4777
 27S  CAJ  C  CH2    0  -0.421  -2.7039   3.1119   0.9465
 27S  CAA  C  CH3    0  -0.677  -1.9245   3.9269  -0.0759
 27S  H2   H  HNH2   0   0.422   4.4627   0.7028   2.7733
 27S  H3   H  HCH1   0   0.283   0.9750   1.4990  -0.0978
 27S  H4   H  HNH1   0   0.406   0.8340  -0.2906  -2.4440
 27S  H5   H  HCH3   0   0.250   2.0856   0.1120  -4.1739
 27S  H6   H  HCH3   0   0.266   2.6819   1.7713  -4.3104
 27S  H7   H  HCH3   0   0.268   3.6971   0.5339  -3.5878
 27S  H8   H  H      0   0.254   0.4076  -2.7739   0.3896
 27S  H10  H  HCH2   0   0.247  -1.4163  -0.4885  -2.3899
 27S  H11  H  HCH2   0   0.267  -2.6580  -0.4617  -1.1980
 27S  H12  H  HCH1   0   0.233  -1.1189   1.5973  -1.4057
 27S  H13  H  HCH1   0   0.198  -3.2958   1.4602  -0.2818
 27S  H14  H  HCH2   0   0.216  -2.9126   0.9659   2.6960
 27S  H15  H  HCH2   0   0.210  -4.4454   1.3688   1.9488
 27S  H16  H  HCH3   0   0.208  -4.3404  -0.7391   0.5826
 27S  H17  H  HCH3   0   0.247  -2.7886  -1.1332   1.3223
 27S  H18  H  HCH3   0   0.223  -4.2520  -1.0891   2.3046
 27S  H19  H  HCH2   0   0.216  -3.7348   3.4746   0.9888
 27S  H20  H  HCH2   0   0.214  -2.2830   3.2765   1.9437
 27S  H21  H  HCH3   0   0.222  -0.8666   3.6616  -0.0843
 27S  H22  H  HCH3   0   0.217  -2.3146   3.7867  -1.0862
 27S  H23  H  HCH3   0   0.234  -1.9873   4.9917   0.1517
 27S  H1   H  HNH2   0   0.427   5.0249   0.0133   1.2963

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  1.319  0.020  1.319
 27S  CAK  CAV  single  1.524  0.020  1.524
 27S  CAK  CAB  single  1.521  0.020  1.521
 27S  CAC  CAQ  single  1.507  0.020  1.507
 27S  CAJ  CAV  single  1.527  0.020  1.527
 27S  CAJ  CAA  single  1.522  0.020  1.522
 27S  CAV  OAO  single  1.418  0.020  1.418
 27S  SAP  CAS  single  1.761  0.020  1.761
 27S  SAP  CAY  single  1.834  0.020  1.834
 27S  CAS  NAM  double  1.299  0.020  1.299
 27S  NAN  CAQ  single  1.350  0.020  1.350
 27S  NAN  CAX  single  1.440  0.020  1.440
 27S  CAQ  OAE  double  1.221  0.020  1.221
 27S  OAO  CAW  single  1.401  0.020  1.401
 27S  CAW  CAX  single  1.529  0.020  1.529
 27S  CAW  CAL  single  1.525  0.020  1.525
 27S  NAM  CAT  single  1.370  0.020  1.370
 27S  CAX  CAY  single  1.556  0.020  1.556
 27S  CAY  CAT  single  1.560  0.020  1.560
 27S  CAY  CAI  single  1.489  0.020  1.489
 27S  CAL  CAU  single  1.499  0.020  1.499
 27S  CAT  OAG  double  1.204  0.020  1.204
 27S  CAI  CAU  double  1.333  0.020  1.333
 27S  CAU  CAR  single  1.527  0.020  1.527
 27S  CAR  OAF  deloc   1.246  0.020  1.246
 27S  CAR  OAH  deloc   1.246  0.020  1.246
 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  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  113.47  3.000
 27S  CAY  CAT  OAG  122.66  3.000
 27S  NAM  CAT  OAG  123.86  3.000
 27S  CAS  NAM  CAT  111.37  3.000
 27S  SAP  CAS  NAD  118.65  3.000
 27S  SAP  CAS  NAM  117.58  3.000
 27S  NAD  CAS  NAM  123.76  3.000
 27S  H1   NAD  H2   117.82  3.000
 27S  H1   NAD  CAS  122.34  3.000
 27S  H2   NAD  CAS  119.85  3.000
 27S  CAY  SAP  CAS   89.09  3.000
 27S  CAI  CAY  CAX  112.07  3.000
 27S  CAI  CAY  SAP  111.45  3.000
 27S  CAX  CAY  SAP  107.45  3.000
 27S  CAI  CAY  CAT  111.33  3.000
 27S  CAX  CAY  CAT  112.70  3.000
 27S  SAP  CAY  CAT  101.29  3.000
 27S  H3   CAX  CAW  109.33  3.000
 27S  H3   CAX  NAN  107.13  3.000
 27S  CAW  CAX  NAN  108.89  3.000
 27S  H3   CAX  CAY  109.27  3.000
 27S  CAW  CAX  CAY  111.44  3.000
 27S  NAN  CAX  CAY  110.69  3.000
 27S  H4   NAN  CAQ  118.08  3.000
 27S  H4   NAN  CAX  118.02  3.000
 27S  CAQ  NAN  CAX  123.79  3.000
 27S  CAC  CAQ  OAE  121.92  3.000
 27S  OAE  CAQ  NAN  123.23  3.000
 27S  CAC  CAQ  NAN  114.86  3.000
 27S  H7   CAC  H6   107.36  3.000
 27S  H7   CAC  H5   108.31  3.000
 27S  H6   CAC  H5   108.64  3.000
 27S  H7   CAC  CAQ  109.06  3.000
 27S  H6   CAC  CAQ  109.63  3.000
 27S  H5   CAC  CAQ  113.65  3.000
 27S  H8   CAI  CAU  119.15  3.000
 27S  H8   CAI  CAY  116.65  3.000
 27S  CAU  CAI  CAY  124.17  3.000
 27S  CAL  CAU  CAR  117.67  3.000
 27S  CAR  CAU  CAI  119.83  3.000
 27S  CAL  CAU  CAI  122.49  3.000
 27S  OAF  CAR  OAH  126.68  3.000
 27S  OAH  CAR  CAU  115.78  3.000
 27S  OAF  CAR  CAU  117.54  3.000
 27S  H11  CAL  H10  103.82  3.000
 27S  H11  CAL  CAW  109.89  3.000
 27S  H10  CAL  CAW  109.07  3.000
 27S  H11  CAL  CAU  109.77  3.000
 27S  H10  CAL  CAU  109.59  3.000
 27S  CAW  CAL  CAU  114.19  3.000
 27S  H12  CAW  OAO  110.90  3.000
 27S  H12  CAW  CAL  108.35  3.000
 27S  OAO  CAW  CAL  113.76  3.000
 27S  H12  CAW  CAX  107.16  3.000
 27S  CAL  CAW  CAX  110.46  3.000
 27S  OAO  CAW  CAX  106.01  3.000
 27S  CAV  OAO  CAW  117.88  3.000
 27S  H13  CAV  CAJ  108.10  3.000
 27S  H13  CAV  CAK  108.65  3.000
 27S  CAJ  CAV  CAK  111.21  3.000
 27S  H13  CAV  OAO  110.22  3.000
 27S  CAJ  CAV  OAO  110.40  3.000
 27S  CAK  CAV  OAO  108.25  3.000
 27S  H15  CAK  H14  106.44  3.000
 27S  H15  CAK  CAB  109.77  3.000
 27S  H14  CAK  CAB  109.52  3.000
 27S  H15  CAK  CAV  108.34  3.000
 27S  H14  CAK  CAV  108.35  3.000
 27S  CAB  CAK  CAV  114.13  3.000
 27S  H18  CAB  H17  107.92  3.000
 27S  H18  CAB  H16  107.43  3.000
 27S  H17  CAB  H16  107.90  3.000
 27S  H18  CAB  CAK  110.94  3.000
 27S  H17  CAB  CAK  111.11  3.000
 27S  H16  CAB  CAK  111.38  3.000
 27S  H20  CAJ  H19  106.10  3.000
 27S  H20  CAJ  CAA  109.54  3.000
 27S  H19  CAJ  CAA  109.33  3.000
 27S  H20  CAJ  CAV  109.19  3.000
 27S  H19  CAJ  CAV  107.57  3.000
 27S  CAA  CAJ  CAV  114.75  3.000
 27S  H23  CAA  H22  107.33  3.000
 27S  H23  CAA  H21  107.16  3.000
 27S  H22  CAA  H21  107.94  3.000
 27S  H23  CAA  CAJ  110.68  3.000
 27S  H22  CAA  CAJ  111.70  3.000
 27S  H21  CAA  CAJ  111.81  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  H4   NAN  CAQ  OAE  180.00   0.0  0
 27S  Var_01    CAY  CAT  NAM  CAS  -21.28  30.0  1
 27S  Var_02    CAL  CAU  CAI  CAY    1.79  30.0  1
 27S  Var_03    CAW  CAL  CAU  CAI  -15.52  30.0  1
 27S  Var_04    OAF  CAR  CAU  CAI    1.23  30.0  2
 27S  Var_05    CAK  CAV  OAO  CAW  132.96  30.0  2
 27S  Var_06    CAB  CAK  CAV  OAO  -65.69  30.0  2
 27S  Var_07    CAA  CAJ  CAV  OAO   56.87  30.0  2
 27S  Var_08    H5   CAC  CAQ  NAN    6.88  30.0  3
 27S  Var_09    H16  CAB  CAK  CAV  -60.75  30.0  3
 27S  Var_10    H21  CAA  CAJ  CAV  -64.43  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

