# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 19:48:51 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: (3~{S},7~{R},10~{R},11~{R},13~{S})-11-methyl-2-oxidanylidene-1,4-diazatricyclo[8.3.0.0^{3,7}]tridec-8-ene-13-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1C[C@H](N2[C@H]1C=C[C@H]3CCN[C@@H]3C2=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
 8SN  8SN  '(3~{S},7~{R},10~{R},11~{R},13~{S})-11-methyl-2-oxidanylidene-1,4-diazatricyclo[8.3.0.0^{3,7}]tridec-8-ene-13-carboxylic acid'  ligand  36  18  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8SN
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
 8SN  N2   N  NR15  0  -0.615   2.9254   0.8389  -1.0819
 8SN  C22  C  CH2   0  -0.278   4.1143   0.4107  -0.3269
 8SN  C23  C  CH2   0  -0.480   3.6701  -0.7651   0.5490
 8SN  C8   C  CR15  0  -0.301   2.1763  -0.5124   0.7441
 8SN  C21  C  CR15  0  -0.193   1.8011   0.0374  -0.6401
 8SN  C25  C  C     0   0.553   0.5156   0.8194  -0.5564
 8SN  O7   O  O     0  -0.492   0.4852   2.0424  -0.6147
 8SN  C7   C  C1    0  -0.197   1.3897  -1.7086   1.1616
 8SN  C6   C  C1    0  -0.221   0.1952  -2.0659   0.7016
 8SN  C5   C  CH1   0  -0.044  -0.7025  -1.3695  -0.2840
 8SN  C4   C  CH1   0  -0.290  -2.1817  -1.5867   0.0856
 8SN  C3   C  CH2   0  -0.463  -2.8778  -0.3781  -0.5223
 8SN  C2   C  CH1   0  -0.207  -1.8763   0.7593  -0.3053
 8SN  N1   N  NT    0  -0.485  -0.5968   0.0910  -0.3684
 8SN  C1   C  C     0   0.556  -2.0624   1.4335   1.0410
 8SN  O2   O  O     0  -0.428  -1.4048   1.2040   2.0215
 8SN  C47  C  CH3   0  -0.665  -2.7294  -2.9193  -0.3886
 8SN  O1   O  OH1   0  -0.593  -3.0700   2.2953   1.0059
 8SN  H1   H  HNR5  0   0.350   2.7300   1.8142  -0.8996
 8SN  H96  H  HCH2  0   0.220   4.9254   0.1183  -0.9979
 8SN  H97  H  HCH2  0   0.224   4.4918   1.2298   0.2896
 8SN  H23  H  HCH2  0   0.235   3.8155  -1.7146   0.0272
 8SN  H95  H  HCH2  0   0.252   4.2199  -0.8193   1.4886
 8SN  H8   H  HCR5  0   0.261   2.0537   0.2874   1.4874
 8SN  H21  H  HCR5  0   0.257   1.6559  -0.8148  -1.3196
 8SN  H7   H  H     0   0.249   1.8535  -2.3510   1.9039
 8SN  H6   H  H     0   0.249  -0.2180  -3.0019   1.0656
 8SN  H5   H  HCH1  0   0.265  -0.5300  -1.7964  -1.2825
 8SN  H41  H  HCH1  0   0.257  -2.2690  -1.5320   1.1763
 8SN  H32  H  HCH2  0   0.259  -3.0208  -0.5197  -1.5963
 8SN  H31  H  HCH2  0   0.273  -3.8553  -0.1794  -0.0841
 8SN  H22  H  HCH1  0   0.302  -1.9650   1.5143  -1.0893
 8SN  H47  H  HCH3  0   0.238  -2.1996  -3.7589   0.0634
 8SN  H93  H  HCH3  0   0.243  -3.7822  -3.0209  -0.1247
 8SN  H94  H  HCH3  0   0.227  -2.6436  -3.0128  -1.4729
 8SN  H3   H  HOH1  0   0.483  -3.2011   2.6932   1.8798

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
 8SN  C22  C23  single  1.532  0.020  1.532
 8SN  C22  N2   single  1.472  0.020  1.472
 8SN  C23  C8   single  1.528  0.020  1.528
 8SN  N2   C21  single  1.450  0.020  1.450
 8SN  C8   C21  single  1.536  0.020  1.536
 8SN  C8   C7   single  1.491  0.020  1.491
 8SN  C21  C25  single  1.507  0.020  1.507
 8SN  C7   C6   double  1.329  0.020  1.329
 8SN  O7   C25  double  1.225  0.020  1.225
 8SN  C25  N1   single  1.343  0.020  1.343
 8SN  C6   C5   single  1.504  0.020  1.504
 8SN  N1   C5   single  1.467  0.020  1.467
 8SN  N1   C2   single  1.445  0.020  1.445
 8SN  C5   C4   single  1.540  0.020  1.540
 8SN  O2   C1   double  1.203  0.020  1.203
 8SN  C2   C1   single  1.517  0.020  1.517
 8SN  C2   C3   single  1.531  0.020  1.531
 8SN  C1   O1   single  1.326  0.020  1.326
 8SN  C4   C3   single  1.521  0.020  1.521
 8SN  C4   C47  single  1.517  0.020  1.517
 8SN  N2   H1   single  0.890  0.020  1.040
 8SN  C22  H96  single  0.970  0.020  1.090
 8SN  C22  H97  single  0.970  0.020  1.090
 8SN  C23  H23  single  0.970  0.020  1.090
 8SN  C23  H95  single  0.970  0.020  1.090
 8SN  C8   H8   single  0.970  0.020  1.090
 8SN  C21  H21  single  0.970  0.020  1.090
 8SN  C7   H7   single  0.930  0.020  1.080
 8SN  C6   H6   single  0.930  0.020  1.080
 8SN  C5   H5   single  0.970  0.020  1.090
 8SN  C4   H41  single  0.970  0.020  1.090
 8SN  C3   H32  single  0.970  0.020  1.090
 8SN  C3   H31  single  0.970  0.020  1.090
 8SN  C2   H22  single  0.970  0.020  1.090
 8SN  C47  H47  single  0.970  0.020  1.090
 8SN  C47  H93  single  0.970  0.020  1.090
 8SN  C47  H94  single  0.970  0.020  1.090
 8SN  O1   H3   single  0.850  0.020  0.980

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
 8SN  H1   N2   C21  109.18  3.000
 8SN  H1   N2   C22  110.13  3.000
 8SN  C21  N2   C22  108.01  3.000
 8SN  H97  C22  H96  106.90  3.000
 8SN  H97  C22  C23  110.67  3.000
 8SN  H96  C22  C23  111.16  3.000
 8SN  H97  C22  N2   110.51  3.000
 8SN  H96  C22  N2   111.25  3.000
 8SN  C23  C22  N2   106.40  3.000
 8SN  H95  C23  H23  107.53  3.000
 8SN  H95  C23  C8   113.04  3.000
 8SN  H23  C23  C8   109.55  3.000
 8SN  H95  C23  C22  112.63  3.000
 8SN  H23  C23  C22  110.81  3.000
 8SN  C8   C23  C22  103.27  3.000
 8SN  H8   C8   C7   109.61  3.000
 8SN  H8   C8   C21  108.77  3.000
 8SN  C7   C8   C21  114.24  3.000
 8SN  H8   C8   C23  108.42  3.000
 8SN  C7   C8   C23  114.77  3.000
 8SN  C21  C8   C23  100.54  3.000
 8SN  H21  C21  C25  108.89  3.000
 8SN  H21  C21  C8   108.16  3.000
 8SN  C25  C21  C8   110.12  3.000
 8SN  H21  C21  N2   110.04  3.000
 8SN  C25  C21  N2   113.05  3.000
 8SN  C8   C21  N2   106.45  3.000
 8SN  N1   C25  O7   121.85  3.000
 8SN  N1   C25  C21  115.65  3.000
 8SN  O7   C25  C21  122.46  3.000
 8SN  H7   C7   C6   117.49  3.000
 8SN  H7   C7   C8   116.15  3.000
 8SN  C6   C7   C8   126.36  3.000
 8SN  H6   C6   C5   113.06  3.000
 8SN  H6   C6   C7   117.24  3.000
 8SN  C5   C6   C7   129.70  3.000
 8SN  H5   C5   N1   108.85  3.000
 8SN  H5   C5   C4   108.29  3.000
 8SN  N1   C5   C4   102.91  3.000
 8SN  H5   C5   C6   108.77  3.000
 8SN  C4   C5   C6   110.53  3.000
 8SN  N1   C5   C6   117.11  3.000
 8SN  H41  C4   C47  109.05  3.000
 8SN  H41  C4   C3   108.76  3.000
 8SN  C47  C4   C3   114.07  3.000
 8SN  H41  C4   C5   107.97  3.000
 8SN  C47  C4   C5   113.30  3.000
 8SN  C3   C4   C5   103.39  3.000
 8SN  H31  C3   H32  107.54  3.000
 8SN  H31  C3   C2   113.23  3.000
 8SN  H32  C3   C2   108.74  3.000
 8SN  H31  C3   C4   113.24  3.000
 8SN  H32  C3   C4   110.47  3.000
 8SN  C2   C3   C4   103.55  3.000
 8SN  H22  C2   C1   108.66  3.000
 8SN  H22  C2   N1   111.12  3.000
 8SN  C1   C2   N1   110.66  3.000
 8SN  H22  C2   C3   111.03  3.000
 8SN  C1   C2   C3   112.07  3.000
 8SN  N1   C2   C3   103.26  3.000
 8SN  C2   N1   C5   113.22  3.000
 8SN  C2   N1   C25  119.26  3.000
 8SN  C5   N1   C25  127.43  3.000
 8SN  O1   C1   O2   124.12  3.000
 8SN  O1   C1   C2   111.00  3.000
 8SN  O2   C1   C2   124.87  3.000
 8SN  H94  C47  H93  107.96  3.000
 8SN  H94  C47  H47  107.91  3.000
 8SN  H93  C47  H47  107.28  3.000
 8SN  H94  C47  C4   110.94  3.000
 8SN  H93  C47  C4   110.79  3.000
 8SN  H47  C47  C4   111.79  3.000
 8SN  H3   O1   C1   110.22  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
 8SN  CONST_01  H3   O1   C1   C2   180.00   0.0  0
 8SN  Var_01    C8   C23  C22  N2   -26.27  30.0  1
 8SN  Var_02    C21  N2   C22  C23    3.36  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
 8SN  chir_01  C8   C23  C21  C7   negativ
 8SN  chir_02  C21  N2   C8   C25  negativ
 8SN  chir_03  C5   N1   C4   C6   positiv
 8SN  chir_04  C4   C5   C3   C47  negativ
 8SN  chir_05  C2   N1   C1   C3   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
 8SN  plan-1  C21  0.020
 8SN  plan-1  C25  0.020
 8SN  plan-1  O7   0.020
 8SN  plan-1  C5   0.020
 8SN  plan-1  C2   0.020
 8SN  plan-1  N1   0.020
 8SN  plan-2  C2   0.020
 8SN  plan-2  C1   0.020
 8SN  plan-2  O2   0.020
 8SN  plan-2  O1   0.020
 8SN  plan-2  H3   0.020

