# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 23:37:22 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: (3~{S},7~{R},10~{R},13~{S})-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: OC(=O)[C@@H]1CC[C@@H]2C=C[C@H]3CCN[C@@H]3C(=O)N12
#
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
 92B  92B  '(3~{S},7~{R},10~{R},13~{S})-2-oxidanylidene-1,4-diazatricyclo[8.3.0.0^{3,7}]tridec-8-ene-13-carboxylic acid'  ligand  33  17  .  2022-07-24  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_92B
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
 92B  N2   N  NR15  0  -0.596   2.5964   1.3112  -0.9172
 92B  C22  C  CH2   0  -0.295   3.8982   0.8906  -0.3791
 92B  C23  C  CH2   0  -0.480   3.6431  -0.2712   0.6059
 92B  C8   C  CR15  0  -0.296   2.1233  -0.2657   0.8046
 92B  C21  C  CR15  0  -0.222   1.6569   0.2710  -0.5567
 92B  C25  C  C     0   0.562   0.2347   0.7622  -0.4886
 92B  O7   O  O     0  -0.492  -0.0497   1.9530  -0.4850
 92B  C7   C  C1    0  -0.189   1.5542  -1.5907   1.1864
 92B  C6   C  C1    0  -0.230   0.4742  -2.1684   0.6696
 92B  C5   C  CH1   0  -0.080  -0.4819  -1.6465  -0.3693
 92B  C4   C  CH2   0  -0.481  -1.8953  -2.1930  -0.1367
 92B  C3   C  CH2   0  -0.482  -2.8081  -1.1392  -0.7401
 92B  C2   C  CH1   0  -0.206  -2.0996   0.1725  -0.3796
 92B  N1   N  NT    0  -0.477  -0.7026  -0.1945  -0.3904
 92B  C1   C  C     0   0.555  -2.5170   0.6765   0.9884
 92B  O2   O  O     0  -0.427  -1.8874   0.5205   2.0012
 92B  OXT  O  OH1   0  -0.593  -3.6930   1.2871   0.9285
 92B  H1   H  HNR5  0   0.346   2.3079   2.1707  -0.4673
 92B  H26  H  HCH2  0   0.223   4.5555   0.5620  -1.1869
 92B  H27  H  HCH2  0   0.235   4.3864   1.7365   0.1049
 92B  H28  H  HCH2  0   0.237   3.9520  -1.2219   0.1654
 92B  H29  H  HCH2  0   0.249   4.1842  -0.1552   1.5449
 92B  H30  H  HCR5  0   0.260   1.8760   0.4794   1.5727
 92B  H31  H  HCR5  0   0.264   1.7252  -0.5459  -1.2885
 92B  H32  H  H     0   0.248   2.0959  -2.1393   1.9510
 92B  H33  H  H     0   0.253   0.2256  -3.1669   1.0159
 92B  H34  H  HCH1  0   0.272  -0.1406  -1.9689  -1.3617
 92B  H42  H  HCH2  0   0.269  -2.0202  -3.1764  -0.5877
 92B  H35  H  HCH2  0   0.251  -2.0823  -2.2961   0.9347
 92B  H36  H  HCH2  0   0.266  -2.8404  -1.2313  -1.8267
 92B  H37  H  HCH1  0   0.303  -2.3063   0.9496  -1.1182
 92B  H3   H  HOH1  0   0.483  -3.9768   1.5597   1.8142
 92B  H2   H  HCH2  0   0.273  -3.8323  -1.1902  -0.3736

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
 92B  O2   C1   double  1.203  0.020  1.203
 92B  C7   C8   single  1.492  0.020  1.492
 92B  C23  C8   single  1.533  0.020  1.533
 92B  C23  C22  single  1.544  0.020  1.544
 92B  C8   C21  single  1.536  0.020  1.536
 92B  C6   C5   single  1.505  0.020  1.505
 92B  C1   OXT  single  1.326  0.020  1.326
 92B  C1   C2   single  1.516  0.020  1.516
 92B  C22  N2   single  1.470  0.020  1.470
 92B  C4   C5   single  1.533  0.020  1.533
 92B  C4   C3   single  1.519  0.020  1.519
 92B  C5   N1   single  1.469  0.020  1.469
 92B  C21  C25  single  1.506  0.020  1.506
 92B  C21  N2   single  1.447  0.020  1.447
 92B  N1   C25  single  1.343  0.020  1.343
 92B  N1   C2   single  1.444  0.020  1.444
 92B  C25  O7   double  1.224  0.020  1.224
 92B  C2   C3   single  1.534  0.020  1.534
 92B  N2   H1   single  0.890  0.020  1.040
 92B  C22  H26  single  0.970  0.020  1.090
 92B  C22  H27  single  0.970  0.020  1.090
 92B  C23  H28  single  0.970  0.020  1.090
 92B  C23  H29  single  0.970  0.020  1.090
 92B  C8   H30  single  0.970  0.020  1.090
 92B  C21  H31  single  0.970  0.020  1.090
 92B  C7   H32  single  0.930  0.020  1.080
 92B  C6   H33  single  0.930  0.020  1.080
 92B  C5   H34  single  0.970  0.020  1.090
 92B  C4   H42  single  0.970  0.020  1.090
 92B  C4   H35  single  0.970  0.020  1.090
 92B  C3   H36  single  0.970  0.020  1.090
 92B  C2   H37  single  0.970  0.020  1.090
 92B  OXT  H3   single  0.850  0.020  0.980
 92B  C3   H2   single  0.970  0.020  1.090
 92B  C6   C7   double  1.329  0.020  1.329

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
 92B  H1   N2   C21  108.34  3.000
 92B  H1   N2   C22  109.43  3.000
 92B  C21  N2   C22  106.14  3.000
 92B  H27  C22  H26  107.00  3.000
 92B  H27  C22  C23  112.00  3.000
 92B  H26  C22  C23  110.18  3.000
 92B  H27  C22  N2   109.70  3.000
 92B  H26  C22  N2   110.39  3.000
 92B  C23  C22  N2   107.60  3.000
 92B  H29  C23  H28  107.43  3.000
 92B  H29  C23  C8   112.35  3.000
 92B  H28  C23  C8   109.62  3.000
 92B  H29  C23  C22  112.79  3.000
 92B  H28  C23  C22  110.53  3.000
 92B  C8   C23  C22  104.11  3.000
 92B  H30  C8   C7   109.73  3.000
 92B  H30  C8   C21  108.33  3.000
 92B  C7   C8   C21  114.92  3.000
 92B  H30  C8   C23  108.44  3.000
 92B  C21  C8   C23  100.80  3.000
 92B  C7   C8   C23  114.10  3.000
 92B  H31  C21  C25  109.35  3.000
 92B  H31  C21  C8   108.15  3.000
 92B  C25  C21  C8   111.14  3.000
 92B  H31  C21  N2   109.15  3.000
 92B  C25  C21  N2   112.94  3.000
 92B  C8   C21  N2   105.95  3.000
 92B  N1   C25  O7   122.04  3.000
 92B  O7   C25  C21  122.46  3.000
 92B  N1   C25  C21  115.47  3.000
 92B  H32  C7   C6   117.36  3.000
 92B  C6   C7   C8   126.61  3.000
 92B  H32  C7   C8   116.01  3.000
 92B  H33  C6   C5   113.17  3.000
 92B  H33  C6   C7   117.50  3.000
 92B  C5   C6   C7   129.33  3.000
 92B  H34  C5   N1   108.91  3.000
 92B  H34  C5   C4   108.61  3.000
 92B  N1   C5   C4   102.48  3.000
 92B  H34  C5   C6   108.94  3.000
 92B  N1   C5   C6   116.62  3.000
 92B  C4   C5   C6   110.93  3.000
 92B  H35  C4   H42  107.54  3.000
 92B  H35  C4   C3   110.62  3.000
 92B  H42  C4   C3   113.14  3.000
 92B  H35  C4   C5   109.89  3.000
 92B  H42  C4   C5   111.39  3.000
 92B  C3   C4   C5   104.26  3.000
 92B  H2   C3   H36  107.66  3.000
 92B  H2   C3   C2   113.29  3.000
 92B  H36  C3   C2   108.66  3.000
 92B  H2   C3   C4   113.51  3.000
 92B  H36  C3   C4   110.78  3.000
 92B  C2   C3   C4   102.85  3.000
 92B  H37  C2   C1   108.76  3.000
 92B  H37  C2   N1   111.03  3.000
 92B  C1   C2   N1   110.94  3.000
 92B  H37  C2   C3   111.24  3.000
 92B  N1   C2   C3   103.16  3.000
 92B  C1   C2   C3   111.66  3.000
 92B  C2   N1   C5   113.35  3.000
 92B  C2   N1   C25  119.64  3.000
 92B  C5   N1   C25  126.90  3.000
 92B  OXT  C1   O2   124.18  3.000
 92B  OXT  C1   C2   110.87  3.000
 92B  O2   C1   C2   124.92  3.000
 92B  H3   OXT  C1   110.36  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
 92B  CONST_01  H3   OXT  C1   C2   180.00   0.0  0
 92B  Var_01    C8   C23  C22  N2   -11.66  30.0  1
 92B  Var_02    C21  N2   C22  C23  -13.35  30.0  1
 92B  Var_03    C2   C3   C4   C5   -37.49  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
 92B  chir_01  C8   C7  C23  C21  negativ
 92B  chir_02  C21  N2  C8   C25  negativ
 92B  chir_03  C5   N1  C6   C4   negativ
 92B  chir_04  C2   N1  C3   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
 92B  plan-1  C21  0.020
 92B  plan-1  C25  0.020
 92B  plan-1  O7   0.020
 92B  plan-1  C5   0.020
 92B  plan-1  C2   0.020
 92B  plan-1  N1   0.020
 92B  plan-2  C2   0.020
 92B  plan-2  C1   0.020
 92B  plan-2  O2   0.020
 92B  plan-2  OXT  0.020
 92B  plan-2  H3   0.020

