# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 13:18:23 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  32  17  .  2022-07-24  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_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  -0.624   2.6601   1.1251  -1.0835
 92B  C22  C  CH2    0  -0.276   3.7646   1.1023  -0.1158
 92B  C23  C  CH2    0  -0.472   3.5991  -0.2089   0.6456
 92B  C8   C  CR15   0  -0.300   2.0820  -0.3617   0.7040
 92B  C21  C  CR15   0  -0.176   1.6803   0.1240  -0.6976
 92B  C25  C  C      0   0.536   0.2644   0.6505  -0.6568
 92B  O7   O  O      0  -0.513   0.0247   1.8531  -0.7318
 92B  C7   C  C1     0  -0.202   1.5853  -1.7321   1.0199
 92B  C6   C  C1     0  -0.221   0.4938  -2.2928   0.5109
 92B  C5   C  CH1    0  -0.070  -0.5249  -1.7236  -0.4380
 92B  C4   C  CH2    0  -0.478  -1.9321  -2.2110  -0.0612
 92B  C3   C  CH2    0  -0.474  -2.8540  -1.1265  -0.5921
 92B  C2   C  CH1    0  -0.201  -2.0702   0.1506  -0.2972
 92B  N1   N  NT     0  -0.463  -0.6924  -0.2673  -0.4941
 92B  C1   C  C      0   0.415  -2.3323   0.6764   1.1345
 92B  O2   O  O      0  -0.583  -1.4181   0.5827   1.9688
 92B  OXT  O  OC    -1  -0.623  -3.4768   1.1436   1.3096
 92B  H1   H  HNR5   0   0.348   2.2211   2.0360  -1.1074
 92B  H26  H  HCH2   0   0.219   4.7340   1.1621  -0.6162
 92B  H27  H  HCH2   0   0.212   3.7083   1.9457   0.5804
 92B  H28  H  HCH2   0   0.231   4.0366  -1.0413   0.0868
 92B  H29  H  HCH2   0   0.248   4.0652  -0.1857   1.6309
 92B  H30  H  HCR5   0   0.261   1.6909   0.3445   1.4485
 92B  H31  H  HCR5   0   0.244   1.7222  -0.7333  -1.3842
 92B  H32  H  H      0   0.241   2.1785  -2.3173   1.7161
 92B  H33  H  H      0   0.245   0.2783  -3.3207   0.7885
 92B  H34  H  HCH1   0   0.258  -0.2927  -2.0920  -1.4468
 92B  H42  H  HCH2   0   0.251  -2.1316  -3.1989  -0.4755
 92B  H35  H  HCH2   0   0.241  -2.0189  -2.2854   1.0255
 92B  H36  H  HCH2   0   0.235  -2.9985  -1.2434  -1.6691
 92B  H37  H  HCH1   0   0.247  -2.3264   0.9395  -1.0077
 92B  H2   H  HCH2   0   0.247  -3.8370  -1.1244  -0.1242

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   deloc   1.241  0.020  1.241
 92B  C7   C8   single  1.491  0.020  1.491
 92B  C23  C8   single  1.526  0.020  1.526
 92B  C23  C22  single  1.525  0.020  1.525
 92B  C8   C21  single  1.537  0.020  1.537
 92B  C6   C5   single  1.504  0.020  1.504
 92B  C1   OXT  deloc   1.249  0.020  1.249
 92B  C1   C2   single  1.548  0.020  1.548
 92B  C22  N2   single  1.469  0.020  1.469
 92B  C4   C5   single  1.536  0.020  1.536
 92B  C4   C3   single  1.519  0.020  1.519
 92B  C5   N1   single  1.467  0.020  1.467
 92B  C21  C25  single  1.511  0.020  1.511
 92B  C21  N2   single  1.453  0.020  1.453
 92B  N1   C25  single  1.336  0.020  1.336
 92B  N1   C2   single  1.453  0.020  1.453
 92B  C25  O7   double  1.229  0.020  1.229
 92B  C2   C3   single  1.527  0.020  1.527
 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  C3   H2   single  0.970  0.020  1.090
 92B  C6   C7   double  1.328  0.020  1.328

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  109.52  3.000
 92B  H1   N2   C22  110.85  3.000
 92B  C21  N2   C22  108.75  3.000
 92B  H27  C22  H26  107.14  3.000
 92B  H27  C22  C23  109.83  3.000
 92B  H26  C22  C23  111.83  3.000
 92B  H27  C22  N2   111.61  3.000
 92B  H26  C22  N2   111.38  3.000
 92B  C23  C22  N2   105.11  3.000
 92B  H29  C23  H28  107.87  3.000
 92B  H29  C23  C8   113.12  3.000
 92B  H28  C23  C8   109.94  3.000
 92B  H29  C23  C22  112.73  3.000
 92B  H28  C23  C22  110.84  3.000
 92B  C8   C23  C22  102.30  3.000
 92B  H30  C8   C7   109.19  3.000
 92B  H30  C8   C21  108.78  3.000
 92B  C7   C8   C21  113.36  3.000
 92B  H30  C8   C23  108.40  3.000
 92B  C21  C8   C23  101.15  3.000
 92B  C7   C8   C23  115.55  3.000
 92B  H31  C21  C25  108.93  3.000
 92B  H31  C21  C8   108.25  3.000
 92B  C25  C21  C8   109.29  3.000
 92B  H31  C21  N2   110.23  3.000
 92B  C25  C21  N2   113.51  3.000
 92B  C8   C21  N2   106.49  3.000
 92B  N1   C25  O7   122.70  3.000
 92B  O7   C25  C21  121.48  3.000
 92B  N1   C25  C21  115.79  3.000
 92B  H32  C7   C6   117.84  3.000
 92B  C6   C7   C8   125.47  3.000
 92B  H32  C7   C8   116.68  3.000
 92B  H33  C6   C5   112.65  3.000
 92B  H33  C6   C7   117.68  3.000
 92B  C5   C6   C7   129.67  3.000
 92B  H34  C5   N1   108.77  3.000
 92B  H34  C5   C4   108.20  3.000
 92B  N1   C5   C4   102.70  3.000
 92B  H34  C5   C6   108.01  3.000
 92B  N1   C5   C6   118.50  3.000
 92B  C4   C5   C6   110.22  3.000
 92B  H35  C4   H42  107.57  3.000
 92B  H35  C4   C3   110.37  3.000
 92B  H42  C4   C3   113.78  3.000
 92B  H35  C4   C5   109.77  3.000
 92B  H42  C4   C5   111.23  3.000
 92B  C3   C4   C5   104.10  3.000
 92B  H2   C3   H36  107.72  3.000
 92B  H2   C3   C2   112.26  3.000
 92B  H36  C3   C2   110.34  3.000
 92B  H2   C3   C4   113.52  3.000
 92B  H36  C3   C4   110.38  3.000
 92B  C2   C3   C4   102.60  3.000
 92B  H37  C2   C1   108.46  3.000
 92B  H37  C2   N1   110.00  3.000
 92B  C1   C2   N1   112.56  3.000
 92B  H37  C2   C3   110.98  3.000
 92B  N1   C2   C3   102.70  3.000
 92B  C1   C2   C3   112.08  3.000
 92B  C2   N1   C5   112.86  3.000
 92B  C2   N1   C25  119.87  3.000
 92B  C5   N1   C25  127.22  3.000
 92B  OXT  C1   O2   127.53  3.000
 92B  OXT  C1   C2   114.34  3.000
 92B  O2   C1   C2   118.13  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  Var_01  C8   C23  C22  N2   -34.60  30.0  1
 92B  Var_02  C21  N2   C22  C23   15.29  30.0  1
 92B  Var_03  C2   C3   C4   C5   -38.45  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

