# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 16:12:52 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: (3aS,4R,9bR)-9-nitro-3a,4,5,9b-tetrahydro-3H-cyclopenta[c]quinoline-4,6-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1Nc2c(ccc(c2[C@@H]3C=CC[C@H]13)[N+]([O-])=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
 BR0  BR0  '(3aS,4R,9bR)-9-nitro-3a,4,5,9b-tetrahydro-3H-cyclopenta[c]quinoline-4,6-dicarboxylic acid'  ligand  34  22  .  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_BR0
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
 BR0  C     C  C      0   0.542  -3.2857  -0.9911   0.4334
 BR0  N     N  NH1    0  -0.718  -1.3823   0.4337   0.0945
 BR0  OXT   O  OH1    0  -0.585  -3.7227  -2.1156   0.9738
 BR0  CA    C  CH1    0  -0.189  -1.8028  -0.8077   0.6775
 BR0  CB    C  CR15   0  -0.273  -0.9904  -1.9485   0.0864
 BR0  CG    C  CR15   0  -0.351   0.5244  -1.6946   0.2325
 BR0  OAA   O  OH1    0  -0.590  -0.1433   4.4180  -0.3314
 BR0  OAC   O  O      0  -0.359   3.2375  -1.5267   1.3706
 BR0  OAD   O  O      0  -0.459  -1.8834   3.0430  -0.2393
 BR0  OAF   O  O     -1  -0.361   4.2250  -0.7517  -0.3595
 BR0  CAG   C  CR16   0  -0.291   1.6785   2.4661  -0.0929
 BR0  CAH   C  CR16   0  -0.283   2.6474   1.5050   0.0629
 BR0  CAI   C  CR15   0  -0.216   0.1108  -2.6697  -1.8766
 BR0  CAK   C  CH2    0  -0.468  -1.2377  -2.2176  -1.4062
 BR0  CAM   C  C      0   0.579  -0.6803   3.2128  -0.2236
 BR0  CAO   C  CR6    0  -0.179   0.3226   2.1385  -0.0823
 BR0  CAP   C  CR6    0   0.199   2.2316   0.1906   0.2306
 BR0  CAQ   C  CR6    0   0.370  -0.0762   0.7850   0.0787
 BR0  NAT   N  N      1   0.319   3.3087  -0.7796   0.4255
 BR0  CD1   C  CR15   0  -0.209   1.0648  -2.4060  -0.9919
 BR0  CD2   C  CR6    0   0.081   0.9131  -0.2243   0.2156
 BR0  O     O  O      0  -0.425  -3.9797  -0.2127  -0.1676
 BR0  HN    H  HNH1   0   0.410  -2.0482   1.1928   0.0585
 BR0  HO    H  HOH1   0   0.491  -4.6726  -2.2222   0.8116
 BR0  HA    H  HCH1   0   0.304  -1.6536  -0.8040   1.7684
 BR0  HB    H  HCR5   0   0.289  -1.2118  -2.8607   0.6416
 BR0  HG    H  HCR5   0   0.295   0.8742  -2.1468   1.1609
 BR0  HOAA  H  HOH1   0   0.492  -0.8430   5.0814  -0.4255
 BR0  HAG   H  HCR6   0   0.283   1.9874   3.4932  -0.2178
 BR0  HAH   H  HCR6   0   0.289   3.6942   1.7704   0.0743
 BR0  HAI   H  HCR5   0   0.254   0.2742  -3.1386  -2.8384
 BR0  HAK   H  HCH2   0   0.256  -2.0129  -2.9715  -1.5588
 BR0  HAKA  H  HCH2   0   0.251  -1.5581  -1.3229  -1.9509
 BR0  HD1   H  HCR5   0   0.254   2.1112  -2.6411  -1.1352

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
 BR0  C    OXT   single    1.322  0.020  1.322
 BR0  CA   C     single    1.514  0.020  1.514
 BR0  CA   N     single    1.434  0.020  1.434
 BR0  CA   CB    single    1.520  0.020  1.520
 BR0  CB   CG    single    1.543  0.020  1.543
 BR0  CB   CAK   single    1.537  0.020  1.537
 BR0  CG   CD1   single    1.516  0.020  1.516
 BR0  OAD  CAM   double    1.215  0.020  1.215
 BR0  OAF  NAT   single    1.207  0.020  1.207
 BR0  CAG  CAH   aromatic  1.373  0.020  1.373
 BR0  CAG  CAO   aromatic  1.395  0.020  1.395
 BR0  CAH  CAP   aromatic  1.389  0.020  1.389
 BR0  CAK  CAI   single    1.498  0.020  1.498
 BR0  CAM  OAA   single    1.324  0.020  1.324
 BR0  CAM  CAO   single    1.476  0.020  1.476
 BR0  CAO  CAQ   aromatic  1.420  0.020  1.420
 BR0  CAP  NAT   single    1.463  0.020  1.463
 BR0  CAP  CD2   aromatic  1.382  0.020  1.382
 BR0  CAQ  N     single    1.353  0.020  1.353
 BR0  CAQ  CD2   aromatic  1.420  0.020  1.420
 BR0  NAT  OAC   double    1.207  0.020  1.207
 BR0  CD1  CAI   double    1.328  0.020  1.328
 BR0  CD2  CG    single    1.521  0.020  1.521
 BR0  O    C     double    1.204  0.020  1.204
 BR0  N    HN    single    0.890  0.020  1.040
 BR0  OXT  HO    single    0.850  0.020  0.980
 BR0  CA   HA    single    0.970  0.020  1.090
 BR0  CB   HB    single    0.970  0.020  1.090
 BR0  CG   HG    single    0.970  0.020  1.090
 BR0  OAA  HOAA  single    0.850  0.020  0.980
 BR0  CAG  HAG   single    0.930  0.020  1.080
 BR0  CAH  HAH   single    0.930  0.020  1.080
 BR0  CAI  HAI   single    0.930  0.020  1.080
 BR0  CAK  HAK   single    0.970  0.020  1.090
 BR0  CAK  HAKA  single    0.970  0.020  1.090
 BR0  CD1  HD1   single    0.930  0.020  1.080

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
 BR0  O     C    CA   124.53  3.000
 BR0  O     C    OXT  124.31  3.000
 BR0  CA    C    OXT  111.16  3.000
 BR0  HN    N    CAQ  116.16  3.000
 BR0  HN    N    CA   118.13  3.000
 BR0  CAQ   N    CA   120.83  3.000
 BR0  HO    OXT  C    110.43  3.000
 BR0  HA    CA   CB   108.38  3.000
 BR0  HA    CA   N    111.10  3.000
 BR0  CB    CA   N    109.56  3.000
 BR0  HA    CA   C    107.03  3.000
 BR0  CB    CA   C    111.71  3.000
 BR0  N     CA   C    109.05  3.000
 BR0  HB    CB   CAK  108.37  3.000
 BR0  HB    CB   CG   106.79  3.000
 BR0  CAK   CB   CG   106.19  3.000
 BR0  HB    CB   CA   108.74  3.000
 BR0  CAK   CB   CA   115.03  3.000
 BR0  CG    CB   CA   111.37  3.000
 BR0  HG    CG   CD2  109.17  3.000
 BR0  HG    CG   CD1  112.26  3.000
 BR0  CD2   CG   CD1  110.71  3.000
 BR0  HG    CG   CB   109.11  3.000
 BR0  CD2   CG   CB   114.14  3.000
 BR0  CD1   CG   CB   101.32  3.000
 BR0  HOAA  OAA  CAM  109.77  3.000
 BR0  HAG   CAG  CAO  120.15  3.000
 BR0  HAG   CAG  CAH  118.49  3.000
 BR0  CAO   CAG  CAH  121.36  3.000
 BR0  HAH   CAH  CAP  121.43  3.000
 BR0  HAH   CAH  CAG  120.86  3.000
 BR0  CAP   CAH  CAG  117.70  3.000
 BR0  HAI   CAI  CD1  124.73  3.000
 BR0  HAI   CAI  CAK  123.07  3.000
 BR0  CD1   CAI  CAK  112.19  3.000
 BR0  HAKA  CAK  HAK  106.66  3.000
 BR0  HAKA  CAK  CAI  110.71  3.000
 BR0  HAK   CAK  CAI  112.75  3.000
 BR0  HAKA  CAK  CB   112.77  3.000
 BR0  HAK   CAK  CB   111.77  3.000
 BR0  CAI   CAK  CB   102.30  3.000
 BR0  CAO   CAM  OAD  124.90  3.000
 BR0  CAO   CAM  OAA  113.25  3.000
 BR0  OAD   CAM  OAA  121.86  3.000
 BR0  CAQ   CAO  CAM  120.91  3.000
 BR0  CAQ   CAO  CAG  119.84  3.000
 BR0  CAM   CAO  CAG  119.25  3.000
 BR0  CD2   CAP  NAT  120.32  3.000
 BR0  CD2   CAP  CAH  124.63  3.000
 BR0  NAT   CAP  CAH  115.05  3.000
 BR0  CD2   CAQ  CAO  119.52  3.000
 BR0  CD2   CAQ  N    119.15  3.000
 BR0  CAO   CAQ  N    121.33  3.000
 BR0  CAP   NAT  OAF  117.20  3.000
 BR0  CAP   NAT  OAC  118.13  3.000
 BR0  OAF   NAT  OAC  124.64  3.000
 BR0  HD1   CD1  CAI  124.30  3.000
 BR0  HD1   CD1  CG   123.63  3.000
 BR0  CAI   CD1  CG   112.05  3.000
 BR0  CAQ   CD2  CAP  116.89  3.000
 BR0  CAQ   CD2  CG   120.68  3.000
 BR0  CAP   CD2  CG   122.26  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
 BR0  CONST_01  CD2   CAP  CAH  CAG     0.00   0.0  0
 BR0  CONST_02  CD2   CAQ  CAO  CAG     0.00   0.0  0
 BR0  CONST_03  CAQ   CAO  CAG  CAH     0.00   0.0  0
 BR0  CONST_04  CAQ   CD2  CAP  CAH     0.00   0.0  0
 BR0  CONST_05  CAP   CAH  CAG  CAO     0.00   0.0  0
 BR0  CONST_06  CAP   CD2  CAQ  CAO     0.00   0.0  0
 BR0  CONST_07  CAM   CAO  CAQ  N       0.00   0.0  0
 BR0  CONST_08  NAT   CAP  CD2  CG      0.00   0.0  0
 BR0  CONST_09  NAT   CAP  CAH  CAG   180.00   0.0  0
 BR0  CONST_10  CAM   CAO  CAG  CAH   180.00   0.0  0
 BR0  CONST_11  CD2   CAQ  CAO  CAM   180.00   0.0  0
 BR0  CONST_12  NAT   CAP  CD2  CAQ   180.00   0.0  0
 BR0  CONST_13  HAH   CAH  CAG  CAO   180.00   0.0  0
 BR0  CONST_14  HAG   CAG  CAH  CAP   180.00   0.0  0
 BR0  CONST_19  HO    OXT  C    CA    180.00   0.0  0
 BR0  CONST_20  HOAA  OAA  CAM  CAO   180.00   0.0  0
 BR0  Var_01    CAO   CAQ  N    CA   -159.42  30.0  1
 BR0  Var_02    CD1   CAI  CAK  CB    -13.91  30.0  1
 BR0  Var_03    CAK   CAI  CD1  CG     -1.23  30.0  1
 BR0  Var_04    CAG   CAO  CAM  OAA    -0.86  30.0  2

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
 BR0  chir_01  CA  C    N    CB   positiv
 BR0  chir_02  CB  CA   CG   CAK  positiv
 BR0  chir_03  CG  CD2  CD1  CB   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
 BR0  plan-1  N     0.020
 BR0  plan-1  CG    0.020
 BR0  plan-1  CAG   0.020
 BR0  plan-1  CAH   0.020
 BR0  plan-1  CAM   0.020
 BR0  plan-1  CAO   0.020
 BR0  plan-1  CAP   0.020
 BR0  plan-1  CAQ   0.020
 BR0  plan-1  NAT   0.020
 BR0  plan-1  CD2   0.020
 BR0  plan-1  HAG   0.020
 BR0  plan-1  HAH   0.020
 BR0  plan-2  OAC   0.020
 BR0  plan-2  OAF   0.020
 BR0  plan-2  CAP   0.020
 BR0  plan-2  NAT   0.020
 BR0  plan-3  C     0.020
 BR0  plan-3  OXT   0.020
 BR0  plan-3  CA    0.020
 BR0  plan-3  O     0.020
 BR0  plan-3  HO    0.020
 BR0  plan-4  OAA   0.020
 BR0  plan-4  OAD   0.020
 BR0  plan-4  CAM   0.020
 BR0  plan-4  CAO   0.020
 BR0  plan-4  HOAA  0.020

