# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 13:41:55 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  32  22  .  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_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   0.402  -3.3192  -1.0387   0.4148
 BR0  N     N  NH1    0  -0.690  -1.3583   0.4029   0.0191
 BR0  OXT   O  OC     0  -0.631  -3.7531  -2.1469   0.7839
 BR0  CA    C  CH1    0  -0.222  -1.8045  -0.8237   0.6194
 BR0  CB    C  CR15   0  -0.234  -0.9799  -1.9674   0.0659
 BR0  CG    C  CR15   0  -0.345   0.5374  -1.7194   0.2278
 BR0  OAA   O  OC    -1  -0.580  -0.1743   4.4059  -0.3612
 BR0  OAC   O  O      0  -0.372   3.2030  -1.5906   1.4388
 BR0  OAD   O  O      0  -0.588  -1.8757   2.9853  -0.2642
 BR0  OAF   O  O     -1  -0.376   4.3071  -0.7233  -0.1678
 BR0  CAG   C  C1     0  -0.304   1.6878   2.4381  -0.0351
 BR0  CAH   C  C1     0  -0.286   2.6659   1.4818   0.1484
 BR0  CAI   C  CR15   0  -0.215   0.1542  -2.6841  -1.8924
 BR0  CAK   C  CH2    0  -0.455  -1.2052  -2.2610  -1.4260
 BR0  CAM   C  C      0   0.436  -0.6536   3.2645  -0.2495
 BR0  CAO   C  C      0  -0.213   0.3378   2.1193  -0.0743
 BR0  CAP   C  C      0   0.175   2.2549   0.1656   0.3011
 BR0  CAQ   C  C      0   0.297  -0.0533   0.7597   0.0661
 BR0  NAT   N  N      1   0.314   3.3269  -0.7952   0.5367
 BR0  CD1   C  CR15   0  -0.195   1.0979  -2.4086  -0.9991
 BR0  CD2   C  C      0   0.068   0.9311  -0.2487   0.2435
 BR0  O     O  O     -1  -0.528  -3.9747  -0.0973  -0.0671
 BR0  HN    H  HNH1   0   0.403  -2.0050   1.1845  -0.0402
 BR0  HA    H  HCH1   0   0.216  -1.6377  -0.7948   1.7112
 BR0  HB    H  HCR5   0   0.240  -1.2201  -2.8702   0.6288
 BR0  HG    H  HCR5   0   0.265   0.8789  -2.1923   1.1491
 BR0  HAG   H  H      0   0.247   1.9757   3.4747  -0.1392
 BR0  HAH   H  H      0   0.248   3.7098   1.7557   0.2015
 BR0  HAI   H  HCR5   0   0.223   0.3363  -3.1399  -2.8581
 BR0  HAK   H  HCH2   0   0.234  -1.9651  -3.0312  -1.5746
 BR0  HAKA  H  HCH2   0   0.242  -1.5477  -1.3776  -1.9763
 BR0  HD1   H  HCR5   0   0.221   2.1509  -2.6167  -1.1424

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   deloc     1.246  0.020  1.246
 BR0  CA   C     single    1.544  0.020  1.544
 BR0  CA   N     single    1.437  0.020  1.437
 BR0  CA   CB    single    1.515  0.020  1.515
 BR0  CB   CG    single    1.546  0.020  1.546
 BR0  CB   CAK   single    1.537  0.020  1.537
 BR0  CG   CD1   single    1.515  0.020  1.515
 BR0  OAD  CAM   deloc     1.254  0.020  1.254
 BR0  OAF  NAT   single    1.209  0.020  1.209
 BR0  CAG  CAH   aromatic  1.380  0.020  1.380
 BR0  CAG  CAO   aromatic  1.388  0.020  1.388
 BR0  CAH  CAP   aromatic  1.387  0.020  1.387
 BR0  CAK  CAI   single    1.498  0.020  1.498
 BR0  CAM  OAA   deloc     1.243  0.020  1.243
 BR0  CAM  CAO   single    1.525  0.020  1.525
 BR0  CAO  CAQ   aromatic  1.422  0.020  1.422
 BR0  CAP  NAT   single    1.459  0.020  1.459
 BR0  CAP  CD2   aromatic  1.388  0.020  1.388
 BR0  CAQ  N     single    1.354  0.020  1.354
 BR0  CAQ  CD2   aromatic  1.420  0.020  1.420
 BR0  NAT  OAC   double    1.209  0.020  1.209
 BR0  CD1  CAI   double    1.328  0.020  1.328
 BR0  CD2  CG    single    1.523  0.020  1.523
 BR0  O    C     deloc     1.244  0.020  1.244
 BR0  N    HN    single    0.890  0.020  1.040
 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  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   117.57  3.000
 BR0  O     C    OXT  127.18  3.000
 BR0  CA    C    OXT  115.23  3.000
 BR0  HN    N    CAQ  114.37  3.000
 BR0  HN    N    CA   118.91  3.000
 BR0  CAQ   N    CA   120.66  3.000
 BR0  HA    CA   CB   107.38  3.000
 BR0  HA    CA   N    110.10  3.000
 BR0  CB    CA   N    108.84  3.000
 BR0  HA    CA   C    106.42  3.000
 BR0  CB    CA   C    112.37  3.000
 BR0  N     CA   C    111.61  3.000
 BR0  HB    CB   CAK  108.09  3.000
 BR0  HB    CB   CG   107.15  3.000
 BR0  CAK   CB   CG   106.03  3.000
 BR0  HB    CB   CA   108.46  3.000
 BR0  CAK   CB   CA   114.78  3.000
 BR0  CG    CB   CA   112.02  3.000
 BR0  HG    CG   CD2  109.22  3.000
 BR0  HG    CG   CD1  111.79  3.000
 BR0  CD2   CG   CD1  110.62  3.000
 BR0  HG    CG   CB   109.04  3.000
 BR0  CD2   CG   CB   114.20  3.000
 BR0  CD1   CG   CB   101.85  3.000
 BR0  HAG   CAG  CAO  118.47  3.000
 BR0  HAG   CAG  CAH  119.25  3.000
 BR0  CAO   CAG  CAH  122.28  3.000
 BR0  HAH   CAH  CAP  121.42  3.000
 BR0  HAH   CAH  CAG  121.04  3.000
 BR0  CAP   CAH  CAG  117.52  3.000
 BR0  HAI   CAI  CD1  124.57  3.000
 BR0  HAI   CAI  CAK  123.29  3.000
 BR0  CD1   CAI  CAK  112.13  3.000
 BR0  HAKA  CAK  HAK  106.42  3.000
 BR0  HAKA  CAK  CAI  110.79  3.000
 BR0  HAK   CAK  CAI  112.94  3.000
 BR0  HAKA  CAK  CB   112.29  3.000
 BR0  HAK   CAK  CB   111.64  3.000
 BR0  CAI   CAK  CB   102.89  3.000
 BR0  CAO   CAM  OAD  117.90  3.000
 BR0  CAO   CAM  OAA  116.69  3.000
 BR0  OAD   CAM  OAA  125.41  3.000
 BR0  CAQ   CAO  CAM  123.41  3.000
 BR0  CAQ   CAO  CAG  118.98  3.000
 BR0  CAM   CAO  CAG  117.60  3.000
 BR0  CD2   CAP  NAT  120.72  3.000
 BR0  CD2   CAP  CAH  124.13  3.000
 BR0  NAT   CAP  CAH  115.15  3.000
 BR0  CD2   CAQ  CAO  120.04  3.000
 BR0  CD2   CAQ  N    119.03  3.000
 BR0  CAO   CAQ  N    120.92  3.000
 BR0  CAP   NAT  OAF  117.54  3.000
 BR0  CAP   NAT  OAC  118.59  3.000
 BR0  OAF   NAT  OAC  123.84  3.000
 BR0  HD1   CD1  CAI  124.19  3.000
 BR0  HD1   CD1  CG   123.67  3.000
 BR0  CAI   CD1  CG   112.10  3.000
 BR0  CAQ   CD2  CAP  117.01  3.000
 BR0  CAQ   CD2  CG   120.35  3.000
 BR0  CAP   CD2  CG   122.36  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
 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  Var_01    CAO  CAQ  N    CA   -157.38  30.0  1
 BR0  Var_02    CD1  CAI  CAK  CB    -12.82  30.0  1
 BR0  Var_03    CAK  CAI  CD1  CG     -1.13  30.0  1
 BR0  Var_04    CAG  CAO  CAM  OAA     0.84  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-4  OAA  0.020
 BR0  plan-4  OAD  0.020
 BR0  plan-4  CAM  0.020
 BR0  plan-4  CAO  0.020

