# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 09:52:06 2020
#   Inital geometry file: a 95 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NN=C(CN2CCOCC2)c3c[nH]c4cccc1c34
#
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
 G9D  G9D  'None                     '  ligand  37  21  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G9D
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
 G9D  N11   N  NR6   0  -0.422   2.8138   0.3558   0.2160
 G9D  N12   N  N     0  -0.256   0.4965  -1.0384   0.3650
 G9D  N13   N  NH1   0  -0.539  -0.4572  -2.0017   0.4314
 G9D  N14   N  NR15  0  -0.685  -2.4233   2.5363  -0.3386
 G9D  OAA   O  O     0  -0.461  -2.2813  -3.2518   0.5031
 G9D  CAB   C  CR16  0  -0.274  -4.9753  -0.1136  -0.0476
 G9D  CAC   C  CR16  0  -0.288  -4.5278   1.1816  -0.2248
 G9D  CAD   C  CR16  0  -0.307  -4.0819  -1.1731   0.1473
 G9D  CAE   C  CR15  0  -0.045  -1.1029   2.2563  -0.2364
 G9D  CAF   C  C     0  -0.188   5.1757   0.4135   0.7823
 G9D  CAG   C  C     0  -0.187   4.4637  -1.0659  -0.8618
 G9D  CAH   C  C     0  -0.306   3.8998   1.2217   0.6423
 G9D  CAI   C  C     0  -0.308   3.1722  -0.2905  -1.0347
 G9D  CAJ   C  CH2   0  -0.322   1.5667   1.0695   0.1379
 G9D  OAN   O  O     0  -0.486   5.5166  -0.2344  -0.4236
 G9D  CAO   C  C     0   0.101   0.3238   0.2062   0.1614
 G9D  CAP   C  C     0   0.487  -1.8205  -2.1273   0.3766
 G9D  CAQ   C  CR56  0   0.356  -3.1523   1.3893  -0.1988
 G9D  CAR   C  CR5   0  -0.060  -0.9288   0.9063  -0.0282
 G9D  CAS   C  CR6   0  -0.129  -2.7118  -0.9644   0.1723
 G9D  CAT   C  CR56  0   0.152  -2.2373   0.3370  -0.0019
 G9D  HN13  H  HNH1  0   0.405  -0.0200  -2.8979   0.5883
 G9D  HAB   H  HCR6  0   0.261  -6.0379  -0.3152  -0.0603
 G9D  HAC   H  HCR6  0   0.274  -5.2200   1.9997  -0.3756
 G9D  HAD   H  HCR6  0   0.261  -4.4717  -2.1722   0.2818
 G9D  HAE   H  HCR5  0   0.302  -0.3736   3.0458  -0.3169
 G9D  HAF   H  H     0   0.236   6.0073   1.0679   1.0484
 G9D  HAFA  H  H     0   0.200   5.0487  -0.3210   1.5901
 G9D  HAG   H  H     0   0.200   4.2988  -1.8860  -0.1486
 G9D  HAGA  H  H     0   0.235   4.7687  -1.5041  -1.8133
 G9D  HAH   H  H     0   0.197   4.0652   2.0546  -0.0627
 G9D  HAHA  H  H     0   0.243   3.6553   1.6628   1.6118
 G9D  HAI   H  H     0   0.249   2.3869  -0.9844  -1.3338
 G9D  HAIA  H  H     0   0.197   3.2898   0.4482  -1.8469
 G9D  HAJ   H  HCH2  0   0.266   1.5025   1.7491   0.9949
 G9D  HAJA  H  HCH2  0   0.220   1.5198   1.7171  -0.7549
 G9D  HN14  H  HNR5  0   0.422  -2.8023   3.4576  -0.4866

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
 G9D  CAI  N11   single    1.453  0.020  1.453
 G9D  CAH  N11   single    1.453  0.020  1.453
 G9D  N11  CAJ   single    1.439  0.020  1.439
 G9D  CAO  N12   double    1.273  0.020  1.273
 G9D  N12  N13   single    1.357  0.020  1.357
 G9D  N13  CAP   single    1.370  0.020  1.370
 G9D  N13  HN13  single    0.860  0.020  1.020
 G9D  CAE  N14   aromatic  1.354  0.020  1.354
 G9D  N14  CAQ   aromatic  1.366  0.020  1.366
 G9D  CAP  OAA   double    1.222  0.020  1.222
 G9D  CAC  CAB   aromatic  1.382  0.020  1.382
 G9D  CAB  CAD   aromatic  1.400  0.020  1.400
 G9D  CAB  HAB   single    0.930  0.020  1.080
 G9D  CAQ  CAC   aromatic  1.391  0.020  1.391
 G9D  CAC  HAC   single    0.930  0.020  1.080
 G9D  CAS  CAD   aromatic  1.386  0.020  1.386
 G9D  CAD  HAD   single    0.930  0.020  1.080
 G9D  CAE  CAR   aromatic  1.377  0.020  1.377
 G9D  CAE  HAE   single    0.930  0.020  1.080
 G9D  OAN  CAF   single    1.411  0.020  1.411
 G9D  CAF  CAH   single    1.517  0.020  1.517
 G9D  CAF  HAF   single    0.970  0.020  1.090
 G9D  CAF  HAFA  single    0.970  0.020  1.090
 G9D  OAN  CAG   single    1.411  0.020  1.411
 G9D  CAG  CAI   single    1.516  0.020  1.516
 G9D  CAG  HAG   single    0.970  0.020  1.090
 G9D  CAG  HAGA  single    0.970  0.020  1.090
 G9D  CAH  HAH   single    0.970  0.020  1.090
 G9D  CAH  HAHA  single    0.970  0.020  1.090
 G9D  CAI  HAI   single    0.970  0.020  1.090
 G9D  CAI  HAIA  single    0.970  0.020  1.090
 G9D  CAJ  CAO   single    1.513  0.020  1.513
 G9D  CAJ  HAJ   single    0.970  0.020  1.090
 G9D  CAJ  HAJA  single    0.970  0.020  1.090
 G9D  CAO  CAR   single    1.447  0.020  1.447
 G9D  CAS  CAP   single    1.479  0.020  1.479
 G9D  CAQ  CAT   aromatic  1.408  0.020  1.408
 G9D  CAR  CAT   aromatic  1.427  0.020  1.427
 G9D  CAT  CAS   aromatic  1.396  0.020  1.396
 G9D  N14  HN14  single    0.860  0.020  1.020

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
 G9D  CAJ   N11  CAI  112.82  3.000
 G9D  CAJ   N11  CAH  111.60  3.000
 G9D  CAI   N11  CAH  109.47  3.000
 G9D  CAO   N12  N13  127.34  3.000
 G9D  HN13  N13  CAP  110.84  3.000
 G9D  HN13  N13  N12  109.48  3.000
 G9D  CAP   N13  N12  139.67  3.000
 G9D  HN14  N14  CAQ  125.61  3.000
 G9D  HN14  N14  CAE  124.57  3.000
 G9D  CAQ   N14  CAE  109.82  3.000
 G9D  HAB   CAB  CAD  119.19  3.000
 G9D  HAB   CAB  CAC  119.44  3.000
 G9D  CAD   CAB  CAC  121.38  3.000
 G9D  HAC   CAC  CAQ  121.47  3.000
 G9D  HAC   CAC  CAB  121.28  3.000
 G9D  CAQ   CAC  CAB  117.24  3.000
 G9D  HAD   CAD  CAS  119.56  3.000
 G9D  HAD   CAD  CAB  119.13  3.000
 G9D  CAS   CAD  CAB  121.30  3.000
 G9D  HAE   CAE  CAR  130.08  3.000
 G9D  HAE   CAE  N14  120.19  3.000
 G9D  CAR   CAE  N14  109.73  3.000
 G9D  HAFA  CAF  HAF  108.03  3.000
 G9D  HAFA  CAF  OAN  110.44  3.000
 G9D  HAF   CAF  OAN  107.44  3.000
 G9D  HAFA  CAF  CAH  109.07  3.000
 G9D  HAF   CAF  CAH  110.13  3.000
 G9D  OAN   CAF  CAH  111.66  3.000
 G9D  HAGA  CAG  HAG  107.94  3.000
 G9D  HAGA  CAG  OAN  107.39  3.000
 G9D  HAG   CAG  OAN  110.48  3.000
 G9D  HAGA  CAG  CAI  110.13  3.000
 G9D  HAG   CAG  CAI  109.13  3.000
 G9D  OAN   CAG  CAI  111.69  3.000
 G9D  HAHA  CAH  HAH  107.19  3.000
 G9D  HAHA  CAH  CAF  108.74  3.000
 G9D  HAH   CAH  CAF  109.57  3.000
 G9D  HAHA  CAH  N11  109.49  3.000
 G9D  HAH   CAH  N11  111.99  3.000
 G9D  CAF   CAH  N11  109.77  3.000
 G9D  HAIA  CAI  HAI  107.51  3.000
 G9D  HAIA  CAI  CAG  109.59  3.000
 G9D  HAI   CAI  CAG  108.63  3.000
 G9D  HAIA  CAI  N11  111.22  3.000
 G9D  HAI   CAI  N11  109.98  3.000
 G9D  CAG   CAI  N11  109.85  3.000
 G9D  HAJA  CAJ  HAJ  105.44  3.000
 G9D  HAJA  CAJ  CAO  108.20  3.000
 G9D  HAJ   CAJ  CAO  107.07  3.000
 G9D  HAJA  CAJ  N11  111.82  3.000
 G9D  HAJ   CAJ  N11  108.42  3.000
 G9D  CAO   CAJ  N11  115.33  3.000
 G9D  CAG   OAN  CAF  110.84  3.000
 G9D  CAR   CAO  CAJ  115.64  3.000
 G9D  CAR   CAO  N12  127.68  3.000
 G9D  CAJ   CAO  N12  116.67  3.000
 G9D  CAS   CAP  OAA  120.70  3.000
 G9D  CAS   CAP  N13  122.20  3.000
 G9D  OAA   CAP  N13  117.09  3.000
 G9D  CAT   CAQ  CAC  122.24  3.000
 G9D  CAT   CAQ  N14  107.15  3.000
 G9D  CAC   CAQ  N14  130.61  3.000
 G9D  CAT   CAR  CAO  126.73  3.000
 G9D  CAT   CAR  CAE  106.13  3.000
 G9D  CAO   CAR  CAE  127.12  3.000
 G9D  CAT   CAS  CAP  123.04  3.000
 G9D  CAT   CAS  CAD  118.30  3.000
 G9D  CAP   CAS  CAD  118.66  3.000
 G9D  CAS   CAT  CAR  133.29  3.000
 G9D  CAS   CAT  CAQ  119.55  3.000
 G9D  CAR   CAT  CAQ  107.16  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
 G9D  CONST_01  CAB   CAC  CAQ  N14   180.00   0.0  0
 G9D  CONST_02  CAT   CAQ  CAC  CAB     0.00   0.0  0
 G9D  CONST_03  CAS   CAD  CAB  CAC     0.00   0.0  0
 G9D  CONST_04  CAE   N14  CAQ  CAC   180.00   0.0  0
 G9D  CONST_05  CAQ   CAC  CAB  CAD     0.00   0.0  0
 G9D  CONST_06  CAT   CAQ  N14  CAE     0.00   0.0  0
 G9D  CONST_07  CAR   CAE  N14  CAQ     0.00   0.0  0
 G9D  CONST_08  HAC   CAC  CAQ  N14     0.00   0.0  0
 G9D  CONST_09  HAD   CAD  CAB  CAC   180.00   0.0  0
 G9D  CONST_10  HN14  N14  CAQ  CAC     0.00   0.0  0
 G9D  CONST_11  HAE   CAE  N14  CAQ   180.00   0.0  0
 G9D  CONST_12  HAB   CAB  CAC  CAQ   180.00   0.0  0
 G9D  Var_01    OAN   CAG  CAI  N11   -57.41  30.0  1
 G9D  Var_02    OAN   CAF  CAH  N11    57.59  30.0  1
 G9D  Var_03    CAI   CAG  OAN  CAF    56.87  30.0  1
 G9D  Var_04    CAI   N11  CAH  CAF   -57.41  30.0  1
 G9D  Var_05    CAH   CAF  OAN  CAG   -56.96  30.0  1
 G9D  Var_06    CAH   N11  CAI  CAG    57.34  30.0  1
 G9D  Var_07    CAO   CAJ  N11  CAH  -160.41  30.0  3

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
 G9D  plan-1  N12   0.020
 G9D  plan-1  N13   0.020
 G9D  plan-1  OAA   0.020
 G9D  plan-1  CAP   0.020
 G9D  plan-1  CAS   0.020
 G9D  plan-1  HN13  0.020
 G9D  plan-2  N14   0.020
 G9D  plan-2  CAB   0.020
 G9D  plan-2  CAC   0.020
 G9D  plan-2  CAD   0.020
 G9D  plan-2  CAE   0.020
 G9D  plan-2  CAO   0.020
 G9D  plan-2  CAP   0.020
 G9D  plan-2  CAQ   0.020
 G9D  plan-2  CAR   0.020
 G9D  plan-2  CAS   0.020
 G9D  plan-2  CAT   0.020
 G9D  plan-2  HAB   0.020
 G9D  plan-2  HAC   0.020
 G9D  plan-2  HAD   0.020
 G9D  plan-2  HAE   0.020
 G9D  plan-2  HN14  0.020

