# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 22:58:09 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: N~2~,N~2~-dimethyl-N-(6-oxo-5,6-dihydrophenanthridin-2-yl)glycinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CC(=O)Nc1ccc2NC(=O)c3ccccc3c2c1
#
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
 P34  P34  N~2~,N~2~-dimethyl-N-(6-oxo-5,6-dihydrophenanthridin-2-yl)glycinamide  ligand  39  22  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P34
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
 P34  CAA   C  CH3   0  -0.521   6.8661  -0.5724  -0.4470
 P34  N     N  NT    0  -0.397   5.4966  -0.7332  -0.0053
 P34  CAB   C  CH3   0  -0.529   5.4158  -0.7631   1.4406
 P34  CA    C  CH2   0  -0.404   4.6523   0.2895  -0.5635
 P34  C     C  C     0   0.518   3.1736  -0.0382  -0.4154
 P34  O     O  O     0  -0.458   2.7443  -1.1747  -0.4749
 P34  NAM   N  NH1   0  -0.749   2.3998   1.0636  -0.2578
 P34  CAP   C  CR6   0   0.409   1.0073   1.1688  -0.1865
 P34  CAK   C  CR16  0  -0.458   0.1371   0.0906  -0.1749
 P34  CAU   C  CR66  0   0.058  -1.2475   0.2827  -0.0906
 P34  CAT   C  CR66  0   0.277  -2.1999  -0.8215  -0.0705
 P34  CAI   C  CR16  0  -0.348  -1.8033  -2.1638  -0.1400
 P34  CAF   C  CR16  0  -0.222  -2.7337  -3.1816  -0.1138
 P34  CAE   C  CR16  0  -0.261  -4.0951  -2.8942  -0.0186
 P34  CAH   C  CR16  0  -0.274  -4.5075  -1.5809   0.0479
 P34  CAS   C  CR66  0  -0.186  -3.5732  -0.5428   0.0236
 P34  CAQ   C  CR6   0   0.508  -4.0704   0.8404   0.0999
 P34  OAD   O  OC    0  -0.471  -5.2560   1.1301   0.1813
 P34  NAN   N  NR16  0  -0.766  -3.1097   1.7994   0.0740
 P34  CAR   C  CR66  0   0.338  -1.7502   1.5833  -0.0149
 P34  CAJ   C  CR16  0  -0.302  -0.8764   2.6707  -0.0277
 P34  CAG   C  CR16  0  -0.359   0.4794   2.4657  -0.1128
 P34  HAA1  H  HCH3  0   0.236   7.4802  -1.3796  -0.0459
 P34  HAA2  H  HCH3  0   0.236   6.9202  -0.6209  -1.5355
 P34  HAA3  H  HCH3  0   0.196   7.3182   0.3799  -0.1290
 P34  HAB1  H  HCH3  0   0.239   4.3981  -0.9765   1.7682
 P34  HAB2  H  HCH3  0   0.239   6.0546  -1.5567   1.8291
 P34  HAB3  H  HCH3  0   0.197   5.7299   0.1830   1.9089
 P34  HA1   H  HCH2  0   0.225   4.8685   1.2888  -0.1475
 P34  HA2   H  HCH2  0   0.285   4.8438   0.3632  -1.6398
 P34  HAM   H  HNH1  0   0.417   2.8930   1.9415  -0.1958
 P34  HAK   H  HCR6  0   0.284   0.5318  -0.9092  -0.2284
 P34  HAI   H  HCR6  0   0.260  -0.7566  -2.4225  -0.2177
 P34  HAF   H  HCR6  0   0.270  -2.4008  -4.2097  -0.1694
 P34  HAE   H  HCR6  0   0.267  -4.8215  -3.6950   0.0022
 P34  HAH   H  HCR6  0   0.266  -5.5607  -1.3461   0.1207
 P34  HAN   H  HNR6  0   0.416  -3.4307   2.7569   0.1313
 P34  HAJ   H  HCR6  0   0.282  -1.2653   3.6795   0.0317
 P34  HAG   H  HCR6  0   0.281   1.1438   3.3211  -0.1232

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
 P34  CAA  N     single    1.448  0.020  1.448
 P34  CAA  HAA1  single    0.970  0.020  1.090
 P34  CAA  HAA2  single    0.970  0.020  1.090
 P34  CAA  HAA3  single    0.970  0.020  1.090
 P34  N    CAB   single    1.448  0.020  1.448
 P34  N    CA    single    1.439  0.020  1.439
 P34  CAB  HAB1  single    0.970  0.020  1.090
 P34  CAB  HAB2  single    0.970  0.020  1.090
 P34  CAB  HAB3  single    0.970  0.020  1.090
 P34  CA   C     single    1.522  0.020  1.522
 P34  CA   HA1   single    0.970  0.020  1.090
 P34  CA   HA2   single    0.970  0.020  1.090
 P34  C    O     double    1.216  0.020  1.216
 P34  C    NAM   single    1.356  0.020  1.356
 P34  NAM  CAP   single    1.398  0.020  1.398
 P34  NAM  HAM   single    0.860  0.020  1.020
 P34  CAP  CAK   aromatic  1.386  0.020  1.386
 P34  CAP  CAG   aromatic  1.402  0.020  1.402
 P34  CAK  CAU   aromatic  1.400  0.020  1.400
 P34  CAK  HAK   single    0.930  0.020  1.080
 P34  CAU  CAT   aromatic  1.458  0.020  1.458
 P34  CAU  CAR   aromatic  1.396  0.020  1.396
 P34  CAT  CAI   aromatic  1.401  0.020  1.401
 P34  CAT  CAS   aromatic  1.404  0.020  1.404
 P34  CAI  CAF   aromatic  1.379  0.020  1.379
 P34  CAI  HAI   single    0.930  0.020  1.080
 P34  CAF  CAE   aromatic  1.395  0.020  1.395
 P34  CAF  HAF   single    0.930  0.020  1.080
 P34  CAE  CAH   aromatic  1.378  0.020  1.378
 P34  CAE  HAE   single    0.930  0.020  1.080
 P34  CAH  CAS   aromatic  1.397  0.020  1.397
 P34  CAH  HAH   single    0.930  0.020  1.080
 P34  CAS  CAQ   aromatic  1.472  0.020  1.472
 P34  CAQ  OAD   double    1.223  0.020  1.223
 P34  CAQ  NAN   aromatic  1.358  0.020  1.358
 P34  NAN  CAR   aromatic  1.379  0.020  1.379
 P34  NAN  HAN   single    0.860  0.020  1.020
 P34  CAR  CAJ   aromatic  1.395  0.020  1.395
 P34  CAJ  CAG   aromatic  1.374  0.020  1.374
 P34  CAJ  HAJ   single    0.930  0.020  1.080
 P34  CAG  HAG   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
 P34  HAA3  CAA  HAA2  107.83  3.000
 P34  HAA3  CAA  HAA1  107.62  3.000
 P34  HAA2  CAA  HAA1  107.83  3.000
 P34  HAA3  CAA  N     113.35  3.000
 P34  HAA2  CAA  N     110.27  3.000
 P34  HAA1  CAA  N     109.77  3.000
 P34  CA    N    CAB   111.66  3.000
 P34  CA    N    CAA   110.96  3.000
 P34  CAB   N    CAA   111.07  3.000
 P34  HAB3  CAB  HAB2  107.85  3.000
 P34  HAB3  CAB  HAB1  107.86  3.000
 P34  HAB2  CAB  HAB1  107.30  3.000
 P34  HAB3  CAB  N     113.01  3.000
 P34  HAB2  CAB  N     109.75  3.000
 P34  HAB1  CAB  N     110.86  3.000
 P34  HA2   CA   HA1   105.97  3.000
 P34  HA2   CA   C     106.26  3.000
 P34  HA1   CA   C     110.40  3.000
 P34  HA2   CA   N     109.04  3.000
 P34  HA1   CA   N     112.48  3.000
 P34  C     CA   N     112.29  3.000
 P34  NAM   C    O     124.31  3.000
 P34  NAM   C    CA    113.01  3.000
 P34  O     C    CA    122.64  3.000
 P34  HAM   NAM  CAP   114.72  3.000
 P34  HAM   NAM  C     115.81  3.000
 P34  CAP   NAM  C     129.46  3.000
 P34  CAG   CAP  CAK   118.87  3.000
 P34  CAG   CAP  NAM   116.57  3.000
 P34  CAK   CAP  NAM   124.56  3.000
 P34  HAK   CAK  CAU   119.54  3.000
 P34  HAK   CAK  CAP   119.48  3.000
 P34  CAU   CAK  CAP   120.98  3.000
 P34  CAR   CAU  CAT   117.99  3.000
 P34  CAR   CAU  CAK   119.14  3.000
 P34  CAT   CAU  CAK   122.87  3.000
 P34  CAS   CAT  CAI   118.04  3.000
 P34  CAS   CAT  CAU   119.29  3.000
 P34  CAI   CAT  CAU   122.67  3.000
 P34  HAI   CAI  CAF   118.55  3.000
 P34  HAI   CAI  CAT   120.45  3.000
 P34  CAF   CAI  CAT   121.00  3.000
 P34  HAF   CAF  CAE   119.97  3.000
 P34  HAF   CAF  CAI   119.52  3.000
 P34  CAE   CAF  CAI   120.51  3.000
 P34  HAE   CAE  CAH   120.24  3.000
 P34  HAE   CAE  CAF   120.30  3.000
 P34  CAH   CAE  CAF   119.46  3.000
 P34  HAH   CAH  CAS   119.41  3.000
 P34  HAH   CAH  CAE   120.11  3.000
 P34  CAS   CAH  CAE   120.48  3.000
 P34  CAQ   CAS  CAH   118.14  3.000
 P34  CAQ   CAS  CAT   121.35  3.000
 P34  CAH   CAS  CAT   120.51  3.000
 P34  NAN   CAQ  OAD   121.32  3.000
 P34  NAN   CAQ  CAS   115.07  3.000
 P34  OAD   CAQ  CAS   123.60  3.000
 P34  HAN   NAN  CAR   117.69  3.000
 P34  HAN   NAN  CAQ   116.30  3.000
 P34  CAR   NAN  CAQ   126.01  3.000
 P34  CAJ   CAR  NAN   119.72  3.000
 P34  CAJ   CAR  CAU   120.00  3.000
 P34  NAN   CAR  CAU   120.28  3.000
 P34  HAJ   CAJ  CAG   119.80  3.000
 P34  HAJ   CAJ  CAR   120.05  3.000
 P34  CAG   CAJ  CAR   120.16  3.000
 P34  HAG   CAG  CAJ   119.21  3.000
 P34  HAG   CAG  CAP   119.93  3.000
 P34  CAJ   CAG  CAP   120.86  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
 P34  CONST_01  CAT   CAU  CAK  CAP   180.00   0.0  0
 P34  CONST_02  CAR   CAU  CAK  CAP     0.00   0.0  0
 P34  CONST_03  CAR   CAJ  CAG  CAP     0.00   0.0  0
 P34  CONST_04  CAJ   CAG  CAP  CAK     0.00   0.0  0
 P34  CONST_05  CAI   CAT  CAU  CAK     0.00   0.0  0
 P34  CONST_06  CAS   CAT  CAU  CAK   180.00   0.0  0
 P34  CONST_07  NAN   CAR  CAU  CAK   180.00   0.0  0
 P34  CONST_08  CAJ   CAR  CAU  CAK     0.00   0.0  0
 P34  CONST_09  CAG   CAP  CAK  CAU     0.00   0.0  0
 P34  CONST_10  CAF   CAI  CAT  CAU   180.00   0.0  0
 P34  CONST_11  CAH   CAS  CAT  CAU   180.00   0.0  0
 P34  CONST_12  CAQ   CAS  CAT  CAU     0.00   0.0  0
 P34  CONST_13  CAQ   NAN  CAR  CAU     0.00   0.0  0
 P34  CONST_14  CAG   CAJ  CAR  CAU     0.00   0.0  0
 P34  CONST_15  NAN   CAR  CAU  CAT     0.00   0.0  0
 P34  CONST_16  CAJ   CAR  CAU  CAT   180.00   0.0  0
 P34  CONST_17  CAE   CAF  CAI  CAT     0.00   0.0  0
 P34  CONST_18  CAE   CAH  CAS  CAT     0.00   0.0  0
 P34  CONST_19  NAN   CAQ  CAS  CAT     0.00   0.0  0
 P34  CONST_20  CAR   CAU  CAT  CAI   180.00   0.0  0
 P34  CONST_21  CAH   CAS  CAT  CAI     0.00   0.0  0
 P34  CONST_22  CAQ   CAS  CAT  CAI   180.00   0.0  0
 P34  CONST_23  CAH   CAE  CAF  CAI     0.00   0.0  0
 P34  CONST_24  CAS   CAT  CAI  CAF     0.00   0.0  0
 P34  CONST_25  CAS   CAH  CAE  CAF     0.00   0.0  0
 P34  CONST_26  CAQ   CAS  CAH  CAE   180.00   0.0  0
 P34  CONST_27  NAN   CAQ  CAS  CAH   180.00   0.0  0
 P34  CONST_28  CAR   CAU  CAT  CAS     0.00   0.0  0
 P34  CONST_29  CAR   NAN  CAQ  CAS     0.00   0.0  0
 P34  CONST_30  CAJ   CAR  NAN  CAQ   180.00   0.0  0
 P34  CONST_31  CAG   CAJ  CAR  NAN   180.00   0.0  0
 P34  CONST_32  CAU   CAK  CAP  NAM   180.00   0.0  0
 P34  CONST_33  CAJ   CAG  CAP  NAM   180.00   0.0  0
 P34  CONST_34  OAD   CAQ  CAS  CAT   180.00   0.0  0
 P34  CONST_35  OAD   CAQ  CAS  CAH     0.00   0.0  0
 P34  CONST_36  CAR   NAN  CAQ  OAD   180.00   0.0  0
 P34  CONST_37  HAJ   CAJ  CAG  CAP   180.00   0.0  0
 P34  CONST_38  HAG   CAG  CAP  CAK   180.00   0.0  0
 P34  CONST_39  HAI   CAI  CAT  CAU     0.00   0.0  0
 P34  CONST_40  HAN   NAN  CAR  CAU   180.00   0.0  0
 P34  CONST_41  HAK   CAK  CAU  CAT     0.00   0.0  0
 P34  CONST_42  HAF   CAF  CAI  CAT   180.00   0.0  0
 P34  CONST_43  HAH   CAH  CAS  CAT   180.00   0.0  0
 P34  CONST_44  HAE   CAE  CAF  CAI   180.00   0.0  0
 P34  CONST_45  CAK   CAP  NAM  C       0.00   0.0  0
 P34  CONST_46  CAG   CAP  NAM  C     180.00   0.0  0
 P34  CONST_47  HAM   NAM  CAP  CAK   180.00   0.0  0
 P34  CONST_48  CAP   NAM  C    CA    180.00   0.0  0
 P34  CONST_49  CAP   NAM  C    O       0.00   0.0  0
 P34  Var_01    C     CA   N    CAA   165.62  30.0  3
 P34  Var_02    O     C    CA   N     -34.43  30.0  3
 P34  Var_03    HAB1  CAB  N    CAA  -174.74  30.0  3
 P34  Var_04    HAA1  CAA  N    CAB    57.45  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
 P34  plan-1  NAM  0.020
 P34  plan-1  CAP  0.020
 P34  plan-1  CAK  0.020
 P34  plan-1  CAU  0.020
 P34  plan-1  CAT  0.020
 P34  plan-1  CAI  0.020
 P34  plan-1  CAF  0.020
 P34  plan-1  CAE  0.020
 P34  plan-1  CAH  0.020
 P34  plan-1  CAS  0.020
 P34  plan-1  CAQ  0.020
 P34  plan-1  OAD  0.020
 P34  plan-1  NAN  0.020
 P34  plan-1  CAR  0.020
 P34  plan-1  CAJ  0.020
 P34  plan-1  CAG  0.020
 P34  plan-1  HAK  0.020
 P34  plan-1  HAI  0.020
 P34  plan-1  HAF  0.020
 P34  plan-1  HAE  0.020
 P34  plan-1  HAH  0.020
 P34  plan-1  HAN  0.020
 P34  plan-1  HAJ  0.020
 P34  plan-1  HAG  0.020
 P34  plan-2  CA   0.020
 P34  plan-2  C    0.020
 P34  plan-2  O    0.020
 P34  plan-2  NAM  0.020
 P34  plan-2  CAP  0.020
 P34  plan-2  HAM  0.020

