# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 23:32:09 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: N-1,10-phenanthrolin-5-ylacetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1cc2cccnc2c3ncccc13
#
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
 PXX  PXX  N-1,10-phenanthrolin-5-ylacetamide  ligand  29  18  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PXX
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
 PXX  CAA   C  CH3   0  -0.786   4.8198   0.5343  -0.0144
 PXX  CAM   C  C     0   0.503   3.3818   0.8642   0.2887
 PXX  OAB   O  O     0  -0.467   3.0557   1.6802   1.1294
 PXX  NAL   N  NH1   0  -0.751   2.4802   0.1414  -0.4326
 PXX  CAN   C  CR6   0   0.328   1.0864   0.2049  -0.2826
 PXX  CAP   C  CR66  0   0.020   0.3646  -1.0283  -0.1040
 PXX  CAH   C  CR16  0  -0.174   1.0075  -2.2747  -0.0071
 PXX  CAD   C  CR16  0  -0.313   0.2572  -3.4120   0.1450
 PXX  CAF   C  CR16  0  -0.080  -1.1363  -3.2883   0.2010
 PXX  NAK   N  N     0  -0.403  -1.7635  -2.1379   0.1357
 PXX  CAR   C  CR66  0   0.152  -1.0434  -1.0162  -0.0058
 PXX  CAQ   C  CR66  0   0.145  -1.7458   0.2489  -0.0357
 PXX  NAJ   N  N     0  -0.400  -3.0821   0.2508   0.0702
 PXX  CAE   C  CR16  0  -0.083  -3.7103   1.4030   0.0464
 PXX  CAC   C  CR16  0  -0.318  -3.0628   2.6402  -0.0842
 PXX  CAG   C  CR16  0  -0.189  -1.6968   2.6511  -0.1943
 PXX  CAO   C  CR66  0   0.069  -0.9963   1.4325  -0.1706
 PXX  CAI   C  CR16  0  -0.371   0.4215   1.3854  -0.3065
 PXX  HAA   H  HCH3  0   0.277   5.1810  -0.1897   0.7182
 PXX  HAAA  H  HCH3  0   0.256   4.9615   0.1062  -1.0053
 PXX  HAAB  H  HCH3  0   0.269   5.4321   1.4288   0.0751
 PXX  HNAL  H  HNH1  0   0.414   2.8442  -0.5295  -1.0917
 PXX  HAH   H  HCR6  0   0.263   2.0862  -2.3443  -0.0383
 PXX  HAD   H  HCR6  0   0.278   0.7222  -4.3844   0.2268
 PXX  HAF   H  HCR6  0   0.268  -1.7531  -4.1734   0.3127
 PXX  HAE   H  HCR6  0   0.265  -4.7910   1.3693   0.1325
 PXX  HAC   H  HCR6  0   0.276  -3.6389   3.5548  -0.0982
 PXX  HAG   H  HCR6  0   0.277  -1.1519   3.5808  -0.3027
 PXX  HAI   H  HCR6  0   0.274   0.9551   2.3142  -0.4569

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
 PXX  CAA  CAM   single    1.506  0.020  1.506
 PXX  CAM  OAB   double    1.216  0.020  1.216
 PXX  CAM  NAL   single    1.362  0.020  1.362
 PXX  NAL  CAN   single    1.403  0.020  1.403
 PXX  CAN  CAP   aromatic  1.440  0.020  1.440
 PXX  CAN  CAI   aromatic  1.355  0.020  1.355
 PXX  CAP  CAH   aromatic  1.406  0.020  1.406
 PXX  CAP  CAR   aromatic  1.411  0.020  1.411
 PXX  CAH  CAD   aromatic  1.371  0.020  1.371
 PXX  CAD  CAF   aromatic  1.400  0.020  1.400
 PXX  CAF  NAK   aromatic  1.312  0.020  1.312
 PXX  NAK  CAR   aromatic  1.340  0.020  1.340
 PXX  CAR  CAQ   aromatic  1.447  0.020  1.447
 PXX  CAQ  NAJ   aromatic  1.341  0.020  1.341
 PXX  CAQ  CAO   aromatic  1.407  0.020  1.407
 PXX  NAJ  CAE   aromatic  1.313  0.020  1.313
 PXX  CAE  CAC   aromatic  1.402  0.020  1.402
 PXX  CAC  CAG   aromatic  1.370  0.020  1.370
 PXX  CAG  CAO   aromatic  1.406  0.020  1.406
 PXX  CAO  CAI   aromatic  1.425  0.020  1.425
 PXX  CAA  HAA   single    0.970  0.020  1.090
 PXX  CAA  HAAA  single    0.970  0.020  1.090
 PXX  CAA  HAAB  single    0.970  0.020  1.090
 PXX  NAL  HNAL  single    0.860  0.020  1.020
 PXX  CAH  HAH   single    0.930  0.020  1.080
 PXX  CAD  HAD   single    0.930  0.020  1.080
 PXX  CAF  HAF   single    0.930  0.020  1.080
 PXX  CAE  HAE   single    0.930  0.020  1.080
 PXX  CAC  HAC   single    0.930  0.020  1.080
 PXX  CAG  HAG   single    0.930  0.020  1.080
 PXX  CAI  HAI   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
 PXX  HAAB  CAA  HAAA  108.97  3.000
 PXX  HAAB  CAA  HAA   107.69  3.000
 PXX  HAAA  CAA  HAA   107.88  3.000
 PXX  HAAB  CAA  CAM   109.93  3.000
 PXX  HAAA  CAA  CAM   113.18  3.000
 PXX  HAA   CAA  CAM   109.04  3.000
 PXX  NAL   CAM  OAB   122.99  3.000
 PXX  NAL   CAM  CAA   114.15  3.000
 PXX  OAB   CAM  CAA   122.83  3.000
 PXX  HNAL  NAL  CAN   117.29  3.000
 PXX  HNAL  NAL  CAM   117.40  3.000
 PXX  CAN   NAL  CAM   125.23  3.000
 PXX  CAI   CAN  CAP   120.16  3.000
 PXX  CAI   CAN  NAL   121.66  3.000
 PXX  CAP   CAN  NAL   118.19  3.000
 PXX  CAR   CAP  CAH   117.32  3.000
 PXX  CAR   CAP  CAN   120.08  3.000
 PXX  CAH   CAP  CAN   122.59  3.000
 PXX  HAH   CAH  CAD   119.72  3.000
 PXX  HAH   CAH  CAP   120.75  3.000
 PXX  CAD   CAH  CAP   119.53  3.000
 PXX  HAD   CAD  CAF   120.31  3.000
 PXX  HAD   CAD  CAH   121.28  3.000
 PXX  CAF   CAD  CAH   118.42  3.000
 PXX  HAF   CAF  NAK   116.67  3.000
 PXX  HAF   CAF  CAD   119.87  3.000
 PXX  NAK   CAF  CAD   123.46  3.000
 PXX  CAR   NAK  CAF   118.83  3.000
 PXX  CAQ   CAR  NAK   118.22  3.000
 PXX  CAQ   CAR  CAP   119.35  3.000
 PXX  NAK   CAR  CAP   122.42  3.000
 PXX  CAO   CAQ  NAJ   122.50  3.000
 PXX  CAO   CAQ  CAR   118.60  3.000
 PXX  NAJ   CAQ  CAR   118.90  3.000
 PXX  CAE   NAJ  CAQ   118.48  3.000
 PXX  HAE   CAE  CAC   119.66  3.000
 PXX  HAE   CAE  NAJ   116.62  3.000
 PXX  CAC   CAE  NAJ   123.72  3.000
 PXX  HAC   CAC  CAG   121.57  3.000
 PXX  HAC   CAC  CAE   120.10  3.000
 PXX  CAG   CAC  CAE   118.34  3.000
 PXX  HAG   CAG  CAO   119.67  3.000
 PXX  HAG   CAG  CAC   121.09  3.000
 PXX  CAO   CAG  CAC   119.24  3.000
 PXX  CAI   CAO  CAG   121.52  3.000
 PXX  CAI   CAO  CAQ   120.74  3.000
 PXX  CAG   CAO  CAQ   117.72  3.000
 PXX  HAI   CAI  CAO   118.40  3.000
 PXX  HAI   CAI  CAN   120.57  3.000
 PXX  CAO   CAI  CAN   121.01  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
 PXX  CONST_01  CAD  CAH  CAP  CAN  180.00   0.0  0
 PXX  CONST_02  NAK  CAR  CAP  CAN  180.00   0.0  0
 PXX  CONST_03  CAQ  CAR  CAP  CAN    0.00   0.0  0
 PXX  CONST_04  CAQ  CAO  CAI  CAN    0.00   0.0  0
 PXX  CONST_05  CAG  CAO  CAI  CAN  180.00   0.0  0
 PXX  CONST_06  CAO  CAI  CAN  CAP    0.00   0.0  0
 PXX  CONST_07  CAF  CAD  CAH  CAP    0.00   0.0  0
 PXX  CONST_08  CAF  NAK  CAR  CAP    0.00   0.0  0
 PXX  CONST_09  NAJ  CAQ  CAR  CAP  180.00   0.0  0
 PXX  CONST_10  CAO  CAQ  CAR  CAP    0.00   0.0  0
 PXX  CONST_11  CAI  CAN  CAP  CAH  180.00   0.0  0
 PXX  CONST_12  NAK  CAR  CAP  CAH    0.00   0.0  0
 PXX  CONST_13  CAQ  CAR  CAP  CAH  180.00   0.0  0
 PXX  CONST_14  NAK  CAF  CAD  CAH    0.00   0.0  0
 PXX  CONST_15  CAR  CAP  CAH  CAD    0.00   0.0  0
 PXX  CONST_16  CAR  NAK  CAF  CAD    0.00   0.0  0
 PXX  CONST_17  CAQ  CAR  NAK  CAF  180.00   0.0  0
 PXX  CONST_18  NAJ  CAQ  CAR  NAK    0.00   0.0  0
 PXX  CONST_19  CAO  CAQ  CAR  NAK  180.00   0.0  0
 PXX  CONST_20  CAI  CAN  CAP  CAR    0.00   0.0  0
 PXX  CONST_21  CAE  NAJ  CAQ  CAR  180.00   0.0  0
 PXX  CONST_22  CAG  CAO  CAQ  CAR  180.00   0.0  0
 PXX  CONST_23  CAI  CAO  CAQ  CAR    0.00   0.0  0
 PXX  CONST_24  CAC  CAE  NAJ  CAQ    0.00   0.0  0
 PXX  CONST_25  CAC  CAG  CAO  CAQ    0.00   0.0  0
 PXX  CONST_26  CAG  CAO  CAQ  NAJ    0.00   0.0  0
 PXX  CONST_27  CAI  CAO  CAQ  NAJ  180.00   0.0  0
 PXX  CONST_28  CAG  CAC  CAE  NAJ    0.00   0.0  0
 PXX  CONST_29  CAO  CAQ  NAJ  CAE    0.00   0.0  0
 PXX  CONST_30  CAO  CAG  CAC  CAE    0.00   0.0  0
 PXX  CONST_31  CAI  CAO  CAG  CAC  180.00   0.0  0
 PXX  CONST_32  CAH  CAP  CAN  NAL    0.00   0.0  0
 PXX  CONST_33  CAR  CAP  CAN  NAL  180.00   0.0  0
 PXX  CONST_34  CAO  CAI  CAN  NAL  180.00   0.0  0
 PXX  CONST_35  HAH  CAH  CAP  CAN    0.00   0.0  0
 PXX  CONST_36  HAI  CAI  CAN  CAP  180.00   0.0  0
 PXX  CONST_37  HAD  CAD  CAH  CAP  180.00   0.0  0
 PXX  CONST_38  HAF  CAF  CAD  CAH  180.00   0.0  0
 PXX  CONST_39  HAE  CAE  NAJ  CAQ  180.00   0.0  0
 PXX  CONST_40  HAG  CAG  CAO  CAQ  180.00   0.0  0
 PXX  CONST_41  HAC  CAC  CAE  NAJ  180.00   0.0  0
 PXX  CONST_45  CAN  NAL  CAM  CAA  180.00   0.0  0
 PXX  CONST_46  CAN  NAL  CAM  OAB    0.00   0.0  0
 PXX  Var_01    HAA  CAA  CAM  OAB   82.26  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
 PXX  plan-1  NAL   0.020
 PXX  plan-1  CAN   0.020
 PXX  plan-1  CAP   0.020
 PXX  plan-1  CAH   0.020
 PXX  plan-1  CAD   0.020
 PXX  plan-1  CAF   0.020
 PXX  plan-1  NAK   0.020
 PXX  plan-1  CAR   0.020
 PXX  plan-1  CAQ   0.020
 PXX  plan-1  NAJ   0.020
 PXX  plan-1  CAE   0.020
 PXX  plan-1  CAC   0.020
 PXX  plan-1  CAG   0.020
 PXX  plan-1  CAO   0.020
 PXX  plan-1  CAI   0.020
 PXX  plan-1  HAH   0.020
 PXX  plan-1  HAD   0.020
 PXX  plan-1  HAF   0.020
 PXX  plan-1  HAE   0.020
 PXX  plan-1  HAC   0.020
 PXX  plan-1  HAG   0.020
 PXX  plan-1  HAI   0.020
 PXX  plan-2  CAA   0.020
 PXX  plan-2  CAM   0.020
 PXX  plan-2  OAB   0.020
 PXX  plan-2  NAL   0.020
 PXX  plan-2  CAN   0.020
 PXX  plan-2  HNAL  0.020

