# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 15:37:07 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: (2S)-2-(4-propan-2-ylphenyl)-2,3-dihydro-1H-pyrido[2,3-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)c1ccc(cc1)[C@@H]2NC(=O)c3cccnc3N2
#
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
 O53  O53  (2S)-2-(4-propan-2-ylphenyl)-2,3-dihydro-1H-pyrido[2,3-d]pyrimidin-4-one  ligand  37  20  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_O53
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
 O53  CAS   C  CH3   0  -0.643   4.6207   2.0162  -0.5860
 O53  CAR   C  CH1   0  -0.328   4.4065   0.5098  -0.7346
 O53  CAT   C  CH3   0  -0.645   5.5506  -0.2714  -0.0882
 O53  CAA   C  CR6   0   0.166   3.0673   0.0914  -0.1763
 O53  CAD   C  CR16  0  -0.316   2.0857  -0.4564  -0.9939
 O53  CAE   C  CR16  0  -0.286   0.8507  -0.8429  -0.4847
 O53  CAC   C  CR16  0  -0.299   2.7766   0.2392   1.1809
 O53  CAB   C  CR16  0  -0.285   1.5481  -0.1426   1.6913
 O53  CAF   C  CR6   0   0.118   0.5652  -0.6828   0.8642
 O53  CAG   C  CH1   0  -0.031  -0.7839  -1.0216   1.4792
 O53  NAI   N  NH1   0  -0.646  -1.5445  -1.9840   0.7202
 O53  CAH   C  C     0   0.522  -2.3575  -1.6664  -0.3122
 O53  OAK   O  O     0  -0.473  -2.8326  -2.5071  -1.0619
 O53  CAQ   C  CR6   0  -0.205  -2.6618  -0.2276  -0.4296
 O53  CAL   C  CR16  0  -0.164  -3.3872   0.2819  -1.4927
 O53  CAM   C  CR16  0  -0.351  -3.7137   1.6288  -1.5085
 O53  CAN   C  CR16  0  -0.050  -3.3101   2.4029  -0.4301
 O53  NAO   N  N     0  -0.451  -2.6140   1.9418   0.6009
 O53  CAP   C  CR6   0   0.484  -2.2841   0.6541   0.5994
 O53  NAJ   N  NH1   0  -0.645  -1.6007   0.1609   1.6653
 O53  HAS1  H  HCH3  0   0.231   3.8233   2.5823  -1.0686
 O53  HAS2  H  HCH3  0   0.220   4.6507   2.3117   0.4647
 O53  HAS3  H  HCH3  0   0.230   5.5669   2.3156  -1.0396
 O53  HAR   H  HCH1  0   0.241   4.4046   0.2762  -1.8037
 O53  HAT1  H  HCH3  0   0.220   5.6109  -0.0758   0.9844
 O53  HAT2  H  HCH3  0   0.232   5.4265  -1.3462  -0.2255
 O53  HAT3  H  HCH3  0   0.231   6.5069   0.0149  -0.5289
 O53  HAD   H  HCR6  0   0.249   2.2856  -0.5925  -2.0504
 O53  HAC   H  HCR6  0   0.250   3.5204   0.6523   1.8528
 O53  HAE   H  HCR6  0   0.255   0.1266  -1.2821  -1.1587
 O53  HAB   H  HCR6  0   0.252   1.3529  -0.0222   2.7516
 O53  HAG   H  HCH1  0   0.298  -0.6104  -1.4497   2.4675
 O53  HAI   H  HNH1  0   0.410  -1.2812  -2.9535   0.8206
 O53  HAJ   H  HNH1  0   0.395  -1.2412   0.8462   2.3133
 O53  HAL   H  HCR6  0   0.275  -3.6988  -0.3733  -2.2958
 O53  HAM   H  HCR6  0   0.269  -4.2718   2.0678  -2.3224
 O53  HAN   H  HCR6  0   0.270  -3.5615   3.4573  -0.3966

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
 O53  CAS  CAR   single    1.529  0.020  1.529
 O53  CAR  CAT   single    1.529  0.020  1.529
 O53  CAR  CAA   single    1.510  0.020  1.510
 O53  CAA  CAD   aromatic  1.390  0.020  1.390
 O53  CAA  CAC   aromatic  1.396  0.020  1.396
 O53  CAD  CAE   aromatic  1.391  0.020  1.391
 O53  CAE  CAF   aromatic  1.388  0.020  1.388
 O53  CAC  CAB   aromatic  1.384  0.020  1.384
 O53  CAB  CAF   aromatic  1.394  0.020  1.394
 O53  CAF  CAG   single    1.521  0.020  1.521
 O53  CAG  NAI   single    1.442  0.020  1.442
 O53  CAG  NAJ   single    1.449  0.020  1.449
 O53  NAI  CAH   single    1.352  0.020  1.352
 O53  CAH  OAK   double    1.223  0.020  1.223
 O53  CAH  CAQ   single    1.475  0.020  1.475
 O53  CAQ  CAL   aromatic  1.384  0.020  1.384
 O53  CAQ  CAP   aromatic  1.407  0.020  1.407
 O53  CAL  CAM   aromatic  1.386  0.020  1.386
 O53  CAM  CAN   aromatic  1.387  0.020  1.387
 O53  CAN  NAO   aromatic  1.327  0.020  1.327
 O53  NAO  CAP   aromatic  1.329  0.020  1.329
 O53  CAP  NAJ   single    1.359  0.020  1.359
 O53  CAS  HAS1  single    0.970  0.020  1.090
 O53  CAS  HAS2  single    0.970  0.020  1.090
 O53  CAS  HAS3  single    0.970  0.020  1.090
 O53  CAR  HAR   single    0.970  0.020  1.090
 O53  CAT  HAT1  single    0.970  0.020  1.090
 O53  CAT  HAT2  single    0.970  0.020  1.090
 O53  CAT  HAT3  single    0.970  0.020  1.090
 O53  CAD  HAD   single    0.930  0.020  1.080
 O53  CAC  HAC   single    0.930  0.020  1.080
 O53  CAE  HAE   single    0.930  0.020  1.080
 O53  CAB  HAB   single    0.930  0.020  1.080
 O53  CAG  HAG   single    0.970  0.020  1.090
 O53  NAI  HAI   single    0.860  0.020  1.020
 O53  NAJ  HAJ   single    0.890  0.020  1.040
 O53  CAL  HAL   single    0.930  0.020  1.080
 O53  CAM  HAM   single    0.930  0.020  1.080
 O53  CAN  HAN   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
 O53  HAS3  CAS  HAS2  107.57  3.000
 O53  HAS3  CAS  HAS1  107.91  3.000
 O53  HAS2  CAS  HAS1  107.78  3.000
 O53  HAS3  CAS  CAR   110.58  3.000
 O53  HAS2  CAS  CAR   111.35  3.000
 O53  HAS1  CAS  CAR   111.47  3.000
 O53  HAR   CAR  CAA   107.48  3.000
 O53  HAR   CAR  CAT   107.78  3.000
 O53  CAA   CAR  CAT   111.46  3.000
 O53  HAR   CAR  CAS   107.79  3.000
 O53  CAA   CAR  CAS   111.18  3.000
 O53  CAT   CAR  CAS   110.95  3.000
 O53  HAT3  CAT  HAT2  107.91  3.000
 O53  HAT3  CAT  HAT1  107.53  3.000
 O53  HAT2  CAT  HAT1  107.85  3.000
 O53  HAT3  CAT  CAR   110.55  3.000
 O53  HAT2  CAT  CAR   111.43  3.000
 O53  HAT1  CAT  CAR   111.42  3.000
 O53  CAC   CAA  CAD   117.81  3.000
 O53  CAC   CAA  CAR   120.99  3.000
 O53  CAD   CAA  CAR   121.20  3.000
 O53  HAD   CAD  CAE   119.06  3.000
 O53  HAD   CAD  CAA   119.51  3.000
 O53  CAE   CAD  CAA   121.42  3.000
 O53  HAE   CAE  CAF   120.96  3.000
 O53  HAE   CAE  CAD   118.61  3.000
 O53  CAF   CAE  CAD   120.42  3.000
 O53  HAC   CAC  CAB   119.05  3.000
 O53  HAC   CAC  CAA   120.00  3.000
 O53  CAB   CAC  CAA   120.95  3.000
 O53  HAB   CAB  CAF   119.75  3.000
 O53  HAB   CAB  CAC   119.31  3.000
 O53  CAF   CAB  CAC   120.94  3.000
 O53  CAG   CAF  CAB   118.17  3.000
 O53  CAG   CAF  CAE   123.34  3.000
 O53  CAB   CAF  CAE   118.45  3.000
 O53  HAG   CAG  NAJ   107.06  3.000
 O53  HAG   CAG  NAI   107.38  3.000
 O53  NAJ   CAG  NAI   108.35  3.000
 O53  HAG   CAG  CAF   108.22  3.000
 O53  NAJ   CAG  CAF   111.73  3.000
 O53  NAI   CAG  CAF   113.81  3.000
 O53  HAI   NAI  CAH   117.28  3.000
 O53  HAI   NAI  CAG   116.80  3.000
 O53  CAH   NAI  CAG   124.20  3.000
 O53  CAQ   CAH  OAK   122.80  3.000
 O53  CAQ   CAH  NAI   114.45  3.000
 O53  OAK   CAH  NAI   122.72  3.000
 O53  CAP   CAQ  CAL   118.15  3.000
 O53  CAP   CAQ  CAH   119.85  3.000
 O53  CAL   CAQ  CAH   121.88  3.000
 O53  HAL   CAL  CAM   120.80  3.000
 O53  HAL   CAL  CAQ   119.87  3.000
 O53  CAM   CAL  CAQ   119.33  3.000
 O53  HAM   CAM  CAN   120.61  3.000
 O53  HAM   CAM  CAL   121.69  3.000
 O53  CAN   CAM  CAL   117.70  3.000
 O53  HAN   CAN  NAO   115.82  3.000
 O53  HAN   CAN  CAM   119.94  3.000
 O53  NAO   CAN  CAM   124.24  3.000
 O53  CAP   NAO  CAN   117.78  3.000
 O53  NAJ   CAP  NAO   118.39  3.000
 O53  NAJ   CAP  CAQ   118.77  3.000
 O53  NAO   CAP  CAQ   122.78  3.000
 O53  HAJ   NAJ  CAP   115.87  3.000
 O53  HAJ   NAJ  CAG   115.83  3.000
 O53  CAP   NAJ  CAG   118.61  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
 O53  CONST_01  CAF   CAE  CAD  CAA    0.00   0.0  0
 O53  CONST_02  CAF   CAB  CAC  CAA    0.00   0.0  0
 O53  CONST_03  CAB   CAC  CAA  CAD    0.00   0.0  0
 O53  CONST_04  CAB   CAF  CAE  CAD    0.00   0.0  0
 O53  CONST_05  CAC   CAA  CAD  CAE    0.00   0.0  0
 O53  CONST_06  CAC   CAB  CAF  CAE    0.00   0.0  0
 O53  CONST_07  CAN   CAM  CAL  CAQ    0.00   0.0  0
 O53  CONST_08  CAN   NAO  CAP  CAQ    0.00   0.0  0
 O53  CONST_09  NAO   CAP  CAQ  CAL    0.00   0.0  0
 O53  CONST_10  NAO   CAN  CAM  CAL    0.00   0.0  0
 O53  CONST_11  CAP   CAQ  CAL  CAM    0.00   0.0  0
 O53  CONST_12  CAP   NAO  CAN  CAM    0.00   0.0  0
 O53  CONST_13  CAG   CAF  CAE  CAD  180.00   0.0  0
 O53  CONST_14  CAG   CAF  CAB  CAC  180.00   0.0  0
 O53  CONST_15  CAQ   CAH  NAI  CAG    0.00   0.0  0
 O53  CONST_16  CAE   CAD  CAA  CAR  180.00   0.0  0
 O53  CONST_17  CAB   CAC  CAA  CAR  180.00   0.0  0
 O53  CONST_18  OAK   CAH  NAI  CAG  180.00   0.0  0
 O53  CONST_19  HAE   CAE  CAD  CAA  180.00   0.0  0
 O53  CONST_20  HAB   CAB  CAC  CAA  180.00   0.0  0
 O53  CONST_21  HAC   CAC  CAA  CAD  180.00   0.0  0
 O53  CONST_22  HAD   CAD  CAA  CAC  180.00   0.0  0
 O53  CONST_23  HAL   CAL  CAQ  CAH    0.00   0.0  0
 O53  CONST_24  HAM   CAM  CAL  CAQ  180.00   0.0  0
 O53  CONST_25  HAN   CAN  CAM  CAL  180.00   0.0  0
 O53  CONST_26  HAI   NAI  CAH  CAQ  180.00   0.0  0
 O53  Var_01    CAQ   CAP  NAJ  CAG   27.18  30.0  1
 O53  Var_02    CAL   CAQ  CAH  NAI  174.58  30.0  1
 O53  Var_03    CAD   CAA  CAR  CAS  116.61  30.0  2
 O53  Var_04    HAS1  CAS  CAR  CAA  -56.94  30.0  3
 O53  Var_05    HAT1  CAT  CAR  CAA  -62.65  30.0  3

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
 O53  chir_01  CAG  CAF  NAI  NAJ  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
 O53  plan-1  CAR  0.020
 O53  plan-1  CAA  0.020
 O53  plan-1  CAD  0.020
 O53  plan-1  CAE  0.020
 O53  plan-1  CAC  0.020
 O53  plan-1  CAB  0.020
 O53  plan-1  CAF  0.020
 O53  plan-1  CAG  0.020
 O53  plan-1  HAD  0.020
 O53  plan-1  HAC  0.020
 O53  plan-1  HAE  0.020
 O53  plan-1  HAB  0.020
 O53  plan-2  CAH  0.020
 O53  plan-2  CAQ  0.020
 O53  plan-2  CAL  0.020
 O53  plan-2  CAM  0.020
 O53  plan-2  CAN  0.020
 O53  plan-2  NAO  0.020
 O53  plan-2  CAP  0.020
 O53  plan-2  NAJ  0.020
 O53  plan-2  HAL  0.020
 O53  plan-2  HAM  0.020
 O53  plan-2  HAN  0.020
 O53  plan-3  CAG  0.020
 O53  plan-3  NAI  0.020
 O53  plan-3  CAH  0.020
 O53  plan-3  OAK  0.020
 O53  plan-3  CAQ  0.020
 O53  plan-3  HAI  0.020

