# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 16:03:47 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: (2S)-2-(4-tert-butylphenyl)-2,3-dihydro-1H-pyrido[2,3-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(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
 GN5  GN5  (2S)-2-(4-tert-butylphenyl)-2,3-dihydro-1H-pyrido[2,3-d]pyrimidin-4-one  ligand  40  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 PERFECT
;

data_comp_GN5
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
 GN5  CAA   C  CH3   0  -0.631   4.0649  -1.3401   1.6193
 GN5  CAB   C  CT    0  -0.172   4.2409  -0.4713   0.3658
 GN5  CAC   C  CH3   0  -0.630   5.0214   0.8006   0.7225
 GN5  CAD   C  CH3   0  -0.667   5.0574  -1.2675  -0.6523
 GN5  CAE   C  CR6   0   0.188   2.8665  -0.0843  -0.1672
 GN5  CAJ   C  CR16  0  -0.291   1.9907   0.6459   0.6366
 GN5  CAI   C  CR16  0  -0.291   0.7274   1.0130   0.1971
 GN5  CAF   C  CR16  0  -0.326   2.4238  -0.4231  -1.4442
 GN5  CAG   C  CR16  0  -0.277   1.1610  -0.0576  -1.8883
 GN5  CAH   C  CR6   0   0.108   0.2901   0.6550  -1.0727
 GN5  CAK   C  CH1   0  -0.025  -1.1033   0.9684  -1.5986
 GN5  NAL   N  NH1   0  -0.647  -1.7929   1.9859  -0.8438
 GN5  CAM   C  C     0   0.523  -2.4879   1.7389   0.2895
 GN5  OAN   O  O     0  -0.473  -2.8898   2.6271   1.0272
 GN5  CAO   C  CR6   0  -0.206  -2.7664   0.3105   0.5344
 GN5  CAU   C  CR16  0  -0.163  -3.3673  -0.1273   1.7021
 GN5  CAT   C  CR16  0  -0.351  -3.6883  -1.4687   1.8385
 GN5  CAS   C  CR16  0  -0.050  -3.4082  -2.3107   0.7715
 GN5  NAR   N  N     0  -0.450  -2.8323  -1.9190  -0.3576
 GN5  CAP   C  CR6   0   0.484  -2.5043  -0.6361  -0.4726
 GN5  NAQ   N  NH1   0  -0.644  -1.9414  -0.2131  -1.6352
 GN5  HAA1  H  HCH3  0   0.228   3.5241  -0.8178   2.4091
 GN5  HAA2  H  HCH3  0   0.229   3.5158  -2.2541   1.3857
 GN5  HAA3  H  HCH3  0   0.228   5.0386  -1.6300   2.0196
 GN5  HAC1  H  HCH3  0   0.227   6.0114   0.5448   1.1057
 GN5  HAC2  H  HCH3  0   0.228   5.1574   1.4360  -0.1547
 GN5  HAC3  H  HCH3  0   0.228   4.5169   1.3934   1.4872
 GN5  HAD1  H  HCH3  0   0.231   4.5638  -2.1996  -0.9327
 GN5  HAD2  H  HCH3  0   0.231   5.2515  -0.6994  -1.5638
 GN5  HAD3  H  HCH3  0   0.239   6.0239  -1.5277  -0.2180
 GN5  HAJ   H  HCR6  0   0.248   2.2928   0.9462   1.6327
 GN5  HAF   H  HCR6  0   0.253   3.0609  -0.9800  -2.1174
 GN5  HAI   H  HCR6  0   0.256   0.1004   1.5962   0.8585
 GN5  HAG   H  HCR6  0   0.251   0.8581  -0.3363  -2.8920
 GN5  HAK   H  HCH1  0   0.300  -1.0118   1.3295  -2.6237
 GN5  HAL   H  HNH1  0   0.410  -1.5546   2.9463  -1.0438
 GN5  HAQ   H  HNH1  0   0.395  -1.6582  -0.9398  -2.2759
 GN5  HAU   H  HCR6  0   0.275  -3.5860   0.5792   2.4922
 GN5  HAT   H  HCR6  0   0.269  -4.1516  -1.8533   2.7351
 GN5  HAS   H  HCR6  0   0.270  -3.6616  -3.3634   0.8322

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
 GN5  CAA  CAB   single    1.535  0.020  1.535
 GN5  CAB  CAC   single    1.534  0.020  1.534
 GN5  CAB  CAD   single    1.529  0.020  1.529
 GN5  CAB  CAE   single    1.524  0.020  1.524
 GN5  CAE  CAJ   aromatic  1.395  0.020  1.395
 GN5  CAE  CAF   aromatic  1.393  0.020  1.393
 GN5  CAJ  CAI   aromatic  1.387  0.020  1.387
 GN5  CAI  CAH   aromatic  1.390  0.020  1.390
 GN5  CAF  CAG   aromatic  1.388  0.020  1.388
 GN5  CAG  CAH   aromatic  1.390  0.020  1.390
 GN5  CAH  CAK   single    1.522  0.020  1.522
 GN5  CAK  NAL   single    1.442  0.020  1.442
 GN5  CAK  NAQ   single    1.449  0.020  1.449
 GN5  NAL  CAM   single    1.352  0.020  1.352
 GN5  CAM  OAN   double    1.223  0.020  1.223
 GN5  CAM  CAO   single    1.476  0.020  1.476
 GN5  CAO  CAU   aromatic  1.384  0.020  1.384
 GN5  CAO  CAP   aromatic  1.407  0.020  1.407
 GN5  CAU  CAT   aromatic  1.386  0.020  1.386
 GN5  CAT  CAS   aromatic  1.388  0.020  1.388
 GN5  CAS  NAR   aromatic  1.327  0.020  1.327
 GN5  NAR  CAP   aromatic  1.329  0.020  1.329
 GN5  CAP  NAQ   single    1.359  0.020  1.359
 GN5  CAA  HAA1  single    0.970  0.020  1.090
 GN5  CAA  HAA2  single    0.970  0.020  1.090
 GN5  CAA  HAA3  single    0.970  0.020  1.090
 GN5  CAC  HAC1  single    0.970  0.020  1.090
 GN5  CAC  HAC2  single    0.970  0.020  1.090
 GN5  CAC  HAC3  single    0.970  0.020  1.090
 GN5  CAD  HAD1  single    0.970  0.020  1.090
 GN5  CAD  HAD2  single    0.970  0.020  1.090
 GN5  CAD  HAD3  single    0.970  0.020  1.090
 GN5  CAJ  HAJ   single    0.930  0.020  1.080
 GN5  CAF  HAF   single    0.930  0.020  1.080
 GN5  CAI  HAI   single    0.930  0.020  1.080
 GN5  CAG  HAG   single    0.930  0.020  1.080
 GN5  CAK  HAK   single    0.970  0.020  1.090
 GN5  NAL  HAL   single    0.860  0.020  1.020
 GN5  NAQ  HAQ   single    0.890  0.020  1.040
 GN5  CAU  HAU   single    0.930  0.020  1.080
 GN5  CAT  HAT   single    0.930  0.020  1.080
 GN5  CAS  HAS   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
 GN5  HAA3  CAA  HAA2  107.74  3.000
 GN5  HAA3  CAA  HAA1  107.70  3.000
 GN5  HAA2  CAA  HAA1  107.85  3.000
 GN5  HAA3  CAA  CAB   110.33  3.000
 GN5  HAA2  CAA  CAB   110.90  3.000
 GN5  HAA1  CAA  CAB   112.16  3.000
 GN5  CAE   CAB  CAD   112.39  3.000
 GN5  CAE   CAB  CAC   109.24  3.000
 GN5  CAD   CAB  CAC   108.35  3.000
 GN5  CAE   CAB  CAA   109.02  3.000
 GN5  CAD   CAB  CAA   108.07  3.000
 GN5  CAC   CAB  CAA   109.73  3.000
 GN5  HAC3  CAC  HAC2  107.73  3.000
 GN5  HAC3  CAC  HAC1  107.49  3.000
 GN5  HAC2  CAC  HAC1  107.79  3.000
 GN5  HAC3  CAC  CAB   112.21  3.000
 GN5  HAC2  CAC  CAB   111.04  3.000
 GN5  HAC1  CAC  CAB   110.40  3.000
 GN5  HAD3  CAD  HAD2  107.40  3.000
 GN5  HAD3  CAD  HAD1  107.41  3.000
 GN5  HAD2  CAD  HAD1  108.08  3.000
 GN5  HAD3  CAD  CAB   109.40  3.000
 GN5  HAD2  CAD  CAB   112.34  3.000
 GN5  HAD1  CAD  CAB   111.99  3.000
 GN5  CAF   CAE  CAJ   117.12  3.000
 GN5  CAF   CAE  CAB   123.04  3.000
 GN5  CAJ   CAE  CAB   119.84  3.000
 GN5  HAJ   CAJ  CAI   118.16  3.000
 GN5  HAJ   CAJ  CAE   119.98  3.000
 GN5  CAI   CAJ  CAE   121.85  3.000
 GN5  HAI   CAI  CAH   121.00  3.000
 GN5  HAI   CAI  CAJ   118.47  3.000
 GN5  CAH   CAI  CAJ   120.52  3.000
 GN5  HAF   CAF  CAG   118.20  3.000
 GN5  HAF   CAF  CAE   120.58  3.000
 GN5  CAG   CAF  CAE   121.23  3.000
 GN5  HAG   CAG  CAH   119.99  3.000
 GN5  HAG   CAG  CAF   118.85  3.000
 GN5  CAH   CAG  CAF   121.16  3.000
 GN5  CAK   CAH  CAG   118.46  3.000
 GN5  CAK   CAH  CAI   123.41  3.000
 GN5  CAG   CAH  CAI   118.11  3.000
 GN5  HAK   CAK  NAQ   107.14  3.000
 GN5  HAK   CAK  NAL   107.36  3.000
 GN5  NAQ   CAK  NAL   108.17  3.000
 GN5  HAK   CAK  CAH   108.43  3.000
 GN5  NAQ   CAK  CAH   111.74  3.000
 GN5  NAL   CAK  CAH   113.72  3.000
 GN5  HAL   NAL  CAM   117.45  3.000
 GN5  HAL   NAL  CAK   117.04  3.000
 GN5  CAM   NAL  CAK   123.75  3.000
 GN5  CAO   CAM  OAN   122.76  3.000
 GN5  CAO   CAM  NAL   114.38  3.000
 GN5  OAN   CAM  NAL   122.82  3.000
 GN5  CAP   CAO  CAU   118.16  3.000
 GN5  CAP   CAO  CAM   119.83  3.000
 GN5  CAU   CAO  CAM   121.87  3.000
 GN5  HAU   CAU  CAT   120.88  3.000
 GN5  HAU   CAU  CAO   119.80  3.000
 GN5  CAT   CAU  CAO   119.31  3.000
 GN5  HAT   CAT  CAS   120.58  3.000
 GN5  HAT   CAT  CAU   121.71  3.000
 GN5  CAS   CAT  CAU   117.70  3.000
 GN5  HAS   CAS  NAR   115.83  3.000
 GN5  HAS   CAS  CAT   119.92  3.000
 GN5  NAR   CAS  CAT   124.25  3.000
 GN5  CAP   NAR  CAS   117.76  3.000
 GN5  NAQ   CAP  NAR   118.46  3.000
 GN5  NAQ   CAP  CAO   118.69  3.000
 GN5  NAR   CAP  CAO   122.79  3.000
 GN5  HAQ   NAQ  CAP   115.79  3.000
 GN5  HAQ   NAQ  CAK   116.16  3.000
 GN5  CAP   NAQ  CAK   118.14  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
 GN5  CONST_01  CAH   CAI  CAJ  CAE     0.00   0.0  0
 GN5  CONST_02  CAH   CAG  CAF  CAE     0.00   0.0  0
 GN5  CONST_03  CAG   CAF  CAE  CAJ     0.00   0.0  0
 GN5  CONST_04  CAG   CAH  CAI  CAJ     0.00   0.0  0
 GN5  CONST_05  CAF   CAE  CAJ  CAI     0.00   0.0  0
 GN5  CONST_06  CAF   CAG  CAH  CAI     0.00   0.0  0
 GN5  CONST_07  CAS   CAT  CAU  CAO     0.00   0.0  0
 GN5  CONST_08  CAS   NAR  CAP  CAO     0.00   0.0  0
 GN5  CONST_09  NAR   CAP  CAO  CAU     0.00   0.0  0
 GN5  CONST_10  NAR   CAS  CAT  CAU     0.00   0.0  0
 GN5  CONST_11  CAP   CAO  CAU  CAT     0.00   0.0  0
 GN5  CONST_12  CAP   NAR  CAS  CAT     0.00   0.0  0
 GN5  CONST_13  CAK   CAH  CAI  CAJ   180.00   0.0  0
 GN5  CONST_14  CAK   CAH  CAG  CAF   180.00   0.0  0
 GN5  CONST_15  CAO   CAM  NAL  CAK     0.00   0.0  0
 GN5  CONST_16  CAI   CAJ  CAE  CAB   180.00   0.0  0
 GN5  CONST_17  CAG   CAF  CAE  CAB   180.00   0.0  0
 GN5  CONST_18  OAN   CAM  NAL  CAK   180.00   0.0  0
 GN5  CONST_19  HAI   CAI  CAJ  CAE   180.00   0.0  0
 GN5  CONST_20  HAG   CAG  CAF  CAE   180.00   0.0  0
 GN5  CONST_21  HAF   CAF  CAE  CAJ   180.00   0.0  0
 GN5  CONST_22  HAJ   CAJ  CAE  CAF   180.00   0.0  0
 GN5  CONST_23  HAU   CAU  CAO  CAM     0.00   0.0  0
 GN5  CONST_24  HAT   CAT  CAU  CAO   180.00   0.0  0
 GN5  CONST_25  HAS   CAS  CAT  CAU   180.00   0.0  0
 GN5  CONST_26  HAL   NAL  CAM  CAO   180.00   0.0  0
 GN5  Var_01    CAO   CAP  NAQ  CAK    27.61  30.0  1
 GN5  Var_02    CAU   CAO  CAM  NAL   174.46  30.0  1
 GN5  Var_03    CAJ   CAE  CAB  CAA    60.14  30.0  2
 GN5  Var_04    HAA1  CAA  CAB  CAE   -59.95  30.0  3
 GN5  Var_05    HAC1  CAC  CAB  CAE  -179.92  30.0  3
 GN5  Var_06    HAD1  CAD  CAB  CAE   -60.40  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
 GN5  chir_01  CAK  CAH  NAL  NAQ  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
 GN5  plan-1  CAB  0.020
 GN5  plan-1  CAE  0.020
 GN5  plan-1  CAJ  0.020
 GN5  plan-1  CAI  0.020
 GN5  plan-1  CAF  0.020
 GN5  plan-1  CAG  0.020
 GN5  plan-1  CAH  0.020
 GN5  plan-1  CAK  0.020
 GN5  plan-1  HAJ  0.020
 GN5  plan-1  HAF  0.020
 GN5  plan-1  HAI  0.020
 GN5  plan-1  HAG  0.020
 GN5  plan-2  CAM  0.020
 GN5  plan-2  CAO  0.020
 GN5  plan-2  CAU  0.020
 GN5  plan-2  CAT  0.020
 GN5  plan-2  CAS  0.020
 GN5  plan-2  NAR  0.020
 GN5  plan-2  CAP  0.020
 GN5  plan-2  NAQ  0.020
 GN5  plan-2  HAU  0.020
 GN5  plan-2  HAT  0.020
 GN5  plan-2  HAS  0.020
 GN5  plan-3  CAK  0.020
 GN5  plan-3  NAL  0.020
 GN5  plan-3  CAM  0.020
 GN5  plan-3  OAN  0.020
 GN5  plan-3  CAO  0.020
 GN5  plan-3  HAL  0.020

