# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 19:45:33 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 1-methyl-7-phenyl-2,3,4,6-tetrahydro-1,6-naphthyridin-5(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCCC2=C1C=C(NC2=O)c3ccccc3
#
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
 3GX  3GX  1-methyl-7-phenyl-2,3,4,6-tetrahydro-1,6-naphthyridin-5(1H)-one  ligand  34  18  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3GX
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
 3GX  CAH  C  CR16  0  -0.519  -0.1009   0.8421  -0.0155
 3GX  CAG  C  CR6   0   0.541  -1.5024   0.5529  -0.0057
 3GX  NAB  N  NT    0  -0.521  -2.3958   1.5721  -0.0990
 3GX  CAA  C  CH3   0  -0.542  -1.9610   2.9259  -0.3606
 3GX  CAC  C  CH2   0  -0.285  -3.7956   1.2676  -0.3376
 3GX  CAD  C  CH2   0  -0.470  -4.2280   0.0559   0.4635
 3GX  CAE  C  CH2   0  -0.457  -3.3693  -1.1463   0.1077
 3GX  CAF  C  CR6   0  -0.255  -1.9164  -0.7725   0.0868
 3GX  CAK  C  CR6   0   0.469  -0.9651  -1.8279   0.1800
 3GX  OAL  O  O     0  -0.529  -1.2414  -3.0301   0.2623
 3GX  NAJ  N  NR16  0  -0.732   0.3668  -1.4461   0.1855
 3GX  CAI  C  CR6   0   0.399   0.8024  -0.1680   0.0852
 3GX  CAM  C  CR6   0   0.061   2.2581   0.0546   0.0557
 3GX  CAN  C  CR16  0  -0.305   3.1080  -0.8493  -0.5836
 3GX  CAO  C  CR16  0  -0.239   4.4766  -0.6265  -0.6136
 3GX  CAP  C  CR16  0  -0.257   5.0148   0.4998  -0.0061
 3GX  CAQ  C  CR16  0  -0.239   4.1754   1.4035   0.6329
 3GX  CAR  C  CR16  0  -0.299   2.8075   1.1828   0.6658
 3GX  H1   H  HCR6  0   0.281   0.2631   1.8487  -0.1458
 3GX  H3   H  HCH3  0   0.236  -1.5129   3.0454  -1.3518
 3GX  H4   H  HCH3  0   0.259  -2.8227   3.5861  -0.3026
 3GX  H5   H  HCH3  0   0.246  -1.2440   3.2702   0.3850
 3GX  H6   H  HCH2  0   0.249  -4.3845   2.1386  -0.0488
 3GX  H7   H  HCH2  0   0.230  -3.9769   1.0967  -1.4067
 3GX  H8   H  HCH2  0   0.234  -4.1394   0.2810   1.5292
 3GX  H9   H  HCH2  0   0.244  -5.2810  -0.1489   0.2653
 3GX  H10  H  HCH2  0   0.242  -3.5376  -1.9517   0.8256
 3GX  H11  H  HCH2  0   0.234  -3.6764  -1.5450  -0.8656
 3GX  H12  H  HCR6  0   0.264   2.7080  -1.7219  -1.0852
 3GX  H13  H  HCR6  0   0.265   5.1214  -1.3332  -1.1192
 3GX  H14  H  HCR6  0   0.264   6.0826   0.6731  -0.0301
 3GX  H15  H  HCR6  0   0.264   4.5873   2.2798   1.1156
 3GX  H16  H  HCR6  0   0.261   2.1651   1.8819   1.1856
 3GX  H2   H  HNR6  0   0.409   1.0396  -2.1900   0.3091

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
 3GX  CAP  CAQ  aromatic  1.389  0.020  1.389
 3GX  CAP  CAO  aromatic  1.388  0.020  1.388
 3GX  CAQ  CAR  aromatic  1.386  0.020  1.386
 3GX  CAO  CAN  aromatic  1.387  0.020  1.387
 3GX  CAR  CAM  aromatic  1.395  0.020  1.395
 3GX  CAN  CAM  aromatic  1.396  0.020  1.396
 3GX  CAM  CAI  single    1.473  0.020  1.473
 3GX  CAI  CAH  double    1.359  0.020  1.359
 3GX  CAI  NAJ  single    1.354  0.020  1.354
 3GX  CAH  CAG  single    1.431  0.020  1.431
 3GX  NAJ  CAK  single    1.385  0.020  1.385
 3GX  CAA  NAB  single    1.446  0.020  1.446
 3GX  CAG  NAB  single    1.359  0.020  1.359
 3GX  CAG  CAF  double    1.392  0.020  1.392
 3GX  CAK  CAF  single    1.424  0.020  1.424
 3GX  CAK  OAL  double    1.236  0.020  1.236
 3GX  NAB  CAC  single    1.452  0.020  1.452
 3GX  CAF  CAE  single    1.500  0.020  1.500
 3GX  CAC  CAD  single    1.516  0.020  1.516
 3GX  CAE  CAD  single    1.520  0.020  1.520
 3GX  CAH  H1   single    0.930  0.020  1.080
 3GX  CAA  H3   single    0.970  0.020  1.090
 3GX  CAA  H4   single    0.970  0.020  1.090
 3GX  CAA  H5   single    0.970  0.020  1.090
 3GX  CAC  H6   single    0.970  0.020  1.090
 3GX  CAC  H7   single    0.970  0.020  1.090
 3GX  CAD  H8   single    0.970  0.020  1.090
 3GX  CAD  H9   single    0.970  0.020  1.090
 3GX  CAE  H10  single    0.970  0.020  1.090
 3GX  CAE  H11  single    0.970  0.020  1.090
 3GX  CAN  H12  single    0.930  0.020  1.080
 3GX  CAO  H13  single    0.930  0.020  1.080
 3GX  CAP  H14  single    0.930  0.020  1.080
 3GX  CAQ  H15  single    0.930  0.020  1.080
 3GX  CAR  H16  single    0.930  0.020  1.080
 3GX  NAJ  H2   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
 3GX  H1   CAH  CAI  118.58  3.000
 3GX  H1   CAH  CAG  121.34  3.000
 3GX  CAI  CAH  CAG  120.02  3.000
 3GX  CAF  CAG  NAB  121.57  3.000
 3GX  CAF  CAG  CAH  118.96  3.000
 3GX  NAB  CAG  CAH  119.47  3.000
 3GX  CAC  NAB  CAA  117.16  3.000
 3GX  CAC  NAB  CAG  119.20  3.000
 3GX  CAA  NAB  CAG  121.14  3.000
 3GX  H5   CAA  H4   107.04  3.000
 3GX  H5   CAA  H3   108.40  3.000
 3GX  H4   CAA  H3   107.86  3.000
 3GX  H5   CAA  NAB  111.70  3.000
 3GX  H4   CAA  NAB  108.70  3.000
 3GX  H3   CAA  NAB  112.91  3.000
 3GX  H7   CAC  H6   107.05  3.000
 3GX  H7   CAC  CAD  110.07  3.000
 3GX  H6   CAC  CAD  110.15  3.000
 3GX  H7   CAC  NAB  110.60  3.000
 3GX  H6   CAC  NAB  108.03  3.000
 3GX  CAD  CAC  NAB  110.84  3.000
 3GX  H9   CAD  H8   107.10  3.000
 3GX  H9   CAD  CAE  110.76  3.000
 3GX  H8   CAD  CAE  110.21  3.000
 3GX  H9   CAD  CAC  109.24  3.000
 3GX  H8   CAD  CAC  109.13  3.000
 3GX  CAE  CAD  CAC  110.34  3.000
 3GX  H11  CAE  H10  105.81  3.000
 3GX  H11  CAE  CAF  110.47  3.000
 3GX  H10  CAE  CAF  110.01  3.000
 3GX  H11  CAE  CAD  109.72  3.000
 3GX  H10  CAE  CAD  110.03  3.000
 3GX  CAF  CAE  CAD  110.69  3.000
 3GX  CAK  CAF  CAE  117.48  3.000
 3GX  CAE  CAF  CAG  121.76  3.000
 3GX  CAK  CAF  CAG  120.76  3.000
 3GX  NAJ  CAK  OAL  118.85  3.000
 3GX  OAL  CAK  CAF  125.15  3.000
 3GX  NAJ  CAK  CAF  115.99  3.000
 3GX  H2   NAJ  CAI  119.32  3.000
 3GX  H2   NAJ  CAK  115.95  3.000
 3GX  CAI  NAJ  CAK  124.69  3.000
 3GX  CAM  CAI  NAJ  117.53  3.000
 3GX  NAJ  CAI  CAH  119.55  3.000
 3GX  CAM  CAI  CAH  122.90  3.000
 3GX  CAR  CAM  CAN  118.95  3.000
 3GX  CAN  CAM  CAI  120.87  3.000
 3GX  CAR  CAM  CAI  120.17  3.000
 3GX  H12  CAN  CAO  118.93  3.000
 3GX  H12  CAN  CAM  120.60  3.000
 3GX  CAO  CAN  CAM  120.45  3.000
 3GX  H13  CAO  CAP  120.22  3.000
 3GX  H13  CAO  CAN  119.55  3.000
 3GX  CAP  CAO  CAN  120.22  3.000
 3GX  H14  CAP  CAQ  120.16  3.000
 3GX  H14  CAP  CAO  120.18  3.000
 3GX  CAQ  CAP  CAO  119.66  3.000
 3GX  H15  CAQ  CAR  119.61  3.000
 3GX  H15  CAQ  CAP  120.14  3.000
 3GX  CAR  CAQ  CAP  120.25  3.000
 3GX  H16  CAR  CAQ  119.62  3.000
 3GX  H16  CAR  CAM  119.90  3.000
 3GX  CAQ  CAR  CAM  120.47  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
 3GX  CONST_01  CAP  CAQ  CAR  CAM    0.00   0.0  0
 3GX  CONST_02  CAP  CAO  CAN  CAM    0.00   0.0  0
 3GX  CONST_03  CAQ  CAP  CAO  CAN    0.00   0.0  0
 3GX  CONST_04  CAQ  CAR  CAM  CAN    0.00   0.0  0
 3GX  CONST_05  CAR  CAQ  CAP  CAO    0.00   0.0  0
 3GX  CONST_06  CAR  CAM  CAN  CAO    0.00   0.0  0
 3GX  CONST_07  CAQ  CAR  CAM  CAI  180.00   0.0  0
 3GX  CONST_08  CAO  CAN  CAM  CAI  180.00   0.0  0
 3GX  CONST_09  CAI  NAJ  CAK  CAF    0.00   0.0  0
 3GX  CONST_10  CAI  NAJ  CAK  OAL  180.00   0.0  0
 3GX  CONST_11  H16  CAR  CAM  CAI    0.00   0.0  0
 3GX  CONST_12  H12  CAN  CAM  CAI    0.00   0.0  0
 3GX  CONST_13  H15  CAQ  CAR  CAM  180.00   0.0  0
 3GX  CONST_14  H13  CAO  CAN  CAM  180.00   0.0  0
 3GX  CONST_15  H14  CAP  CAO  CAN  180.00   0.0  0
 3GX  CONST_16  H2   NAJ  CAK  CAF  180.00   0.0  0
 3GX  Var_01    CAR  CAM  CAI  CAH   36.98  30.0  3
 3GX  Var_02    CAC  NAB  CAG  CAH  168.68  30.0  1
 3GX  Var_03    CAD  CAC  NAB  CAG   40.32  30.0  1
 3GX  Var_04    CAD  CAE  CAF  CAG  -18.17  30.0  1
 3GX  Var_05    CAE  CAD  CAC  NAB  -58.03  30.0  1
 3GX  Var_06    CAF  CAE  CAD  CAC   46.33  30.0  1
 3GX  Var_07    H3   CAA  NAB  CAG   65.54  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
 3GX  plan-1  CAI  0.020
 3GX  plan-1  CAM  0.020
 3GX  plan-1  CAN  0.020
 3GX  plan-1  CAO  0.020
 3GX  plan-1  CAP  0.020
 3GX  plan-1  CAQ  0.020
 3GX  plan-1  CAR  0.020
 3GX  plan-1  H12  0.020
 3GX  plan-1  H13  0.020
 3GX  plan-1  H14  0.020
 3GX  plan-1  H15  0.020
 3GX  plan-1  H16  0.020
 3GX  plan-2  CAG  0.020
 3GX  plan-2  NAB  0.020
 3GX  plan-2  CAA  0.020
 3GX  plan-2  CAC  0.020
 3GX  plan-3  CAH  0.020
 3GX  plan-3  CAG  0.020
 3GX  plan-3  NAB  0.020
 3GX  plan-3  CAE  0.020
 3GX  plan-3  CAF  0.020
 3GX  plan-3  CAK  0.020
 3GX  plan-3  OAL  0.020
 3GX  plan-3  NAJ  0.020
 3GX  plan-3  CAI  0.020
 3GX  plan-3  CAM  0.020
 3GX  plan-3  H1   0.020
 3GX  plan-3  H2   0.020

