# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 14:38:48 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 1-methyl-3-(trifluoromethyl)benzo[c][1,8]naphthyridin-6(5H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(nc2NC(=O)c3ccccc3c12)C(F)(F)F
#
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
 M3F  M3F  1-methyl-3-(trifluoromethyl)benzo[c][1,8]naphthyridin-6(5H)-one  ligand  29  20  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_M3F
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
 M3F  CAA   C  CH3   0  -0.799  -0.0986   3.0886   0.2096
 M3F  OAB   O  O     0  -0.452  -2.6126  -2.9819   0.3696
 M3F  FAC   F  F     0  -0.309   4.0111  -0.9272   0.9329
 M3F  FAD   F  F     0  -0.297   4.3920   0.8857  -0.1644
 M3F  FAE   F  F     0  -0.309   3.9006  -0.9289  -1.2144
 M3F  CAF   C  CR16  0  -0.256  -4.8356   0.5305  -0.0460
 M3F  CAG   C  CR16  0  -0.218  -4.1470   1.7179  -0.2681
 M3F  CAH   C  CR16  0  -0.262  -4.1195  -0.6341   0.1320
 M3F  CAI   C  CR16  0  -0.357  -2.7657   1.7442  -0.2683
 M3F  CAJ   C  CR16  0  -0.374   1.6983   1.4208   0.0212
 M3F  NAK   N  N     0  -0.460   1.3698  -0.9285  -0.0375
 M3F  NAL   N  NR16  0  -0.732  -0.6876  -1.8558   0.0855
 M3F  CAM   C  CR6   0   0.178   0.3239   1.6585   0.0612
 M3F  CAN   C  CR6   0  -0.002   2.1604   0.1264  -0.0523
 M3F  CAO   C  CR6   0   0.529  -2.0397  -1.9166   0.2182
 M3F  CAP   C  CR66  0  -0.175  -2.7254  -0.6195   0.1191
 M3F  CAQ   C  CR66  0   0.468   0.0685  -0.7152   0.0072
 M3F  CAR   C  CR66  0   0.234  -2.0112   0.5842  -0.0418
 M3F  CAS   C  CR66  0  -0.078  -0.5471   0.5561  -0.0016
 M3F  CAT   C  CT    0   1.055   3.6262  -0.2060  -0.1245
 M3F  HAA   H  HCH3  0   0.273  -0.4783   3.5016  -0.7262
 M3F  HAAA  H  HCH3  0   0.269  -0.8691   3.2126   0.9694
 M3F  HAAB  H  HCH3  0   0.279   0.7560   3.6961   0.5005
 M3F  HAF   H  HCR6  0   0.270  -5.9168   0.5153  -0.0350
 M3F  HAG   H  HCR6  0   0.274  -4.6909   2.6348  -0.4519
 M3F  HAH   H  HCR6  0   0.271  -4.6361  -1.5737   0.2708
 M3F  HAI   H  HCR6  0   0.276  -2.2885   2.6841  -0.4797
 M3F  HAJ   H  HCR6  0   0.285   2.3797   2.2583   0.0570
 M3F  HNAL  H  HNR6  0   0.418  -0.1755  -2.7290   0.1057

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
 M3F  CAA  CAM   single    1.499  0.020  1.499
 M3F  OAB  CAO   double    1.219  0.020  1.219
 M3F  FAC  CAT   single    1.337  0.020  1.337
 M3F  FAD  CAT   single    1.334  0.020  1.334
 M3F  FAE  CAT   single    1.336  0.020  1.336
 M3F  CAF  CAG   aromatic  1.390  0.020  1.390
 M3F  CAF  CAH   aromatic  1.379  0.020  1.379
 M3F  CAG  CAI   aromatic  1.382  0.020  1.382
 M3F  CAH  CAP   aromatic  1.394  0.020  1.394
 M3F  CAI  CAR   aromatic  1.402  0.020  1.402
 M3F  CAJ  CAM   aromatic  1.395  0.020  1.395
 M3F  CAJ  CAN   aromatic  1.376  0.020  1.376
 M3F  NAK  CAN   aromatic  1.318  0.020  1.318
 M3F  NAK  CAQ   aromatic  1.319  0.020  1.319
 M3F  NAL  CAO   single    1.360  0.020  1.360
 M3F  NAL  CAQ   single    1.371  0.020  1.371
 M3F  CAM  CAS   aromatic  1.406  0.020  1.406
 M3F  CAN  CAT   single    1.505  0.020  1.505
 M3F  CAO  CAP   single    1.471  0.020  1.471
 M3F  CAP  CAR   aromatic  1.409  0.020  1.409
 M3F  CAQ  CAS   aromatic  1.412  0.020  1.412
 M3F  CAR  CAS   aromatic  1.465  0.020  1.465
 M3F  CAA  HAA   single    0.970  0.020  1.090
 M3F  CAA  HAAA  single    0.970  0.020  1.090
 M3F  CAA  HAAB  single    0.970  0.020  1.090
 M3F  CAF  HAF   single    0.930  0.020  1.080
 M3F  CAG  HAG   single    0.930  0.020  1.080
 M3F  CAH  HAH   single    0.930  0.020  1.080
 M3F  CAI  HAI   single    0.930  0.020  1.080
 M3F  CAJ  HAJ   single    0.930  0.020  1.080
 M3F  NAL  HNAL  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
 M3F  HAAB  CAA  HAAA  107.79  3.000
 M3F  HAAB  CAA  HAA   106.94  3.000
 M3F  HAAA  CAA  HAA   108.00  3.000
 M3F  HAAB  CAA  CAM   109.75  3.000
 M3F  HAAA  CAA  CAM   112.16  3.000
 M3F  HAA   CAA  CAM   111.99  3.000
 M3F  HAF   CAF  CAH   120.41  3.000
 M3F  HAF   CAF  CAG   120.58  3.000
 M3F  CAH   CAF  CAG   118.99  3.000
 M3F  HAG   CAG  CAI   119.11  3.000
 M3F  HAG   CAG  CAF   120.13  3.000
 M3F  CAI   CAG  CAF   120.76  3.000
 M3F  HAH   CAH  CAP   119.21  3.000
 M3F  HAH   CAH  CAF   120.17  3.000
 M3F  CAP   CAH  CAF   120.62  3.000
 M3F  HAI   CAI  CAR   121.07  3.000
 M3F  HAI   CAI  CAG   117.42  3.000
 M3F  CAR   CAI  CAG   121.48  3.000
 M3F  HAJ   CAJ  CAN   121.27  3.000
 M3F  HAJ   CAJ  CAM   119.23  3.000
 M3F  CAN   CAJ  CAM   119.50  3.000
 M3F  CAQ   NAK  CAN   117.55  3.000
 M3F  HNAL  NAL  CAQ   116.10  3.000
 M3F  HNAL  NAL  CAO   117.53  3.000
 M3F  CAQ   NAL  CAO   126.24  3.000
 M3F  CAS   CAM  CAJ   118.37  3.000
 M3F  CAS   CAM  CAA   125.30  3.000
 M3F  CAJ   CAM  CAA   116.30  3.000
 M3F  CAT   CAN  NAK   114.08  3.000
 M3F  CAT   CAN  CAJ   122.50  3.000
 M3F  NAK   CAN  CAJ   123.41  3.000
 M3F  CAP   CAO  NAL   114.68  3.000
 M3F  CAP   CAO  OAB   124.06  3.000
 M3F  NAL   CAO  OAB   121.23  3.000
 M3F  CAR   CAP  CAO   121.66  3.000
 M3F  CAR   CAP  CAH   121.12  3.000
 M3F  CAO   CAP  CAH   117.15  3.000
 M3F  CAS   CAQ  NAL   120.59  3.000
 M3F  CAS   CAQ  NAK   125.11  3.000
 M3F  NAL   CAQ  NAK   114.29  3.000
 M3F  CAS   CAR  CAP   119.15  3.000
 M3F  CAS   CAR  CAI   123.92  3.000
 M3F  CAP   CAR  CAI   116.90  3.000
 M3F  CAR   CAS  CAQ   116.94  3.000
 M3F  CAR   CAS  CAM   127.24  3.000
 M3F  CAQ   CAS  CAM   115.81  3.000
 M3F  CAN   CAT  FAE   111.02  3.000
 M3F  CAN   CAT  FAD   112.32  3.000
 M3F  FAE   CAT  FAD   107.48  3.000
 M3F  CAN   CAT  FAC   111.21  3.000
 M3F  FAE   CAT  FAC   107.11  3.000
 M3F  FAD   CAT  FAC   107.45  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
 M3F  CONST_01  CAR   CAI  CAG  CAF    0.00   0.0  0
 M3F  CONST_02  CAR   CAP  CAH  CAF    0.00   0.0  0
 M3F  CONST_03  CAP   CAH  CAF  CAG    0.00   0.0  0
 M3F  CONST_04  CAP   CAR  CAI  CAG    0.00   0.0  0
 M3F  CONST_05  CAS   CAR  CAI  CAG  180.00   0.0  0
 M3F  CONST_06  CAI   CAG  CAF  CAH    0.00   0.0  0
 M3F  CONST_07  CAI   CAR  CAP  CAH    0.00   0.0  0
 M3F  CONST_08  CAS   CAR  CAP  CAH  180.00   0.0  0
 M3F  CONST_09  CAM   CAS  CAR  CAI    0.00   0.0  0
 M3F  CONST_10  CAQ   CAS  CAR  CAI  180.00   0.0  0
 M3F  CONST_11  CAQ   CAS  CAM  CAJ    0.00   0.0  0
 M3F  CONST_12  CAR   CAS  CAM  CAJ  180.00   0.0  0
 M3F  CONST_13  CAQ   NAK  CAN  CAJ    0.00   0.0  0
 M3F  CONST_14  CAM   CAJ  CAN  NAK    0.00   0.0  0
 M3F  CONST_15  CAM   CAS  CAQ  NAK    0.00   0.0  0
 M3F  CONST_16  CAR   CAS  CAQ  NAK  180.00   0.0  0
 M3F  CONST_17  CAP   CAR  CAS  CAM  180.00   0.0  0
 M3F  CONST_18  CAS   CAM  CAJ  CAN    0.00   0.0  0
 M3F  CONST_19  CAS   CAQ  NAK  CAN    0.00   0.0  0
 M3F  CONST_20  CAQ   CAS  CAR  CAP    0.00   0.0  0
 M3F  CONST_21  CAQ   NAL  CAO  CAP    0.00   0.0  0
 M3F  CONST_22  CAN   CAJ  CAM  CAA  180.00   0.0  0
 M3F  CONST_23  CAQ   CAS  CAM  CAA  180.00   0.0  0
 M3F  CONST_24  CAR   CAS  CAM  CAA    0.00   0.0  0
 M3F  CONST_25  CAT   CAN  CAJ  CAM  180.00   0.0  0
 M3F  CONST_26  CAT   CAN  NAK  CAQ  180.00   0.0  0
 M3F  CONST_27  CAQ   NAL  CAO  OAB  180.00   0.0  0
 M3F  CONST_28  HAI   CAI  CAG  CAF  180.00   0.0  0
 M3F  CONST_29  HAH   CAH  CAF  CAG  180.00   0.0  0
 M3F  CONST_30  HAG   CAG  CAF  CAH  180.00   0.0  0
 M3F  CONST_31  HAF   CAF  CAG  CAI  180.00   0.0  0
 M3F  CONST_32  HAJ   CAJ  CAN  NAK  180.00   0.0  0
 M3F  CONST_33  HNAL  NAL  CAO  CAP  180.00   0.0  0
 M3F  Var_01    CAJ   CAN  CAT  FAC  117.87  30.0  1
 M3F  Var_02    HAA   CAA  CAM  CAJ  105.12  30.0  2

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
 M3F  plan-1  CAA   0.020
 M3F  plan-1  OAB   0.020
 M3F  plan-1  CAF   0.020
 M3F  plan-1  CAG   0.020
 M3F  plan-1  CAH   0.020
 M3F  plan-1  CAI   0.020
 M3F  plan-1  CAJ   0.020
 M3F  plan-1  NAK   0.020
 M3F  plan-1  NAL   0.020
 M3F  plan-1  CAM   0.020
 M3F  plan-1  CAN   0.020
 M3F  plan-1  CAO   0.020
 M3F  plan-1  CAP   0.020
 M3F  plan-1  CAQ   0.020
 M3F  plan-1  CAR   0.020
 M3F  plan-1  CAS   0.020
 M3F  plan-1  CAT   0.020
 M3F  plan-1  HAF   0.020
 M3F  plan-1  HAG   0.020
 M3F  plan-1  HAH   0.020
 M3F  plan-1  HAI   0.020
 M3F  plan-1  HAJ   0.020
 M3F  plan-1  HNAL  0.020

