# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 19:15:32 2022
#   Inital geometry file: a 118 line input string
#   Ligand name: 7-[(1R,5S,6s)-6-amino-3-azabicyclo[3.1.0]hex-3-yl]-1-(2,4-difluorophenyl)-6-fluoro-4-oxo-1,4-dihydro-1,8-naphthyridine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1[C@@H]2CN(C[C@H]12)c3nc4N(C=C(C(O)=O)C(=O)c4cc3F)c5ccc(F)cc5F
#
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
 TR6  TR6  '7-[(1R,5S,6s)-6-amino-3-azabicyclo[3.1.0]hex-3-yl]-1-(2,4-difluorophenyl)-6-fluoro-4-oxo-1,4-dihydro-1,8-naphthyridine-3-carboxylic acid'  ligand  44  30  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_TR6
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
 TR6  C01   C  CR16   0  -0.234   1.0979  -2.6261  -1.2754
 TR6  C02   C  CR16   0  -0.428   0.5261  -3.8883  -1.3365
 TR6  C03   C  CR6    0   0.553  -0.2529  -4.3054  -0.2756
 TR6  F04   F  F      0  -0.305  -0.8167  -5.5169  -0.3188
 TR6  C05   C  CR16   0  -0.574  -0.4739  -3.5205   0.8414
 TR6  C06   C  CR6    0   0.586   0.1236  -2.2784   0.8737
 TR6  F07   F  F      0  -0.290  -0.0501  -1.5054   1.9441
 TR6  C08   C  CR6    0   0.085   0.9063  -1.8114  -0.1716
 TR6  N09   N  NR6    0  -0.608   1.5127  -0.5314  -0.0966
 TR6  C10   C  CR66   0   0.498   0.7410   0.6084  -0.1840
 TR6  N11   N  N      0  -0.505  -0.5607   0.4342  -0.3276
 TR6  C12   C  CR6    0   0.406  -1.3791   1.4756  -0.4137
 TR6  N13   N  NR5    0  -0.515  -2.6923   1.2030  -0.5134
 TR6  C14   C  CH2    0  -0.253  -3.1343  -0.1893  -0.5932
 TR6  C15   C  CR15   0  -0.297  -4.6352  -0.1076  -0.5404
 TR6  C16   C  CH1    0  -0.073  -5.2313   0.5963   0.6395
 TR6  N17   N  NH2    0  -0.807  -6.5808   0.2580   0.9724
 TR6  C18   C  CR15   0  -0.295  -5.0265   1.3332  -0.6474
 TR6  C19   C  CH2    0  -0.264  -3.7714   2.1573  -0.7693
 TR6  C20   C  CR6    0   0.426  -0.8135   2.7839  -0.3894
 TR6  C21   C  CR16   0  -0.347   0.5247   2.9586  -0.2500
 TR6  C22   C  CR66   0  -0.183   1.3753   1.8459  -0.1315
 TR6  C23   C  CR6    0   0.390   2.8241   1.9998   0.0197
 TR6  C24   C  CR6    0  -0.390   3.5537   0.7410   0.0939
 TR6  C25   C  CR16   0   0.021   2.8592  -0.4259   0.0336
 TR6  C26   C  C      0   0.410   5.0667   0.6301   0.2454
 TR6  O27   O  OC    -1  -0.581   5.7163   1.6848   0.3258
 TR6  O28   O  O      0  -0.603   5.5305  -0.5296   0.2779
 TR6  O29   O  O      0  -0.462   3.3194   3.1233   0.0740
 TR6  F30   F  F      0  -0.310  -1.6033   3.8652  -0.5124
 TR6  H011  H  HCR6   0   0.293   1.7013  -2.2694  -2.0999
 TR6  H021  H  HCR6   0   0.293   0.6788  -4.5274  -2.1952
 TR6  H051  H  HCR6   0   0.311  -1.0811  -3.8687   1.6666
 TR6  H141  H  HCH2   0   0.243  -2.7982  -0.6559  -1.5247
 TR6  H142  H  HCH2   0   0.251  -2.7079  -0.7669   0.2289
 TR6  H151  H  HCR5   0   0.268  -5.2111  -0.8848  -1.0261
 TR6  H161  H  HCH1   0   0.231  -4.5413   0.8417   1.4514
 TR6  H171  H  HNH2   0   0.348  -6.5933  -0.5314   1.6055
 TR6  H172  H  HNH2   0   0.348  -7.0199   1.0266   1.4628
 TR6  H181  H  HCR5   0   0.270  -5.8967   1.6429  -1.2119
 TR6  H191  H  HCH2   0   0.254  -3.7572   2.9728  -0.0469
 TR6  H192  H  HCH2   0   0.247  -3.6970   2.5859  -1.7729
 TR6  H211  H  HCR6   0   0.287   0.9360   3.9601  -0.2317
 TR6  H251  H  HCR6   0   0.306   3.3898  -1.3655   0.0970

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
 TR6  F30  C20   single    1.345  0.020  1.345
 TR6  O29  C23   double    1.229  0.020  1.229
 TR6  C21  C20   aromatic  1.357  0.020  1.357
 TR6  C21  C22   aromatic  1.406  0.020  1.406
 TR6  N17  C16   single    1.431  0.020  1.431
 TR6  C20  C12   aromatic  1.426  0.020  1.426
 TR6  F07  C06   single    1.332  0.020  1.332
 TR6  C16  C18   single    1.497  0.020  1.497
 TR6  C16  C15   single    1.498  0.020  1.498
 TR6  C23  C22   single    1.465  0.020  1.465
 TR6  C23  C24   single    1.457  0.020  1.457
 TR6  O28  C26   deloc     1.249  0.020  1.249
 TR6  C22  C10   aromatic  1.392  0.020  1.392
 TR6  C19  N13   single    1.463  0.020  1.463
 TR6  C19  C18   single    1.506  0.020  1.506
 TR6  C12  N13   single    1.345  0.020  1.345
 TR6  C12  N11   aromatic  1.327  0.020  1.327
 TR6  C26  C24   single    1.525  0.020  1.525
 TR6  C26  O27   deloc     1.241  0.020  1.241
 TR6  N13  C14   single    1.463  0.020  1.463
 TR6  C24  C25   double    1.359  0.020  1.359
 TR6  C18  C15   single    1.497  0.020  1.497
 TR6  C10  N11   aromatic  1.321  0.020  1.321
 TR6  C10  N09   single    1.379  0.020  1.379
 TR6  C06  C05   aromatic  1.379  0.020  1.379
 TR6  C06  C08   aromatic  1.387  0.020  1.387
 TR6  C25  N09   single    1.357  0.020  1.357
 TR6  N09  C08   single    1.418  0.020  1.418
 TR6  C14  C15   single    1.504  0.020  1.504
 TR6  C05  C03   aromatic  1.383  0.020  1.383
 TR6  C08  C01   aromatic  1.385  0.020  1.385
 TR6  C03  F04   single    1.337  0.020  1.337
 TR6  C03  C02   aromatic  1.381  0.020  1.381
 TR6  C01  C02   aromatic  1.387  0.020  1.387
 TR6  C01  H011  single    0.930  0.020  1.080
 TR6  C02  H021  single    0.930  0.020  1.080
 TR6  C05  H051  single    0.930  0.020  1.080
 TR6  C14  H141  single    0.970  0.020  1.090
 TR6  C14  H142  single    0.970  0.020  1.090
 TR6  C15  H151  single    0.970  0.020  1.090
 TR6  C16  H161  single    0.970  0.020  1.090
 TR6  N17  H171  single    0.890  0.020  1.040
 TR6  N17  H172  single    0.890  0.020  1.040
 TR6  C18  H181  single    0.970  0.020  1.090
 TR6  C19  H191  single    0.970  0.020  1.090
 TR6  C19  H192  single    0.970  0.020  1.090
 TR6  C21  H211  single    0.930  0.020  1.080
 TR6  C25  H251  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
 TR6  H011  C01  C08   119.36  3.000
 TR6  H011  C01  C02   119.75  3.000
 TR6  C08   C01  C02   120.88  3.000
 TR6  H021  C02  C03   120.75  3.000
 TR6  H021  C02  C01   120.97  3.000
 TR6  C03   C02  C01   118.27  3.000
 TR6  C05   C03  F04   118.23  3.000
 TR6  F04   C03  C02   119.13  3.000
 TR6  C05   C03  C02   122.64  3.000
 TR6  H051  C05  C06   121.02  3.000
 TR6  H051  C05  C03   121.53  3.000
 TR6  C06   C05  C03   117.45  3.000
 TR6  C08   C06  F07   118.95  3.000
 TR6  C08   C06  C05   122.03  3.000
 TR6  F07   C06  C05   119.03  3.000
 TR6  N09   C08  C06   120.35  3.000
 TR6  N09   C08  C01   120.92  3.000
 TR6  C06   C08  C01   118.73  3.000
 TR6  C25   N09  C10   119.81  3.000
 TR6  C25   N09  C08   119.96  3.000
 TR6  C10   N09  C08   120.21  3.000
 TR6  C22   C10  N11   124.79  3.000
 TR6  N11   C10  N09   116.69  3.000
 TR6  C22   C10  N09   118.52  3.000
 TR6  C12   N11  C10   120.74  3.000
 TR6  C20   C12  N13   125.08  3.000
 TR6  N13   C12  N11   116.60  3.000
 TR6  C20   C12  N11   118.32  3.000
 TR6  C19   N13  C14   112.85  3.000
 TR6  C14   N13  C12   119.47  3.000
 TR6  C19   N13  C12   126.94  3.000
 TR6  H142  C14  H141  107.18  3.000
 TR6  H142  C14  C15   113.09  3.000
 TR6  H141  C14  C15   111.06  3.000
 TR6  H142  C14  N13   110.15  3.000
 TR6  H141  C14  N13   111.06  3.000
 TR6  C15   C14  N13   104.35  3.000
 TR6  H151  C15  C18   121.33  3.000
 TR6  H151  C15  C16   118.64  3.000
 TR6  C18   C15  C16    59.99  3.000
 TR6  H151  C15  C14   118.44  3.000
 TR6  C18   C15  C14   108.10  3.000
 TR6  C16   C15  C14   116.77  3.000
 TR6  H161  C16  C18   116.20  3.000
 TR6  H161  C16  N17   118.39  3.000
 TR6  C18   C16  N17   116.46  3.000
 TR6  H161  C16  C15   116.06  3.000
 TR6  C18   C16  C15    59.98  3.000
 TR6  N17   C16  C15   116.59  3.000
 TR6  H172  N17  H171  106.49  3.000
 TR6  H172  N17  C16   110.03  3.000
 TR6  H171  N17  C16   109.98  3.000
 TR6  H181  C18  C19   118.10  3.000
 TR6  H181  C18  C16   118.63  3.000
 TR6  C19   C18  C16   116.93  3.000
 TR6  H181  C18  C15   121.52  3.000
 TR6  C19   C18  C15   108.34  3.000
 TR6  C16   C18  C15    60.03  3.000
 TR6  H192  C19  H191  108.31  3.000
 TR6  H192  C19  C18   110.20  3.000
 TR6  H191  C19  C18   111.51  3.000
 TR6  H192  C19  N13   111.46  3.000
 TR6  H191  C19  N13   111.25  3.000
 TR6  C18   C19  N13   104.10  3.000
 TR6  F30   C20  C21   119.03  3.000
 TR6  C21   C20  C12   120.75  3.000
 TR6  F30   C20  C12   120.22  3.000
 TR6  H211  C21  C22   120.06  3.000
 TR6  H211  C21  C20   119.70  3.000
 TR6  C22   C21  C20   120.24  3.000
 TR6  C23   C22  C21   121.61  3.000
 TR6  C23   C22  C10   123.24  3.000
 TR6  C21   C22  C10   115.15  3.000
 TR6  O29   C23  C24   125.86  3.000
 TR6  C24   C23  C22   114.19  3.000
 TR6  O29   C23  C22   119.95  3.000
 TR6  C26   C24  C25   116.68  3.000
 TR6  C25   C24  C23   118.92  3.000
 TR6  C26   C24  C23   124.40  3.000
 TR6  H251  C25  C24   119.52  3.000
 TR6  H251  C25  N09   115.16  3.000
 TR6  C24   C25  N09   125.31  3.000
 TR6  O28   C26  O27   126.35  3.000
 TR6  O27   C26  C24   117.64  3.000
 TR6  O28   C26  C24   116.01  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
 TR6  CONST_01  C05   C06  C08  C01     0.00   0.0  0
 TR6  CONST_02  C05   C03  C02  C01     0.00   0.0  0
 TR6  CONST_03  C06   C05  C03  C02     0.00   0.0  0
 TR6  CONST_04  C06   C08  C01  C02     0.00   0.0  0
 TR6  CONST_05  C08   C06  C05  C03     0.00   0.0  0
 TR6  CONST_06  C08   C01  C02  C03     0.00   0.0  0
 TR6  CONST_07  C20   C21  C22  C10     0.00   0.0  0
 TR6  CONST_08  C20   C12  N11  C10     0.00   0.0  0
 TR6  CONST_09  C21   C20  C12  N11     0.00   0.0  0
 TR6  CONST_10  C21   C22  C10  N11     0.00   0.0  0
 TR6  CONST_11  C22   C21  C20  C12     0.00   0.0  0
 TR6  CONST_12  C22   C10  N11  C12     0.00   0.0  0
 TR6  CONST_13  N09   C08  C01  C02   180.00   0.0  0
 TR6  CONST_14  N09   C08  C06  C05   180.00   0.0  0
 TR6  CONST_15  N13   C12  N11  C10   180.00   0.0  0
 TR6  CONST_16  C21   C20  C12  N13   180.00   0.0  0
 TR6  CONST_17  F07   C06  C08  C01   180.00   0.0  0
 TR6  CONST_18  F04   C03  C02  C01   180.00   0.0  0
 TR6  CONST_19  F07   C06  C05  C03   180.00   0.0  0
 TR6  CONST_20  C06   C05  C03  F04   180.00   0.0  0
 TR6  CONST_21  N09   C08  C06  F07     0.00   0.0  0
 TR6  CONST_22  F30   C20  C12  N11   180.00   0.0  0
 TR6  CONST_23  F30   C20  C12  N13     0.00   0.0  0
 TR6  CONST_24  F30   C20  C21  C22   180.00   0.0  0
 TR6  CONST_25  H051  C05  C03  C02   180.00   0.0  0
 TR6  CONST_26  H011  C01  C02  C03   180.00   0.0  0
 TR6  CONST_27  H021  C02  C03  C05   180.00   0.0  0
 TR6  CONST_28  H211  C21  C22  C10   180.00   0.0  0
 TR6  Var_01    C10   N09  C08  C01   110.07  30.0  2
 TR6  Var_02    C19   N13  C12  N11  -172.63  30.0  2
 TR6  Var_03    C18   C19  N13  C12  -174.82  30.0  1
 TR6  Var_04    C15   C14  N13  C12   174.00  30.0  1
 TR6  Var_05    C16   C18  C19  N13    56.22  30.0  1
 TR6  Var_06    C16   C15  C14  N13   -56.16  30.0  1
 TR6  Var_07    C18   C16  C15  C14    96.34  30.0  1
 TR6  Var_08    O28   C26  C24  C23  -179.23  30.0  3
 TR6  Var_09    H171  N17  C16  C15    88.51  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
 TR6  chir_01  C15  C16  C18  C14  both
 TR6  chir_02  C16  N17  C18  C15  both
 TR6  chir_03  C18  C15  C19  C16  both

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
 TR6  plan-1  C01   0.020
 TR6  plan-1  C02   0.020
 TR6  plan-1  C03   0.020
 TR6  plan-1  F04   0.020
 TR6  plan-1  C05   0.020
 TR6  plan-1  C06   0.020
 TR6  plan-1  F07   0.020
 TR6  plan-1  C08   0.020
 TR6  plan-1  N09   0.020
 TR6  plan-1  H011  0.020
 TR6  plan-1  H021  0.020
 TR6  plan-1  H051  0.020
 TR6  plan-2  C08   0.020
 TR6  plan-2  N09   0.020
 TR6  plan-2  C10   0.020
 TR6  plan-2  N11   0.020
 TR6  plan-2  C12   0.020
 TR6  plan-2  N13   0.020
 TR6  plan-2  C20   0.020
 TR6  plan-2  C21   0.020
 TR6  plan-2  C22   0.020
 TR6  plan-2  C23   0.020
 TR6  plan-2  C24   0.020
 TR6  plan-2  C25   0.020
 TR6  plan-2  C26   0.020
 TR6  plan-2  O29   0.020
 TR6  plan-2  F30   0.020
 TR6  plan-2  H211  0.020
 TR6  plan-2  H251  0.020
 TR6  plan-3  C24   0.020
 TR6  plan-3  C26   0.020
 TR6  plan-3  O27   0.020
 TR6  plan-3  O28   0.020

