# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 18:11:41 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: (7aR,8R)-8-amino-4-cyclopropyl-12-fluoro-1-oxo-4,7,7a,8,9,10-hexahydro-1H-pyrrolo[1',2':1,7]azepino[2,3-h]quinoline-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1CCN2[C@@H]1CC=Cc3c2c(F)cc4C(=O)C(=CN(C5CC5)c34)C(O)=O
#
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
 AF5  AF5  '(7aR,8R)-8-amino-4-cyclopropyl-12-fluoro-1-oxo-4,7,7a,8,9,10-hexahydro-1H-pyrrolo[1',2':1,7]azepino[2,3-h]quinoline-2-carboxylic acid'  ligand  46  27  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_AF5
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
 AF5  N01   N  NR6    0  -0.542  -1.6661  -1.1299  -0.1724
 AF5  C02   C  CH1    0  -0.112  -1.1371  -2.3878  -0.6748
 AF5  C03   C  CH2    0  -0.521  -1.9869  -3.4391  -1.3074
 AF5  C04   C  CH2    0  -0.479  -1.3445  -3.6868   0.0277
 AF5  C05   C  CR16   0   0.017  -2.9975  -0.9102  -0.1887
 AF5  C06   C  CR6    0  -0.378  -3.6173   0.2975  -0.0872
 AF5  C07   C  C      0   0.404  -5.1381   0.2934  -0.0457
 AF5  O08   O  OC    -1  -0.585  -5.7146   1.3824   0.1126
 AF5  O09   O  O      0  -0.605  -5.6886  -0.8231  -0.1618
 AF5  C10   C  CR6    0   0.389  -2.7955   1.4884  -0.0959
 AF5  O11   O  O      0  -0.468  -3.2070   2.6458  -0.1732
 AF5  C12   C  CR6    0  -0.148  -1.3516   1.2262   0.0126
 AF5  C13   C  CR6    0   0.323  -0.8113  -0.0608   0.0668
 AF5  C14   C  C      0  -0.083   0.5555  -0.2659   0.3960
 AF5  C15   C  C1     0  -0.206   0.9135  -1.5195   1.0668
 AF5  C16   C  C1     0  -0.236   2.0875  -2.1132   1.2993
 AF5  C17   C  CH2    0  -0.471   3.4310  -1.7523   0.7820
 AF5  C18   C  CH1    0  -0.102   3.3968  -0.5845  -0.1868
 AF5  N19   N  NT     0  -0.519   2.7948   0.6092   0.4099
 AF5  C20   C  CH2    0  -0.272   3.8098   1.6256   0.7169
 AF5  C21   C  CH2    0  -0.497   5.1223   0.8812   0.5509
 AF5  C22   C  CH1    0  -0.098   4.8034  -0.1010  -0.5756
 AF5  N23   N  NH2    0  -0.799   5.7316  -1.1835  -0.8194
 AF5  C24   C  C      0   0.201   1.4533   0.8242   0.3264
 AF5  C25   C  C      0   0.494   0.8700   2.1079   0.2034
 AF5  F26   F  F      0  -0.320   1.6578   3.2019   0.2041
 AF5  C27   C  C1     0  -0.489  -0.4712   2.3097   0.1090
 AF5  H021  H  HCH1   0   0.302  -0.1747  -2.2366  -1.1440
 AF5  H031  H  HCH2   0   0.267  -3.0634  -3.3404  -1.3430
 AF5  H032  H  HCH2   0   0.275  -1.5696  -3.9213  -2.1818
 AF5  H041  H  HCH2   0   0.265  -0.5073  -4.3684   0.1016
 AF5  H042  H  HCH2   0   0.267  -2.0000  -3.6784   0.8908
 AF5  H051  H  HCR6   0   0.291  -3.6206  -1.7845  -0.3006
 AF5  H151  H  H      0   0.259   0.0620  -2.0038   1.5294
 AF5  H161  H  H      0   0.242   2.0547  -3.0018   1.9212
 AF5  H172  H  HCH2   0   0.241   4.0943  -1.5278   1.6247
 AF5  H171  H  HCH2   0   0.244   3.8646  -2.6290   0.2892
 AF5  H181  H  HCH1   0   0.257   2.8228  -0.8739  -1.0732
 AF5  H201  H  HCH2   0   0.237   3.7862   2.4550   0.0102
 AF5  H202  H  HCH2   0   0.246   3.6686   2.0294   1.7205
 AF5  H211  H  HCH2   0   0.255   5.9412   1.5574   0.3051
 AF5  H212  H  HCH2   0   0.233   5.4022   0.3412   1.4595
 AF5  H221  H  HCH1   0   0.250   4.7138   0.4649  -1.5081
 AF5  H231  H  HNH2   0   0.354   6.5696  -0.8155  -1.2511
 AF5  H232  H  HNH2   0   0.345   6.0314  -1.5949   0.0568
 AF5  H271  H  H      0   0.273  -0.8555   3.3200   0.0550

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
 AF5  C16  C17   single    1.484  0.020  1.484
 AF5  C16  C15   double    1.336  0.020  1.336
 AF5  C17  C18   single    1.518  0.020  1.518
 AF5  C02  C04   single    1.491  0.020  1.491
 AF5  C02  N01   single    1.454  0.020  1.454
 AF5  C02  C03   single    1.493  0.020  1.493
 AF5  C04  C03   single    1.502  0.020  1.502
 AF5  C15  C14   single    1.466  0.020  1.466
 AF5  C21  C20   single    1.518  0.020  1.518
 AF5  C21  C22   single    1.528  0.020  1.528
 AF5  N01  C05   single    1.349  0.020  1.349
 AF5  N01  C13   single    1.390  0.020  1.390
 AF5  C18  N19   single    1.464  0.020  1.464
 AF5  C18  C22   single    1.537  0.020  1.537
 AF5  C14  C13   aromatic  1.421  0.020  1.421
 AF5  C14  C24   aromatic  1.414  0.020  1.414
 AF5  C20  N19   single    1.469  0.020  1.469
 AF5  C05  C06   double    1.361  0.020  1.361
 AF5  N19  C24   single    1.361  0.020  1.361
 AF5  C13  C12   aromatic  1.397  0.020  1.397
 AF5  O09  C07   deloc     1.250  0.020  1.250
 AF5  C24  C25   aromatic  1.415  0.020  1.415
 AF5  N23  C22   single    1.447  0.020  1.447
 AF5  C06  C07   single    1.521  0.020  1.521
 AF5  C06  C10   single    1.447  0.020  1.447
 AF5  C12  C10   single    1.472  0.020  1.472
 AF5  C12  C27   aromatic  1.399  0.020  1.399
 AF5  C07  O08   deloc     1.242  0.020  1.242
 AF5  C25  C27   aromatic  1.360  0.020  1.360
 AF5  C25  F26   single    1.348  0.020  1.348
 AF5  C10  O11   double    1.231  0.020  1.231
 AF5  C02  H021  single    0.970  0.020  1.090
 AF5  C03  H031  single    0.970  0.020  1.090
 AF5  C03  H032  single    0.970  0.020  1.090
 AF5  C04  H041  single    0.970  0.020  1.090
 AF5  C04  H042  single    0.970  0.020  1.090
 AF5  C05  H051  single    0.930  0.020  1.080
 AF5  C15  H151  single    0.930  0.020  1.080
 AF5  C16  H161  single    0.930  0.020  1.080
 AF5  C17  H172  single    0.970  0.020  1.090
 AF5  C17  H171  single    0.970  0.020  1.090
 AF5  C18  H181  single    0.970  0.020  1.090
 AF5  C20  H201  single    0.970  0.020  1.090
 AF5  C20  H202  single    0.970  0.020  1.090
 AF5  C21  H211  single    0.970  0.020  1.090
 AF5  C21  H212  single    0.970  0.020  1.090
 AF5  C22  H221  single    0.970  0.020  1.090
 AF5  N23  H231  single    0.890  0.020  1.040
 AF5  N23  H232  single    0.890  0.020  1.040
 AF5  C27  H271  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
 AF5  C13   N01  C05   118.93  3.000
 AF5  C13   N01  C02   120.08  3.000
 AF5  C05   N01  C02   119.71  3.000
 AF5  H021  C02  C04   116.74  3.000
 AF5  H021  C02  C03   114.92  3.000
 AF5  C04   C02  C03    60.45  3.000
 AF5  H021  C02  N01   110.66  3.000
 AF5  C03   C02  N01   123.27  3.000
 AF5  C04   C02  N01   122.69  3.000
 AF5  H032  C03  H031  113.45  3.000
 AF5  H032  C03  C04   118.67  3.000
 AF5  H031  C03  C04   118.03  3.000
 AF5  H032  C03  C02   115.89  3.000
 AF5  H031  C03  C02   121.09  3.000
 AF5  C04   C03  C02    59.73  3.000
 AF5  H042  C04  H041  114.74  3.000
 AF5  H042  C04  C03   116.60  3.000
 AF5  H041  C04  C03   119.70  3.000
 AF5  H042  C04  C02   116.90  3.000
 AF5  H041  C04  C02   118.24  3.000
 AF5  C03   C04  C02    59.81  3.000
 AF5  H051  C05  C06   117.62  3.000
 AF5  H051  C05  N01   116.03  3.000
 AF5  C06   C05  N01   126.35  3.000
 AF5  C10   C06  C07   124.76  3.000
 AF5  C10   C06  C05   118.11  3.000
 AF5  C07   C06  C05   117.05  3.000
 AF5  O09   C07  O08   126.18  3.000
 AF5  O08   C07  C06   117.71  3.000
 AF5  O09   C07  C06   116.11  3.000
 AF5  C12   C10  O11   120.02  3.000
 AF5  O11   C10  C06   125.76  3.000
 AF5  C12   C10  C06   114.21  3.000
 AF5  C27   C12  C13   117.86  3.000
 AF5  C27   C12  C10   118.97  3.000
 AF5  C13   C12  C10   123.13  3.000
 AF5  C14   C13  C12   120.94  3.000
 AF5  C12   C13  N01   117.66  3.000
 AF5  C14   C13  N01   121.37  3.000
 AF5  C24   C14  C15   121.78  3.000
 AF5  C24   C14  C13   119.22  3.000
 AF5  C15   C14  C13   117.66  3.000
 AF5  H151  C15  C16   114.69  3.000
 AF5  H151  C15  C14   112.68  3.000
 AF5  C16   C15  C14   132.39  3.000
 AF5  H161  C16  C17   115.23  3.000
 AF5  H161  C16  C15   115.92  3.000
 AF5  C17   C16  C15   128.81  3.000
 AF5  H171  C17  H172  105.69  3.000
 AF5  H171  C17  C18   109.73  3.000
 AF5  H172  C17  C18   110.30  3.000
 AF5  H171  C17  C16   108.69  3.000
 AF5  H172  C17  C16   109.26  3.000
 AF5  C18   C17  C16   112.90  3.000
 AF5  H181  C18  C22   110.97  3.000
 AF5  H181  C18  N19   109.27  3.000
 AF5  C22   C18  N19   102.87  3.000
 AF5  H181  C18  C17   108.98  3.000
 AF5  C22   C18  C17   112.51  3.000
 AF5  N19   C18  C17   112.12  3.000
 AF5  C24   N19  C20   125.77  3.000
 AF5  C24   N19  C18   120.60  3.000
 AF5  C20   N19  C18   111.43  3.000
 AF5  H202  C20  H201  108.18  3.000
 AF5  H202  C20  C21   113.21  3.000
 AF5  H201  C20  C21   108.72  3.000
 AF5  H202  C20  N19   111.04  3.000
 AF5  H201  C20  N19   112.09  3.000
 AF5  C21   C20  N19   103.61  3.000
 AF5  H212  C21  H211  107.54  3.000
 AF5  H212  C21  C22   110.40  3.000
 AF5  H211  C21  C22   112.91  3.000
 AF5  H212  C21  C20   111.88  3.000
 AF5  H211  C21  C20   111.71  3.000
 AF5  C22   C21  C20   102.43  3.000
 AF5  H221  C22  N23   107.21  3.000
 AF5  H221  C22  C21   108.23  3.000
 AF5  N23   C22  C21   118.11  3.000
 AF5  H221  C22  C18   107.65  3.000
 AF5  N23   C22  C18   113.23  3.000
 AF5  C21   C22  C18   101.93  3.000
 AF5  H232  N23  H231  105.76  3.000
 AF5  H232  N23  C22   110.36  3.000
 AF5  H231  N23  C22   109.34  3.000
 AF5  C25   C24  N19   123.69  3.000
 AF5  C25   C24  C14   116.22  3.000
 AF5  N19   C24  C14   120.07  3.000
 AF5  C27   C25  F26   117.13  3.000
 AF5  F26   C25  C24   119.68  3.000
 AF5  C27   C25  C24   123.18  3.000
 AF5  H271  C27  C25   119.49  3.000
 AF5  H271  C27  C12   119.73  3.000
 AF5  C25   C27  C12   120.70  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
 AF5  CONST_01  C24   C25  C27  C12    0.00   0.0  0
 AF5  CONST_02  C25   C27  C12  C13    0.00   0.0  0
 AF5  CONST_03  C27   C12  C13  C14    0.00   0.0  0
 AF5  CONST_04  F26   C25  C27  C12  180.00   0.0  0
 AF5  CONST_05  H271  C27  C12  C10    0.00   0.0  0
 AF5  Var_01    C03   C04  C02  N01  112.68  30.0  1
 AF5  Var_02    C05   N01  C02  C03    4.37  30.0  3
 AF5  Var_03    C22   C21  C20  N19   33.26  30.0  1
 AF5  Var_04    O09   C07  C06  C05   -2.70  30.0  2

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
 AF5  chir_02  C18  C17  N19  C22  negativ
 AF5  chir_03  C22  N23  C21  C18  positiv
 AF5  chir_04  C02  C04  N01  C03  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
 AF5  plan-1  N01   0.020
 AF5  plan-1  C02   0.020
 AF5  plan-1  C05   0.020
 AF5  plan-1  C06   0.020
 AF5  plan-1  C07   0.020
 AF5  plan-1  C10   0.020
 AF5  plan-1  O11   0.020
 AF5  plan-1  C12   0.020
 AF5  plan-1  C13   0.020
 AF5  plan-1  C14   0.020
 AF5  plan-1  C15   0.020
 AF5  plan-1  N19   0.020
 AF5  plan-1  C24   0.020
 AF5  plan-1  C25   0.020
 AF5  plan-1  F26   0.020
 AF5  plan-1  C27   0.020
 AF5  plan-1  H051  0.020
 AF5  plan-1  H271  0.020
 AF5  plan-2  C06   0.020
 AF5  plan-2  C07   0.020
 AF5  plan-2  O08   0.020
 AF5  plan-2  O09   0.020

