# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 09:07:30 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: (1R,5S)-1,2,3,4,5,6-hexahydro-8H-1,5-methanopyrido[1,2-a][1,5]diazocin-8-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1C=CC=C2[C@H]3CNC[C@H](C3)CN12
#
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
 C5E  C5E  (1R,5S)-1,2,3,4,5,6-hexahydro-8H-1,5-methanopyrido[1,2-a][1,5]diazocin-8-one  ligand  28  14  .  2021-08-07  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C5E
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
 C5E  O     O  O     0  -0.528  -2.2696  -2.0127  -0.0274
 C5E  C     C  CR6   0   0.554  -1.9850  -0.8156  -0.0534
 C5E  N     N  NR6   0  -0.567  -0.6574  -0.4225  -0.2663
 C5E  C5    C  CH2   0  -0.288   0.2807  -1.5386  -0.4788
 C5E  C6    C  CH1   0  -0.296   1.7462  -1.1385  -0.5613
 C5E  C10   C  CH2   0  -0.312   2.4110  -0.9566   0.8080
 C5E  N1    N  NH1   0  -0.582   1.9337   0.1790   1.5764
 C5E  C9    C  CH2   0  -0.298   1.8727   1.3923   0.7920
 C5E  C8    C  CH1   0  -0.360   1.1658   1.2254  -0.5695
 C5E  C7    C  CH2   0  -0.445   1.8750   0.1430  -1.3699
 C5E  C4    C  CR6   0   0.446  -0.2806   0.8848  -0.3579
 C5E  C3    C  CR16  0  -0.429  -1.2064   1.8792  -0.2134
 C5E  C2    C  CR16  0  -0.108  -2.5491   1.5480   0.0363
 C5E  C1    C  CR16  0  -0.467  -2.9300   0.2455   0.1190
 C5E  H1    H  HCR6  0   0.263  -3.9584  -0.0350   0.3011
 C5E  H51C  H  HCH2  0   0.262   0.1295  -2.2620   0.3227
 C5E  H52C  H  HCH2  0   0.267  -0.0115  -2.0335  -1.4071
 C5E  H6    H  HCH1  0   0.263   2.2574  -1.9614  -1.0675
 C5E  H101  H  HCH2  0   0.243   2.2873  -1.8593   1.4101
 C5E  H102  H  HCH2  0   0.230   3.4882  -0.8350   0.6447
 C5E  H71C  H  HCH2  0   0.252   2.9249   0.4117  -1.5108
 C5E  H72C  H  HCH2  0   0.252   1.4355   0.0318  -2.3647
 C5E  HA    H  HNH1  0   0.351   1.0305  -0.0216   1.9866
 C5E  H91C  H  HCH2  0   0.251   1.3819   2.1706   1.3790
 C5E  H92C  H  HCH2  0   0.236   2.8927   1.7391   0.5922
 C5E  H8    H  HCH1  0   0.274   1.2024   2.1841  -1.0911
 C5E  H2    H  HCR6  0   0.270  -3.2820   2.3357   0.1569
 C5E  H3    H  HCR6  0   0.265  -0.8888   2.9090  -0.2923

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
 C5E  O    C     double  1.231  0.020  1.231
 C5E  C    N     single  1.401  0.020  1.401
 C5E  C    C1    single  1.431  0.020  1.431
 C5E  N    C5    single  1.473  0.020  1.473
 C5E  N    C4    single  1.364  0.020  1.364
 C5E  C5   C6    single  1.521  0.020  1.521
 C5E  C6   C10   single  1.533  0.020  1.533
 C5E  C6   C7    single  1.521  0.020  1.521
 C5E  C10  N1    single  1.452  0.020  1.452
 C5E  N1   C9    single  1.446  0.020  1.446
 C5E  C9   C8    single  1.543  0.020  1.543
 C5E  C8   C7    single  1.522  0.020  1.522
 C5E  C8   C4    single  1.501  0.020  1.501
 C5E  C4   C3    double  1.366  0.020  1.366
 C5E  C3   C2    single  1.405  0.020  1.405
 C5E  C2   C1    double  1.360  0.020  1.360
 C5E  C1   H1    single  0.930  0.020  1.080
 C5E  C5   H51C  single  0.970  0.020  1.090
 C5E  C5   H52C  single  0.970  0.020  1.090
 C5E  C6   H6    single  0.970  0.020  1.090
 C5E  C10  H101  single  0.970  0.020  1.090
 C5E  C10  H102  single  0.970  0.020  1.090
 C5E  C7   H71C  single  0.970  0.020  1.090
 C5E  C7   H72C  single  0.970  0.020  1.090
 C5E  N1   HA    single  0.890  0.020  1.040
 C5E  C9   H91C  single  0.970  0.020  1.090
 C5E  C9   H92C  single  0.970  0.020  1.090
 C5E  C8   H8    single  0.970  0.020  1.090
 C5E  C3   H3    single  0.930  0.020  1.080
 C5E  C2   H2    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
 C5E  C1    C    N     115.85  3.000
 C5E  C1    C    O     124.45  3.000
 C5E  N     C    O     119.69  3.000
 C5E  C4    N    C5    122.73  3.000
 C5E  C4    N    C     122.76  3.000
 C5E  C5    N    C     114.38  3.000
 C5E  H52C  C5   H51C  106.68  3.000
 C5E  H52C  C5   C6    109.32  3.000
 C5E  H51C  C5   C6    110.36  3.000
 C5E  H52C  C5   N     107.19  3.000
 C5E  H51C  C5   N     107.96  3.000
 C5E  C6    C5   N     114.96  3.000
 C5E  H6    C6   C7    110.40  3.000
 C5E  H6    C6   C10   107.47  3.000
 C5E  C7    C6   C10   109.77  3.000
 C5E  H6    C6   C5    106.13  3.000
 C5E  C7    C6   C5    109.39  3.000
 C5E  C10   C6   C5    113.61  3.000
 C5E  H102  C10  H101  106.56  3.000
 C5E  H102  C10  N1    108.37  3.000
 C5E  H101  C10  N1    108.51  3.000
 C5E  H102  C10  C6    107.84  3.000
 C5E  H101  C10  C6    110.20  3.000
 C5E  N1    C10  C6    115.03  3.000
 C5E  HA    N1   C9    110.40  3.000
 C5E  HA    N1   C10   110.67  3.000
 C5E  C9    N1   C10   112.52  3.000
 C5E  H92C  C9   H91C  106.91  3.000
 C5E  H92C  C9   C8    107.45  3.000
 C5E  H91C  C9   C8    110.22  3.000
 C5E  H92C  C9   N1    108.99  3.000
 C5E  H91C  C9   N1    109.00  3.000
 C5E  C8    C9   N1    114.03  3.000
 C5E  H8    C8   C4    107.39  3.000
 C5E  H8    C8   C7    110.96  3.000
 C5E  C4    C8   C7    111.21  3.000
 C5E  H8    C8   C9    108.13  3.000
 C5E  C4    C8   C9    109.98  3.000
 C5E  C7    C8   C9    109.12  3.000
 C5E  H72C  C7   H71C  107.09  3.000
 C5E  H72C  C7   C8    111.32  3.000
 C5E  H71C  C7   C8    109.92  3.000
 C5E  H72C  C7   C6    111.35  3.000
 C5E  H71C  C7   C6    110.92  3.000
 C5E  C8    C7   C6    106.28  3.000
 C5E  C3    C4   C8    120.18  3.000
 C5E  C3    C4   N     120.22  3.000
 C5E  C8    C4   N     119.56  3.000
 C5E  H3    C3   C2    121.22  3.000
 C5E  H3    C3   C4    119.13  3.000
 C5E  C2    C3   C4    119.65  3.000
 C5E  H2    C2   C1    120.04  3.000
 C5E  H2    C2   C3    119.68  3.000
 C5E  C1    C2   C3    120.28  3.000
 C5E  H1    C1   C2    121.68  3.000
 C5E  H1    C1   C     117.12  3.000
 C5E  C2    C1   C     121.19  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
 C5E  CONST_01  C1  C   N    C5    180.00   0.0  0
 C5E  CONST_02  C1  C   N    C4      0.00   0.0  0
 C5E  CONST_03  C5  N   C    O       0.00   0.0  0
 C5E  CONST_04  C4  N   C    O     180.00   0.0  0
 C5E  Var_01    C6  C5  N    C    -173.69  30.0  1
 C5E  Var_02    C9  N1  C10  C6    -47.53  30.0  3
 C5E  Var_03    C8  C9  N1   C10    48.70  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
 C5E  chir_01  C6  C5  C10  C7  positiv
 C5E  chir_02  C8  C4  C7   C9  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
 C5E  plan-1  O   0.020
 C5E  plan-1  C   0.020
 C5E  plan-1  N   0.020
 C5E  plan-1  C5  0.020
 C5E  plan-1  C8  0.020
 C5E  plan-1  C4  0.020
 C5E  plan-1  C3  0.020
 C5E  plan-1  C2  0.020
 C5E  plan-1  C1  0.020
 C5E  plan-1  H1  0.020
 C5E  plan-1  H2  0.020
 C5E  plan-1  H3  0.020

