# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 15:16:45 2021
#   Inital geometry file: a 72 line input string
#   Ligand name: 2,3,5,6,7,8-hexahydro-1~{H}-cyclopenta[b]quinolin-9-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1c2CCCCc2nc3CCCc13
#
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
 R9W  R9W  2,3,5,6,7,8-hexahydro-1~{H}-cyclopenta[b]quinolin-9-amine  ligand  30  14  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_R9W
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
 R9W  C1   C  CH2   0  -0.440  6.9161  33.4100  -1.2883
 R9W  C2   C  CH2   0  -0.446  7.5266  32.4171  -2.2633
 R9W  C3   C  CH2   0  -0.499  7.5765  31.0383  -1.6236
 R9W  C4   C  CR6   0   0.157  6.2659  30.6199  -1.0081
 R9W  C5   C  CR6   0  -0.025  5.2839  31.5599  -0.7056
 R9W  C6   C  CH2   0  -0.512  5.4757  33.0318  -0.9686
 R9W  C7   C  CR6   0   0.327  4.0628  31.1052  -0.1577
 R9W  C8   C  CR56  0  -0.024  3.9482  29.7409   0.1020
 R9W  C9   C  CH2   0  -0.498  2.7995  28.9645   0.6757
 R9W  C10  C  CH2   0  -0.459  3.4532  27.6146   1.0331
 R9W  C11  C  CH2   0  -0.497  4.6618  27.4787   0.0941
 R9W  C12  C  CR56  0   0.154  5.0034  28.9090  -0.2257
 R9W  N1   N  N     0  -0.486  6.1372  29.3061  -0.7774
 R9W  N2   N  NH2   0  -0.855  3.0183  31.9535   0.0661
 R9W  H1   H  HCH2  0   0.222  7.5089  33.4180  -0.3684
 R9W  H2   H  HCH2  0   0.236  6.9449  34.4251  -1.6884
 R9W  H3   H  HCH2  0   0.235  8.5313  32.7284  -2.5559
 R9W  H4   H  HCH2  0   0.221  6.9283  32.3834  -3.1795
 R9W  H5   H  HCH2  0   0.243  7.8767  30.2801  -2.3501
 R9W  H6   H  HCH2  0   0.239  8.3461  31.0291  -0.8435
 R9W  H7   H  HCH2  0   0.238  5.1459  33.6125  -0.1005
 R9W  H8   H  HCH2  0   0.242  4.8255  33.3420  -1.7954
 R9W  H9   H  HCH2  0   0.239  2.3416  29.4383   1.5479
 R9W  H10  H  HCH2  0   0.243  2.0035  28.8391  -0.0662
 R9W  H11  H  HCH2  0   0.236  2.7573  26.7803   0.9537
 R9W  H12  H  HCH2  0   0.238  3.8027  27.6496   2.0667
 R9W  H13  H  HCH2  0   0.245  4.3950  26.9480  -0.8259
 R9W  H14  H  HCH2  0   0.245  5.4940  26.9352   0.5438
 R9W  H15  H  HNH2  0   0.389  2.2877  31.6390   0.6829
 R9W  H16  H  HNH2  0   0.392  3.2039  32.9392   0.1435

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
 R9W  C2   C3   single    1.521  0.020  1.521
 R9W  C2   C1   single    1.520  0.020  1.520
 R9W  C3   C4   single    1.507  0.020  1.507
 R9W  C1   C6   single    1.523  0.020  1.523
 R9W  C4   N1   aromatic  1.340  0.020  1.340
 R9W  C4   C5   aromatic  1.393  0.020  1.393
 R9W  C6   C5   single    1.508  0.020  1.508
 R9W  N1   C12  aromatic  1.322  0.020  1.322
 R9W  C5   C7   aromatic  1.414  0.020  1.414
 R9W  C12  C8   aromatic  1.383  0.020  1.383
 R9W  C12  C11  single    1.505  0.020  1.505
 R9W  C7   C8   aromatic  1.394  0.020  1.394
 R9W  C7   N2   single    1.364  0.020  1.364
 R9W  C8   C9   single    1.500  0.020  1.500
 R9W  C11  C10  single    1.537  0.020  1.537
 R9W  C9   C10  single    1.542  0.020  1.542
 R9W  C1   H1   single    0.970  0.020  1.090
 R9W  C1   H2   single    0.970  0.020  1.090
 R9W  C2   H3   single    0.970  0.020  1.090
 R9W  C2   H4   single    0.970  0.020  1.090
 R9W  C3   H5   single    0.970  0.020  1.090
 R9W  C3   H6   single    0.970  0.020  1.090
 R9W  C6   H7   single    0.970  0.020  1.090
 R9W  C6   H8   single    0.970  0.020  1.090
 R9W  C9   H9   single    0.970  0.020  1.090
 R9W  C9   H10  single    0.970  0.020  1.090
 R9W  C10  H11  single    0.970  0.020  1.090
 R9W  C10  H12  single    0.970  0.020  1.090
 R9W  C11  H13  single    0.970  0.020  1.090
 R9W  C11  H14  single    0.970  0.020  1.090
 R9W  N2   H15  single    0.890  0.020  1.040
 R9W  N2   H16  single    0.890  0.020  1.040

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
 R9W  H2   C1   H1   106.67  3.000
 R9W  H2   C1   C6   109.44  3.000
 R9W  H1   C1   C6   109.73  3.000
 R9W  H2   C1   C2   111.22  3.000
 R9W  H1   C1   C2   109.06  3.000
 R9W  C6   C1   C2   110.63  3.000
 R9W  H4   C2   H3   106.71  3.000
 R9W  H4   C2   C3   110.00  3.000
 R9W  H3   C2   C3   109.94  3.000
 R9W  H4   C2   C1   109.72  3.000
 R9W  H3   C2   C1   110.81  3.000
 R9W  C3   C2   C1   109.61  3.000
 R9W  H6   C3   H5   105.94  3.000
 R9W  H6   C3   C4   108.52  3.000
 R9W  H5   C3   C4   108.54  3.000
 R9W  H6   C3   C2   109.28  3.000
 R9W  H5   C3   C2   111.01  3.000
 R9W  C4   C3   C2   113.27  3.000
 R9W  N1   C4   C5   123.82  3.000
 R9W  C5   C4   C3   120.96  3.000
 R9W  N1   C4   C3   115.21  3.000
 R9W  C7   C5   C6   119.44  3.000
 R9W  C7   C5   C4   118.44  3.000
 R9W  C6   C5   C4   122.11  3.000
 R9W  H8   C6   H7   105.61  3.000
 R9W  H8   C6   C5   109.41  3.000
 R9W  H7   C6   C5   109.94  3.000
 R9W  H8   C6   C1   109.40  3.000
 R9W  H7   C6   C1   108.63  3.000
 R9W  C5   C6   C1   113.54  3.000
 R9W  N2   C7   C8   121.02  3.000
 R9W  N2   C7   C5   121.67  3.000
 R9W  C8   C7   C5   117.27  3.000
 R9W  C12  C8   C9   111.31  3.000
 R9W  C9   C8   C7   129.85  3.000
 R9W  C12  C8   C7   118.81  3.000
 R9W  H10  C9   H9   106.60  3.000
 R9W  H10  C9   C10  111.40  3.000
 R9W  H9   C9   C10  111.85  3.000
 R9W  H10  C9   C8   110.89  3.000
 R9W  H9   C9   C8   113.67  3.000
 R9W  C10  C9   C8   102.54  3.000
 R9W  H12  C10  H11  107.34  3.000
 R9W  H12  C10  C11  109.24  3.000
 R9W  H11  C10  C11  112.96  3.000
 R9W  H12  C10  C9   109.10  3.000
 R9W  H11  C10  C9   112.51  3.000
 R9W  C11  C10  C9   105.62  3.000
 R9W  H14  C11  H13  106.90  3.000
 R9W  H14  C11  C12  112.83  3.000
 R9W  H13  C11  C12  109.72  3.000
 R9W  H14  C11  C10  113.09  3.000
 R9W  H13  C11  C10  111.38  3.000
 R9W  C12  C11  C10  102.96  3.000
 R9W  N1   C12  C11  124.67  3.000
 R9W  C11  C12  C8   110.37  3.000
 R9W  N1   C12  C8   124.93  3.000
 R9W  C12  N1   C4   116.66  3.000
 R9W  H16  N2   H15  113.13  3.000
 R9W  H16  N2   C7   118.73  3.000
 R9W  H15  N2   C7   117.52  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
 R9W  CONST_01  C8   C12  N1   C4      0.00   0.0  0
 R9W  CONST_02  C8   C7   C5   C4      0.00   0.0  0
 R9W  CONST_03  C12  N1   C4   C5      0.00   0.0  0
 R9W  CONST_04  C12  C8   C7   C5      0.00   0.0  0
 R9W  CONST_05  N1   C4   C5   C7      0.00   0.0  0
 R9W  CONST_06  N1   C12  C8   C7      0.00   0.0  0
 R9W  CONST_07  N2   C7   C5   C4    180.00   0.0  0
 R9W  CONST_08  N2   C7   C5   C6      0.00   0.0  0
 R9W  CONST_09  N2   C7   C8   C9      0.00   0.0  0
 R9W  CONST_10  N2   C7   C8   C12   180.00   0.0  0
 R9W  Var_01    C4   C3   C2   C1     49.45  30.0  1
 R9W  Var_02    C4   C5   C6   C1    -12.88  30.0  1
 R9W  Var_03    N1   C4   C3   C2    161.86  30.0  1
 R9W  Var_04    C5   C6   C1   C2     44.15  30.0  1
 R9W  Var_05    C6   C1   C2   C3    -62.97  30.0  1
 R9W  Var_06    C10  C9   C8   C7   -165.76  30.0  1
 R9W  Var_07    C10  C11  C12  C8    -16.44  30.0  1
 R9W  Var_08    C11  C10  C9   C8    -25.50  30.0  1
 R9W  Var_09    C12  C11  C10  C9     25.72  30.0  1

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
 R9W  plan-1  C3   0.020
 R9W  plan-1  C4   0.020
 R9W  plan-1  C5   0.020
 R9W  plan-1  C6   0.020
 R9W  plan-1  C7   0.020
 R9W  plan-1  C8   0.020
 R9W  plan-1  C9   0.020
 R9W  plan-1  C11  0.020
 R9W  plan-1  C12  0.020
 R9W  plan-1  N1   0.020
 R9W  plan-1  N2   0.020
 R9W  plan-2  C7   0.020
 R9W  plan-2  N2   0.020
 R9W  plan-2  H15  0.020
 R9W  plan-2  H16  0.020

