# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 15:43:13 2021
#   Inital geometry file: a 71 line input string
#   Ligand name: 1-(1-methyl-1,2,3,4-tetrahydroquinolin-6-yl)methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCCc2cc(CN)ccc12
#
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
 R9Y  R9Y  1-(1-methyl-1,2,3,4-tetrahydroquinolin-6-yl)methanamine  ligand  29  13  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_R9Y
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
 R9Y  C4   C  CR6   0   0.041  24.5288   0.7305  59.7019
 R9Y  C5   C  CR6   0   0.349  23.4518   1.4717  60.2287
 R9Y  C6   C  CR16  0  -0.355  23.7245   2.7581  60.7260
 R9Y  N1   N  NH2   0  -0.791  27.4632   4.4718  59.4714
 R9Y  C7   C  CR16  0  -0.289  24.9999   3.2951  60.6768
 R9Y  C8   C  CR6   0   0.085  26.0661   2.5781  60.1445
 R9Y  C9   C  CR16  0  -0.373  25.7938   1.3033  59.6627
 R9Y  C10  C  CH2   0  -0.350  27.4559   3.1546  60.0942
 R9Y  C3   C  CH2   0  -0.482  24.3246  -0.6719  59.1917
 R9Y  C2   C  CH2   0  -0.463  22.8648  -0.9355  58.8629
 R9Y  C1   C  CH2   0  -0.283  21.9922  -0.4638  60.0107
 R9Y  N    N  NT    0  -0.514  22.1716   0.9562  60.2351
 R9Y  C    C  CH3   0  -0.534  21.1394   1.6309  60.9810
 R9Y  H1   H  HCR6  0   0.256  22.9351   3.3552  61.1619
 R9Y  H2   H  HNH2  0   0.347  28.4074   4.8375  59.4743
 R9Y  H3   H  HNH2  0   0.338  27.2042   4.3808  58.4967
 R9Y  H5   H  HCR6  0   0.236  25.1640   4.2936  61.0642
 R9Y  H6   H  HCR6  0   0.231  26.6030   0.7196  59.2326
 R9Y  H7   H  HCH2  0   0.207  28.1175   2.4279  59.6024
 R9Y  H8   H  HCH2  0   0.226  27.8419   3.2713  61.1119
 R9Y  H9   H  HCH2  0   0.240  24.6544  -1.3866  59.9532
 R9Y  H10  H  HCH2  0   0.246  24.9579  -0.8480  58.3194
 R9Y  H11  H  HCH2  0   0.231  22.5755  -0.4069  57.9509
 R9Y  H12  H  HCH2  0   0.241  22.6955  -1.9988  58.6873
 R9Y  H13  H  HCH2  0   0.242  20.9410  -0.6402  59.7787
 R9Y  H14  H  HCH2  0   0.214  22.2220  -1.0483  60.9136
 R9Y  H15  H  HCH3  0   0.238  20.9943   2.6532  60.6270
 R9Y  H16  H  HCH3  0   0.248  20.1977   1.1048  60.8362
 R9Y  H17  H  HCH3  0   0.219  21.3394   1.6738  62.0590

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
 R9Y  C2   C3   single    1.519  0.020  1.519
 R9Y  C2   C1   single    1.517  0.020  1.517
 R9Y  N1   C10  single    1.457  0.020  1.457
 R9Y  C3   C4   single    1.506  0.020  1.506
 R9Y  C4   C9   aromatic  1.389  0.020  1.389
 R9Y  C4   C5   aromatic  1.410  0.020  1.410
 R9Y  C9   C8   aromatic  1.390  0.020  1.390
 R9Y  C1   N    single    1.449  0.020  1.449
 R9Y  C8   C10  single    1.505  0.020  1.505
 R9Y  C8   C7   aromatic  1.391  0.020  1.391
 R9Y  N    C5   single    1.380  0.020  1.380
 R9Y  N    C    single    1.441  0.020  1.441
 R9Y  C5   C6   aromatic  1.406  0.020  1.406
 R9Y  C7   C6   aromatic  1.385  0.020  1.385
 R9Y  C6   H1   single    0.930  0.020  1.080
 R9Y  N1   H2   single    0.890  0.020  1.040
 R9Y  N1   H3   single    0.890  0.020  1.040
 R9Y  C7   H5   single    0.930  0.020  1.080
 R9Y  C9   H6   single    0.930  0.020  1.080
 R9Y  C10  H7   single    0.970  0.020  1.090
 R9Y  C10  H8   single    0.970  0.020  1.090
 R9Y  C3   H9   single    0.970  0.020  1.090
 R9Y  C3   H10  single    0.970  0.020  1.090
 R9Y  C2   H11  single    0.970  0.020  1.090
 R9Y  C2   H12  single    0.970  0.020  1.090
 R9Y  C1   H13  single    0.970  0.020  1.090
 R9Y  C1   H14  single    0.970  0.020  1.090
 R9Y  C    H15  single    0.970  0.020  1.090
 R9Y  C    H16  single    0.970  0.020  1.090
 R9Y  C    H17  single    0.970  0.020  1.090

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
 R9Y  C3   C4   C9   119.86  3.000
 R9Y  C9   C4   C5   119.31  3.000
 R9Y  C3   C4   C5   120.83  3.000
 R9Y  N    C5   C6   121.34  3.000
 R9Y  C6   C5   C4   117.72  3.000
 R9Y  N    C5   C4   120.94  3.000
 R9Y  H1   C6   C7   118.19  3.000
 R9Y  H1   C6   C5   120.41  3.000
 R9Y  C7   C6   C5   121.40  3.000
 R9Y  H3   N1   H2   105.89  3.000
 R9Y  H3   N1   C10  109.20  3.000
 R9Y  H2   N1   C10  109.26  3.000
 R9Y  H5   C7   C8   119.72  3.000
 R9Y  H5   C7   C6   118.96  3.000
 R9Y  C8   C7   C6   121.32  3.000
 R9Y  C10  C8   C9   121.37  3.000
 R9Y  C10  C8   C7   121.54  3.000
 R9Y  C9   C8   C7   117.09  3.000
 R9Y  H6   C9   C8   118.95  3.000
 R9Y  H6   C9   C4   117.89  3.000
 R9Y  C8   C9   C4   123.15  3.000
 R9Y  H8   C10  H7   105.92  3.000
 R9Y  H8   C10  C8   109.59  3.000
 R9Y  H7   C10  C8   108.51  3.000
 R9Y  H8   C10  N1   107.41  3.000
 R9Y  H7   C10  N1   113.79  3.000
 R9Y  C8   C10  N1   111.41  3.000
 R9Y  H10  C3   H9   105.99  3.000
 R9Y  H10  C3   C2   110.87  3.000
 R9Y  H9   C3   C2   109.06  3.000
 R9Y  H10  C3   C4   110.00  3.000
 R9Y  H9   C3   C4   109.34  3.000
 R9Y  C2   C3   C4   111.41  3.000
 R9Y  H12  C2   H11  107.21  3.000
 R9Y  H12  C2   C1   109.61  3.000
 R9Y  H11  C2   C1   109.19  3.000
 R9Y  H12  C2   C3   110.67  3.000
 R9Y  H11  C2   C3   110.54  3.000
 R9Y  C1   C2   C3   109.57  3.000
 R9Y  H14  C1   H13  106.86  3.000
 R9Y  H14  C1   N    111.59  3.000
 R9Y  H13  C1   N    108.10  3.000
 R9Y  H14  C1   C2   109.62  3.000
 R9Y  H13  C1   C2   110.06  3.000
 R9Y  N    C1   C2   110.54  3.000
 R9Y  C    N    C1   116.76  3.000
 R9Y  C    N    C5   119.47  3.000
 R9Y  C1   N    C5   118.70  3.000
 R9Y  H17  C    H16  107.90  3.000
 R9Y  H17  C    H15  107.83  3.000
 R9Y  H16  C    H15  107.13  3.000
 R9Y  H17  C    N    113.35  3.000
 R9Y  H16  C    N    108.94  3.000
 R9Y  H15  C    N    111.45  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
 R9Y  CONST_01  C7   C8  C9   C4    0.00   0.0  0
 R9Y  CONST_02  C7   C6  C5   C4    0.00   0.0  0
 R9Y  CONST_03  C8   C9  C4   C5    0.00   0.0  0
 R9Y  CONST_04  C8   C7  C6   C5    0.00   0.0  0
 R9Y  CONST_05  C9   C4  C5   C6    0.00   0.0  0
 R9Y  CONST_06  C9   C8  C7   C6    0.00   0.0  0
 R9Y  CONST_07  C10  C8  C9   C4  180.00   0.0  0
 R9Y  CONST_08  C10  C8  C7   C6  180.00   0.0  0
 R9Y  CONST_09  H1   C6  C5   C4  180.00   0.0  0
 R9Y  CONST_10  H6   C9  C4   C5  180.00   0.0  0
 R9Y  CONST_11  H5   C7  C6   C5  180.00   0.0  0
 R9Y  Var_01    C1   C2  C3   C4  -47.72  30.0  1
 R9Y  Var_02    C1   N   C5   C4   15.34  30.0  1
 R9Y  Var_03    C2   C3  C4   C5   20.42  30.0  1
 R9Y  Var_04    C2   C1  N    C5  -44.15  30.0  1
 R9Y  Var_05    N    C1  C2   C3   60.09  30.0  1
 R9Y  Var_06    C9   C8  C10  N1  128.24  30.0  3
 R9Y  Var_07    H15  C   N    C5   59.77  30.0  3
 R9Y  Var_08    H2   N1  C10  C8  178.67  30.0  3

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
 R9Y  plan-1  C4   0.020
 R9Y  plan-1  C5   0.020
 R9Y  plan-1  C6   0.020
 R9Y  plan-1  C7   0.020
 R9Y  plan-1  C8   0.020
 R9Y  plan-1  C9   0.020
 R9Y  plan-1  C10  0.020
 R9Y  plan-1  C3   0.020
 R9Y  plan-1  N    0.020
 R9Y  plan-1  H1   0.020
 R9Y  plan-1  H5   0.020
 R9Y  plan-1  H6   0.020

