# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 10:58:46 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: (1R)-1,2,3,4-tetrahydronaphthalen-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1CCCc2ccccc12
#
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
 1Y5  1Y5  (1R)-1,2,3,4-tetrahydronaphthalen-1-amine  ligand  24  11  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1Y5
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
 1Y5  N32  N  NH2   0  -0.799  -1.4997   2.1600   0.4348
 1Y5  C33  C  CH1   0  -0.148  -1.2874   0.9103  -0.2903
 1Y5  C34  C  CH2   0  -0.449  -2.3002  -0.1200   0.1912
 1Y5  C35  C  CH2   0  -0.451  -1.9832  -1.4983  -0.3628
 1Y5  C36  C  CH2   0  -0.496  -0.6481  -1.9765   0.1839
 1Y5  C37  C  CR6   0   0.065   0.4355  -0.9342   0.0704
 1Y5  C38  C  CR16  0  -0.298   1.7680  -1.3342   0.1822
 1Y5  C39  C  CR16  0  -0.262   2.8074  -0.4233   0.1043
 1Y5  C40  C  CR16  0  -0.259   2.5184   0.9209  -0.0933
 1Y5  C41  C  CR16  0  -0.304   1.1991   1.3283  -0.2046
 1Y5  C42  C  CR6   0   0.102   0.1411   0.4202  -0.1219
 1Y5  H36  H  HNH2  0   0.348  -0.9933   2.9144  -0.0108
 1Y5  H37  H  HCH1  0   0.216  -1.4491   1.0360  -1.3736
 1Y5  H38  H  HCH2  0   0.220  -2.2894  -0.1472   1.2861
 1Y5  H39  H  HCH2  0   0.237  -3.3022   0.1986  -0.1080
 1Y5  H40  H  HCH2  0   0.239  -2.7689  -2.2091  -0.1009
 1Y5  H41  H  HCH2  0   0.223  -1.9492  -1.4582  -1.4561
 1Y5  H42  H  HCH2  0   0.242  -0.7693  -2.2433   1.2395
 1Y5  H43  H  HCH2  0   0.246  -0.3280  -2.8917  -0.3198
 1Y5  H44  H  HCR6  0   0.243   1.9867  -2.3856   0.3327
 1Y5  H45  H  HCR6  0   0.249   3.8332  -0.7576   0.1923
 1Y5  H46  H  HCR6  0   0.250   3.3162   1.6490  -0.1628
 1Y5  H47  H  HCR6  0   0.238   1.0025   2.3807  -0.3694
 1Y5  H2   H  HNH2  0   0.347  -2.4757   2.4177   0.3417

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
 1Y5  C35  C34  single    1.519  0.020  1.519
 1Y5  C35  C36  single    1.520  0.020  1.520
 1Y5  C34  C33  single    1.523  0.020  1.523
 1Y5  C36  C37  single    1.508  0.020  1.508
 1Y5  N32  C33  single    1.460  0.020  1.460
 1Y5  C33  C42  single    1.520  0.020  1.520
 1Y5  C37  C42  aromatic  1.399  0.020  1.399
 1Y5  C37  C38  aromatic  1.396  0.020  1.396
 1Y5  C42  C41  aromatic  1.397  0.020  1.397
 1Y5  C38  C39  aromatic  1.384  0.020  1.384
 1Y5  C41  C40  aromatic  1.385  0.020  1.385
 1Y5  C39  C40  aromatic  1.389  0.020  1.389
 1Y5  N32  H36  single    0.890  0.020  1.040
 1Y5  C33  H37  single    0.970  0.020  1.090
 1Y5  C34  H38  single    0.970  0.020  1.090
 1Y5  C34  H39  single    0.970  0.020  1.090
 1Y5  C35  H40  single    0.970  0.020  1.090
 1Y5  C35  H41  single    0.970  0.020  1.090
 1Y5  C36  H42  single    0.970  0.020  1.090
 1Y5  C36  H43  single    0.970  0.020  1.090
 1Y5  C38  H44  single    0.930  0.020  1.080
 1Y5  C39  H45  single    0.930  0.020  1.080
 1Y5  C40  H46  single    0.930  0.020  1.080
 1Y5  C41  H47  single    0.930  0.020  1.080
 1Y5  N32  H2   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
 1Y5  H2   N32  H36  104.59  3.000
 1Y5  H2   N32  C33  108.18  3.000
 1Y5  H36  N32  C33  110.27  3.000
 1Y5  H37  C33  C42  106.47  3.000
 1Y5  H37  C33  C34  106.87  3.000
 1Y5  C42  C33  C34  111.84  3.000
 1Y5  H37  C33  N32  111.65  3.000
 1Y5  C42  C33  N32  110.96  3.000
 1Y5  C34  C33  N32  108.98  3.000
 1Y5  H39  C34  H38  106.85  3.000
 1Y5  H39  C34  C35  110.85  3.000
 1Y5  H38  C34  C35  109.88  3.000
 1Y5  H39  C34  C33  109.02  3.000
 1Y5  H38  C34  C33  109.04  3.000
 1Y5  C35  C34  C33  111.09  3.000
 1Y5  H41  C35  H40  106.61  3.000
 1Y5  H41  C35  C36  110.09  3.000
 1Y5  H40  C35  C36  109.95  3.000
 1Y5  H41  C35  C34  109.73  3.000
 1Y5  H40  C35  C34  110.69  3.000
 1Y5  C36  C35  C34  109.73  3.000
 1Y5  H43  C36  H42  105.82  3.000
 1Y5  H43  C36  C37  109.50  3.000
 1Y5  H42  C36  C37  108.69  3.000
 1Y5  H43  C36  C35  110.79  3.000
 1Y5  H42  C36  C35  109.03  3.000
 1Y5  C37  C36  C35  112.75  3.000
 1Y5  C42  C37  C38  119.29  3.000
 1Y5  C38  C37  C36  118.81  3.000
 1Y5  C42  C37  C36  121.89  3.000
 1Y5  H44  C38  C39  119.63  3.000
 1Y5  H44  C38  C37  118.79  3.000
 1Y5  C39  C38  C37  121.58  3.000
 1Y5  H45  C39  C40  120.50  3.000
 1Y5  H45  C39  C38  120.25  3.000
 1Y5  C40  C39  C38  119.25  3.000
 1Y5  H46  C40  C41  119.93  3.000
 1Y5  H46  C40  C39  120.45  3.000
 1Y5  C41  C40  C39  119.62  3.000
 1Y5  H47  C41  C42  120.22  3.000
 1Y5  H47  C41  C40  118.08  3.000
 1Y5  C42  C41  C40  121.69  3.000
 1Y5  C41  C42  C37  118.56  3.000
 1Y5  C41  C42  C33  119.72  3.000
 1Y5  C37  C42  C33  121.68  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
 1Y5  CONST_01  C40  C41  C42  C37    0.00   0.0  0
 1Y5  CONST_02  C40  C39  C38  C37    0.00   0.0  0
 1Y5  CONST_03  C41  C42  C37  C38    0.00   0.0  0
 1Y5  CONST_04  C41  C40  C39  C38    0.00   0.0  0
 1Y5  CONST_05  C42  C37  C38  C39    0.00   0.0  0
 1Y5  CONST_06  C42  C41  C40  C39    0.00   0.0  0
 1Y5  CONST_07  H47  C41  C42  C33    0.00   0.0  0
 1Y5  CONST_08  H44  C38  C37  C36    0.00   0.0  0
 1Y5  CONST_09  H45  C39  C38  C37  180.00   0.0  0
 1Y5  CONST_10  H46  C40  C39  C38  180.00   0.0  0
 1Y5  Var_01    C36  C35  C34  C33   64.42  30.0  1
 1Y5  Var_02    C37  C36  C35  C34  -48.04  30.0  1
 1Y5  Var_03    C42  C37  C36  C35   18.39  30.0  1

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
 1Y5  chir_01  C33  C34  N32  C42  negativ

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
 1Y5  plan-1  C33  0.020
 1Y5  plan-1  C36  0.020
 1Y5  plan-1  C37  0.020
 1Y5  plan-1  C38  0.020
 1Y5  plan-1  C39  0.020
 1Y5  plan-1  C40  0.020
 1Y5  plan-1  C41  0.020
 1Y5  plan-1  C42  0.020
 1Y5  plan-1  H44  0.020
 1Y5  plan-1  H45  0.020
 1Y5  plan-1  H46  0.020
 1Y5  plan-1  H47  0.020

