# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 11:30:08 2022
#   Inital geometry file: a 61 line input string
#   Ligand name: (1~{S})-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
 STQ  STQ  "(1~{S})-1,2,3,4-tetrahydronaphthalen-1-amine"
  ligand  24  11  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_STQ
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
 STQ  N1   N  NH2   0  -0.780  35.6042  14.6109  -62.0073
 STQ  C10  C  CH1   0  -0.194  36.2123  15.8374  -62.5236
 STQ  C5   C  CR6   0   0.098  36.8189  16.7018  -61.4303
 STQ  C6   C  CR16  0  -0.302  37.9984  16.2760  -60.8169
 STQ  C1   C  CR16  0  -0.261  38.5724  16.9886  -59.7782
 STQ  C9   C  CH2   0  -0.435  35.1972  16.6175  -63.3504
 STQ  C8   C  CH2   0  -0.459  34.2180  17.3708  -62.4594
 STQ  C7   C  CH2   0  -0.494  34.9623  18.4160  -61.6420
 STQ  C4   C  CR6   0   0.070  36.2099  17.8784  -60.9876
 STQ  C3   C  CR16  0  -0.295  36.7930  18.5884  -59.9358
 STQ  C2   C  CR16  0  -0.258  37.9610  18.1551  -59.3316
 STQ  H1   H  HNH2  0   0.346  36.2997  14.0775  -61.4992
 STQ  H2   H  HNH2  0   0.338  34.8936  14.8429  -61.3225
 STQ  H4   H  HCH1  0   0.242  37.0231  15.5199  -63.1864
 STQ  H5   H  HCR6  0   0.244  38.4762  15.3664  -61.1664
 STQ  H6   H  HCR6  0   0.246  39.4895  16.6411  -59.3198
 STQ  H7   H  HCH2  0   0.226  35.7224  17.3364  -63.9873
 STQ  H8   H  HCH2  0   0.233  34.6776  15.9266  -64.0174
 STQ  H9   H  HCH2  0   0.239  33.4476  17.8533  -63.0636
 STQ  H10  H  HCH2  0   0.223  33.6936  16.6780  -61.7940
 STQ  H11  H  HCH2  0   0.241  35.2458  19.2451  -62.3002
 STQ  H12  H  HCH2  0   0.245  34.3079  18.8499  -60.8825
 STQ  H13  H  HCR6  0   0.241  36.3162  19.4992  -59.5905
 STQ  H14  H  HCR6  0   0.247  38.3937  18.7236  -58.5180

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
 STQ  C9   C10  single    1.524  0.020  1.524
 STQ  C9   C8   single    1.523  0.020  1.523
 STQ  C10  N1   single    1.463  0.020  1.463
 STQ  C10  C5   single    1.520  0.020  1.520
 STQ  C8   C7   single    1.521  0.020  1.521
 STQ  C7   C4   single    1.508  0.020  1.508
 STQ  C5   C4   aromatic  1.397  0.020  1.397
 STQ  C5   C6   aromatic  1.396  0.020  1.396
 STQ  C4   C3   aromatic  1.397  0.020  1.397
 STQ  C6   C1   aromatic  1.384  0.020  1.384
 STQ  C3   C2   aromatic  1.385  0.020  1.385
 STQ  C1   C2   aromatic  1.391  0.020  1.391
 STQ  N1   H1   single    0.890  0.020  1.040
 STQ  N1   H2   single    0.890  0.020  1.040
 STQ  C10  H4   single    0.970  0.020  1.090
 STQ  C6   H5   single    0.930  0.020  1.080
 STQ  C1   H6   single    0.930  0.020  1.080
 STQ  C9   H7   single    0.970  0.020  1.090
 STQ  C9   H8   single    0.970  0.020  1.090
 STQ  C8   H9   single    0.970  0.020  1.090
 STQ  C8   H10  single    0.970  0.020  1.090
 STQ  C7   H11  single    0.970  0.020  1.090
 STQ  C7   H12  single    0.970  0.020  1.090
 STQ  C3   H13  single    0.930  0.020  1.080
 STQ  C2   H14  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
 STQ  H2   N1   H1   105.24  3.000
 STQ  H2   N1   C10  109.75  3.000
 STQ  H1   N1   C10  109.45  3.000
 STQ  H4   C10  C9   108.27  3.000
 STQ  H4   C10  C5   107.76  3.000
 STQ  C9   C10  C5   111.41  3.000
 STQ  H4   C10  N1   106.17  3.000
 STQ  C5   C10  N1   112.88  3.000
 STQ  C9   C10  N1   110.10  3.000
 STQ  C4   C5   C6   119.08  3.000
 STQ  C6   C5   C10  118.67  3.000
 STQ  C4   C5   C10  122.21  3.000
 STQ  H5   C6   C1   119.38  3.000
 STQ  H5   C6   C5   119.08  3.000
 STQ  C1   C6   C5   121.54  3.000
 STQ  H6   C1   C2   120.38  3.000
 STQ  H6   C1   C6   120.25  3.000
 STQ  C2   C1   C6   119.37  3.000
 STQ  H8   C9   H7   106.77  3.000
 STQ  H8   C9   C8   111.37  3.000
 STQ  H7   C9   C8   108.90  3.000
 STQ  H8   C9   C10  108.94  3.000
 STQ  H7   C9   C10  109.40  3.000
 STQ  C8   C9   C10  111.35  3.000
 STQ  H10  C8   H9   106.15  3.000
 STQ  H10  C8   C7   110.03  3.000
 STQ  H9   C8   C7   109.81  3.000
 STQ  H10  C8   C9   110.53  3.000
 STQ  H9   C8   C9   110.40  3.000
 STQ  C7   C8   C9   109.85  3.000
 STQ  H12  C7   H11  105.79  3.000
 STQ  H12  C7   C4   109.61  3.000
 STQ  H11  C7   C4   108.44  3.000
 STQ  H12  C7   C8   110.69  3.000
 STQ  H11  C7   C8   108.88  3.000
 STQ  C4   C7   C8   113.14  3.000
 STQ  C3   C4   C7   119.41  3.000
 STQ  C3   C4   C5   119.01  3.000
 STQ  C7   C4   C5   121.57  3.000
 STQ  H13  C3   C2   119.65  3.000
 STQ  H13  C3   C4   118.90  3.000
 STQ  C2   C3   C4   121.45  3.000
 STQ  H14  C2   C3   120.05  3.000
 STQ  H14  C2   C1   120.40  3.000
 STQ  C3   C2   C1   119.55  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
 STQ  CONST_01  C2   C3  C4  C5      0.00   0.0  0
 STQ  CONST_02  C2   C1  C6  C5      0.00   0.0  0
 STQ  CONST_03  C3   C4  C5  C6      0.00   0.0  0
 STQ  CONST_04  C3   C2  C1  C6      0.00   0.0  0
 STQ  CONST_05  C4   C5  C6  C1      0.00   0.0  0
 STQ  CONST_06  C4   C3  C2  C1      0.00   0.0  0
 STQ  CONST_07  H5   C6  C5  C10     0.00   0.0  0
 STQ  CONST_08  H13  C3  C4  C5    180.00   0.0  0
 STQ  CONST_09  H6   C1  C6  C5    180.00   0.0  0
 STQ  CONST_10  H14  C2  C1  C6    180.00   0.0  0
 STQ  CONST_11  H13  C3  C2  C1    180.00   0.0  0
 STQ  CONST_12  H13  C3  C4  C7      0.00   0.0  0
 STQ  CONST_13  H5   C6  C5  C4    180.00   0.0  0
 STQ  CONST_14  H14  C2  C3  C4    180.00   0.0  0
 STQ  CONST_15  H6   C1  C2  C3    180.00   0.0  0
 STQ  CONST_16  H5   C6  C1  C2    180.00   0.0  0
 STQ  Var_01    C7   C8  C9  C10    63.62  30.0  1
 STQ  Var_02    C8   C7  C4  C5     18.86  30.0  1
 STQ  Var_03    C4   C7  C8  C9    -47.19  30.0  1
 STQ  Var_04    C3   C4  C7  C8   -162.80  30.0  1
 STQ  Var_05    H9   C8  C9  C10  -175.13  30.0  1
 STQ  Var_06    H10  C8  C9  C10   -57.99  30.0  1
 STQ  Var_07    H11  C7  C4  C5   -102.04  30.0  1
 STQ  Var_08    H12  C7  C4  C5    142.93  30.0  1
 STQ  Var_09    H11  C7  C8  C9     73.46  30.0  1
 STQ  Var_10    H12  C7  C8  C9   -170.66  30.0  1
 STQ  Var_11    H7   C9  C8  C7    -57.10  30.0  1
 STQ  Var_12    H8   C9  C8  C7   -174.58  30.0  1
 STQ  Var_13    H9   C8  C7  C4   -168.79  30.0  1
 STQ  Var_14    H10  C8  C7  C4     74.72  30.0  1
 STQ  Var_15    H11  C7  C4  C3     76.31  30.0  1
 STQ  Var_16    H12  C7  C4  C3    -38.73  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
 STQ  chir_01  C10  C9  N1  C5  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
 STQ  plan-1  C10  0.020
 STQ  plan-1  C5   0.020
 STQ  plan-1  C6   0.020
 STQ  plan-1  C1   0.020
 STQ  plan-1  C7   0.020
 STQ  plan-1  C4   0.020
 STQ  plan-1  C3   0.020
 STQ  plan-1  C2   0.020
 STQ  plan-1  H5   0.020
 STQ  plan-1  H6   0.020
 STQ  plan-1  H13  0.020
 STQ  plan-1  H14  0.020

