# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 05:26:49 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 2-hydroxy-N-[(1R)-1,2,3,4-tetrahydronaphthalen-1-yl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC(=O)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
 67Y  67Y  2-hydroxy-N-[(1R)-1,2,3,4-tetrahydronaphthalen-1-yl]acetamide  ligand  30  15  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_67Y
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
 67Y  C6   C  CH1   0  -0.119  -0.0101   0.7745   0.2742
 67Y  C7   C  CH2   0  -0.438   0.5647   2.1250  -0.1424
 67Y  C8   C  CH2   0  -0.454   1.9704   2.2984   0.4079
 67Y  C10  C  CR6   0   0.071   2.3300  -0.1348  -0.1415
 67Y  C13  C  CR16  0  -0.261   1.3606  -2.7585  -0.0481
 67Y  C15  C  CR6   0   0.063   0.9667  -0.3693   0.0581
 67Y  O1   O  OH1   0  -0.658  -4.8298   0.5152  -0.1162
 67Y  C2   C  CH2   0  -0.271  -3.6196   0.3126  -0.7834
 67Y  C3   C  C     0   0.504  -2.4764   0.5997   0.1769
 67Y  O4   O  O     0  -0.488  -2.6596   0.8631   1.3527
 67Y  N5   N  NH1   0  -0.636  -1.2644   0.5148  -0.3999
 67Y  C9   C  CH2   0  -0.497   2.8967   1.2606  -0.2065
 67Y  C11  C  CR16  0  -0.302   3.1859  -1.2262  -0.2972
 67Y  C12  C  CR16  0  -0.256   2.7151  -2.5273  -0.2550
 67Y  C14  C  CR16  0  -0.284   0.5011  -1.6840   0.1070
 67Y  H1   H  HCH1  0   0.268  -0.2363   0.8187   1.3428
 67Y  H2   H  HCH2  0   0.226   0.5871   2.1943  -1.2353
 67Y  H3   H  HCH2  0   0.246  -0.0997   2.9153   0.2125
 67Y  H4   H  HCH2  0   0.243   2.3423   3.3022   0.1956
 67Y  H5   H  HCH2  0   0.227   1.9583   2.1917   1.4971
 67Y  H6   H  HCR6  0   0.251   0.9774  -3.7699  -0.0044
 67Y  H7   H  HOH1  0   0.461  -5.5396   0.3356  -0.7394
 67Y  H8   H  HCH2  0   0.236  -3.5061  -0.7185  -1.1462
 67Y  H9   H  HCH2  0   0.233  -3.5083   0.9636  -1.6609
 67Y  H10  H  HNH1  0   0.398  -1.2180   0.3390  -1.3928
 67Y  H11  H  HCH2  0   0.245   3.0779   1.5191  -1.2555
 67Y  H12  H  HCH2  0   0.249   3.8744   1.2786   0.2802
 67Y  H13  H  HCR6  0   0.246   4.2440  -1.0457  -0.4507
 67Y  H14  H  HCR6  0   0.252   3.4002  -3.3564  -0.3768
 67Y  H15  H  HCR6  0   0.247  -0.5541  -1.8679   0.2686

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
 67Y  O1   C2   single    1.397  0.020  1.397
 67Y  C2   C3   single    1.520  0.020  1.520
 67Y  O4   C3   double    1.219  0.020  1.219
 67Y  C3   N5   single    1.345  0.020  1.345
 67Y  N5   C6   single    1.447  0.020  1.447
 67Y  C14  C13  aromatic  1.385  0.020  1.385
 67Y  C14  C15  aromatic  1.396  0.020  1.396
 67Y  C6   C15  single    1.520  0.020  1.520
 67Y  C6   C7   single    1.526  0.020  1.526
 67Y  C13  C12  aromatic  1.390  0.020  1.390
 67Y  C15  C10  aromatic  1.398  0.020  1.398
 67Y  C7   C8   single    1.519  0.020  1.519
 67Y  C12  C11  aromatic  1.384  0.020  1.384
 67Y  C10  C11  aromatic  1.396  0.020  1.396
 67Y  C10  C9   single    1.507  0.020  1.507
 67Y  C8   C9   single    1.521  0.020  1.521
 67Y  C6   H1   single    0.970  0.020  1.090
 67Y  C7   H2   single    0.970  0.020  1.090
 67Y  C7   H3   single    0.970  0.020  1.090
 67Y  C8   H4   single    0.970  0.020  1.090
 67Y  C8   H5   single    0.970  0.020  1.090
 67Y  C13  H6   single    0.930  0.020  1.080
 67Y  O1   H7   single    0.850  0.020  0.980
 67Y  C2   H8   single    0.970  0.020  1.090
 67Y  C2   H9   single    0.970  0.020  1.090
 67Y  N5   H10  single    0.860  0.020  1.020
 67Y  C9   H11  single    0.970  0.020  1.090
 67Y  C9   H12  single    0.970  0.020  1.090
 67Y  C11  H13  single    0.930  0.020  1.080
 67Y  C12  H14  single    0.930  0.020  1.080
 67Y  C14  H15  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
 67Y  H1   C6   N5   106.45  3.000
 67Y  H1   C6   C15  107.60  3.000
 67Y  N5   C6   C15  110.84  3.000
 67Y  H1   C6   C7   108.00  3.000
 67Y  C15  C6   C7   112.66  3.000
 67Y  N5   C6   C7   110.99  3.000
 67Y  H3   C7   H2   106.92  3.000
 67Y  H3   C7   C8   111.27  3.000
 67Y  H2   C7   C8   109.59  3.000
 67Y  H3   C7   C6   108.83  3.000
 67Y  H2   C7   C6   109.64  3.000
 67Y  C8   C7   C6   110.53  3.000
 67Y  H5   C8   H4   106.68  3.000
 67Y  H5   C8   C9   110.01  3.000
 67Y  H4   C8   C9   109.97  3.000
 67Y  H5   C8   C7   109.82  3.000
 67Y  H4   C8   C7   110.47  3.000
 67Y  C9   C8   C7   109.84  3.000
 67Y  C11  C10  C9   119.24  3.000
 67Y  C9   C10  C15  121.88  3.000
 67Y  C11  C10  C15  118.88  3.000
 67Y  H6   C13  C14  120.05  3.000
 67Y  H6   C13  C12  120.43  3.000
 67Y  C14  C13  C12  119.51  3.000
 67Y  C14  C15  C10  119.24  3.000
 67Y  C10  C15  C6   121.41  3.000
 67Y  C14  C15  C6   119.31  3.000
 67Y  H7   O1   C2   107.64  3.000
 67Y  H9   C2   H8   106.37  3.000
 67Y  H9   C2   C3   108.45  3.000
 67Y  H8   C2   C3   107.94  3.000
 67Y  H9   C2   O1   112.55  3.000
 67Y  H8   C2   O1   112.54  3.000
 67Y  C3   C2   O1   108.81  3.000
 67Y  N5   C3   O4   124.25  3.000
 67Y  N5   C3   C2   113.25  3.000
 67Y  O4   C3   C2   122.49  3.000
 67Y  H10  N5   C3   118.31  3.000
 67Y  H10  N5   C6   116.71  3.000
 67Y  C3   N5   C6   124.74  3.000
 67Y  H12  C9   H11  105.95  3.000
 67Y  H12  C9   C10  109.42  3.000
 67Y  H11  C9   C10  108.78  3.000
 67Y  H12  C9   C8   110.73  3.000
 67Y  H11  C9   C8   109.06  3.000
 67Y  C10  C9   C8   112.66  3.000
 67Y  H13  C11  C12  119.51  3.000
 67Y  H13  C11  C10  118.95  3.000
 67Y  C12  C11  C10  121.53  3.000
 67Y  H14  C12  C11  120.09  3.000
 67Y  H14  C12  C13  120.41  3.000
 67Y  C11  C12  C13  119.50  3.000
 67Y  H15  C14  C15  119.35  3.000
 67Y  H15  C14  C13  119.32  3.000
 67Y  C15  C14  C13  121.33  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
 67Y  CONST_01  C13  C14  C15  C10    0.00   0.0  0
 67Y  CONST_02  C13  C12  C11  C10    0.00   0.0  0
 67Y  CONST_03  C12  C13  C14  C15    0.00   0.0  0
 67Y  CONST_04  C12  C11  C10  C15    0.00   0.0  0
 67Y  CONST_05  C14  C13  C12  C11    0.00   0.0  0
 67Y  CONST_06  C14  C15  C10  C11    0.00   0.0  0
 67Y  CONST_07  H15  C14  C15  C6     0.00   0.0  0
 67Y  CONST_08  H14  C12  C11  C10  180.00   0.0  0
 67Y  CONST_09  H13  C11  C12  C13  180.00   0.0  0
 67Y  CONST_10  H6   C13  C14  C15  180.00   0.0  0
 67Y  CONST_11  C2   C3   N5   C6   180.00   0.0  0
 67Y  CONST_12  O4   C3   N5   C6     0.00   0.0  0
 67Y  CONST_13  H10  N5   C3   C2     0.00   0.0  0
 67Y  Var_01    C9   C8   C7   C6    64.21  30.0  1
 67Y  Var_02    C10  C9   C8   C7   -49.09  30.0  1
 67Y  Var_03    C15  C10  C9   C8    19.01  30.0  1
 67Y  Var_04    O4   C3   C2   O1     4.84  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
 67Y  chir_01  C6  N5  C15  C7  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
 67Y  plan-1  C6   0.020
 67Y  plan-1  C2   0.020
 67Y  plan-1  C3   0.020
 67Y  plan-1  O4   0.020
 67Y  plan-1  N5   0.020
 67Y  plan-1  H10  0.020
 67Y  plan-2  C6   0.020
 67Y  plan-2  C10  0.020
 67Y  plan-2  C13  0.020
 67Y  plan-2  C15  0.020
 67Y  plan-2  C9   0.020
 67Y  plan-2  C11  0.020
 67Y  plan-2  C12  0.020
 67Y  plan-2  C14  0.020
 67Y  plan-2  H6   0.020
 67Y  plan-2  H13  0.020
 67Y  plan-2  H14  0.020
 67Y  plan-2  H15  0.020

