# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 02:32:38 2022
#   Inital geometry file: a 66 line input string
#   Ligand name: 5,6,7,8-tetrahydronaphthalene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc2CCCCc2c1
#
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
 NY5  NY5  '5,6,7,8-tetrahydronaphthalene-2-carboxylic acid'  ligand  24  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 GRAND
;

data_comp_NY5
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
 NY5  C1   C  CR16   0  -0.286  -13.0419  24.7420  -0.6734
 NY5  C2   C  CR6    0   0.059  -11.6554  24.6066  -0.7551
 NY5  C3   C  CR6    0   0.092  -10.9709  25.3205  -1.7416
 NY5  C4   C  CR16   0  -0.346  -11.6894  26.1528  -2.5989
 NY5  C5   C  CR6    0  -0.096  -13.0687  26.2954  -2.5176
 NY5  C6   C  C      0   0.389  -13.8207  27.2230  -3.4671
 NY5  C10  C  CH2    0  -0.494  -10.9299  23.7260   0.2311
 NY5  O1   O  O      0  -0.589  -13.1308  27.8654  -4.2830
 NY5  O    O  OC    -1  -0.591  -15.0607  27.2607  -3.3427
 NY5  C    C  CR16   0  -0.301  -13.7410  25.5671  -1.5367
 NY5  C7   C  CH2    0  -0.494   -9.4777  25.1878  -1.9159
 NY5  C8   C  CH2    0  -0.441   -8.7825  24.5950  -0.6986
 NY5  C9   C  CH2    0  -0.442   -9.5247  23.3549  -0.2218
 NY5  H1   H  HCR6   0   0.231  -13.5798  24.1848   0.0864
 NY5  H2   H  HCR6   0   0.225  -11.1509  26.7109  -3.3567
 NY5  H9   H  HCH2   0   0.237  -10.8678  24.2520   1.1904
 NY5  H10  H  HCH2   0   0.242  -11.5205  22.8270   0.4246
 NY5  H    H  HCR6   0   0.231  -14.8164  25.6483  -1.4505
 NY5  H4   H  HCH2   0   0.235   -9.2805  24.5471  -2.7825
 NY5  H3   H  HCH2   0   0.241   -9.0499  26.1624  -2.1638
 NY5  H5   H  HCH2   0   0.232   -7.7460  24.3568  -0.9457
 NY5  H6   H  HCH2   0   0.218   -8.7491  25.3318   0.1106
 NY5  H8   H  HCH2   0   0.218   -9.5781  22.6277  -1.0383
 NY5  H7   H  HCH2   0   0.232   -8.9885  22.8699   0.5962

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
 NY5  O1   C6   deloc     1.247  0.020  1.247
 NY5  C6   O    deloc     1.247  0.020  1.247
 NY5  C6   C5   single    1.526  0.020  1.526
 NY5  C4   C5   aromatic  1.389  0.020  1.389
 NY5  C4   C3   aromatic  1.394  0.020  1.394
 NY5  C5   C    aromatic  1.394  0.020  1.394
 NY5  C7   C3   single    1.509  0.020  1.509
 NY5  C7   C8   single    1.522  0.020  1.522
 NY5  C3   C2   aromatic  1.397  0.020  1.397
 NY5  C    C1   aromatic  1.384  0.020  1.384
 NY5  C2   C1   aromatic  1.395  0.020  1.395
 NY5  C2   C10  single    1.508  0.020  1.508
 NY5  C8   C9   single    1.522  0.020  1.522
 NY5  C9   C10  single    1.522  0.020  1.522
 NY5  C1   H1   single    0.930  0.020  1.080
 NY5  C4   H2   single    0.930  0.020  1.080
 NY5  C10  H9   single    0.970  0.020  1.090
 NY5  C10  H10  single    0.970  0.020  1.090
 NY5  C    H    single    0.930  0.020  1.080
 NY5  C7   H4   single    0.970  0.020  1.090
 NY5  C7   H3   single    0.970  0.020  1.090
 NY5  C8   H5   single    0.970  0.020  1.090
 NY5  C8   H6   single    0.970  0.020  1.090
 NY5  C9   H8   single    0.970  0.020  1.090
 NY5  C9   H7   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
 NY5  H1   C1   C    119.51  3.000
 NY5  H1   C1   C2   118.94  3.000
 NY5  C    C1   C2   121.55  3.000
 NY5  C10  C2   C3   121.64  3.000
 NY5  C10  C2   C1   119.76  3.000
 NY5  C3   C2   C1   118.59  3.000
 NY5  C7   C3   C4   119.43  3.000
 NY5  C7   C3   C2   121.43  3.000
 NY5  C4   C3   C2   119.13  3.000
 NY5  H2   C4   C5   118.77  3.000
 NY5  H2   C4   C3   118.75  3.000
 NY5  C5   C4   C3   122.48  3.000
 NY5  C    C5   C6   121.18  3.000
 NY5  C    C5   C4   117.79  3.000
 NY5  C6   C5   C4   121.03  3.000
 NY5  O    C6   O1   126.87  3.000
 NY5  O    C6   C5   116.52  3.000
 NY5  O1   C6   C5   116.61  3.000
 NY5  H10  C10  H9   105.70  3.000
 NY5  H10  C10  C9   110.55  3.000
 NY5  H9   C10  C9   108.97  3.000
 NY5  H10  C10  C2   109.64  3.000
 NY5  H9   C10  C2   108.62  3.000
 NY5  C9   C10  C2   113.07  3.000
 NY5  H    C    C5   119.74  3.000
 NY5  H    C    C1   119.81  3.000
 NY5  C5   C    C1   120.45  3.000
 NY5  H3   C7   H4   105.76  3.000
 NY5  H3   C7   C8   110.49  3.000
 NY5  H4   C7   C8   108.82  3.000
 NY5  H3   C7   C3   109.58  3.000
 NY5  H4   C7   C3   108.71  3.000
 NY5  C8   C7   C3   113.19  3.000
 NY5  H6   C8   H5   106.57  3.000
 NY5  H6   C8   C9   109.37  3.000
 NY5  H5   C8   C9   110.86  3.000
 NY5  H6   C8   C7   110.06  3.000
 NY5  H5   C8   C7   109.73  3.000
 NY5  C9   C8   C7   110.19  3.000
 NY5  H7   C9   H8   106.72  3.000
 NY5  H7   C9   C8   110.93  3.000
 NY5  H8   C9   C8   109.35  3.000
 NY5  H7   C9   C10  109.80  3.000
 NY5  H8   C9   C10  109.81  3.000
 NY5  C8   C9   C10  110.17  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
 NY5  CONST_01  C4  C5   C    C1     0.00   0.0  0
 NY5  CONST_02  C4  C3   C2   C1     0.00   0.0  0
 NY5  CONST_03  C5  C4   C3   C2     0.00   0.0  0
 NY5  CONST_04  C5  C    C1   C2     0.00   0.0  0
 NY5  CONST_05  C   C5   C4   C3     0.00   0.0  0
 NY5  CONST_06  C   C1   C2   C3     0.00   0.0  0
 NY5  CONST_07  C6  C5   C    C1   180.00   0.0  0
 NY5  CONST_08  C6  C5   C4   C3   180.00   0.0  0
 NY5  CONST_09  H2  C4   C3   C2   180.00   0.0  0
 NY5  CONST_10  H   C    C1   C2   180.00   0.0  0
 NY5  CONST_11  H1  C1   C2   C3   180.00   0.0  0
 NY5  Var_01    C9  C10  C2   C1   162.98  30.0  1
 NY5  Var_02    C8  C7   C3   C2   -18.13  30.0  1
 NY5  Var_03    C8  C9   C10  C2    47.70  30.0  1
 NY5  Var_04    C9  C8   C7   C3    47.48  30.0  1
 NY5  Var_05    C7  C8   C9   C10  -63.17  30.0  1
 NY5  Var_06    O1  C6   C5   C4    -1.97  30.0  2

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
 NY5  plan-1  C5   0.020
 NY5  plan-1  C6   0.020
 NY5  plan-1  O1   0.020
 NY5  plan-1  O    0.020
 NY5  plan-2  C1   0.020
 NY5  plan-2  C2   0.020
 NY5  plan-2  C3   0.020
 NY5  plan-2  C4   0.020
 NY5  plan-2  C5   0.020
 NY5  plan-2  C6   0.020
 NY5  plan-2  C10  0.020
 NY5  plan-2  C    0.020
 NY5  plan-2  C7   0.020
 NY5  plan-2  H1   0.020
 NY5  plan-2  H2   0.020
 NY5  plan-2  H    0.020

