# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 21:00:53 2021
#   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  25  13  .  2022-03-23  2022-11-17
;
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  -0.282  -13.0017  24.7877  -0.6540
 NY5  C2   C  CR6   0   0.077  -11.6204  24.6193  -0.7611
 NY5  C3   C  CR6   0   0.093  -10.9246  25.3308  -1.7441
 NY5  C4   C  CR16  0  -0.310  -11.6287  26.1899  -2.5804
 NY5  C5   C  CR6   0  -0.083  -13.0040  26.3572  -2.4672
 NY5  C6   C  C     0   0.528  -13.6780  27.2946  -3.3947
 NY5  C10  C  CH2   0  -0.500  -10.9076  23.7034   0.1991
 NY5  O1   O  O     0  -0.443  -13.1048  27.9311  -4.2480
 NY5  O    O  OH1   0  -0.596  -14.9882  27.3712  -3.1982
 NY5  C    C  CR16  0  -0.269  -13.6960  25.6414  -1.4893
 NY5  C7   C  CH2   0  -0.497   -9.4374  25.1661  -1.9336
 NY5  C8   C  CH2   0  -0.446   -8.7483  24.5474  -0.7260
 NY5  C9   C  CH2   0  -0.446   -9.5115  23.3135  -0.2663
 NY5  H1   H  HCR6  0   0.252  -13.5435  24.2349   0.1046
 NY5  H2   H  HCR6  0   0.253  -11.0857  26.7402  -3.3399
 NY5  H9   H  HCH2  0   0.249  -10.8343  24.2138   1.1659
 NY5  H10  H  HCH2  0   0.253  -11.5177  22.8150   0.3782
 NY5  H11  H  HOH1  0   0.486  -15.3777  27.9974  -3.8263
 NY5  H    H  HCR6  0   0.261  -14.7661  25.7432  -1.3724
 NY5  H4   H  HCH2  0   0.245   -9.2670  24.5262  -2.8061
 NY5  H3   H  HCH2  0   0.250   -8.9918  26.1328  -2.1794
 NY5  H5   H  HCH2  0   0.238   -7.7182  24.2940  -0.9825
 NY5  H6   H  HCH2  0   0.223   -8.7004  25.2735   0.0917
 NY5  H8   H  HCH2  0   0.224   -9.5812  22.5996  -1.0929
 NY5  H7   H  HCH2  0   0.239   -8.9833  22.8068   0.5432

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   double    1.209  0.020  1.209
 NY5  C6   O    single    1.327  0.020  1.327
 NY5  C6   C5   single    1.481  0.020  1.481
 NY5  C4   C5   aromatic  1.390  0.020  1.390
 NY5  C4   C3   aromatic  1.390  0.020  1.390
 NY5  C5   C    aromatic  1.395  0.020  1.395
 NY5  C7   C3   single    1.508  0.020  1.508
 NY5  C7   C8   single    1.522  0.020  1.522
 NY5  C3   C2   aromatic  1.399  0.020  1.399
 NY5  C    C1   aromatic  1.382  0.020  1.382
 NY5  C2   C1   aromatic  1.396  0.020  1.396
 NY5  C2   C10  single    1.506  0.020  1.506
 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  O    H11  single    0.850  0.020  0.980
 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    119.15  3.000
 NY5  H1   C1   C2   119.15  3.000
 NY5  C    C1   C2   121.70  3.000
 NY5  C10  C2   C3   121.46  3.000
 NY5  C10  C2   C1   119.52  3.000
 NY5  C3   C2   C1   119.01  3.000
 NY5  C7   C3   C4   119.42  3.000
 NY5  C7   C3   C2   121.55  3.000
 NY5  C4   C3   C2   119.02  3.000
 NY5  H2   C4   C5   119.45  3.000
 NY5  H2   C4   C3   118.79  3.000
 NY5  C5   C4   C3   121.76  3.000
 NY5  C    C5   C6   122.54  3.000
 NY5  C    C5   C4   119.07  3.000
 NY5  C6   C5   C4   118.39  3.000
 NY5  O    C6   O1   122.83  3.000
 NY5  O    C6   C5   113.15  3.000
 NY5  O1   C6   C5   124.02  3.000
 NY5  H10  C10  H9   105.75  3.000
 NY5  H10  C10  C9   110.73  3.000
 NY5  H9   C10  C9   109.13  3.000
 NY5  H10  C10  C2   109.55  3.000
 NY5  H9   C10  C2   108.12  3.000
 NY5  C9   C10  C2   113.25  3.000
 NY5  H11  O    C6   109.77  3.000
 NY5  H    C    C5   121.21  3.000
 NY5  H    C    C1   119.35  3.000
 NY5  C5   C    C1   119.44  3.000
 NY5  H3   C7   H4   105.92  3.000
 NY5  H3   C7   C8   110.71  3.000
 NY5  H4   C7   C8   108.91  3.000
 NY5  H3   C7   C3   109.50  3.000
 NY5  H4   C7   C3   108.50  3.000
 NY5  C8   C7   C3   113.03  3.000
 NY5  H6   C8   H5   106.76  3.000
 NY5  H6   C8   C9   109.52  3.000
 NY5  H5   C8   C9   110.86  3.000
 NY5  H6   C8   C7   110.05  3.000
 NY5  H5   C8   C7   109.59  3.000
 NY5  C9   C8   C7   110.01  3.000
 NY5  H7   C9   H8   106.75  3.000
 NY5  H7   C9   C8   110.96  3.000
 NY5  H8   C9   C8   109.43  3.000
 NY5  H7   C9   C10  109.64  3.000
 NY5  H8   C9   C10  109.85  3.000
 NY5  C8   C9   C10  110.16  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  CONST_12  H11  O    C6   C5   180.00   0.0  0
 NY5  Var_01    C9   C10  C2   C1   163.72  30.0  1
 NY5  Var_02    C8   C7   C3   C2   -18.47  30.0  1
 NY5  Var_03    C8   C9   C10  C2    47.36  30.0  1
 NY5  Var_04    C9   C8   C7   C3    48.07  30.0  1
 NY5  Var_05    C7   C8   C9   C10  -63.42  30.0  1
 NY5  Var_06    O1   C6   C5   C4    -0.20  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-1  H11  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

