# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 00:38:24 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: (1R,2S)-1,2-dihydronaphthalene-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1C=Cc2ccccc2[C@H]1O
#
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
 NDH  NDH  (1R,2S)-1,2-dihydronaphthalene-1,2-diol  ligand  22  12  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NDH
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
 NDH  OH2  O  OH1   0  -0.663  -1.3861  -2.0942  -0.2944
 NDH  C1   C  CH1   0   0.011  -1.1031  -0.7652  -0.6335
 NDH  C2   C  CH1   0  -0.041  -2.0876   0.2283  -0.0266
 NDH  OH1  O  OH1   0  -0.660  -2.1274   0.0338   1.3720
 NDH  C3   C  C1    0  -0.289  -1.6469   1.6282  -0.3733
 NDH  C4   C  C1    0  -0.259  -0.3499   1.9326  -0.4477
 NDH  C4A  C  CR6   0   0.130   0.6831   0.9206  -0.2400
 NDH  C8A  C  CR6   0   0.011   0.3176  -0.4336  -0.2554
 NDH  C8   C  CR16  0  -0.314   1.2775  -1.4028  -0.0104
 NDH  C5   C  CR16  0  -0.317   2.0079   1.2741   0.0009
 NDH  C6   C  CR16  0  -0.256   2.9648   0.2987   0.2459
 NDH  C7   C  CR16  0  -0.254   2.5966  -1.0385   0.2462
 NDH  HH2  H  HOH1  0   0.458  -2.2068  -2.3507  -0.7265
 NDH  H1   H  HCH1  0   0.234  -1.1783  -0.6126  -1.7236
 NDH  H2   H  HCH1  0   0.223  -3.0739   0.0369  -0.4711
 NDH  HH1  H  HOH1  0   0.452  -2.7992   0.6184   1.7366
 NDH  H3   H  H     0   0.261  -2.3997   2.3998  -0.4809
 NDH  H4   H  H     0   0.257  -0.0314   2.9529  -0.6295
 NDH  H8   H  HCR6  0   0.254   1.0110  -2.4508  -0.0240
 NDH  H5   H  HCR6  0   0.253   2.2874   2.3213   0.0064
 NDH  H6   H  HCR6  0   0.255   3.9913   0.5825   0.4382
 NDH  H7   H  HCR6  0   0.255   3.3356  -1.8056   0.4387

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
 NDH  OH2  C1   single    1.400  0.020  1.400
 NDH  OH2  HH2  single    0.850  0.020  0.980
 NDH  C1   C2   single    1.525  0.020  1.525
 NDH  C1   C8A  single    1.507  0.020  1.507
 NDH  C1   H1   single    0.970  0.020  1.090
 NDH  C2   OH1  single    1.413  0.020  1.413
 NDH  C2   C3   single    1.508  0.020  1.508
 NDH  C2   H2   single    0.970  0.020  1.090
 NDH  OH1  HH1  single    0.850  0.020  0.980
 NDH  C3   C4   double    1.334  0.020  1.334
 NDH  C3   H3   single    0.930  0.020  1.080
 NDH  C4   C4A  single    1.461  0.020  1.461
 NDH  C4   H4   single    0.930  0.020  1.080
 NDH  C4A  C8A  aromatic  1.403  0.020  1.403
 NDH  C4A  C5   aromatic  1.392  0.020  1.392
 NDH  C8A  C8   aromatic  1.386  0.020  1.386
 NDH  C8   C7   aromatic  1.392  0.020  1.392
 NDH  C8   H8   single    0.930  0.020  1.080
 NDH  C5   C6   aromatic  1.388  0.020  1.388
 NDH  C5   H5   single    0.930  0.020  1.080
 NDH  C6   C7   aromatic  1.387  0.020  1.387
 NDH  C6   H6   single    0.930  0.020  1.080
 NDH  C7   H7   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
 NDH  HH2  OH2  C1   108.46  3.000
 NDH  H1   C1   C8A  106.36  3.000
 NDH  H1   C1   C2   105.02  3.000
 NDH  C8A  C1   C2   111.44  3.000
 NDH  H1   C1   OH2  110.90  3.000
 NDH  C8A  C1   OH2  109.79  3.000
 NDH  C2   C1   OH2  113.05  3.000
 NDH  H2   C2   C3   109.33  3.000
 NDH  H2   C2   OH1  110.57  3.000
 NDH  C3   C2   OH1  111.33  3.000
 NDH  H2   C2   C1   107.77  3.000
 NDH  C3   C2   C1   108.95  3.000
 NDH  OH1  C2   C1   108.82  3.000
 NDH  HH1  OH1  C2   108.13  3.000
 NDH  H3   C3   C4   120.49  3.000
 NDH  H3   C3   C2   118.75  3.000
 NDH  C4   C3   C2   120.57  3.000
 NDH  H4   C4   C4A  117.90  3.000
 NDH  H4   C4   C3   120.63  3.000
 NDH  C4A  C4   C3   121.42  3.000
 NDH  C5   C4A  C8A  119.67  3.000
 NDH  C5   C4A  C4   121.44  3.000
 NDH  C8A  C4A  C4   118.87  3.000
 NDH  C8   C8A  C4A  119.51  3.000
 NDH  C8   C8A  C1   122.92  3.000
 NDH  C4A  C8A  C1   117.44  3.000
 NDH  H8   C8   C7   119.30  3.000
 NDH  H8   C8   C8A  120.31  3.000
 NDH  C7   C8   C8A  120.39  3.000
 NDH  H5   C5   C6   120.02  3.000
 NDH  H5   C5   C4A  119.44  3.000
 NDH  C6   C5   C4A  120.54  3.000
 NDH  H6   C6   C7   120.30  3.000
 NDH  H6   C6   C5   120.06  3.000
 NDH  C7   C6   C5   119.64  3.000
 NDH  H7   C7   C6   120.14  3.000
 NDH  H7   C7   C8   119.61  3.000
 NDH  C6   C7   C8   120.24  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
 NDH  CONST_01  C7   C8   C8A  C4A    0.00   0.0  0
 NDH  CONST_02  C7   C6   C5   C4A    0.00   0.0  0
 NDH  CONST_03  C6   C5   C4A  C8A    0.00   0.0  0
 NDH  CONST_04  C6   C7   C8   C8A    0.00   0.0  0
 NDH  CONST_05  C5   C4A  C8A  C8     0.00   0.0  0
 NDH  CONST_06  C5   C6   C7   C8     0.00   0.0  0
 NDH  CONST_07  H8   C8   C8A  C1     0.00   0.0  0
 NDH  CONST_08  H5   C5   C4A  C4     0.00   0.0  0
 NDH  CONST_09  H6   C6   C5   C4A  180.00   0.0  0
 NDH  CONST_10  H7   C7   C8   C8A  180.00   0.0  0
 NDH  Var_01    C4A  C4   C3   C2     1.96  30.0  1
 NDH  Var_02    C8A  C4A  C4   C3    14.12  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
 NDH  chir_01  C1  OH2  C2  C8A  negativ
 NDH  chir_02  C2  OH1  C3  C1   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
 NDH  plan-1  C1   0.020
 NDH  plan-1  C4   0.020
 NDH  plan-1  C4A  0.020
 NDH  plan-1  C8A  0.020
 NDH  plan-1  C8   0.020
 NDH  plan-1  C5   0.020
 NDH  plan-1  C6   0.020
 NDH  plan-1  C7   0.020
 NDH  plan-1  H8   0.020
 NDH  plan-1  H5   0.020
 NDH  plan-1  H6   0.020
 NDH  plan-1  H7   0.020

