# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 15:43:08 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 4-[(1~{R})-2-(naphthalen-2-ylmethylamino)-1-oxidanyl-ethyl]benzene-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H](CNCc1ccc2ccccc2c1)c3ccc(O)c(O)c3
#
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
 946  946  4-[(1~{R})-2-(naphthalen-2-ylmethylamino)-1-oxidanyl-ethyl]benzene-1,2-diol  ligand  42  23  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_946
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
 946  C1   C  CR6   0   0.309   5.2625  -1.4343  -0.2665
 946  O1   O  OH1   0  -0.636   5.7716  -2.6466  -0.5730
 946  C2   C  CR6   0   0.242   6.0382  -0.2712  -0.3415
 946  O2   O  OH1   0  -0.645   7.3215  -0.4322  -0.7403
 946  C3   C  CR16  0  -0.358   5.4718   0.9493  -0.0106
 946  O3   O  OH1   0  -0.658   1.6945   0.6050   2.0898
 946  C4   C  CR16  0  -0.342   4.1435   1.0269   0.3896
 946  C5   C  CR6   0   0.137   3.3636  -0.1202   0.4652
 946  C6   C  CH1   0  -0.092   1.9061  -0.0611   0.8602
 946  C7   C  CH2   0  -0.264   1.0684   0.5476  -0.2601
 946  C8   C  CH2   0  -0.288  -1.1735   1.0433  -0.9903
 946  C9   C  CR6   0   0.064  -2.6435   0.7986  -0.7704
 946  C10  C  CR66  0   0.146  -4.4932  -0.4670   0.1649
 946  C11  C  CR16  0  -0.317  -4.9831  -1.5358   0.9526
 946  C12  C  CR16  0  -0.258  -6.3291  -1.7355   1.1012
 946  C13  C  CR16  0  -0.262  -7.2520  -0.8740   0.4713
 946  C14  C  CR16  0  -0.310  -6.8076   0.1688  -0.2959
 946  C15  C  CR66  0   0.097  -5.4225   0.3965  -0.4694
 946  C16  C  CR16  0  -0.300  -4.9249   1.4632  -1.2547
 946  C17  C  CR16  0  -0.295  -3.5801   1.6573  -1.3962
 946  C18  C  CR16  0  -0.406   3.9391  -1.3440   0.1361
 946  C19  C  CR16  0  -0.383  -3.1065  -0.2405  -0.0062
 946  N1   N  NH1   0  -0.606  -0.3456   0.4271   0.0208
 946  H1   H  HOH1  0   0.472   6.6906  -2.5646  -0.8535
 946  H2   H  HOH1  0   0.482   7.7653   0.4188  -0.8255
 946  H3   H  HCR6  0   0.274   6.0721   1.8504  -0.0677
 946  H4   H  HOH1  0   0.447   1.9013   1.5393   1.9802
 946  H5   H  HCR6  0   0.245   3.7364   2.0007   0.6331
 946  H6   H  HCH1  0   0.243   1.5504  -1.0828   1.0234
 946  H7   H  HCH2  0   0.196   1.3897   1.5920  -0.4261
 946  H8   H  HCH2  0   0.236   1.2893   0.0113  -1.1873
 946  H9   H  HCH2  0   0.246  -0.8929   0.6219  -1.9624
 946  H10  H  HCH2  0   0.215  -1.0032   2.1277  -1.0828
 946  H11  H  HCR6  0   0.252  -4.2760  -2.1973   1.4389
 946  H12  H  HCR6  0   0.257  -6.6919  -2.5583   1.7037
 946  H13  H  HCR6  0   0.257  -8.3135  -1.0428   0.5981
 946  H14  H  HCR6  0   0.254  -7.5138   0.8326  -0.7809
 946  H15  H  HCR6  0   0.253  -5.6251   2.1323  -1.7406
 946  H16  H  HCR6  0   0.249  -3.2188   2.4875  -1.9923
 946  H17  H  HCR6  0   0.260   3.3497  -2.2525   0.1925
 946  H18  H  HCR6  0   0.245  -2.4036  -0.9045   0.4829
 946  H19  H  HNH1  0   0.344  -0.5462   0.8539   0.9175

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
 946  C13  C12  aromatic  1.411  0.020  1.411
 946  C13  C14  aromatic  1.369  0.020  1.369
 946  C12  C11  aromatic  1.369  0.020  1.369
 946  C14  C15  aromatic  1.414  0.020  1.414
 946  C11  C10  aromatic  1.415  0.020  1.415
 946  C15  C10  aromatic  1.418  0.020  1.418
 946  C15  C16  aromatic  1.415  0.020  1.415
 946  C10  C19  aromatic  1.416  0.020  1.416
 946  C16  C17  aromatic  1.366  0.020  1.366
 946  C19  C9   aromatic  1.370  0.020  1.370
 946  C17  C9   aromatic  1.417  0.020  1.417
 946  C9   C8   single    1.506  0.020  1.506
 946  C8   N1   single    1.445  0.020  1.445
 946  N1   C7   single    1.447  0.020  1.447
 946  C7   C6   single    1.525  0.020  1.525
 946  C6   C5   single    1.511  0.020  1.511
 946  C6   O3   single    1.414  0.020  1.414
 946  C4   C5   aromatic  1.389  0.020  1.389
 946  C4   C3   aromatic  1.389  0.020  1.389
 946  C5   C18  aromatic  1.392  0.020  1.392
 946  C3   C2   aromatic  1.386  0.020  1.386
 946  C18  C1   aromatic  1.386  0.020  1.386
 946  C2   C1   aromatic  1.400  0.020  1.400
 946  C2   O2   single    1.353  0.020  1.353
 946  C1   O1   single    1.350  0.020  1.350
 946  O1   H1   single    0.850  0.020  0.980
 946  O2   H2   single    0.850  0.020  0.980
 946  C3   H3   single    0.930  0.020  1.080
 946  O3   H4   single    0.850  0.020  0.980
 946  C4   H5   single    0.930  0.020  1.080
 946  C6   H6   single    0.970  0.020  1.090
 946  C7   H7   single    0.970  0.020  1.090
 946  C7   H8   single    0.970  0.020  1.090
 946  C8   H9   single    0.970  0.020  1.090
 946  C8   H10  single    0.970  0.020  1.090
 946  C11  H11  single    0.930  0.020  1.080
 946  C12  H12  single    0.930  0.020  1.080
 946  C13  H13  single    0.930  0.020  1.080
 946  C14  H14  single    0.930  0.020  1.080
 946  C16  H15  single    0.930  0.020  1.080
 946  C17  H16  single    0.930  0.020  1.080
 946  C18  H17  single    0.930  0.020  1.080
 946  C19  H18  single    0.930  0.020  1.080
 946  N1   H19  single    0.890  0.020  1.040

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
 946  C18  C1   C2   119.36  3.000
 946  C2   C1   O1   121.66  3.000
 946  C18  C1   O1   118.98  3.000
 946  H1   O1   C1   110.43  3.000
 946  C3   C2   O2   124.24  3.000
 946  O2   C2   C1   116.25  3.000
 946  C3   C2   C1   119.51  3.000
 946  H2   O2   C2   110.96  3.000
 946  H3   C3   C4   119.87  3.000
 946  H3   C3   C2   119.55  3.000
 946  C4   C3   C2   120.58  3.000
 946  H4   O3   C6   109.01  3.000
 946  H5   C4   C5   121.27  3.000
 946  H5   C4   C3   118.31  3.000
 946  C5   C4   C3   120.42  3.000
 946  C18  C5   C6   119.68  3.000
 946  C18  C5   C4   118.75  3.000
 946  C6   C5   C4   121.56  3.000
 946  H6   C6   C7   107.67  3.000
 946  H6   C6   C5   108.42  3.000
 946  C7   C6   C5   110.68  3.000
 946  H6   C6   O3   105.16  3.000
 946  C5   C6   O3   112.95  3.000
 946  C7   C6   O3   111.62  3.000
 946  H8   C7   H7   106.10  3.000
 946  H8   C7   N1   108.73  3.000
 946  H7   C7   N1   113.08  3.000
 946  H8   C7   C6   108.43  3.000
 946  H7   C7   C6   109.13  3.000
 946  N1   C7   C6   111.15  3.000
 946  H10  C8   H9   105.33  3.000
 946  H10  C8   N1   112.95  3.000
 946  H9   C8   N1   108.05  3.000
 946  H10  C8   C9   108.85  3.000
 946  H9   C8   C9   108.48  3.000
 946  N1   C8   C9   112.81  3.000
 946  C19  C9   C17  118.86  3.000
 946  C17  C9   C8   118.83  3.000
 946  C19  C9   C8   122.30  3.000
 946  C19  C10  C15  119.37  3.000
 946  C19  C10  C11  121.82  3.000
 946  C15  C10  C11  118.81  3.000
 946  H11  C11  C12  120.26  3.000
 946  H11  C11  C10  119.01  3.000
 946  C12  C11  C10  120.73  3.000
 946  H12  C12  C13  119.56  3.000
 946  H12  C12  C11  120.06  3.000
 946  C13  C12  C11  120.38  3.000
 946  H13  C13  C14  120.20  3.000
 946  H13  C13  C12  119.61  3.000
 946  C14  C13  C12  120.20  3.000
 946  H14  C14  C15  118.99  3.000
 946  H14  C14  C13  120.39  3.000
 946  C15  C14  C13  120.62  3.000
 946  C16  C15  C14  122.26  3.000
 946  C16  C15  C10  118.47  3.000
 946  C14  C15  C10  119.26  3.000
 946  H15  C16  C17  120.13  3.000
 946  H15  C16  C15  119.15  3.000
 946  C17  C16  C15  120.72  3.000
 946  H16  C17  C16  119.60  3.000
 946  H16  C17  C9   119.13  3.000
 946  C16  C17  C9   121.27  3.000
 946  H17  C18  C5   119.97  3.000
 946  H17  C18  C1   118.64  3.000
 946  C5   C18  C1   121.38  3.000
 946  H18  C19  C10  118.87  3.000
 946  H18  C19  C9   119.82  3.000
 946  C10  C19  C9   121.31  3.000
 946  H19  N1   C8   109.04  3.000
 946  H19  N1   C7   109.28  3.000
 946  C8   N1   C7   112.87  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
 946  CONST_01  C4   C5   C18  C1     0.00   0.0  0
 946  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 946  CONST_03  C5   C4   C3   C2     0.00   0.0  0
 946  CONST_04  C5   C18  C1   C2     0.00   0.0  0
 946  CONST_05  C18  C5   C4   C3     0.00   0.0  0
 946  CONST_06  C18  C1   C2   C3     0.00   0.0  0
 946  CONST_07  C11  C10  C19  C9   180.00   0.0  0
 946  CONST_08  C15  C10  C19  C9     0.00   0.0  0
 946  CONST_09  C15  C16  C17  C9     0.00   0.0  0
 946  CONST_10  C13  C12  C11  C10    0.00   0.0  0
 946  CONST_11  C13  C14  C15  C10    0.00   0.0  0
 946  CONST_12  C17  C16  C15  C10    0.00   0.0  0
 946  CONST_13  C17  C9   C19  C10    0.00   0.0  0
 946  CONST_14  C14  C13  C12  C11    0.00   0.0  0
 946  CONST_15  C14  C15  C10  C11    0.00   0.0  0
 946  CONST_16  C16  C15  C10  C11  180.00   0.0  0
 946  CONST_17  C15  C14  C13  C12    0.00   0.0  0
 946  CONST_18  C15  C10  C11  C12    0.00   0.0  0
 946  CONST_19  C19  C10  C11  C12  180.00   0.0  0
 946  CONST_20  C16  C15  C14  C13  180.00   0.0  0
 946  CONST_21  C19  C10  C15  C14  180.00   0.0  0
 946  CONST_22  C17  C16  C15  C14  180.00   0.0  0
 946  CONST_23  C19  C10  C15  C16    0.00   0.0  0
 946  CONST_24  C19  C9   C17  C16    0.00   0.0  0
 946  CONST_25  C6   C5   C18  C1   180.00   0.0  0
 946  CONST_26  C5   C18  C1   O1   180.00   0.0  0
 946  CONST_27  C3   C2   C1   O1   180.00   0.0  0
 946  CONST_28  C4   C3   C2   O2   180.00   0.0  0
 946  CONST_29  C18  C1   C2   O2   180.00   0.0  0
 946  CONST_30  C6   C5   C4   C3   180.00   0.0  0
 946  CONST_31  C10  C19  C9   C8   180.00   0.0  0
 946  CONST_32  C16  C17  C9   C8   180.00   0.0  0
 946  CONST_33  H3   C3   C2   C1   180.00   0.0  0
 946  CONST_34  H5   C4   C3   C2   180.00   0.0  0
 946  CONST_35  H17  C18  C1   C2   180.00   0.0  0
 946  CONST_36  H15  C16  C17  C9   180.00   0.0  0
 946  CONST_37  H12  C12  C11  C10  180.00   0.0  0
 946  CONST_38  H14  C14  C15  C10  180.00   0.0  0
 946  CONST_39  H13  C13  C12  C11  180.00   0.0  0
 946  CONST_40  H18  C19  C10  C11    0.00   0.0  0
 946  CONST_41  H11  C11  C12  C13  180.00   0.0  0
 946  CONST_42  H16  C17  C16  C15  180.00   0.0  0
 946  Var_01    N1   C8   C9   C17  160.18  30.0  2
 946  Var_02    C9   C8   N1   C7   174.24  30.0  1
 946  Var_03    C8   N1   C7   C6   177.51  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
 946  chir_01  C6  C7  C5  O3  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
 946  plan-1  C1   0.020
 946  plan-1  O1   0.020
 946  plan-1  C2   0.020
 946  plan-1  O2   0.020
 946  plan-1  C3   0.020
 946  plan-1  C4   0.020
 946  plan-1  C5   0.020
 946  plan-1  C6   0.020
 946  plan-1  C18  0.020
 946  plan-1  H3   0.020
 946  plan-1  H5   0.020
 946  plan-1  H17  0.020
 946  plan-2  C8   0.020
 946  plan-2  C9   0.020
 946  plan-2  C10  0.020
 946  plan-2  C11  0.020
 946  plan-2  C12  0.020
 946  plan-2  C13  0.020
 946  plan-2  C14  0.020
 946  plan-2  C15  0.020
 946  plan-2  C16  0.020
 946  plan-2  C17  0.020
 946  plan-2  C19  0.020
 946  plan-2  H11  0.020
 946  plan-2  H12  0.020
 946  plan-2  H13  0.020
 946  plan-2  H14  0.020
 946  plan-2  H15  0.020
 946  plan-2  H16  0.020
 946  plan-2  H18  0.020

