# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 14:50:03 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: (naphthalen-1-yloxy)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)COc1cccc2ccccc12
#
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
 NOA  NOA  '(naphthalen-1-yloxy)acetic acid'  ligand  24  15  .  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_NOA
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
 NOA  C    C  C      0   0.382   0.6944   0.0211   3.4995
 NOA  CA   C  CH2    0  -0.329  -0.3870   0.0183   2.4071
 NOA  C1   C  C      0   0.369  -0.5820   0.0093   0.0419
 NOA  C2   C  C1     0  -0.411  -1.9570   0.0124   0.0656
 NOA  C3   C  C1     0  -0.244  -2.6851   0.0113  -1.1429
 NOA  C4   C  C1     0  -0.349  -2.0555   0.0069  -2.3539
 NOA  C4A  C  CR6    0   0.128  -0.6402   0.0040  -2.4111
 NOA  C5   C  CR16   0  -0.318   0.0504   0.0007  -3.6456
 NOA  C6   C  CR16   0  -0.252   1.4183  -0.0018  -3.6868
 NOA  C7   C  CR16   0  -0.259   2.1612  -0.0011  -2.4901
 NOA  C8   C  CR16   0  -0.287   1.5234   0.0028  -1.2776
 NOA  C1A  C  CR6    0  -0.029   0.1112   0.0052  -1.2086
 NOA  O    O  O      0  -0.589   1.8835   0.0268   3.1513
 NOA  OXT  O  OC    -1  -0.622   0.2299   0.0188   4.6562
 NOA  O1   O  O2     0  -0.449   0.2051   0.0103   1.1231
 NOA  HA1  H  HCH2   0   0.228  -1.0315  -0.8596   2.5362
 NOA  HA2  H  HCH2   0   0.229  -1.0255   0.9019   2.5280
 NOA  H2   H  H      0   0.277  -2.5031   0.0159   0.9988
 NOA  H3   H  H      0   0.257  -3.7663   0.0140  -1.0937
 NOA  H4   H  H      0   0.248  -2.6258   0.0047  -3.2742
 NOA  H5   H  HCR6   0   0.253  -0.5255   0.0004  -4.5636
 NOA  H6   H  HCR6   0   0.256   1.9330  -0.0041  -4.6391
 NOA  H7   H  HCR6   0   0.256   3.2426  -0.0036  -2.5302
 NOA  H8   H  HCR6   0   0.255   2.1062   0.0062  -0.3663

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
 NOA  C    CA   single    1.537  0.020  1.537
 NOA  C    O    deloc     1.239  0.020  1.239
 NOA  C    OXT  deloc     1.246  0.020  1.246
 NOA  CA   O1   single    1.414  0.020  1.414
 NOA  CA   HA1  single    0.970  0.020  1.090
 NOA  CA   HA2  single    0.970  0.020  1.090
 NOA  C1   C2   aromatic  1.375  0.020  1.375
 NOA  C1   C1A  aromatic  1.430  0.020  1.430
 NOA  C1   O1   single    1.337  0.020  1.337
 NOA  C2   C3   aromatic  1.411  0.020  1.411
 NOA  C2   H2   single    0.930  0.020  1.080
 NOA  C3   C4   aromatic  1.365  0.020  1.365
 NOA  C3   H3   single    0.930  0.020  1.080
 NOA  C4   C4A  aromatic  1.416  0.020  1.416
 NOA  C4   H4   single    0.930  0.020  1.080
 NOA  C4A  C5   aromatic  1.414  0.020  1.414
 NOA  C4A  C1A  aromatic  1.418  0.020  1.418
 NOA  C5   C6   aromatic  1.369  0.020  1.369
 NOA  C5   H5   single    0.930  0.020  1.080
 NOA  C6   C7   aromatic  1.408  0.020  1.408
 NOA  C6   H6   single    0.930  0.020  1.080
 NOA  C7   C8   aromatic  1.370  0.020  1.370
 NOA  C7   H7   single    0.930  0.020  1.080
 NOA  C8   C1A  aromatic  1.414  0.020  1.414
 NOA  C8   H8   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
 NOA  OXT  C    O    128.20  3.000
 NOA  OXT  C    CA   113.41  3.000
 NOA  O    C    CA   118.39  3.000
 NOA  HA2  CA   HA1  106.84  3.000
 NOA  HA2  CA   O1   110.39  3.000
 NOA  HA1  CA   O1   110.40  3.000
 NOA  HA2  CA   C    109.25  3.000
 NOA  HA1  CA   C    109.34  3.000
 NOA  O1   CA   C    110.54  3.000
 NOA  O1   C1   C1A  114.94  3.000
 NOA  O1   C1   C2   125.06  3.000
 NOA  C1A  C1   C2   119.99  3.000
 NOA  H2   C2   C3   118.60  3.000
 NOA  H2   C2   C1   121.32  3.000
 NOA  C3   C2   C1   120.08  3.000
 NOA  H3   C3   C4   120.08  3.000
 NOA  H3   C3   C2   118.46  3.000
 NOA  C4   C3   C2   121.46  3.000
 NOA  H4   C4   C4A  119.47  3.000
 NOA  H4   C4   C3   120.74  3.000
 NOA  C4A  C4   C3   119.79  3.000
 NOA  C1A  C4A  C5   118.78  3.000
 NOA  C1A  C4A  C4   119.68  3.000
 NOA  C5   C4A  C4   121.54  3.000
 NOA  H5   C5   C6   120.37  3.000
 NOA  H5   C5   C4A  118.68  3.000
 NOA  C6   C5   C4A  120.95  3.000
 NOA  H6   C6   C7   119.78  3.000
 NOA  H6   C6   C5   120.11  3.000
 NOA  C7   C6   C5   120.11  3.000
 NOA  H7   C7   C8   119.87  3.000
 NOA  H7   C7   C6   119.71  3.000
 NOA  C8   C7   C6   120.43  3.000
 NOA  H8   C8   C1A  119.80  3.000
 NOA  H8   C8   C7   119.66  3.000
 NOA  C1A  C8   C7   120.54  3.000
 NOA  C8   C1A  C4A  119.20  3.000
 NOA  C8   C1A  C1   121.80  3.000
 NOA  C4A  C1A  C1   119.00  3.000
 NOA  C1   O1   CA   119.19  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
 NOA  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 NOA  CONST_02  C4   C4A  C1A  C1     0.00   0.0  0
 NOA  CONST_03  C5   C4A  C1A  C1   180.00   0.0  0
 NOA  CONST_04  C7   C8   C1A  C1   180.00   0.0  0
 NOA  CONST_05  C4A  C1A  C1   C2     0.00   0.0  0
 NOA  CONST_06  C8   C1A  C1   C2   180.00   0.0  0
 NOA  CONST_07  C4A  C4   C3   C2     0.00   0.0  0
 NOA  CONST_08  C1A  C1   C2   C3     0.00   0.0  0
 NOA  CONST_09  C5   C4A  C4   C3   180.00   0.0  0
 NOA  CONST_10  C1A  C4A  C4   C3     0.00   0.0  0
 NOA  CONST_11  C6   C5   C4A  C4   180.00   0.0  0
 NOA  CONST_12  C8   C1A  C4A  C4   180.00   0.0  0
 NOA  CONST_13  C7   C6   C5   C4A    0.00   0.0  0
 NOA  CONST_14  C7   C8   C1A  C4A    0.00   0.0  0
 NOA  CONST_15  C8   C1A  C4A  C5     0.00   0.0  0
 NOA  CONST_16  C8   C7   C6   C5     0.00   0.0  0
 NOA  CONST_17  C1A  C4A  C5   C6     0.00   0.0  0
 NOA  CONST_18  C1A  C8   C7   C6     0.00   0.0  0
 NOA  CONST_19  O1   C1   C2   C3   180.00   0.0  0
 NOA  CONST_20  O1   C1   C1A  C4A  180.00   0.0  0
 NOA  CONST_21  O1   C1   C1A  C8     0.00   0.0  0
 NOA  CONST_22  H3   C3   C2   C1   180.00   0.0  0
 NOA  CONST_23  H8   C8   C1A  C1     0.00   0.0  0
 NOA  CONST_24  H4   C4   C3   C2   180.00   0.0  0
 NOA  CONST_25  H2   C2   C3   C4   180.00   0.0  0
 NOA  CONST_26  H5   C5   C4A  C4     0.00   0.0  0
 NOA  CONST_27  H6   C6   C5   C4A  180.00   0.0  0
 NOA  CONST_28  H7   C7   C6   C5   180.00   0.0  0
 NOA  Var_01    C2   C1   O1   CA    -0.15  30.0  2
 NOA  Var_02    HA1  CA   O1   C1    59.01  30.0  1
 NOA  Var_03    O1   CA   C    O      0.55  30.0  3

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
 NOA  plan-1  C1   0.020
 NOA  plan-1  C2   0.020
 NOA  plan-1  C3   0.020
 NOA  plan-1  C4   0.020
 NOA  plan-1  C4A  0.020
 NOA  plan-1  C5   0.020
 NOA  plan-1  C6   0.020
 NOA  plan-1  C7   0.020
 NOA  plan-1  C8   0.020
 NOA  plan-1  C1A  0.020
 NOA  plan-1  O1   0.020
 NOA  plan-1  H2   0.020
 NOA  plan-1  H3   0.020
 NOA  plan-1  H4   0.020
 NOA  plan-1  H5   0.020
 NOA  plan-1  H6   0.020
 NOA  plan-1  H7   0.020
 NOA  plan-1  H8   0.020
 NOA  plan-2  C    0.020
 NOA  plan-2  CA   0.020
 NOA  plan-2  O    0.020
 NOA  plan-2  OXT  0.020

