# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 23:08:54 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: naphthalen-2-yl hydrogen (R)-hexylphosphonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC[P](O)(=O)Oc1ccc2ccccc2c1
#
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
 HLN  HLN  'naphthalen-2-yl hydrogen (R)-hexylphosphonate'  ligand  40  20  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HLN
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
 HLN  CAA  C  CH3    0  -0.662   8.6785  -0.2460  -0.4802
 HLN  CAB  C  CH2    0  -0.418   7.4314  -0.0699   0.3747
 HLN  CAC  C  CH2    0  -0.406   6.1420  -0.1819  -0.4296
 HLN  CAD  C  CH2    0  -0.403   4.8880   0.0054   0.4142
 HLN  CAE  C  CH2    0  -0.428   3.5996  -0.1167  -0.3899
 HLN  CAF  C  CH2    0  -0.721   2.3525   0.0997   0.4644
 HLN  PAG  P  P      0   1.260   0.8274  -0.0511  -0.5168
 HLN  OAH  O  OP    -1  -0.788   0.5939  -1.4752  -0.9389
 HLN  OAI  O  O      0  -0.789   0.7267   1.0518  -1.5336
 HLN  OAJ  O  O2     0  -0.656  -0.2569   0.3011   0.7381
 HLN  CAR  C  CR6    0   0.391  -1.5740   0.4080   0.4378
 HLN  CAQ  C  CR16   0  -0.415  -2.4008  -0.6837   0.4993
 HLN  CAK  C  CR66   0   0.129  -3.7844  -0.5539   0.2398
 HLN  CAP  C  CR16   0  -0.321  -4.6642  -1.6610   0.3107
 HLN  CAO  C  CR16   0  -0.258  -6.0003  -1.5105   0.0552
 HLN  CAN  C  CR16   0  -0.265  -6.5251  -0.2457  -0.2855
 HLN  CAM  C  CR16   0  -0.308  -5.6982   0.8421  -0.3640
 HLN  CAL  C  CR66   0   0.095  -4.3134   0.7173  -0.1053
 HLN  CAT  C  CR16   0  -0.308  -3.4315   1.8219  -0.1734
 HLN  CAS  C  CR16   0  -0.327  -2.0979   1.6740   0.0831
 HLN  H1   H  HCH3   0   0.225   9.5893  -0.1760   0.1159
 HLN  H2   H  HCH3   0   0.215   8.6827  -1.2202  -0.9736
 HLN  H3   H  HCH3   0   0.216   8.7346   0.5161  -1.2598
 HLN  H4   H  HCH2   0   0.210   7.4258  -0.8191   1.1727
 HLN  H5   H  HCH2   0   0.210   7.4623   0.9035   0.8745
 HLN  H6   H  HCH2   0   0.206   6.1524   0.5609  -1.2354
 HLN  H7   H  HCH2   0   0.206   6.1075  -1.1604  -0.9222
 HLN  H8   H  HCH2   0   0.208   4.8798  -0.7326   1.2241
 HLN  H9   H  HCH2   0   0.207   4.9187   0.9872   0.8996
 HLN  H10  H  HCH2   0   0.217   3.6117   0.6102  -1.2077
 HLN  H11  H  HCH2   0   0.216   3.5578  -1.1044  -0.8596
 HLN  H12  H  HCH2   0   0.240   2.3316  -0.6273   1.2817
 HLN  H13  H  HCH2   0   0.240   2.3886   1.0915   0.9244
 HLN  H15  H  HCR6   0   0.253  -1.9985  -1.6522   0.7704
 HLN  H16  H  HCR6   0   0.252  -4.2646  -2.6330   0.5739
 HLN  H17  H  HCR6   0   0.256  -6.6627  -2.3643   0.1139
 HLN  H18  H  HCR6   0   0.255  -7.5837  -0.1402  -0.4834
 HLN  H19  H  HCR6   0   0.253  -6.0965   1.8147  -0.6280
 HLN  H20  H  HCR6   0   0.255  -3.8267   2.7949  -0.4391
 HLN  H21  H  HCR6   0   0.259  -1.4294   2.5233   0.0338

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
 HLN  CAA  CAB  single    1.522  0.020  1.522
 HLN  CAB  CAC  single    1.524  0.020  1.524
 HLN  CAC  CAD  single    1.523  0.020  1.523
 HLN  CAD  CAE  single    1.524  0.020  1.524
 HLN  CAE  CAF  single    1.527  0.020  1.527
 HLN  CAF  PAG  single    1.820  0.020  1.820
 HLN  CAT  CAS  aromatic  1.366  0.020  1.366
 HLN  CAT  CAL  aromatic  1.415  0.020  1.415
 HLN  CAS  CAR  aromatic  1.415  0.020  1.415
 HLN  OAI  PAG  deloc     1.503  0.020  1.503
 HLN  PAG  OAJ  single    1.695  0.020  1.695
 HLN  PAG  OAH  deloc     1.504  0.020  1.504
 HLN  CAM  CAL  aromatic  1.414  0.020  1.414
 HLN  CAM  CAN  aromatic  1.369  0.020  1.369
 HLN  CAL  CAK  aromatic  1.419  0.020  1.419
 HLN  CAR  OAJ  single    1.355  0.020  1.355
 HLN  CAR  CAQ  aromatic  1.371  0.020  1.371
 HLN  CAN  CAO  aromatic  1.411  0.020  1.411
 HLN  CAK  CAQ  aromatic  1.414  0.020  1.414
 HLN  CAK  CAP  aromatic  1.416  0.020  1.416
 HLN  CAO  CAP  aromatic  1.369  0.020  1.369
 HLN  CAA  H1   single    0.970  0.020  1.090
 HLN  CAA  H2   single    0.970  0.020  1.090
 HLN  CAA  H3   single    0.970  0.020  1.090
 HLN  CAB  H4   single    0.970  0.020  1.090
 HLN  CAB  H5   single    0.970  0.020  1.090
 HLN  CAC  H6   single    0.970  0.020  1.090
 HLN  CAC  H7   single    0.970  0.020  1.090
 HLN  CAD  H8   single    0.970  0.020  1.090
 HLN  CAD  H9   single    0.970  0.020  1.090
 HLN  CAE  H10  single    0.970  0.020  1.090
 HLN  CAE  H11  single    0.970  0.020  1.090
 HLN  CAF  H12  single    0.970  0.020  1.090
 HLN  CAF  H13  single    0.970  0.020  1.090
 HLN  CAQ  H15  single    0.930  0.020  1.080
 HLN  CAP  H16  single    0.930  0.020  1.080
 HLN  CAO  H17  single    0.930  0.020  1.080
 HLN  CAN  H18  single    0.930  0.020  1.080
 HLN  CAM  H19  single    0.930  0.020  1.080
 HLN  CAT  H20  single    0.930  0.020  1.080
 HLN  CAS  H21  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
 HLN  H3   CAA  H2   107.46  3.000
 HLN  H3   CAA  H1   107.61  3.000
 HLN  H2   CAA  H1   107.52  3.000
 HLN  H3   CAA  CAB  111.24  3.000
 HLN  H2   CAA  CAB  111.11  3.000
 HLN  H1   CAA  CAB  111.70  3.000
 HLN  H5   CAB  H4   106.02  3.000
 HLN  H5   CAB  CAC  109.29  3.000
 HLN  H4   CAB  CAC  109.28  3.000
 HLN  H5   CAB  CAA  109.64  3.000
 HLN  H4   CAB  CAA  109.54  3.000
 HLN  CAC  CAB  CAA  112.85  3.000
 HLN  H7   CAC  H6   105.96  3.000
 HLN  H7   CAC  CAD  109.44  3.000
 HLN  H6   CAC  CAD  109.38  3.000
 HLN  H7   CAC  CAB  109.24  3.000
 HLN  H6   CAC  CAB  109.28  3.000
 HLN  CAD  CAC  CAB  113.28  3.000
 HLN  H9   CAD  H8   106.03  3.000
 HLN  H9   CAD  CAE  109.23  3.000
 HLN  H8   CAD  CAE  109.25  3.000
 HLN  H9   CAD  CAC  109.43  3.000
 HLN  H8   CAD  CAC  109.45  3.000
 HLN  CAE  CAD  CAC  113.21  3.000
 HLN  H11  CAE  H10  106.20  3.000
 HLN  H11  CAE  CAF  109.68  3.000
 HLN  H10  CAE  CAF  109.45  3.000
 HLN  H11  CAE  CAD  109.34  3.000
 HLN  H10  CAE  CAD  109.38  3.000
 HLN  CAF  CAE  CAD  112.58  3.000
 HLN  H13  CAF  H12  106.80  3.000
 HLN  H13  CAF  PAG  109.24  3.000
 HLN  H12  CAF  PAG  109.37  3.000
 HLN  H13  CAF  CAE  109.68  3.000
 HLN  H12  CAF  CAE  109.84  3.000
 HLN  PAG  CAF  CAE  111.78  3.000
 HLN  OAJ  PAG  OAI  107.78  3.000
 HLN  OAJ  PAG  OAH  107.77  3.000
 HLN  OAI  PAG  OAH  119.64  3.000
 HLN  OAH  PAG  CAF  111.10  3.000
 HLN  OAJ  PAG  CAF   96.87  3.000
 HLN  OAI  PAG  CAF  111.10  3.000
 HLN  CAR  OAJ  PAG  118.29  3.000
 HLN  CAS  CAR  CAQ  120.03  3.000
 HLN  CAQ  CAR  OAJ  120.89  3.000
 HLN  CAS  CAR  OAJ  119.07  3.000
 HLN  H15  CAQ  CAK  119.44  3.000
 HLN  H15  CAQ  CAR  119.95  3.000
 HLN  CAK  CAQ  CAR  120.59  3.000
 HLN  CAL  CAK  CAP  118.74  3.000
 HLN  CAP  CAK  CAQ  121.81  3.000
 HLN  CAL  CAK  CAQ  119.45  3.000
 HLN  H16  CAP  CAO  120.27  3.000
 HLN  H16  CAP  CAK  118.98  3.000
 HLN  CAO  CAP  CAK  120.75  3.000
 HLN  H17  CAO  CAN  119.51  3.000
 HLN  H17  CAO  CAP  120.05  3.000
 HLN  CAN  CAO  CAP  120.44  3.000
 HLN  H18  CAN  CAM  120.20  3.000
 HLN  H18  CAN  CAO  119.69  3.000
 HLN  CAM  CAN  CAO  120.10  3.000
 HLN  H19  CAM  CAL  118.92  3.000
 HLN  H19  CAM  CAN  120.35  3.000
 HLN  CAL  CAM  CAN  120.73  3.000
 HLN  CAT  CAL  CAM  122.18  3.000
 HLN  CAM  CAL  CAK  119.24  3.000
 HLN  CAT  CAL  CAK  118.59  3.000
 HLN  H20  CAT  CAS  119.96  3.000
 HLN  H20  CAT  CAL  119.05  3.000
 HLN  CAS  CAT  CAL  120.99  3.000
 HLN  H21  CAS  CAT  120.64  3.000
 HLN  H21  CAS  CAR  119.01  3.000
 HLN  CAT  CAS  CAR  120.34  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
 HLN  CONST_01  CAL  CAT  CAS  CAR     0.00   0.0  0
 HLN  CONST_02  CAL  CAK  CAQ  CAR     0.00   0.0  0
 HLN  CONST_03  CAP  CAK  CAQ  CAR   180.00   0.0  0
 HLN  CONST_04  CAT  CAS  CAR  CAQ     0.00   0.0  0
 HLN  CONST_05  CAT  CAL  CAK  CAQ     0.00   0.0  0
 HLN  CONST_06  CAM  CAL  CAK  CAQ   180.00   0.0  0
 HLN  CONST_07  CAO  CAP  CAK  CAQ   180.00   0.0  0
 HLN  CONST_08  CAS  CAT  CAL  CAK     0.00   0.0  0
 HLN  CONST_09  CAN  CAM  CAL  CAK     0.00   0.0  0
 HLN  CONST_10  CAS  CAR  CAQ  CAK     0.00   0.0  0
 HLN  CONST_11  CAN  CAO  CAP  CAK     0.00   0.0  0
 HLN  CONST_12  CAT  CAL  CAK  CAP   180.00   0.0  0
 HLN  CONST_13  CAM  CAL  CAK  CAP     0.00   0.0  0
 HLN  CONST_14  CAM  CAN  CAO  CAP     0.00   0.0  0
 HLN  CONST_15  CAL  CAM  CAN  CAO     0.00   0.0  0
 HLN  CONST_16  CAL  CAK  CAP  CAO     0.00   0.0  0
 HLN  CONST_17  CAT  CAL  CAM  CAN   180.00   0.0  0
 HLN  CONST_18  CAS  CAT  CAL  CAM   180.00   0.0  0
 HLN  CONST_19  CAT  CAS  CAR  OAJ   180.00   0.0  0
 HLN  CONST_20  CAK  CAQ  CAR  OAJ   180.00   0.0  0
 HLN  CONST_21  H20  CAT  CAS  CAR   180.00   0.0  0
 HLN  CONST_22  H21  CAS  CAR  CAQ   180.00   0.0  0
 HLN  CONST_23  H16  CAP  CAK  CAQ     0.00   0.0  0
 HLN  CONST_24  H19  CAM  CAL  CAK   180.00   0.0  0
 HLN  CONST_25  H17  CAO  CAP  CAK   180.00   0.0  0
 HLN  CONST_26  H15  CAQ  CAK  CAP     0.00   0.0  0
 HLN  CONST_27  H18  CAN  CAO  CAP   180.00   0.0  0
 HLN  Var_01    CAS  CAR  OAJ  PAG   -90.51  30.0  2
 HLN  Var_02    CAD  CAC  CAB  CAA  -179.48  30.0  3
 HLN  Var_03    CAE  CAD  CAC  CAB  -179.59  30.0  3
 HLN  Var_04    CAF  CAE  CAD  CAC  -178.91  30.0  3
 HLN  Var_05    PAG  CAF  CAE  CAD  -179.99  30.0  3
 HLN  Var_06    OAI  PAG  CAF  CAE   -65.93  30.0  3
 HLN  Var_07    H1   CAA  CAB  CAC  -179.23  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
 HLN  plan-1  OAJ  0.020
 HLN  plan-1  CAR  0.020
 HLN  plan-1  CAQ  0.020
 HLN  plan-1  CAK  0.020
 HLN  plan-1  CAP  0.020
 HLN  plan-1  CAO  0.020
 HLN  plan-1  CAN  0.020
 HLN  plan-1  CAM  0.020
 HLN  plan-1  CAL  0.020
 HLN  plan-1  CAT  0.020
 HLN  plan-1  CAS  0.020
 HLN  plan-1  H15  0.020
 HLN  plan-1  H16  0.020
 HLN  plan-1  H17  0.020
 HLN  plan-1  H18  0.020
 HLN  plan-1  H19  0.020
 HLN  plan-1  H20  0.020
 HLN  plan-1  H21  0.020

