# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 00:12:01 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: N-{[6-(pentyloxy)naphthalen-2-yl]sulfonyl}-D-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCOc1ccc2cc(ccc2c1)[S](=O)(=O)N[C@H](CCC(O)=O)C(O)=O
#
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
 LK3  LK3  'N-{[6-(pentyloxy)naphthalen-2-yl]sulfonyl}-D-glutamic acid'  ligand  52  29  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LK3
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
 LK3  O28   O  OS     0  -0.672  -1.3612   3.0361    2.5240
 LK3  S11   S  S      0   1.367  -1.6153   2.0937    1.4427
 LK3  O27   O  OS     0  -0.662  -2.9057   1.4233    1.3691
 LK3  N     N  NC1    0  -0.732  -0.4531   0.9548    1.5369
 LK3  CA    C  CH1    0  -0.252  -0.3628  -0.0737    0.4990
 LK3  C     C  C      0   0.438   1.1234  -0.1809    0.0664
 LK3  OXT   O  OC    -1  -0.596   1.3790  -1.0462   -0.7856
 LK3  O     O  O      0  -0.594   1.9218   0.6133    0.6050
 LK3  CB    C  CH2    0  -0.379  -0.9324  -1.4043    0.9828
 LK3  CG    C  CH2    0  -0.590  -0.1798  -1.9958    2.1631
 LK3  CD    C  C      0   0.411  -0.7869  -3.2797    2.7555
 LK3  OE2   O  O      0  -0.611  -1.9733  -3.5464    2.4771
 LK3  OE1   O  OC    -1  -0.633  -0.0378  -3.9521    3.4961
 LK3  C12   C  CR6    0  -0.214  -1.3639   2.9467   -0.0890
 LK3  C17   C  CR16   0  -0.241  -0.2114   3.7563   -0.2226
 LK3  C16   C  CR16   0  -0.311   0.0287   4.3994   -1.3997
 LK3  C15   C  CR66   0   0.153  -0.8608   4.2700   -2.4986
 LK3  C21   C  CR16   0  -0.436  -0.6271   4.9213   -3.7209
 LK3  C20   C  CR6    0   0.414  -1.5061   4.7809   -4.7739
 LK3  C19   C  CR16   0  -0.375  -2.6616   3.9775   -4.6226
 LK3  C18   C  CR16   0  -0.287  -2.8998   3.3360   -3.4375
 LK3  C14   C  CR66   0   0.106  -2.0146   3.4577   -2.3469
 LK3  C13   C  CR16   0  -0.291  -2.2468   2.7956   -1.1206
 LK3  O22   O  O2     0  -0.473  -1.2010   5.4293   -5.9077
 LK3  C23   C  CH2    0  -0.174  -2.0934   5.3847   -7.0144
 LK3  C24   C  CH2    0  -0.456  -1.4772   6.1809   -8.1452
 LK3  C25   C  CH2    0  -0.420  -2.4037   6.2465   -9.3535
 LK3  C26   C  CH2    0  -0.419  -1.7913   7.0092  -10.5225
 LK3  C30   C  CH3    0  -0.663  -2.7278   7.0963  -11.7193
 LK3  H     H  HNC1   0   0.402   0.4824   1.3458    1.6839
 LK3  HA    H  HCH1   0   0.257  -0.9218   0.2341   -0.3955
 LK3  HBC1  H  HCH2   0   0.210  -0.9220  -2.1020    0.1431
 LK3  HBC2  H  HCH2   0   0.216  -1.9811  -1.2595    1.2456
 LK3  HGC1  H  HCH2   0   0.214   0.8577  -2.2024    1.8837
 LK3  HGC2  H  HCH2   0   0.224  -0.1227  -1.2524    2.9672
 LK3  H17   H  HCR6   0   0.277   0.4782   3.8735    0.6033
 LK3  H13   H  HCR6   0   0.279  -3.1275   2.1741   -1.0182
 LK3  H16   H  HCR6   0   0.264   0.9085   5.0219   -1.5036
 LK3  H21   H  HCR6   0   0.263   0.2539   5.5416   -3.8371
 LK3  H19   H  HCR6   0   0.287  -3.3679   3.8554   -5.4319
 LK3  H18   H  HCR6   0   0.269  -3.7847   2.7201   -3.3350
 LK3  H231  H  HCH2   0   0.225  -2.2601   4.3496   -7.3322
 LK3  H232  H  HCH2   0   0.224  -3.0643   5.8093   -6.7349
 LK3  H241  H  HCH2   0   0.230  -1.2557   7.1944   -7.7983
 LK3  H242  H  HCH2   0   0.230  -0.5255   5.7253   -8.4342
 LK3  H251  H  HCH2   0   0.216  -3.3474   6.7222   -9.0664
 LK3  H252  H  HCH2   0   0.216  -2.6596   5.2327   -9.6792
 LK3  H261  H  HCH2   0   0.214  -1.5209   8.0170  -10.1933
 LK3  H262  H  HCH2   0   0.215  -0.8559   6.5246  -10.8178
 LK3  H301  H  HCH3   0   0.217  -2.9858   6.1035  -12.0925
 LK3  H302  H  HCH3   0   0.217  -3.6589   7.5999  -11.4522
 LK3  H303  H  HCH3   0   0.228  -2.2772   7.6517  -12.5423

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
 LK3  O27  S11   double    1.456  0.020  1.456
 LK3  S11  N     single    1.630  0.020  1.630
 LK3  N    CA    single    1.464  0.020  1.464
 LK3  CA   C     single    1.552  0.020  1.552
 LK3  C    OXT   deloc     1.241  0.020  1.241
 LK3  C    O     deloc     1.248  0.020  1.248
 LK3  CA   CB    single    1.526  0.020  1.526
 LK3  CB   CG    single    1.520  0.020  1.520
 LK3  CG   CD    single    1.539  0.020  1.539
 LK3  CD   OE2   deloc     1.247  0.020  1.247
 LK3  CD   OE1   deloc     1.250  0.020  1.250
 LK3  S11  C12   single    1.771  0.020  1.771
 LK3  C12  C17   aromatic  1.415  0.020  1.415
 LK3  C17  C16   aromatic  1.363  0.020  1.363
 LK3  C16  C15   aromatic  1.420  0.020  1.420
 LK3  C15  C21   single    1.405  0.020  1.405
 LK3  C21  C20   double    1.379  0.020  1.379
 LK3  C20  C19   single    1.415  0.020  1.415
 LK3  C19  C18   double    1.368  0.020  1.368
 LK3  C15  C14   aromatic  1.419  0.020  1.419
 LK3  C18  C14   single    1.410  0.020  1.410
 LK3  C12  C13   aromatic  1.366  0.020  1.366
 LK3  C14  C13   aromatic  1.413  0.020  1.413
 LK3  C20  O22   single    1.341  0.020  1.341
 LK3  O22  C23   single    1.422  0.020  1.422
 LK3  S11  O28   double    1.457  0.020  1.457
 LK3  C23  C24   single    1.514  0.020  1.514
 LK3  C24  C25   single    1.524  0.020  1.524
 LK3  C25  C26   single    1.524  0.020  1.524
 LK3  C26  C30   single    1.522  0.020  1.522
 LK3  N    H     single    0.860  0.020  1.020
 LK3  CB   HBC1  single    0.970  0.020  1.090
 LK3  CB   HBC2  single    0.970  0.020  1.090
 LK3  CG   HGC1  single    0.970  0.020  1.090
 LK3  CG   HGC2  single    0.970  0.020  1.090
 LK3  C17  H17   single    0.930  0.020  1.080
 LK3  C13  H13   single    0.930  0.020  1.080
 LK3  C16  H16   single    0.930  0.020  1.080
 LK3  C21  H21   single    0.930  0.020  1.080
 LK3  C19  H19   single    0.930  0.020  1.080
 LK3  C18  H18   single    0.930  0.020  1.080
 LK3  C23  H231  single    0.970  0.020  1.090
 LK3  C23  H232  single    0.970  0.020  1.090
 LK3  C24  H241  single    0.970  0.020  1.090
 LK3  C24  H242  single    0.970  0.020  1.090
 LK3  C25  H251  single    0.970  0.020  1.090
 LK3  C25  H252  single    0.970  0.020  1.090
 LK3  C26  H261  single    0.970  0.020  1.090
 LK3  C26  H262  single    0.970  0.020  1.090
 LK3  C30  H301  single    0.970  0.020  1.090
 LK3  C30  H302  single    0.970  0.020  1.090
 LK3  C30  H303  single    0.970  0.020  1.090
 LK3  CA   HA    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
 LK3  C12   S11  N     106.58  3.000
 LK3  C12   S11  O27   107.69  3.000
 LK3  N     S11  O27   108.25  3.000
 LK3  C12   S11  O28   107.80  3.000
 LK3  N     S11  O28   106.55  3.000
 LK3  O27   S11  O28   119.33  3.000
 LK3  H     N    CA    108.27  3.000
 LK3  H     N    S11   113.12  3.000
 LK3  CA    N    S11   119.60  3.000
 LK3  HA    CA   CB    108.21  3.000
 LK3  HA    CA   C     106.24  3.000
 LK3  CB    CA   C     112.68  3.000
 LK3  HA    CA   N     110.42  3.000
 LK3  CB    CA   N     111.39  3.000
 LK3  C     CA   N     107.78  3.000
 LK3  O     C    OXT   127.45  3.000
 LK3  O     C    CA    116.64  3.000
 LK3  OXT   C    CA    115.91  3.000
 LK3  HBC2  CB   HBC1  106.21  3.000
 LK3  HBC2  CB   CG    109.92  3.000
 LK3  HBC1  CB   CG    110.12  3.000
 LK3  HBC2  CB   CA    108.63  3.000
 LK3  HBC1  CB   CA    108.05  3.000
 LK3  CG    CB   CA    113.63  3.000
 LK3  HGC2  CG   HGC1  105.41  3.000
 LK3  HGC2  CG   CD    107.69  3.000
 LK3  HGC1  CG   CD    108.35  3.000
 LK3  HGC2  CG   CB    109.36  3.000
 LK3  HGC1  CG   CB    110.17  3.000
 LK3  CD    CG   CB    115.37  3.000
 LK3  OE1   CD   OE2   125.97  3.000
 LK3  OE1   CD   CG    116.14  3.000
 LK3  OE2   CD   CG    117.89  3.000
 LK3  C13   C12  C17   121.23  3.000
 LK3  C13   C12  S11   120.53  3.000
 LK3  C17   C12  S11   118.22  3.000
 LK3  H17   C17  C16   119.73  3.000
 LK3  H17   C17  C12   120.59  3.000
 LK3  C16   C17  C12   119.68  3.000
 LK3  H16   C16  C15   119.15  3.000
 LK3  H16   C16  C17   119.83  3.000
 LK3  C15   C16  C17   121.02  3.000
 LK3  C14   C15  C21   119.58  3.000
 LK3  C14   C15  C16   118.61  3.000
 LK3  C21   C15  C16   121.81  3.000
 LK3  H21   C21  C20   119.65  3.000
 LK3  H21   C21  C15   119.60  3.000
 LK3  C20   C21  C15   120.75  3.000
 LK3  O22   C20  C19   123.40  3.000
 LK3  O22   C20  C21   116.83  3.000
 LK3  C19   C20  C21   119.78  3.000
 LK3  H19   C19  C18   118.79  3.000
 LK3  H19   C19  C20   121.16  3.000
 LK3  C18   C19  C20   120.05  3.000
 LK3  H18   C18  C14   119.27  3.000
 LK3  H18   C18  C19   119.39  3.000
 LK3  C14   C18  C19   121.34  3.000
 LK3  C13   C14  C18   121.86  3.000
 LK3  C13   C14  C15   119.65  3.000
 LK3  C18   C14  C15   118.50  3.000
 LK3  H13   C13  C14   119.00  3.000
 LK3  H13   C13  C12   121.18  3.000
 LK3  C14   C13  C12   119.83  3.000
 LK3  C23   O22  C20   119.99  3.000
 LK3  H232  C23  H231  107.77  3.000
 LK3  H232  C23  C24   110.32  3.000
 LK3  H231  C23  C24   110.01  3.000
 LK3  H232  C23  O22   110.20  3.000
 LK3  H231  C23  O22   110.54  3.000
 LK3  C24   C23  O22   108.02  3.000
 LK3  H242  C24  H241  107.07  3.000
 LK3  H242  C24  C25   109.71  3.000
 LK3  H241  C24  C25   109.55  3.000
 LK3  H242  C24  C23   109.41  3.000
 LK3  H241  C24  C23   109.44  3.000
 LK3  C25   C24  C23   111.56  3.000
 LK3  H252  C25  H251  106.18  3.000
 LK3  H252  C25  C26   109.21  3.000
 LK3  H251  C25  C26   109.26  3.000
 LK3  H252  C25  C24   109.75  3.000
 LK3  H251  C25  C24   109.55  3.000
 LK3  C26   C25  C24   112.67  3.000
 LK3  H262  C26  H261  106.13  3.000
 LK3  H262  C26  C30   109.83  3.000
 LK3  H261  C26  C30   109.63  3.000
 LK3  H262  C26  C25   109.20  3.000
 LK3  H261  C26  C25   109.23  3.000
 LK3  C30   C26  C25   112.61  3.000
 LK3  H303  C30  H302  107.58  3.000
 LK3  H303  C30  H301  107.63  3.000
 LK3  H302  C30  H301  107.55  3.000
 LK3  H303  C30  C26   111.61  3.000
 LK3  H302  C30  C26   111.03  3.000
 LK3  H301  C30  C26   111.23  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
 LK3  CONST_01  C15   C16  C17  C12     0.00   0.0  0
 LK3  CONST_02  C15   C14  C13  C12     0.00   0.0  0
 LK3  CONST_03  C14   C13  C12  C17     0.00   0.0  0
 LK3  CONST_04  C14   C15  C16  C17     0.00   0.0  0
 LK3  CONST_05  C13   C12  C17  C16     0.00   0.0  0
 LK3  CONST_06  C13   C14  C15  C16     0.00   0.0  0
 LK3  CONST_07  C16   C17  C12  S11   180.00   0.0  0
 LK3  CONST_08  C14   C13  C12  S11   180.00   0.0  0
 LK3  CONST_09  H16   C16  C17  C12   180.00   0.0  0
 LK3  CONST_10  H13   C13  C12  C17   180.00   0.0  0
 LK3  CONST_11  H17   C17  C16  C15   180.00   0.0  0
 LK3  Var_01    C17   C12  S11  O28    45.62  30.0  2
 LK3  Var_02    C12   S11  N    CA    -59.38  30.0  2
 LK3  Var_03    C24   C23  O22  C20  -179.09  30.0  3
 LK3  Var_04    CD    CG   CB   CA    175.30  30.0  3
 LK3  Var_05    OE2   CD   CG   CB    -17.56  30.0  3
 LK3  Var_06    C25   C24  C23  O22  -177.07  30.0  3
 LK3  Var_07    C26   C25  C24  C23  -178.36  30.0  3
 LK3  Var_08    C30   C26  C25  C24  -178.93  30.0  3
 LK3  Var_09    H301  C30  C26  C25   -60.24  30.0  3

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
 LK3  chir_01  CA  N  C  CB  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
 LK3  plan-1  S11  0.020
 LK3  plan-1  C12  0.020
 LK3  plan-1  C17  0.020
 LK3  plan-1  C16  0.020
 LK3  plan-1  C15  0.020
 LK3  plan-1  C21  0.020
 LK3  plan-1  C20  0.020
 LK3  plan-1  C19  0.020
 LK3  plan-1  C18  0.020
 LK3  plan-1  C14  0.020
 LK3  plan-1  C13  0.020
 LK3  plan-1  O22  0.020
 LK3  plan-1  H17  0.020
 LK3  plan-1  H13  0.020
 LK3  plan-1  H16  0.020
 LK3  plan-1  H21  0.020
 LK3  plan-1  H19  0.020
 LK3  plan-1  H18  0.020
 LK3  plan-2  CA   0.020
 LK3  plan-2  C    0.020
 LK3  plan-2  OXT  0.020
 LK3  plan-2  O    0.020
 LK3  plan-3  CG   0.020
 LK3  plan-3  CD   0.020
 LK3  plan-3  OE2  0.020
 LK3  plan-3  OE1  0.020

