# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 15 19:29:39 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: N-[(6-butoxynaphthalen-2-yl)sulfonyl]-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCOc1ccc2cc(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
 LK1  LK1  'N-[(6-butoxynaphthalen-2-yl)sulfonyl]-L-glutamic acid'  ligand  51  28  .  2021-08-13  2021-08-13  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LK1
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
 LK1  O28   O  OS    0  -0.656  0.3279   4.0844   1.0597
 LK1  S11   S  S     0   1.373  1.2577   5.1559   0.7413
 LK1  O27   O  OS    0  -0.645  0.7614   6.3646   0.0979
 LK1  N     N  NC1   0  -0.726  2.4652   4.4589  -0.1449
 LK1  CA    C  CH1   0  -0.233  3.3688   5.3217  -0.8728
 LK1  C     C  C     0   0.565  2.8440   5.6095  -2.2701
 LK1  OXT   O  OH1   0  -0.586  3.5205   6.5893  -2.8465
 LK1  O     O  O     0  -0.427  1.9435   5.0068  -2.7928
 LK1  CB    C  CH2   0  -0.438  4.7732   4.7043  -0.9208
 LK1  CG    C  CH2   0  -0.585  5.3602   4.4716   0.4611
 LK1  CD    C  C     0   0.558  5.6813   5.7358   1.2125
 LK1  OE2   O  OH1   0  -0.588  6.0864   5.4800   2.4512
 LK1  OE1   O  O     0  -0.439  5.6078   6.8526   0.7627
 LK1  C12   C  CR6   0  -0.217  2.1409   5.6253   2.1935
 LK1  C17   C  CR16  0  -0.232  2.5047   4.6109   3.1108
 LK1  C16   C  CR16  0  -0.304  3.2478   4.9333   4.2048
 LK1  C15   C  CR66  0   0.153  3.6743   6.2683   4.4320
 LK1  C21   C  CR16  0  -0.438  4.4844   6.6072   5.5267
 LK1  C20   C  CR6   0   0.414  4.9088   7.9064   5.7145
 LK1  C19   C  CR16  0  -0.377  4.5088   8.9150   4.8048
 LK1  C18   C  CR16  0  -0.284  3.7205   8.5967   3.7325
 LK1  C14   C  CR66  0   0.102  3.2874   7.2742   3.5089
 LK1  C13   C  CR16  0  -0.284  2.5063   6.9275   2.3850
 LK1  O22   O  O2    0  -0.471  5.6977   8.1360   6.7726
 LK1  C23   C  CH2   0  -0.175  6.1673   9.4526   7.0386
 LK1  C24   C  CH2   0  -0.450  7.1244   9.3825   8.2098
 LK1  C25   C  CH2   0  -0.432  7.6162  10.7671   8.6154
 LK1  C26   C  CH3   0  -0.661  8.6428  10.7139   9.7379
 LK1  H     H  HNC1  0   0.416  2.1531   3.6284  -0.6383
 LK1  HA    H  HCH1  0   0.305  3.4457   6.2781  -0.3503
 LK1  HBC1  H  HCH2  0   0.267  5.4300   5.3499  -1.5039
 LK1  HBC2  H  HCH2  0   0.266  4.7257   3.7479  -1.4459
 LK1  HXT   H  HOH1  0   0.489  3.2007   6.7368  -3.7496
 LK1  HGC1  H  HCH2  0   0.286  4.6951   3.8568   1.0714
 LK1  HGC2  H  HCH2  0   0.305  6.2882   3.8996   0.3686
 LK1  HE2   H  HOH1  0   0.473  6.2750   6.3091   2.9155
 LK1  H17   H  HCR6  0   0.282  2.1993   3.5864   2.9455
 LK1  H13   H  HCR6  0   0.284  2.2221   7.7017   1.6833
 LK1  H16   H  HCR6  0   0.265  3.5306   4.1625   4.9105
 LK1  H21   H  HCR6  0   0.265  4.7868   5.8378   6.2272
 LK1  H19   H  HCR6  0   0.290  4.8196   9.9416   4.9388
 LK1  H18   H  HCR6  0   0.270  3.4273   9.3738   3.0378
 LK1  H231  H  HCH2  0   0.225  5.3241  10.1138   7.2688
 LK1  H232  H  HCH2  0   0.226  6.6810   9.8597   6.1611
 LK1  H241  H  HCH2  0   0.229  7.9771   8.7514   7.9409
 LK1  H242  H  HCH2  0   0.230  6.6293   8.9060   9.0607
 LK1  H251  H  HCH2  0   0.221  6.7641  11.3788   8.9266
 LK1  H252  H  HCH2  0   0.220  8.0524  11.2713   7.7481
 LK1  H261  H  HCH3  0   0.219  8.2336  10.2333  10.6279
 LK1  H262  H  HCH3  0   0.219  9.5269  10.1496   9.4364
 LK1  H263  H  HCH3  0   0.230  8.9703  11.7137  10.0232

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
 LK1  O28  S11   double    1.454  0.020  1.454
 LK1  S11  O27   double    1.456  0.020  1.456
 LK1  S11  N     single    1.652  0.020  1.652
 LK1  S11  C12   single    1.763  0.020  1.763
 LK1  N    CA    single    1.446  0.020  1.446
 LK1  N    H     single    0.860  0.020  1.020
 LK1  CA   C     single    1.520  0.020  1.520
 LK1  CA   CB    single    1.535  0.020  1.535
 LK1  CA   HA    single    0.970  0.020  1.090
 LK1  C    OXT   single    1.323  0.020  1.323
 LK1  C    O     double    1.203  0.020  1.203
 LK1  OXT  HXT   single    0.850  0.020  0.980
 LK1  CB   CG    single    1.519  0.020  1.519
 LK1  CB   HBC1  single    0.970  0.020  1.090
 LK1  CB   HBC2  single    0.970  0.020  1.090
 LK1  CG   CD    single    1.505  0.020  1.505
 LK1  CG   HGC1  single    0.970  0.020  1.090
 LK1  CG   HGC2  single    0.970  0.020  1.090
 LK1  CD   OE2   single    1.328  0.020  1.328
 LK1  CD   OE1   double    1.206  0.020  1.206
 LK1  OE2  HE2   single    0.850  0.020  0.980
 LK1  C12  C17   aromatic  1.415  0.020  1.415
 LK1  C12  C13   aromatic  1.366  0.020  1.366
 LK1  C17  C16   aromatic  1.361  0.020  1.361
 LK1  C17  H17   single    0.930  0.020  1.080
 LK1  C16  C15   aromatic  1.420  0.020  1.420
 LK1  C16  H16   single    0.930  0.020  1.080
 LK1  C15  C21   aromatic  1.403  0.020  1.403
 LK1  C15  C14   aromatic  1.419  0.020  1.419
 LK1  C21  C20   aromatic  1.380  0.020  1.380
 LK1  C21  H21   single    0.930  0.020  1.080
 LK1  C20  C19   aromatic  1.416  0.020  1.416
 LK1  C20  O22   single    1.340  0.020  1.340
 LK1  C19  C18   aromatic  1.368  0.020  1.368
 LK1  C19  H19   single    0.930  0.020  1.080
 LK1  C18  C14   aromatic  1.409  0.020  1.409
 LK1  C18  H18   single    0.930  0.020  1.080
 LK1  C14  C13   aromatic  1.412  0.020  1.412
 LK1  C13  H13   single    0.930  0.020  1.080
 LK1  O22  C23   single    1.423  0.020  1.423
 LK1  C23  C24   single    1.514  0.020  1.514
 LK1  C23  H231  single    0.970  0.020  1.090
 LK1  C23  H232  single    0.970  0.020  1.090
 LK1  C24  C25   single    1.524  0.020  1.524
 LK1  C24  H241  single    0.970  0.020  1.090
 LK1  C24  H242  single    0.970  0.020  1.090
 LK1  C25  C26   single    1.522  0.020  1.522
 LK1  C25  H251  single    0.970  0.020  1.090
 LK1  C25  H252  single    0.970  0.020  1.090
 LK1  C26  H261  single    0.970  0.020  1.090
 LK1  C26  H262  single    0.970  0.020  1.090
 LK1  C26  H263  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
 LK1  C12   S11  N     100.83  3.000
 LK1  C12   S11  O27   108.28  3.000
 LK1  N     S11  O27   111.24  3.000
 LK1  C12   S11  O28   109.64  3.000
 LK1  N     S11  O28   105.90  3.000
 LK1  O27   S11  O28   119.37  3.000
 LK1  H     N    CA    115.82  3.000
 LK1  H     N    S11   112.41  3.000
 LK1  CA    N    S11   118.36  3.000
 LK1  HA    CA   CB    107.62  3.000
 LK1  HA    CA   C     107.35  3.000
 LK1  CB    CA   C     111.31  3.000
 LK1  HA    CA   N     109.00  3.000
 LK1  CB    CA   N     110.33  3.000
 LK1  C     CA   N     111.10  3.000
 LK1  O     C    OXT   124.37  3.000
 LK1  O     C    CA    124.26  3.000
 LK1  OXT   C    CA    111.36  3.000
 LK1  HXT   OXT  C     110.48  3.000
 LK1  HBC2  CB   HBC1  106.72  3.000
 LK1  HBC2  CB   CG    108.66  3.000
 LK1  HBC1  CB   CG    110.15  3.000
 LK1  HBC2  CB   CA    109.12  3.000
 LK1  HBC1  CB   CA    109.25  3.000
 LK1  CG    CB   CA    112.75  3.000
 LK1  HGC2  CG   HGC1  105.63  3.000
 LK1  HGC2  CG   CD    107.48  3.000
 LK1  HGC1  CG   CD    108.89  3.000
 LK1  HGC2  CG   CB    109.33  3.000
 LK1  HGC1  CG   CB    111.05  3.000
 LK1  CD    CG   CB    114.07  3.000
 LK1  OE1   CD   OE2   123.01  3.000
 LK1  OE1   CD   CG    125.34  3.000
 LK1  OE2   CD   CG    111.65  3.000
 LK1  HE2   OE2  CD    109.97  3.000
 LK1  C13   C12  C17   121.58  3.000
 LK1  C13   C12  S11   120.21  3.000
 LK1  C17   C12  S11   118.15  3.000
 LK1  H17   C17  C16   120.09  3.000
 LK1  H17   C17  C12   120.48  3.000
 LK1  C16   C17  C12   119.44  3.000
 LK1  H16   C16  C15   119.12  3.000
 LK1  H16   C16  C17   119.86  3.000
 LK1  C15   C16  C17   121.02  3.000
 LK1  C14   C15  C21   119.58  3.000
 LK1  C14   C15  C16   118.72  3.000
 LK1  C21   C15  C16   121.69  3.000
 LK1  H21   C21  C20   119.66  3.000
 LK1  H21   C21  C15   119.60  3.000
 LK1  C20   C21  C15   120.74  3.000
 LK1  O22   C20  C19   123.49  3.000
 LK1  O22   C20  C21   116.75  3.000
 LK1  C19   C20  C21   119.77  3.000
 LK1  H19   C19  C18   118.93  3.000
 LK1  H19   C19  C20   121.04  3.000
 LK1  C18   C19  C20   120.03  3.000
 LK1  H18   C18  C14   119.24  3.000
 LK1  H18   C18  C19   119.46  3.000
 LK1  C14   C18  C19   121.30  3.000
 LK1  C13   C14  C18   121.78  3.000
 LK1  C13   C14  C15   119.65  3.000
 LK1  C18   C14  C15   118.57  3.000
 LK1  H13   C13  C14   119.05  3.000
 LK1  H13   C13  C12   121.37  3.000
 LK1  C14   C13  C12   119.58  3.000
 LK1  C23   O22  C20   120.04  3.000
 LK1  H232  C23  H231  107.75  3.000
 LK1  H232  C23  C24   109.90  3.000
 LK1  H231  C23  C24   110.60  3.000
 LK1  H232  C23  O22   110.43  3.000
 LK1  H231  C23  O22   110.10  3.000
 LK1  C24   C23  O22   108.08  3.000
 LK1  H242  C24  H241  107.02  3.000
 LK1  H242  C24  C25   109.56  3.000
 LK1  H241  C24  C25   109.75  3.000
 LK1  H242  C24  C23   109.62  3.000
 LK1  H241  C24  C23   109.22  3.000
 LK1  C25   C24  C23   111.57  3.000
 LK1  H252  C25  H251  106.17  3.000
 LK1  H252  C25  C26   109.38  3.000
 LK1  H251  C25  C26   109.58  3.000
 LK1  H252  C25  C24   109.65  3.000
 LK1  H251  C25  C24   109.41  3.000
 LK1  C26   C25  C24   112.46  3.000
 LK1  H263  C26  H262  107.65  3.000
 LK1  H263  C26  H261  107.65  3.000
 LK1  H262  C26  H261  107.55  3.000
 LK1  H263  C26  C25   111.32  3.000
 LK1  H262  C26  C25   111.15  3.000
 LK1  H261  C26  C25   111.35  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
 LK1  CONST_01  C15   C16  C17  C12     0.00   0.0  0
 LK1  CONST_02  C15   C14  C13  C12     0.00   0.0  0
 LK1  CONST_03  C18   C14  C13  C12   180.00   0.0  0
 LK1  CONST_04  C14   C13  C12  C17     0.00   0.0  0
 LK1  CONST_05  C21   C15  C16  C17   180.00   0.0  0
 LK1  CONST_06  C14   C15  C16  C17     0.00   0.0  0
 LK1  CONST_07  C13   C12  C17  C16     0.00   0.0  0
 LK1  CONST_08  C20   C21  C15  C16   180.00   0.0  0
 LK1  CONST_09  C18   C14  C15  C16   180.00   0.0  0
 LK1  CONST_10  C13   C14  C15  C16     0.00   0.0  0
 LK1  CONST_11  C19   C20  C21  C15     0.00   0.0  0
 LK1  CONST_12  C19   C18  C14  C15     0.00   0.0  0
 LK1  CONST_13  C18   C14  C15  C21     0.00   0.0  0
 LK1  CONST_14  C13   C14  C15  C21   180.00   0.0  0
 LK1  CONST_15  C18   C19  C20  C21     0.00   0.0  0
 LK1  CONST_16  C14   C15  C21  C20     0.00   0.0  0
 LK1  CONST_17  C14   C18  C19  C20     0.00   0.0  0
 LK1  CONST_18  C13   C14  C18  C19   180.00   0.0  0
 LK1  CONST_19  C16   C17  C12  S11   180.00   0.0  0
 LK1  CONST_20  C14   C13  C12  S11   180.00   0.0  0
 LK1  CONST_21  O22   C20  C21  C15   180.00   0.0  0
 LK1  CONST_22  O22   C20  C19  C18   180.00   0.0  0
 LK1  CONST_23  H16   C16  C17  C12   180.00   0.0  0
 LK1  CONST_24  H13   C13  C12  C17   180.00   0.0  0
 LK1  CONST_25  H21   C21  C15  C16     0.00   0.0  0
 LK1  CONST_26  H17   C17  C16  C15   180.00   0.0  0
 LK1  CONST_27  H18   C18  C14  C15   180.00   0.0  0
 LK1  CONST_28  H19   C19  C20  C21   180.00   0.0  0
 LK1  CONST_29  HXT   OXT  C    CA    180.00   0.0  0
 LK1  CONST_30  HE2   OE2  CD   CG    180.00   0.0  0
 LK1  Var_01    C17   C12  S11  O28    36.86  30.0  2
 LK1  Var_02    C12   S11  N    CA    -80.24  30.0  2
 LK1  Var_03    C24   C23  O22  C20  -175.05  30.0  3
 LK1  Var_04    CD    CG   CB   CA    -67.96  30.0  3
 LK1  Var_05    OE2   CD   CG   CB    174.82  30.0  3
 LK1  Var_06    C25   C24  C23  O22  -176.72  30.0  3
 LK1  Var_07    C26   C25  C24  C23  -176.63  30.0  3
 LK1  Var_08    H261  C26  C25  C24   -59.02  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
 LK1  chir_01  CA  N  C  CB  positiv

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
 LK1  plan-1  S11  0.020
 LK1  plan-1  C12  0.020
 LK1  plan-1  C17  0.020
 LK1  plan-1  C16  0.020
 LK1  plan-1  C15  0.020
 LK1  plan-1  C21  0.020
 LK1  plan-1  C20  0.020
 LK1  plan-1  C19  0.020
 LK1  plan-1  C18  0.020
 LK1  plan-1  C14  0.020
 LK1  plan-1  C13  0.020
 LK1  plan-1  O22  0.020
 LK1  plan-1  H17  0.020
 LK1  plan-1  H13  0.020
 LK1  plan-1  H16  0.020
 LK1  plan-1  H21  0.020
 LK1  plan-1  H19  0.020
 LK1  plan-1  H18  0.020
 LK1  plan-2  CA   0.020
 LK1  plan-2  C    0.020
 LK1  plan-2  OXT  0.020
 LK1  plan-2  O    0.020
 LK1  plan-2  HXT  0.020
 LK1  plan-3  CG   0.020
 LK1  plan-3  CD   0.020
 LK1  plan-3  OE2  0.020
 LK1  plan-3  OE1  0.020
 LK1  plan-3  HE2  0.020

