# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 15 07:28:53 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: N-[(6-butoxynaphthalen-2-yl)sulfonyl]-D-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
 LK2  LK2  'N-[(6-butoxynaphthalen-2-yl)sulfonyl]-D-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 PERFECT
;

data_comp_LK2
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
 LK2  O32   O  OS    0  -0.653  -0.6658   2.8034   2.9593
 LK2  S11   S  S     0   1.374  -1.4570   2.1631   1.9231
 LK2  O33   O  OS    0  -0.648  -2.8393   1.7963   2.1806
 LK2  N     N  NC1   0  -0.716  -0.6529   0.7683   1.5557
 LK2  CA    C  CH1   0  -0.253  -1.1357  -0.0641   0.4700
 LK2  C     C  C     0   0.556  -0.3734   0.2236  -0.8151
 LK2  O     O  O     0  -0.422   0.6606   0.8374  -0.8626
 LK2  OXT   O  OH1   0  -0.581  -0.9721  -0.3160  -1.8624
 LK2  CB    C  CH2   0  -0.415  -1.0547  -1.5487   0.8500
 LK2  CG    C  CH2   0  -0.605   0.3577  -2.0086   1.1712
 LK2  CD    C  C     0   0.562   0.4133  -3.4505   1.5978
 LK2  OE2   O  OH1   0  -0.594   1.6543  -3.8284   1.8827
 LK2  OE1   O  O     0  -0.440  -0.5371  -4.1872   1.6776
 LK2  C12   C  CR6   0  -0.226  -1.4194   3.1723   0.4755
 LK2  C13   C  CR16  0  -0.225  -0.2194   3.8452   0.1477
 LK2  C14   C  CR16  0  -0.312  -0.1642   4.6052  -0.9812
 LK2  C15   C  CR66  0   0.157  -1.2913   4.7316  -1.8357
 LK2  C16   C  CR66  0   0.108  -2.4867   4.0482  -1.4907
 LK2  C17   C  CR16  0  -0.291  -2.5293   3.2644  -0.3183
 LK2  C21   C  CR16  0  -0.436  -1.2547   5.5179  -2.9984
 LK2  C20   C  CR6   0   0.415  -2.3672   5.6339  -3.8057
 LK2  C19   C  CR16  0  -0.375  -3.5607   4.9538  -3.4619
 LK2  C18   C  CR16  0  -0.284  -3.6093   4.1830  -2.3333
 LK2  O22   O  O2    0  -0.472  -2.2483   6.4035  -4.8971
 LK2  C23   C  CH2   0  -0.176  -3.3812   6.6178  -5.7326
 LK2  C24   C  CH2   0  -0.450  -2.9739   7.5400  -6.8617
 LK2  C29   C  CH2   0  -0.430  -4.1445   7.8315  -7.7934
 LK2  C44   C  CH3   0  -0.660  -3.7552   8.7438  -8.9480
 LK2  H     H  HNC1  0   0.415   0.3539   0.8944   1.5794
 LK2  HA    H  HCH1  0   0.321  -2.1923   0.1559   0.2972
 LK2  HBC1  H  HCH2  0   0.266  -1.4773  -2.1447   0.0406
 LK2  HBC2  H  HCH2  0   0.270  -1.7009  -1.6875   1.7170
 LK2  HXT   H  HOH1  0   0.490  -0.4529  -0.1604  -2.6665
 LK2  HGC1  H  HCH2  0   0.290   1.0289  -1.8905   0.3148
 LK2  HGC2  H  HCH2  0   0.287   0.7912  -1.4070   1.9758
 LK2  HE2   H  HOH1  0   0.481   1.6639  -4.7579   2.1559
 LK2  H13   H  HCR6  0   0.279   0.6478   3.7684   0.7893
 LK2  H17   H  HCR6  0   0.285  -3.4497   2.7563  -0.0595
 LK2  H14   H  HCR6  0   0.266   0.7499   5.1275  -1.2343
 LK2  H21   H  HCR6  0   0.265  -0.3445   6.0430  -3.2629
 LK2  H18   H  HCR6  0   0.270  -4.5264   3.6662  -2.0791
 LK2  H19   H  HCR6  0   0.290  -4.4443   5.0300  -4.0796
 LK2  H231  H  HCH2  0   0.226  -4.1974   7.0631  -5.1525
 LK2  H232  H  HCH2  0   0.225  -3.7404   5.6645  -6.1359
 LK2  H241  H  HCH2  0   0.229  -2.1583   7.0822  -7.4291
 LK2  H242  H  HCH2  0   0.230  -2.5908   8.4780  -6.4492
 LK2  H291  H  HCH2  0   0.220  -4.9573   8.2912  -7.2237
 LK2  H292  H  HCH2  0   0.220  -4.5416   6.8918  -8.1882
 LK2  H441  H  HCH3  0   0.219  -3.3811   9.7028  -8.5855
 LK2  H442  H  HCH3  0   0.219  -2.9719   8.2944  -9.5611
 LK2  H443  H  HCH3  0   0.229  -4.6080   8.9459  -9.5969

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
 LK2  O32  S11   double    1.453  0.020  1.453
 LK2  S11  O33   double    1.453  0.020  1.453
 LK2  S11  N     single    1.651  0.020  1.651
 LK2  S11  C12   single    1.765  0.020  1.765
 LK2  N    CA    single    1.451  0.020  1.451
 LK2  N    H     single    0.860  0.020  1.020
 LK2  CA   C     single    1.522  0.020  1.522
 LK2  CA   CB    single    1.535  0.020  1.535
 LK2  CA   HA    single    0.970  0.020  1.090
 LK2  C    O     double    1.203  0.020  1.203
 LK2  C    OXT   single    1.321  0.020  1.321
 LK2  OXT  HXT   single    0.850  0.020  0.980
 LK2  CB   CG    single    1.520  0.020  1.520
 LK2  CB   HBC1  single    0.970  0.020  1.090
 LK2  CB   HBC2  single    0.970  0.020  1.090
 LK2  CG   CD    single    1.505  0.020  1.505
 LK2  CG   HGC1  single    0.970  0.020  1.090
 LK2  CG   HGC2  single    0.970  0.020  1.090
 LK2  CD   OE2   single    1.328  0.020  1.328
 LK2  CD   OE1   double    1.205  0.020  1.205
 LK2  OE2  HE2   single    0.850  0.020  0.980
 LK2  C12  C13   aromatic  1.414  0.020  1.414
 LK2  C12  C17   aromatic  1.368  0.020  1.368
 LK2  C13  C14   aromatic  1.362  0.020  1.362
 LK2  C13  H13   single    0.930  0.020  1.080
 LK2  C14  C15   aromatic  1.420  0.020  1.420
 LK2  C14  H14   single    0.930  0.020  1.080
 LK2  C15  C16   aromatic  1.420  0.020  1.420
 LK2  C15  C21   aromatic  1.404  0.020  1.404
 LK2  C16  C17   aromatic  1.411  0.020  1.411
 LK2  C16  C18   aromatic  1.410  0.020  1.410
 LK2  C17  H17   single    0.930  0.020  1.080
 LK2  C21  C20   aromatic  1.379  0.020  1.379
 LK2  C21  H21   single    0.930  0.020  1.080
 LK2  C20  C19   aromatic  1.416  0.020  1.416
 LK2  C20  O22   single    1.341  0.020  1.341
 LK2  C19  C18   aromatic  1.368  0.020  1.368
 LK2  C19  H19   single    0.930  0.020  1.080
 LK2  C18  H18   single    0.930  0.020  1.080
 LK2  O22  C23   single    1.424  0.020  1.424
 LK2  C23  C24   single    1.514  0.020  1.514
 LK2  C23  H231  single    0.970  0.020  1.090
 LK2  C23  H232  single    0.970  0.020  1.090
 LK2  C24  C29   single    1.524  0.020  1.524
 LK2  C24  H241  single    0.970  0.020  1.090
 LK2  C24  H242  single    0.970  0.020  1.090
 LK2  C29  C44   single    1.522  0.020  1.522
 LK2  C29  H291  single    0.970  0.020  1.090
 LK2  C29  H292  single    0.970  0.020  1.090
 LK2  C44  H441  single    0.970  0.020  1.090
 LK2  C44  H442  single    0.970  0.020  1.090
 LK2  C44  H443  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
 LK2  C12   S11  N     106.86  3.000
 LK2  C12   S11  O33   108.06  3.000
 LK2  N     S11  O33   106.82  3.000
 LK2  C12   S11  O32   108.75  3.000
 LK2  N     S11  O32   105.41  3.000
 LK2  O33   S11  O32   120.20  3.000
 LK2  H     N    CA    114.76  3.000
 LK2  H     N    S11   111.89  3.000
 LK2  CA    N    S11   119.28  3.000
 LK2  HA    CA   CB    106.55  3.000
 LK2  HA    CA   C     108.22  3.000
 LK2  CB    CA   C     111.45  3.000
 LK2  HA    CA   N     108.94  3.000
 LK2  CB    CA   N     110.62  3.000
 LK2  C     CA   N     110.91  3.000
 LK2  OXT   C    O     124.49  3.000
 LK2  OXT   C    CA    111.42  3.000
 LK2  O     C    CA    124.07  3.000
 LK2  HXT   OXT  C     110.43  3.000
 LK2  HBC2  CB   HBC1  106.92  3.000
 LK2  HBC2  CB   CG    110.14  3.000
 LK2  HBC1  CB   CG    110.59  3.000
 LK2  HBC2  CB   CA    106.79  3.000
 LK2  HBC1  CB   CA    108.94  3.000
 LK2  CG    CB   CA    113.21  3.000
 LK2  HGC2  CG   HGC1  105.85  3.000
 LK2  HGC2  CG   CD    107.68  3.000
 LK2  HGC1  CG   CD    107.61  3.000
 LK2  HGC2  CG   CB    110.93  3.000
 LK2  HGC1  CG   CB    111.83  3.000
 LK2  CD    CG   CB    112.60  3.000
 LK2  OE1   CD   OE2   123.28  3.000
 LK2  OE1   CD   CG    125.13  3.000
 LK2  OE2   CD   CG    111.59  3.000
 LK2  HE2   OE2  CD    110.04  3.000
 LK2  C17   C12  C13   121.47  3.000
 LK2  C17   C12  S11   119.82  3.000
 LK2  C13   C12  S11   118.70  3.000
 LK2  H13   C13  C14   119.92  3.000
 LK2  H13   C13  C12   120.61  3.000
 LK2  C14   C13  C12   119.47  3.000
 LK2  H14   C14  C15   119.11  3.000
 LK2  H14   C14  C13   119.81  3.000
 LK2  C15   C14  C13   121.08  3.000
 LK2  C21   C15  C16   119.52  3.000
 LK2  C21   C15  C14   121.84  3.000
 LK2  C16   C15  C14   118.64  3.000
 LK2  C18   C16  C17   121.71  3.000
 LK2  C18   C16  C15   118.63  3.000
 LK2  C17   C16  C15   119.66  3.000
 LK2  H17   C17  C16   119.01  3.000
 LK2  H17   C17  C12   121.30  3.000
 LK2  C16   C17  C12   119.68  3.000
 LK2  H21   C21  C20   119.59  3.000
 LK2  H21   C21  C15   119.69  3.000
 LK2  C20   C21  C15   120.71  3.000
 LK2  O22   C20  C19   123.24  3.000
 LK2  O22   C20  C21   116.94  3.000
 LK2  C19   C20  C21   119.82  3.000
 LK2  H19   C19  C18   118.84  3.000
 LK2  H19   C19  C20   121.10  3.000
 LK2  C18   C19  C20   120.06  3.000
 LK2  H18   C18  C19   119.52  3.000
 LK2  H18   C18  C16   119.23  3.000
 LK2  C19   C18  C16   121.25  3.000
 LK2  C23   O22  C20   119.57  3.000
 LK2  H232  C23  H231  107.71  3.000
 LK2  H232  C23  C24   110.10  3.000
 LK2  H231  C23  C24   110.34  3.000
 LK2  H232  C23  O22   110.24  3.000
 LK2  H231  C23  O22   110.07  3.000
 LK2  C24   C23  O22   108.38  3.000
 LK2  H242  C24  H241  107.06  3.000
 LK2  H242  C24  C29   109.59  3.000
 LK2  H241  C24  C29   109.61  3.000
 LK2  H242  C24  C23   109.59  3.000
 LK2  H241  C24  C23   109.42  3.000
 LK2  C29   C24  C23   111.46  3.000
 LK2  H292  C29  H291  106.22  3.000
 LK2  H292  C29  C44   109.51  3.000
 LK2  H291  C29  C44   109.47  3.000
 LK2  H292  C29  C24   109.57  3.000
 LK2  H291  C29  C24   109.43  3.000
 LK2  C44   C29  C24   112.45  3.000
 LK2  H443  C44  H442  107.65  3.000
 LK2  H443  C44  H441  107.64  3.000
 LK2  H442  C44  H441  107.60  3.000
 LK2  H443  C44  C29   111.25  3.000
 LK2  H442  C44  C29   111.27  3.000
 LK2  H441  C44  C29   111.24  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
 LK2  CONST_01  C15   C14  C13  C12     0.00   0.0  0
 LK2  CONST_02  C15   C16  C17  C12     0.00   0.0  0
 LK2  CONST_03  C18   C16  C17  C12   180.00   0.0  0
 LK2  CONST_04  C16   C17  C12  C13     0.00   0.0  0
 LK2  CONST_05  C16   C15  C14  C13     0.00   0.0  0
 LK2  CONST_06  C21   C15  C14  C13   180.00   0.0  0
 LK2  CONST_07  C17   C12  C13  C14     0.00   0.0  0
 LK2  CONST_08  C17   C16  C15  C14     0.00   0.0  0
 LK2  CONST_09  C18   C16  C15  C14   180.00   0.0  0
 LK2  CONST_10  C20   C21  C15  C14   180.00   0.0  0
 LK2  CONST_11  C19   C18  C16  C15     0.00   0.0  0
 LK2  CONST_12  C19   C20  C21  C15     0.00   0.0  0
 LK2  CONST_13  C20   C21  C15  C16     0.00   0.0  0
 LK2  CONST_14  C20   C19  C18  C16     0.00   0.0  0
 LK2  CONST_15  C21   C15  C16  C17   180.00   0.0  0
 LK2  CONST_16  C19   C18  C16  C17   180.00   0.0  0
 LK2  CONST_17  C18   C16  C15  C21     0.00   0.0  0
 LK2  CONST_18  C18   C19  C20  C21     0.00   0.0  0
 LK2  CONST_19  C14   C13  C12  S11   180.00   0.0  0
 LK2  CONST_20  C16   C17  C12  S11   180.00   0.0  0
 LK2  CONST_21  O22   C20  C21  C15   180.00   0.0  0
 LK2  CONST_22  O22   C20  C19  C18   180.00   0.0  0
 LK2  CONST_23  H14   C14  C13  C12   180.00   0.0  0
 LK2  CONST_24  H17   C17  C12  C13   180.00   0.0  0
 LK2  CONST_25  H21   C21  C15  C14     0.00   0.0  0
 LK2  CONST_26  H13   C13  C14  C15   180.00   0.0  0
 LK2  CONST_27  H18   C18  C16  C15   180.00   0.0  0
 LK2  CONST_28  H19   C19  C18  C16   180.00   0.0  0
 LK2  CONST_29  HXT   OXT  C    CA    180.00   0.0  0
 LK2  CONST_30  HE2   OE2  CD   CG    180.00   0.0  0
 LK2  Var_01    C13   C12  S11  O32    37.28  30.0  2
 LK2  Var_02    C12   S11  N    CA    -59.75  30.0  2
 LK2  Var_03    C24   C23  O22  C20   178.75  30.0  3
 LK2  Var_04    CD    CG   CB   CA    177.59  30.0  3
 LK2  Var_05    OE2   CD   CG   CB   -179.55  30.0  3
 LK2  Var_06    C29   C24  C23  O22  -179.28  30.0  3
 LK2  Var_07    C44   C29  C24  C23  -179.28  30.0  3
 LK2  Var_08    H441  C44  C29  C24   -59.55  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
 LK2  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
 LK2  plan-1  S11  0.020
 LK2  plan-1  C12  0.020
 LK2  plan-1  C13  0.020
 LK2  plan-1  C14  0.020
 LK2  plan-1  C15  0.020
 LK2  plan-1  C16  0.020
 LK2  plan-1  C17  0.020
 LK2  plan-1  C21  0.020
 LK2  plan-1  C20  0.020
 LK2  plan-1  C19  0.020
 LK2  plan-1  C18  0.020
 LK2  plan-1  O22  0.020
 LK2  plan-1  H13  0.020
 LK2  plan-1  H17  0.020
 LK2  plan-1  H14  0.020
 LK2  plan-1  H21  0.020
 LK2  plan-1  H18  0.020
 LK2  plan-1  H19  0.020
 LK2  plan-2  CA   0.020
 LK2  plan-2  C    0.020
 LK2  plan-2  O    0.020
 LK2  plan-2  OXT  0.020
 LK2  plan-2  HXT  0.020
 LK2  plan-3  CG   0.020
 LK2  plan-3  CD   0.020
 LK2  plan-3  OE2  0.020
 LK2  plan-3  OE1  0.020
 LK2  plan-3  HE2  0.020

