# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 17:22:56 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  49  28  .  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_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  -0.674  -0.3738   2.7442   2.7474
 LK2  S11   S  S      0   1.369  -1.0413   2.0307   1.6669
 LK2  O33   O  OS     0  -0.662  -2.3697   1.4789   1.8931
 LK2  N     N  NC1    0  -0.731  -0.0486   0.8148   1.2312
 LK2  CA    C  CH1    0  -0.251  -0.3633   0.0051   0.0538
 LK2  C     C  C      0   0.437   0.9415  -0.1598  -0.7697
 LK2  O     O  O      0  -0.595   1.9565   0.4227  -0.3354
 LK2  OXT   O  OC    -1  -0.596   0.8482  -0.8539  -1.7940
 LK2  CB    C  CH2    0  -0.377  -0.9858  -1.3338   0.4391
 LK2  CG    C  CH2    0  -0.595  -0.0788  -2.2042   1.2900
 LK2  CD    C  C      0   0.413  -0.6870  -3.5355   1.7646
 LK2  OE2   O  OC    -1  -0.635   0.0704  -4.2731   2.4317
 LK2  OE1   O  O      0  -0.609  -1.8714  -3.7812   1.4617
 LK2  C12   C  CR6    0  -0.216  -1.1447   3.1205   0.2743
 LK2  C13   C  CR16   0  -0.241   0.0198   3.8234  -0.1152
 LK2  C14   C  CR16   0  -0.310  -0.0201   4.6446  -1.2019
 LK2  C15   C  CR66   0   0.153  -1.2143   4.8068  -1.9530
 LK2  C16   C  CR66   0   0.106  -2.3745   4.0980  -1.5460
 LK2  C17   C  CR16   0  -0.291  -2.3147   3.2483  -0.4193
 LK2  C21   C  CR16   0  -0.436  -1.2729   5.6424  -3.0805
 LK2  C20   C  CR6    0   0.413  -2.4441   5.7804  -3.7954
 LK2  C19   C  CR16   0  -0.375  -3.6046   5.0810  -3.3858
 LK2  C18   C  CR16   0  -0.286  -3.5605   4.2628  -2.2901
 LK2  O22   O  O2     0  -0.473  -2.4108   6.5897  -4.8649
 LK2  C23   C  CH2    0  -0.175  -3.5858   6.7751  -5.6454
 LK2  C24   C  CH2    0  -0.450  -3.2436   7.6764  -6.8126
 LK2  C29   C  CH2    0  -0.430  -4.4631   7.9416  -7.6874
 LK2  C44   C  CH3    0  -0.660  -4.1406   8.8220  -8.8867
 LK2  H     H  HNC1   0   0.402   0.9365   1.0905   1.1843
 LK2  HA    H  HCH1   0   0.256  -1.0703   0.5372  -0.5975
 LK2  HBC1  H  HCH2   0   0.209  -1.2583  -1.8545  -0.4801
 LK2  HBC2  H  HCH2   0   0.214  -1.9223  -1.1429   0.9660
 LK2  HGC1  H  HCH2   0   0.220   0.8443  -2.4331   0.7456
 LK2  HGC2  H  HCH2   0   0.223   0.2427  -1.6464   2.1760
 LK2  H13   H  HCR6   0   0.277   0.9398   3.7179   0.4448
 LK2  H17   H  HCR6   0   0.279  -3.2029   2.7065  -0.1202
 LK2  H14   H  HCR6   0   0.264   0.8688   5.1851  -1.5024
 LK2  H21   H  HCR6   0   0.263  -0.3877   6.1831  -3.3942
 LK2  H18   H  HCR6   0   0.269  -4.4527   3.7286  -1.9877
 LK2  H19   H  HCR6   0   0.288  -4.5350   5.1784  -3.9272
 LK2  H231  H  HCH2   0   0.224  -4.3775   7.2246  -5.0351
 LK2  H232  H  HCH2   0   0.225  -3.9547   5.8105  -6.0113
 LK2  H241  H  HCH2   0   0.229  -2.4554   7.2105  -7.4112
 LK2  H242  H  HCH2   0   0.229  -2.8459   8.6249  -6.4399
 LK2  H291  H  HCH2   0   0.220  -5.2448   8.4160  -7.0872
 LK2  H292  H  HCH2   0   0.220  -4.8789   6.9912  -8.0347
 LK2  H441  H  HCH3   0   0.219  -3.7418   9.7880  -8.5724
 LK2  H442  H  HCH3   0   0.219  -3.3975   8.3530  -9.5342
 LK2  H443  H  HCH3   0   0.229  -5.0305   9.0114  -9.4875

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    1.457  0.020  1.457
 LK2  S11  O33   double    1.456  0.020  1.456
 LK2  S11  N     single    1.629  0.020  1.629
 LK2  S11  C12   single    1.771  0.020  1.771
 LK2  N    CA    single    1.463  0.020  1.463
 LK2  N    H     single    0.860  0.020  1.020
 LK2  CA   C     single    1.552  0.020  1.552
 LK2  CA   CB    single    1.526  0.020  1.526
 LK2  CA   HA    single    0.970  0.020  1.090
 LK2  C    O     deloc     1.248  0.020  1.248
 LK2  C    OXT   deloc     1.241  0.020  1.241
 LK2  CB   CG    single    1.518  0.020  1.518
 LK2  CB   HBC1  single    0.970  0.020  1.090
 LK2  CB   HBC2  single    0.970  0.020  1.090
 LK2  CG   CD    single    1.539  0.020  1.539
 LK2  CG   HGC1  single    0.970  0.020  1.090
 LK2  CG   HGC2  single    0.970  0.020  1.090
 LK2  CD   OE2   deloc     1.250  0.020  1.250
 LK2  CD   OE1   deloc     1.247  0.020  1.247
 LK2  C12  C13   aromatic  1.415  0.020  1.415
 LK2  C12  C17   aromatic  1.366  0.020  1.366
 LK2  C13  C14   aromatic  1.363  0.020  1.363
 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  1.419  0.020  1.419
 LK2  C15  C21   aromatic  1.405  0.020  1.405
 LK2  C16  C17   aromatic  1.412  0.020  1.412
 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    1.342  0.020  1.342
 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    1.423  0.020  1.423
 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     106.53  3.000
 LK2  C12   S11  O33   107.58  3.000
 LK2  N     S11  O33   108.34  3.000
 LK2  C12   S11  O32   107.97  3.000
 LK2  N     S11  O32   106.54  3.000
 LK2  O33   S11  O32   119.23  3.000
 LK2  H     N    CA    108.60  3.000
 LK2  H     N    S11   113.43  3.000
 LK2  CA    N    S11   119.81  3.000
 LK2  HA    CA   CB    108.19  3.000
 LK2  HA    CA   C     106.14  3.000
 LK2  CB    CA   C     112.57  3.000
 LK2  HA    CA   N     110.33  3.000
 LK2  CB    CA   N     111.73  3.000
 LK2  C     CA   N     107.76  3.000
 LK2  OXT   C    O     127.55  3.000
 LK2  OXT   C    CA    115.74  3.000
 LK2  O     C    CA    116.71  3.000
 LK2  HBC2  CB   HBC1  106.01  3.000
 LK2  HBC2  CB   CG    110.02  3.000
 LK2  HBC1  CB   CG    110.36  3.000
 LK2  HBC2  CB   CA    108.57  3.000
 LK2  HBC1  CB   CA    107.93  3.000
 LK2  CG    CB   CA    113.63  3.000
 LK2  HGC2  CG   HGC1  105.13  3.000
 LK2  HGC2  CG   CD    107.88  3.000
 LK2  HGC1  CG   CD    107.79  3.000
 LK2  HGC2  CG   CB    109.69  3.000
 LK2  HGC1  CG   CB    110.16  3.000
 LK2  CD    CG   CB    115.65  3.000
 LK2  OE1   CD   OE2   126.07  3.000
 LK2  OE1   CD   CG    118.10  3.000
 LK2  OE2   CD   CG    115.83  3.000
 LK2  C17   C12  C13   121.24  3.000
 LK2  C17   C12  S11   120.45  3.000
 LK2  C13   C12  S11   118.30  3.000
 LK2  H13   C13  C14   119.75  3.000
 LK2  H13   C13  C12   120.58  3.000
 LK2  C14   C13  C12   119.66  3.000
 LK2  H14   C14  C15   119.11  3.000
 LK2  H14   C14  C13   119.88  3.000
 LK2  C15   C14  C13   121.01  3.000
 LK2  C21   C15  C16   119.55  3.000
 LK2  C21   C15  C14   121.85  3.000
 LK2  C16   C15  C14   118.60  3.000
 LK2  C18   C16  C17   121.80  3.000
 LK2  C18   C16  C15   118.55  3.000
 LK2  C17   C16  C15   119.64  3.000
 LK2  H17   C17  C16   119.13  3.000
 LK2  H17   C17  C12   121.03  3.000
 LK2  C16   C17  C12   119.84  3.000
 LK2  H21   C21  C20   119.59  3.000
 LK2  H21   C21  C15   119.67  3.000
 LK2  C20   C21  C15   120.74  3.000
 LK2  O22   C20  C19   123.30  3.000
 LK2  O22   C20  C21   116.91  3.000
 LK2  C19   C20  C21   119.79  3.000
 LK2  H19   C19  C18   118.87  3.000
 LK2  H19   C19  C20   121.08  3.000
 LK2  C18   C19  C20   120.05  3.000
 LK2  H18   C18  C19   119.48  3.000
 LK2  H18   C18  C16   119.20  3.000
 LK2  C19   C18  C16   121.31  3.000
 LK2  C23   O22  C20   119.69  3.000
 LK2  H232  C23  H231  107.69  3.000
 LK2  H232  C23  C24   110.05  3.000
 LK2  H231  C23  C24   110.39  3.000
 LK2  H232  C23  O22   110.28  3.000
 LK2  H231  C23  O22   110.16  3.000
 LK2  C24   C23  O22   108.29  3.000
 LK2  H242  C24  H241  107.08  3.000
 LK2  H242  C24  C29   109.61  3.000
 LK2  H241  C24  C29   109.66  3.000
 LK2  H242  C24  C23   109.62  3.000
 LK2  H241  C24  C23   109.34  3.000
 LK2  C29   C24  C23   111.42  3.000
 LK2  H292  C29  H291  106.23  3.000
 LK2  H292  C29  C44   109.45  3.000
 LK2  H291  C29  C44   109.44  3.000
 LK2  H292  C29  C24   109.58  3.000
 LK2  H291  C29  C24   109.41  3.000
 LK2  C44   C29  C24   112.54  3.000
 LK2  H443  C44  H442  107.66  3.000
 LK2  H443  C44  H441  107.65  3.000
 LK2  H442  C44  H441  107.61  3.000
 LK2  H443  C44  C29   111.20  3.000
 LK2  H442  C44  C29   111.29  3.000
 LK2  H441  C44  C29   111.25  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  Var_01    C13   C12  S11  O32    47.81  30.0  2
 LK2  Var_02    C12   S11  N    CA    -57.56  30.0  2
 LK2  Var_03    C24   C23  O22  C20  -177.37  30.0  3
 LK2  Var_04    CD    CG   CB   CA    177.04  30.0  3
 LK2  Var_05    OE2   CD   CG   CB    177.92  30.0  3
 LK2  Var_06    C29   C24  C23  O22  -179.08  30.0  3
 LK2  Var_07    C44   C29  C24  C23  -178.77  30.0  3
 LK2  Var_08    H441  C44  C29  C24   -59.06  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-3  CG   0.020
 LK2  plan-3  CD   0.020
 LK2  plan-3  OE2  0.020
 LK2  plan-3  OE1  0.020

