# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 18:15:01 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  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 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  -0.680  0.2234   4.4516   1.1876
 LK1  S11   S  S      0   1.365  1.2567   5.3897   0.7595
 LK1  O27   O  OS     0  -0.663  0.8196   6.6390   0.1410
 LK1  N     N  NC1    0  -0.715  2.2993   4.5236  -0.1737
 LK1  CA    C  CH1    0  -0.238  3.3393   5.2787  -0.8816
 LK1  C     C  C      0   0.427  2.8512   5.7223  -2.2780
 LK1  OXT   O  OC    -1  -0.610  3.4960   6.6389  -2.8194
 LK1  O     O  O      0  -0.605  1.8895   5.0914  -2.7614
 LK1  CB    C  CH2    0  -0.404  4.5876   4.4045  -1.0108
 LK1  CG    C  CH2    0  -0.593  5.2228   4.0203   0.3165
 LK1  CD    C  C      0   0.438  5.9378   5.1476   1.0875
 LK1  OE2   O  OC    -1  -0.624  6.4069   4.8300   2.1988
 LK1  OE1   O  O      0  -0.613  6.0310   6.2650   0.5385
 LK1  C12   C  CR6    0  -0.215  2.2869   5.7950   2.1322
 LK1  C17   C  CR16   0  -0.224  2.8009   4.7410   2.9220
 LK1  C16   C  CR16   0  -0.284  3.6135   5.0275   3.9745
 LK1  C15   C  CR66   0   0.174  3.9290   6.3691   4.3088
 LK1  C21   C  CR16   0  -0.441  4.7542   6.6843   5.4002
 LK1  C20   C  CR6    0   0.409  5.0380   7.9960   5.7153
 LK1  C19   C  CR16   0  -0.379  4.4914   9.0415   4.9333
 LK1  C18   C  CR16   0  -0.291  3.6907   8.7476   3.8629
 LK1  C14   C  CR66   0   0.112  3.3870   7.4149   3.5189
 LK1  C13   C  CR16   0  -0.292  2.5637   7.1008   2.4161
 LK1  O22   O  O2     0  -0.475  5.8374   8.2066   6.7735
 LK1  C23   C  CH2    0  -0.174  6.1587   9.5361   7.1619
 LK1  C24   C  CH2    0  -0.450  7.1135   9.4682   8.3349
 LK1  C25   C  CH2    0  -0.432  7.4936  10.8596   8.8285
 LK1  C26   C  CH3    0  -0.661  8.4896  10.8164   9.9788
 LK1  H     H  HNC1   0   0.389  1.7613   3.9794  -0.8503
 LK1  HA    H  HCH1   0   0.255  3.6180   6.1535  -0.2910
 LK1  HBC1  H  HCH2   0   0.218  5.3103   4.9443  -1.6241
 LK1  HBC2  H  HCH2   0   0.205  4.3191   3.5000  -1.5682
 LK1  HGC1  H  HCH2   0   0.228  4.4773   3.5651   0.9742
 LK1  HGC2  H  HCH2   0   0.222  5.9621   3.2304   0.1386
 LK1  H17   H  HCR6   0   0.272  2.5673   3.7138   2.6767
 LK1  H13   H  HCR6   0   0.275  2.1683   7.9041   1.8077
 LK1  H16   H  HCR6   0   0.251  4.0230   4.2253   4.5748
 LK1  H21   H  HCR6   0   0.259  5.1708   5.8863   6.0033
 LK1  H19   H  HCR6   0   0.286  4.6949  10.0772   5.1671
 LK1  H18   H  HCR6   0   0.266  3.2808   9.5542   3.2674
 LK1  H231  H  HCH2   0   0.223  5.2486  10.0793   7.4412
 LK1  H232  H  HCH2   0   0.224  6.6251  10.0753   6.3301
 LK1  H241  H  HCH2   0   0.228  8.0151   8.9251   8.0356
 LK1  H242  H  HCH2   0   0.229  6.6542   8.9022   9.1505
 LK1  H251  H  HCH2   0   0.220  6.5930  11.3937   9.1455
 LK1  H252  H  HCH2   0   0.220  7.9160  11.4380   8.0016
 LK1  H261  H  HCH3   0   0.219  8.0850  10.2702  10.8325
 LK1  H262  H  HCH3   0   0.219  9.4156  10.3220   9.6807
 LK1  H263  H  HCH3   0   0.230  8.7449  11.8198  10.3202

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    1.460  0.020  1.460
 LK1  S11  O27   double    1.461  0.020  1.461
 LK1  S11  N     single    1.646  0.020  1.646
 LK1  S11  C12   single    1.763  0.020  1.763
 LK1  N    CA    single    1.467  0.020  1.467
 LK1  N    H     single    0.860  0.020  1.020
 LK1  CA   C     single    1.544  0.020  1.544
 LK1  CA   CB    single    1.529  0.020  1.529
 LK1  CA   HA    single    0.970  0.020  1.090
 LK1  C    OXT   deloc     1.245  0.020  1.245
 LK1  C    O     deloc     1.248  0.020  1.248
 LK1  CB   CG    single    1.521  0.020  1.521
 LK1  CB   HBC1  single    0.970  0.020  1.090
 LK1  CB   HBC2  single    0.970  0.020  1.090
 LK1  CG   CD    single    1.542  0.020  1.542
 LK1  CG   HGC1  single    0.970  0.020  1.090
 LK1  CG   HGC2  single    0.970  0.020  1.090
 LK1  CD   OE2   deloc     1.247  0.020  1.247
 LK1  CD   OE1   deloc     1.248  0.020  1.248
 LK1  C12  C17   aromatic  1.414  0.020  1.414
 LK1  C12  C13   aromatic  1.365  0.020  1.365
 LK1  C17  C16   aromatic  1.360  0.020  1.360
 LK1  C17  H17   single    0.930  0.020  1.080
 LK1  C16  C15   aromatic  1.418  0.020  1.418
 LK1  C16  H16   single    0.930  0.020  1.080
 LK1  C15  C21   aromatic  1.404  0.020  1.404
 LK1  C15  C14   aromatic  1.418  0.020  1.418
 LK1  C21  C20   aromatic  1.379  0.020  1.379
 LK1  C21  H21   single    0.930  0.020  1.080
 LK1  C20  C19   aromatic  1.415  0.020  1.415
 LK1  C20  O22   single    1.343  0.020  1.343
 LK1  C19  C18   aromatic  1.369  0.020  1.369
 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    1.422  0.020  1.422
 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    1.525  0.020  1.525
 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     101.09  3.000
 LK1  C12   S11  O27   107.93  3.000
 LK1  N     S11  O27   113.55  3.000
 LK1  C12   S11  O28   109.45  3.000
 LK1  N     S11  O28   106.06  3.000
 LK1  O27   S11  O28   117.51  3.000
 LK1  H     N    CA    109.14  3.000
 LK1  H     N    S11   108.80  3.000
 LK1  CA    N    S11   116.86  3.000
 LK1  HA    CA   CB    107.17  3.000
 LK1  HA    CA   C     109.86  3.000
 LK1  CB    CA   C     110.22  3.000
 LK1  HA    CA   N     109.42  3.000
 LK1  CB    CA   N     108.97  3.000
 LK1  C     CA   N     111.11  3.000
 LK1  O     C    OXT   127.10  3.000
 LK1  O     C    CA    116.66  3.000
 LK1  OXT   C    CA    116.18  3.000
 LK1  HBC2  CB   HBC1  106.55  3.000
 LK1  HBC2  CB   CG    109.74  3.000
 LK1  HBC1  CB   CG    109.82  3.000
 LK1  HBC2  CB   CA    108.34  3.000
 LK1  HBC1  CB   CA    107.79  3.000
 LK1  CG    CB   CA    114.30  3.000
 LK1  HGC2  CG   HGC1  104.91  3.000
 LK1  HGC2  CG   CD    107.17  3.000
 LK1  HGC1  CG   CD    108.66  3.000
 LK1  HGC2  CG   CB    108.79  3.000
 LK1  HGC1  CG   CB    110.21  3.000
 LK1  CD    CG   CB    116.45  3.000
 LK1  OE1   CD   OE2   126.27  3.000
 LK1  OE1   CD   CG    117.98  3.000
 LK1  OE2   CD   CG    115.71  3.000
 LK1  C13   C12  C17   121.56  3.000
 LK1  C13   C12  S11   120.02  3.000
 LK1  C17   C12  S11   118.42  3.000
 LK1  H17   C17  C16   120.30  3.000
 LK1  H17   C17  C12   120.19  3.000
 LK1  C16   C17  C12   119.50  3.000
 LK1  H16   C16  C15   119.09  3.000
 LK1  H16   C16  C17   119.94  3.000
 LK1  C15   C16  C17   120.97  3.000
 LK1  C14   C15  C21   119.47  3.000
 LK1  C14   C15  C16   118.77  3.000
 LK1  C21   C15  C16   121.76  3.000
 LK1  H21   C21  C20   119.63  3.000
 LK1  H21   C21  C15   119.55  3.000
 LK1  C20   C21  C15   120.81  3.000
 LK1  O22   C20  C19   123.33  3.000
 LK1  O22   C20  C21   116.86  3.000
 LK1  C19   C20  C21   119.81  3.000
 LK1  H19   C19  C18   119.01  3.000
 LK1  H19   C19  C20   121.03  3.000
 LK1  C18   C19  C20   119.96  3.000
 LK1  H18   C18  C14   119.23  3.000
 LK1  H18   C18  C19   119.43  3.000
 LK1  C14   C18  C19   121.33  3.000
 LK1  C13   C14  C18   121.79  3.000
 LK1  C13   C14  C15   119.60  3.000
 LK1  C18   C14  C15   118.62  3.000
 LK1  H13   C13  C14   119.14  3.000
 LK1  H13   C13  C12   121.27  3.000
 LK1  C14   C13  C12   119.59  3.000
 LK1  C23   O22  C20   119.76  3.000
 LK1  H232  C23  H231  107.64  3.000
 LK1  H232  C23  C24   109.99  3.000
 LK1  H231  C23  C24   110.40  3.000
 LK1  H232  C23  O22   110.43  3.000
 LK1  H231  C23  O22   110.21  3.000
 LK1  C24   C23  O22   108.19  3.000
 LK1  H242  C24  H241  107.04  3.000
 LK1  H242  C24  C25   109.60  3.000
 LK1  H241  C24  C25   109.64  3.000
 LK1  H242  C24  C23   109.64  3.000
 LK1  H241  C24  C23   109.27  3.000
 LK1  C25   C24  C23   111.54  3.000
 LK1  H252  C25  H251  106.19  3.000
 LK1  H252  C25  C26   109.48  3.000
 LK1  H251  C25  C26   109.48  3.000
 LK1  H252  C25  C24   109.52  3.000
 LK1  H251  C25  C24   109.52  3.000
 LK1  C26   C25  C24   112.45  3.000
 LK1  H263  C26  H262  107.69  3.000
 LK1  H263  C26  H261  107.60  3.000
 LK1  H262  C26  H261  107.55  3.000
 LK1  H263  C26  C25   111.33  3.000
 LK1  H262  C26  C25   111.20  3.000
 LK1  H261  C26  C25   111.27  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  Var_01    C17   C12  S11  O28    49.01  30.0  2
 LK1  Var_02    C12   S11  N    CA    -73.84  30.0  2
 LK1  Var_03    C24   C23  O22  C20  -177.60  30.0  3
 LK1  Var_04    CD    CG   CB   CA    -71.05  30.0  3
 LK1  Var_05    OE2   CD   CG   CB    177.22  30.0  3
 LK1  Var_06    C25   C24  C23  O22  -179.15  30.0  3
 LK1  Var_07    C26   C25  C24  C23  -178.11  30.0  3
 LK1  Var_08    H261  C26  C25  C24   -59.70  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-3  CG   0.020
 LK1  plan-3  CD   0.020
 LK1  plan-3  OE2  0.020
 LK1  plan-3  OE1  0.020

