# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 10:57:00 2022
#   Inital geometry file: a 124 line input string
#   Ligand name: N~6~-{[5-(dimethylamino)naphthalen-1-yl]sulfonyl}-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1cccc2c1cccc2[S](=O)(=O)NCCCC[C@H](N)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
 DNS  DNS  N~6~-{[5-(dimethylamino)naphthalen-1-yl]sulfonyl}-L-lysine  L-peptide  50  26  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_DNS
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
 DNS  C1    C  CH3    0  -0.545  70.0704  20.3967  -40.0804
 DNS  N1    N  NT     0  -0.489  69.4925  19.1714  -40.5897
 DNS  C2    C  CH3    0  -0.543  69.7172  19.0352  -42.0228
 DNS  C3    C  CR6    0   0.295  69.7401  18.0094  -39.8467
 DNS  C4    C  CR16   0  -0.339  70.8190  17.8824  -39.0036
 DNS  C5    C  CR16   0  -0.226  71.0365  16.6900  -38.2973
 DNS  C6    C  CR16   0  -0.370  70.2159  15.6076  -38.4493
 DNS  C7    C  CR66   0   0.175  69.0866  15.6879  -39.2974
 DNS  C8    C  CR6    0  -0.279  68.1810  14.6089  -39.5304
 DNS  S     S  S      0   1.364  68.5467  12.9579  -38.9636
 DNS  OA    O  OS     0  -0.652  68.8659  12.9831  -37.5451
 DNS  OB    O  OS     0  -0.646  67.4806  12.0875  -39.4314
 DNS  NZ    N  NC1    0  -0.734  69.9010  12.5024  -39.7659
 DNS  CE    C  CH2    0  -0.274  69.8367  12.3791  -41.2266
 DNS  CD    C  CH2    0  -0.473  71.1774  12.7026  -41.8639
 DNS  CG    C  CH2    0  -0.436  71.6109  14.1550  -41.6960
 DNS  CB    C  CH2    0  -0.399  72.8589  14.4818  -42.5029
 DNS  CA    C  CH1    0  -0.205  73.3634  15.9179  -42.3449
 DNS  C     C  C      0   0.417  74.2264  16.1477  -41.0760
 DNS  OXT   O  OC    -1  -0.608  75.0725  17.0629  -41.1423
 DNS  O     O  O      0  -0.595  73.9915  15.4344  -40.0803
 DNS  N     N  NH2    0  -0.813  74.1268  16.2926  -43.5304
 DNS  C9    C  CR16   0  -0.239  67.0443  14.7725  -40.2770
 DNS  C10   C  CR16   0  -0.250  66.7349  16.0297  -40.8210
 DNS  C11   C  CR16   0  -0.288  67.6071  17.0704  -40.6740
 DNS  C12   C  CR66   0   0.043  68.8152  16.9205  -39.9554
 DNS  H11A  H  HCH3   0   0.249  69.6199  21.2406  -40.6035
 DNS  H12   H  HCH3   0   0.212  71.1572  20.4652  -40.2218
 DNS  H13   H  HCH3   0   0.247  69.8551  20.5060  -39.0182
 DNS  H21   H  HCH3   0   0.252  69.2758  18.1190  -42.4089
 DNS  H22   H  HCH3   0   0.222  70.7872  19.0224  -42.2699
 DNS  H23   H  HCH3   0   0.241  69.2582  19.8744  -42.5461
 DNS  H4    H  HCR6   0   0.269  71.5243  18.6935  -38.8827
 DNS  H5    H  HCR6   0   0.262  71.8885  16.6214  -37.6339
 DNS  H6    H  HCR6   0   0.261  70.4281  14.7172  -37.8791
 DNS  HZ    H  HNC1   0   0.416  70.7479  12.9218  -39.4003
 DNS  HE3   H  HCH2   0   0.239  69.0838  13.0560  -41.6444
 DNS  HE2   H  HCH2   0   0.258  69.5335  11.3627  -41.4792
 DNS  HD3   H  HCH2   0   0.239  71.0864  12.4682  -42.9279
 DNS  HD2   H  HCH2   0   0.232  71.9467  12.0311  -41.4697
 DNS  HG3   H  HCH2   0   0.229  71.7991  14.3864  -40.6471
 DNS  HG2   H  HCH2   0   0.203  70.7936  14.8135  -42.0133
 DNS  HB3   H  HCH2   0   0.203  72.6274  14.3134  -43.5608
 DNS  HB2   H  HCH2   0   0.204  73.6592  13.7766  -42.2572
 DNS  HA    H  HCH1   0   0.187  72.4727  16.5642  -42.2154
 DNS  H     H  HNH2   0   0.329  74.5953  17.1683  -43.3397
 DNS  H2    H  HNH2   0   0.326  73.4930  16.4600  -44.3016
 DNS  H9    H  HCR6   0   0.286  66.3727  13.9434  -40.4494
 DNS  H10   H  HCR6   0   0.268  65.8088  16.1622  -41.3633
 DNS  H11   H  HCR6   0   0.276  67.3626  18.0367  -41.0928

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
 DNS  C1   N1    single    1.447  0.020  1.447
 DNS  C1   H11A  single    0.970  0.020  1.090
 DNS  C1   H12   single    0.970  0.020  1.090
 DNS  C1   H13   single    0.970  0.020  1.090
 DNS  N1   C2    single    1.457  0.020  1.457
 DNS  N1   C3    single    1.401  0.020  1.401
 DNS  C2   H21   single    0.970  0.020  1.090
 DNS  C2   H22   single    0.970  0.020  1.090
 DNS  C2   H23   single    0.970  0.020  1.090
 DNS  C3   C4    aromatic  1.375  0.020  1.375
 DNS  C3   C12   aromatic  1.433  0.020  1.433
 DNS  C4   C5    aromatic  1.403  0.020  1.403
 DNS  C4   H4    single    0.930  0.020  1.080
 DNS  C5   C6    aromatic  1.367  0.020  1.367
 DNS  C5   H5    single    0.930  0.020  1.080
 DNS  C6   C7    aromatic  1.415  0.020  1.415
 DNS  C6   H6    single    0.930  0.020  1.080
 DNS  C7   C8    aromatic  1.428  0.020  1.428
 DNS  C7   C12   aromatic  1.423  0.020  1.423
 DNS  C8   S     single    1.783  0.020  1.783
 DNS  C8   C9    aromatic  1.370  0.020  1.370
 DNS  S    OA    double    1.454  0.020  1.454
 DNS  S    OB    double    1.454  0.020  1.454
 DNS  S    NZ    single    1.639  0.020  1.639
 DNS  NZ   CE    single    1.467  0.020  1.467
 DNS  NZ   HZ    single    0.890  0.020  1.040
 DNS  CE   CD    single    1.519  0.020  1.519
 DNS  CE   HE3   single    0.970  0.020  1.090
 DNS  CE   HE2   single    0.970  0.020  1.090
 DNS  CD   CG    single    1.525  0.020  1.525
 DNS  CD   HD3   single    0.970  0.020  1.090
 DNS  CD   HD2   single    0.970  0.020  1.090
 DNS  CG   CB    single    1.522  0.020  1.522
 DNS  CG   HG3   single    0.970  0.020  1.090
 DNS  CG   HG2   single    0.970  0.020  1.090
 DNS  CB   CA    single    1.530  0.020  1.530
 DNS  CB   HB3   single    0.970  0.020  1.090
 DNS  CB   HB2   single    0.970  0.020  1.090
 DNS  CA   C     single    1.525  0.021  1.525
 DNS  CA   N     single    1.458  0.019  1.458
 DNS  CA   HA    single    0.970  0.020  0.970
 DNS  C    OXT   deloc     1.248  0.020  1.248
 DNS  C    O     deloc     1.231  0.020  1.231
 DNS  N    H     single    0.860  0.020  0.860
 DNS  N    H2    single    0.890  0.020  1.040
 DNS  C9   C10   aromatic  1.404  0.020  1.404
 DNS  C9   H9    single    0.930  0.020  1.080
 DNS  C10  C11   aromatic  1.366  0.020  1.366
 DNS  C10  H10   single    0.930  0.020  1.080
 DNS  C11  C12   aromatic  1.414  0.020  1.414
 DNS  C11  H11   single    0.930  0.020  1.080

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
 DNS  H13   C1   H12   108.35  3.000
 DNS  H13   C1   H11A  107.97  3.000
 DNS  H12   C1   H11A  107.39  3.000
 DNS  H13   C1   N1    110.44  3.000
 DNS  H12   C1   N1    113.75  3.000
 DNS  H11A  C1   N1    108.75  3.000
 DNS  C3    N1   C2    114.63  3.000
 DNS  C3    N1   C1    116.42  3.000
 DNS  C2    N1   C1    111.33  3.000
 DNS  H23   C2   H22   108.13  3.000
 DNS  H23   C2   H21   107.89  3.000
 DNS  H22   C2   H21   107.80  3.000
 DNS  H23   C2   N1    109.58  3.000
 DNS  H22   C2   N1    111.88  3.000
 DNS  H21   C2   N1    111.42  3.000
 DNS  C12   C3   C4    118.87  3.000
 DNS  C12   C3   N1    118.42  3.000
 DNS  C4    C3   N1    122.70  3.000
 DNS  H4    C4   C5    118.69  3.000
 DNS  H4    C4   C3    120.72  3.000
 DNS  C5    C4   C3    120.58  3.000
 DNS  H5    C5   C6    119.39  3.000
 DNS  H5    C5   C4    118.99  3.000
 DNS  C6    C5   C4    121.61  3.000
 DNS  H6    C6   C7    121.39  3.000
 DNS  H6    C6   C5    118.49  3.000
 DNS  C7    C6   C5    120.07  3.000
 DNS  C12   C7   C8    117.26  3.000
 DNS  C12   C7   C6    118.59  3.000
 DNS  C8    C7   C6    124.15  3.000
 DNS  C9    C8   S     117.00  3.000
 DNS  C9    C8   C7    121.67  3.000
 DNS  S     C8   C7    121.17  3.000
 DNS  NZ    S    OB    106.38  3.000
 DNS  NZ    S    OA    107.52  3.000
 DNS  OB    S    OA    119.03  3.000
 DNS  NZ    S    C8    105.73  3.000
 DNS  OB    S    C8    107.55  3.000
 DNS  OA    S    C8    109.82  3.000
 DNS  HZ    NZ   CE    115.50  3.000
 DNS  HZ    NZ   S     113.51  3.000
 DNS  CE    NZ   S     118.34  3.000
 DNS  HE2   CE   HE3   107.25  3.000
 DNS  HE2   CE   CD    110.29  3.000
 DNS  HE3   CE   CD    108.36  3.000
 DNS  HE2   CE   NZ    108.74  3.000
 DNS  HE3   CE   NZ    110.97  3.000
 DNS  CD    CE   NZ    111.17  3.000
 DNS  HD2   CD   HD3   106.11  3.000
 DNS  HD2   CD   CG    110.17  3.000
 DNS  HD3   CD   CG    109.57  3.000
 DNS  HD2   CD   CE    109.78  3.000
 DNS  HD3   CD   CE    106.81  3.000
 DNS  CG    CD   CE    114.05  3.000
 DNS  HG2   CG   HG3   106.23  3.000
 DNS  HG2   CG   CB    109.20  3.000
 DNS  HG3   CG   CB    108.84  3.000
 DNS  HG2   CG   CD    109.16  3.000
 DNS  HG3   CG   CD    110.92  3.000
 DNS  CB    CG   CD    112.29  3.000
 DNS  HB2   CB   HB3   105.79  3.000
 DNS  HB2   CB   CA    109.90  3.000
 DNS  HB3   CB   CA    108.27  3.000
 DNS  HB2   CB   CG    110.01  3.000
 DNS  HB3   CB   CG    107.79  3.000
 DNS  CA    CB   CG    114.66  3.000
 DNS  HA    CA   N     110.00  3.000
 DNS  HA    CA   C     109.00  3.000
 DNS  N     CA   C     111.00  2.800
 DNS  HA    CA   CB    109.00  3.000
 DNS  N     CA   CB    110.50  1.700
 DNS  C     CA   CB    110.10  1.900
 DNS  O     C    OXT   126.12  3.000
 DNS  O     C    CA    120.80  1.700
 DNS  OXT   C    CA    116.25  3.000
 DNS  H2    N    H     106.89  3.000
 DNS  H2    N    CA    109.51  3.000
 DNS  H     N    CA    114.00  3.000
 DNS  H9    C9   C10   119.21  3.000
 DNS  H9    C9   C8    120.73  3.000
 DNS  C10   C9   C8    120.06  3.000
 DNS  H10   C10  C11   120.50  3.000
 DNS  H10   C10  C9    119.52  3.000
 DNS  C11   C10  C9    119.98  3.000
 DNS  H11   C11  C12   119.00  3.000
 DNS  H11   C11  C10   119.66  3.000
 DNS  C12   C11  C10   121.31  3.000
 DNS  C11   C12  C7    119.32  3.000
 DNS  C11   C12  C3    120.64  3.000
 DNS  C7    C12  C3    120.00  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
 DNS  CONST_01  C6    C5   C4   C3     0.00   0.0  0
 DNS  CONST_02  C6    C7   C12  C3     0.00   0.0  0
 DNS  CONST_03  C8    C7   C12  C3   180.00   0.0  0
 DNS  CONST_04  C10   C11  C12  C3   180.00   0.0  0
 DNS  CONST_05  C7    C12  C3   C4     0.00   0.0  0
 DNS  CONST_06  C11   C12  C3   C4   180.00   0.0  0
 DNS  CONST_07  C7    C6   C5   C4     0.00   0.0  0
 DNS  CONST_08  C12   C3   C4   C5     0.00   0.0  0
 DNS  CONST_09  C8    C7   C6   C5   180.00   0.0  0
 DNS  CONST_10  C12   C7   C6   C5     0.00   0.0  0
 DNS  CONST_11  C9    C8   C7   C6   180.00   0.0  0
 DNS  CONST_12  C11   C12  C7   C6   180.00   0.0  0
 DNS  CONST_13  C10   C9   C8   C7     0.00   0.0  0
 DNS  CONST_14  C10   C11  C12  C7     0.00   0.0  0
 DNS  CONST_15  C11   C12  C7   C8     0.00   0.0  0
 DNS  CONST_16  C11   C10  C9   C8     0.00   0.0  0
 DNS  CONST_17  C12   C7   C8   C9     0.00   0.0  0
 DNS  CONST_18  C12   C11  C10  C9     0.00   0.0  0
 DNS  CONST_19  C5    C4   C3   N1   180.00   0.0  0
 DNS  CONST_20  C7    C12  C3   N1   180.00   0.0  0
 DNS  CONST_21  C11   C12  C3   N1     0.00   0.0  0
 DNS  CONST_22  S     C8   C7   C6     0.00   0.0  0
 DNS  CONST_23  C12   C7   C8   S    180.00   0.0  0
 DNS  CONST_24  C10   C9   C8   S    180.00   0.0  0
 DNS  CONST_25  H5    C5   C4   C3   180.00   0.0  0
 DNS  CONST_26  H11   C11  C12  C3     0.00   0.0  0
 DNS  CONST_27  H6    C6   C5   C4   180.00   0.0  0
 DNS  CONST_28  H4    C4   C5   C6   180.00   0.0  0
 DNS  CONST_29  H9    C9   C8   C7   180.00   0.0  0
 DNS  CONST_30  H10   C10  C9   C8   180.00   0.0  0
 DNS  Var_01    OA    S    C8   C7    52.77  30.0  2
 DNS  Var_02    CE    NZ   S    C8   -63.63  30.0  3
 DNS  Var_03    H11A  C1   N1   C3  -166.98  30.0  3
 DNS  Var_04    H21   C2   N1   C3    45.73  30.0  3
 DNS  Var_05    CD    CE   NZ   S    149.07  30.0  3
 DNS  Var_06    CG    CD   CE   NZ   -65.79  30.0  3
 DNS  Var_07    CB    CG   CD   CE  -172.31  30.0  3
 DNS  Var_08    CA    CB   CG   CD  -178.47  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
 DNS  chir_01  CA  CB  C  N  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
 DNS  plan-1  N1   0.020
 DNS  plan-1  C3   0.020
 DNS  plan-1  C4   0.020
 DNS  plan-1  C5   0.020
 DNS  plan-1  C6   0.020
 DNS  plan-1  C7   0.020
 DNS  plan-1  C8   0.020
 DNS  plan-1  S    0.020
 DNS  plan-1  C9   0.020
 DNS  plan-1  C10  0.020
 DNS  plan-1  C11  0.020
 DNS  plan-1  C12  0.020
 DNS  plan-1  H4   0.020
 DNS  plan-1  H5   0.020
 DNS  plan-1  H6   0.020
 DNS  plan-1  H9   0.020
 DNS  plan-1  H10  0.020
 DNS  plan-1  H11  0.020
 DNS  plan-2  C1   0.020
 DNS  plan-2  N1   0.020
 DNS  plan-2  C2   0.020
 DNS  plan-2  C3   0.020
 DNS  plan-3  CA   0.020
 DNS  plan-3  C    0.020
 DNS  plan-3  OXT  0.020
 DNS  plan-3  O    0.020

