# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 14:17:03 2022
#   Inital geometry file: a 102 line input string
#   Ligand name: N-{[5-(dimethylamino)naphthalen-1-yl]sulfonyl}-N-methylglycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1cccc2c1cccc2[S](=O)(=O)N(C)CC(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
 9DS  9DS  N-{[5-(dimethylamino)naphthalen-1-yl]sulfonyl}-N-methylglycine  L-peptide  39  22  .  2012-08-28  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9DS
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
 9DS  N     N  N      0  -0.556  55.5654  33.2717  76.4516
 9DS  CA    C  CH2    0  -0.445  54.5902  33.4653  77.5161
 9DS  C     C  C      0   0.407  54.0725  32.1922  78.2174
 9DS  O     O  O      0  -0.587  54.3446  31.1016  77.6886
 9DS  OXT   O  OC    -1  -0.609  53.4045  32.4060  79.2461
 9DS  C6    C  CH3    0  -0.513  56.9192  32.9470  76.8707
 9DS  S8    S  S      0   1.370  55.0759  32.5719  75.0444
 9DS  O9    O  OS     0  -0.645  55.6189  31.2318  74.8649
 9DS  O10   O  OS     0  -0.662  53.6356  32.7570  74.9275
 9DS  C11   C  CR6    0  -0.264  55.8873  33.5970  73.8240
 9DS  C12   C  CR16   0  -0.256  56.7498  32.9669  72.9669
 9DS  C13   C  CR16   0  -0.247  57.4000  33.6920  71.9553
 9DS  C14   C  CR16   0  -0.291  57.2141  35.0408  71.8554
 9DS  C15   C  CR66   0   0.045  56.3669  35.7326  72.7514
 9DS  C16   C  CR66   0   0.188  55.6336  34.9987  73.7272
 9DS  C17   C  CR16   0  -0.354  54.6897  35.6913  74.5223
 9DS  C18   C  CR16   0  -0.236  54.5016  37.0341  74.3520
 9DS  C19   C  CR16   0  -0.339  55.2637  37.7735  73.4330
 9DS  C20   C  CR6    0   0.294  56.2076  37.1530  72.6506
 9DS  N21   N  NT     0  -0.490  57.0092  37.8499  71.7332
 9DS  C23   C  CH3    0  -0.544  56.4796  39.1002  71.2330
 9DS  C22   C  CH3    0  -0.541  58.4050  37.9875  72.1262
 9DS  HA    H  HCH2   0   0.266  53.7352  34.0279  77.1351
 9DS  HA2   H  HCH2   0   0.255  55.0683  34.1224  78.2458
 9DS  H61C  H  HCH3   0   0.250  57.6105  32.9973  76.0298
 9DS  H62C  H  HCH3   0   0.252  57.2365  33.6974  77.5929
 9DS  H63C  H  HCH3   0   0.238  56.9935  31.9612  77.3321
 9DS  H12   H  HCR6   0   0.283  56.9300  31.9051  73.0523
 9DS  H13   H  HCR6   0   0.266  58.0434  33.1733  71.2578
 9DS  H14   H  HCR6   0   0.274  57.7002  35.5920  71.0626
 9DS  H17   H  HCR6   0   0.254  54.0868  35.1748  75.2506
 9DS  H18   H  HCR6   0   0.260  53.7649  37.5483  74.9558
 9DS  H19   H  HCR6   0   0.266  55.1082  38.8419  73.3657
 9DS  H221  H  HCH3   0   0.239  58.9997  38.2871  71.2627
 9DS  H222  H  HCH3   0   0.220  58.5378  38.7448  72.9102
 9DS  H223  H  HCH3   0   0.251  58.8080  37.0483  72.4992
 9DS  H231  H  HCH3   0   0.210  56.5059  39.9180  71.9656
 9DS  H232  H  HCH3   0   0.248  57.0743  39.4141  70.3744
 9DS  H233  H  HCH3   0   0.246  55.4507  38.9721  70.8988

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
 9DS  C    OXT   deloc     1.245  0.020  1.245
 9DS  C    O     deloc     1.231  0.020  1.231
 9DS  C    CA    single    1.516  0.018  1.516
 9DS  C6   N     single    1.454  0.020  1.454
 9DS  N    S8    single    1.646  0.020  1.646
 9DS  N    CA    single    1.451  0.016  1.451
 9DS  S8   O9    double    1.457  0.020  1.457
 9DS  S8   O10   double    1.457  0.020  1.457
 9DS  S8   C11   single    1.788  0.020  1.788
 9DS  C11  C12   aromatic  1.370  0.020  1.370
 9DS  C11  C16   aromatic  1.428  0.020  1.428
 9DS  C12  C13   aromatic  1.404  0.020  1.404
 9DS  C13  C14   aromatic  1.365  0.020  1.365
 9DS  C14  C15   aromatic  1.414  0.020  1.414
 9DS  C15  C16   aromatic  1.424  0.020  1.424
 9DS  C15  C20   aromatic  1.433  0.020  1.433
 9DS  C16  C17   aromatic  1.415  0.020  1.415
 9DS  C17  C18   aromatic  1.367  0.020  1.367
 9DS  C18  C19   aromatic  1.404  0.020  1.404
 9DS  C19  C20   aromatic  1.374  0.020  1.374
 9DS  C20  N21   single    1.403  0.020  1.403
 9DS  N21  C22   single    1.457  0.020  1.457
 9DS  N21  C23   single    1.447  0.020  1.447
 9DS  CA   HA    single    0.970  0.020  1.090
 9DS  CA   HA2   single    0.970  0.020  1.090
 9DS  C6   H61C  single    0.970  0.020  1.090
 9DS  C6   H62C  single    0.970  0.020  1.090
 9DS  C6   H63C  single    0.970  0.020  1.090
 9DS  C12  H12   single    0.930  0.020  1.080
 9DS  C13  H13   single    0.930  0.020  1.080
 9DS  C14  H14   single    0.930  0.020  1.080
 9DS  C17  H17   single    0.930  0.020  1.080
 9DS  C18  H18   single    0.930  0.020  1.080
 9DS  C19  H19   single    0.930  0.020  1.080
 9DS  C22  H221  single    0.970  0.020  1.090
 9DS  C22  H222  single    0.970  0.020  1.090
 9DS  C22  H223  single    0.970  0.020  1.090
 9DS  C23  H231  single    0.970  0.020  1.090
 9DS  C23  H232  single    0.970  0.020  1.090
 9DS  C23  H233  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
 9DS  S8    N    C6    115.37  3.000
 9DS  S8    N    CA    118.83  3.000
 9DS  C6    N    CA    116.26  3.000
 9DS  HA2   CA   HA    105.41  3.000
 9DS  HA2   CA   C     109.85  3.000
 9DS  HA    CA   C     108.72  3.000
 9DS  HA2   CA   N     105.97  3.000
 9DS  HA    CA   N     109.74  3.000
 9DS  C     CA   N     113.30  2.900
 9DS  OXT   C    O     128.31  3.000
 9DS  O     C    CA    120.80  2.100
 9DS  OXT   C    CA    114.45  3.000
 9DS  H63C  C6   H62C  108.81  3.000
 9DS  H63C  C6   H61C  108.96  3.000
 9DS  H62C  C6   H61C  107.17  3.000
 9DS  H63C  C6   N     112.78  3.000
 9DS  H62C  C6   N     107.98  3.000
 9DS  H61C  C6   N     110.98  3.000
 9DS  C11   S8   O10   108.72  3.000
 9DS  C11   S8   O9    105.91  3.000
 9DS  O10   S8   O9    118.38  3.000
 9DS  C11   S8   N     101.82  3.000
 9DS  O10   S8   N     107.97  3.000
 9DS  O9    S8   N     112.67  3.000
 9DS  C16   C11  C12   121.41  3.000
 9DS  C16   C11  S8    121.90  3.000
 9DS  C12   C11  S8    116.68  3.000
 9DS  H12   C12  C13   119.16  3.000
 9DS  H12   C12  C11   120.52  3.000
 9DS  C13   C12  C11   120.32  3.000
 9DS  H13   C13  C14   120.51  3.000
 9DS  H13   C13  C12   119.50  3.000
 9DS  C14   C13  C12   119.99  3.000
 9DS  H14   C14  C15   118.99  3.000
 9DS  H14   C14  C13   119.75  3.000
 9DS  C15   C14  C13   121.25  3.000
 9DS  C20   C15  C16   120.12  3.000
 9DS  C20   C15  C14   120.47  3.000
 9DS  C16   C15  C14   119.37  3.000
 9DS  C17   C16  C15   118.43  3.000
 9DS  C17   C16  C11   124.11  3.000
 9DS  C15   C16  C11   117.44  3.000
 9DS  H17   C17  C18   118.58  3.000
 9DS  H17   C17  C16   121.23  3.000
 9DS  C18   C17  C16   120.17  3.000
 9DS  H18   C18  C19   118.97  3.000
 9DS  H18   C18  C17   119.40  3.000
 9DS  C19   C18  C17   121.62  3.000
 9DS  H19   C19  C20   120.62  3.000
 9DS  H19   C19  C18   118.86  3.000
 9DS  C20   C19  C18   120.51  3.000
 9DS  N21   C20  C19   122.70  3.000
 9DS  N21   C20  C15   118.34  3.000
 9DS  C19   C20  C15   118.94  3.000
 9DS  C22   N21  C23   111.24  3.000
 9DS  C23   N21  C20   116.49  3.000
 9DS  C22   N21  C20   114.70  3.000
 9DS  H233  C23  H232  107.90  3.000
 9DS  H233  C23  H231  108.35  3.000
 9DS  H232  C23  H231  107.33  3.000
 9DS  H233  C23  N21   110.49  3.000
 9DS  H232  C23  N21   108.74  3.000
 9DS  H231  C23  N21   113.83  3.000
 9DS  H223  C22  H222  107.81  3.000
 9DS  H223  C22  H221  107.86  3.000
 9DS  H222  C22  H221  108.05  3.000
 9DS  H223  C22  N21   111.46  3.000
 9DS  H222  C22  N21   111.94  3.000
 9DS  H221  C22  N21   109.57  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
 9DS  CONST_01  C14   C13  C12  C11     0.00   0.0  0
 9DS  CONST_02  C14   C15  C16  C11     0.00   0.0  0
 9DS  CONST_03  C20   C15  C16  C11   180.00   0.0  0
 9DS  CONST_04  C18   C17  C16  C11   180.00   0.0  0
 9DS  CONST_05  C15   C16  C11  C12     0.00   0.0  0
 9DS  CONST_06  C17   C16  C11  C12   180.00   0.0  0
 9DS  CONST_07  C15   C14  C13  C12     0.00   0.0  0
 9DS  CONST_08  C16   C11  C12  C13     0.00   0.0  0
 9DS  CONST_09  C16   C15  C14  C13     0.00   0.0  0
 9DS  CONST_10  C20   C15  C14  C13   180.00   0.0  0
 9DS  CONST_11  C17   C16  C15  C14   180.00   0.0  0
 9DS  CONST_12  C19   C20  C15  C14   180.00   0.0  0
 9DS  CONST_13  C18   C17  C16  C15     0.00   0.0  0
 9DS  CONST_14  C18   C19  C20  C15     0.00   0.0  0
 9DS  CONST_15  C19   C20  C15  C16     0.00   0.0  0
 9DS  CONST_16  C19   C18  C17  C16     0.00   0.0  0
 9DS  CONST_17  C20   C15  C16  C17     0.00   0.0  0
 9DS  CONST_18  C20   C19  C18  C17     0.00   0.0  0
 9DS  CONST_19  C13   C12  C11  S8    180.00   0.0  0
 9DS  CONST_20  C15   C16  C11  S8    180.00   0.0  0
 9DS  CONST_21  C17   C16  C11  S8      0.00   0.0  0
 9DS  CONST_22  N21   C20  C15  C14     0.00   0.0  0
 9DS  CONST_23  N21   C20  C15  C16   180.00   0.0  0
 9DS  CONST_24  N21   C20  C19  C18   180.00   0.0  0
 9DS  CONST_25  H13   C13  C12  C11   180.00   0.0  0
 9DS  CONST_26  H17   C17  C16  C11     0.00   0.0  0
 9DS  CONST_27  H14   C14  C13  C12   180.00   0.0  0
 9DS  CONST_28  H12   C12  C13  C14   180.00   0.0  0
 9DS  CONST_29  H19   C19  C20  C15   180.00   0.0  0
 9DS  CONST_30  H18   C18  C17  C16   180.00   0.0  0
 9DS  Var_01    C12   C11  S8   N     121.07  30.0  2
 9DS  Var_02    C11   S8   N    CA    137.03  30.0  3
 9DS  Var_03    H221  C22  N21  C20   164.67  30.0  3
 9DS  Var_04    H231  C23  N21  C20    73.48  30.0  3
 9DS  Var_05    OXT   C    CA   N     169.56  30.0  3
 9DS  Var_06    C6    N    CA   C     -75.51  30.0  3
 9DS  Var_07    H61C  C6   N    CA   -169.80  30.0  3

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
 9DS  plan-1  S8   0.020
 9DS  plan-1  C11  0.020
 9DS  plan-1  C12  0.020
 9DS  plan-1  C13  0.020
 9DS  plan-1  C14  0.020
 9DS  plan-1  C15  0.020
 9DS  plan-1  C16  0.020
 9DS  plan-1  C17  0.020
 9DS  plan-1  C18  0.020
 9DS  plan-1  C19  0.020
 9DS  plan-1  C20  0.020
 9DS  plan-1  N21  0.020
 9DS  plan-1  H12  0.020
 9DS  plan-1  H13  0.020
 9DS  plan-1  H14  0.020
 9DS  plan-1  H17  0.020
 9DS  plan-1  H18  0.020
 9DS  plan-1  H19  0.020
 9DS  plan-2  C20  0.020
 9DS  plan-2  N21  0.020
 9DS  plan-2  C23  0.020
 9DS  plan-2  C22  0.020
 9DS  plan-3  CA   0.020
 9DS  plan-3  C    0.020
 9DS  plan-3  O    0.020
 9DS  plan-3  OXT  0.020

