# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 14:12:49 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 5-(dimethylamino)naphthalene-2-sulfonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1cccc2cc(ccc12)[S](O)(=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
 DSY  DSY  '5-(dimethylamino)naphthalene-2-sulfonic acid'  ligand  29  17  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DSY
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
 DSY  C1    C  CR16   0  -0.336  -1.1043   0.0529  -0.8628
 DSY  C2    C  CR6    0  -0.210   0.1151   0.1443  -1.4698
 DSY  C3    C  CR16   0  -0.251   1.2979   0.0772  -0.7022
 DSY  C4    C  CR16   0  -0.302   1.2264  -0.0466   0.6562
 DSY  C4A   C  CR66   0   0.066  -0.0215  -0.1064   1.3240
 DSY  C5    C  CR6    0   0.283  -0.1209  -0.2266   2.7462
 DSY  C6    C  CR16   0  -0.343  -1.3637  -0.4108   3.3097
 DSY  C7    C  CR16   0  -0.251  -2.5295  -0.4342   2.5196
 DSY  C8    C  CR16   0  -0.338  -2.4621  -0.2534   1.1672
 DSY  C8A   C  CR66   0   0.123  -1.2041  -0.0914   0.5422
 DSY  N     N  NT     0  -0.488   1.0601  -0.1765   3.5049
 DSY  CM1   C  CH3    0  -0.542   1.6626   1.1456   3.6013
 DSY  CM2   C  CH3    0  -0.545   1.0274  -0.8335   4.7931
 DSY  S     S  S      0   1.414   0.2614   0.3109  -3.2437
 DSY  O1S   O  OS     0  -0.755   1.0117  -0.8830  -3.6701
 DSY  O2S   O  OS    -1  -0.755   1.0095   1.5634  -3.4462
 DSY  O3S   O  OS     0  -0.744  -1.1153   0.3561  -3.7651
 DSY  H1    H  HCR6   0   0.263  -2.0143   0.0807  -1.4488
 DSY  H3    H  HCR6   0   0.264   2.2656   0.1099  -1.1864
 DSY  H4    H  HCR6   0   0.266   2.1381  -0.1287   1.2322
 DSY  H6    H  HCR6   0   0.264  -1.4662  -0.5205   4.3814
 DSY  H7    H  HCR6   0   0.257  -3.4874  -0.5773   3.0029
 DSY  H8    H  HCR6   0   0.252  -3.3594  -0.2473   0.5606
 DSY  HM11  H  HCH3   0   0.238   2.6859   1.0549   3.9672
 DSY  HM12  H  HCH3   0   0.250   1.6992   1.6367   2.6312
 DSY  HM13  H  HCH3   0   0.218   1.1116   1.8014   4.2887
 DSY  HM21  H  HCH3   0   0.246   0.6387  -1.8465   4.6933
 DSY  HM22  H  HCH3   0   0.247   2.0457  -0.9008   5.1776
 DSY  HM23  H  HCH3   0   0.209   0.4275  -0.3061   5.5469

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
 DSY  C1   C2    aromatic  1.365  0.020  1.365
 DSY  C1   C8A   aromatic  1.416  0.020  1.416
 DSY  C1   H1    single    0.930  0.020  1.080
 DSY  C2   C3    aromatic  1.412  0.020  1.412
 DSY  C2   S     single    1.788  0.020  1.788
 DSY  C3   C4    aromatic  1.366  0.020  1.366
 DSY  C3   H3    single    0.930  0.020  1.080
 DSY  C4   C4A   aromatic  1.417  0.020  1.417
 DSY  C4   H4    single    0.930  0.020  1.080
 DSY  C4A  C5    aromatic  1.431  0.020  1.431
 DSY  C4A  C8A   aromatic  1.418  0.020  1.418
 DSY  C5   C6    aromatic  1.377  0.020  1.377
 DSY  C5   N     single    1.405  0.020  1.405
 DSY  C6   C7    aromatic  1.409  0.020  1.409
 DSY  C6   H6    single    0.930  0.020  1.080
 DSY  C7   C8    aromatic  1.366  0.020  1.366
 DSY  C7   H7    single    0.930  0.020  1.080
 DSY  C8   C8A   aromatic  1.414  0.020  1.414
 DSY  C8   H8    single    0.930  0.020  1.080
 DSY  N    CM1   single    1.456  0.020  1.456
 DSY  N    CM2   single    1.446  0.020  1.446
 DSY  CM1  HM11  single    0.970  0.020  1.090
 DSY  CM1  HM12  single    0.970  0.020  1.090
 DSY  CM1  HM13  single    0.970  0.020  1.090
 DSY  CM2  HM21  single    0.970  0.020  1.090
 DSY  CM2  HM22  single    0.970  0.020  1.090
 DSY  CM2  HM23  single    0.970  0.020  1.090
 DSY  S    O1S   deloc     1.473  0.020  1.473
 DSY  S    O2S   deloc     1.473  0.020  1.473
 DSY  S    O3S   deloc     1.473  0.020  1.473

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
 DSY  H1    C1   C8A   118.71  3.000
 DSY  H1    C1   C2    120.55  3.000
 DSY  C8A   C1   C2    120.73  3.000
 DSY  S     C2   C3    118.39  3.000
 DSY  S     C2   C1    121.37  3.000
 DSY  C3    C2   C1    120.22  3.000
 DSY  H3    C3   C4    119.63  3.000
 DSY  H3    C3   C2    120.29  3.000
 DSY  C4    C3   C2    120.08  3.000
 DSY  H4    C4   C4A   119.22  3.000
 DSY  H4    C4   C3    119.51  3.000
 DSY  C4A   C4   C3    121.25  3.000
 DSY  C8A   C4A  C5    119.42  3.000
 DSY  C8A   C4A  C4    118.32  3.000
 DSY  C5    C4A  C4    122.23  3.000
 DSY  N     C5   C6    122.86  3.000
 DSY  N     C5   C4A   118.40  3.000
 DSY  C6    C5   C4A   118.73  3.000
 DSY  H6    C6   C7    118.39  3.000
 DSY  H6    C6   C5    120.29  3.000
 DSY  C7    C6   C5    121.31  3.000
 DSY  H7    C7   C8    120.21  3.000
 DSY  H7    C7   C6    118.96  3.000
 DSY  C8    C7   C6    120.81  3.000
 DSY  H8    C8   C8A   119.26  3.000
 DSY  H8    C8   C7    120.95  3.000
 DSY  C8A   C8   C7    119.78  3.000
 DSY  C8    C8A  C4A   119.81  3.000
 DSY  C8    C8A  C1    120.86  3.000
 DSY  C4A   C8A  C1    119.31  3.000
 DSY  CM2   N    CM1   111.27  3.000
 DSY  CM2   N    C5    116.48  3.000
 DSY  CM1   N    C5    114.59  3.000
 DSY  HM13  CM1  HM12  107.78  3.000
 DSY  HM13  CM1  HM11  108.09  3.000
 DSY  HM12  CM1  HM11  107.77  3.000
 DSY  HM13  CM1  N     112.09  3.000
 DSY  HM12  CM1  N     111.39  3.000
 DSY  HM11  CM1  N     109.57  3.000
 DSY  HM23  CM2  HM22  107.32  3.000
 DSY  HM23  CM2  HM21  108.33  3.000
 DSY  HM22  CM2  HM21  107.94  3.000
 DSY  HM23  CM2  N     113.92  3.000
 DSY  HM22  CM2  N     108.72  3.000
 DSY  HM21  CM2  N     110.42  3.000
 DSY  O3S   S    O2S   113.58  3.000
 DSY  O3S   S    O1S   113.48  3.000
 DSY  O2S   S    O1S   113.00  3.000
 DSY  O3S   S    C2    106.12  3.000
 DSY  O2S   S    C2    104.91  3.000
 DSY  O1S   S    C2    104.67  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
 DSY  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 DSY  CONST_02  C4    C4A  C8A  C1      0.00   0.0  0
 DSY  CONST_03  C5    C4A  C8A  C1    180.00   0.0  0
 DSY  CONST_04  C7    C8   C8A  C1    180.00   0.0  0
 DSY  CONST_05  C4A   C8A  C1   C2      0.00   0.0  0
 DSY  CONST_06  C8    C8A  C1   C2    180.00   0.0  0
 DSY  CONST_07  C4A   C4   C3   C2      0.00   0.0  0
 DSY  CONST_08  C8A   C1   C2   C3      0.00   0.0  0
 DSY  CONST_09  C5    C4A  C4   C3    180.00   0.0  0
 DSY  CONST_10  C8A   C4A  C4   C3      0.00   0.0  0
 DSY  CONST_11  C6    C5   C4A  C4    180.00   0.0  0
 DSY  CONST_12  C8    C8A  C4A  C4    180.00   0.0  0
 DSY  CONST_13  C7    C6   C5   C4A     0.00   0.0  0
 DSY  CONST_14  C7    C8   C8A  C4A     0.00   0.0  0
 DSY  CONST_15  C8    C8A  C4A  C5      0.00   0.0  0
 DSY  CONST_16  C8    C7   C6   C5      0.00   0.0  0
 DSY  CONST_17  C8A   C4A  C5   C6      0.00   0.0  0
 DSY  CONST_18  C8A   C8   C7   C6      0.00   0.0  0
 DSY  CONST_19  S     C2   C3   C4    180.00   0.0  0
 DSY  CONST_20  N     C5   C4A  C4      0.00   0.0  0
 DSY  CONST_21  N     C5   C6   C7    180.00   0.0  0
 DSY  CONST_22  S     C2   C1   C8A   180.00   0.0  0
 DSY  CONST_23  N     C5   C4A  C8A   180.00   0.0  0
 DSY  CONST_24  H3    C3   C2   C1    180.00   0.0  0
 DSY  CONST_25  H8    C8   C8A  C1      0.00   0.0  0
 DSY  CONST_26  H4    C4   C3   C2    180.00   0.0  0
 DSY  CONST_27  H1    C1   C2   C3    180.00   0.0  0
 DSY  CONST_28  H6    C6   C5   C4A   180.00   0.0  0
 DSY  CONST_29  H7    C7   C6   C5    180.00   0.0  0
 DSY  Var_01    O1S   S    C2   C1   -118.77  30.0  2
 DSY  Var_02    HM11  CM1  N    C5   -165.07  30.0  3
 DSY  Var_03    HM21  CM2  N    C5     50.11  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
 DSY  plan-1  C1   0.020
 DSY  plan-1  C2   0.020
 DSY  plan-1  C3   0.020
 DSY  plan-1  C4   0.020
 DSY  plan-1  C4A  0.020
 DSY  plan-1  C5   0.020
 DSY  plan-1  C6   0.020
 DSY  plan-1  C7   0.020
 DSY  plan-1  C8   0.020
 DSY  plan-1  C8A  0.020
 DSY  plan-1  N    0.020
 DSY  plan-1  S    0.020
 DSY  plan-1  H1   0.020
 DSY  plan-1  H3   0.020
 DSY  plan-1  H4   0.020
 DSY  plan-1  H6   0.020
 DSY  plan-1  H7   0.020
 DSY  plan-1  H8   0.020
 DSY  plan-2  C5   0.020
 DSY  plan-2  N    0.020
 DSY  plan-2  CM1  0.020
 DSY  plan-2  CM2  0.020

