# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 19:38:12 2021
#   Inital geometry file: a 67 line input string
#   Ligand name: N-[4-(aminomethyl)phenyl]methanesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)Nc1ccc(CN)cc1
#
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
 RY4  RY4  N-[4-(aminomethyl)phenyl]methanesulfonamide  ligand  25  13  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RY4
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
 RY4  N1   N  NC1   0  -0.845  7.6795  17.8842   5.2095
 RY4  C4   C  CR16  0  -0.313  6.7893  19.6583   8.3346
 RY4  C5   C  CR6   0   0.096  5.4077  19.7640   8.2274
 RY4  C6   C  CR16  0  -0.290  4.7933  19.2246   7.0977
 RY4  C7   C  CR16  0  -0.253  5.5337  18.5993   6.1092
 RY4  C8   C  CH2   0  -0.342  4.5968  20.4229   9.3137
 RY4  C1   C  CH3   0  -0.783  7.1962  16.1237   3.2341
 RY4  C2   C  CR6   0   0.301  6.9148  18.4856   6.2394
 RY4  C3   C  CR16  0  -0.277  7.5402  19.0129   7.3611
 RY4  N2   N  NH2   0  -0.792  3.5642  21.2862   8.7663
 RY4  O1   O  OS    0  -0.661  8.9352  15.6715   5.1411
 RY4  O2   O  OS    0  -0.654  6.4954  15.7076   5.7338
 RY4  S1   S  S     0   1.323  7.6048  16.2317   4.9543
 RY4  H1   H  HNC1  0   0.420  8.6374  18.2136   5.1562
 RY4  H2   H  HCR6  0   0.253  7.2945  20.0821   9.1945
 RY4  H3   H  HCR6  0   0.250  3.7216  19.3160   6.9766
 RY4  H4   H  HCR6  0   0.260  5.0370  18.2182   5.2266
 RY4  H5   H  HCH2  0   0.239  4.0974  19.6475   9.9022
 RY4  H6   H  HCH2  0   0.215  5.2853  20.9276  10.0046
 RY4  H7   H  HCH3  0   0.301  7.1295  15.0689   2.9725
 RY4  H8   H  HCH3  0   0.293  6.2413  16.6136   3.0614
 RY4  H9   H  HCH3  0   0.296  7.9774  16.6019   2.6482
 RY4  H10  H  HCR6  0   0.266  8.6150  18.9348   7.4707
 RY4  H11  H  HNH2  0   0.353  2.9823  21.6289   9.5195
 RY4  H12  H  HNH2  0   0.343  3.9883  22.1033   8.3452

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
 RY4  C1  S1   single    1.771  0.020  1.771
 RY4  N1  S1   single    1.674  0.020  1.674
 RY4  N1  C2   single    1.417  0.020  1.417
 RY4  S1  O1   double    1.456  0.020  1.456
 RY4  S1  O2   double    1.454  0.020  1.454
 RY4  C7  C2   aromatic  1.392  0.020  1.392
 RY4  C7  C6   aromatic  1.384  0.020  1.384
 RY4  C2  C3   aromatic  1.388  0.020  1.388
 RY4  C6  C5   aromatic  1.394  0.020  1.394
 RY4  C3  C4   aromatic  1.389  0.020  1.389
 RY4  C5  C4   aromatic  1.390  0.020  1.390
 RY4  C5  C8   single    1.507  0.020  1.507
 RY4  N2  C8   single    1.453  0.020  1.453
 RY4  N1  H1   single    0.890  0.020  1.040
 RY4  C4  H2   single    0.930  0.020  1.080
 RY4  C6  H3   single    0.930  0.020  1.080
 RY4  C7  H4   single    0.930  0.020  1.080
 RY4  C8  H5   single    0.970  0.020  1.090
 RY4  C8  H6   single    0.970  0.020  1.090
 RY4  C1  H7   single    0.970  0.020  1.090
 RY4  C1  H8   single    0.970  0.020  1.090
 RY4  C1  H9   single    0.970  0.020  1.090
 RY4  C3  H10  single    0.930  0.020  1.080
 RY4  N2  H11  single    0.890  0.020  1.040
 RY4  N2  H12  single    0.890  0.020  1.040

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
 RY4  H1   N1  S1   110.78  3.000
 RY4  H1   N1  C2   114.21  3.000
 RY4  S1   N1  C2   120.39  3.000
 RY4  H2   C4  C3   119.08  3.000
 RY4  H2   C4  C5   119.66  3.000
 RY4  C3   C4  C5   121.25  3.000
 RY4  C8   C5  C6   121.06  3.000
 RY4  C8   C5  C4   120.83  3.000
 RY4  C6   C5  C4   118.11  3.000
 RY4  H3   C6  C7   119.20  3.000
 RY4  H3   C6  C5   119.62  3.000
 RY4  C7   C6  C5   121.16  3.000
 RY4  H4   C7  C2   120.20  3.000
 RY4  H4   C7  C6   119.73  3.000
 RY4  C2   C7  C6   120.06  3.000
 RY4  H6   C8  H5   105.87  3.000
 RY4  H6   C8  N2   114.18  3.000
 RY4  H5   C8  N2   107.42  3.000
 RY4  H6   C8  C5   108.48  3.000
 RY4  H5   C8  C5   108.87  3.000
 RY4  N2   C8  C5   111.75  3.000
 RY4  H9   C1  H8   110.32  3.000
 RY4  H9   C1  H7   109.91  3.000
 RY4  H8   C1  H7   110.16  3.000
 RY4  H9   C1  S1   109.31  3.000
 RY4  H8   C1  S1   109.24  3.000
 RY4  H7   C1  S1   107.85  3.000
 RY4  C3   C2  C7   119.44  3.000
 RY4  C3   C2  N1   120.36  3.000
 RY4  C7   C2  N1   120.15  3.000
 RY4  H10  C3  C2   120.09  3.000
 RY4  H10  C3  C4   119.94  3.000
 RY4  C2   C3  C4   119.96  3.000
 RY4  H12  N2  H11  106.09  3.000
 RY4  H12  N2  C8   109.79  3.000
 RY4  H11  N2  C8   109.24  3.000
 RY4  O2   S1  O1   119.34  3.000
 RY4  O2   S1  C1   108.82  3.000
 RY4  O1   S1  C1   108.18  3.000
 RY4  O2   S1  N1   107.95  3.000
 RY4  O1   S1  N1   108.64  3.000
 RY4  C1   S1  N1   102.63  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
 RY4  CONST_01  C7   C2  C3  C4    0.00   0.0  0
 RY4  CONST_02  C7   C6  C5  C4    0.00   0.0  0
 RY4  CONST_03  C2   C7  C6  C5    0.00   0.0  0
 RY4  CONST_04  C2   C3  C4  C5    0.00   0.0  0
 RY4  CONST_05  C3   C2  C7  C6    0.00   0.0  0
 RY4  CONST_06  C3   C4  C5  C6    0.00   0.0  0
 RY4  CONST_07  C6   C7  C2  N1  180.00   0.0  0
 RY4  CONST_08  C4   C3  C2  N1  180.00   0.0  0
 RY4  CONST_09  C8   C5  C6  C7  180.00   0.0  0
 RY4  CONST_10  C3   C4  C5  C8  180.00   0.0  0
 RY4  CONST_11  H3   C6  C5  C4  180.00   0.0  0
 RY4  CONST_12  H4   C7  C6  C5  180.00   0.0  0
 RY4  CONST_13  H10  C3  C4  C5  180.00   0.0  0
 RY4  CONST_14  H2   C4  C5  C6  180.00   0.0  0
 RY4  Var_01    N2   C8  C5  C4  137.80  30.0  2
 RY4  Var_02    C2   N1  S1  C1  126.17  30.0  2
 RY4  Var_03    H11  N2  C8  C5  173.97  30.0  3
 RY4  Var_04    H7   C1  S1  N1  179.76  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
 RY4  plan-1  N1   0.020
 RY4  plan-1  C4   0.020
 RY4  plan-1  C5   0.020
 RY4  plan-1  C6   0.020
 RY4  plan-1  C7   0.020
 RY4  plan-1  C8   0.020
 RY4  plan-1  C2   0.020
 RY4  plan-1  C3   0.020
 RY4  plan-1  H2   0.020
 RY4  plan-1  H3   0.020
 RY4  plan-1  H4   0.020
 RY4  plan-1  H10  0.020
 RY4  plan-2  N1   0.020
 RY4  plan-2  C2   0.020
 RY4  plan-2  S1   0.020
 RY4  plan-2  H1   0.020

