# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 17:02:55 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 4-(aminomethyl)-~{N}-(pyridin-2-ylmethyl)benzenesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccc(cc1)[S](=O)(=O)NCc2ccccn2
#
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
 9RT  9RT  4-(aminomethyl)-~{N}-(pyridin-2-ylmethyl)benzenesulfonamide  ligand  34  19  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9RT
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
 9RT  N1   N  NH2   0  -0.794   5.6269   1.8514  -0.8938
 9RT  C1   C  CH2   0  -0.334   4.7933   1.8667   0.2918
 9RT  C2   C  CR6   0   0.099   3.6535   0.8845   0.2093
 9RT  C3   C  CR16  0  -0.291   3.1158   0.3441   1.3767
 9RT  C4   C  CR16  0  -0.221   2.0384  -0.5231   1.3344
 9RT  C5   C  CR6   0  -0.220   1.4925  -0.8621   0.1018
 9RT  S1   S  S     0   1.370   0.0828  -1.9292   0.0463
 9RT  O1   O  OS    0  -0.654  -0.0470  -2.4286  -1.3126
 9RT  O2   O  OS    0  -0.655   0.1624  -2.8600   1.1597
 9RT  N2   N  NC1   0  -0.720  -1.2405  -0.9881   0.3417
 9RT  C6   C  CH2   0  -0.350  -1.5326   0.1116  -0.5741
 9RT  C7   C  CR6   0   0.234  -2.9084   0.6441  -0.2780
 9RT  C8   C  CR16  0  -0.332  -3.0752   1.9058   0.2768
 9RT  C9   C  CR16  0  -0.147  -4.3613   2.3550   0.5427
 9RT  C10  C  CR16  0  -0.323  -5.4293   1.5260   0.2451
 9RT  C11  C  CR16  0  -0.077  -5.1588   0.2810  -0.3083
 9RT  N3   N  N     0  -0.405  -3.9337  -0.1536  -0.5652
 9RT  C12  C  CR16  0  -0.215   2.0169  -0.3454  -1.0750
 9RT  C13  C  CR16  0  -0.279   3.0961   0.5228  -1.0136
 9RT  H1   H  HNH2  0   0.359   6.2630   2.6368  -0.8653
 9RT  H2   H  HNH2  0   0.348   6.2031   1.0194  -0.8954
 9RT  H4   H  HCH2  0   0.223   5.3392   1.6909   1.2283
 9RT  H5   H  HCH2  0   0.253   4.3615   2.8675   0.3876
 9RT  H6   H  HCR6  0   0.263   3.5501   0.5981   2.3361
 9RT  H7   H  HCR6  0   0.283   1.6432  -0.9339   2.2542
 9RT  H8   H  HNC1  0   0.413  -1.2941  -0.7230   1.3206
 9RT  H9   H  HCH2  0   0.260  -0.7948   0.9162  -0.4998
 9RT  H10  H  HCH2  0   0.281  -1.5096  -0.2709  -1.5942
 9RT  H11  H  HCR6  0   0.273  -2.2149   2.5244   0.4960
 9RT  H12  H  HCR6  0   0.277  -4.5231   3.3333   0.9756
 9RT  H13  H  HCR6  0   0.274  -6.4497   1.8304   0.4318
 9RT  H14  H  HCR6  0   0.265  -5.9721  -0.3918  -0.5571
 9RT  H15  H  HCR6  0   0.282   1.5995  -0.6149  -2.0356
 9RT  H16  H  HCR6  0   0.264   3.5152   0.9192  -1.9282

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
 9RT  C11  C10  aromatic  1.389  0.020  1.389
 9RT  C11  N3   aromatic  1.325  0.020  1.325
 9RT  C10  C9   aromatic  1.384  0.020  1.384
 9RT  O2   S1   double    1.453  0.020  1.453
 9RT  N3   C7   aromatic  1.330  0.020  1.330
 9RT  C9   C8   aromatic  1.388  0.020  1.388
 9RT  C7   C8   aromatic  1.388  0.020  1.388
 9RT  C7   C6   single    1.505  0.020  1.505
 9RT  N2   S1   single    1.650  0.020  1.650
 9RT  N2   C6   single    1.461  0.020  1.461
 9RT  S1   O1   double    1.454  0.020  1.454
 9RT  S1   C5   single    1.769  0.020  1.769
 9RT  C12  C5   aromatic  1.388  0.020  1.388
 9RT  C12  C13  aromatic  1.386  0.020  1.386
 9RT  C5   C4   aromatic  1.390  0.020  1.390
 9RT  C13  C2   aromatic  1.392  0.020  1.392
 9RT  C4   C3   aromatic  1.384  0.020  1.384
 9RT  C2   C3   aromatic  1.394  0.020  1.394
 9RT  C2   C1   single    1.507  0.020  1.507
 9RT  N1   C1   single    1.449  0.020  1.449
 9RT  N1   H1   single    0.890  0.020  1.040
 9RT  N1   H2   single    0.890  0.020  1.040
 9RT  C1   H4   single    0.970  0.020  1.090
 9RT  C1   H5   single    0.970  0.020  1.090
 9RT  C3   H6   single    0.930  0.020  1.080
 9RT  C4   H7   single    0.930  0.020  1.080
 9RT  N2   H8   single    0.890  0.020  1.040
 9RT  C6   H9   single    0.970  0.020  1.090
 9RT  C6   H10  single    0.970  0.020  1.090
 9RT  C8   H11  single    0.930  0.020  1.080
 9RT  C9   H12  single    0.930  0.020  1.080
 9RT  C10  H13  single    0.930  0.020  1.080
 9RT  C11  H14  single    0.930  0.020  1.080
 9RT  C12  H15  single    0.930  0.020  1.080
 9RT  C13  H16  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
 9RT  H2   N1   H1   106.28  3.000
 9RT  H2   N1   C1   109.72  3.000
 9RT  H1   N1   C1   109.30  3.000
 9RT  H5   C1   H4   105.55  3.000
 9RT  H5   C1   C2   107.61  3.000
 9RT  H4   C1   C2   108.56  3.000
 9RT  H5   C1   N1   107.95  3.000
 9RT  H4   C1   N1   114.21  3.000
 9RT  C2   C1   N1   112.54  3.000
 9RT  C13  C2   C3   118.72  3.000
 9RT  C3   C2   C1   119.90  3.000
 9RT  C13  C2   C1   121.37  3.000
 9RT  H6   C3   C4   119.09  3.000
 9RT  H6   C3   C2   119.74  3.000
 9RT  C4   C3   C2   121.17  3.000
 9RT  H7   C4   C5   121.17  3.000
 9RT  H7   C4   C3   119.76  3.000
 9RT  C5   C4   C3   119.06  3.000
 9RT  C12  C5   S1   119.93  3.000
 9RT  C12  C5   C4   120.84  3.000
 9RT  S1   C5   C4   119.20  3.000
 9RT  N2   S1   O2   105.78  3.000
 9RT  N2   S1   O1   106.95  3.000
 9RT  O2   S1   O1   120.07  3.000
 9RT  O1   S1   C5   107.93  3.000
 9RT  N2   S1   C5   106.82  3.000
 9RT  O2   S1   C5   108.58  3.000
 9RT  H8   N2   C6   113.41  3.000
 9RT  H8   N2   S1   111.33  3.000
 9RT  C6   N2   S1   118.52  3.000
 9RT  H10  C6   H9   107.90  3.000
 9RT  H10  C6   C7   109.13  3.000
 9RT  H9   C6   C7   110.06  3.000
 9RT  H10  C6   N2   108.57  3.000
 9RT  H9   C6   N2   112.10  3.000
 9RT  C7   C6   N2   109.03  3.000
 9RT  N3   C7   C8   122.58  3.000
 9RT  C8   C7   C6   120.67  3.000
 9RT  N3   C7   C6   116.74  3.000
 9RT  H11  C8   C9   120.85  3.000
 9RT  H11  C8   C7   120.33  3.000
 9RT  C9   C8   C7   118.82  3.000
 9RT  H12  C9   C10  120.80  3.000
 9RT  H12  C9   C8   120.53  3.000
 9RT  C10  C9   C8   118.68  3.000
 9RT  H13  C10  C11  120.33  3.000
 9RT  H13  C10  C9   121.50  3.000
 9RT  C11  C10  C9   118.17  3.000
 9RT  H14  C11  N3   116.45  3.000
 9RT  H14  C11  C10  120.09  3.000
 9RT  N3   C11  C10  123.46  3.000
 9RT  C11  N3   C7   118.29  3.000
 9RT  H15  C12  C13  119.72  3.000
 9RT  H15  C12  C5   120.97  3.000
 9RT  C13  C12  C5   119.31  3.000
 9RT  H16  C13  C12  119.59  3.000
 9RT  H16  C13  C2   119.51  3.000
 9RT  C12  C13  C2   120.90  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
 9RT  CONST_01  C5   C12  C13  C2     0.00   0.0  0
 9RT  CONST_02  C5   C4   C3   C2     0.00   0.0  0
 9RT  CONST_03  C12  C5   C4   C3     0.00   0.0  0
 9RT  CONST_04  C12  C13  C2   C3     0.00   0.0  0
 9RT  CONST_05  C13  C12  C5   C4     0.00   0.0  0
 9RT  CONST_06  C13  C2   C3   C4     0.00   0.0  0
 9RT  CONST_07  C10  C11  N3   C7     0.00   0.0  0
 9RT  CONST_08  C10  C9   C8   C7     0.00   0.0  0
 9RT  CONST_09  C11  C10  C9   C8     0.00   0.0  0
 9RT  CONST_10  C11  N3   C7   C8     0.00   0.0  0
 9RT  CONST_11  N3   C11  C10  C9     0.00   0.0  0
 9RT  CONST_12  N3   C7   C8   C9     0.00   0.0  0
 9RT  CONST_13  C12  C13  C2   C1   180.00   0.0  0
 9RT  CONST_14  C4   C3   C2   C1   180.00   0.0  0
 9RT  CONST_15  S1   C5   C4   C3   180.00   0.0  0
 9RT  CONST_16  C13  C12  C5   S1   180.00   0.0  0
 9RT  CONST_17  C11  N3   C7   C6   180.00   0.0  0
 9RT  CONST_18  C9   C8   C7   C6   180.00   0.0  0
 9RT  CONST_19  H15  C12  C13  C2   180.00   0.0  0
 9RT  CONST_20  H7   C4   C3   C2   180.00   0.0  0
 9RT  CONST_21  H16  C13  C2   C3   180.00   0.0  0
 9RT  CONST_22  H6   C3   C4   C5   180.00   0.0  0
 9RT  CONST_23  H14  C11  N3   C7   180.00   0.0  0
 9RT  CONST_24  H12  C9   C8   C7   180.00   0.0  0
 9RT  CONST_25  H13  C10  C9   C8   180.00   0.0  0
 9RT  CONST_26  H11  C8   C9   C10  180.00   0.0  0
 9RT  Var_01    C13  C2   C1   N1   -28.86  30.0  2
 9RT  Var_02    O2   S1   C5   C4   -32.20  30.0  2
 9RT  Var_03    N3   C7   C6   N2   -68.56  30.0  3
 9RT  Var_04    C6   N2   S1   C5    60.57  30.0  1
 9RT  Var_05    C7   C6   N2   S1   168.67  30.0  3
 9RT  Var_06    H1   N1   C1   C2   169.47  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
 9RT  plan-1  C6   0.020
 9RT  plan-1  C7   0.020
 9RT  plan-1  C8   0.020
 9RT  plan-1  C9   0.020
 9RT  plan-1  C10  0.020
 9RT  plan-1  C11  0.020
 9RT  plan-1  N3   0.020
 9RT  plan-1  H11  0.020
 9RT  plan-1  H12  0.020
 9RT  plan-1  H13  0.020
 9RT  plan-1  H14  0.020
 9RT  plan-2  C1   0.020
 9RT  plan-2  C2   0.020
 9RT  plan-2  C3   0.020
 9RT  plan-2  C4   0.020
 9RT  plan-2  C5   0.020
 9RT  plan-2  S1   0.020
 9RT  plan-2  C12  0.020
 9RT  plan-2  C13  0.020
 9RT  plan-2  H6   0.020
 9RT  plan-2  H7   0.020
 9RT  plan-2  H15  0.020
 9RT  plan-2  H16  0.020

