# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 21:01:20 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: 3-[(thiomorpholin-4-yl)methyl]phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cccc(CN2CCSCC2)c1
#
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
 NSJ  NSJ  3-[(thiomorpholin-4-yl)methyl]phenol  ligand  29  14  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NSJ
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
 NSJ  N1   N  NT    0  -0.411  -1.1391   0.5562   0.3257
 NSJ  C4   C  CR16  0  -0.310   1.5144   0.8111  -0.8444
 NSJ  C5   C  CR6   0   0.090   1.3163   0.4143   0.4772
 NSJ  C6   C  CH2   0  -0.314   0.0156   0.7021   1.1862
 NSJ  C7   C  CH2   0  -0.263  -1.3738  -0.8356  -0.0142
 NSJ  C8   C  CH2   0  -0.566  -2.3969  -0.9897  -1.1228
 NSJ  C10  C  CH2   0  -0.260  -2.3125   1.1997   0.8886
 NSJ  C1   C  CR6   0   0.367   3.5761  -0.4412   0.5478
 NSJ  C11  C  CR16  0  -0.399   2.3462  -0.2146   1.1631
 NSJ  C2   C  CR16  0  -0.398   3.7728  -0.0446  -0.7713
 NSJ  C3   C  CR16  0  -0.230   2.7362   0.5768  -1.4557
 NSJ  C9   C  CH2   0  -0.568  -3.4468   1.2910  -0.1146
 NSJ  O1   O  OH1   0  -0.636   4.5335  -1.0542   1.2746
 NSJ  S1   S  S2    0  -0.043  -4.0202  -0.3465  -0.6374
 NSJ  H3   H  HCH2  0   0.254   0.0404   1.7370   1.5415
 NSJ  H4   H  HCH2  0   0.214  -0.0503   0.0728   2.0892
 NSJ  H5   H  HCH2  0   0.251  -0.4339  -1.2700  -0.3634
 NSJ  H6   H  HCH2  0   0.204  -1.6948  -1.4195   0.8647
 NSJ  H7   H  HCH2  0   0.262  -2.0563  -0.4768  -2.0244
 NSJ  H8   H  HCH2  0   0.278  -2.5332  -2.0439  -1.3642
 NSJ  H9   H  HCH2  0   0.200  -2.6696   0.6884   1.7973
 NSJ  H10  H  HCH2  0   0.245  -2.0354   2.2164   1.1796
 NSJ  H11  H  HCR6  0   0.253   2.1985  -0.5379   2.1878
 NSJ  H12  H  HCR6  0   0.267   4.7229  -0.2225  -1.2630
 NSJ  H13  H  HCR6  0   0.255   2.8927   0.8812  -2.4829
 NSJ  H14  H  HCH2  0   0.279  -4.3020   1.8002   0.3298
 NSJ  H15  H  HCH2  0   0.262  -3.1298   1.8617  -0.9900
 NSJ  H16  H  HOH1  0   0.473   5.3377  -1.1517   0.7533
 NSJ  H2   H  HCR6  0   0.242   0.7088   1.2878  -1.3870

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
 NSJ  O1   C1   single    1.349  0.020  1.349
 NSJ  C2   C1   aromatic  1.391  0.020  1.391
 NSJ  C2   C3   aromatic  1.389  0.020  1.389
 NSJ  C1   C11  aromatic  1.394  0.020  1.394
 NSJ  C3   C4   aromatic  1.386  0.020  1.386
 NSJ  C11  C5   aromatic  1.388  0.020  1.388
 NSJ  C4   C5   aromatic  1.394  0.020  1.394
 NSJ  C5   C6   single    1.509  0.020  1.509
 NSJ  C6   N1   single    1.447  0.020  1.447
 NSJ  C7   N1   single    1.452  0.020  1.452
 NSJ  C7   C8   single    1.516  0.020  1.516
 NSJ  N1   C10  single    1.452  0.020  1.452
 NSJ  C8   S1   single    1.812  0.020  1.812
 NSJ  C10  C9   single    1.517  0.020  1.517
 NSJ  C9   S1   single    1.812  0.020  1.812
 NSJ  C4   H2   single    0.930  0.020  1.080
 NSJ  C6   H3   single    0.970  0.020  1.090
 NSJ  C6   H4   single    0.970  0.020  1.090
 NSJ  C7   H5   single    0.970  0.020  1.090
 NSJ  C7   H6   single    0.970  0.020  1.090
 NSJ  C8   H7   single    0.970  0.020  1.090
 NSJ  C8   H8   single    0.970  0.020  1.090
 NSJ  C10  H9   single    0.970  0.020  1.090
 NSJ  C10  H10  single    0.970  0.020  1.090
 NSJ  C11  H11  single    0.930  0.020  1.080
 NSJ  C2   H12  single    0.930  0.020  1.080
 NSJ  C3   H13  single    0.930  0.020  1.080
 NSJ  C9   H14  single    0.970  0.020  1.090
 NSJ  C9   H15  single    0.970  0.020  1.090
 NSJ  O1   H16  single    0.850  0.020  0.980

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
 NSJ  C10  N1   C7   112.65  3.000
 NSJ  C10  N1   C6   111.69  3.000
 NSJ  C7   N1   C6   111.39  3.000
 NSJ  H2   C4   C3   120.63  3.000
 NSJ  H2   C4   C5   119.67  3.000
 NSJ  C3   C4   C5   119.69  3.000
 NSJ  C11  C5   C6   119.58  3.000
 NSJ  C6   C5   C4   120.91  3.000
 NSJ  C11  C5   C4   119.47  3.000
 NSJ  H4   C6   H3   105.97  3.000
 NSJ  H4   C6   C5   109.12  3.000
 NSJ  H3   C6   C5   108.26  3.000
 NSJ  H4   C6   N1   112.44  3.000
 NSJ  H3   C6   N1   107.84  3.000
 NSJ  C5   C6   N1   112.90  3.000
 NSJ  H6   C7   H5   107.13  3.000
 NSJ  H6   C7   C8   109.42  3.000
 NSJ  H5   C7   C8   107.84  3.000
 NSJ  H6   C7   N1   111.59  3.000
 NSJ  H5   C7   N1   108.48  3.000
 NSJ  C8   C7   N1   112.19  3.000
 NSJ  H8   C8   H7   108.09  3.000
 NSJ  H8   C8   S1   106.89  3.000
 NSJ  H7   C8   S1   109.51  3.000
 NSJ  H8   C8   C7   110.15  3.000
 NSJ  H7   C8   C7   110.21  3.000
 NSJ  S1   C8   C7   111.87  3.000
 NSJ  H10  C10  H9   107.10  3.000
 NSJ  H10  C10  C9   108.04  3.000
 NSJ  H9   C10  C9   109.33  3.000
 NSJ  H10  C10  N1   108.09  3.000
 NSJ  H9   C10  N1   112.08  3.000
 NSJ  C9   C10  N1   112.00  3.000
 NSJ  O1   C1   C2   122.67  3.000
 NSJ  C2   C1   C11  119.79  3.000
 NSJ  O1   C1   C11  117.53  3.000
 NSJ  H11  C11  C1   119.26  3.000
 NSJ  H11  C11  C5   120.06  3.000
 NSJ  C1   C11  C5   120.68  3.000
 NSJ  H12  C2   C3   120.26  3.000
 NSJ  H12  C2   C1   120.45  3.000
 NSJ  C3   C2   C1   119.29  3.000
 NSJ  H13  C3   C2   119.04  3.000
 NSJ  H13  C3   C4   119.89  3.000
 NSJ  C2   C3   C4   121.07  3.000
 NSJ  H15  C9   H14  108.09  3.000
 NSJ  H15  C9   S1   109.44  3.000
 NSJ  H14  C9   S1   106.95  3.000
 NSJ  H15  C9   C10  110.15  3.000
 NSJ  H14  C9   C10  110.19  3.000
 NSJ  S1   C9   C10  111.90  3.000
 NSJ  H16  O1   C1   110.30  3.000
 NSJ  C9   S1   C8    96.58  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
 NSJ  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 NSJ  CONST_02  C1   C11  C5   C4      0.00   0.0  0
 NSJ  CONST_03  C2   C1   C11  C5      0.00   0.0  0
 NSJ  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 NSJ  CONST_05  C3   C2   C1   C11     0.00   0.0  0
 NSJ  CONST_06  C3   C4   C5   C11     0.00   0.0  0
 NSJ  CONST_07  O1   C1   C11  C5    180.00   0.0  0
 NSJ  CONST_08  C1   C11  C5   C6    180.00   0.0  0
 NSJ  CONST_09  C3   C4   C5   C6    180.00   0.0  0
 NSJ  CONST_10  O1   C1   C2   C3    180.00   0.0  0
 NSJ  CONST_11  H12  C2   C3   C4    180.00   0.0  0
 NSJ  CONST_12  H11  C11  C5   C4    180.00   0.0  0
 NSJ  CONST_13  H13  C3   C4   C5    180.00   0.0  0
 NSJ  CONST_14  H2   C4   C5   C11   180.00   0.0  0
 NSJ  Var_01    S1   C8   C7   N1    -62.35  30.0  1
 NSJ  Var_02    S1   C9   C10  N1     62.56  30.0  1
 NSJ  Var_03    C9   C10  N1   C7    -64.95  30.0  1
 NSJ  Var_04    C10  N1   C7   C8     64.92  30.0  1
 NSJ  Var_05    C10  C9   S1   C8    -52.85  30.0  1
 NSJ  Var_06    C11  C5   C6   N1   -143.98  30.0  3
 NSJ  Var_07    C7   N1   C6   C5     69.86  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
 NSJ  plan-1  C4   0.020
 NSJ  plan-1  C5   0.020
 NSJ  plan-1  C6   0.020
 NSJ  plan-1  C1   0.020
 NSJ  plan-1  C11  0.020
 NSJ  plan-1  C2   0.020
 NSJ  plan-1  C3   0.020
 NSJ  plan-1  O1   0.020
 NSJ  plan-1  H11  0.020
 NSJ  plan-1  H12  0.020
 NSJ  plan-1  H13  0.020
 NSJ  plan-1  H2   0.020

