# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 02:02:56 2022
#   Inital geometry file: a 123 line input string
#   Ligand name: (3S)-N-hydroxy-2,2-dimethyl-4-{[4-(pyridin-4-yloxy)phenyl]sulfonyl}thiomorpholine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)SCCN([C@H]1C(=O)NO)[S](=O)(=O)c2ccc(Oc3ccncc3)cc2
#
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
 PN0  PN0  (3S)-N-hydroxy-2,2-dimethyl-4-{[4-(pyridin-4-yloxy)phenyl]sulfonyl}thiomorpholine-3-carboxamide  ligand  49  28  .  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_PN0
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
 PN0  N1    N  N     0  -0.599  -2.0473   0.2199  -0.4828
 PN0  N3    N  NH1   0  -0.368  -1.6525  -2.6104  -0.7398
 PN0  C4    C  CH2   0  -0.555  -3.4368   2.2038  -0.9955
 PN0  C5    C  CR6   0  -0.160   0.5275   0.4493   0.2387
 PN0  C6    C  CR16  0  -0.241   1.1425   1.6458  -0.1033
 PN0  C7    C  CR16  0  -0.290   2.4300   1.6273  -0.6163
 PN0  C8    C  CR6   0   0.318   3.0816   0.4149  -0.7698
 PN0  C10   C  CR16  0  -0.243   1.1901  -0.7644   0.0998
 PN0  C13   C  CR16  0  -0.060   7.7861   0.2370  -0.3346
 PN0  C15   C  CR16  0  -0.407   5.3651   0.4504   0.8699
 PN0  C17   C  CH3   0  -0.642  -4.5180   0.1230   1.4635
 PN0  C1    C  CT    0  -0.212  -4.4950  -0.2515  -0.0113
 PN0  C2    C  CH1   0  -0.179  -3.1385  -0.7601  -0.5364
 PN0  C3    C  CH2   0  -0.319  -2.2232   1.3746  -1.3643
 PN0  S1    S  S2    0   0.001  -4.9486   1.2096  -1.0487
 PN0  S2    S  S     0   1.375  -1.1257   0.4619   0.8772
 PN0  C9    C  CR16  0  -0.283   2.4775  -0.7806  -0.4063
 PN0  O1    O  O2    0  -0.497   4.3344   0.3957  -1.3230
 PN0  C11   C  CR6   0   0.456   5.4188   0.3678  -0.5152
 PN0  C12   C  CR16  0  -0.396   6.6592   0.2591  -1.1344
 PN0  N2    N  N     0  -0.416   7.7589   0.3130   0.9935
 PN0  C14   C  CR16  0  -0.062   6.5664   0.4174   1.5637
 PN0  O2    O  OS    0  -0.630  -1.3503   1.7877   1.4333
 PN0  O3    O  OS    0  -0.632  -1.3047  -0.7059   1.7219
 PN0  C16   C  C     0   0.548  -2.6928  -2.1398  -0.0206
 PN0  O4    O  OH1   0  -0.540  -0.9896  -3.7182  -0.3065
 PN0  O5    O  O     0  -0.442  -3.2624  -2.7823   0.8335
 PN0  C18   C  CH3   0  -0.652  -5.6045  -1.2548  -0.3302
 PN0  HN3   H  HNH1  0   0.414  -1.1214  -2.0164  -1.3613
 PN0  H4    H  HCH2  0   0.278  -3.3132   2.6712  -0.0195
 PN0  H4A   H  HCH2  0   0.295  -3.5763   2.9983  -1.7295
 PN0  H6    H  HCR6  0   0.298   0.6411   2.5938   0.0339
 PN0  H7    H  HCR6  0   0.295   2.9180   2.5520  -0.8938
 PN0  H10   H  HCR6  0   0.296   0.7307  -1.6973   0.3946
 PN0  H15   H  HCR6  0   0.293   4.4370   0.5423   1.4168
 PN0  H17   H  HCH3  0   0.232  -3.8376   0.9365   1.7079
 PN0  H17A  H  HCH3  0   0.243  -5.5209   0.4485   1.7385
 PN0  H17B  H  HCH3  0   0.248  -4.2570  -0.7342   2.0818
 PN0  H2    H  HCH1  0   0.316  -3.2874  -0.9088  -1.6133
 PN0  H3    H  HCH2  0   0.283  -1.3242   1.9922  -1.3542
 PN0  H3A   H  HCH2  0   0.283  -2.3209   0.9889  -2.3805
 PN0  H9    H  HCR6  0   0.296   3.0038  -1.7188  -0.5227
 PN0  H12   H  HCR6  0   0.286   6.7432   0.1942  -2.2108
 PN0  H14   H  HCR6  0   0.271   6.5483   0.4809   2.6459
 PN0  HO4   H  HOH1  0   0.482  -1.2963  -4.4482  -0.8597
 PN0  H18   H  HCH3  0   0.244  -6.5821  -0.7815  -0.2212
 PN0  H18A  H  HCH3  0   0.243  -5.5284  -1.6292  -1.3524
 PN0  H18B  H  HCH3  0   0.261  -5.5748  -2.1008   0.3519
 PN0  H13   H  HCR6  0   0.271   8.7636   0.1524  -0.7959

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
 PN0  N1   C2    single    1.468  0.020  1.468
 PN0  N1   C3    single    1.463  0.020  1.463
 PN0  N1   S2    single    1.661  0.020  1.661
 PN0  N3   C16   single    1.349  0.020  1.349
 PN0  N3   O4    single    1.362  0.020  1.362
 PN0  C4   C3    single    1.515  0.020  1.515
 PN0  C4   S1    single    1.810  0.020  1.810
 PN0  C5   C6    aromatic  1.388  0.020  1.388
 PN0  C5   C10   aromatic  1.390  0.020  1.390
 PN0  C5   S2    single    1.772  0.020  1.772
 PN0  C6   C7    aromatic  1.386  0.020  1.386
 PN0  C7   C8    aromatic  1.385  0.020  1.385
 PN0  C8   C9    aromatic  1.388  0.020  1.388
 PN0  C8   O1    single    1.370  0.020  1.370
 PN0  C10  C9    aromatic  1.383  0.020  1.383
 PN0  C13  C12   aromatic  1.382  0.020  1.382
 PN0  C13  N2    aromatic  1.331  0.020  1.331
 PN0  C15  C11   aromatic  1.389  0.020  1.389
 PN0  C15  C14   aromatic  1.388  0.020  1.388
 PN0  C17  C1    single    1.522  0.020  1.522
 PN0  C1   C2    single    1.541  0.020  1.541
 PN0  C1   S1    single    1.848  0.020  1.848
 PN0  C1   C18   single    1.529  0.020  1.529
 PN0  C2   C16   single    1.539  0.020  1.539
 PN0  S2   O2    double    1.455  0.020  1.455
 PN0  S2   O3    double    1.452  0.020  1.452
 PN0  O1   C11   single    1.352  0.020  1.352
 PN0  C11  C12   aromatic  1.391  0.020  1.391
 PN0  N2   C14   aromatic  1.326  0.020  1.326
 PN0  C16  O5    double    1.211  0.020  1.211
 PN0  N3   HN3   single    0.890  0.020  1.040
 PN0  C4   H4    single    0.970  0.020  1.090
 PN0  C4   H4A   single    0.970  0.020  1.090
 PN0  C6   H6    single    0.930  0.020  1.080
 PN0  C7   H7    single    0.930  0.020  1.080
 PN0  C10  H10   single    0.930  0.020  1.080
 PN0  C13  H13   single    0.930  0.020  1.080
 PN0  C15  H15   single    0.930  0.020  1.080
 PN0  C17  H17   single    0.970  0.020  1.090
 PN0  C17  H17A  single    0.970  0.020  1.090
 PN0  C17  H17B  single    0.970  0.020  1.090
 PN0  C2   H2    single    0.970  0.020  1.090
 PN0  C3   H3    single    0.970  0.020  1.090
 PN0  C3   H3A   single    0.970  0.020  1.090
 PN0  C9   H9    single    0.930  0.020  1.080
 PN0  C12  H12   single    0.930  0.020  1.080
 PN0  C14  H14   single    0.930  0.020  1.080
 PN0  O4   HO4   single    0.850  0.020  0.980
 PN0  C18  H18   single    0.970  0.020  1.090
 PN0  C18  H18A  single    0.970  0.020  1.090
 PN0  C18  H18B  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
 PN0  S2    N1   C3    116.43  3.000
 PN0  S2    N1   C2    122.67  3.000
 PN0  C3    N1   C2    114.56  3.000
 PN0  HN3   N3   O4    114.71  3.000
 PN0  HN3   N3   C16   121.87  3.000
 PN0  O4    N3   C16   119.30  3.000
 PN0  H4A   C4   H4    107.76  3.000
 PN0  H4A   C4   S1    105.87  3.000
 PN0  H4    C4   S1    110.91  3.000
 PN0  H4A   C4   C3    109.71  3.000
 PN0  H4    C4   C3    111.22  3.000
 PN0  S1    C4   C3    111.17  3.000
 PN0  S2    C5   C10   119.14  3.000
 PN0  S2    C5   C6    119.73  3.000
 PN0  C10   C5   C6    121.13  3.000
 PN0  H6    C6   C7    119.30  3.000
 PN0  H6    C6   C5    121.27  3.000
 PN0  C7    C6   C5    119.42  3.000
 PN0  H7    C7   C8    120.50  3.000
 PN0  H7    C7   C6    120.17  3.000
 PN0  C8    C7   C6    119.32  3.000
 PN0  O1    C8   C9    119.47  3.000
 PN0  O1    C8   C7    119.17  3.000
 PN0  C9    C8   C7    121.35  3.000
 PN0  H10   C10  C9    119.02  3.000
 PN0  H10   C10  C5    121.60  3.000
 PN0  C9    C10  C5    119.37  3.000
 PN0  H13   C13  N2    116.59  3.000
 PN0  H13   C13  C12   119.35  3.000
 PN0  N2    C13  C12   124.06  3.000
 PN0  H15   C15  C14   119.49  3.000
 PN0  H15   C15  C11   122.87  3.000
 PN0  C14   C15  C11   117.64  3.000
 PN0  H17B  C17  H17A  108.21  3.000
 PN0  H17B  C17  H17   108.13  3.000
 PN0  H17A  C17  H17   107.18  3.000
 PN0  H17B  C17  C1    110.67  3.000
 PN0  H17A  C17  C1    109.39  3.000
 PN0  H17   C17  C1    113.09  3.000
 PN0  C18   C1   S1    102.91  3.000
 PN0  C18   C1   C2    110.55  3.000
 PN0  S1    C1   C2    106.60  3.000
 PN0  C18   C1   C17   110.64  3.000
 PN0  S1    C1   C17   110.22  3.000
 PN0  C2    C1   C17   115.13  3.000
 PN0  H2    C2   C16   104.28  3.000
 PN0  H2    C2   C1    105.05  3.000
 PN0  C16   C2   C1    115.89  3.000
 PN0  H2    C2   N1    103.13  3.000
 PN0  C16   C2   N1    111.79  3.000
 PN0  C1    C2   N1    114.94  3.000
 PN0  H3A   C3   H3    106.41  3.000
 PN0  H3A   C3   C4    110.38  3.000
 PN0  H3    C3   C4    110.36  3.000
 PN0  H3A   C3   N1    107.03  3.000
 PN0  H3    C3   N1    110.01  3.000
 PN0  C4    C3   N1    112.42  3.000
 PN0  C1    S1   C4    102.28  3.000
 PN0  O3    S2   O2    119.42  3.000
 PN0  O3    S2   C5    108.59  3.000
 PN0  O2    S2   C5    106.75  3.000
 PN0  O3    S2   N1    106.90  3.000
 PN0  O2    S2   N1    111.11  3.000
 PN0  C5    S2   N1    102.80  3.000
 PN0  H9    C9   C10   120.14  3.000
 PN0  H9    C9   C8    120.46  3.000
 PN0  C10   C9   C8    119.40  3.000
 PN0  C11   O1   C8    119.50  3.000
 PN0  C12   C11  O1    116.80  3.000
 PN0  C12   C11  C15   118.90  3.000
 PN0  O1    C11  C15   124.31  3.000
 PN0  H12   C12  C11   121.14  3.000
 PN0  H12   C12  C13   120.78  3.000
 PN0  C11   C12  C13   118.09  3.000
 PN0  C14   N2   C13   116.88  3.000
 PN0  H14   C14  N2    116.67  3.000
 PN0  H14   C14  C15   118.89  3.000
 PN0  N2    C14  C15   124.44  3.000
 PN0  O5    C16  C2    125.16  3.000
 PN0  O5    C16  N3    123.60  3.000
 PN0  C2    C16  N3    110.93  3.000
 PN0  HO4   O4   N3    106.14  3.000
 PN0  H18B  C18  H18A  108.58  3.000
 PN0  H18B  C18  H18   107.42  3.000
 PN0  H18A  C18  H18   107.74  3.000
 PN0  H18B  C18  C1    111.09  3.000
 PN0  H18A  C18  C1    111.70  3.000
 PN0  H18   C18  C1    110.15  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
 PN0  CONST_01  C8   C7   C6   C5      0.00   0.0  0
 PN0  CONST_02  C8   C9   C10  C5      0.00   0.0  0
 PN0  CONST_03  C9   C10  C5   C6      0.00   0.0  0
 PN0  CONST_04  C9   C8   C7   C6      0.00   0.0  0
 PN0  CONST_05  C10  C5   C6   C7      0.00   0.0  0
 PN0  CONST_06  C10  C9   C8   C7      0.00   0.0  0
 PN0  CONST_07  C15  C11  C12  C13     0.00   0.0  0
 PN0  CONST_08  C15  C14  N2   C13     0.00   0.0  0
 PN0  CONST_09  N2   C14  C15  C11     0.00   0.0  0
 PN0  CONST_10  N2   C13  C12  C11     0.00   0.0  0
 PN0  CONST_11  C14  N2   C13  C12     0.00   0.0  0
 PN0  CONST_12  C14  C15  C11  C12     0.00   0.0  0
 PN0  CONST_13  O1   C8   C7   C6    180.00   0.0  0
 PN0  CONST_14  S2   C5   C6   C7    180.00   0.0  0
 PN0  CONST_15  O1   C8   C9   C10   180.00   0.0  0
 PN0  CONST_16  O1   C11  C12  C13   180.00   0.0  0
 PN0  CONST_17  C9   C10  C5   S2    180.00   0.0  0
 PN0  CONST_18  C14  C15  C11  O1    180.00   0.0  0
 PN0  CONST_19  H7   C7   C6   C5    180.00   0.0  0
 PN0  CONST_20  H9   C9   C10  C5    180.00   0.0  0
 PN0  CONST_21  H10  C10  C5   C6    180.00   0.0  0
 PN0  CONST_22  H6   C6   C7   C8    180.00   0.0  0
 PN0  CONST_23  H14  C14  N2   C13   180.00   0.0  0
 PN0  CONST_24  H12  C12  C11  C15   180.00   0.0  0
 PN0  CONST_25  H13  C13  C12  C11   180.00   0.0  0
 PN0  CONST_26  H15  C15  C11  C12   180.00   0.0  0
 PN0  CONST_27  O4   N3   C16  C2    180.00   0.0  0
 PN0  CONST_28  HN3  N3   C16  C2      0.00   0.0  0
 PN0  Var_01    S1   C4   C3   N1    -58.29  30.0  1
 PN0  Var_02    C2   N1   C3   C4     63.15  30.0  1
 PN0  Var_03    C2   C1   S1   C4    -49.78  30.0  1
 PN0  Var_04    C3   C4   S1   C1     51.33  30.0  1
 PN0  Var_05    C6   C5   S2   N1     94.05  30.0  2
 PN0  Var_06    C15  C11  O1   C8     -4.68  30.0  2
 PN0  Var_07    H17  C17  C1   C2     61.79  30.0  3
 PN0  Var_08    H18  C18  C1   C2   -163.90  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 PN0  chir_01  C2  N1  C1  C16  positiv

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
 PN0  plan-1  C5   0.020
 PN0  plan-1  C6   0.020
 PN0  plan-1  C7   0.020
 PN0  plan-1  C8   0.020
 PN0  plan-1  C10  0.020
 PN0  plan-1  S2   0.020
 PN0  plan-1  C9   0.020
 PN0  plan-1  O1   0.020
 PN0  plan-1  H6   0.020
 PN0  plan-1  H7   0.020
 PN0  plan-1  H10  0.020
 PN0  plan-1  H9   0.020
 PN0  plan-2  C13  0.020
 PN0  plan-2  C15  0.020
 PN0  plan-2  O1   0.020
 PN0  plan-2  C11  0.020
 PN0  plan-2  C12  0.020
 PN0  plan-2  N2   0.020
 PN0  plan-2  C14  0.020
 PN0  plan-2  H15  0.020
 PN0  plan-2  H12  0.020
 PN0  plan-2  H14  0.020
 PN0  plan-2  H13  0.020
 PN0  plan-3  N3   0.020
 PN0  plan-3  C2   0.020
 PN0  plan-3  C16  0.020
 PN0  plan-3  O4   0.020
 PN0  plan-3  O5   0.020
 PN0  plan-3  HN3  0.020

