# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 09:40:47 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: (2S,3S)-3-{3-[4-(methylsulfonyl)phenyl]-1,2,4-oxadiazol-5-yl}-1-oxo-1-pyrrolidin-1-ylbutan-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]([C@H](N)C(=O)N1CCCC1)c2onc(n2)c3ccc(cc3)[S](C)(=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
 3TP  3TP  (2S,3S)-3-{3-[4-(methylsulfonyl)phenyl]-1,2,4-oxadiazol-5-yl}-1-oxo-1-pyrrolidin-1-ylbutan-2-amine  ligand  48  26  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3TP
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
 3TP  C2    C  CH1   0  -0.183   0.0822  -2.8117   4.2899
 3TP  C3    C  C     0   0.550   1.0465  -3.9508   3.9459
 3TP  O5    O  O     0  -0.518   0.6021  -5.0915   3.8244
 3TP  C10   C  CH2   0  -0.264   3.2587  -4.7019   3.2716
 3TP  C11   C  CH2   0  -0.485   4.5394  -3.9311   2.9794
 3TP  C12   C  CH2   0  -0.475   4.4822  -2.7824   3.9798
 3TP  C13   C  CH2   0  -0.288   3.0088  -2.3928   3.9700
 3TP  C20   C  CR5   0   0.557   0.1603  -3.5668   6.6370
 3TP  C22   C  CR5   0   0.334   1.6823  -3.7420   8.0378
 3TP  C25   C  CR6   0   0.022   2.9592  -3.5259   8.7176
 3TP  C26   C  CR16  0  -0.266   3.2690  -4.2057   9.8947
 3TP  C27   C  CR16  0  -0.213   4.4803  -3.9865  10.5257
 3TP  C29   C  CR16  0  -0.212   5.0894  -2.4035   8.7996
 3TP  C30   C  CR16  0  -0.277   3.8731  -2.6255   8.1765
 3TP  C1    C  CH1   0  -0.370  -0.7510  -3.1953   5.5227
 3TP  N4    N  NR5   0  -0.466   2.3309  -3.6644   3.7180
 3TP  N6    N  NH2   0  -0.778  -0.8039  -2.5294   3.1761
 3TP  N21   N  N     0  -0.460   1.3294  -3.0860   6.8965
 3TP  N23   N  N     0  -0.148   0.7786  -4.5755   8.4575
 3TP  O24   O  O     0  -0.321  -0.2225  -4.4634   7.5369
 3TP  C28   C  CR6   0  -0.207   5.3820  -3.0892   9.9683
 3TP  S34   S  S     0   1.218   6.9405  -2.8035  10.7743
 3TP  O35   O  OS    0  -0.665   7.4300  -1.4906  10.3607
 3TP  O36   O  OS    0  -0.665   6.7725  -3.0742  12.1999
 3TP  C37   C  CH3   0  -0.790   8.0052  -4.0468  10.0831
 3TP  C44   C  CH3   0  -0.650  -1.6710  -2.0562   5.9690
 3TP  H2    H  HCH1  0   0.263   0.6179  -1.8903   4.5192
 3TP  H11   H  HCH2  0   0.240   4.5216  -3.5419   1.9590
 3TP  H12   H  HCH2  0   0.235   4.7678  -3.1358   4.9736
 3TP  H13   H  HCH2  0   0.264   2.6931  -1.9597   4.9178
 3TP  H26   H  HCR6  0   0.276   2.5654  -4.9027  10.3291
 3TP  H27   H  HCR6  0   0.292   4.7081  -4.5094  11.4446
 3TP  H29   H  HCR6  0   0.292   5.7891  -1.6990   8.3718
 3TP  H30   H  HCR6  0   0.280   3.6326  -2.0886   7.2695
 3TP  H1    H  HCH1  0   0.286  -1.3623  -4.0686   5.2804
 3TP  HN61  H  HNH2  0   0.348  -1.1882  -3.3912   2.8072
 3TP  HN62  H  HNH2  0   0.361  -0.2889  -2.0931   2.4223
 3TP  H371  H  HCH3  0   0.298   8.0546  -3.9201   9.0041
 3TP  H372  H  HCH3  0   0.314   8.9929  -3.9075  10.5223
 3TP  H373  H  HCH3  0   0.298   7.6210  -5.0328  10.3337
 3TP  H441  H  HCH3  0   0.233  -1.0958  -1.1709   6.2427
 3TP  H442  H  HCH3  0   0.247  -2.2743  -2.3510   6.8270
 3TP  H443  H  HCH3  0   0.255  -2.3424  -1.7926   5.1553
 3TP  H10A  H  HCH2  0   0.237   3.4106  -5.4426   4.0621
 3TP  H11A  H  HCH2  0   0.253   5.4267  -4.5541   3.0833
 3TP  H12A  H  HCH2  0   0.254   5.1293  -1.9452   3.7220
 3TP  H13A  H  HCH2  0   0.244   2.8013  -1.6726   3.1735
 3TP  H10   H  HCH2  0   0.248   2.8691  -5.2250   2.3980

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
 3TP  C2   C3    single    1.532  0.020  1.532
 3TP  C2   C1    single    1.537  0.020  1.537
 3TP  C2   N6    single    1.451  0.020  1.451
 3TP  C2   H2    single    0.970  0.020  1.090
 3TP  C3   O5    double    1.230  0.020  1.230
 3TP  C3   N4    single    1.336  0.020  1.336
 3TP  C10  C11   aromatic  1.523  0.020  1.523
 3TP  C10  N4    aromatic  1.462  0.020  1.462
 3TP  C10  H10   single    0.970  0.020  1.090
 3TP  C11  C12   aromatic  1.524  0.020  1.524
 3TP  C11  H11   single    0.970  0.020  1.090
 3TP  C12  C13   aromatic  1.524  0.020  1.524
 3TP  C12  H12   single    0.970  0.020  1.090
 3TP  C13  N4    aromatic  1.463  0.020  1.463
 3TP  C13  H13   single    0.970  0.020  1.090
 3TP  C20  C1    single    1.487  0.020  1.487
 3TP  C20  N21   aromatic  1.291  0.020  1.291
 3TP  C20  O24   aromatic  1.327  0.020  1.327
 3TP  C22  C25   single    1.463  0.020  1.463
 3TP  C22  N21   aromatic  1.363  0.020  1.363
 3TP  C22  N23   aromatic  1.299  0.020  1.299
 3TP  C25  C26   aromatic  1.394  0.020  1.394
 3TP  C25  C30   aromatic  1.392  0.020  1.392
 3TP  C26  C27   aromatic  1.383  0.020  1.383
 3TP  C26  H26   single    0.930  0.020  1.080
 3TP  C27  C28   aromatic  1.389  0.020  1.389
 3TP  C27  H27   single    0.930  0.020  1.080
 3TP  C29  C30   aromatic  1.384  0.020  1.384
 3TP  C29  C28   aromatic  1.386  0.020  1.386
 3TP  C29  H29   single    0.930  0.020  1.080
 3TP  C30  H30   single    0.930  0.020  1.080
 3TP  C1   C44   single    1.531  0.020  1.531
 3TP  C1   H1    single    0.970  0.020  1.090
 3TP  N6   HN61  single    0.890  0.020  1.040
 3TP  N6   HN62  single    0.890  0.020  1.040
 3TP  N23  O24   aromatic  1.365  0.020  1.365
 3TP  C28  S34   single    1.778  0.020  1.778
 3TP  S34  O35   double    1.461  0.020  1.461
 3TP  S34  O36   double    1.461  0.020  1.461
 3TP  S34  C37   single    1.777  0.020  1.777
 3TP  C37  H371  single    0.970  0.020  1.090
 3TP  C37  H372  single    0.970  0.020  1.090
 3TP  C37  H373  single    0.970  0.020  1.090
 3TP  C44  H441  single    0.970  0.020  1.090
 3TP  C44  H442  single    0.970  0.020  1.090
 3TP  C44  H443  single    0.970  0.020  1.090
 3TP  C10  H10A  single    0.970  0.020  1.090
 3TP  C11  H11A  single    0.970  0.020  1.090
 3TP  C12  H12A  single    0.970  0.020  1.090
 3TP  C13  H13A  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
 3TP  H2    C2   N6    107.28  3.000
 3TP  H2    C2   C1    107.98  3.000
 3TP  N6    C2   C1    109.47  3.000
 3TP  H2    C2   C3    111.49  3.000
 3TP  N6    C2   C3    110.90  3.000
 3TP  C1    C2   C3    109.63  3.000
 3TP  N4    C3   O5    121.97  3.000
 3TP  N4    C3   C2    118.97  3.000
 3TP  O5    C3   C2    118.97  3.000
 3TP  H10A  C10  H10   107.69  3.000
 3TP  H10A  C10  N4    110.38  3.000
 3TP  H10   C10  N4    111.01  3.000
 3TP  H10A  C10  C11   111.38  3.000
 3TP  H10   C10  C11   112.93  3.000
 3TP  N4    C10  C11   103.47  3.000
 3TP  H11A  C11  H11   107.83  3.000
 3TP  H11A  C11  C12   113.51  3.000
 3TP  H11   C11  C12   110.12  3.000
 3TP  H11A  C11  C10   112.16  3.000
 3TP  H11   C11  C10   110.24  3.000
 3TP  C12   C11  C10   102.94  3.000
 3TP  H12A  C12  H12   107.98  3.000
 3TP  H12A  C12  C13   112.11  3.000
 3TP  H12   C12  C13   109.95  3.000
 3TP  H12A  C12  C11   113.68  3.000
 3TP  H12   C12  C11   110.08  3.000
 3TP  C13   C12  C11   102.98  3.000
 3TP  H13A  C13  H13   108.48  3.000
 3TP  H13A  C13  N4    111.04  3.000
 3TP  H13   C13  N4    111.18  3.000
 3TP  H13A  C13  C12   110.88  3.000
 3TP  H13   C13  C12   112.11  3.000
 3TP  N4    C13  C12   103.11  3.000
 3TP  O24   C20  N21   112.13  3.000
 3TP  O24   C20  C1    120.03  3.000
 3TP  N21   C20  C1    127.80  3.000
 3TP  N23   C22  N21   113.53  3.000
 3TP  N23   C22  C25   123.50  3.000
 3TP  N21   C22  C25   122.97  3.000
 3TP  C30   C25  C26   119.84  3.000
 3TP  C30   C25  C22   119.21  3.000
 3TP  C26   C25  C22   120.96  3.000
 3TP  H26   C26  C27   119.25  3.000
 3TP  H26   C26  C25   120.58  3.000
 3TP  C27   C26  C25   120.17  3.000
 3TP  H27   C27  C28   121.11  3.000
 3TP  H27   C27  C26   119.70  3.000
 3TP  C28   C27  C26   119.19  3.000
 3TP  H29   C29  C28   121.28  3.000
 3TP  H29   C29  C30   119.67  3.000
 3TP  C28   C29  C30   119.05  3.000
 3TP  H30   C30  C29   119.57  3.000
 3TP  H30   C30  C25   120.07  3.000
 3TP  C29   C30  C25   120.36  3.000
 3TP  H1    C1   C44   108.85  3.000
 3TP  H1    C1   C20   108.02  3.000
 3TP  C44   C1   C20   109.62  3.000
 3TP  H1    C1   C2    108.95  3.000
 3TP  C44   C1   C2    111.97  3.000
 3TP  C20   C1   C2    109.35  3.000
 3TP  C13   N4   C10   112.06  3.000
 3TP  C13   N4   C3    127.06  3.000
 3TP  C10   N4   C3    120.68  3.000
 3TP  HN62  N6   HN61  106.77  3.000
 3TP  HN62  N6   C2    110.18  3.000
 3TP  HN61  N6   C2    110.22  3.000
 3TP  C22   N21  C20   102.92  3.000
 3TP  O24   N23  C22   103.87  3.000
 3TP  N23   O24  C20   107.54  3.000
 3TP  S34   C28  C29   119.20  3.000
 3TP  S34   C28  C27   119.41  3.000
 3TP  C29   C28  C27   121.40  3.000
 3TP  C37   S34  O36   108.60  3.000
 3TP  C37   S34  O35   108.53  3.000
 3TP  O36   S34  O35   118.77  3.000
 3TP  C37   S34  C28   103.68  3.000
 3TP  O36   S34  C28   108.17  3.000
 3TP  O35   S34  C28   108.05  3.000
 3TP  H373  C37  H372  110.07  3.000
 3TP  H373  C37  H371  110.51  3.000
 3TP  H372  C37  H371  110.11  3.000
 3TP  H373  C37  S34   109.46  3.000
 3TP  H372  C37  S34   107.27  3.000
 3TP  H371  C37  S34   109.37  3.000
 3TP  H443  C44  H442  108.24  3.000
 3TP  H443  C44  H441  108.46  3.000
 3TP  H442  C44  H441  108.30  3.000
 3TP  H443  C44  C1    109.46  3.000
 3TP  H442  C44  C1    111.17  3.000
 3TP  H441  C44  C1    111.12  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
 3TP  CONST_02  C12   C13  N4   C10     0.00   0.0  0
 3TP  CONST_03  C13   N4   C10  C11     0.00   0.0  0
 3TP  CONST_06  C25   C22  N21  C20   180.00   0.0  0
 3TP  CONST_07  N23   C22  N21  C20     0.00   0.0  0
 3TP  CONST_08  C22   N23  O24  C20     0.00   0.0  0
 3TP  CONST_09  C27   C26  C25  C22   180.00   0.0  0
 3TP  CONST_10  C29   C30  C25  C22   180.00   0.0  0
 3TP  CONST_11  O24   C20  N21  C22     0.00   0.0  0
 3TP  CONST_12  O24   N23  C22  C25   180.00   0.0  0
 3TP  CONST_13  C28   C27  C26  C25     0.00   0.0  0
 3TP  CONST_14  C28   C29  C30  C25     0.00   0.0  0
 3TP  CONST_15  N21   C22  C25  C26   180.00   0.0  0
 3TP  CONST_16  N23   C22  C25  C26     0.00   0.0  0
 3TP  CONST_17  C29   C30  C25  C26     0.00   0.0  0
 3TP  CONST_18  C29   C28  C27  C26     0.00   0.0  0
 3TP  CONST_19  C30   C25  C26  C27     0.00   0.0  0
 3TP  CONST_20  C30   C29  C28  C27     0.00   0.0  0
 3TP  CONST_21  N21   C22  C25  C30     0.00   0.0  0
 3TP  CONST_22  N23   C22  C25  C30   180.00   0.0  0
 3TP  CONST_23  N23   O24  C20  N21     0.00   0.0  0
 3TP  CONST_24  O24   N23  C22  N21     0.00   0.0  0
 3TP  CONST_25  C11   C10  N4   C3    180.00   0.0  0
 3TP  CONST_27  C1    C20  N21  C22   180.00   0.0  0
 3TP  CONST_28  S34   C28  C27  C26   180.00   0.0  0
 3TP  CONST_29  S34   C28  C29  C30   180.00   0.0  0
 3TP  CONST_30  N23   O24  C20  C1    180.00   0.0  0
 3TP  CONST_31  H26   C26  C25  C22     0.00   0.0  0
 3TP  CONST_32  H30   C30  C25  C22     0.00   0.0  0
 3TP  CONST_33  H27   C27  C26  C25   180.00   0.0  0
 3TP  CONST_34  H29   C29  C30  C25   180.00   0.0  0
 3TP  CONST_35  C10   N4   C3   C2    180.00   0.0  0
 3TP  CONST_36  C13   N4   C3   C2      0.00   0.0  0
 3TP  CONST_37  C10   N4   C3   O5      0.00   0.0  0
 3TP  CONST_38  C13   N4   C3   O5    180.00   0.0  0
 3TP  Var_01    O35   S34  C28  C27  -156.51  30.0  2
 3TP  Var_02    H371  C37  S34  C28    59.17  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
 3TP  chir_01  C2  C3  C1   N6   positiv
 3TP  chir_02  C1  C2  C20  C44  negativ

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
 3TP  plan-1  C20  0.020
 3TP  plan-1  C22  0.020
 3TP  plan-1  C25  0.020
 3TP  plan-1  C1   0.020
 3TP  plan-1  N21  0.020
 3TP  plan-1  N23  0.020
 3TP  plan-1  O24  0.020
 3TP  plan-2  C22  0.020
 3TP  plan-2  C25  0.020
 3TP  plan-2  C26  0.020
 3TP  plan-2  C27  0.020
 3TP  plan-2  C29  0.020
 3TP  plan-2  C30  0.020
 3TP  plan-2  C28  0.020
 3TP  plan-2  S34  0.020
 3TP  plan-2  H26  0.020
 3TP  plan-2  H27  0.020
 3TP  plan-2  H29  0.020
 3TP  plan-2  H30  0.020
 3TP  plan-3  C2   0.020
 3TP  plan-3  C3   0.020
 3TP  plan-3  O5   0.020
 3TP  plan-3  C10  0.020
 3TP  plan-3  C13  0.020
 3TP  plan-3  N4   0.020

