# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 15:00:48 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 5-(4-methoxybiphenyl-3-yl)-1,2,5-thiadiazolidin-3-one 1,1-dioxide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1N2CC(=O)N[S]2(=O)=O)c3ccccc3
#
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
 T1D  T1D  '5-(4-methoxybiphenyl-3-yl)-1,2,5-thiadiazolidin-3-one 1,1-dioxide'  ligand  36  22  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_T1D
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
 T1D  O     O  O     0  -0.418  -4.4772  -1.3238   1.9034
 T1D  C     C  C     0   0.561  -3.5800  -1.0434   1.1505
 T1D  N     N  NC1   0  -0.810  -3.5398  -1.3645  -0.1761
 T1D  S     S  S     0   1.559  -2.2065  -0.8365  -1.0293
 T1D  O1    O  OS    0  -0.620  -1.4956  -1.9526  -1.6134
 T1D  O2    O  OS    0  -0.615  -2.5660   0.2376  -1.9301
 T1D  N1    N  N     0  -0.746  -1.4730  -0.3193   0.3485
 T1D  C1    C  CH2   0  -0.368  -2.3349  -0.2746   1.5160
 T1D  C2    C  CR6   0   0.231  -0.2819   0.4346   0.2203
 T1D  C3    C  CR16  0  -0.321   0.9297  -0.2325   0.1701
 T1D  C4    C  CR6   0   0.072   2.1350   0.4575   0.0565
 T1D  C5    C  CR16  0  -0.293   2.0750   1.8484   0.0061
 T1D  C6    C  CR16  0  -0.372   0.8713   2.5341   0.0593
 T1D  C7    C  CR6   0   0.389  -0.3294   1.8358   0.1561
 T1D  O3    O  O2    0  -0.454  -1.5403   2.3960   0.2044
 T1D  C8    C  CH3   0  -0.440  -1.6428   3.8088   0.1621
 T1D  C9    C  CR6   0   0.094   3.4216  -0.2622   0.0009
 T1D  C10   C  CR16  0  -0.313   4.5608   0.2611   0.6157
 T1D  C11   C  CR16  0  -0.239   5.7708  -0.4151   0.5640
 T1D  C12   C  CR16  0  -0.267   5.8652  -1.6307  -0.1010
 T1D  C13   C  CR16  0  -0.240   4.7387  -2.1627  -0.7148
 T1D  C14   C  CR16  0  -0.312   3.5297  -1.4845  -0.6657
 T1D  H     H  HNC1  0   0.459  -4.2867  -1.8627  -0.6488
 T1D  H1    H  HCH2  0   0.304  -2.6173   0.7428   1.7959
 T1D  H11A  H  HCH2  0   0.315  -1.8461  -0.7490   2.3680
 T1D  H3    H  HCR6  0   0.269   0.9195  -1.3119   0.2511
 T1D  H5    H  HCR6  0   0.266   2.9862   2.4244  -0.0946
 T1D  H6    H  HCR6  0   0.291   0.8862   3.6137   0.0065
 T1D  H8C1  H  HCH3  0   0.236  -1.2440   4.2151  -0.7702
 T1D  H8C2  H  HCH3  0   0.266  -2.7028   4.0389   0.2224
 T1D  H8C3  H  HCH3  0   0.236  -1.1300   4.2775   1.0051
 T1D  H10   H  HCR6  0   0.254   4.5000   1.1968   1.1580
 T1D  H11   H  HCR6  0   0.258   6.6401   0.0056   1.0525
 T1D  H12   H  HCR6  0   0.258   6.8090  -2.1585  -0.1430
 T1D  H13   H  HCR6  0   0.258   4.8023  -3.1050  -1.2435
 T1D  H14   H  HCR6  0   0.252   2.6682  -1.9022  -1.1723

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
 T1D  O    C     double    1.204  0.020  1.204
 T1D  C    N     single    1.365  0.020  1.365
 T1D  C    C1    single    1.508  0.020  1.508
 T1D  N    S     single    1.669  0.020  1.669
 T1D  N    H     single    0.860  0.020  1.020
 T1D  S    O1    double    1.447  0.020  1.447
 T1D  S    O2    double    1.447  0.020  1.447
 T1D  S    N1    single    1.644  0.020  1.644
 T1D  N1   C1    single    1.452  0.020  1.452
 T1D  N1   C2    single    1.415  0.020  1.415
 T1D  C1   H1    single    0.970  0.020  1.090
 T1D  C1   H11A  single    0.970  0.020  1.090
 T1D  C2   C3    aromatic  1.384  0.020  1.384
 T1D  C2   C7    aromatic  1.403  0.020  1.403
 T1D  C3   C4    aromatic  1.393  0.020  1.393
 T1D  C3   H3    single    0.930  0.020  1.080
 T1D  C4   C5    aromatic  1.393  0.020  1.393
 T1D  C4   C9    single    1.475  0.020  1.475
 T1D  C5   C6    aromatic  1.386  0.020  1.386
 T1D  C5   H5    single    0.930  0.020  1.080
 T1D  C6   C7    aromatic  1.392  0.020  1.392
 T1D  C6   H6    single    0.930  0.020  1.080
 T1D  C7   O3    single    1.335  0.020  1.335
 T1D  O3   C8    single    1.417  0.020  1.417
 T1D  C8   H8C1  single    0.970  0.020  1.090
 T1D  C8   H8C2  single    0.970  0.020  1.090
 T1D  C8   H8C3  single    0.970  0.020  1.090
 T1D  C9   C10   aromatic  1.396  0.020  1.396
 T1D  C9   C14   aromatic  1.396  0.020  1.396
 T1D  C10  C11   aromatic  1.387  0.020  1.387
 T1D  C10  H10   single    0.930  0.020  1.080
 T1D  C11  C12   aromatic  1.389  0.020  1.389
 T1D  C11  H11   single    0.930  0.020  1.080
 T1D  C12  C13   aromatic  1.389  0.020  1.389
 T1D  C12  H12   single    0.930  0.020  1.080
 T1D  C13  C14   aromatic  1.387  0.020  1.387
 T1D  C13  H13   single    0.930  0.020  1.080
 T1D  C14  H14   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
 T1D  C1    C    N     109.33  3.000
 T1D  C1    C    O     125.60  3.000
 T1D  N     C    O     125.06  3.000
 T1D  H     N    S     120.35  3.000
 T1D  H     N    C     123.12  3.000
 T1D  S     N    C     116.48  3.000
 T1D  N1    S    O2    113.51  3.000
 T1D  N1    S    O1    111.21  3.000
 T1D  O2    S    O1    116.32  3.000
 T1D  N1    S    N      91.58  3.000
 T1D  O2    S    N     110.77  3.000
 T1D  O1    S    N     110.80  3.000
 T1D  C2    N1   C1    123.78  3.000
 T1D  C2    N1   S     117.84  3.000
 T1D  C1    N1   S     114.75  3.000
 T1D  H11A  C1   H1    108.71  3.000
 T1D  H11A  C1   N1    110.40  3.000
 T1D  H1    C1   N1    112.84  3.000
 T1D  H11A  C1   C     109.72  3.000
 T1D  H1    C1   C     108.87  3.000
 T1D  N1    C1   C     106.23  3.000
 T1D  C7    C2   C3    120.61  3.000
 T1D  C7    C2   N1    120.50  3.000
 T1D  C3    C2   N1    118.90  3.000
 T1D  H3    C3   C4    120.53  3.000
 T1D  H3    C3   C2    118.01  3.000
 T1D  C4    C3   C2    121.43  3.000
 T1D  C9    C4   C5    121.55  3.000
 T1D  C9    C4   C3    121.05  3.000
 T1D  C5    C4   C3    117.40  3.000
 T1D  H5    C5   C6    118.11  3.000
 T1D  H5    C5   C4    119.89  3.000
 T1D  C6    C5   C4    121.99  3.000
 T1D  H6    C6   C7    121.07  3.000
 T1D  H6    C6   C5    118.70  3.000
 T1D  C7    C6   C5    120.22  3.000
 T1D  O3    C7   C6    125.05  3.000
 T1D  O3    C7   C2    116.61  3.000
 T1D  C6    C7   C2    118.34  3.000
 T1D  C8    O3   C7    118.87  3.000
 T1D  H8C3  C8   H8C2  108.93  3.000
 T1D  H8C3  C8   H8C1  109.13  3.000
 T1D  H8C2  C8   H8C1  108.96  3.000
 T1D  H8C3  C8   O3    111.76  3.000
 T1D  H8C2  C8   O3    106.26  3.000
 T1D  H8C1  C8   O3    111.71  3.000
 T1D  C14   C9   C10   118.36  3.000
 T1D  C14   C9   C4    120.83  3.000
 T1D  C10   C9   C4    120.81  3.000
 T1D  H10   C10  C11   119.26  3.000
 T1D  H10   C10  C9    119.89  3.000
 T1D  C11   C10  C9    120.84  3.000
 T1D  H11   C11  C12   120.12  3.000
 T1D  H11   C11  C10   119.63  3.000
 T1D  C12   C11  C10   120.26  3.000
 T1D  H12   C12  C13   120.23  3.000
 T1D  H12   C12  C11   120.31  3.000
 T1D  C13   C12  C11   119.45  3.000
 T1D  H13   C13  C14   119.61  3.000
 T1D  H13   C13  C12   120.11  3.000
 T1D  C14   C13  C12   120.27  3.000
 T1D  H14   C14  C13   119.22  3.000
 T1D  H14   C14  C9    119.95  3.000
 T1D  C13   C14  C9    120.82  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
 T1D  CONST_01  C5    C4   C3   C2     0.00   0.0  0
 T1D  CONST_02  C9    C4   C3   C2   180.00   0.0  0
 T1D  CONST_03  C5    C6   C7   C2     0.00   0.0  0
 T1D  CONST_04  C6    C7   C2   C3     0.00   0.0  0
 T1D  CONST_05  C6    C5   C4   C3     0.00   0.0  0
 T1D  CONST_08  C7    C2   C3   C4     0.00   0.0  0
 T1D  CONST_09  C7    C6   C5   C4     0.00   0.0  0
 T1D  CONST_10  C11   C10  C9   C4   180.00   0.0  0
 T1D  CONST_11  C13   C14  C9   C4   180.00   0.0  0
 T1D  CONST_14  C9    C4   C5   C6   180.00   0.0  0
 T1D  CONST_15  C12   C11  C10  C9     0.00   0.0  0
 T1D  CONST_16  C12   C13  C14  C9     0.00   0.0  0
 T1D  CONST_17  C13   C14  C9   C10    0.00   0.0  0
 T1D  CONST_18  C13   C12  C11  C10    0.00   0.0  0
 T1D  CONST_19  C14   C9   C10  C11    0.00   0.0  0
 T1D  CONST_20  C14   C13  C12  C11    0.00   0.0  0
 T1D  CONST_21  C4    C3   C2   N1   180.00   0.0  0
 T1D  CONST_22  C6    C7   C2   N1   180.00   0.0  0
 T1D  CONST_23  C1    C    N    S      0.00   0.0  0
 T1D  CONST_24  O3    C7   C2   N1     0.00   0.0  0
 T1D  CONST_25  O3    C7   C2   C3   180.00   0.0  0
 T1D  CONST_26  O3    C7   C6   C5   180.00   0.0  0
 T1D  CONST_27  S     N    C    O    180.00   0.0  0
 T1D  CONST_28  H3    C3   C2   N1     0.00   0.0  0
 T1D  CONST_29  H6    C6   C7   C2   180.00   0.0  0
 T1D  CONST_30  H5    C5   C4   C3   180.00   0.0  0
 T1D  CONST_31  H10   C10  C9   C4     0.00   0.0  0
 T1D  CONST_32  H14   C14  C9   C4     0.00   0.0  0
 T1D  CONST_33  H11   C11  C10  C9   180.00   0.0  0
 T1D  CONST_34  H13   C13  C14  C9   180.00   0.0  0
 T1D  CONST_35  H12   C12  C11  C10  180.00   0.0  0
 T1D  CONST_36  H     N    C    C1   180.00   0.0  0
 T1D  Var_01    N1    S    N    C      7.48  30.0  1
 T1D  Var_02    S     N1   C1   C     13.29  30.0  1
 T1D  Var_03    N1    C1   C    N     -7.42  30.0  1
 T1D  Var_04    C1    N1   S    N    -12.21  30.0  1
 T1D  Var_05    C3    C2   N1   S    -88.73  30.0  2
 T1D  Var_06    H8C1  C8   O3   C7    61.80  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
 T1D  plan-1  N1   0.020
 T1D  plan-1  C2   0.020
 T1D  plan-1  C3   0.020
 T1D  plan-1  C4   0.020
 T1D  plan-1  C5   0.020
 T1D  plan-1  C6   0.020
 T1D  plan-1  C7   0.020
 T1D  plan-1  O3   0.020
 T1D  plan-1  C9   0.020
 T1D  plan-1  H3   0.020
 T1D  plan-1  H5   0.020
 T1D  plan-1  H6   0.020
 T1D  plan-2  C4   0.020
 T1D  plan-2  C9   0.020
 T1D  plan-2  C10  0.020
 T1D  plan-2  C11  0.020
 T1D  plan-2  C12  0.020
 T1D  plan-2  C13  0.020
 T1D  plan-2  C14  0.020
 T1D  plan-2  H10  0.020
 T1D  plan-2  H11  0.020
 T1D  plan-2  H12  0.020
 T1D  plan-2  H13  0.020
 T1D  plan-2  H14  0.020
 T1D  plan-3  S    0.020
 T1D  plan-3  N1   0.020
 T1D  plan-3  C1   0.020
 T1D  plan-3  C2   0.020
 T1D  plan-4  O    0.020
 T1D  plan-4  C    0.020
 T1D  plan-4  N    0.020
 T1D  plan-4  S    0.020
 T1D  plan-4  C1   0.020
 T1D  plan-4  H    0.020

