# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 21:12:00 2022
#   Inital geometry file: a 69 line input string
#   Ligand name: 2-methyl-4-(phenylmethyl)-1,2,4-thiadiazolidine-3,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1SC(=O)N(Cc2ccccc2)C1=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
 U3W  U3W  "2-methyl-4-(phenylmethyl)-1,2,4-thiadiazolidine-3,5-dione"
  ligand  25  15  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U3W
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
 U3W  C02  C  CR5   0   0.387   2.3983   -7.6400  7.6965
 U3W  C05  C  CH3   0  -0.504   1.9659  -11.3299  6.5658
 U3W  C06  C  CR5   0   0.811   0.7620   -9.2415  7.1660
 U3W  C08  C  CH2   0  -0.429   0.0392   -6.9473  7.8177
 U3W  C09  C  CR6   0   0.135  -0.2549   -6.1325  6.5861
 U3W  C10  C  CR16  0  -0.292   0.4081   -4.9302  6.3577
 U3W  C11  C  CR16  0  -0.240   0.1533   -4.1921  5.2096
 U3W  C12  C  CR16  0  -0.260  -0.7697   -4.6490  4.2787
 U3W  C13  C  CR16  0  -0.239  -1.4406   -5.8440  4.5032
 U3W  C14  C  CR16  0  -0.293  -1.1838   -6.5814  5.6507
 U3W  N04  N  NR5   0  -0.646   1.9027   -9.9380  6.9539
 U3W  N07  N  NR5   0  -0.529   1.0756   -7.9480  7.5809
 U3W  O01  O  O     0  -0.414   2.8790   -6.5883  8.0292
 U3W  O15  O  O     0  -0.472  -0.3676   -9.6567  7.0251
 U3W  S03  S  S2    0   0.318   3.3380   -9.0719  7.2741
 U3W  H1   H  HCH3  0   0.262   2.3649  -11.9426  7.3736
 U3W  H2   H  HCH3  0   0.276   0.9624  -11.6696  6.3283
 U3W  H3   H  HCH3  0   0.264   2.5911  -11.4474  5.6821
 U3W  H4   H  HCH2  0   0.295   0.3711   -6.3124  8.6380
 U3W  H5   H  HCH2  0   0.296  -0.8486   -7.4764  8.1586
 U3W  H6   H  HCR6  0   0.254   1.1252   -4.5651  7.0823
 U3W  H7   H  HCR6  0   0.256   0.6743   -3.2578  5.0443
 U3W  H8   H  HCR6  0   0.257  -0.9702   -4.0728  3.3846
 U3W  H9   H  HCR6  0   0.256  -2.1676   -6.2019  3.7855
 U3W  H10  H  HCR6  0   0.254  -1.7106   -7.5117  5.8226

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
 U3W  C12  C13  aromatic  1.389  0.020  1.389
 U3W  C12  C11  aromatic  1.388  0.020  1.388
 U3W  C13  C14  aromatic  1.388  0.020  1.388
 U3W  C11  C10  aromatic  1.388  0.020  1.388
 U3W  C14  C09  aromatic  1.393  0.020  1.393
 U3W  C05  N04  single    1.446  0.020  1.446
 U3W  C10  C09  aromatic  1.392  0.020  1.392
 U3W  C09  C08  single    1.506  0.020  1.506
 U3W  N04  S03  single    1.707  0.020  1.707
 U3W  N04  C06  single    1.353  0.020  1.353
 U3W  S03  C02  single    1.764  0.020  1.764
 U3W  O15  C06  double    1.212  0.020  1.212
 U3W  C06  N07  single    1.394  0.020  1.394
 U3W  C02  N07  single    1.363  0.020  1.363
 U3W  C02  O01  double    1.203  0.020  1.203
 U3W  N07  C08  single    1.460  0.020  1.460
 U3W  C05  H1   single    0.970  0.020  1.090
 U3W  C05  H2   single    0.970  0.020  1.090
 U3W  C05  H3   single    0.970  0.020  1.090
 U3W  C08  H4   single    0.970  0.020  1.090
 U3W  C08  H5   single    0.970  0.020  1.090
 U3W  C10  H6   single    0.930  0.020  1.080
 U3W  C11  H7   single    0.930  0.020  1.080
 U3W  C12  H8   single    0.930  0.020  1.080
 U3W  C13  H9   single    0.930  0.020  1.080
 U3W  C14  H10  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
 U3W  S03  C02  O01  124.25  3.000
 U3W  O01  C02  N07  127.49  3.000
 U3W  S03  C02  N07  108.25  3.000
 U3W  H3   C05  H2   108.62  3.000
 U3W  H3   C05  H1   109.31  3.000
 U3W  H2   C05  H1   108.95  3.000
 U3W  H3   C05  N04  110.28  3.000
 U3W  H2   C05  N04  108.63  3.000
 U3W  H1   C05  N04  110.99  3.000
 U3W  O15  C06  N07  124.21  3.000
 U3W  N07  C06  N04  109.55  3.000
 U3W  O15  C06  N04  126.24  3.000
 U3W  H5   C08  H4   107.23  3.000
 U3W  H5   C08  N07  107.26  3.000
 U3W  H4   C08  N07  107.79  3.000
 U3W  H5   C08  C09  111.10  3.000
 U3W  H4   C08  C09  111.11  3.000
 U3W  N07  C08  C09  112.14  3.000
 U3W  C14  C09  C10  119.07  3.000
 U3W  C10  C09  C08  120.57  3.000
 U3W  C14  C09  C08  120.35  3.000
 U3W  H6   C10  C11  119.71  3.000
 U3W  H6   C10  C09  119.79  3.000
 U3W  C11  C10  C09  120.50  3.000
 U3W  H7   C11  C12  120.11  3.000
 U3W  H7   C11  C10  119.79  3.000
 U3W  C12  C11  C10  120.10  3.000
 U3W  H8   C12  C13  120.14  3.000
 U3W  H8   C12  C11  120.12  3.000
 U3W  C13  C12  C11  119.73  3.000
 U3W  H9   C13  C14  119.79  3.000
 U3W  H9   C13  C12  120.12  3.000
 U3W  C14  C13  C12  120.09  3.000
 U3W  H10  C14  C13  119.85  3.000
 U3W  H10  C14  C09  119.65  3.000
 U3W  C13  C14  C09  120.50  3.000
 U3W  S03  N04  C06  114.72  3.000
 U3W  C06  N04  C05  125.04  3.000
 U3W  S03  N04  C05  120.13  3.000
 U3W  C08  N07  C06  121.64  3.000
 U3W  C08  N07  C02  121.35  3.000
 U3W  C06  N07  C02  116.95  3.000
 U3W  N04  S03  C02   90.51  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
 U3W  CONST_01  C12  C13  C14  C09     0.00   0.0  0
 U3W  CONST_02  C12  C11  C10  C09     0.00   0.0  0
 U3W  CONST_03  C13  C12  C11  C10     0.00   0.0  0
 U3W  CONST_04  C13  C14  C09  C10     0.00   0.0  0
 U3W  CONST_05  C14  C13  C12  C11     0.00   0.0  0
 U3W  CONST_06  C14  C09  C10  C11     0.00   0.0  0
 U3W  CONST_07  C06  N04  S03  C02     0.00   0.0  0
 U3W  CONST_08  N04  C06  N07  C02     0.00   0.0  0
 U3W  CONST_09  S03  C02  N07  C06     0.00   0.0  0
 U3W  CONST_10  N07  C02  S03  N04     0.00   0.0  0
 U3W  CONST_11  S03  N04  C06  N07     0.00   0.0  0
 U3W  CONST_12  C13  C14  C09  C08   180.00   0.0  0
 U3W  CONST_13  C11  C10  C09  C08   180.00   0.0  0
 U3W  CONST_14  C05  N04  S03  C02   180.00   0.0  0
 U3W  CONST_15  O15  C06  N07  C02   180.00   0.0  0
 U3W  CONST_16  N07  C06  N04  C05   180.00   0.0  0
 U3W  CONST_17  N04  C06  N07  C08   180.00   0.0  0
 U3W  CONST_18  S03  C02  N07  C08   180.00   0.0  0
 U3W  CONST_19  S03  N04  C06  O15   180.00   0.0  0
 U3W  CONST_20  H9   C13  C14  C09   180.00   0.0  0
 U3W  CONST_21  H7   C11  C10  C09   180.00   0.0  0
 U3W  CONST_22  H8   C12  C11  C10   180.00   0.0  0
 U3W  CONST_23  H10  C14  C09  C10   180.00   0.0  0
 U3W  CONST_24  H9   C13  C12  C11   180.00   0.0  0
 U3W  CONST_25  H10  C14  C13  C12   180.00   0.0  0
 U3W  CONST_26  H6   C10  C11  C12   180.00   0.0  0
 U3W  CONST_27  H7   C11  C12  C13   180.00   0.0  0
 U3W  CONST_28  H8   C12  C13  C14   180.00   0.0  0
 U3W  CONST_29  H6   C10  C09  C14   180.00   0.0  0
 U3W  CONST_30  O15  C06  N04  C05     0.00   0.0  0
 U3W  CONST_31  O15  C06  N07  C08     0.00   0.0  0
 U3W  Var_01    C09  C08  N07  C02    85.69  30.0  3
 U3W  Var_02    C09  C08  N07  C06   -91.24  30.0  3
 U3W  Var_03    N07  C08  C09  C10   -92.56  30.0  2
 U3W  Var_04    N07  C08  C09  C14    86.65  30.0  2
 U3W  Var_05    H4   C08  N07  C02   -36.91  30.0  3
 U3W  Var_06    H5   C08  N07  C02  -152.08  30.0  3
 U3W  Var_07    H1   C05  N04  C06  -111.19  30.0  3
 U3W  Var_08    H2   C05  N04  C06     8.57  30.0  3
 U3W  Var_09    H3   C05  N04  C06   127.51  30.0  3
 U3W  Var_10    H4   C08  N07  C06   146.16  30.0  3
 U3W  Var_11    H5   C08  N07  C06    30.99  30.0  3
 U3W  Var_12    H4   C08  C09  C10    28.14  30.0  2
 U3W  Var_13    H5   C08  C09  C10   147.42  30.0  2
 U3W  Var_14    H4   C08  C09  C14  -152.66  30.0  2
 U3W  Var_15    H5   C08  C09  C14   -33.37  30.0  2
 U3W  Var_16    H1   C05  N04  S03    64.98  30.0  3
 U3W  Var_17    H2   C05  N04  S03  -175.26  30.0  3
 U3W  Var_18    H3   C05  N04  S03   -56.32  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
 U3W  plan-1  C08  0.020
 U3W  plan-1  C09  0.020
 U3W  plan-1  C10  0.020
 U3W  plan-1  C11  0.020
 U3W  plan-1  C12  0.020
 U3W  plan-1  C13  0.020
 U3W  plan-1  C14  0.020
 U3W  plan-1  H6   0.020
 U3W  plan-1  H7   0.020
 U3W  plan-1  H8   0.020
 U3W  plan-1  H9   0.020
 U3W  plan-1  H10  0.020
 U3W  plan-2  C02  0.020
 U3W  plan-2  C05  0.020
 U3W  plan-2  C06  0.020
 U3W  plan-2  C08  0.020
 U3W  plan-2  N04  0.020
 U3W  plan-2  N07  0.020
 U3W  plan-2  O01  0.020
 U3W  plan-2  O15  0.020
 U3W  plan-2  S03  0.020

