# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 23:16:12 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: N-hydroxy-3-[(6-oxo-4-phenyl-1,6-dihydropyrimidin-2-yl)sulfanyl]propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)CCSC1=NC(=CC(=O)N1)c2ccccc2
#
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
 77J  77J  N-hydroxy-3-[(6-oxo-4-phenyl-1,6-dihydropyrimidin-2-yl)sulfanyl]propanamide  ligand  33  20  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_77J
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
 77J  C     C  CR6   0   0.364  -0.5140   1.7104   0.0484
 77J  N     N  NR16  0  -0.689  -1.4314   2.7010   0.0225
 77J  O     O  O     0  -0.479  -3.5915   3.3931  -0.0172
 77J  S     S  S2    0   0.080   1.1506   2.2375   0.1126
 77J  C1    C  CR6   0   0.302  -2.1421   0.1245  -0.0009
 77J  N1    N  N     0  -0.465  -0.8202   0.4584   0.0316
 77J  O1    O  OH1   0  -0.543   6.4072  -1.2605  -0.2070
 77J  C2    C  CR16  0  -0.502  -3.1295   1.0647  -0.0051
 77J  N2    N  NH1   0  -0.376   5.4986  -0.2532  -0.3339
 77J  O2    O  O     0  -0.468   3.8503  -1.4246   0.6791
 77J  C3    C  CR6   0   0.562  -2.8035   2.4613  -0.0032
 77J  C4    C  CR6   0   0.058  -2.4235  -1.3249  -0.0083
 77J  C5    C  CR16  0  -0.280  -1.4441  -2.2243   0.4169
 77J  C6    C  CR16  0  -0.239  -1.6994  -3.5868   0.4393
 77J  C7    C  CR16  0  -0.256  -2.9314  -4.0737   0.0243
 77J  C8    C  CR16  0  -0.238  -3.9075  -3.1881  -0.4151
 77J  C9    C  CR16  0  -0.313  -3.6567  -1.8253  -0.4308
 77J  C10   C  CH2   0  -0.551   2.0205   0.6455   0.0480
 77J  C11   C  CH2   0  -0.599   3.5016   0.9181   0.2575
 77J  C12   C  C     0   0.544   4.2853  -0.3788   0.2357
 77J  HN    H  HNR6  0   0.432  -1.1356   3.6705   0.0259
 77J  HO1   H  HOH1  0   0.479   6.3965  -1.7372  -1.0467
 77J  H2    H  HCR6  0   0.277  -4.1762   0.7987   0.0045
 77J  HN2   H  HNH1  0   0.417   5.9007   0.6512  -0.5366
 77J  H5    H  HCR6  0   0.263  -0.4818  -1.8530   0.7409
 77J  H6    H  HCR6  0   0.261  -0.9320  -4.2695   0.7802
 77J  H7    H  HCR6  0   0.263  -3.1295  -5.1375   0.0381
 77J  H8    H  HCR6  0   0.263  -4.8655  -3.5592  -0.7540
 77J  H9    H  HCR6  0   0.257  -4.4256  -1.1561  -0.7950
 77J  H10   H  HCH2  0   0.300   1.6255  -0.0007   0.8273
 77J  H10A  H  HCH2  0   0.297   1.8313   0.1846  -0.9201
 77J  H11   H  HCH2  0   0.280   3.8831   1.6154  -0.4913
 77J  H11A  H  HCH2  0   0.298   3.6655   1.3835   1.2340

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
 77J  C    N     single    1.350  0.020  1.350
 77J  C    S     single    1.747  0.020  1.747
 77J  C    N1    double    1.289  0.020  1.289
 77J  N    C3    single    1.393  0.020  1.393
 77J  O    C3    double    1.220  0.020  1.220
 77J  S    C10   single    1.815  0.020  1.815
 77J  C1   N1    single    1.364  0.020  1.364
 77J  C1   C2    double    1.364  0.020  1.364
 77J  C1   C4    single    1.477  0.020  1.477
 77J  O1   N2    single    1.362  0.020  1.362
 77J  C2   C3    single    1.434  0.020  1.434
 77J  N2   C12   single    1.346  0.020  1.346
 77J  O2   C12   double    1.216  0.020  1.216
 77J  C4   C5    aromatic  1.396  0.020  1.396
 77J  C4   C9    aromatic  1.396  0.020  1.396
 77J  C5   C6    aromatic  1.386  0.020  1.386
 77J  C6   C7    aromatic  1.388  0.020  1.388
 77J  C7   C8    aromatic  1.389  0.020  1.389
 77J  C8   C9    aromatic  1.386  0.020  1.386
 77J  C10  C11   single    1.520  0.020  1.520
 77J  C11  C12   single    1.515  0.020  1.515
 77J  N    HN    single    0.860  0.020  1.020
 77J  O1   HO1   single    0.850  0.020  0.980
 77J  C2   H2    single    0.930  0.020  1.080
 77J  N2   HN2   single    0.890  0.020  1.040
 77J  C5   H5    single    0.930  0.020  1.080
 77J  C6   H6    single    0.930  0.020  1.080
 77J  C7   H7    single    0.930  0.020  1.080
 77J  C8   H8    single    0.930  0.020  1.080
 77J  C9   H9    single    0.930  0.020  1.080
 77J  C10  H10   single    0.970  0.020  1.090
 77J  C10  H10A  single    0.970  0.020  1.090
 77J  C11  H11   single    0.970  0.020  1.090
 77J  C11  H11A  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
 77J  N1    C    S    121.32  3.000
 77J  N1    C    N    123.42  3.000
 77J  S     C    N    115.25  3.000
 77J  HN    N    C3   116.88  3.000
 77J  HN    N    C    120.22  3.000
 77J  C3    N    C    122.91  3.000
 77J  C10   S    C    100.99  3.000
 77J  C4    C1   C2   122.61  3.000
 77J  C4    C1   N1   115.16  3.000
 77J  C2    C1   N1   122.22  3.000
 77J  C1    N1   C    117.93  3.000
 77J  HO1   O1   N2   106.06  3.000
 77J  H2    C2   C3   117.40  3.000
 77J  H2    C2   C1   122.14  3.000
 77J  C3    C2   C1   120.45  3.000
 77J  HN2   N2   C12  121.81  3.000
 77J  HN2   N2   O1   114.52  3.000
 77J  C12   N2   O1   119.52  3.000
 77J  C2    C3   O    126.63  3.000
 77J  C2    C3   N    113.05  3.000
 77J  O     C3   N    120.32  3.000
 77J  C9    C4   C5   118.74  3.000
 77J  C9    C4   C1   121.44  3.000
 77J  C5    C4   C1   119.81  3.000
 77J  H5    C5   C6   119.77  3.000
 77J  H5    C5   C4   119.64  3.000
 77J  C6    C5   C4   120.59  3.000
 77J  H6    C6   C7   120.15  3.000
 77J  H6    C6   C5   119.63  3.000
 77J  C7    C6   C5   120.22  3.000
 77J  H7    C7   C8   120.14  3.000
 77J  H7    C7   C6   120.23  3.000
 77J  C8    C7   C6   119.63  3.000
 77J  H8    C8   C9   119.61  3.000
 77J  H8    C8   C7   120.16  3.000
 77J  C9    C8   C7   120.22  3.000
 77J  H9    C9   C8   118.90  3.000
 77J  H9    C9   C4   120.50  3.000
 77J  C8    C9   C4   120.58  3.000
 77J  H10A  C10  H10  108.83  3.000
 77J  H10A  C10  C11  111.57  3.000
 77J  H10   C10  C11  111.22  3.000
 77J  H10A  C10  S    108.63  3.000
 77J  H10   C10  S    108.77  3.000
 77J  C11   C10  S    107.74  3.000
 77J  H11A  C11  H11  106.74  3.000
 77J  H11A  C11  C12  107.42  3.000
 77J  H11   C11  C12  110.85  3.000
 77J  H11A  C11  C10  110.19  3.000
 77J  H11   C11  C10  111.12  3.000
 77J  C12   C11  C10  110.38  3.000
 77J  C11   C12  O2   123.07  3.000
 77J  C11   C12  N2   113.10  3.000
 77J  O2    C12  N2   123.83  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
 77J  CONST_01  C7   C6   C5   C4     0.00   0.0  0
 77J  CONST_02  C7   C8   C9   C4     0.00   0.0  0
 77J  CONST_03  C8   C9   C4   C5     0.00   0.0  0
 77J  CONST_04  C8   C7   C6   C5     0.00   0.0  0
 77J  CONST_05  C9   C4   C5   C6     0.00   0.0  0
 77J  CONST_06  C9   C8   C7   C6     0.00   0.0  0
 77J  CONST_07  C6   C5   C4   C1   180.00   0.0  0
 77J  CONST_08  C8   C9   C4   C1   180.00   0.0  0
 77J  CONST_09  C2   C3   N    C      0.00   0.0  0
 77J  CONST_10  C1   N1   C    N      0.00   0.0  0
 77J  CONST_11  C3   N    C    N1     0.00   0.0  0
 77J  CONST_12  O    C3   N    C    180.00   0.0  0
 77J  CONST_13  C3   N    C    S    180.00   0.0  0
 77J  CONST_14  C1   N1   C    S    180.00   0.0  0
 77J  CONST_15  H5   C5   C4   C1     0.00   0.0  0
 77J  CONST_16  H9   C9   C4   C1     0.00   0.0  0
 77J  CONST_17  H6   C6   C5   C4   180.00   0.0  0
 77J  CONST_18  H8   C8   C9   C4   180.00   0.0  0
 77J  CONST_19  H7   C7   C6   C5   180.00   0.0  0
 77J  CONST_20  HN   N    C    N1   180.00   0.0  0
 77J  CONST_21  O2   C12  N2   O1     0.00   0.0  0
 77J  CONST_22  C11  C12  N2   O1   180.00   0.0  0
 77J  CONST_23  HN2  N2   C12  O2   180.00   0.0  0
 77J  Var_01    C5   C4   C1   N1    19.35  30.0  2
 77J  Var_02    C11  C10  S    C   -173.56  30.0  3
 77J  Var_03    C12  C11  C10  S    179.14  30.0  3
 77J  Var_04    C10  C11  C12  N2   144.24  30.0  2

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
 77J  plan-1  C    0.020
 77J  plan-1  N    0.020
 77J  plan-1  O    0.020
 77J  plan-1  S    0.020
 77J  plan-1  C1   0.020
 77J  plan-1  N1   0.020
 77J  plan-1  C2   0.020
 77J  plan-1  C3   0.020
 77J  plan-1  C4   0.020
 77J  plan-1  HN   0.020
 77J  plan-1  H2   0.020
 77J  plan-2  C1   0.020
 77J  plan-2  C4   0.020
 77J  plan-2  C5   0.020
 77J  plan-2  C6   0.020
 77J  plan-2  C7   0.020
 77J  plan-2  C8   0.020
 77J  plan-2  C9   0.020
 77J  plan-2  H5   0.020
 77J  plan-2  H6   0.020
 77J  plan-2  H7   0.020
 77J  plan-2  H8   0.020
 77J  plan-2  H9   0.020
 77J  plan-3  O1   0.020
 77J  plan-3  N2   0.020
 77J  plan-3  O2   0.020
 77J  plan-3  C11  0.020
 77J  plan-3  C12  0.020
 77J  plan-3  HN2  0.020

