# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 09:25:48 2020
#   Inital geometry file: a 155 line input string
#   Ligand name: 2-[(2S)-1-(3,5-dichloropyridine-4-carbonyl)pyrrolidin-2-yl]-5-hydroxy-6-oxo-N-[2-(phenylsulfonyl)ethyl]-1,6-dihydropyrimidine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC1=C(N=C(NC1=O)[C@@H]2CCCN2C(=O)c3c(Cl)cncc3Cl)C(=O)NCC[S](=O)(=O)c4ccccc4
#
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
 KU0  KU0  2-[(2S)-1-(3,5-dichloropyridine-4-carbonyl)pyrrolidin-2-yl]-5-hydroxy-6-oxo-N-[2-(phenylsulfonyl)ethyl]-1,6-dihydropyrimidine-4-carboxamide  ligand  58  37  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KU0
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
 KU0  C1   C   CR6   0  -0.158  -5.8572  -0.5526   0.7868
 KU0  C10  C   CR6   0  -0.170   6.6242  -1.0914  -0.3686
 KU0  C11  C   CR16  0  -0.233   7.1277  -0.9842  -1.6581
 KU0  C12  C   CR16  0  -0.241   7.5295  -2.1368  -2.3165
 KU0  C13  C   CR16  0  -0.233   7.4239  -3.3711  -1.6886
 KU0  C14  C   CR16  0  -0.242   6.9188  -3.4618  -0.3976
 KU0  C15  C   CR16  0  -0.230   6.5163  -2.3178   0.2744
 KU0  C16  C   CR6   0   0.239  -0.7915   3.6255   0.4284
 KU0  C17  C   CR6   0   0.484  -2.1712   3.3756   0.0182
 KU0  C18  C   CH2   0  -0.478  -1.8748   0.0260  -2.8281
 KU0  C19  C   CH2   0  -0.478  -2.8952  -1.0439  -3.1953
 KU0  C2   C   CR6   0   0.189  -4.7460  -1.3662   0.6427
 KU0  C20  C   CH2   0  -0.277  -3.9132  -0.9597  -2.0676
 KU0  C21  C   CR6   0  -0.162  -4.9331  -2.7269   0.8314
 KU0  C22  C   CR16  0  -0.008  -6.1920  -3.2117   1.1536
 KU0  C23  C   CR16  0  -0.008  -7.0850  -1.1096   1.1138
 KU0  C3   C   C     0   0.509  -3.3802  -0.8025   0.3714
 KU0  C4   C   CH1   0  -0.148  -1.7664  -0.0995  -1.3009
 KU0  C5   C   CR6   0   0.511  -1.4045   1.1986  -0.6391
 KU0  C6   C   CR6   0  -0.004   0.1342   2.6398   0.2622
 KU0  C7   C   C     0   0.556   1.5676   2.8050   0.6542
 KU0  C8   C   CH2   0  -0.236   3.7196   1.6732   0.7739
 KU0  C9   C   CH2   0  -0.649   4.3478   0.4624   0.0985
 KU0  N1   N   NT    0  -0.484  -3.0874  -0.5839  -0.9154
 KU0  N2   N   N     0  -0.473  -0.1990   1.4230  -0.2715
 KU0  N3   N   NH1   0  -0.663   2.3184   1.7160   0.4347
 KU0  N4   N   NR16  0  -0.679  -2.3792   2.1374  -0.5176
 KU0  N5   N   N     0  -0.394  -7.2363  -2.4112   1.2931
 KU0  O1   O   O     0  -0.433  -2.6253  -0.5566   1.2941
 KU0  O2   O   O     0  -0.476   2.0074   3.8417   1.1282
 KU0  O3   O   OS    0  -0.665   6.2437   0.1640   1.9152
 KU0  O4   O   OS    0  -0.664   6.7531   1.5283  -0.1337
 KU0  O6   O   O     0  -0.464  -3.0521   4.2107   0.1446
 KU0  S1   S   S     0   1.210   6.0971   0.3734   0.4761
 KU0  CL1  CL  CL    0  -0.081  -5.7237   1.1497   0.5527
 KU0  CL2  CL  CL    0  -0.073  -3.6121  -3.8105   0.6330
 KU0  H1   H   HCR6  0   0.286   7.2140  -0.0226  -2.1458
 KU0  H2   H   HCR6  0   0.276   7.9284  -2.0678  -3.3195
 KU0  H3   H   HCR6  0   0.275   7.7371  -4.2676  -2.2069
 KU0  H4   H   HCR6  0   0.276   6.8393  -4.4239   0.0900
 KU0  H5   H   HCR6  0   0.287   6.1293  -2.3890   1.2821
 KU0  H6   H   HCH2  0   0.282  -0.9063  -0.1130  -3.3037
 KU0  H7   H   HCH2  0   0.262  -2.2476   1.0146  -3.1059
 KU0  H8   H   HCH2  0   0.272  -3.3502  -0.8766  -4.1697
 KU0  H9   H   HCH2  0   0.257  -2.4271  -2.0297  -3.2033
 KU0  H10  H   HCH2  0   0.261  -4.6670  -0.1926  -2.2613
 KU0  H11  H   HCH2  0   0.275  -4.4241  -1.9063  -1.8995
 KU0  H12  H   HCR6  0   0.303  -6.3501  -4.2735   1.2990
 KU0  H13  H   HCR6  0   0.303  -7.9594  -0.4804   1.2302
 KU0  H14  H   HCH1  0   0.310  -0.9968  -0.8258  -1.0280
 KU0  H15  H   HCH2  0   0.262   3.8556   1.6128   1.8566
 KU0  H16  H   HCH2  0   0.264   4.2051   2.5876   0.4306
 KU0  H17  H   HCH2  0   0.315   3.8999  -0.4712   0.4446
 KU0  H18  H   HCH2  0   0.317   4.2549   0.5162  -0.9877
 KU0  H19  H   HNH1  0   0.415   1.8560   0.8884   0.0879
 KU0  H20  H   HNR6  0   0.418  -3.3218   1.9233  -0.8222
 KU0  H21  H   HOH1  0   0.477  -1.3852   5.3193   0.9641
 KU0  O5   O   OH1   0  -0.585  -0.5509   4.8235   0.9433

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
 KU0  O1   C3   double    1.217  0.020  1.217
 KU0  CL2  C21  single    1.720  0.020  1.720
 KU0  C3   C2   single    1.502  0.020  1.502
 KU0  C3   N1   single    1.338  0.020  1.338
 KU0  C21  C2   aromatic  1.386  0.020  1.386
 KU0  C21  C22  aromatic  1.387  0.020  1.387
 KU0  C2   C1   aromatic  1.385  0.020  1.385
 KU0  C20  N1   single    1.467  0.020  1.467
 KU0  C20  C19  single    1.522  0.020  1.522
 KU0  C22  N5   aromatic  1.323  0.020  1.323
 KU0  C1   CL1  single    1.724  0.020  1.724
 KU0  C1   C23  aromatic  1.387  0.020  1.387
 KU0  N1   C4   single    1.459  0.020  1.459
 KU0  C8   N3   single    1.442  0.020  1.442
 KU0  C8   C9   single    1.522  0.020  1.522
 KU0  N5   C23  aromatic  1.323  0.020  1.323
 KU0  N3   C7   single    1.341  0.020  1.341
 KU0  O3   S1   double    1.462  0.020  1.462
 KU0  C19  C18  single    1.523  0.020  1.523
 KU0  C9   S1   single    1.792  0.020  1.792
 KU0  C7   O2   double    1.222  0.020  1.222
 KU0  C7   C6   single    1.495  0.020  1.495
 KU0  C4   C18  single    1.536  0.020  1.536
 KU0  C4   C5   single    1.501  0.020  1.501
 KU0  N2   C6   single    1.370  0.020  1.370
 KU0  N2   C5   double    1.280  0.020  1.280
 KU0  C6   C16  double    1.362  0.020  1.362
 KU0  C5   N4   single    1.359  0.020  1.359
 KU0  S1   O4   double    1.461  0.020  1.461
 KU0  S1   C10  single    1.771  0.020  1.771
 KU0  N4   C17  single    1.365  0.020  1.365
 KU0  C16  O5   single    1.326  0.020  1.326
 KU0  C16  C17  single    1.461  0.020  1.461
 KU0  C10  C11  aromatic  1.388  0.020  1.388
 KU0  C10  C15  aromatic  1.389  0.020  1.389
 KU0  C11  C12  aromatic  1.387  0.020  1.387
 KU0  C17  O6   double    1.220  0.020  1.220
 KU0  C12  C13  aromatic  1.389  0.020  1.389
 KU0  C15  C14  aromatic  1.387  0.020  1.387
 KU0  C13  C14  aromatic  1.389  0.020  1.389
 KU0  C11  H1   single    0.930  0.020  1.080
 KU0  C12  H2   single    0.930  0.020  1.080
 KU0  C13  H3   single    0.930  0.020  1.080
 KU0  C14  H4   single    0.930  0.020  1.080
 KU0  C15  H5   single    0.930  0.020  1.080
 KU0  C18  H6   single    0.970  0.020  1.090
 KU0  C18  H7   single    0.970  0.020  1.090
 KU0  C19  H8   single    0.970  0.020  1.090
 KU0  C19  H9   single    0.970  0.020  1.090
 KU0  C20  H10  single    0.970  0.020  1.090
 KU0  C20  H11  single    0.970  0.020  1.090
 KU0  C22  H12  single    0.930  0.020  1.080
 KU0  C23  H13  single    0.930  0.020  1.080
 KU0  C4   H14  single    0.970  0.020  1.090
 KU0  C8   H15  single    0.970  0.020  1.090
 KU0  C8   H16  single    0.970  0.020  1.090
 KU0  C9   H17  single    0.970  0.020  1.090
 KU0  C9   H18  single    0.970  0.020  1.090
 KU0  N3   H19  single    0.860  0.020  1.020
 KU0  N4   H20  single    0.860  0.020  1.020
 KU0  O5   H21  single    0.850  0.020  0.980

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
 KU0  CL1  C1   C23  119.81  3.000
 KU0  C23  C1   C2   119.92  3.000
 KU0  CL1  C1   C2   120.27  3.000
 KU0  S1   C10  C15  119.10  3.000
 KU0  C15  C10  C11  121.75  3.000
 KU0  S1   C10  C11  119.15  3.000
 KU0  H1   C11  C12  120.11  3.000
 KU0  H1   C11  C10  121.09  3.000
 KU0  C12  C11  C10  118.80  3.000
 KU0  H2   C12  C13  120.26  3.000
 KU0  H2   C12  C11  119.61  3.000
 KU0  C13  C12  C11  120.13  3.000
 KU0  H3   C13  C14  119.75  3.000
 KU0  H3   C13  C12  119.86  3.000
 KU0  C14  C13  C12  120.38  3.000
 KU0  H4   C14  C15  119.62  3.000
 KU0  H4   C14  C13  120.25  3.000
 KU0  C15  C14  C13  120.13  3.000
 KU0  H5   C15  C14  120.07  3.000
 KU0  H5   C15  C10  121.14  3.000
 KU0  C14  C15  C10  118.79  3.000
 KU0  O5   C16  C6   125.29  3.000
 KU0  O5   C16  C17  115.78  3.000
 KU0  C6   C16  C17  118.93  3.000
 KU0  O6   C17  N4   123.46  3.000
 KU0  O6   C17  C16  122.38  3.000
 KU0  N4   C17  C16  114.16  3.000
 KU0  H7   C18  H6   107.95  3.000
 KU0  H7   C18  C4   110.54  3.000
 KU0  H6   C18  C4   111.18  3.000
 KU0  H7   C18  C19  110.23  3.000
 KU0  H6   C18  C19  113.65  3.000
 KU0  C4   C18  C19  103.27  3.000
 KU0  H9   C19  H8   108.16  3.000
 KU0  H9   C19  C20  110.02  3.000
 KU0  H8   C19  C20  112.04  3.000
 KU0  H9   C19  C18  110.42  3.000
 KU0  H8   C19  C18  112.82  3.000
 KU0  C20  C19  C18  103.33  3.000
 KU0  C3   C2   C21  121.04  3.000
 KU0  C21  C2   C1   117.02  3.000
 KU0  C3   C2   C1   121.86  3.000
 KU0  H11  C20  H10  108.31  3.000
 KU0  H11  C20  N1   111.45  3.000
 KU0  H10  C20  N1   110.35  3.000
 KU0  H11  C20  C19  112.35  3.000
 KU0  H10  C20  C19  111.65  3.000
 KU0  N1   C20  C19  102.69  3.000
 KU0  CL2  C21  C22  120.25  3.000
 KU0  C22  C21  C2   119.81  3.000
 KU0  CL2  C21  C2   119.93  3.000
 KU0  H12  C22  N5   117.62  3.000
 KU0  H12  C22  C21  120.41  3.000
 KU0  N5   C22  C21  121.97  3.000
 KU0  H13  C23  N5   117.69  3.000
 KU0  H13  C23  C1   120.42  3.000
 KU0  N5   C23  C1   121.89  3.000
 KU0  O1   C3   N1   124.09  3.000
 KU0  N1   C3   C2   115.73  3.000
 KU0  O1   C3   C2   120.18  3.000
 KU0  H14  C4   N1   110.55  3.000
 KU0  H14  C4   C5   107.15  3.000
 KU0  N1   C4   C5   112.88  3.000
 KU0  H14  C4   C18  110.63  3.000
 KU0  C5   C4   C18  112.62  3.000
 KU0  N1   C4   C18  103.06  3.000
 KU0  N4   C5   N2   121.92  3.000
 KU0  N4   C5   C4   117.64  3.000
 KU0  N2   C5   C4   120.34  3.000
 KU0  N2   C6   C7   115.69  3.000
 KU0  N2   C6   C16  121.67  3.000
 KU0  C7   C6   C16  122.65  3.000
 KU0  O2   C7   N3   123.44  3.000
 KU0  O2   C7   C6   122.72  3.000
 KU0  N3   C7   C6   113.84  3.000
 KU0  H16  C8   H15  107.63  3.000
 KU0  H16  C8   N3   109.48  3.000
 KU0  H15  C8   N3   110.82  3.000
 KU0  H16  C8   C9   110.10  3.000
 KU0  H15  C8   C9   110.14  3.000
 KU0  N3   C8   C9   108.67  3.000
 KU0  H18  C9   H17  108.83  3.000
 KU0  H18  C9   S1   107.17  3.000
 KU0  H17  C9   S1   106.93  3.000
 KU0  H18  C9   C8   111.55  3.000
 KU0  H17  C9   C8   111.73  3.000
 KU0  S1   C9   C8   110.42  3.000
 KU0  C4   N1   C3   120.44  3.000
 KU0  C4   N1   C20  112.79  3.000
 KU0  C3   N1   C20  126.20  3.000
 KU0  C6   N2   C5   119.77  3.000
 KU0  H19  N3   C8   120.10  3.000
 KU0  H19  N3   C7   117.75  3.000
 KU0  C8   N3   C7   121.98  3.000
 KU0  H20  N4   C5   119.63  3.000
 KU0  H20  N4   C17  116.83  3.000
 KU0  C5   N4   C17  123.54  3.000
 KU0  C23  N5   C22  119.39  3.000
 KU0  O4   S1   O3   118.62  3.000
 KU0  O4   S1   C9   108.12  3.000
 KU0  O3   S1   C9   108.21  3.000
 KU0  O4   S1   C10  108.72  3.000
 KU0  C9   S1   C10  103.36  3.000
 KU0  O3   S1   C10  108.74  3.000
 KU0  H21  O5   C16  108.29  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
 KU0  CONST_01  C22  C21  C2   C1      0.00   0.0  0
 KU0  CONST_02  C22  N5   C23  C1      0.00   0.0  0
 KU0  CONST_03  C13  C12  C11  C10     0.00   0.0  0
 KU0  CONST_04  C13  C14  C15  C10     0.00   0.0  0
 KU0  CONST_05  C14  C15  C10  C11     0.00   0.0  0
 KU0  CONST_06  C14  C13  C12  C11     0.00   0.0  0
 KU0  CONST_07  C15  C10  C11  C12     0.00   0.0  0
 KU0  CONST_08  C15  C14  C13  C12     0.00   0.0  0
 KU0  CONST_09  N5   C22  C21  C2      0.00   0.0  0
 KU0  CONST_10  N5   C23  C1   C2      0.00   0.0  0
 KU0  CONST_11  C23  C1   C2   C21     0.00   0.0  0
 KU0  CONST_12  C23  N5   C22  C21     0.00   0.0  0
 KU0  CONST_13  C5   N4   C17  C16     0.00   0.0  0
 KU0  CONST_14  C4   C5   N4   C17   180.00   0.0  0
 KU0  CONST_15  N2   C5   N4   C17     0.00   0.0  0
 KU0  CONST_16  C6   N2   C5   C4    180.00   0.0  0
 KU0  CONST_17  N4   C5   N2   C6      0.00   0.0  0
 KU0  CONST_18  CL2  C21  C2   C1    180.00   0.0  0
 KU0  CONST_19  S1   C10  C11  C12   180.00   0.0  0
 KU0  CONST_20  S1   C10  C15  C14   180.00   0.0  0
 KU0  CONST_21  CL1  C1   C2   C21   180.00   0.0  0
 KU0  CONST_22  C3   C2   C21  C22   180.00   0.0  0
 KU0  CONST_23  C3   C2   C1   C23   180.00   0.0  0
 KU0  CONST_24  CL2  C21  C22  N5    180.00   0.0  0
 KU0  CONST_25  CL1  C1   C23  N5    180.00   0.0  0
 KU0  CONST_26  C20  N1   C3   C2      0.00   0.0  0
 KU0  CONST_27  C4   N1   C3   C2    180.00   0.0  0
 KU0  CONST_28  O6   C17  N4   C5    180.00   0.0  0
 KU0  CONST_29  H2   C12  C11  C10   180.00   0.0  0
 KU0  CONST_30  H4   C14  C15  C10   180.00   0.0  0
 KU0  CONST_31  H5   C15  C10  C11   180.00   0.0  0
 KU0  CONST_32  H3   C13  C12  C11   180.00   0.0  0
 KU0  CONST_33  H1   C11  C12  C13   180.00   0.0  0
 KU0  CONST_34  H12  C22  C21  C2    180.00   0.0  0
 KU0  CONST_35  H13  C23  C1   C2    180.00   0.0  0
 KU0  CONST_36  H20  N4   C17  C16   180.00   0.0  0
 KU0  CONST_37  O1   C3   N1   C20   180.00   0.0  0
 KU0  CONST_38  O1   C3   N1   C4      0.00   0.0  0
 KU0  CONST_39  C8   N3   C7   C6    180.00   0.0  0
 KU0  CONST_40  H19  N3   C7   C6      0.00   0.0  0
 KU0  CONST_41  O2   C7   N3   C8      0.00   0.0  0
 KU0  Var_01    N1   C20  C19  C18   -32.89  30.0  1
 KU0  Var_02    C4   N1   C20  C19    15.09  30.0  1
 KU0  Var_03    C4   C18  C19  C20    38.81  30.0  1
 KU0  Var_04    N1   C3   C2   C1    -86.30  30.0  2
 KU0  Var_05    O3   S1   C10  C11  -152.35  30.0  2
 KU0  Var_06    N3   C7   C6   C16   178.87  30.0  2
 KU0  Var_07    C8   C9   S1   C10   179.18  30.0  1
 KU0  Var_08    C9   C8   N3   C7   -166.15  30.0  2
 KU0  Var_09    S1   C9   C8   N3    179.42  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
 KU0  chir_01  C4  N1  C18  C5  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
 KU0  plan-1  C10  0.020
 KU0  plan-1  C11  0.020
 KU0  plan-1  C12  0.020
 KU0  plan-1  C13  0.020
 KU0  plan-1  C14  0.020
 KU0  plan-1  C15  0.020
 KU0  plan-1  S1   0.020
 KU0  plan-1  H1   0.020
 KU0  plan-1  H2   0.020
 KU0  plan-1  H3   0.020
 KU0  plan-1  H4   0.020
 KU0  plan-1  H5   0.020
 KU0  plan-2  C1   0.020
 KU0  plan-2  C2   0.020
 KU0  plan-2  C21  0.020
 KU0  plan-2  C22  0.020
 KU0  plan-2  C23  0.020
 KU0  plan-2  C3   0.020
 KU0  plan-2  N5   0.020
 KU0  plan-2  CL1  0.020
 KU0  plan-2  CL2  0.020
 KU0  plan-2  H12  0.020
 KU0  plan-2  H13  0.020
 KU0  plan-3  C16  0.020
 KU0  plan-3  C17  0.020
 KU0  plan-3  C4   0.020
 KU0  plan-3  C5   0.020
 KU0  plan-3  C6   0.020
 KU0  plan-3  C7   0.020
 KU0  plan-3  N2   0.020
 KU0  plan-3  N4   0.020
 KU0  plan-3  O6   0.020
 KU0  plan-3  H20  0.020
 KU0  plan-3  O5   0.020
 KU0  plan-4  C6   0.020
 KU0  plan-4  C7   0.020
 KU0  plan-4  C8   0.020
 KU0  plan-4  N3   0.020
 KU0  plan-4  O2   0.020
 KU0  plan-4  H19  0.020
 KU0  plan-5  C2   0.020
 KU0  plan-5  C20  0.020
 KU0  plan-5  C3   0.020
 KU0  plan-5  C4   0.020
 KU0  plan-5  N1   0.020
 KU0  plan-5  O1   0.020

