# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 01:58:46 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 2-{(2S)-1-[(4-chlorophenyl)acetyl]pyrrolidin-2-yl}-5-hydroxy-6-oxo-1,6-dihydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C1=C(O)C(=O)NC(=N1)[C@@H]2CCCN2C(=O)Cc3ccc(Cl)cc3
#
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
 GY4  GY4  '2-{(2S)-1-[(4-chlorophenyl)acetyl]pyrrolidin-2-yl}-5-hydroxy-6-oxo-1,6-dihydropyrimidine-4-carboxylic acid'  ligand  41  26  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GY4
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
 GY4  C1   C   CR6    0   0.452  -3.2916   1.1990  -1.4977
 GY4  C10  C   CR16   0  -0.288   1.8379  -0.3770   0.7946
 GY4  C11  C   CR16   0  -0.199   2.5614   0.7780   1.0465
 GY4  C12  C   CR6    0  -0.056   3.7962   0.9469   0.4390
 GY4  C13  C   CR16   0  -0.198   4.3087  -0.0129  -0.4174
 GY4  C14  C   CR16   0  -0.333   3.5675  -1.1616  -0.6625
 GY4  C15  C   CH2    0  -0.276  -0.8372  -3.4187   1.2723
 GY4  C16  C   CH2    0  -0.476  -2.2862  -3.8465   1.4507
 GY4  C17  C   CH2    0  -0.475  -3.0672  -2.6496   0.9241
 GY4  C2   C   CR6    0   0.195  -2.4713   2.0228  -0.6350
 GY4  C3   C   CR6    0  -0.044  -1.6400   1.4401   0.2781
 GY4  C4   C   C      0   0.418  -0.7327   2.2375   1.2116
 GY4  C5   C   CR6    0   0.498  -2.2631  -0.6591  -0.3921
 GY4  C6   C   CH1    0  -0.139  -2.2228  -2.1603  -0.2635
 GY4  C8   C   CH2    0  -0.647   1.5473  -2.6259  -0.3066
 GY4  C9   C   CR6    0   0.136   2.3309  -1.3614  -0.0602
 GY4  N1   N   N      0  -0.404  -1.5762   0.0806   0.3977
 GY4  N2   N   NT     0  -0.471  -0.8829  -2.6252   0.0485
 GY4  N3   N   NR16   0  -0.689  -3.1052  -0.1443  -1.3222
 GY4  O1   O   O      0  -0.501  -4.0741   1.6608  -2.3248
 GY4  O2   O   OH1    0  -0.614  -2.6192   3.3476  -0.7890
 GY4  O3   O   O      0  -0.587  -0.3106   3.3218   0.7758
 GY4  O4   O   OC    -1  -0.594  -0.5012   1.7159   2.3153
 GY4  O5   O   O      0  -0.487  -0.0501  -1.6891  -1.8067
 GY4  H2   H   HCR6   0   0.273   2.1521   1.5309   1.7056
 GY4  H3   H   HCR6   0   0.276   5.2697   0.1276  -0.8932
 GY4  H4   H   HCR6   0   0.261   3.9685  -1.9099  -1.3349
 GY4  H5   H   HCH2   0   0.245  -0.4948  -2.8173   2.1195
 GY4  H6   H   HCH2   0   0.262  -0.1705  -4.2727   1.1683
 GY4  H7   H   HCH2   0   0.247  -2.4932  -4.7347   0.8507
 GY4  H8   H   HCH2   0   0.260  -2.5213  -4.0792   2.4881
 GY4  H9   H   HCH2   0   0.267  -4.0836  -2.8933   0.6196
 GY4  H10  H   HCH2   0   0.256  -3.1213  -1.8717   1.6887
 GY4  H11  H   HCH1   0   0.285  -2.5749  -2.6161  -1.1951
 GY4  H12  H   HCH2   0   0.281   1.5703  -3.2466   0.5890
 GY4  H13  H   HCH2   0   0.289   2.0227  -3.2061  -1.0999
 GY4  H14  H   HNR6   0   0.427  -3.6294  -0.7675  -1.9247
 GY4  H15  H   HOH1   0   0.462  -3.3008   3.4883  -1.4629
 GY4  C7   C   C      0   0.550   0.1388  -2.2885  -0.7560
 GY4  CL1  CL  CL     0  -0.139   4.7103   2.3902   0.7501
 GY4  H1   H   HCR6   0   0.278   0.8636  -0.4832   1.2561

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
 GY4  O1   C1   double    1.229  0.020  1.229
 GY4  C16  C17  single    1.523  0.020  1.523
 GY4  C16  C15  single    1.521  0.020  1.521
 GY4  C1   N3   single    1.367  0.020  1.367
 GY4  C1   C2   single    1.448  0.020  1.448
 GY4  C17  C6   single    1.537  0.020  1.537
 GY4  N3   C5   single    1.356  0.020  1.356
 GY4  C15  N2   single    1.459  0.020  1.459
 GY4  O2   C2   single    1.342  0.020  1.342
 GY4  C2   C3   double    1.365  0.020  1.365
 GY4  C5   C6   single    1.507  0.020  1.507
 GY4  C5   N1   double    1.282  0.020  1.282
 GY4  C6   N2   single    1.452  0.020  1.452
 GY4  N2   C7   single    1.343  0.020  1.343
 GY4  C3   N1   single    1.366  0.020  1.366
 GY4  C3   C4   single    1.527  0.020  1.527
 GY4  O3   C4   deloc     1.243  0.020  1.243
 GY4  C8   C7   single    1.516  0.020  1.516
 GY4  C8   C9   single    1.508  0.020  1.508
 GY4  C7   O5   double    1.224  0.020  1.224
 GY4  C4   O4   deloc     1.242  0.020  1.242
 GY4  C9   C10  aromatic  1.394  0.020  1.394
 GY4  C9   C14  aromatic  1.390  0.020  1.390
 GY4  C10  C11  aromatic  1.386  0.020  1.386
 GY4  C14  C13  aromatic  1.389  0.020  1.389
 GY4  C11  C12  aromatic  1.386  0.020  1.386
 GY4  C13  C12  aromatic  1.385  0.020  1.385
 GY4  C12  CL1  single    1.737  0.020  1.737
 GY4  C10  H1   single    0.930  0.020  1.080
 GY4  C11  H2   single    0.930  0.020  1.080
 GY4  C13  H3   single    0.930  0.020  1.080
 GY4  C14  H4   single    0.930  0.020  1.080
 GY4  C15  H5   single    0.970  0.020  1.090
 GY4  C15  H6   single    0.970  0.020  1.090
 GY4  C16  H7   single    0.970  0.020  1.090
 GY4  C16  H8   single    0.970  0.020  1.090
 GY4  C17  H9   single    0.970  0.020  1.090
 GY4  C17  H10  single    0.970  0.020  1.090
 GY4  C6   H11  single    0.970  0.020  1.090
 GY4  C8   H12  single    0.970  0.020  1.090
 GY4  C8   H13  single    0.970  0.020  1.090
 GY4  N3   H14  single    0.860  0.020  1.020
 GY4  O2   H15  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
 GY4  O1   C1   N3   122.85  3.000
 GY4  N3   C1   C2   113.90  3.000
 GY4  O1   C1   C2   123.24  3.000
 GY4  H1   C10  C9   120.67  3.000
 GY4  H1   C10  C11  118.28  3.000
 GY4  C9   C10  C11  121.02  3.000
 GY4  H2   C11  C12  121.30  3.000
 GY4  H2   C11  C10  119.58  3.000
 GY4  C12  C11  C10  119.13  3.000
 GY4  CL1  C12  C13  119.48  3.000
 GY4  CL1  C12  C11  119.44  3.000
 GY4  C13  C12  C11  121.08  3.000
 GY4  H3   C13  C14  120.27  3.000
 GY4  H3   C13  C12  120.73  3.000
 GY4  C14  C13  C12  119.00  3.000
 GY4  H4   C14  C9   119.95  3.000
 GY4  H4   C14  C13  118.91  3.000
 GY4  C9   C14  C13  121.15  3.000
 GY4  H6   C15  H5   108.28  3.000
 GY4  H6   C15  N2   111.45  3.000
 GY4  H5   C15  N2   111.12  3.000
 GY4  H6   C15  C16  111.96  3.000
 GY4  H5   C15  C16  111.22  3.000
 GY4  N2   C15  C16  102.79  3.000
 GY4  H8   C16  H7   107.99  3.000
 GY4  H8   C16  C17  112.74  3.000
 GY4  H7   C16  C17  110.61  3.000
 GY4  H8   C16  C15  112.18  3.000
 GY4  H7   C16  C15  110.18  3.000
 GY4  C17  C16  C15  103.11  3.000
 GY4  H10  C17  H9   108.00  3.000
 GY4  H10  C17  C6   109.97  3.000
 GY4  H9   C17  C6   111.60  3.000
 GY4  H10  C17  C16  110.06  3.000
 GY4  H9   C17  C16  113.55  3.000
 GY4  C6   C17  C16  103.62  3.000
 GY4  O2   C2   C3   124.41  3.000
 GY4  C3   C2   C1   120.04  3.000
 GY4  O2   C2   C1   115.53  3.000
 GY4  N1   C3   C4   116.00  3.000
 GY4  C4   C3   C2   123.22  3.000
 GY4  N1   C3   C2   120.77  3.000
 GY4  O4   C4   O3   127.93  3.000
 GY4  O4   C4   C3   115.76  3.000
 GY4  O3   C4   C3   116.31  3.000
 GY4  N3   C5   N1   122.43  3.000
 GY4  N1   C5   C6   120.52  3.000
 GY4  N3   C5   C6   116.95  3.000
 GY4  H11  C6   N2   110.25  3.000
 GY4  H11  C6   C5   109.47  3.000
 GY4  N2   C6   C5   111.21  3.000
 GY4  H11  C6   C17  110.37  3.000
 GY4  N2   C6   C17  103.83  3.000
 GY4  C5   C6   C17  111.60  3.000
 GY4  H13  C8   H12  106.57  3.000
 GY4  H13  C8   C9   109.76  3.000
 GY4  H12  C8   C9   109.41  3.000
 GY4  H13  C8   C7   107.90  3.000
 GY4  H12  C8   C7   112.94  3.000
 GY4  C9   C8   C7   110.15  3.000
 GY4  C8   C9   C14  120.80  3.000
 GY4  C14  C9   C10  118.61  3.000
 GY4  C8   C9   C10  120.58  3.000
 GY4  C5   N1   C3   119.69  3.000
 GY4  C7   N2   C6   119.53  3.000
 GY4  C7   N2   C15  127.93  3.000
 GY4  C6   N2   C15  112.53  3.000
 GY4  H14  N3   C5   119.72  3.000
 GY4  H14  N3   C1   117.22  3.000
 GY4  C5   N3   C1   123.07  3.000
 GY4  H15  O2   C2   107.50  3.000
 GY4  O5   C7   N2   121.29  3.000
 GY4  O5   C7   C8   120.43  3.000
 GY4  N2   C7   C8   118.24  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
 GY4  CONST_01  C13  C14  C9   C10     0.00   0.0  0
 GY4  CONST_02  C13  C12  C11  C10     0.00   0.0  0
 GY4  CONST_03  C14  C9   C10  C11     0.00   0.0  0
 GY4  CONST_04  C14  C13  C12  C11     0.00   0.0  0
 GY4  CONST_05  C9   C10  C11  C12     0.00   0.0  0
 GY4  CONST_06  C9   C14  C13  C12     0.00   0.0  0
 GY4  CONST_07  C6   C5   N3   C1    180.00   0.0  0
 GY4  CONST_08  N1   C5   N3   C1      0.00   0.0  0
 GY4  CONST_09  C5   N3   C1   C2      0.00   0.0  0
 GY4  CONST_10  N3   C5   N1   C3      0.00   0.0  0
 GY4  CONST_11  C6   C5   N1   C3    180.00   0.0  0
 GY4  CONST_12  CL1  C12  C11  C10   180.00   0.0  0
 GY4  CONST_13  C8   C9   C10  C11   180.00   0.0  0
 GY4  CONST_14  C8   C9   C14  C13   180.00   0.0  0
 GY4  CONST_15  CL1  C12  C13  C14   180.00   0.0  0
 GY4  CONST_16  O1   C1   N3   C5    180.00   0.0  0
 GY4  CONST_17  H4   C14  C9   C10   180.00   0.0  0
 GY4  CONST_18  H3   C13  C12  C11   180.00   0.0  0
 GY4  CONST_19  H1   C10  C11  C12   180.00   0.0  0
 GY4  CONST_20  H2   C11  C12  C13   180.00   0.0  0
 GY4  CONST_21  H14  N3   C1   C2    180.00   0.0  0
 GY4  CONST_22  C8   C7   N2   C15     0.00   0.0  0
 GY4  CONST_23  O5   C7   N2   C15   180.00   0.0  0
 GY4  CONST_24  C8   C7   N2   C6    180.00   0.0  0
 GY4  CONST_25  O5   C7   N2   C6      0.00   0.0  0
 GY4  Var_01    C6   C17  C16  C15    36.92  30.0  1
 GY4  Var_02    C6   N2   C15  C16    19.62  30.0  1
 GY4  Var_03    N2   C15  C16  C17   -34.41  30.0  1
 GY4  Var_04    C7   C8   C9   C10    53.65  30.0  2
 GY4  Var_05    O3   C4   C3   C2    -30.96  30.0  2
 GY4  Var_06    N2   C7   C8   C9   -114.62  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
 GY4  chir_01  C6  C17  C5  N2  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
 GY4  plan-1  C1   0.020
 GY4  plan-1  C2   0.020
 GY4  plan-1  C3   0.020
 GY4  plan-1  C4   0.020
 GY4  plan-1  C5   0.020
 GY4  plan-1  C6   0.020
 GY4  plan-1  N1   0.020
 GY4  plan-1  N3   0.020
 GY4  plan-1  O1   0.020
 GY4  plan-1  O2   0.020
 GY4  plan-1  H14  0.020
 GY4  plan-2  C10  0.020
 GY4  plan-2  C11  0.020
 GY4  plan-2  C12  0.020
 GY4  plan-2  C13  0.020
 GY4  plan-2  C14  0.020
 GY4  plan-2  C8   0.020
 GY4  plan-2  C9   0.020
 GY4  plan-2  H2   0.020
 GY4  plan-2  H3   0.020
 GY4  plan-2  H4   0.020
 GY4  plan-2  CL1  0.020
 GY4  plan-2  H1   0.020
 GY4  plan-3  C15  0.020
 GY4  plan-3  C6   0.020
 GY4  plan-3  C8   0.020
 GY4  plan-3  N2   0.020
 GY4  plan-3  O5   0.020
 GY4  plan-3  C7   0.020
 GY4  plan-4  C3   0.020
 GY4  plan-4  C4   0.020
 GY4  plan-4  O3   0.020
 GY4  plan-4  O4   0.020

