# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 06:55:51 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 5-hydroxy-2-[(2S)-1-{[(naphthalen-1-yl)oxy]acetyl}pyrrolidin-2-yl]-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)COc3cccc4ccccc34
#
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
 9KU  9KU  '5-hydroxy-2-[(2S)-1-{[(naphthalen-1-yl)oxy]acetyl}pyrrolidin-2-yl]-6-oxo-1,6-dihydropyrimidine-4-carboxylic acid'  ligand  48  30  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9KU
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
 9KU  C1   C  CR6    0   0.453  -4.2398   1.1209  -1.3930
 9KU  C10  C  CR16   0  -0.402   3.9172  -1.7981   0.9264
 9KU  C11  C  CR16   0  -0.245   5.2731  -1.7221   1.3113
 9KU  C12  C  CR16   0  -0.343   6.0717  -0.6976   0.8936
 9KU  C13  C  CR66   0   0.127   5.5422   0.3157   0.0574
 9KU  C14  C  CR66   0  -0.022   4.1839   0.2562  -0.3454
 9KU  C15  C  CR16   0  -0.287   3.6644   1.2744  -1.1781
 9KU  C16  C  CR16   0  -0.256   4.4623   2.3085  -1.5910
 9KU  C17  C  CR16   0  -0.251   5.8122   2.3709  -1.1938
 9KU  C18  C  CR16   0  -0.317   6.3374   1.3965  -0.3890
 9KU  C19  C  CH2    0  -0.284  -1.0633  -3.2746   1.0096
 9KU  C2   C  CR6    0   0.198  -3.8806   1.9000  -0.2282
 9KU  C20  C  CH2    0  -0.473  -2.3399  -4.0714   0.7839
 9KU  C21  C  CH2    0  -0.476  -3.3329  -3.0011   0.3485
 9KU  C3   C  CR6    0  -0.043  -3.1096   1.3464   0.7526
 9KU  C4   C  C      0   0.387  -2.6968   2.1005   2.0127
 9KU  C5   C  CR6    0   0.496  -2.9378  -0.6258  -0.3945
 9KU  C6   C  CH1    0  -0.140  -2.4890  -2.0582  -0.5253
 9KU  C8   C  CH2    0  -0.311   1.2222  -1.7918   0.1403
 9KU  C9   C  CR6    0   0.367   3.3818  -0.8319   0.1120
 9KU  N1   N  N      0  -0.411  -2.6600   0.0588   0.6536
 9KU  N2   N  NT     0  -0.481  -1.1407  -2.2519  -0.0266
 9KU  N3   N  NR16   0  -0.689  -3.7038  -0.1375  -1.4013
 9KU  O1   O  O      0  -0.499  -4.9502   1.5491  -2.2986
 9KU  O2   O  OH1    0  -0.614  -4.3767   3.1461  -0.1846
 9KU  O3   O  OC    -1  -0.589  -2.6076   1.4144   3.0434
 9KU  O4   O  O      0  -0.590  -2.4821   3.3180   1.8842
 9KU  O5   O  O2     0  -0.456   2.1080  -0.8107  -0.3193
 9KU  O6   O  O      0  -0.476  -0.2658  -0.7040  -1.4013
 9KU  H3   H  HCR6   0   0.252   7.1100  -0.6453   1.1960
 9KU  H4   H  HCR6   0   0.256   2.6299   1.2382  -1.4913
 9KU  H5   H  HCR6   0   0.258   4.0534   3.0841  -2.2252
 9KU  H6   H  HCR6   0   0.258   6.4328   3.1922  -1.5278
 9KU  H7   H  HCR6   0   0.255   7.3745   1.4425  -0.0796
 9KU  H8   H  HCH2   0   0.253  -1.0495  -2.8208   2.0049
 9KU  H9   H  HCH2   0   0.264  -0.1695  -3.8891   0.9019
 9KU  H10  H  HCH2   0   0.248  -2.1886  -4.8044  -0.0108
 9KU  H11  H  HCH2   0   0.261  -2.6576  -4.6032   1.6792
 9KU  H12  H  HCH2   0   0.270  -4.1892  -3.3929  -0.1976
 9KU  H13  H  HCH2   0   0.257  -3.7036  -2.4608   1.2213
 9KU  H14  H  HCH1   0   0.288  -2.5485  -2.3616  -1.5766
 9KU  H15  H  HCH2   0   0.265   1.1293  -1.7647   1.2331
 9KU  H16  H  HCH2   0   0.267   1.5601  -2.8009  -0.1311
 9KU  H17  H  HNR6   0   0.427  -3.8991  -0.7188  -2.2076
 9KU  H18  H  HOH1   0   0.463  -4.9315   3.2689  -0.9690
 9KU  C7   C  C      0   0.539  -0.1251  -1.5208  -0.5068
 9KU  H1   H  HCR6   0   0.283   3.3237  -2.6265   1.2883
 9KU  H2   H  HCR6   0   0.260   5.6735  -2.4988   1.9497

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
 9KU  C20  C19  single    1.522  0.020  1.522
 9KU  C20  C21  single    1.524  0.020  1.524
 9KU  O1   C1   double    1.228  0.020  1.228
 9KU  C19  N2   single    1.458  0.020  1.458
 9KU  C21  C6   single    1.538  0.020  1.538
 9KU  C1   N3   single    1.368  0.020  1.368
 9KU  C1   C2   single    1.447  0.020  1.447
 9KU  N3   C5   single    1.356  0.020  1.356
 9KU  O2   C2   single    1.342  0.020  1.342
 9KU  C2   C3   double    1.365  0.020  1.365
 9KU  C5   C6   single    1.507  0.020  1.507
 9KU  C5   N1   double    1.282  0.020  1.282
 9KU  N2   C6   single    1.451  0.020  1.451
 9KU  N2   C7   single    1.340  0.020  1.340
 9KU  C8   C7   single    1.519  0.020  1.519
 9KU  C8   O5   single    1.399  0.020  1.399
 9KU  C3   N1   single    1.367  0.020  1.367
 9KU  C3   C4   single    1.525  0.020  1.525
 9KU  C7   O6   double    1.219  0.020  1.219
 9KU  O4   C4   deloc     1.243  0.020  1.243
 9KU  C4   O3   deloc     1.241  0.020  1.241
 9KU  O5   C9   single    1.345  0.020  1.345
 9KU  C10  C9   aromatic  1.372  0.020  1.372
 9KU  C10  C11  aromatic  1.412  0.020  1.412
 9KU  C9   C14  aromatic  1.427  0.020  1.427
 9KU  C11  C12  aromatic  1.364  0.020  1.364
 9KU  C14  C15  aromatic  1.414  0.020  1.414
 9KU  C14  C13  aromatic  1.418  0.020  1.418
 9KU  C15  C16  aromatic  1.370  0.020  1.370
 9KU  C12  C13  aromatic  1.416  0.020  1.416
 9KU  C13  C18  aromatic  1.414  0.020  1.414
 9KU  C16  C17  aromatic  1.409  0.020  1.409
 9KU  C18  C17  aromatic  1.369  0.020  1.369
 9KU  C10  H1   single    0.930  0.020  1.080
 9KU  C11  H2   single    0.930  0.020  1.080
 9KU  C12  H3   single    0.930  0.020  1.080
 9KU  C15  H4   single    0.930  0.020  1.080
 9KU  C16  H5   single    0.930  0.020  1.080
 9KU  C17  H6   single    0.930  0.020  1.080
 9KU  C18  H7   single    0.930  0.020  1.080
 9KU  C19  H8   single    0.970  0.020  1.090
 9KU  C19  H9   single    0.970  0.020  1.090
 9KU  C20  H10  single    0.970  0.020  1.090
 9KU  C20  H11  single    0.970  0.020  1.090
 9KU  C21  H12  single    0.970  0.020  1.090
 9KU  C21  H13  single    0.970  0.020  1.090
 9KU  C6   H14  single    0.970  0.020  1.090
 9KU  C8   H15  single    0.970  0.020  1.090
 9KU  C8   H16  single    0.970  0.020  1.090
 9KU  N3   H17  single    0.860  0.020  1.020
 9KU  O2   H18  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
 9KU  O1   C1   N3   122.89  3.000
 9KU  N3   C1   C2   113.77  3.000
 9KU  O1   C1   C2   123.34  3.000
 9KU  H1   C10  C9   121.59  3.000
 9KU  H1   C10  C11  118.50  3.000
 9KU  C9   C10  C11  119.91  3.000
 9KU  H2   C11  C12  120.19  3.000
 9KU  H2   C11  C10  118.53  3.000
 9KU  C12  C11  C10  121.27  3.000
 9KU  H3   C12  C13  119.26  3.000
 9KU  H3   C12  C11  120.80  3.000
 9KU  C13  C12  C11  119.94  3.000
 9KU  C18  C13  C14  118.75  3.000
 9KU  C18  C13  C12  121.53  3.000
 9KU  C14  C13  C12  119.72  3.000
 9KU  C9   C14  C15  122.09  3.000
 9KU  C15  C14  C13  119.27  3.000
 9KU  C9   C14  C13  118.64  3.000
 9KU  H4   C15  C16  119.68  3.000
 9KU  H4   C15  C14  119.85  3.000
 9KU  C16  C15  C14  120.47  3.000
 9KU  H5   C16  C17  119.71  3.000
 9KU  H5   C16  C15  119.84  3.000
 9KU  C17  C16  C15  120.44  3.000
 9KU  H6   C17  C18  120.12  3.000
 9KU  H6   C17  C16  119.75  3.000
 9KU  C18  C17  C16  120.13  3.000
 9KU  H7   C18  C17  120.34  3.000
 9KU  H7   C18  C13  118.73  3.000
 9KU  C17  C18  C13  120.93  3.000
 9KU  H9   C19  H8   108.26  3.000
 9KU  H9   C19  N2   111.64  3.000
 9KU  H8   C19  N2   110.87  3.000
 9KU  H9   C19  C20  112.21  3.000
 9KU  H8   C19  C20  111.27  3.000
 9KU  N2   C19  C20  102.55  3.000
 9KU  O2   C2   C3   124.20  3.000
 9KU  C3   C2   C1   120.03  3.000
 9KU  O2   C2   C1   115.75  3.000
 9KU  H11  C20  H10  108.13  3.000
 9KU  H11  C20  C21  112.83  3.000
 9KU  H10  C20  C21  110.73  3.000
 9KU  H11  C20  C19  112.24  3.000
 9KU  H10  C20  C19  110.08  3.000
 9KU  C21  C20  C19  102.79  3.000
 9KU  H13  C21  H12  108.19  3.000
 9KU  H13  C21  C6   109.71  3.000
 9KU  H12  C21  C6   111.55  3.000
 9KU  H13  C21  C20  109.92  3.000
 9KU  H12  C21  C20  113.78  3.000
 9KU  C6   C21  C20  103.62  3.000
 9KU  N1   C3   C4   115.87  3.000
 9KU  C4   C3   C2   123.09  3.000
 9KU  N1   C3   C2   121.04  3.000
 9KU  O4   C4   O3   127.94  3.000
 9KU  O3   C4   C3   115.60  3.000
 9KU  O4   C4   C3   116.46  3.000
 9KU  N3   C5   N1   122.48  3.000
 9KU  N1   C5   C6   120.93  3.000
 9KU  N3   C5   C6   116.50  3.000
 9KU  H14  C6   N2   110.08  3.000
 9KU  H14  C6   C5   109.29  3.000
 9KU  N2   C6   C5   111.96  3.000
 9KU  H14  C6   C21  110.22  3.000
 9KU  N2   C6   C21  103.47  3.000
 9KU  C5   C6   C21  111.72  3.000
 9KU  H16  C8   H15  107.16  3.000
 9KU  H16  C8   O5   111.61  3.000
 9KU  H15  C8   O5   111.31  3.000
 9KU  H16  C8   C7   109.36  3.000
 9KU  H15  C8   C7   110.17  3.000
 9KU  O5   C8   C7   107.24  3.000
 9KU  O5   C9   C14  114.68  3.000
 9KU  C14  C9   C10  120.51  3.000
 9KU  O5   C9   C10  124.81  3.000
 9KU  C5   N1   C3   119.38  3.000
 9KU  C7   N2   C6   120.55  3.000
 9KU  C7   N2   C19  126.66  3.000
 9KU  C6   N2   C19  112.79  3.000
 9KU  H17  N3   C5   119.55  3.000
 9KU  H17  N3   C1   117.21  3.000
 9KU  C5   N3   C1   123.24  3.000
 9KU  H18  O2   C2   107.64  3.000
 9KU  C9   O5   C8   118.89  3.000
 9KU  O6   C7   N2   122.74  3.000
 9KU  O6   C7   C8   122.30  3.000
 9KU  N2   C7   C8   114.96  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
 9KU  CONST_01  C15  C14  C9   C10   180.00   0.0  0
 9KU  CONST_02  C13  C14  C9   C10     0.00   0.0  0
 9KU  CONST_03  C13  C12  C11  C10     0.00   0.0  0
 9KU  CONST_04  C14  C9   C10  C11     0.00   0.0  0
 9KU  CONST_05  C14  C13  C12  C11     0.00   0.0  0
 9KU  CONST_06  C18  C13  C12  C11   180.00   0.0  0
 9KU  CONST_07  C9   C10  C11  C12     0.00   0.0  0
 9KU  CONST_08  C9   C14  C13  C12     0.00   0.0  0
 9KU  CONST_09  C15  C14  C13  C12   180.00   0.0  0
 9KU  CONST_10  C17  C18  C13  C12   180.00   0.0  0
 9KU  CONST_11  C16  C15  C14  C13     0.00   0.0  0
 9KU  CONST_12  C16  C17  C18  C13     0.00   0.0  0
 9KU  CONST_13  C17  C16  C15  C14     0.00   0.0  0
 9KU  CONST_14  C17  C18  C13  C14     0.00   0.0  0
 9KU  CONST_15  C18  C13  C14  C15     0.00   0.0  0
 9KU  CONST_16  C18  C17  C16  C15     0.00   0.0  0
 9KU  CONST_17  C9   C14  C15  C16   180.00   0.0  0
 9KU  CONST_18  C9   C14  C13  C18   180.00   0.0  0
 9KU  CONST_19  C6   C5   N3   C1    180.00   0.0  0
 9KU  CONST_20  N1   C5   N3   C1      0.00   0.0  0
 9KU  CONST_21  C5   N3   C1   C2      0.00   0.0  0
 9KU  CONST_22  N3   C5   N1   C3      0.00   0.0  0
 9KU  CONST_23  C6   C5   N1   C3    180.00   0.0  0
 9KU  CONST_24  O5   C9   C10  C11   180.00   0.0  0
 9KU  CONST_25  O5   C9   C14  C13   180.00   0.0  0
 9KU  CONST_26  O5   C9   C14  C15     0.00   0.0  0
 9KU  CONST_27  O1   C1   N3   C5    180.00   0.0  0
 9KU  CONST_28  H3   C12  C11  C10   180.00   0.0  0
 9KU  CONST_29  H1   C10  C11  C12   180.00   0.0  0
 9KU  CONST_30  H7   C18  C13  C12     0.00   0.0  0
 9KU  CONST_31  H4   C15  C14  C13   180.00   0.0  0
 9KU  CONST_32  H2   C11  C12  C13   180.00   0.0  0
 9KU  CONST_33  H6   C17  C18  C13   180.00   0.0  0
 9KU  CONST_34  H5   C16  C15  C14   180.00   0.0  0
 9KU  CONST_35  H17  N3   C1   C2    180.00   0.0  0
 9KU  CONST_36  C8   C7   N2   C19     0.00   0.0  0
 9KU  CONST_37  O6   C7   N2   C19   180.00   0.0  0
 9KU  CONST_38  C8   C7   N2   C6    180.00   0.0  0
 9KU  CONST_39  O6   C7   N2   C6      0.00   0.0  0
 9KU  Var_01    C6   C21  C20  C19    37.76  30.0  1
 9KU  Var_02    C6   N2   C19  C20    20.10  30.0  1
 9KU  Var_03    N2   C19  C20  C21   -35.12  30.0  1
 9KU  Var_04    O4   C4   C3   C2    -34.62  30.0  2
 9KU  Var_05    O5   C8   C7   N2   -170.75  30.0  1
 9KU  Var_06    H15  C8   O5   C9     59.47  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
 9KU  chir_01  C6  C21  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
 9KU  plan-1  C1   0.020
 9KU  plan-1  C2   0.020
 9KU  plan-1  C3   0.020
 9KU  plan-1  C4   0.020
 9KU  plan-1  C5   0.020
 9KU  plan-1  C6   0.020
 9KU  plan-1  N1   0.020
 9KU  plan-1  N3   0.020
 9KU  plan-1  O1   0.020
 9KU  plan-1  O2   0.020
 9KU  plan-1  H17  0.020
 9KU  plan-2  C10  0.020
 9KU  plan-2  C11  0.020
 9KU  plan-2  C12  0.020
 9KU  plan-2  C13  0.020
 9KU  plan-2  C14  0.020
 9KU  plan-2  C15  0.020
 9KU  plan-2  C16  0.020
 9KU  plan-2  C17  0.020
 9KU  plan-2  C18  0.020
 9KU  plan-2  C9   0.020
 9KU  plan-2  O5   0.020
 9KU  plan-2  H3   0.020
 9KU  plan-2  H4   0.020
 9KU  plan-2  H5   0.020
 9KU  plan-2  H6   0.020
 9KU  plan-2  H7   0.020
 9KU  plan-2  H1   0.020
 9KU  plan-2  H2   0.020
 9KU  plan-3  C19  0.020
 9KU  plan-3  C6   0.020
 9KU  plan-3  C8   0.020
 9KU  plan-3  N2   0.020
 9KU  plan-3  O6   0.020
 9KU  plan-3  C7   0.020
 9KU  plan-4  C3   0.020
 9KU  plan-4  C4   0.020
 9KU  plan-4  O3   0.020
 9KU  plan-4  O4   0.020

