# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 17:44:29 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 5-ethyl-5-[(2S)-pentan-2-yl]pyrimidine-2,4,6(1H,3H,5H)-trione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[C@H](C)C1(CC)C(=O)NC(=O)NC1=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
 RAV  RAV  5-ethyl-5-[(2S)-pentan-2-yl]pyrimidine-2,4,6(1H,3H,5H)-trione  ligand  34  16  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RAV
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
 RAV  C1    C  CT    0  -0.384   0.0740   0.4213   0.2887
 RAV  C2    C  C     0   0.615   1.1190   1.1235  -0.5669
 RAV  N3    N  NH1   0  -0.703   2.2538   0.4298  -0.8915
 RAV  C4    C  C     0   0.692   2.5766  -0.8524  -0.5213
 RAV  N5    N  NH1   0  -0.704   1.6693  -1.4672   0.3043
 RAV  C6    C  C     0   0.622   0.5139  -0.9315   0.8131
 RAV  O7    O  O     0  -0.411  -0.1253  -1.5455   1.6352
 RAV  O8    O  O     0  -0.414   0.9602   2.2530  -0.9676
 RAV  O9    O  O     0  -0.440   3.5910  -1.3942  -0.8872
 RAV  C12   C  CH2   0  -0.421  -0.2281   1.3383   1.4920
 RAV  C13   C  CH1   0  -0.216  -1.1791   0.2316  -0.6425
 RAV  C14   C  CH3   0  -0.694  -0.8719  -0.7061  -1.8100
 RAV  C15   C  CH2   0  -0.411  -2.4541  -0.1931   0.0899
 RAV  C16   C  CH2   0  -0.427  -3.7064  -0.0799  -0.7779
 RAV  C17   C  CH3   0  -0.662  -4.9738  -0.3451   0.0235
 RAV  C18   C  CH3   0  -0.685   0.9904   1.6717   2.3433
 RAV  HN3   H  HNH1  0   0.433   2.9280   0.8999  -1.4841
 RAV  HN5   H  HNH1  0   0.433   1.9233  -2.3954   0.6218
 RAV  H12   H  HCH2  0   0.255  -0.6831   2.2557   1.1148
 RAV  H12A  H  HCH2  0   0.260  -0.9767   0.8560   2.1178
 RAV  H13   H  HCH1  0   0.254  -1.3668   1.2321  -1.0452
 RAV  H14   H  HCH3  0   0.241   0.0275  -0.4234  -2.3584
 RAV  H14A  H  HCH3  0   0.233  -0.7526  -1.7392  -1.4771
 RAV  H14B  H  HCH3  0   0.260  -1.6855  -0.6940  -2.5326
 RAV  H15   H  HCH2  0   0.226  -2.3660  -1.2180   0.4573
 RAV  H15A  H  HCH2  0   0.231  -2.6051   0.4402   0.9660
 RAV  H16   H  HCH2  0   0.215  -3.7542   0.9201  -1.2201
 RAV  H16A  H  HCH2  0   0.222  -3.6610  -0.7822  -1.6135
 RAV  H17   H  HCH3  0   0.218  -4.9552  -1.3403   0.4719
 RAV  H17A  H  HCH3  0   0.218  -5.0899   0.3780   0.8330
 RAV  H17B  H  HCH3  0   0.229  -5.8628  -0.2843  -0.6051
 RAV  H18   H  HCH3  0   0.252   0.6920   2.2897   3.1897
 RAV  H18A  H  HCH3  0   0.231   1.4647   0.7781   2.7520
 RAV  H18B  H  HCH3  0   0.234   1.7484   2.2291   1.7917

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
 RAV  C6   C1    single  1.516  0.020  1.516
 RAV  C2   C1    single  1.522  0.020  1.522
 RAV  C1   C13   single  1.573  0.020  1.573
 RAV  C1   C12   single  1.543  0.020  1.543
 RAV  N3   C2    single  1.369  0.020  1.369
 RAV  C2   O8    double  1.209  0.020  1.209
 RAV  C4   N3    single  1.373  0.020  1.373
 RAV  N3   HN3   single  0.860  0.020  1.020
 RAV  O9   C4    double  1.207  0.020  1.207
 RAV  C4   N5    single  1.372  0.020  1.372
 RAV  N5   C6    single  1.371  0.020  1.371
 RAV  N5   HN5   single  0.860  0.020  1.020
 RAV  C6   O7    double  1.209  0.020  1.209
 RAV  C12  C18   single  1.523  0.020  1.523
 RAV  C12  H12   single  0.970  0.020  1.090
 RAV  C12  H12A  single  0.970  0.020  1.090
 RAV  C15  C13   single  1.531  0.020  1.531
 RAV  C13  C14   single  1.529  0.020  1.529
 RAV  C13  H13   single  0.970  0.020  1.090
 RAV  C14  H14   single  0.970  0.020  1.090
 RAV  C14  H14A  single  0.970  0.020  1.090
 RAV  C14  H14B  single  0.970  0.020  1.090
 RAV  C15  C16   single  1.528  0.020  1.528
 RAV  C15  H15   single  0.970  0.020  1.090
 RAV  C15  H15A  single  0.970  0.020  1.090
 RAV  C17  C16   single  1.523  0.020  1.523
 RAV  C16  H16   single  0.970  0.020  1.090
 RAV  C16  H16A  single  0.970  0.020  1.090
 RAV  C17  H17   single  0.970  0.020  1.090
 RAV  C17  H17A  single  0.970  0.020  1.090
 RAV  C17  H17B  single  0.970  0.020  1.090
 RAV  C18  H18   single  0.970  0.020  1.090
 RAV  C18  H18A  single  0.970  0.020  1.090
 RAV  C18  H18B  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
 RAV  C13   C1   C12   112.18  3.000
 RAV  C12   C1   C6    108.50  3.000
 RAV  C13   C1   C6    109.17  3.000
 RAV  C12   C1   C2    107.38  3.000
 RAV  C13   C1   C2    105.65  3.000
 RAV  C6    C1   C2    114.01  3.000
 RAV  O8    C2   N3    120.25  3.000
 RAV  O8    C2   C1    121.81  3.000
 RAV  N3    C2   C1    117.94  3.000
 RAV  HN3   N3   C4    115.76  3.000
 RAV  HN3   N3   C2    117.07  3.000
 RAV  C4    N3   C2    127.17  3.000
 RAV  O9    C4   N5    122.49  3.000
 RAV  N5    C4   N3    115.17  3.000
 RAV  O9    C4   N3    122.35  3.000
 RAV  HN5   N5   C6    116.92  3.000
 RAV  HN5   N5   C4    115.67  3.000
 RAV  C6    N5   C4    127.25  3.000
 RAV  O7    C6   N5    119.96  3.000
 RAV  O7    C6   C1    122.34  3.000
 RAV  N5    C6   C1    117.69  3.000
 RAV  H12A  C12  H12   106.53  3.000
 RAV  H12A  C12  C18   109.01  3.000
 RAV  H12   C12  C18   110.04  3.000
 RAV  H12A  C12  C1    108.65  3.000
 RAV  H12   C12  C1    108.16  3.000
 RAV  C18   C12  C1    114.16  3.000
 RAV  H13   C13  C15   106.67  3.000
 RAV  H13   C13  C14   108.31  3.000
 RAV  C15   C13  C14   111.26  3.000
 RAV  H13   C13  C1    104.13  3.000
 RAV  C14   C13  C1    111.47  3.000
 RAV  C15   C13  C1    114.45  3.000
 RAV  H14B  C14  H14A  107.14  3.000
 RAV  H14B  C14  H14   106.25  3.000
 RAV  H14A  C14  H14   107.96  3.000
 RAV  H14B  C14  C13   110.49  3.000
 RAV  H14A  C14  C13   111.69  3.000
 RAV  H14   C14  C13   113.00  3.000
 RAV  H15A  C15  H15   106.59  3.000
 RAV  H15A  C15  C16   107.43  3.000
 RAV  H15   C15  C16   109.07  3.000
 RAV  H15A  C15  C13   109.77  3.000
 RAV  H15   C15  C13   110.74  3.000
 RAV  C16   C15  C13   112.98  3.000
 RAV  H16A  C16  H16   106.27  3.000
 RAV  H16A  C16  C17   108.98  3.000
 RAV  H16   C16  C17   109.60  3.000
 RAV  H16A  C16  C15   110.66  3.000
 RAV  H16   C16  C15   109.45  3.000
 RAV  C17   C16  C15   111.74  3.000
 RAV  H17B  C17  H17A  107.69  3.000
 RAV  H17B  C17  H17   107.55  3.000
 RAV  H17A  C17  H17   107.52  3.000
 RAV  H17B  C17  C16   111.43  3.000
 RAV  H17A  C17  C16   111.31  3.000
 RAV  H17   C17  C16   111.15  3.000
 RAV  H18B  C18  H18A  107.81  3.000
 RAV  H18B  C18  H18   107.06  3.000
 RAV  H18A  C18  H18   107.01  3.000
 RAV  H18B  C18  C12   112.65  3.000
 RAV  H18A  C18  C12   112.19  3.000
 RAV  H18   C18  C12   109.83  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
 RAV  CONST_01  C4   N3   C2   C1      0.00   0.0  0
 RAV  CONST_02  N5   C4   N3   C2      0.00   0.0  0
 RAV  CONST_03  C6   N5   C4   N3      0.00   0.0  0
 RAV  CONST_04  O9   C4   N3   C2    180.00   0.0  0
 RAV  CONST_05  O8   C2   N3   C4    180.00   0.0  0
 RAV  CONST_06  O9   C4   N5   C6    180.00   0.0  0
 RAV  CONST_07  HN3  N3   C2   C1    180.00   0.0  0
 RAV  CONST_08  HN5  N5   C4   N3    180.00   0.0  0
 RAV  Var_01    O7   C6   N5   C4   -172.72  30.0  1
 RAV  Var_02    H18  C18  C12  C1   -177.94  30.0  3
 RAV  Var_03    C17  C16  C15  C13  -173.07  30.0  3
 RAV  Var_04    H17  C17  C16  C15   -58.83  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
 RAV  chir_01  C1   C2  C6   C12  negativ
 RAV  chir_02  C13  C1  C15  C14  positiv

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
 RAV  plan-1  C1   0.020
 RAV  plan-1  N5   0.020
 RAV  plan-1  C6   0.020
 RAV  plan-1  O7   0.020
 RAV  plan-2  C1   0.020
 RAV  plan-2  C2   0.020
 RAV  plan-2  N3   0.020
 RAV  plan-2  C4   0.020
 RAV  plan-2  N5   0.020
 RAV  plan-2  C6   0.020
 RAV  plan-2  O8   0.020
 RAV  plan-2  O9   0.020
 RAV  plan-2  HN3  0.020
 RAV  plan-2  HN5  0.020

