# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 03:13:44 2022
#   Inital geometry file: a 84 line input string
#   Ligand name: 5-ethyl-5-[(2R)-pentan-2-yl]-2-thioxodihydropyrimidine-4,6(1H,5H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[C@@H](C)C1(CC)C(=O)NC(=S)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
 EDP  EDP  5-ethyl-5-[(2R)-pentan-2-yl]-2-thioxodihydropyrimidine-4,6(1H,5H)-dione  ligand  34  16  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EDP
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
 EDP  C1    C  CT    0  -0.391  -0.2611  -0.5367   0.2293
 EDP  C2    C  C     0   0.623   0.3003   0.6455   0.9911
 EDP  N3    N  NH1   0  -0.659   1.5452   1.1107   0.6240
 EDP  C4    C  C     0   0.365   2.4069   0.5392  -0.2534
 EDP  N5    N  NH1   0  -0.658   1.9692  -0.5935  -0.8590
 EDP  C6    C  C     0   0.614   0.7394  -1.1929  -0.7075
 EDP  O7    O  O     0  -0.402   0.4840  -2.2013  -1.3201
 EDP  O8    O  O     0  -0.400  -0.3013   1.1952   1.8815
 EDP  S9    S  S1    0  -0.245   3.8949   1.1733  -0.5572
 EDP  C12   C  CH2   0  -0.422  -0.7179  -1.6050   1.2452
 EDP  C13   C  CH3   0  -0.687   0.4198  -2.2626   2.0162
 EDP  C14   C  CH1   0  -0.215  -1.4445  -0.0497  -0.6860
 EDP  C15   C  CH3   0  -0.692  -0.9859   1.0248  -1.6712
 EDP  C16   C  CH2   0  -0.412  -2.6953   0.3937   0.0763
 EDP  C17   C  CH2   0  -0.428  -3.9249   0.5049  -0.8237
 EDP  C18   C  CH3   0  -0.662  -5.1838   0.8126  -0.0242
 EDP  HN3   H  HNH1  0   0.436   1.8831   1.9348   1.1065
 EDP  HN5   H  HNH1  0   0.437   2.6149  -1.0325  -1.5046
 EDP  H12   H  HCH2  0   0.263  -1.4002  -1.1361   1.9516
 EDP  H12A  H  HCH2  0   0.258  -1.2944  -2.3592   0.7073
 EDP  H13   H  HCH3  0   0.236   1.0891  -2.8326   1.3714
 EDP  H13A  H  HCH3  0   0.232   1.0207  -1.5348   2.5647
 EDP  H13B  H  HCH3  0   0.254   0.0122  -2.9577   2.7494
 EDP  H14   H  HCH1  0   0.257  -1.7232  -0.9430  -1.2541
 EDP  H15   H  HCH3  0   0.234  -0.7819   1.9737  -1.1705
 EDP  H15A  H  HCH3  0   0.242  -0.0933   0.7402  -2.2297
 EDP  H15B  H  HCH3  0   0.261  -1.7597   1.2144  -2.4129
 EDP  H16   H  HCH2  0   0.234  -2.9278  -0.3267   0.8631
 EDP  H16A  H  HCH2  0   0.225  -2.5240   1.3523   0.5716
 EDP  H17   H  HCH2  0   0.223  -3.7810   1.2818  -1.5780
 EDP  H17A  H  HCH2  0   0.215  -4.0582  -0.4338  -1.3705
 EDP  H18   H  HCH3  0   0.218  -5.0947   1.7649   0.5019
 EDP  H18A  H  HCH3  0   0.229  -6.0609   0.8735  -0.6692
 EDP  H18B  H  HCH3  0   0.218  -5.3750   0.0407   0.7237

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
 EDP  C6   C1    single  1.520  0.020  1.520
 EDP  C2   C1    single  1.514  0.020  1.514
 EDP  C1   C14   single  1.573  0.020  1.573
 EDP  C1   C12   single  1.543  0.020  1.543
 EDP  N3   C2    single  1.379  0.020  1.379
 EDP  C2   O8    double  1.207  0.020  1.207
 EDP  C4   N3    single  1.356  0.020  1.356
 EDP  N3   HN3   single  0.860  0.020  1.020
 EDP  S9   C4    double  1.646  0.020  1.646
 EDP  C4   N5    single  1.357  0.020  1.357
 EDP  N5   C6    single  1.376  0.020  1.376
 EDP  N5   HN5   single  0.860  0.020  1.020
 EDP  C6   O7    double  1.207  0.020  1.207
 EDP  C12  C13   single  1.524  0.020  1.524
 EDP  C12  H12   single  0.970  0.020  1.090
 EDP  C12  H12A  single  0.970  0.020  1.090
 EDP  C13  H13   single  0.970  0.020  1.090
 EDP  C13  H13A  single  0.970  0.020  1.090
 EDP  C13  H13B  single  0.970  0.020  1.090
 EDP  C15  C14   single  1.528  0.020  1.528
 EDP  C14  C16   single  1.530  0.020  1.530
 EDP  C14  H14   single  0.970  0.020  1.090
 EDP  C15  H15   single  0.970  0.020  1.090
 EDP  C15  H15A  single  0.970  0.020  1.090
 EDP  C15  H15B  single  0.970  0.020  1.090
 EDP  C16  C17   single  1.528  0.020  1.528
 EDP  C16  H16   single  0.970  0.020  1.090
 EDP  C16  H16A  single  0.970  0.020  1.090
 EDP  C18  C17   single  1.523  0.020  1.523
 EDP  C17  H17   single  0.970  0.020  1.090
 EDP  C17  H17A  single  0.970  0.020  1.090
 EDP  C18  H18   single  0.970  0.020  1.090
 EDP  C18  H18A  single  0.970  0.020  1.090
 EDP  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
 EDP  C14   C1   C12   112.00  3.000
 EDP  C12   C1   C6    107.56  3.000
 EDP  C14   C1   C6    105.68  3.000
 EDP  C12   C1   C2    108.60  3.000
 EDP  C14   C1   C2    109.26  3.000
 EDP  C6    C1   C2    113.77  3.000
 EDP  O8    C2   N3    119.52  3.000
 EDP  O8    C2   C1    122.81  3.000
 EDP  N3    C2   C1    117.66  3.000
 EDP  HN3   N3   C4    116.04  3.000
 EDP  HN3   N3   C2    116.67  3.000
 EDP  C4    N3   C2    127.15  3.000
 EDP  S9    C4   N5    122.07  3.000
 EDP  N5    C4   N3    115.82  3.000
 EDP  S9    C4   N3    122.11  3.000
 EDP  HN5   N5   C6    116.80  3.000
 EDP  HN5   N5   C4    116.13  3.000
 EDP  C6    N5   C4    127.05  3.000
 EDP  O7    C6   N5    119.79  3.000
 EDP  O7    C6   C1    122.30  3.000
 EDP  N5    C6   C1    117.91  3.000
 EDP  H12A  C12  H12   106.66  3.000
 EDP  H12A  C12  C13   110.22  3.000
 EDP  H12   C12  C13   109.00  3.000
 EDP  H12A  C12  C1    108.08  3.000
 EDP  H12   C12  C1    108.34  3.000
 EDP  C13   C12  C1    114.26  3.000
 EDP  H13B  C13  H13A  107.05  3.000
 EDP  H13B  C13  H13   107.10  3.000
 EDP  H13A  C13  H13   107.92  3.000
 EDP  H13B  C13  C12   109.67  3.000
 EDP  H13A  C13  C12   112.19  3.000
 EDP  H13   C13  C12   112.63  3.000
 EDP  H14   C14  C16   106.67  3.000
 EDP  H14   C14  C15   108.39  3.000
 EDP  C16   C14  C15   111.27  3.000
 EDP  H14   C14  C1    103.93  3.000
 EDP  C16   C14  C1    114.49  3.000
 EDP  C15   C14  C1    111.53  3.000
 EDP  H15B  C15  H15A  106.16  3.000
 EDP  H15B  C15  H15   107.08  3.000
 EDP  H15A  C15  H15   107.97  3.000
 EDP  H15B  C15  C14   110.39  3.000
 EDP  H15A  C15  C14   113.10  3.000
 EDP  H15   C15  C14   111.81  3.000
 EDP  H16A  C16  H16   106.60  3.000
 EDP  H16A  C16  C17   109.23  3.000
 EDP  H16   C16  C17   107.52  3.000
 EDP  H16A  C16  C14   110.60  3.000
 EDP  H16   C16  C14   109.99  3.000
 EDP  C17   C16  C14   112.67  3.000
 EDP  H17A  C17  H17   106.32  3.000
 EDP  H17A  C17  C18   109.57  3.000
 EDP  H17   C17  C18   109.13  3.000
 EDP  H17A  C17  C16   109.27  3.000
 EDP  H17   C17  C16   110.64  3.000
 EDP  C18   C17  C16   111.76  3.000
 EDP  H18B  C18  H18A  107.69  3.000
 EDP  H18B  C18  H18   107.52  3.000
 EDP  H18A  C18  H18   107.58  3.000
 EDP  H18B  C18  C17   111.19  3.000
 EDP  H18A  C18  C17   111.45  3.000
 EDP  H18   C18  C17   111.22  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
 EDP  CONST_01  C4   N5   C6   C1     0.00   0.0  0
 EDP  CONST_02  C4   N3   C2   C1     0.00   0.0  0
 EDP  CONST_03  N5   C4   N3   C2     0.00   0.0  0
 EDP  CONST_04  C6   N5   C4   N3     0.00   0.0  0
 EDP  CONST_05  S9   C4   N3   C2   180.00   0.0  0
 EDP  CONST_06  O8   C2   N3   C4   180.00   0.0  0
 EDP  CONST_07  O7   C6   N5   C4   180.00   0.0  0
 EDP  CONST_08  S9   C4   N5   C6   180.00   0.0  0
 EDP  CONST_09  HN5  N5   C6   C1   180.00   0.0  0
 EDP  CONST_10  HN3  N3   C2   C1   180.00   0.0  0
 EDP  Var_01    H13  C13  C12  C1   -64.13  30.0  3
 EDP  Var_02    C18  C17  C16  C14  174.38  30.0  3
 EDP  Var_03    H18  C18  C17  C16   60.96  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
 EDP  chir_01  C1   C2  C6   C12  negativ
 EDP  chir_02  C14  C1  C15  C16  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
 EDP  plan-1  C1   0.020
 EDP  plan-1  C2   0.020
 EDP  plan-1  N3   0.020
 EDP  plan-1  C4   0.020
 EDP  plan-1  N5   0.020
 EDP  plan-1  C6   0.020
 EDP  plan-1  O7   0.020
 EDP  plan-1  O8   0.020
 EDP  plan-1  S9   0.020
 EDP  plan-1  HN3  0.020
 EDP  plan-1  HN5  0.020

