# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 15 19:47:05 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: 6-pyrrolidin-1-yl-5~{H}-pyrimidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1CC(=NC(=O)N1)N2CCCC2
#
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
 M1Z  M1Z  6-pyrrolidin-1-yl-5~{H}-pyrimidine-2,4-dione  ligand  24  13  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M1Z
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
 M1Z  CAC  C  CH2   0  -0.720   0.5805   1.2749  -0.0521
 M1Z  CAD  C  CH2   0  -0.475  -3.6600   0.7713   0.3647
 M1Z  CAE  C  CH2   0  -0.487  -3.7099  -0.6290  -0.2361
 M1Z  CAF  C  CH2   0  -0.281  -2.2646   1.2539  -0.0066
 M1Z  CAG  C  CH2   0  -0.264  -2.3103  -1.1740   0.0222
 M1Z  CAJ  C  C     0   0.549  -0.1538  -0.0296   0.0014
 M1Z  CAK  C  C     0   0.579   2.0732   1.1452  -0.1448
 M1Z  CAL  C  C     0   0.578   1.7799  -1.2921   0.0162
 M1Z  NAH  N  N     0  -0.539   0.4294  -1.1993   0.0471
 M1Z  NAI  N  NH1   0  -0.700   2.5459  -0.1249  -0.0887
 M1Z  NAM  N  NT    0  -0.452  -1.4721   0.0245   0.0059
 M1Z  OAA  O  O     0  -0.447   2.8003   2.1095  -0.2519
 M1Z  OAB  O  O     0  -0.477   2.3657  -2.3567   0.0718
 M1Z  H1   H  HCH2  0   0.332   0.2352   1.8714  -0.9001
 M1Z  H2   H  HCH2  0   0.338   0.3542   1.8657   0.8410
 M1Z  H4   H  HCH2  0   0.247  -3.7637   0.7262   1.4507
 M1Z  H5   H  HCH2  0   0.259  -4.4799  -1.2603   0.2045
 M1Z  H6   H  HCH2  0   0.245  -3.8985  -0.5714  -1.3101
 M1Z  H7   H  HCH2  0   0.260  -2.2527   1.7017  -1.0044
 M1Z  H8   H  HCH2  0   0.269  -1.8703   1.9864   0.6971
 M1Z  H9   H  HCH2  0   0.252  -2.2384  -1.6635   0.9965
 M1Z  H10  H  HCH2  0   0.261  -1.9781  -1.8855  -0.7323
 M1Z  H11  H  HNH1  0   0.415   3.5496  -0.2502  -0.1310
 M1Z  H3   H  HCH2  0   0.260  -4.4331   1.4350  -0.0190

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
 M1Z  OAB  CAL  double  1.216  0.020  1.216
 M1Z  CAL  NAI  single  1.400  0.020  1.400
 M1Z  CAL  NAH  single  1.354  0.020  1.354
 M1Z  NAI  CAK  single  1.356  0.020  1.356
 M1Z  NAH  CAJ  double  1.308  0.020  1.308
 M1Z  CAK  OAA  double  1.212  0.020  1.212
 M1Z  CAK  CAC  single  1.501  0.020  1.501
 M1Z  CAJ  CAC  single  1.498  0.020  1.498
 M1Z  CAJ  NAM  single  1.319  0.020  1.319
 M1Z  CAG  NAM  single  1.463  0.020  1.463
 M1Z  CAG  CAE  single  1.524  0.020  1.524
 M1Z  NAM  CAF  single  1.463  0.020  1.463
 M1Z  CAE  CAD  single  1.525  0.020  1.525
 M1Z  CAF  CAD  single  1.522  0.020  1.522
 M1Z  CAC  H1   single  0.970  0.020  1.090
 M1Z  CAC  H2   single  0.970  0.020  1.090
 M1Z  CAD  H3   single  0.970  0.020  1.090
 M1Z  CAD  H4   single  0.970  0.020  1.090
 M1Z  CAE  H5   single  0.970  0.020  1.090
 M1Z  CAE  H6   single  0.970  0.020  1.090
 M1Z  CAF  H7   single  0.970  0.020  1.090
 M1Z  CAF  H8   single  0.970  0.020  1.090
 M1Z  CAG  H9   single  0.970  0.020  1.090
 M1Z  CAG  H10  single  0.970  0.020  1.090
 M1Z  NAI  H11  single  0.860  0.020  1.020

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
 M1Z  H2   CAC  H1   105.85  3.000
 M1Z  H2   CAC  CAK  107.62  3.000
 M1Z  H1   CAC  CAK  108.27  3.000
 M1Z  H2   CAC  CAJ  109.85  3.000
 M1Z  H1   CAC  CAJ  110.37  3.000
 M1Z  CAK  CAC  CAJ  114.48  3.000
 M1Z  H4   CAD  H3   107.95  3.000
 M1Z  H4   CAD  CAF  110.04  3.000
 M1Z  H3   CAD  CAF  111.82  3.000
 M1Z  H4   CAD  CAE  110.55  3.000
 M1Z  H3   CAD  CAE  113.44  3.000
 M1Z  CAF  CAD  CAE  103.01  3.000
 M1Z  H6   CAE  H5   107.84  3.000
 M1Z  H6   CAE  CAG  110.13  3.000
 M1Z  H5   CAE  CAG  111.93  3.000
 M1Z  H6   CAE  CAD  110.17  3.000
 M1Z  H5   CAE  CAD  113.34  3.000
 M1Z  CAG  CAE  CAD  103.39  3.000
 M1Z  H8   CAF  H7   108.06  3.000
 M1Z  H8   CAF  NAM  111.32  3.000
 M1Z  H7   CAF  NAM  110.24  3.000
 M1Z  H8   CAF  CAD  112.79  3.000
 M1Z  H7   CAF  CAD  111.23  3.000
 M1Z  NAM  CAF  CAD  103.18  3.000
 M1Z  H10  CAG  H9   107.76  3.000
 M1Z  H10  CAG  NAM  110.66  3.000
 M1Z  H9   CAG  NAM  109.83  3.000
 M1Z  H10  CAG  CAE  113.35  3.000
 M1Z  H9   CAG  CAE  111.82  3.000
 M1Z  NAM  CAG  CAE  103.37  3.000
 M1Z  NAM  CAJ  NAH  118.82  3.000
 M1Z  NAM  CAJ  CAC  117.01  3.000
 M1Z  NAH  CAJ  CAC  124.16  3.000
 M1Z  OAA  CAK  NAI  122.64  3.000
 M1Z  OAA  CAK  CAC  122.21  3.000
 M1Z  NAI  CAK  CAC  115.15  3.000
 M1Z  OAB  CAL  NAI  118.01  3.000
 M1Z  NAI  CAL  NAH  119.36  3.000
 M1Z  OAB  CAL  NAH  122.64  3.000
 M1Z  CAL  NAH  CAJ  120.35  3.000
 M1Z  H11  NAI  CAL  116.26  3.000
 M1Z  H11  NAI  CAK  117.37  3.000
 M1Z  CAL  NAI  CAK  126.37  3.000
 M1Z  CAJ  NAM  CAG  122.62  3.000
 M1Z  CAG  NAM  CAF  112.23  3.000
 M1Z  CAJ  NAM  CAF  125.15  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
 M1Z  CONST_01  CAL  NAI  CAK  CAC     0.00   0.0  0
 M1Z  CONST_02  CAL  NAH  CAJ  CAC     0.00   0.0  0
 M1Z  CONST_03  CAG  NAM  CAJ  CAC   180.00   0.0  0
 M1Z  CONST_04  CAF  NAM  CAJ  CAC     0.00   0.0  0
 M1Z  CONST_05  NAH  CAJ  NAM  CAF   180.00   0.0  0
 M1Z  CONST_06  NAH  CAJ  NAM  CAG     0.00   0.0  0
 M1Z  CONST_07  NAI  CAL  NAH  CAJ     0.00   0.0  0
 M1Z  CONST_08  NAH  CAL  NAI  CAK     0.00   0.0  0
 M1Z  CONST_09  NAM  CAJ  NAH  CAL   180.00   0.0  0
 M1Z  CONST_10  OAB  CAL  NAH  CAJ   180.00   0.0  0
 M1Z  CONST_11  OAB  CAL  NAI  CAK   180.00   0.0  0
 M1Z  CONST_12  OAA  CAK  NAI  CAL   180.00   0.0  0
 M1Z  CONST_13  H11  NAI  CAK  CAC   180.00   0.0  0
 M1Z  Var_01    NAM  CAG  CAE  CAD   -29.88  30.0  1
 M1Z  Var_02    CAJ  NAM  CAF  CAD  -165.96  30.0  1
 M1Z  Var_03    NAM  CAF  CAD  CAE   -32.26  30.0  1
 M1Z  Var_04    CAG  CAE  CAD  CAF    38.76  30.0  1
 M1Z  Var_05    H1   CAC  CAJ  NAH   126.44  30.0  1

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
 M1Z  plan-1  CAC  0.020
 M1Z  plan-1  CAF  0.020
 M1Z  plan-1  CAG  0.020
 M1Z  plan-1  CAJ  0.020
 M1Z  plan-1  CAK  0.020
 M1Z  plan-1  CAL  0.020
 M1Z  plan-1  NAH  0.020
 M1Z  plan-1  NAI  0.020
 M1Z  plan-1  NAM  0.020
 M1Z  plan-1  OAA  0.020
 M1Z  plan-1  OAB  0.020
 M1Z  plan-1  H11  0.020

