# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 11:31:29 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: (4R)-2-oxo-1,2,3,4-tetrahydropyrimidine-4,6-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1NC(=O)NC(=C1)C(O)=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
 OTD  OTD  '(4R)-2-oxo-1,2,3,4-tetrahydropyrimidine-4,6-dicarboxylic acid'  ligand  17  13  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_OTD
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
 OTD  N1   N  NR16   0  -0.638   3.8052  -2.9138   0.4150
 OTD  N3   N  NR16   0  -0.717   1.5738  -2.8943   0.9409
 OTD  C4   C  CR6    0   0.173   1.4311  -1.6363   0.3621
 OTD  C5   C  CR16   0  -0.351   2.4072  -1.1411  -0.3966
 OTD  C6   C  CR16   0  -0.212   3.6318  -1.9592  -0.6647
 OTD  C61  C  C      0   0.411   3.5114  -2.6129  -2.0693
 OTD  O62  O  OC    -1  -0.614   3.5392  -1.8074  -3.0203
 OTD  C41  C  C      0   0.393   0.1191  -0.9255   0.6512
 OTD  O42  O  OC    -1  -0.604  -0.6838  -1.5555   1.3689
 OTD  O41  O  O      0  -0.583  -0.0335   0.2003   0.1500
 OTD  C2   C  CR6    0   0.612   2.7723  -3.5395   1.0310
 OTD  O2   O  O      0  -0.542   2.9035  -4.5788   1.6720
 OTD  HN1  H  HNR6   0   0.384   4.6453  -3.4695   0.3738
 OTD  HN3  H  HNR6   0   0.386   0.8124  -3.2175   1.5179
 OTD  H5   H  HCR6   0   0.245   2.3053  -0.1688  -0.8528
 OTD  H6   H  HCR6   0   0.250   4.5100  -1.3058  -0.6735
 OTD  O61  O  O      0  -0.592   3.3800  -3.8461  -2.1164

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
 OTD  N1   C2   single  1.356  0.020  1.356
 OTD  N1   C6   single  1.452  0.020  1.452
 OTD  N1   HN1  single  0.890  0.020  1.040
 OTD  N3   C4   single  1.392  0.020  1.392
 OTD  N3   C2   single  1.364  0.020  1.364
 OTD  N3   HN3  single  0.860  0.020  1.020
 OTD  C4   C41  single  1.520  0.020  1.520
 OTD  C4   C5   double  1.332  0.020  1.332
 OTD  C5   C6   single  1.497  0.020  1.497
 OTD  C5   H5   single  0.930  0.020  1.080
 OTD  C6   C61  single  1.554  0.020  1.554
 OTD  C6   H6   single  0.970  0.020  1.090
 OTD  O61  C61  deloc   1.241  0.020  1.241
 OTD  C61  O62  deloc   1.247  0.020  1.247
 OTD  C41  O41  deloc   1.242  0.020  1.242
 OTD  C41  O42  deloc   1.248  0.020  1.248
 OTD  C2   O2   double  1.228  0.020  1.228

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
 OTD  HN1  N1   C2   113.53  3.000
 OTD  HN1  N1   C6   115.57  3.000
 OTD  C2   N1   C6   123.40  3.000
 OTD  HN3  N3   C2   118.29  3.000
 OTD  HN3  N3   C4   116.75  3.000
 OTD  C2   N3   C4   123.02  3.000
 OTD  C41  C4   C5   124.55  3.000
 OTD  C5   C4   N3   119.85  3.000
 OTD  C41  C4   N3   115.59  3.000
 OTD  H5   C5   C6   119.61  3.000
 OTD  H5   C5   C4   120.45  3.000
 OTD  C6   C5   C4   119.89  3.000
 OTD  H6   C6   C61  107.82  3.000
 OTD  H6   C6   C5   109.36  3.000
 OTD  C61  C6   C5   109.17  3.000
 OTD  H6   C6   N1   107.62  3.000
 OTD  C61  C6   N1   113.89  3.000
 OTD  C5   C6   N1   108.90  3.000
 OTD  O62  C61  O61  127.99  3.000
 OTD  O62  C61  C6   114.58  3.000
 OTD  O61  C61  C6   117.42  3.000
 OTD  O41  C41  O42  127.65  3.000
 OTD  O42  C41  C4   115.39  3.000
 OTD  O41  C41  C4   116.95  3.000
 OTD  O2   C2   N3   121.91  3.000
 OTD  O2   C2   N1   123.11  3.000
 OTD  N3   C2   N1   114.91  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
 OTD  CONST_01  C4   N3   C2  N1    0.00   0.0  0
 OTD  CONST_03  O2   C2   N3  C4  180.00   0.0  0
 OTD  CONST_05  HN3  N3   C2  N1  180.00   0.0  0
 OTD  CONST_06  HN1  N1   C2  N3  180.00   0.0  0
 OTD  Var_01    C6   C5   C4  N3    2.24  30.0  1
 OTD  Var_02    C2   N3   C4  C5   15.22  30.0  1
 OTD  Var_03    O41  C41  C4  N3  179.81  30.0  2

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
 OTD  chir_01  C6  N1  C5  C61  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
 OTD  plan-1  N1   0.020
 OTD  plan-1  N3   0.020
 OTD  plan-1  C4   0.020
 OTD  plan-1  C6   0.020
 OTD  plan-1  C2   0.020
 OTD  plan-1  O2   0.020
 OTD  plan-1  HN1  0.020
 OTD  plan-1  HN3  0.020
 OTD  plan-2  C6   0.020
 OTD  plan-2  C61  0.020
 OTD  plan-2  O62  0.020
 OTD  plan-2  O61  0.020
 OTD  plan-3  C4   0.020
 OTD  plan-3  C41  0.020
 OTD  plan-3  O42  0.020
 OTD  plan-3  O41  0.020

