# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:29:04 2022
#   Inital geometry file: a 49 line input string
#   Ligand name: 5-(hydroxymethyl)pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC1=CNC(=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
 HMU  HMU  5-(hydroxymethyl)pyrimidine-2,4(1H,3H)-dione  ligand  16  10  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_HMU
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
 HMU  N1    N  NR16  0  -0.672   1.3938  -0.0169  -1.0179
 HMU  C2    C  CR6   0   0.680   0.3602  -0.0240  -1.9100
 HMU  O2    O  O     0  -0.482   0.5130  -0.0258  -3.1147
 HMU  N3    N  NR16  0  -0.717  -0.8756  -0.0295  -1.3128
 HMU  C4    C  CR6   0   0.572  -1.1580  -0.0260   0.0423
 HMU  O3    O  OH1   0  -0.668   1.0202   0.0439   3.0375
 HMU  O4    O  O     0  -0.458  -2.3117  -0.0328   0.4350
 HMU  C5    C  CR6   0  -0.240   0.0052  -0.0143   0.9056
 HMU  CM5   C  CH2   0  -0.158  -0.2213  -0.0075   2.3852
 HMU  C6    C  CR16  0   0.058   1.2225  -0.0106   0.3346
 HMU  H1    H  HNR6  0   0.436   2.3298  -0.0063  -1.3954
 HMU  H2    H  HNR6  0   0.426  -1.6678  -0.0364  -1.9433
 HMU  H3    H  HOH1  0   0.466   0.8622   0.0165   3.9853
 HMU  HM51  H  HCH2  0   0.220  -0.7894  -0.9046   2.6647
 HMU  HM52  H  HCH2  0   0.219  -0.8539   0.8514   2.6462
 HMU  H6    H  HCR6  0   0.317   2.1373  -0.0033   0.9079

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
 HMU  N1   C2    single  1.365  0.020  1.365
 HMU  N1   C6    single  1.363  0.020  1.363
 HMU  N1   H1    single  0.860  0.020  1.020
 HMU  C2   O2    double  1.214  0.020  1.214
 HMU  C2   N3    single  1.373  0.020  1.373
 HMU  N3   C4    single  1.384  0.020  1.384
 HMU  N3   H2    single  0.860  0.020  1.020
 HMU  C4   O4    double  1.219  0.020  1.219
 HMU  C4   C5    single  1.449  0.020  1.449
 HMU  O3   CM5   single  1.403  0.020  1.403
 HMU  O3   H3    single  0.850  0.020  0.980
 HMU  C5   CM5   single  1.497  0.020  1.497
 HMU  C5   C6    double  1.345  0.020  1.345
 HMU  CM5  HM51  single  0.970  0.020  1.090
 HMU  CM5  HM52  single  0.970  0.020  1.090
 HMU  C6   H6    single  0.930  0.020  1.080

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
 HMU  H1    N1   C6    119.18  3.000
 HMU  H1    N1   C2    117.24  3.000
 HMU  C6    N1   C2    123.58  3.000
 HMU  N3    C2   O2    123.02  3.000
 HMU  N3    C2   N1    113.41  3.000
 HMU  O2    C2   N1    123.57  3.000
 HMU  H2    N3   C4    116.75  3.000
 HMU  H2    N3   C2    115.69  3.000
 HMU  C4    N3   C2    127.56  3.000
 HMU  C5    C4   O4    124.62  3.000
 HMU  C5    C4   N3    114.81  3.000
 HMU  O4    C4   N3    120.57  3.000
 HMU  H3    O3   CM5   108.17  3.000
 HMU  C6    C5   CM5   123.83  3.000
 HMU  C6    C5   C4    118.29  3.000
 HMU  CM5   C5   C4    117.88  3.000
 HMU  HM52  CM5  HM51  106.28  3.000
 HMU  HM52  CM5  C5    109.01  3.000
 HMU  HM51  CM5  C5    109.04  3.000
 HMU  HM52  CM5  O3    111.75  3.000
 HMU  HM51  CM5  O3    111.67  3.000
 HMU  C5    CM5  O3    109.02  3.000
 HMU  H6    C6   C5    122.80  3.000
 HMU  H6    C6   N1    114.86  3.000
 HMU  C5    C6   N1    122.35  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
 HMU  CONST_01  C4  N3   C2  N1     0.00   0.0  0
 HMU  CONST_02  C5  C4   N3  C2     0.00   0.0  0
 HMU  CONST_03  C6  N1   C2  N3     0.00   0.0  0
 HMU  CONST_04  O4  C4   N3  C2   180.00   0.0  0
 HMU  CONST_05  C6  N1   C2  O2   180.00   0.0  0
 HMU  CONST_06  C4  N3   C2  O2   180.00   0.0  0
 HMU  CONST_07  H2  N3   C2  N1   180.00   0.0  0
 HMU  CONST_08  H1  N1   C2  N3   180.00   0.0  0
 HMU  Var_01    O3  CM5  C5  C4  -178.25  30.0  3

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
 HMU  plan-1  N1   0.020
 HMU  plan-1  C2   0.020
 HMU  plan-1  O2   0.020
 HMU  plan-1  N3   0.020
 HMU  plan-1  C4   0.020
 HMU  plan-1  O4   0.020
 HMU  plan-1  C5   0.020
 HMU  plan-1  CM5  0.020
 HMU  plan-1  C6   0.020
 HMU  plan-1  H1   0.020
 HMU  plan-1  H2   0.020
 HMU  plan-1  H6   0.020

