# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 11:10:25 2022
#   Inital geometry file: a 26 line input string
#   Ligand name: urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(N)=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
 URE  URE  'urea                     '  ligand  8  4  .  2020-03-20  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_URE
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
 URE  C     C  C     0   0.603  -4.6549   0.6993  15.1883
 URE  O     O  O     0  -0.528  -4.3707   1.7879  15.6720
 URE  N1    N  NH2   0  -0.821  -5.1997  -0.3110  15.9233
 URE  N2    N  NH2   0  -0.821  -4.4501   0.4073  13.8725
 URE  HN11  H  HNH2  0   0.393  -5.6559  -1.0815  15.4635
 URE  HN12  H  HNH2  0   0.391  -5.5859  -0.0620  16.8180
 URE  HN21  H  HNH2  0   0.391  -3.8366   1.0216  13.3644
 URE  HN22  H  HNH2  0   0.393  -4.4482  -0.5495  13.5593

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
 URE  C   O     double  1.225  0.020  1.225
 URE  C   N1    single  1.363  0.020  1.363
 URE  C   N2    single  1.363  0.020  1.363
 URE  N1  HN11  single  0.890  0.020  1.040
 URE  N1  HN12  single  0.890  0.020  1.040
 URE  N2  HN21  single  0.890  0.020  1.040
 URE  N2  HN22  single  0.890  0.020  1.040

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
 URE  N2    C   N1    114.95  3.000
 URE  N2    C   O     122.46  3.000
 URE  N1    C   O     122.59  3.000
 URE  HN12  N1  HN11  114.95  3.000
 URE  HN12  N1  C     116.72  3.000
 URE  HN11  N1  C     120.15  3.000
 URE  HN22  N2  HN21  114.97  3.000
 URE  HN22  N2  C     120.27  3.000
 URE  HN21  N2  C     116.64  3.000

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
 URE  plan-1  C     0.020
 URE  plan-1  O     0.020
 URE  plan-1  N1    0.020
 URE  plan-1  N2    0.020
 URE  plan-1  HN11  0.020
 URE  plan-1  HN12  0.020
 URE  plan-1  HN21  0.020
 URE  plan-1  HN22  0.020

