# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:14:30 2022
#   Inital geometry file: a 50 line input string
#   Ligand name: 1-(2,5-dioxo-2,5-dihydro-1H-imidazol-4-yl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)NC1=NC(=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
 2AL  2AL  1-(2,5-dioxo-2,5-dihydro-1H-imidazol-4-yl)urea  ligand  15  11  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2AL
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
 2AL  C4    C  CR5   0   0.430  -0.0301  -0.1022  -0.0076
 2AL  C5    C  CR5   0   0.514  -1.0972  -1.1929   0.0121
 2AL  O5    O  O     0  -0.383  -0.9207  -2.3817   0.0183
 2AL  N7    N  NR15  0  -0.708  -2.2342  -0.4665   0.0195
 2AL  C8    C  CR5   0   0.619  -1.9284   0.8993   0.0075
 2AL  O8    O  O     0  -0.401  -2.7444   1.7784   0.0122
 2AL  N9    N  N     0  -0.470  -0.5431   1.0765  -0.0092
 2AL  N3    N  NH1   0  -0.716   1.2430  -0.4908  -0.0175
 2AL  C2    C  C     0   0.693   2.3706   0.3552  -0.0561
 2AL  N1    N  NH2   0  -0.834   3.5226  -0.3246  -0.0453
 2AL  O2    O  O     0  -0.464   2.2615   1.5600  -0.0975
 2AL  HN7   H  HNR5  0   0.441  -3.1730  -0.8408   0.0306
 2AL  HN3   H  HNH1  0   0.437   1.3876  -1.4932  -0.0096
 2AL  HN11  H  HNH2  0   0.421   4.3894   0.1865  -0.0630
 2AL  HN12  H  HNH2  0   0.421   3.5794  -1.3276   0.0097

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
 2AL  C4  C5    single  1.526  0.020  1.526
 2AL  C4  N9    double  1.286  0.020  1.286
 2AL  C4  N3    single  1.331  0.020  1.331
 2AL  C5  O5    double  1.202  0.020  1.202
 2AL  C5  N7    single  1.349  0.020  1.349
 2AL  N7  C8    single  1.400  0.020  1.400
 2AL  N7  HN7   single  0.860  0.020  1.020
 2AL  C8  O8    double  1.199  0.020  1.199
 2AL  C8  N9    single  1.397  0.020  1.397
 2AL  N3  C2    single  1.410  0.020  1.410
 2AL  N3  HN3   single  0.860  0.020  1.020
 2AL  C2  N1    single  1.338  0.020  1.338
 2AL  C2  O2    double  1.210  0.020  1.210
 2AL  N1  HN11  single  0.860  0.020  1.020
 2AL  N1  HN12  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
 2AL  N3    C4  N9    130.49  3.000
 2AL  N3    C4  C5    117.40  3.000
 2AL  N9    C4  C5    112.11  3.000
 2AL  N7    C5  O5    131.01  3.000
 2AL  N7    C5  C4    101.80  3.000
 2AL  O5    C5  C4    127.19  3.000
 2AL  HN7   N7  C8    124.36  3.000
 2AL  HN7   N7  C5    125.69  3.000
 2AL  C8    N7  C5    109.95  3.000
 2AL  N9    C8  O8    125.58  3.000
 2AL  N9    C8  N7    109.91  3.000
 2AL  O8    C8  N7    124.51  3.000
 2AL  C8    N9  C4    106.23  3.000
 2AL  HN3   N3  C2    118.67  3.000
 2AL  HN3   N3  C4    115.17  3.000
 2AL  C2    N3  C4    126.15  3.000
 2AL  O2    C2  N1    125.72  3.000
 2AL  O2    C2  N3    121.73  3.000
 2AL  N1    C2  N3    112.55  3.000
 2AL  HN12  N1  HN11  117.29  3.000
 2AL  HN12  N1  C2    123.76  3.000
 2AL  HN11  N1  C2    118.91  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
 2AL  CONST_01  C8    N7  C5  C4    0.00  0.0  0
 2AL  CONST_02  N7    C8  N9  C4    0.00  0.0  0
 2AL  CONST_03  C8    N9  C4  C5    0.00  0.0  0
 2AL  CONST_04  N9    C8  N7  C5    0.00  0.0  0
 2AL  CONST_05  N9    C4  C5  N7    0.00  0.0  0
 2AL  CONST_06  O8    C8  N9  C4  180.00  0.0  0
 2AL  CONST_07  O8    C8  N7  C5  180.00  0.0  0
 2AL  CONST_08  C8    N7  C5  O5  180.00  0.0  0
 2AL  CONST_09  N3    C4  N9  C8  180.00  0.0  0
 2AL  CONST_10  HN7   N7  C5  C4  180.00  0.0  0
 2AL  CONST_11  C2    N3  C4  C5  180.00  0.0  0
 2AL  CONST_12  C2    N3  C4  N9    0.00  0.0  0
 2AL  CONST_13  HN3   N3  C4  C5    0.00  0.0  0
 2AL  CONST_14  O2    C2  N3  C4    0.00  0.0  0
 2AL  CONST_15  N1    C2  N3  C4  180.00  0.0  0
 2AL  CONST_16  HN11  N1  C2  O2    0.00  0.0  0
 2AL  CONST_17  HN12  N1  C2  O2  180.00  0.0  0

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
 2AL  plan-1  C4    0.020
 2AL  plan-1  C5    0.020
 2AL  plan-1  O5    0.020
 2AL  plan-1  N7    0.020
 2AL  plan-1  C8    0.020
 2AL  plan-1  O8    0.020
 2AL  plan-1  N9    0.020
 2AL  plan-1  N3    0.020
 2AL  plan-1  C2    0.020
 2AL  plan-1  N1    0.020
 2AL  plan-1  O2    0.020
 2AL  plan-1  HN7   0.020
 2AL  plan-1  HN3   0.020
 2AL  plan-1  HN11  0.020
 2AL  plan-1  HN12  0.020

