# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:27:15 2022
#   Inital geometry file: a 50 line input string
#   Ligand name: 1-[(4S)-2,5-dioxoimidazolidin-4-yl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)N[C@H]1NC(=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
 3AL  3AL  1-[(4S)-2,5-dioxoimidazolidin-4-yl]urea  ligand  17  11  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_3AL
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
 3AL  C4    C  CR15  0   0.003   0.0124   0.0013  -0.3807
 3AL  C5    C  CR5   0   0.541   0.9026  -1.2078  -0.0737
 3AL  O5    O  O     0  -0.416   0.5431  -2.3554  -0.0054
 3AL  N7    N  NR15  0  -0.700   2.1543  -0.7154   0.1069
 3AL  C8    C  CR5   0   0.681   2.2083   0.6753   0.0071
 3AL  O8    O  O     0  -0.470   3.2133   1.3403   0.1057
 3AL  N9    N  NR15  0  -0.670   0.9414   1.0918  -0.2085
 3AL  N3    N  NH1   0  -0.668  -1.1310   0.0530   0.4579
 3AL  C2    C  C     0   0.696  -2.3930   0.2552  -0.0386
 3AL  N1    N  NH2   0  -0.845  -3.3498   0.3821   0.9039
 3AL  O2    O  O     0  -0.532  -2.6226   0.3225  -1.2396
 3AL  H4    H  HCR5  0   0.316  -0.3295  -0.0710  -1.4160
 3AL  HN7   H  HNR5  0   0.431   2.9618  -1.2774   0.3376
 3AL  HN9   H  HNR5  0   0.419   0.7397   2.0321  -0.5096
 3AL  HN3   H  HNH1  0   0.406  -0.9811   0.0638   1.4553
 3AL  HN11  H  HNH2  0   0.404  -3.1729   0.2262   1.8812
 3AL  HN12  H  HNH2  0   0.405  -4.3113   0.4090   0.6129

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
 3AL  C4  C5    single  1.533  0.020  1.533
 3AL  C4  N9    single  1.443  0.020  1.443
 3AL  C4  N3    single  1.419  0.020  1.419
 3AL  C4  H4    single  0.970  0.020  1.090
 3AL  C5  O5    double  1.205  0.020  1.205
 3AL  C5  N7    single  1.357  0.020  1.357
 3AL  N7  C8    single  1.395  0.020  1.395
 3AL  N7  HN7   single  0.860  0.020  1.020
 3AL  C8  O8    double  1.209  0.020  1.209
 3AL  C8  N9    single  1.351  0.020  1.351
 3AL  N9  HN9   single  0.860  0.020  1.020
 3AL  N3  C2    single  1.371  0.020  1.371
 3AL  N3  HN3   single  0.860  0.020  1.020
 3AL  C2  N1    single  1.349  0.020  1.349
 3AL  C2  O2    double  1.225  0.020  1.225
 3AL  N1  HN11  single  0.860  0.020  1.020
 3AL  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
 3AL  H4    C4  N3    108.08  3.000
 3AL  H4    C4  N9    111.38  3.000
 3AL  N3    C4  N9    114.89  3.000
 3AL  H4    C4  C5    108.62  3.000
 3AL  N3    C4  C5    112.23  3.000
 3AL  N9    C4  C5    101.44  3.000
 3AL  N7    C5  O5    127.83  3.000
 3AL  N7    C5  C4    106.03  3.000
 3AL  O5    C5  C4    126.14  3.000
 3AL  HN7   N7  C8    122.66  3.000
 3AL  HN7   N7  C5    124.45  3.000
 3AL  C8    N7  C5    112.81  3.000
 3AL  N9    C8  O8    128.53  3.000
 3AL  N9    C8  N7    106.40  3.000
 3AL  O8    C8  N7    125.06  3.000
 3AL  HN9   N9  C8    121.54  3.000
 3AL  HN9   N9  C4    122.73  3.000
 3AL  C8    N9  C4    112.95  3.000
 3AL  HN3   N3  C2    119.56  3.000
 3AL  HN3   N3  C4    117.71  3.000
 3AL  C2    N3  C4    122.22  3.000
 3AL  O2    C2  N1    123.17  3.000
 3AL  O2    C2  N3    122.39  3.000
 3AL  N1    C2  N3    114.44  3.000
 3AL  HN12  N1  HN11  117.01  3.000
 3AL  HN12  N1  C2    118.60  3.000
 3AL  HN11  N1  C2    122.66  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
 3AL  CONST_01  C8    N7  C5  C4    0.00  0.0  0
 3AL  CONST_02  N7    C8  N9  C4    0.00  0.0  0
 3AL  CONST_03  N9    C8  N7  C5    0.00  0.0  0
 3AL  CONST_04  O8    C8  N9  C4  180.00  0.0  0
 3AL  CONST_05  O8    C8  N7  C5  180.00  0.0  0
 3AL  CONST_06  C8    N7  C5  O5  180.00  0.0  0
 3AL  CONST_07  HN7   N7  C5  C4  180.00  0.0  0
 3AL  CONST_08  HN9   N9  C8  N7  180.00  0.0  0
 3AL  CONST_09  O2    C2  N3  C4    0.00  0.0  0
 3AL  CONST_10  N1    C2  N3  C4  180.00  0.0  0
 3AL  CONST_11  HN3   N3  C2  O2  180.00  0.0  0
 3AL  CONST_12  HN11  N1  C2  O2  180.00  0.0  0
 3AL  CONST_13  HN12  N1  C2  O2    0.00  0.0  0

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
 3AL  chir_01  C4  C5  N9  N3  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
 3AL  plan-1  C4    0.020
 3AL  plan-1  N3    0.020
 3AL  plan-1  C2    0.020
 3AL  plan-1  N1    0.020
 3AL  plan-1  O2    0.020
 3AL  plan-1  HN3   0.020
 3AL  plan-1  HN11  0.020
 3AL  plan-1  HN12  0.020
 3AL  plan-2  C4    0.020
 3AL  plan-2  C5    0.020
 3AL  plan-2  O5    0.020
 3AL  plan-2  N7    0.020
 3AL  plan-2  C8    0.020
 3AL  plan-2  O8    0.020
 3AL  plan-2  N9    0.020
 3AL  plan-2  HN7   0.020
 3AL  plan-2  HN9   0.020

