# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 17:03:12 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 1-methyl-3-(N-methylcarbamimidoyl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=N)NC(=O)NC
#
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
 XRG  XRG  1-methyl-3-(N-methylcarbamimidoyl)urea  ligand  19  9  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_XRG
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
 XRG  CAB   C  CH3   0  -0.506   3.6533   0.2586  -0.1035
 XRG  NAF   N  NH1   0  -0.668   2.2925   0.6521   0.1667
 XRG  CAI   C  C     0   0.728   1.2636  -0.2067  -0.0091
 XRG  OAD   O  O     0  -0.508   1.4290  -1.3737  -0.3165
 XRG  NAG   N  NH1   0  -0.755   0.0285   0.3825   0.1899
 XRG  CAH   C  C     0   0.600  -1.2168  -0.2406   0.1693
 XRG  NAC   N  N     0  -0.676  -1.3474  -1.4896   0.3787
 XRG  NAE   N  NH1   0  -0.655  -2.2195   0.6740  -0.0216
 XRG  CAA   C  CH3   0  -0.546  -3.5943   0.2461  -0.1023
 XRG  HAB   H  HCH3  0   0.236   3.9480  -0.6050   0.4921
 XRG  HABA  H  HCH3  0   0.232   3.8177   0.0206  -1.1562
 XRG  HABB  H  HCH3  0   0.248   4.3036   1.0875   0.1620
 XRG  HNAF  H  HNH1  0   0.400   2.1171   1.6235   0.3585
 XRG  HNAG  H  HNH1  0   0.405   0.0141   1.3773   0.3524
 XRG  HNAC  H  H     0   0.338  -2.3127  -1.7773   0.2671
 XRG  HNAE  H  HNH1  0   0.392  -1.9866   1.4851  -0.5725
 XRG  HAA   H  HCH3  0   0.230  -3.7900  -0.4300  -0.9407
 XRG  HAAA  H  HCH3  0   0.243  -3.8974  -0.2553   0.8174
 XRG  HAAB  H  HCH3  0   0.261  -4.2217   1.1251  -0.2221

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
 XRG  CAB  NAF   single  1.442  0.020  1.442
 XRG  NAF  CAI   single  1.352  0.020  1.352
 XRG  CAI  OAD   double  1.218  0.020  1.218
 XRG  CAI  NAG   single  1.383  0.020  1.383
 XRG  NAG  CAH   single  1.393  0.020  1.393
 XRG  CAH  NAC   double  1.273  0.020  1.273
 XRG  CAH  NAE   single  1.371  0.020  1.371
 XRG  NAE  CAA   single  1.442  0.020  1.442
 XRG  CAB  HAB   single  0.970  0.020  1.090
 XRG  CAB  HABA  single  0.970  0.020  1.090
 XRG  CAB  HABB  single  0.970  0.020  1.090
 XRG  NAF  HNAF  single  0.860  0.020  1.020
 XRG  NAG  HNAG  single  0.860  0.020  1.020
 XRG  NAC  HNAC  single  0.890  0.020  1.040
 XRG  NAE  HNAE  single  0.890  0.020  1.040
 XRG  CAA  HAA   single  0.970  0.020  1.090
 XRG  CAA  HAAA  single  0.970  0.020  1.090
 XRG  CAA  HAAB  single  0.970  0.020  1.090

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
 XRG  HABB  CAB  HABA  108.17  3.000
 XRG  HABB  CAB  HAB   108.01  3.000
 XRG  HABA  CAB  HAB   108.27  3.000
 XRG  HABB  CAB  NAF   108.11  3.000
 XRG  HABA  CAB  NAF   112.47  3.000
 XRG  HAB   CAB  NAF   111.66  3.000
 XRG  HNAF  NAF  CAI   120.38  3.000
 XRG  HNAF  NAF  CAB   117.64  3.000
 XRG  CAI   NAF  CAB   121.37  3.000
 XRG  NAG   CAI  OAD   124.46  3.000
 XRG  NAG   CAI  NAF   112.98  3.000
 XRG  OAD   CAI  NAF   122.56  3.000
 XRG  HNAG  NAG  CAH   115.54  3.000
 XRG  HNAG  NAG  CAI   117.16  3.000
 XRG  CAH   NAG  CAI   127.29  3.000
 XRG  NAE   CAH  NAC   127.05  3.000
 XRG  NAE   CAH  NAG   110.96  3.000
 XRG  NAC   CAH  NAG   121.89  3.000
 XRG  HNAC  NAC  CAH   110.98  3.000
 XRG  HNAE  NAE  CAA   115.38  3.000
 XRG  HNAE  NAE  CAH   116.37  3.000
 XRG  CAA   NAE  CAH   120.48  3.000
 XRG  HAAB  CAA  HAAA  107.73  3.000
 XRG  HAAB  CAA  HAA   108.18  3.000
 XRG  HAAA  CAA  HAA   108.19  3.000
 XRG  HAAB  CAA  NAE   108.46  3.000
 XRG  HAAA  CAA  NAE   110.75  3.000
 XRG  HAA   CAA  NAE   113.36  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
 XRG  CONST_01  OAD   CAI  NAF  CAB    0.00   0.0  0
 XRG  CONST_02  CAH   NAG  CAI  OAD    0.00   0.0  0
 XRG  CONST_03  NAG   CAI  NAF  CAB  180.00   0.0  0
 XRG  CONST_04  CAH   NAG  CAI  NAF  180.00   0.0  0
 XRG  CONST_07  CAA   NAE  CAH  NAG  180.00   0.0  0
 XRG  CONST_08  CAA   NAE  CAH  NAC    0.00   0.0  0
 XRG  CONST_09  HNAF  NAF  CAI  OAD  180.00   0.0  0
 XRG  CONST_10  HNAG  NAG  CAI  OAD  180.00   0.0  0
 XRG  CONST_11  HNAC  NAC  CAH  NAG  180.00   0.0  0
 XRG  Var_01    HAB   CAB  NAF  CAI  -58.15  30.0  3
 XRG  Var_02    HAA   CAA  NAE  CAH  -61.64  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
 XRG  plan-1  CAB   0.020
 XRG  plan-1  NAF   0.020
 XRG  plan-1  CAI   0.020
 XRG  plan-1  OAD   0.020
 XRG  plan-1  NAG   0.020
 XRG  plan-1  CAH   0.020
 XRG  plan-1  NAC   0.020
 XRG  plan-1  NAE   0.020
 XRG  plan-1  CAA   0.020
 XRG  plan-1  HNAF  0.020
 XRG  plan-1  HNAG  0.020
 XRG  plan-1  HNAC  0.020
 XRG  plan-1  HNAE  0.020

