# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 10:22:03 2022
#   Inital geometry file: a 60 line input string
#   Ligand name: 1-[(3~{S})-3-azanyl-4-oxidanylidene-butoxy]guanidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCONC(N)=N)C=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
 ON8  ON8  1-[(3~{S})-3-azanyl-4-oxidanylidene-butoxy]guanidine  ligand  23  11  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ON8
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
 ON8  N    N  NH2   0  -0.779  46.9121  -36.2873   -9.4805
 ON8  CA   C  CH1   0  -0.212  45.7266  -36.4927  -10.2760
 ON8  CB   C  CH2   0  -0.495  45.9683  -36.1426  -11.7488
 ON8  CG   C  CH2   0  -0.112  46.4221  -34.7062  -11.9162
 ON8  C    C  C1    0   0.172  45.1388  -37.8853  -10.2206
 ON8  OD   O  O2    0  -0.416  46.4852  -34.4479  -13.3136
 ON8  NE   N  NH1   0  -0.375  47.1074  -33.2347  -13.5582
 ON8  CZ   C  C     0   0.539  48.1860  -33.3051  -14.4441
 ON8  NH1  N  N     0  -0.716  48.4586  -32.2400  -15.1005
 ON8  NH2  N  NH2   0  -0.828  48.8445  -34.4849  -14.4667
 ON8  OA1  O  O     0  -0.365  45.6193  -38.8083   -9.6147
 ON8  H1   H  HNH2  0   0.355  46.7220  -36.4914   -8.5074
 ON8  H2   H  HNH2  0   0.344  47.6382  -36.9331   -9.7676
 ON8  H4   H  HCH1  0   0.267  44.9347  -35.8256   -9.9079
 ON8  H5   H  HCH2  0   0.252  45.0433  -36.3027  -12.3096
 ON8  H6   H  HCH2  0   0.248  46.7191  -36.8204  -12.1685
 ON8  H7   H  HCH2  0   0.219  47.4008  -34.5499  -11.4579
 ON8  H8   H  HCH2  0   0.213  45.7117  -34.0245  -11.4325
 ON8  H9   H  H     0   0.184  44.2027  -38.0055  -10.7986
 ON8  H10  H  HNH1  0   0.383  46.4236  -32.5545  -13.8692
 ON8  H11  H  H     0   0.320  49.3105  -32.3519  -15.6372
 ON8  H12  H  HNH2  0   0.402  48.5958  -35.2470  -13.8624
 ON8  H13  H  HNH2  0   0.400  49.7213  -34.5492  -14.9517

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
 ON8  NH1  CZ   double  1.280  0.020  1.280
 ON8  CZ   NE   single  1.398  0.020  1.398
 ON8  CZ   NH2  single  1.351  0.020  1.351
 ON8  NE   OD   single  1.385  0.020  1.385
 ON8  OD   CG   single  1.422  0.020  1.422
 ON8  CG   CB   single  1.516  0.020  1.516
 ON8  CB   CA   single  1.533  0.020  1.533
 ON8  OA1  C    double  1.204  0.020  1.204
 ON8  CA   C    single  1.513  0.020  1.513
 ON8  CA   N    single  1.442  0.020  1.442
 ON8  N    H1   single  0.890  0.020  1.040
 ON8  N    H2   single  0.890  0.020  1.040
 ON8  CA   H4   single  0.970  0.020  1.090
 ON8  CB   H5   single  0.970  0.020  1.090
 ON8  CB   H6   single  0.970  0.020  1.090
 ON8  CG   H7   single  0.970  0.020  1.090
 ON8  CG   H8   single  0.970  0.020  1.090
 ON8  C    H9   single  0.930  0.020  1.080
 ON8  NE   H10  single  0.890  0.020  1.040
 ON8  NH1  H11  single  0.890  0.020  1.040
 ON8  NH2  H12  single  0.860  0.020  1.020
 ON8  NH2  H13  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
 ON8  H2   N    H1   106.17  3.000
 ON8  H2   N    CA   110.00  3.000
 ON8  H1   N    CA   110.31  3.000
 ON8  H4   CA   C    105.46  3.000
 ON8  H4   CA   CB   107.27  3.000
 ON8  C    CA   CB   107.86  3.000
 ON8  H4   CA   N    108.73  3.000
 ON8  C    CA   N    115.48  3.000
 ON8  CB   CA   N    111.58  3.000
 ON8  H6   CB   H5   107.03  3.000
 ON8  H6   CB   CG   109.82  3.000
 ON8  H5   CB   CG   109.60  3.000
 ON8  H6   CB   CA   109.57  3.000
 ON8  H5   CB   CA   109.02  3.000
 ON8  CG   CB   CA   111.70  3.000
 ON8  H8   CG   H7   107.84  3.000
 ON8  H8   CG   OD   110.43  3.000
 ON8  H7   CG   OD   110.28  3.000
 ON8  H8   CG   CB   110.26  3.000
 ON8  H7   CG   CB   110.95  3.000
 ON8  OD   CG   CB   107.09  3.000
 ON8  H9   C    OA1  121.14  3.000
 ON8  H9   C    CA   114.17  3.000
 ON8  OA1  C    CA   124.69  3.000
 ON8  NE   OD   CG   110.64  3.000
 ON8  H10  NE   CZ   111.11  3.000
 ON8  H10  NE   OD   109.81  3.000
 ON8  CZ   NE   OD   114.48  3.000
 ON8  NH2  CZ   NH1  127.87  3.000
 ON8  NH2  CZ   NE   115.51  3.000
 ON8  NH1  CZ   NE   116.57  3.000
 ON8  H11  NH1  CZ   111.03  3.000
 ON8  H13  NH2  H12  117.28  3.000
 ON8  H13  NH2  CZ   119.31  3.000
 ON8  H12  NH2  CZ   122.14  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
 ON8  CONST_03  H11  NH1  CZ  NE   180.00   0.0  0
 ON8  CONST_04  H12  NH2  CZ  NE     0.00   0.0  0
 ON8  CONST_05  H13  NH2  CZ  NE   180.00   0.0  0
 ON8  Var_01    OD   CG   CB  CA  -174.22  30.0  1
 ON8  Var_02    CZ   NE   OD  CG   126.10  30.0  1

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
 ON8  chir_01  CA  CB  C  N  negativ

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
 ON8  plan-1  OD   0.020
 ON8  plan-1  NE   0.020
 ON8  plan-1  CZ   0.020
 ON8  plan-1  NH1  0.020
 ON8  plan-1  NH2  0.020
 ON8  plan-1  H10  0.020
 ON8  plan-1  H11  0.020
 ON8  plan-1  H12  0.020
 ON8  plan-1  H13  0.020
 ON8  plan-2  CA   0.020
 ON8  plan-2  C    0.020
 ON8  plan-2  OA1  0.020
 ON8  plan-2  H9   0.020

