# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 12:49:47 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: 1-(3-chlorophenyl)cyclobutane-1-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)C1(CCC1)c2cccc(Cl)c2
#
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
 KJM  KJM  1-(3-chlorophenyl)cyclobutane-1-carboximidamide  ligand  27  14  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_KJM
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
 KJM  N1   N   NH2   0  -0.815   2.2158  -0.6609  -1.9876
 KJM  C4   C   C     0  -0.425   1.8182  -0.1721   1.7393
 KJM  C5   C   C     0   0.399   2.0103  -1.0598  -0.7044
 KJM  C6   C   CR16  0  -0.236  -0.8409  -0.4199   0.2731
 KJM  C7   C   CR16  0  -0.324  -0.1553   1.6099  -0.7984
 KJM  C8   C   C     0  -0.440   2.3303   1.2721   1.8544
 KJM  C10  C   CR16  0  -0.243  -1.4815   1.8970  -1.0985
 KJM  C1   C   C     0  -0.202   1.6084   0.0628   0.2261
 KJM  C11  C   CR16  0  -0.232  -2.4977   1.0360  -0.7180
 KJM  C2   C   CR6   0   0.169   0.1797   0.4538  -0.1027
 KJM  C3   C   C     0  -0.455   2.6020   1.2491   0.3428
 KJM  C9   C   CR6   0  -0.026  -2.1556  -0.1220  -0.0350
 KJM  N2   N   N     0  -0.654   2.0678  -2.2533  -0.2571
 KJM  CL1  CL  CL    0  -0.134  -3.4076  -1.2238   0.4472
 KJM  H1   H   HNH2  0   0.391   2.6399  -1.2984  -2.6413
 KJM  H2   H   HNH2  0   0.397   2.3689   0.3133  -2.1864
 KJM  H4   H   H     0   0.237   0.9483  -0.4607   2.3296
 KJM  H5   H   HCR6  0   0.274  -0.6007  -1.3355   0.7983
 KJM  H6   H   HCR6  0   0.253   0.6117   2.3032  -1.1163
 KJM  H7   H   H     0   0.233   1.5310   1.9693   2.1089
 KJM  H8   H   H     0   0.237   3.1781   1.4553   2.5134
 KJM  H9   H   HCR6  0   0.267  -1.7270   2.8035  -1.6359
 KJM  H10  H   HCR6  0   0.279  -3.5302   1.2606  -0.9475
 KJM  H11  H   H     0   0.246   2.4137   2.1550  -0.2319
 KJM  H12  H   H     0   0.248   3.6186   0.9149   0.1290
 KJM  H13  H   H     0   0.316   2.3256  -2.9086  -0.9915
 KJM  H3   H   H     0   0.240   2.6110  -0.8995   1.9099

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
 KJM  C8   C3   single    1.536  0.020  1.536
 KJM  C8   C4   single    1.537  0.020  1.537
 KJM  C3   C1   single    1.552  0.020  1.552
 KJM  C4   C1   single    1.546  0.020  1.546
 KJM  C1   C5   single    1.512  0.020  1.512
 KJM  C1   C2   single    1.517  0.020  1.517
 KJM  C5   N2   double    1.276  0.020  1.276
 KJM  C5   N1   single    1.359  0.020  1.359
 KJM  C2   C6   aromatic  1.395  0.020  1.395
 KJM  C2   C7   aromatic  1.390  0.020  1.390
 KJM  C6   C9   aromatic  1.383  0.020  1.383
 KJM  C7   C10  aromatic  1.390  0.020  1.390
 KJM  C9   CL1  single    1.736  0.020  1.736
 KJM  C9   C11  aromatic  1.387  0.020  1.387
 KJM  C10  C11  aromatic  1.385  0.020  1.385
 KJM  N1   H1   single    0.890  0.020  1.040
 KJM  N1   H2   single    0.890  0.020  1.040
 KJM  C4   H3   single    0.970  0.020  1.090
 KJM  C4   H4   single    0.970  0.020  1.090
 KJM  C6   H5   single    0.930  0.020  1.080
 KJM  C7   H6   single    0.930  0.020  1.080
 KJM  C8   H7   single    0.970  0.020  1.090
 KJM  C8   H8   single    0.970  0.020  1.090
 KJM  C10  H9   single    0.930  0.020  1.080
 KJM  C11  H10  single    0.930  0.020  1.080
 KJM  C3   H11  single    0.970  0.020  1.090
 KJM  C3   H12  single    0.970  0.020  1.090
 KJM  N2   H13  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
 KJM  H2   N1   H1   114.88  3.000
 KJM  H2   N1   C5   119.58  3.000
 KJM  H1   N1   C5   119.39  3.000
 KJM  H4   C4   H3   108.61  3.000
 KJM  H4   C4   C1   117.52  3.000
 KJM  H3   C4   C1   110.70  3.000
 KJM  H4   C4   C8   118.31  3.000
 KJM  H3   C4   C8   111.91  3.000
 KJM  C1   C4   C8    88.61  3.000
 KJM  N2   C5   C1   119.38  3.000
 KJM  N2   C5   N1   126.77  3.000
 KJM  C1   C5   N1   113.77  3.000
 KJM  H5   C6   C9   120.08  3.000
 KJM  H5   C6   C2   119.88  3.000
 KJM  C9   C6   C2   120.04  3.000
 KJM  H6   C7   C2   120.61  3.000
 KJM  H6   C7   C10  118.74  3.000
 KJM  C2   C7   C10  120.65  3.000
 KJM  H8   C8   H7   108.77  3.000
 KJM  H8   C8   C3   117.40  3.000
 KJM  H7   C8   C3   111.64  3.000
 KJM  H8   C8   C4   117.56  3.000
 KJM  H7   C8   C4   111.96  3.000
 KJM  C3   C8   C4    88.35  3.000
 KJM  H9   C10  C11  119.39  3.000
 KJM  H9   C10  C7   119.79  3.000
 KJM  C11  C10  C7   120.82  3.000
 KJM  C3   C1   C2   114.97  3.000
 KJM  C2   C1   C5   107.95  3.000
 KJM  C3   C1   C5   116.33  3.000
 KJM  C2   C1   C4   112.27  3.000
 KJM  C5   C1   C4   116.97  3.000
 KJM  C3   C1   C4    87.46  3.000
 KJM  H10  C11  C9   120.89  3.000
 KJM  H10  C11  C10  120.87  3.000
 KJM  C9   C11  C10  118.24  3.000
 KJM  C1   C2   C7   123.34  3.000
 KJM  C7   C2   C6   118.64  3.000
 KJM  C1   C2   C6   117.97  3.000
 KJM  H12  C3   H11  108.21  3.000
 KJM  H12  C3   C1   110.34  3.000
 KJM  H11  C3   C1   119.04  3.000
 KJM  H12  C3   C8   111.23  3.000
 KJM  H11  C3   C8   118.44  3.000
 KJM  C1   C3   C8    88.41  3.000
 KJM  CL1  C9   C11  119.25  3.000
 KJM  C11  C9   C6   121.60  3.000
 KJM  CL1  C9   C6   119.15  3.000
 KJM  H13  N2   C5   111.16  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
 KJM  CONST_01  C10  C7   C2   C6     0.00   0.0  0
 KJM  CONST_02  C10  C11  C9   C6     0.00   0.0  0
 KJM  CONST_03  C9   C6   C2   C7     0.00   0.0  0
 KJM  CONST_04  C9   C11  C10  C7     0.00   0.0  0
 KJM  CONST_05  C2   C6   C9   C11    0.00   0.0  0
 KJM  CONST_06  C2   C7   C10  C11    0.00   0.0  0
 KJM  CONST_07  C1   C2   C7   C10  180.00   0.0  0
 KJM  CONST_08  C9   C6   C2   C1   180.00   0.0  0
 KJM  CONST_09  CL1  C9   C11  C10  180.00   0.0  0
 KJM  CONST_10  CL1  C9   C6   C2   180.00   0.0  0
 KJM  CONST_11  H6   C7   C2   C6   180.00   0.0  0
 KJM  CONST_12  H10  C11  C9   C6   180.00   0.0  0
 KJM  CONST_13  H5   C6   C2   C7   180.00   0.0  0
 KJM  CONST_14  H9   C10  C7   C2   180.00   0.0  0
 KJM  CONST_15  H13  N2   C5   C1   180.00   0.0  0
 KJM  CONST_16  H1   N1   C5   C1   180.00   0.0  0
 KJM  Var_01    C1   C3   C8   C4    20.10  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
 KJM  chir_01  C1  C4  C3  C2  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
 KJM  plan-1  C6   0.020
 KJM  plan-1  C7   0.020
 KJM  plan-1  C10  0.020
 KJM  plan-1  C1   0.020
 KJM  plan-1  C11  0.020
 KJM  plan-1  C2   0.020
 KJM  plan-1  C9   0.020
 KJM  plan-1  CL1  0.020
 KJM  plan-1  H5   0.020
 KJM  plan-1  H6   0.020
 KJM  plan-1  H9   0.020
 KJM  plan-1  H10  0.020
 KJM  plan-2  N1   0.020
 KJM  plan-2  C5   0.020
 KJM  plan-2  C1   0.020
 KJM  plan-2  N2   0.020
 KJM  plan-2  H1   0.020
 KJM  plan-2  H2   0.020
 KJM  plan-2  H13  0.020

