# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 03:25:26 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: (3R)-3-[(2H-1,3-benzodioxol-4-yl)methyl]piperidine-1-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)N1CCC[C@@H](C1)Cc2cccc3OCOc23
#
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
 7W7  7W7  (3R)-3-[(2H-1,3-benzodioxol-4-yl)methyl]piperidine-1-carboximidamide  ligand  38  19  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7W7
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
 7W7  C1   C  CR6   0   0.040   1.5146   1.2076  -0.0191
 7W7  C2   C  CR16  0  -0.326   2.0383   1.6338   1.2133
 7W7  C3   C  CR16  0  -0.260   3.0942   0.9841   1.8304
 7W7  C11  C  CH1   0  -0.234  -1.0061   1.4893  -0.0893
 7W7  C12  C  CH2   0  -0.248  -1.2649  -0.0039  -0.2705
 7W7  C14  C  CH2   0  -0.301  -3.6608   0.3525  -0.4167
 7W7  C15  C  CH2   0  -0.431  -3.4908   1.8516  -0.2321
 7W7  C16  C  CH2   0  -0.433  -2.1254   2.3050  -0.7296
 7W7  C17  C  C     0   0.551  -2.7459  -1.6048   0.7984
 7W7  C4   C  CR16  0  -0.362   3.6967  -0.1409   1.2533
 7W7  C5   C  CR56  0   0.305   3.1823  -0.5543   0.0494
 7W7  C6   C  CR56  0   0.248   2.1275   0.1029  -0.5645
 7W7  O7   O  O     0  -0.488   3.5842  -1.5880  -0.7334
 7W7  C8   C  CH2   0   0.067   2.5946  -1.7160  -1.7448
 7W7  O9   O  O     0  -0.485   1.8501  -0.5085  -1.7478
 7W7  C10  C  CH2   0  -0.505   0.3522   1.9001  -0.6679
 7W7  N13  N  NT    0  -0.471  -2.5746  -0.3632   0.2338
 7W7  N18  N  N     0  -0.712  -1.7720  -2.4398   0.8508
 7W7  N19  N  NH2   0  -0.841  -4.0225  -1.8617   1.2631
 7W7  H1   H  HCR6  0   0.249   1.5978   2.5013   1.6905
 7W7  H2   H  HCR6  0   0.256   3.4635   1.3490   2.7795
 7W7  H3   H  HCH1  0   0.226  -0.9977   1.6947   0.9886
 7W7  H4   H  HCH2  0   0.202  -1.1769  -0.2649  -1.3368
 7W7  H5   H  HCH2  0   0.258  -0.5203  -0.5920   0.2601
 7W7  H6   H  HCH2  0   0.252  -4.6236   0.0357  -0.0248
 7W7  H7   H  HCH2  0   0.217  -3.6696   0.1168  -1.4911
 7W7  H8   H  HCH2  0   0.235  -4.2868   2.3717  -0.7690
 7W7  H9   H  HCH2  0   0.221  -3.6047   2.0973   0.8278
 7W7  H10  H  HCH2  0   0.236  -1.9788   3.3696  -0.5290
 7W7  H11  H  HCH2  0   0.212  -2.0770   2.1837  -1.8186
 7W7  H12  H  HCR6  0   0.269   4.5216  -0.6528   1.7299
 7W7  H13  H  HCH2  0   0.245   3.0723  -1.8590  -2.7135
 7W7  H14  H  HCH2  0   0.254   0.4648   2.9800  -0.5406
 7W7  H15  H  HCH2  0   0.243   0.3527   1.7179  -1.7461
 7W7  H16  H  H     0   0.314  -2.0346  -3.2507   1.3992
 7W7  H17  H  HNH2  0   0.384  -4.0899  -2.6835   1.8426
 7W7  H18  H  HNH2  0   0.385  -4.5156  -1.0856   1.6769
 7W7  H19  H  HCH2  0   0.228   1.9346  -2.5610  -1.5147

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
 7W7  C8   O7   single    1.421  0.020  1.421
 7W7  C8   O9   single    1.419  0.020  1.419
 7W7  O7   C5   single    1.357  0.020  1.357
 7W7  O9   C6   single    1.361  0.020  1.361
 7W7  C5   C6   aromatic  1.386  0.020  1.386
 7W7  C5   C4   aromatic  1.373  0.020  1.373
 7W7  C6   C1   aromatic  1.376  0.020  1.376
 7W7  C4   C3   aromatic  1.401  0.020  1.401
 7W7  C1   C10  single    1.501  0.020  1.501
 7W7  C1   C2   aromatic  1.405  0.020  1.405
 7W7  C10  C11  single    1.533  0.020  1.533
 7W7  C16  C11  single    1.526  0.020  1.526
 7W7  C16  C15  single    1.522  0.020  1.522
 7W7  C3   C2   aromatic  1.385  0.020  1.385
 7W7  C11  C12  single    1.526  0.020  1.526
 7W7  C15  C14  single    1.520  0.020  1.520
 7W7  C12  N13  single    1.449  0.020  1.449
 7W7  C14  N13  single    1.454  0.020  1.454
 7W7  N13  C17  single    1.375  0.020  1.375
 7W7  C17  N18  double    1.284  0.020  1.284
 7W7  C17  N19  single    1.383  0.020  1.383
 7W7  C2   H1   single    0.930  0.020  1.080
 7W7  C3   H2   single    0.930  0.020  1.080
 7W7  C11  H3   single    0.970  0.020  1.090
 7W7  C12  H4   single    0.970  0.020  1.090
 7W7  C12  H5   single    0.970  0.020  1.090
 7W7  C14  H6   single    0.970  0.020  1.090
 7W7  C14  H7   single    0.970  0.020  1.090
 7W7  C15  H8   single    0.970  0.020  1.090
 7W7  C15  H9   single    0.970  0.020  1.090
 7W7  C16  H10  single    0.970  0.020  1.090
 7W7  C16  H11  single    0.970  0.020  1.090
 7W7  C4   H12  single    0.930  0.020  1.080
 7W7  C8   H13  single    0.970  0.020  1.090
 7W7  C10  H14  single    0.970  0.020  1.090
 7W7  C10  H15  single    0.970  0.020  1.090
 7W7  N18  H16  single    0.890  0.020  1.040
 7W7  N19  H17  single    0.890  0.020  1.040
 7W7  N19  H18  single    0.890  0.020  1.040
 7W7  C8   H19  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
 7W7  C10  C1   C6   122.96  3.000
 7W7  C10  C1   C2   121.87  3.000
 7W7  C6   C1   C2   115.16  3.000
 7W7  H1   C2   C3   119.29  3.000
 7W7  H1   C2   C1   118.52  3.000
 7W7  C3   C2   C1   122.19  3.000
 7W7  H2   C3   C4   119.05  3.000
 7W7  H2   C3   C2   119.54  3.000
 7W7  C4   C3   C2   121.41  3.000
 7W7  H3   C11  C10  108.29  3.000
 7W7  H3   C11  C16  108.53  3.000
 7W7  C10  C11  C16  110.39  3.000
 7W7  H3   C11  C12  107.52  3.000
 7W7  C16  C11  C12  110.41  3.000
 7W7  C10  C11  C12  111.57  3.000
 7W7  H5   C12  H4   106.83  3.000
 7W7  H5   C12  N13  108.37  3.000
 7W7  H4   C12  N13  110.52  3.000
 7W7  H5   C12  C11  110.80  3.000
 7W7  H4   C12  C11  109.47  3.000
 7W7  N13  C12  C11  110.77  3.000
 7W7  H7   C14  H6   106.42  3.000
 7W7  H7   C14  N13  109.72  3.000
 7W7  H6   C14  N13  110.92  3.000
 7W7  H7   C14  C15  109.32  3.000
 7W7  H6   C14  C15  110.05  3.000
 7W7  N13  C14  C15  110.33  3.000
 7W7  H9   C15  H8   107.06  3.000
 7W7  H9   C15  C16  110.07  3.000
 7W7  H8   C15  C16  110.57  3.000
 7W7  H9   C15  C14  109.12  3.000
 7W7  H8   C15  C14  109.18  3.000
 7W7  C16  C15  C14  110.76  3.000
 7W7  H11  C16  H10  106.50  3.000
 7W7  H11  C16  C15  109.34  3.000
 7W7  H10  C16  C15  110.51  3.000
 7W7  H11  C16  C11  108.97  3.000
 7W7  H10  C16  C11  110.20  3.000
 7W7  C15  C16  C11  111.20  3.000
 7W7  N19  C17  N18  124.46  3.000
 7W7  N19  C17  N13  114.90  3.000
 7W7  N18  C17  N13  120.64  3.000
 7W7  H12  C4   C5   121.98  3.000
 7W7  H12  C4   C3   121.78  3.000
 7W7  C5   C4   C3   116.23  3.000
 7W7  O7   C5   C6   109.32  3.000
 7W7  C6   C5   C4   122.05  3.000
 7W7  O7   C5   C4   128.61  3.000
 7W7  O9   C6   C5   109.11  3.000
 7W7  C5   C6   C1   122.96  3.000
 7W7  O9   C6   C1   127.93  3.000
 7W7  C8   O7   C5   105.84  3.000
 7W7  H19  C8   H13  110.45  3.000
 7W7  H19  C8   O9   109.91  3.000
 7W7  H13  C8   O9   109.87  3.000
 7W7  H19  C8   O7   109.83  3.000
 7W7  H13  C8   O7   109.84  3.000
 7W7  O9   C8   O7   106.88  3.000
 7W7  C8   O9   C6   105.88  3.000
 7W7  H15  C10  H14  106.22  3.000
 7W7  H15  C10  C11  109.15  3.000
 7W7  H14  C10  C11  108.18  3.000
 7W7  H15  C10  C1   110.44  3.000
 7W7  H14  C10  C1   109.01  3.000
 7W7  C11  C10  C1   113.56  3.000
 7W7  C17  N13  C14  122.35  3.000
 7W7  C17  N13  C12  118.66  3.000
 7W7  C14  N13  C12  113.42  3.000
 7W7  H16  N18  C17  110.23  3.000
 7W7  H18  N19  H17  111.04  3.000
 7W7  H18  N19  C17  116.51  3.000
 7W7  H17  N19  C17  113.99  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
 7W7  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 7W7  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 7W7  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 7W7  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 7W7  CONST_05  C6   C5   C4   C3     0.00   0.0  0
 7W7  CONST_06  C6   C1   C2   C3     0.00   0.0  0
 7W7  CONST_07  C10  C1   C2   C3   180.00   0.0  0
 7W7  CONST_08  C10  C1   C6   C5   180.00   0.0  0
 7W7  CONST_09  C10  C1   C6   O9     0.00   0.0  0
 7W7  CONST_10  H2   C3   C2   C1   180.00   0.0  0
 7W7  CONST_11  H12  C4   C3   C2   180.00   0.0  0
 7W7  CONST_12  H1   C2   C3   C4   180.00   0.0  0
 7W7  CONST_13  N18  C17  N13  C12    0.00   0.0  0
 7W7  CONST_14  N19  C17  N13  C12  180.00   0.0  0
 7W7  CONST_17  H16  N18  C17  N13  180.00   0.0  0
 7W7  CONST_18  H17  N19  C17  N13  180.00   0.0  0
 7W7  Var_01    C14  C15  C16  C11  -53.19  30.0  1
 7W7  Var_02    C14  N13  C12  C11   58.95  30.0  1
 7W7  Var_03    C15  C14  N13  C12  -59.12  30.0  1
 7W7  Var_04    N13  C14  C15  C16   55.21  30.0  1
 7W7  Var_05    O9   C8   O7   C5    16.75  30.0  1
 7W7  Var_06    O7   C8   O9   C6   -16.80  30.0  1
 7W7  Var_07    C11  C10  C1   C2   -80.35  30.0  2

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
 7W7  chir_01  C11  C10  C16  C12  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
 7W7  plan-1  C12  0.020
 7W7  plan-1  C14  0.020
 7W7  plan-1  C17  0.020
 7W7  plan-1  N13  0.020
 7W7  plan-1  N18  0.020
 7W7  plan-1  N19  0.020
 7W7  plan-1  H16  0.020
 7W7  plan-1  H17  0.020
 7W7  plan-1  H18  0.020
 7W7  plan-2  C1   0.020
 7W7  plan-2  C2   0.020
 7W7  plan-2  C3   0.020
 7W7  plan-2  C4   0.020
 7W7  plan-2  C5   0.020
 7W7  plan-2  C6   0.020
 7W7  plan-2  O7   0.020
 7W7  plan-2  O9   0.020
 7W7  plan-2  C10  0.020
 7W7  plan-2  H1   0.020
 7W7  plan-2  H2   0.020
 7W7  plan-2  H12  0.020

