# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 18:56:31 2022
#   Inital geometry file: a 75 line input string
#   Ligand name: 2-[(cyclopent-3-en-1-yl)amino]pyridine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccnc(NC2CC=CC2)c1
#
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
 WZ7  WZ7  2-[(cyclopent-3-en-1-yl)amino]pyridine-4-carboxamide  ligand  28  15  .  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_WZ7
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
 WZ7  C4   C  CR16  0  -0.403  16.6071  66.4327  36.9630
 WZ7  C5   C  CR6   0   0.066  16.8930  65.5111  37.9777
 WZ7  C6   C  C     0   0.489  17.7945  64.3263  37.7745
 WZ7  C11  C  CH2   0  -0.488  13.2801  67.8946  42.2642
 WZ7  C7   C  CR15  0  -0.059  14.1022  68.1286  40.9838
 WZ7  C8   C  CH2   0  -0.471  14.8742  69.4450  41.2335
 WZ7  C9   C  CR15  0  -0.232  14.0496  70.1121  42.2955
 WZ7  C10  C  CR15  0  -0.232  13.1827  69.2712  42.8522
 WZ7  N1   N  N     0  -0.471  15.2203  67.6781  38.4701
 WZ7  N2   N  NH2   0  -0.809  17.9023  63.8839  36.5137
 WZ7  C3   C  CR16  0  -0.052  15.7723  67.4852  37.2765
 WZ7  N3   N  NH1   0  -0.690  14.9004  66.9787  40.6443
 WZ7  C1   C  CR16  0  -0.426  16.3445  65.7008  39.2254
 WZ7  C2   C  CR6   0   0.552  15.4898  66.8030  39.4374
 WZ7  O1   O  O     0  -0.465  18.3811  63.8144  38.7153
 WZ7  H3   H  HCR6  0   0.259  17.0355  66.3652  35.9729
 WZ7  H12  H  HCH2  0   0.247  12.3107  67.4399  42.0525
 WZ7  H13  H  HCH2  0   0.239  13.7948  67.2183  42.9581
 WZ7  H7   H  HCR5  0   0.252  13.4038  68.3073  40.1637
 WZ7  H9   H  HCH2  0   0.236  15.8905  69.2471  41.5929
 WZ7  H8   H  HCH2  0   0.240  14.9734  70.0381  40.3229
 WZ7  H10  H  HCR5  0   0.240  14.1810  71.1479  42.5823
 WZ7  H11  H  HCR5  0   0.243  12.5067  69.5178  43.6607
 WZ7  H5   H  HNH2  0   0.406  18.4724  63.0770  36.3168
 WZ7  H4   H  HNH2  0   0.413  17.3251  64.2271  35.7655
 WZ7  H2   H  HCR6  0   0.258  15.5370  68.2279  36.5217
 WZ7  H6   H  HNH1  0   0.389  15.2482  66.4193  41.4065
 WZ7  H1   H  HCR6  0   0.269  16.5508  65.0099  40.0328

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
 WZ7  N2   C6   single    1.341  0.020  1.341
 WZ7  C4   C3   aromatic  1.379  0.020  1.379
 WZ7  C4   C5   aromatic  1.400  0.020  1.400
 WZ7  C3   N1   aromatic  1.329  0.020  1.329
 WZ7  C6   C5   single    1.503  0.020  1.503
 WZ7  C6   O1   double    1.221  0.020  1.221
 WZ7  C5   C1   aromatic  1.376  0.020  1.376
 WZ7  N1   C2   aromatic  1.332  0.020  1.332
 WZ7  C1   C2   aromatic  1.411  0.020  1.411
 WZ7  C2   N3   single    1.355  0.020  1.355
 WZ7  N3   C7   single    1.440  0.020  1.440
 WZ7  C7   C8   single    1.546  0.020  1.546
 WZ7  C7   C11  single    1.540  0.020  1.540
 WZ7  C8   C9   single    1.501  0.020  1.501
 WZ7  C9   C10  double    1.330  0.020  1.330
 WZ7  C11  C10  single    1.500  0.020  1.500
 WZ7  C4   H3   single    0.930  0.020  1.080
 WZ7  C11  H12  single    0.970  0.020  1.090
 WZ7  C11  H13  single    0.970  0.020  1.090
 WZ7  C7   H7   single    0.970  0.020  1.090
 WZ7  C8   H9   single    0.970  0.020  1.090
 WZ7  C8   H8   single    0.970  0.020  1.090
 WZ7  C9   H10  single    0.930  0.020  1.080
 WZ7  C10  H11  single    0.930  0.020  1.080
 WZ7  N2   H5   single    0.860  0.020  1.020
 WZ7  N2   H4   single    0.860  0.020  1.020
 WZ7  C3   H2   single    0.930  0.020  1.080
 WZ7  N3   H6   single    0.860  0.020  1.020
 WZ7  C1   H1   single    0.930  0.020  1.080

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
 WZ7  H3   C4   C3   119.71  3.000
 WZ7  H3   C4   C5   122.80  3.000
 WZ7  C3   C4   C5   117.46  3.000
 WZ7  C1   C5   C6   118.07  3.000
 WZ7  C1   C5   C4   119.01  3.000
 WZ7  C6   C5   C4   122.92  3.000
 WZ7  O1   C6   N2   123.21  3.000
 WZ7  O1   C6   C5   120.97  3.000
 WZ7  N2   C6   C5   115.83  3.000
 WZ7  H13  C11  H12  106.41  3.000
 WZ7  H13  C11  C10  110.38  3.000
 WZ7  H12  C11  C10  113.61  3.000
 WZ7  H13  C11  C7   111.66  3.000
 WZ7  H12  C11  C7   112.10  3.000
 WZ7  C10  C11  C7   102.78  3.000
 WZ7  H7   C7   N3   107.95  3.000
 WZ7  H7   C7   C8   107.53  3.000
 WZ7  N3   C7   C8   116.17  3.000
 WZ7  H7   C7   C11  107.94  3.000
 WZ7  C8   C7   C11  105.17  3.000
 WZ7  N3   C7   C11  111.76  3.000
 WZ7  H8   C8   H9   106.71  3.000
 WZ7  H8   C8   C9   113.50  3.000
 WZ7  H9   C8   C9   110.95  3.000
 WZ7  H8   C8   C7   111.92  3.000
 WZ7  H9   C8   C7   111.24  3.000
 WZ7  C9   C8   C7   102.61  3.000
 WZ7  H10  C9   C10  124.97  3.000
 WZ7  H10  C9   C8   123.09  3.000
 WZ7  C10  C9   C8   111.92  3.000
 WZ7  H11  C10  C9   125.16  3.000
 WZ7  H11  C10  C11  122.85  3.000
 WZ7  C9   C10  C11  111.95  3.000
 WZ7  C2   N1   C3   118.22  3.000
 WZ7  H4   N2   H5   116.92  3.000
 WZ7  H4   N2   C6   122.76  3.000
 WZ7  H5   N2   C6   119.58  3.000
 WZ7  H2   C3   N1   115.81  3.000
 WZ7  H2   C3   C4   119.71  3.000
 WZ7  N1   C3   C4   124.48  3.000
 WZ7  H6   N3   C2   116.87  3.000
 WZ7  H6   N3   C7   117.14  3.000
 WZ7  C2   N3   C7   123.69  3.000
 WZ7  H1   C1   C2   120.13  3.000
 WZ7  H1   C1   C5   120.82  3.000
 WZ7  C2   C1   C5   119.04  3.000
 WZ7  C1   C2   N3   119.92  3.000
 WZ7  N3   C2   N1   118.28  3.000
 WZ7  C1   C2   N1   121.78  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
 WZ7  CONST_01  C2   N1   C3   C4     0.00   0.0  0
 WZ7  CONST_02  C2   C1   C5   C4     0.00   0.0  0
 WZ7  CONST_03  N1   C3   C4   C5     0.00   0.0  0
 WZ7  CONST_04  N1   C2   C1   C5     0.00   0.0  0
 WZ7  CONST_05  C1   C5   C4   C3     0.00   0.0  0
 WZ7  CONST_06  C1   C2   N1   C3     0.00   0.0  0
 WZ7  CONST_07  N3   C2   C1   C5   180.00   0.0  0
 WZ7  CONST_08  C3   C4   C5   C6   180.00   0.0  0
 WZ7  CONST_09  C2   C1   C5   C6   180.00   0.0  0
 WZ7  CONST_10  N3   C2   N1   C3   180.00   0.0  0
 WZ7  CONST_11  N1   C2   N3   C7     0.00   0.0  0
 WZ7  CONST_12  C1   C2   N3   C7   180.00   0.0  0
 WZ7  CONST_13  H1   C1   C5   C4   180.00   0.0  0
 WZ7  CONST_14  H2   C3   C4   C5   180.00   0.0  0
 WZ7  CONST_15  H3   C4   C3   N1   180.00   0.0  0
 WZ7  CONST_16  H6   N3   C2   N1   180.00   0.0  0
 WZ7  CONST_17  H5   N2   C6   C5   180.00   0.0  0
 WZ7  CONST_18  H4   N2   C6   C5     0.00   0.0  0
 WZ7  Var_01    C8   C9   C10  C11    0.24  30.0  1
 WZ7  Var_02    C10  C9   C8   C7    14.21  30.0  1
 WZ7  Var_03    C9   C10  C11  C7   -14.66  30.0  1
 WZ7  Var_04    N2   C6   C5   C4   -25.01  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
 WZ7  chir_01  C7  N3  C8  C11  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
 WZ7  plan-1  C4  0.020
 WZ7  plan-1  C5  0.020
 WZ7  plan-1  C6  0.020
 WZ7  plan-1  N1  0.020
 WZ7  plan-1  C3  0.020
 WZ7  plan-1  N3  0.020
 WZ7  plan-1  C1  0.020
 WZ7  plan-1  C2  0.020
 WZ7  plan-1  H3  0.020
 WZ7  plan-1  H2  0.020
 WZ7  plan-1  H1  0.020
 WZ7  plan-2  C7  0.020
 WZ7  plan-2  N3  0.020
 WZ7  plan-2  C2  0.020
 WZ7  plan-2  H6  0.020
 WZ7  plan-3  C5  0.020
 WZ7  plan-3  C6  0.020
 WZ7  plan-3  N2  0.020
 WZ7  plan-3  O1  0.020
 WZ7  plan-3  H5  0.020
 WZ7  plan-3  H4  0.020

