# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 01:29:19 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 4-[4-(3-oxidanylidene-3-pyrrolidin-1-yl-propyl)piperidin-1-yl]benzenecarbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(CCC1CCN(CC1)c2ccc(cc2)C#N)N3CCCC3
#
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
 5TD  5TD  4-[4-(3-oxidanylidene-3-pyrrolidin-1-yl-propyl)piperidin-1-yl]benzenecarbonitrile  ligand  48  23  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5TD
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
 5TD  O    O  O     0  -0.516   4.6202  -1.8896  -0.6234
 5TD  C4   C  C     0   0.575   4.4525  -0.7346  -0.2440
 5TD  N    N  NR5   0  -0.477   5.4657   0.1458  -0.2152
 5TD  C3   C  CH2   0  -0.270   5.3918   1.5288   0.2429
 5TD  C2   C  CH2   0  -0.471   6.8536   1.9003   0.4574
 5TD  C1   C  CH2   0  -0.487   7.5742   1.0933  -0.6185
 5TD  C    C  CH2   0  -0.257   6.8101  -0.2268  -0.6439
 5TD  C5   C  CH2   0  -0.607   3.1042  -0.2234   0.2204
 5TD  C6   C  CH2   0  -0.396   1.9867  -1.2464   0.0791
 5TD  C7   C  CH1   0  -0.246   0.6521  -0.7559   0.6344
 5TD  C11  C  CH2   0  -0.427   0.0986   0.4521  -0.1128
 5TD  C10  C  CH2   0  -0.305  -1.2613   0.8902   0.4163
 5TD  N1   N  NT    0  -0.514  -2.2102  -0.2092   0.3978
 5TD  C9   C  CH2   0  -0.311  -1.7369  -1.3758   1.1290
 5TD  C8   C  CH2   0  -0.418  -0.3964  -1.8620   0.6035
 5TD  C12  C  CR6   0   0.429  -3.5261  -0.0241   0.0943
 5TD  C17  C  CR16  0  -0.350  -4.4100  -1.1179  -0.0618
 5TD  C16  C  CR16  0  -0.225  -5.7260  -0.9373  -0.4159
 5TD  C15  C  CR6   0  -0.044  -6.2428   0.3445  -0.6286
 5TD  C18  C  CSP   0   0.036  -7.6003   0.5283  -0.9986
 5TD  N2   N  NS    0  -0.276  -8.7047   0.6776  -1.3012
 5TD  C14  C  CR16  0  -0.224  -5.3918   1.4391  -0.4654
 5TD  C13  C  CR16  0  -0.365  -4.0739   1.2634  -0.1072
 5TD  H1   H  HCH2  0   0.238   4.9323   2.1688  -0.5172
 5TD  H2   H  HCH2  0   0.252   4.8013   1.6194   1.1546
 5TD  H3   H  HCH2  0   0.251   7.0208   2.9736   0.3778
 5TD  H4   H  HCH2  0   0.239   7.1779   1.5829   1.4510
 5TD  H5   H  HCH2  0   0.238   7.4938   1.5968  -1.5844
 5TD  H6   H  HCH2  0   0.251   8.6334   0.9497  -0.4087
 5TD  H7   H  HCH2  0   0.233   7.2445  -0.9545   0.0474
 5TD  H8   H  HCH2  0   0.243   6.7942  -0.6844  -1.6337
 5TD  H9   H  HCH2  0   0.263   3.1908   0.0843   1.2686
 5TD  H10  H  HCH2  0   0.266   2.8629   0.6917  -0.3286
 5TD  H11  H  HCH2  0   0.218   1.8604  -1.5202  -0.9729
 5TD  H12  H  HCH2  0   0.229   2.2668  -2.1634   0.6036
 5TD  H13  H  HCH1  0   0.215   0.8033  -0.4672   1.6840
 5TD  H14  H  HCH2  0   0.245   0.7762   1.3060  -0.0436
 5TD  H15  H  HCH2  0   0.222   0.0015   0.2080  -1.1761
 5TD  H16  H  HCH2  0   0.227  -1.1574   1.2861   1.4360
 5TD  H17  H  HCH2  0   0.261  -1.6189   1.7044  -0.2087
 5TD  H18  H  HCH2  0   0.232  -1.6383  -1.1110   2.1905
 5TD  H19  H  HCH2  0   0.264  -2.4603  -2.1827   1.0781
 5TD  H20  H  HCH2  0   0.222  -0.5199  -2.2278  -0.4214
 5TD  H21  H  HCH2  0   0.238  -0.0725  -2.7123   1.2093
 5TD  H22  H  HCR6  0   0.275  -4.0632  -2.1326   0.0640
 5TD  H23  H  HCR6  0   0.273  -6.3614  -1.8043  -0.5406
 5TD  H24  H  HCR6  0   0.274  -5.7686   2.4435  -0.6065
 5TD  H25  H  HCR6  0   0.275  -3.4749   2.1503   0.0339

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
 5TD  O    C4   double    1.227  0.020  1.227
 5TD  C3   C2   single    1.523  0.020  1.523
 5TD  C3   N    single    1.459  0.020  1.459
 5TD  C2   C1   single    1.526  0.020  1.526
 5TD  C4   N    single    1.343  0.020  1.343
 5TD  C4   C5   single    1.515  0.020  1.515
 5TD  N    C    single    1.459  0.020  1.459
 5TD  C6   C5   single    1.522  0.020  1.522
 5TD  C6   C7   single    1.527  0.020  1.527
 5TD  N2   C18  triple    1.155  0.020  1.155
 5TD  C11  C7   single    1.524  0.020  1.524
 5TD  C11  C10  single    1.524  0.020  1.524
 5TD  C1   C    single    1.526  0.020  1.526
 5TD  C7   C8   single    1.524  0.020  1.524
 5TD  C18  C15  single    1.419  0.020  1.419
 5TD  C14  C15  aromatic  1.396  0.020  1.396
 5TD  C14  C13  aromatic  1.377  0.020  1.377
 5TD  C15  C16  aromatic  1.398  0.020  1.398
 5TD  C13  C12  aromatic  1.414  0.020  1.414
 5TD  C10  N1   single    1.452  0.020  1.452
 5TD  C16  C17  aromatic  1.375  0.020  1.375
 5TD  C12  C17  aromatic  1.415  0.020  1.415
 5TD  C12  N1   single    1.363  0.020  1.363
 5TD  C8   C9   single    1.520  0.020  1.520
 5TD  N1   C9   single    1.456  0.020  1.456
 5TD  C3   H1   single    0.970  0.020  1.090
 5TD  C3   H2   single    0.970  0.020  1.090
 5TD  C2   H3   single    0.970  0.020  1.090
 5TD  C2   H4   single    0.970  0.020  1.090
 5TD  C1   H5   single    0.970  0.020  1.090
 5TD  C1   H6   single    0.970  0.020  1.090
 5TD  C    H7   single    0.970  0.020  1.090
 5TD  C    H8   single    0.970  0.020  1.090
 5TD  C5   H9   single    0.970  0.020  1.090
 5TD  C5   H10  single    0.970  0.020  1.090
 5TD  C6   H11  single    0.970  0.020  1.090
 5TD  C6   H12  single    0.970  0.020  1.090
 5TD  C7   H13  single    0.970  0.020  1.090
 5TD  C11  H14  single    0.970  0.020  1.090
 5TD  C11  H15  single    0.970  0.020  1.090
 5TD  C10  H16  single    0.970  0.020  1.090
 5TD  C10  H17  single    0.970  0.020  1.090
 5TD  C9   H18  single    0.970  0.020  1.090
 5TD  C9   H19  single    0.970  0.020  1.090
 5TD  C8   H20  single    0.970  0.020  1.090
 5TD  C8   H21  single    0.970  0.020  1.090
 5TD  C17  H22  single    0.930  0.020  1.080
 5TD  C16  H23  single    0.930  0.020  1.080
 5TD  C14  H24  single    0.930  0.020  1.080
 5TD  C13  H25  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
 5TD  C5   C4   N    116.35  3.000
 5TD  C5   C4   O    122.27  3.000
 5TD  N    C4   O    121.38  3.000
 5TD  C    N    C3   112.39  3.000
 5TD  C    N    C4   121.43  3.000
 5TD  C3   N    C4   126.17  3.000
 5TD  H2   C3   H1   107.74  3.000
 5TD  H2   C3   C2   112.45  3.000
 5TD  H1   C3   C2   110.98  3.000
 5TD  H2   C3   N    111.65  3.000
 5TD  H1   C3   N    110.94  3.000
 5TD  C2   C3   N    103.11  3.000
 5TD  H4   C2   H3   107.90  3.000
 5TD  H4   C2   C1   110.34  3.000
 5TD  H3   C2   C1   113.40  3.000
 5TD  H4   C2   C3   110.00  3.000
 5TD  H3   C2   C3   112.16  3.000
 5TD  C1   C2   C3   103.00  3.000
 5TD  H6   C1   H5   107.62  3.000
 5TD  H6   C1   C    112.10  3.000
 5TD  H5   C1   C    110.33  3.000
 5TD  H6   C1   C2   113.15  3.000
 5TD  H5   C1   C2   110.18  3.000
 5TD  C    C1   C2   103.47  3.000
 5TD  H8   C    H7   107.48  3.000
 5TD  H8   C    C1   112.67  3.000
 5TD  H7   C    C1   111.49  3.000
 5TD  H8   C    N    111.12  3.000
 5TD  H7   C    N    110.49  3.000
 5TD  C1   C    N    103.62  3.000
 5TD  H10  C5   H9   105.22  3.000
 5TD  H10  C5   C6   110.72  3.000
 5TD  H9   C5   C6   109.62  3.000
 5TD  H10  C5   C4   108.95  3.000
 5TD  H9   C5   C4   108.52  3.000
 5TD  C6   C5   C4   113.47  3.000
 5TD  H12  C6   H11  106.32  3.000
 5TD  H12  C6   C7   108.61  3.000
 5TD  H11  C6   C7   109.22  3.000
 5TD  H12  C6   C5   109.35  3.000
 5TD  H11  C6   C5   110.02  3.000
 5TD  C7   C6   C5   113.09  3.000
 5TD  H13  C7   C8   107.73  3.000
 5TD  H13  C7   C11  108.06  3.000
 5TD  C8   C7   C11  108.38  3.000
 5TD  H13  C7   C6   108.15  3.000
 5TD  C8   C7   C6   111.15  3.000
 5TD  C11  C7   C6   113.19  3.000
 5TD  H15  C11  H14  106.91  3.000
 5TD  H15  C11  C10  108.79  3.000
 5TD  H14  C11  C10  107.88  3.000
 5TD  H15  C11  C7   109.36  3.000
 5TD  H14  C11  C7   111.30  3.000
 5TD  C10  C11  C7   112.44  3.000
 5TD  H17  C10  H16  107.15  3.000
 5TD  H17  C10  N1   110.16  3.000
 5TD  H16  C10  N1   110.27  3.000
 5TD  H17  C10  C11  108.02  3.000
 5TD  H16  C10  C11  109.96  3.000
 5TD  N1   C10  C11  111.17  3.000
 5TD  C12  N1   C9   122.31  3.000
 5TD  C9   N1   C10  112.81  3.000
 5TD  C12  N1   C10  122.06  3.000
 5TD  H19  C9   H18  106.52  3.000
 5TD  H19  C9   C8   109.51  3.000
 5TD  H18  C9   C8   109.40  3.000
 5TD  H19  C9   N1   110.83  3.000
 5TD  H18  C9   N1   108.74  3.000
 5TD  C8   C9   N1   111.69  3.000
 5TD  H21  C8   H20  106.99  3.000
 5TD  H21  C8   C9   108.58  3.000
 5TD  H20  C8   C9   109.33  3.000
 5TD  H21  C8   C7   110.45  3.000
 5TD  H20  C8   C7   109.81  3.000
 5TD  C9   C8   C7   111.56  3.000
 5TD  C13  C12  C17  116.51  3.000
 5TD  C17  C12  N1   121.51  3.000
 5TD  C13  C12  N1   121.97  3.000
 5TD  H22  C17  C16  117.45  3.000
 5TD  H22  C17  C12  120.87  3.000
 5TD  C16  C17  C12  121.65  3.000
 5TD  H23  C16  C15  119.99  3.000
 5TD  H23  C16  C17  119.11  3.000
 5TD  C15  C16  C17  120.89  3.000
 5TD  C14  C15  C18  120.80  3.000
 5TD  C14  C15  C16  118.41  3.000
 5TD  C18  C15  C16  120.80  3.000
 5TD  N2   C18  C15  180.00  3.000
 5TD  H24  C14  C13  119.05  3.000
 5TD  H24  C14  C15  120.03  3.000
 5TD  C13  C14  C15  120.91  3.000
 5TD  H25  C13  C14  117.40  3.000
 5TD  H25  C13  C12  120.98  3.000
 5TD  C14  C13  C12  121.61  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
 5TD  CONST_01  C15  C14  C13  C12     0.00   0.0  0
 5TD  CONST_02  C15  C16  C17  C12     0.00   0.0  0
 5TD  CONST_03  C14  C15  C16  C17     0.00   0.0  0
 5TD  CONST_04  C14  C13  C12  C17     0.00   0.0  0
 5TD  CONST_05  C13  C14  C15  C16     0.00   0.0  0
 5TD  CONST_06  C13  C12  C17  C16     0.00   0.0  0
 5TD  CONST_07  C14  C13  C12  N1    180.00   0.0  0
 5TD  CONST_08  C16  C17  C12  N1    180.00   0.0  0
 5TD  CONST_09  C18  C15  C16  C17   180.00   0.0  0
 5TD  CONST_10  C13  C14  C15  C18   180.00   0.0  0
 5TD  CONST_11  H25  C13  C12  N1      0.00   0.0  0
 5TD  CONST_12  H22  C17  C12  N1      0.00   0.0  0
 5TD  CONST_13  H24  C14  C13  C12   180.00   0.0  0
 5TD  CONST_14  H23  C16  C17  C12   180.00   0.0  0
 5TD  CONST_15  C3   N    C4   O     180.00   0.0  0
 5TD  CONST_16  C    N    C4   O       0.00   0.0  0
 5TD  CONST_17  C5   C4   N    C3      0.00   0.0  0
 5TD  CONST_18  C5   C4   N    C     180.00   0.0  0
 5TD  Var_01    C1   C2   C3   N      32.79  30.0  1
 5TD  Var_02    C2   C1   C    N      28.31  30.0  1
 5TD  Var_03    C    C1   C2   C3    -38.04  30.0  1
 5TD  Var_04    C1   C    N    C3     -7.91  30.0  1
 5TD  Var_05    C    N    C3   C2    -15.76  30.0  1
 5TD  Var_06    N1   C10  C11  C7    -55.01  30.0  1
 5TD  Var_07    N1   C9   C8   C7     55.99  30.0  1
 5TD  Var_08    C12  N1   C10  C11  -143.07  30.0  1
 5TD  Var_09    C13  C12  N1   C10    -5.63  30.0  3
 5TD  Var_10    C8   C9   N1   C10   -56.48  30.0  1
 5TD  Var_11    C7   C6   C5   C4    176.19  30.0  1
 5TD  Var_12    C6   C5   C4   N     176.39  30.0  3

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
 5TD  chir_01  C7  C6  C11  C8  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
 5TD  plan-1  O    0.020
 5TD  plan-1  C4   0.020
 5TD  plan-1  N    0.020
 5TD  plan-1  C3   0.020
 5TD  plan-1  C    0.020
 5TD  plan-1  C5   0.020
 5TD  plan-2  N1   0.020
 5TD  plan-2  C12  0.020
 5TD  plan-2  C17  0.020
 5TD  plan-2  C16  0.020
 5TD  plan-2  C15  0.020
 5TD  plan-2  C18  0.020
 5TD  plan-2  N2   0.020
 5TD  plan-2  C14  0.020
 5TD  plan-2  C13  0.020
 5TD  plan-2  H22  0.020
 5TD  plan-2  H23  0.020
 5TD  plan-2  H24  0.020
 5TD  plan-2  H25  0.020

