# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 15:34:23 2022
#   Inital geometry file: a 104 line input string
#   Ligand name: N-[(pyridin-3-yl)methyl]-4-(thiophene-2-carbonyl)piperazine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCc1cccnc1)N2CCN(CC2)C(=O)c3sccc3
#
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
 Y44  Y44  N-[(pyridin-3-yl)methyl]-4-(thiophene-2-carbonyl)piperazine-1-carboxamide  ligand  41  23  .  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_Y44
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
 Y44  N1   N  NH1   0  -0.687  -15.3050  16.9220  25.1868
 Y44  N3   N  NR6   0  -0.501  -16.6928  15.2326  25.9371
 Y44  C4   C  CR16  0  -0.194  -14.3909  19.8479  27.1669
 Y44  C5   C  CR16  0  -0.316  -14.9960  20.9468  27.7578
 Y44  C6   C  CR16  0  -0.076  -16.2271  21.3613  27.2748
 Y44  C7   C  CR16  0  -0.090  -16.2622  19.7045  25.7159
 Y44  C8   C  C     0  -0.309  -17.3078  14.4659  27.0008
 Y44  C13  C  CR15  0  -0.177  -23.0385  13.6749  27.8357
 Y44  C15  C  C     0  -0.318  -18.1300  13.8371  24.5318
 Y44  C1   C  C     0   0.748  -15.7383  16.1598  26.2308
 Y44  C11  C  CR5   0  -0.303  -21.3950  13.1420  26.2871
 Y44  C12  C  CR15  0  -0.208  -21.8317  14.0615  27.2032
 Y44  C14  C  CR15  0  -0.456  -23.4962  12.4697  27.3898
 Y44  C16  C  C     0  -0.328  -17.2755  15.0872  24.6151
 Y44  C2   C  CH2   0  -0.363  -14.4009  18.0215  25.4164
 Y44  C3   C  CR6   0   0.023  -15.0279  19.2018  26.1169
 Y44  C9   C  C     0  -0.309  -18.8155  14.4416  26.8301
 Y44  N2   N  N     0  -0.398  -16.8536  20.7529  26.2733
 Y44  N4   N  NR6   0  -0.475  -19.1697  13.8389  25.5504
 Y44  O1   O  O     0  -0.535  -15.2667  16.2889  27.3559
 Y44  O2   O  O     0  -0.493  -20.4052  12.4171  24.3115
 Y44  S1   S  S2    0   0.255  -22.4845  11.8089  26.1879
 Y44  H1   H  HNH1  0   0.413  -15.8137  16.9363  24.3194
 Y44  H4   H  HCR6  0   0.267  -13.4307  19.4922  27.5220
 Y44  H5   H  HCR6  0   0.268  -14.5266  21.4699  28.5798
 Y44  H6   H  HCR6  0   0.260  -16.7296  22.2159  27.7143
 Y44  H7   H  HCR6  0   0.253  -16.8027  19.2308  24.9015
 Y44  H9   H  H     0   0.247  -16.9179  13.4436  27.0326
 Y44  H8   H  H     0   0.278  -17.0790  14.9262  27.9584
 Y44  H16  H  H     0   0.255  -17.5018  12.9453  24.6203
 Y44  H15  H  H     0   0.278  -18.5868  13.8102  23.5449
 Y44  H12  H  HCR5  0   0.280  -21.3376  14.9985  27.4123
 Y44  H14  H  HCR5  0   0.300  -24.3820  11.9424  27.7100
 Y44  H18  H  H     0   0.266  -16.4953  14.9825  23.8564
 Y44  H17  H  H     0   0.252  -17.8809  15.9611  24.3467
 Y44  H2   H  HCH2  0   0.261  -13.5342  17.6810  25.9832
 Y44  H3   H  HCH2  0   0.274  -14.0275  18.3352  24.4403
 Y44  H11  H  H     0   0.274  -19.2444  13.8627  27.6473
 Y44  H10  H  H     0   0.254  -19.1984  15.4635  26.9039
 Y44  C10  C  C     0   0.558  -20.2809  13.1116  25.3159
 Y44  H13  H  HCR5  0   0.273  -23.5414  14.2679  28.5856

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
 Y44  O1   C1   double    1.227  0.020  1.227
 Y44  C1   N1   single    1.363  0.020  1.363
 Y44  N1   C2   single    1.442  0.020  1.442
 Y44  C2   C3   single    1.509  0.020  1.509
 Y44  C3   C4   aromatic  1.388  0.020  1.388
 Y44  C4   C5   aromatic  1.387  0.020  1.387
 Y44  C5   C6   aromatic  1.386  0.020  1.386
 Y44  C6   N2   aromatic  1.329  0.020  1.329
 Y44  N2   C7   aromatic  1.326  0.020  1.326
 Y44  C1   N3   single    1.363  0.020  1.363
 Y44  N3   C8   single    1.448  0.020  1.448
 Y44  C8   C9   single    1.518  0.020  1.518
 Y44  C9   N4   single    1.458  0.020  1.458
 Y44  N4   C10  single    1.349  0.020  1.349
 Y44  C10  O2   double    1.227  0.020  1.227
 Y44  C10  C11  single    1.478  0.020  1.478
 Y44  C11  C12  aromatic  1.369  0.020  1.369
 Y44  C12  C13  aromatic  1.416  0.020  1.416
 Y44  C13  C14  aromatic  1.364  0.020  1.364
 Y44  C14  S1   aromatic  1.704  0.020  1.704
 Y44  N4   C15  single    1.456  0.020  1.456
 Y44  C15  C16  single    1.517  0.020  1.517
 Y44  C3   C7   aromatic  1.392  0.020  1.392
 Y44  N3   C16  single    1.452  0.020  1.452
 Y44  C11  S1   aromatic  1.724  0.020  1.724
 Y44  N1   H1   single    0.860  0.020  1.020
 Y44  C4   H4   single    0.930  0.020  1.080
 Y44  C5   H5   single    0.930  0.020  1.080
 Y44  C6   H6   single    0.930  0.020  1.080
 Y44  C7   H7   single    0.930  0.020  1.080
 Y44  C8   H9   single    0.970  0.020  1.090
 Y44  C8   H8   single    0.970  0.020  1.090
 Y44  C13  H13  single    0.930  0.020  1.080
 Y44  C15  H16  single    0.970  0.020  1.090
 Y44  C15  H15  single    0.970  0.020  1.090
 Y44  C12  H12  single    0.930  0.020  1.080
 Y44  C14  H14  single    0.930  0.020  1.080
 Y44  C16  H18  single    0.970  0.020  1.090
 Y44  C16  H17  single    0.970  0.020  1.090
 Y44  C2   H2   single    0.970  0.020  1.090
 Y44  C2   H3   single    0.970  0.020  1.090
 Y44  C9   H11  single    0.970  0.020  1.090
 Y44  C9   H10  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
 Y44  H1   N1   C2   116.34  3.000
 Y44  H1   N1   C1   120.51  3.000
 Y44  C2   N1   C1   120.24  3.000
 Y44  C16  N3   C1   123.05  3.000
 Y44  C16  N3   C8   116.44  3.000
 Y44  C1   N3   C8   119.96  3.000
 Y44  H4   C4   C3   120.12  3.000
 Y44  H4   C4   C5   120.47  3.000
 Y44  C3   C4   C5   119.41  3.000
 Y44  H5   C5   C6   120.38  3.000
 Y44  H5   C5   C4   121.18  3.000
 Y44  C6   C5   C4   118.43  3.000
 Y44  H6   C6   N2   116.60  3.000
 Y44  H6   C6   C5   120.40  3.000
 Y44  N2   C6   C5   122.99  3.000
 Y44  H7   C7   N2   115.97  3.000
 Y44  H7   C7   C3   119.99  3.000
 Y44  N2   C7   C3   124.04  3.000
 Y44  H8   C8   H9   107.15  3.000
 Y44  H8   C8   C9   108.36  3.000
 Y44  H9   C8   C9   110.01  3.000
 Y44  H8   C8   N3   109.48  3.000
 Y44  H9   C8   N3   111.38  3.000
 Y44  C9   C8   N3   110.36  3.000
 Y44  H13  C13  C14  123.76  3.000
 Y44  H13  C13  C12  123.84  3.000
 Y44  C14  C13  C12  112.40  3.000
 Y44  H15  C15  H16  107.12  3.000
 Y44  H15  C15  N4   109.57  3.000
 Y44  H16  C15  N4   110.76  3.000
 Y44  H15  C15  C16  107.87  3.000
 Y44  H16  C15  C16  110.11  3.000
 Y44  N4   C15  C16  111.28  3.000
 Y44  O1   C1   N3   122.58  3.000
 Y44  N3   C1   N1   115.98  3.000
 Y44  O1   C1   N1   121.42  3.000
 Y44  S1   C11  C12  110.86  3.000
 Y44  S1   C11  C10  114.99  3.000
 Y44  C12  C11  C10  133.91  3.000
 Y44  H12  C12  C11  124.50  3.000
 Y44  H12  C12  C13  122.70  3.000
 Y44  C11  C12  C13  112.78  3.000
 Y44  H14  C14  S1   120.46  3.000
 Y44  H14  C14  C13  127.59  3.000
 Y44  S1   C14  C13  111.96  3.000
 Y44  H17  C16  H18  107.49  3.000
 Y44  H17  C16  C15  109.42  3.000
 Y44  H18  C16  C15  106.56  3.000
 Y44  H17  C16  N3   111.38  3.000
 Y44  H18  C16  N3   110.79  3.000
 Y44  C15  C16  N3   111.02  3.000
 Y44  H3   C2   H2   106.43  3.000
 Y44  H3   C2   C3   109.43  3.000
 Y44  H2   C2   C3   109.47  3.000
 Y44  H3   C2   N1   106.94  3.000
 Y44  H2   C2   N1   110.07  3.000
 Y44  C3   C2   N1   114.20  3.000
 Y44  C2   C3   C7   121.15  3.000
 Y44  C7   C3   C4   117.19  3.000
 Y44  C2   C3   C4   121.65  3.000
 Y44  H10  C9   H11  107.94  3.000
 Y44  H10  C9   N4   111.12  3.000
 Y44  H11  C9   N4   110.07  3.000
 Y44  H10  C9   C8   108.98  3.000
 Y44  H11  C9   C8   108.38  3.000
 Y44  N4   C9   C8   110.28  3.000
 Y44  C7   N2   C6   117.93  3.000
 Y44  C9   N4   C15  116.18  3.000
 Y44  C15  N4   C10  117.79  3.000
 Y44  C9   N4   C10  125.14  3.000
 Y44  C14  S1   C11   91.99  3.000
 Y44  O2   C10  N4   122.06  3.000
 Y44  O2   C10  C11  118.22  3.000
 Y44  N4   C10  C11  119.72  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
 Y44  CONST_01  N2   C7   C3   C4     0.00   0.0  0
 Y44  CONST_02  N2   C6   C5   C4     0.00   0.0  0
 Y44  CONST_03  C7   C3   C4   C5     0.00   0.0  0
 Y44  CONST_04  C7   N2   C6   C5     0.00   0.0  0
 Y44  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 Y44  CONST_06  C3   C7   N2   C6     0.00   0.0  0
 Y44  CONST_07  S1   C11  C12  C13    0.00   0.0  0
 Y44  CONST_08  C11  S1   C14  C13    0.00   0.0  0
 Y44  CONST_09  C14  C13  C12  C11    0.00   0.0  0
 Y44  CONST_10  C14  S1   C11  C12    0.00   0.0  0
 Y44  CONST_11  S1   C14  C13  C12    0.00   0.0  0
 Y44  CONST_12  C2   C3   C4   C5   180.00   0.0  0
 Y44  CONST_13  C13  C12  C11  C10  180.00   0.0  0
 Y44  CONST_14  C14  S1   C11  C10  180.00   0.0  0
 Y44  CONST_15  N2   C7   C3   C2   180.00   0.0  0
 Y44  CONST_16  C11  C10  N4   C15  180.00   0.0  0
 Y44  CONST_17  C9   N4   C10  C11    0.00   0.0  0
 Y44  CONST_18  H7   C7   C3   C4   180.00   0.0  0
 Y44  CONST_19  H6   C6   C5   C4   180.00   0.0  0
 Y44  CONST_20  H4   C4   C5   C6   180.00   0.0  0
 Y44  CONST_21  H13  C13  C12  C11  180.00   0.0  0
 Y44  CONST_22  H14  C14  S1   C11  180.00   0.0  0
 Y44  CONST_23  H12  C12  C13  C14  180.00   0.0  0
 Y44  CONST_24  H5   C5   C4   C3   180.00   0.0  0
 Y44  CONST_25  O1   C1   N3   C8     0.00   0.0  0
 Y44  CONST_26  O2   C10  N4   C15    0.00   0.0  0
 Y44  CONST_27  O1   C1   N3   C16  180.00   0.0  0
 Y44  CONST_28  O2   C10  N4   C9   180.00   0.0  0
 Y44  CONST_29  C8   N3   C1   N1   180.00   0.0  0
 Y44  CONST_30  C16  N3   C1   N1     0.00   0.0  0
 Y44  CONST_31  C2   N1   C1   N3   180.00   0.0  0
 Y44  CONST_32  H1   N1   C1   N3     0.00   0.0  0
 Y44  CONST_33  O1   C1   N1   C2     0.00   0.0  0
 Y44  Var_01    N4   C9   C8   N3    59.74  30.0  1
 Y44  Var_02    N4   C15  C16  N3    56.44  30.0  1
 Y44  Var_03    C15  C16  N3   C8   -17.98  30.0  1
 Y44  Var_04    C15  N4   C9   C8   -21.37  30.0  1
 Y44  Var_05    C9   N4   C15  C16  -34.89  30.0  1
 Y44  Var_06    C9   C8   N3   C16  -38.44  30.0  1
 Y44  Var_07    N4   C10  C11  C12   26.59  30.0  2
 Y44  Var_08    C4   C3   C2   N1   134.92  30.0  2
 Y44  Var_09    C3   C2   N1   C1   -70.99  30.0  3

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
 Y44  plan-1  C13  0.020
 Y44  plan-1  C11  0.020
 Y44  plan-1  C12  0.020
 Y44  plan-1  C14  0.020
 Y44  plan-1  S1   0.020
 Y44  plan-1  H12  0.020
 Y44  plan-1  H14  0.020
 Y44  plan-1  C10  0.020
 Y44  plan-1  H13  0.020
 Y44  plan-2  C4   0.020
 Y44  plan-2  C5   0.020
 Y44  plan-2  C6   0.020
 Y44  plan-2  C7   0.020
 Y44  plan-2  C2   0.020
 Y44  plan-2  C3   0.020
 Y44  plan-2  N2   0.020
 Y44  plan-2  H4   0.020
 Y44  plan-2  H5   0.020
 Y44  plan-2  H6   0.020
 Y44  plan-2  H7   0.020
 Y44  plan-3  N1   0.020
 Y44  plan-3  N3   0.020
 Y44  plan-3  C8   0.020
 Y44  plan-3  C1   0.020
 Y44  plan-3  C16  0.020
 Y44  plan-3  C2   0.020
 Y44  plan-3  O1   0.020
 Y44  plan-3  H1   0.020
 Y44  plan-4  C15  0.020
 Y44  plan-4  C11  0.020
 Y44  plan-4  C9   0.020
 Y44  plan-4  N4   0.020
 Y44  plan-4  O2   0.020
 Y44  plan-4  C10  0.020

