# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 11:23:57 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: N-(cyclopropylmethyl)-4-(thiophene-2-carbonyl)piperazine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCC1CC1)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
 Y0D  Y0D  N-(cyclopropylmethyl)-4-(thiophene-2-carbonyl)piperazine-1-carboxamide  ligand  39  20  .  2022-08-11  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_Y0D
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
 Y0D  N1   N  NH1   0  -0.691  -15.9528  17.0235  26.1402
 Y0D  N3   N  NT    0  -0.462  -19.0340  13.5797  25.4801
 Y0D  C4   C  CH2   0  -0.490  -14.4630  20.3129  25.1246
 Y0D  C5   C  CH2   0  -0.485  -15.0643  19.3767  24.1205
 Y0D  C6   C  CH2   0  -0.237  -17.9506  14.3026  27.5425
 Y0D  C7   C  CH2   0  -0.385  -18.5841  13.1410  26.7874
 Y0D  C8   C  C     0   0.542  -20.2684  13.4318  24.9605
 Y0D  C10  C  CR15  0  -0.209  -21.7201  13.6683  27.0981
 Y0D  C13  C  CH2   0  -0.247  -17.9713  14.0384  24.5917
 Y0D  C1   C  C     0   0.746  -16.6619  16.2861  27.0405
 Y0D  C11  C  CR15  0  -0.178  -22.9905  13.2413  27.5594
 Y0D  C12  C  CR15  0  -0.456  -23.6141  12.4162  26.6712
 Y0D  C14  C  CH2   0  -0.382  -16.7343  14.3687  25.4187
 Y0D  C2   C  CH2   0  -0.250  -15.5193  18.3673  26.4654
 Y0D  C3   C  CH1   0  -0.282  -14.5459  18.8508  25.4268
 Y0D  C9   C  CR5   0  -0.315  -21.4034  13.1547  25.8711
 Y0D  N2   N  NT    0  -0.506  -17.1130  15.0655  26.6301
 Y0D  O1   O  O     0  -0.541  -16.8758  16.6863  28.1810
 Y0D  O2   O  O     0  -0.483  -20.4826  13.5418  23.7590
 Y0D  S1   S  S2    0   0.255  -22.6793  12.1711  25.2647
 Y0D  H1   H  HNH1  0   0.395  -16.0928  16.8575  25.1567
 Y0D  H5   H  HCH2  0   0.246  -15.1297  20.9795  25.6585
 Y0D  H6   H  HCH2  0   0.252  -13.4895  20.7360  24.9145
 Y0D  H7   H  HCH2  0   0.246  -16.1383  19.4098  23.9783
 Y0D  H8   H  HCH2  0   0.250  -14.5037  19.1589  23.2207
 Y0D  H10  H  HCH2  0   0.236  -17.3816  13.9092  28.3906
 Y0D  H9   H  HCH2  0   0.246  -18.7341  14.9472  27.9441
 Y0D  H12  H  HCH2  0   0.273  -17.8685  12.3243  26.6583
 Y0D  H11  H  HCH2  0   0.294  -19.4063  12.7310  27.3649
 Y0D  H17  H  HCH2  0   0.246  -17.7214  13.2820  23.8423
 Y0D  H16  H  HCH2  0   0.252  -18.3105  14.9302  24.0630
 Y0D  H14  H  HCR5  0   0.273  -23.4205  13.5365  28.5054
 Y0D  H15  H  HCR5  0   0.300  -24.5770  11.9398  26.7750
 Y0D  H19  H  HCH2  0   0.264  -16.1848  13.4585  25.6747
 Y0D  H18  H  HCH2  0   0.278  -16.0517  14.9550  24.8097
 Y0D  H3   H  HCH2  0   0.218  -16.3652  19.0633  26.5253
 Y0D  H2   H  HCH2  0   0.243  -15.0431  18.3613  27.4464
 Y0D  H4   H  HCH1  0   0.259  -13.6144  18.2953  25.3852
 Y0D  H13  H  HCR5  0   0.285  -21.0828  14.3477  27.6470

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
 Y0D  O1   C1   double    1.227  0.020  1.227
 Y0D  C1   N1   single    1.363  0.020  1.363
 Y0D  N1   C2   single    1.449  0.020  1.449
 Y0D  C2   C3   single    1.503  0.020  1.503
 Y0D  C3   C4   single    1.495  0.020  1.495
 Y0D  C4   C5   single    1.499  0.020  1.499
 Y0D  C1   N2   single    1.365  0.020  1.365
 Y0D  N2   C6   single    1.455  0.020  1.455
 Y0D  C6   C7   single    1.523  0.020  1.523
 Y0D  C7   N3   single    1.450  0.020  1.450
 Y0D  N3   C8   single    1.347  0.020  1.347
 Y0D  C8   O2   double    1.225  0.020  1.225
 Y0D  C8   C9   single    1.481  0.020  1.481
 Y0D  C9   C10  aromatic  1.367  0.020  1.367
 Y0D  C10  C11  aromatic  1.417  0.020  1.417
 Y0D  C11  C12  aromatic  1.363  0.020  1.363
 Y0D  C12  S1   aromatic  1.706  0.020  1.706
 Y0D  N3   C13  single    1.459  0.020  1.459
 Y0D  C13  C14  single    1.524  0.020  1.524
 Y0D  C3   C5   single    1.501  0.020  1.501
 Y0D  N2   C14  single    1.448  0.020  1.448
 Y0D  C9   S1   aromatic  1.721  0.020  1.721
 Y0D  N1   H1   single    0.890  0.020  1.040
 Y0D  C4   H5   single    0.970  0.020  1.090
 Y0D  C4   H6   single    0.970  0.020  1.090
 Y0D  C5   H7   single    0.970  0.020  1.090
 Y0D  C5   H8   single    0.970  0.020  1.090
 Y0D  C6   H10  single    0.970  0.020  1.090
 Y0D  C6   H9   single    0.970  0.020  1.090
 Y0D  C7   H12  single    0.970  0.020  1.090
 Y0D  C7   H11  single    0.970  0.020  1.090
 Y0D  C10  H13  single    0.930  0.020  1.080
 Y0D  C13  H17  single    0.970  0.020  1.090
 Y0D  C13  H16  single    0.970  0.020  1.090
 Y0D  C11  H14  single    0.930  0.020  1.080
 Y0D  C12  H15  single    0.930  0.020  1.080
 Y0D  C14  H19  single    0.970  0.020  1.090
 Y0D  C14  H18  single    0.970  0.020  1.090
 Y0D  C2   H3   single    0.970  0.020  1.090
 Y0D  C2   H2   single    0.970  0.020  1.090
 Y0D  C3   H4   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
 Y0D  H1   N1   C2   114.44  3.000
 Y0D  H1   N1   C1   118.92  3.000
 Y0D  C2   N1   C1   120.61  3.000
 Y0D  C13  N3   C8   117.84  3.000
 Y0D  C13  N3   C7   114.70  3.000
 Y0D  C8   N3   C7   126.76  3.000
 Y0D  H6   C4   H5   114.13  3.000
 Y0D  H6   C4   C3   118.13  3.000
 Y0D  H5   C4   C3   117.90  3.000
 Y0D  H6   C4   C5   118.36  3.000
 Y0D  H5   C4   C5   117.88  3.000
 Y0D  C3   C4   C5    60.15  3.000
 Y0D  H8   C5   H7   114.22  3.000
 Y0D  H8   C5   C3   118.31  3.000
 Y0D  H7   C5   C3   117.86  3.000
 Y0D  H8   C5   C4   118.35  3.000
 Y0D  H7   C5   C4   117.80  3.000
 Y0D  C3   C5   C4    59.81  3.000
 Y0D  H9   C6   H10  107.48  3.000
 Y0D  H9   C6   N2   109.55  3.000
 Y0D  H10  C6   N2   112.03  3.000
 Y0D  H9   C6   C7   109.53  3.000
 Y0D  H10  C6   C7   109.04  3.000
 Y0D  N2   C6   C7   109.17  3.000
 Y0D  H11  C7   H12  106.05  3.000
 Y0D  H11  C7   C6   109.84  3.000
 Y0D  H12  C7   C6   110.84  3.000
 Y0D  H11  C7   N3   111.04  3.000
 Y0D  H12  C7   N3   108.82  3.000
 Y0D  C6   C7   N3   110.19  3.000
 Y0D  O2   C8   C9   119.05  3.000
 Y0D  C9   C8   N3   119.04  3.000
 Y0D  O2   C8   N3   121.90  3.000
 Y0D  H13  C10  C9   123.71  3.000
 Y0D  H13  C10  C11  123.53  3.000
 Y0D  C9   C10  C11  112.74  3.000
 Y0D  H16  C13  H17  107.71  3.000
 Y0D  H16  C13  C14  109.77  3.000
 Y0D  H17  C13  C14  109.64  3.000
 Y0D  H16  C13  N3   109.00  3.000
 Y0D  H17  C13  N3   111.48  3.000
 Y0D  C14  C13  N3   109.20  3.000
 Y0D  O1   C1   N2   120.90  3.000
 Y0D  N2   C1   N1   117.22  3.000
 Y0D  O1   C1   N1   121.88  3.000
 Y0D  H14  C11  C12  123.63  3.000
 Y0D  H14  C11  C10  124.02  3.000
 Y0D  C12  C11  C10  112.35  3.000
 Y0D  H15  C12  S1   120.30  3.000
 Y0D  H15  C12  C11  127.77  3.000
 Y0D  S1   C12  C11  111.92  3.000
 Y0D  H18  C14  H19  105.35  3.000
 Y0D  H18  C14  N2   111.94  3.000
 Y0D  H19  C14  N2   109.64  3.000
 Y0D  H18  C14  C13  108.83  3.000
 Y0D  H19  C14  C13  110.76  3.000
 Y0D  N2   C14  C13  110.24  3.000
 Y0D  H2   C2   H3   106.93  3.000
 Y0D  H2   C2   C3   109.91  3.000
 Y0D  H3   C2   C3   109.45  3.000
 Y0D  H2   C2   N1   109.11  3.000
 Y0D  H3   C2   N1   111.71  3.000
 Y0D  C3   C2   N1   109.69  3.000
 Y0D  H4   C3   C2   114.68  3.000
 Y0D  H4   C3   C5   116.26  3.000
 Y0D  C2   C3   C5   119.37  3.000
 Y0D  H4   C3   C4   116.43  3.000
 Y0D  C5   C3   C4    60.04  3.000
 Y0D  C2   C3   C4   119.34  3.000
 Y0D  S1   C9   C10  111.04  3.000
 Y0D  S1   C9   C8   117.28  3.000
 Y0D  C10  C9   C8   131.21  3.000
 Y0D  C14  N2   C1   126.56  3.000
 Y0D  C14  N2   C6   115.03  3.000
 Y0D  C1   N2   C6   118.09  3.000
 Y0D  C9   S1   C12   91.93  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
 Y0D  CONST_01  C12  S1   C9   C10    0.00   0.0  0
 Y0D  CONST_02  S1   C12  C11  C10    0.00   0.0  0
 Y0D  CONST_03  S1   C9   C10  C11    0.00   0.0  0
 Y0D  CONST_04  C9   S1   C12  C11    0.00   0.0  0
 Y0D  CONST_05  C9   C10  C11  C12    0.00   0.0  0
 Y0D  CONST_06  C11  C10  C9   C8   180.00   0.0  0
 Y0D  CONST_07  C12  S1   C9   C8   180.00   0.0  0
 Y0D  CONST_09  C9   C8   N3   C13  180.00   0.0  0
 Y0D  CONST_10  H15  C12  C11  C10  180.00   0.0  0
 Y0D  CONST_11  H13  C10  C11  C12  180.00   0.0  0
 Y0D  CONST_12  H14  C11  C10  C9   180.00   0.0  0
 Y0D  CONST_13  O1   C1   N2   C6     0.00   0.0  0
 Y0D  CONST_15  O2   C8   N3   C13    0.00   0.0  0
 Y0D  CONST_16  O1   C1   N2   C14  180.00   0.0  0
 Y0D  CONST_17  C6   N2   C1   N1   180.00   0.0  0
 Y0D  CONST_18  C14  N2   C1   N1     0.00   0.0  0
 Y0D  CONST_19  N2   C1   N1   C2   180.00   0.0  0
 Y0D  CONST_21  O1   C1   N1   C2     0.00   0.0  0
 Y0D  Var_01    N2   C6   C7   N3   -42.02  30.0  1
 Y0D  Var_02    N2   C14  C13  N3   -41.62  30.0  1
 Y0D  Var_03    C13  C14  N2   C6    62.92  30.0  1
 Y0D  Var_04    C13  N3   C7   C6    63.16  30.0  1
 Y0D  Var_05    C14  N2   C6   C7   -18.46  30.0  1
 Y0D  Var_06    C14  C13  N3   C7   -18.70  30.0  1
 Y0D  Var_07    C10  C9   C8   N3    41.18  30.0  2
 Y0D  Var_08    C2   C3   C5   C4   108.94  30.0  1
 Y0D  Var_09    C4   C3   C2   N1   150.31  30.0  3
 Y0D  Var_10    C3   C2   N1   C1   169.14  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
 Y0D  chir_01  C3  C2  C4  C5  both

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
 Y0D  plan-1  C8   0.020
 Y0D  plan-1  C10  0.020
 Y0D  plan-1  C11  0.020
 Y0D  plan-1  C12  0.020
 Y0D  plan-1  C9   0.020
 Y0D  plan-1  S1   0.020
 Y0D  plan-1  H14  0.020
 Y0D  plan-1  H15  0.020
 Y0D  plan-1  H13  0.020
 Y0D  plan-2  N1   0.020
 Y0D  plan-2  C6   0.020
 Y0D  plan-2  C1   0.020
 Y0D  plan-2  C14  0.020
 Y0D  plan-2  C2   0.020
 Y0D  plan-2  N2   0.020
 Y0D  plan-2  O1   0.020
 Y0D  plan-2  H1   0.020
 Y0D  plan-3  N3   0.020
 Y0D  plan-3  C7   0.020
 Y0D  plan-3  C8   0.020
 Y0D  plan-3  C13  0.020
 Y0D  plan-3  C9   0.020
 Y0D  plan-3  O2   0.020

